escher-1.2.1.js

(function (root, factory) {
    if (typeof define === 'function' && define.amd) {
        //Allow using this built library as an AMD module
        //in another project. That other project will only
        //see this AMD call, not the internal modules in
        //the closure below.
        define('escher', factory);
    } else {
        //Browser globals case. Just assign the
        //result to a property on the global.
        root.escher = factory();
    }
}(this, function () {
    //almond, and your modules will be inlined here

/**
 * almond 0.2.6 Copyright (c) 2011-2012, The Dojo Foundation All Rights Reserved.
 * Available via the MIT or new BSD license.
 * see: http://github.com/jrburke/almond for details
 */
//Going sloppy to avoid 'use strict' string cost, but strict practices should
//be followed.
/*jslint sloppy: true */
/*global setTimeout: false */

var requirejs, require, define;
(function (undef) {
    var main, req, makeMap, handlers,
        defined = {},
        waiting = {},
        config = {},
        defining = {},
        hasOwn = Object.prototype.hasOwnProperty,
        aps = [].slice;

    function hasProp(obj, prop) {
        return hasOwn.call(obj, prop);
    }

    /**
     * Given a relative module name, like ./something, normalize it to
     * a real name that can be mapped to a path.
     * @param {String} name the relative name
     * @param {String} baseName a real name that the name arg is relative
     * to.
     * @returns {String} normalized name
     */
    function normalize(name, baseName) {
        var nameParts, nameSegment, mapValue, foundMap,
            foundI, foundStarMap, starI, i, j, part,
            baseParts = baseName && baseName.split("/"),
            map = config.map,
            starMap = (map && map['*']) || {};

        //Adjust any relative paths.
        if (name && name.charAt(0) === ".") {
            //If have a base name, try to normalize against it,
            //otherwise, assume it is a top-level require that will
            //be relative to baseUrl in the end.
            if (baseName) {
                //Convert baseName to array, and lop off the last part,
                //so that . matches that "directory" and not name of the baseName's
                //module. For instance, baseName of "one/two/three", maps to
                //"one/two/three.js", but we want the directory, "one/two" for
                //this normalization.
                baseParts = baseParts.slice(0, baseParts.length - 1);

                name = baseParts.concat(name.split("/"));

                //start trimDots
                for (i = 0; i < name.length; i += 1) {
                    part = name[i];
                    if (part === ".") {
                        name.splice(i, 1);
                        i -= 1;
                    } else if (part === "..") {
                        if (i === 1 && (name[2] === '..' || name[0] === '..')) {
                            //End of the line. Keep at least one non-dot
                            //path segment at the front so it can be mapped
                            //correctly to disk. Otherwise, there is likely
                            //no path mapping for a path starting with '..'.
                            //This can still fail, but catches the most reasonable
                            //uses of ..
                            break;
                        } else if (i > 0) {
                            name.splice(i - 1, 2);
                            i -= 2;
                        }
                    }
                }
                //end trimDots

                name = name.join("/");
            } else if (name.indexOf('./') === 0) {
                // No baseName, so this is ID is resolved relative
                // to baseUrl, pull off the leading dot.
                name = name.substring(2);
            }
        }

        //Apply map config if available.
        if ((baseParts || starMap) && map) {
            nameParts = name.split('/');

            for (i = nameParts.length; i > 0; i -= 1) {
                nameSegment = nameParts.slice(0, i).join("/");

                if (baseParts) {
                    //Find the longest baseName segment match in the config.
                    //So, do joins on the biggest to smallest lengths of baseParts.
                    for (j = baseParts.length; j > 0; j -= 1) {
                        mapValue = map[baseParts.slice(0, j).join('/')];

                        //baseName segment has  config, find if it has one for
                        //this name.
                        if (mapValue) {
                            mapValue = mapValue[nameSegment];
                            if (mapValue) {
                                //Match, update name to the new value.
                                foundMap = mapValue;
                                foundI = i;
                                break;
                            }
                        }
                    }
                }

                if (foundMap) {
                    break;
                }

                //Check for a star map match, but just hold on to it,
                //if there is a shorter segment match later in a matching
                //config, then favor over this star map.
                if (!foundStarMap && starMap && starMap[nameSegment]) {
                    foundStarMap = starMap[nameSegment];
                    starI = i;
                }
            }

            if (!foundMap && foundStarMap) {
                foundMap = foundStarMap;
                foundI = starI;
            }

            if (foundMap) {
                nameParts.splice(0, foundI, foundMap);
                name = nameParts.join('/');
            }
        }

        return name;
    }

    function makeRequire(relName, forceSync) {
        return function () {
            //A version of a require function that passes a moduleName
            //value for items that may need to
            //look up paths relative to the moduleName
            return req.apply(undef, aps.call(arguments, 0).concat([relName, forceSync]));
        };
    }

    function makeNormalize(relName) {
        return function (name) {
            return normalize(name, relName);
        };
    }

    function makeLoad(depName) {
        return function (value) {
            defined[depName] = value;
        };
    }

    function callDep(name) {
        if (hasProp(waiting, name)) {
            var args = waiting[name];
            delete waiting[name];
            defining[name] = true;
            main.apply(undef, args);
        }

        if (!hasProp(defined, name) && !hasProp(defining, name)) {
            throw new Error('No ' + name);
        }
        return defined[name];
    }

    //Turns a plugin!resource to [plugin, resource]
    //with the plugin being undefined if the name
    //did not have a plugin prefix.
    function splitPrefix(name) {
        var prefix,
            index = name ? name.indexOf('!') : -1;
        if (index > -1) {
            prefix = name.substring(0, index);
            name = name.substring(index + 1, name.length);
        }
        return [prefix, name];
    }

    /**
     * Makes a name map, normalizing the name, and using a plugin
     * for normalization if necessary. Grabs a ref to plugin
     * too, as an optimization.
     */
    makeMap = function (name, relName) {
        var plugin,
            parts = splitPrefix(name),
            prefix = parts[0];

        name = parts[1];

        if (prefix) {
            prefix = normalize(prefix, relName);
            plugin = callDep(prefix);
        }

        //Normalize according
        if (prefix) {
            if (plugin && plugin.normalize) {
                name = plugin.normalize(name, makeNormalize(relName));
            } else {
                name = normalize(name, relName);
            }
        } else {
            name = normalize(name, relName);
            parts = splitPrefix(name);
            prefix = parts[0];
            name = parts[1];
            if (prefix) {
                plugin = callDep(prefix);
            }
        }

        //Using ridiculous property names for space reasons
        return {
            f: prefix ? prefix + '!' + name : name, //fullName
            n: name,
            pr: prefix,
            p: plugin
        };
    };

    function makeConfig(name) {
        return function () {
            return (config && config.config && config.config[name]) || {};
        };
    }

    handlers = {
        require: function (name) {
            return makeRequire(name);
        },
        exports: function (name) {
            var e = defined[name];
            if (typeof e !== 'undefined') {
                return e;
            } else {
                return (defined[name] = {});
            }
        },
        module: function (name) {
            return {
                id: name,
                uri: '',
                exports: defined[name],
                config: makeConfig(name)
            };
        }
    };

    main = function (name, deps, callback, relName) {
        var cjsModule, depName, ret, map, i,
            args = [],
            usingExports;

        //Use name if no relName
        relName = relName || name;

        //Call the callback to define the module, if necessary.
        if (typeof callback === 'function') {

            //Pull out the defined dependencies and pass the ordered
            //values to the callback.
            //Default to [require, exports, module] if no deps
            deps = !deps.length && callback.length ? ['require', 'exports', 'module'] : deps;
            for (i = 0; i < deps.length; i += 1) {
                map = makeMap(deps[i], relName);
                depName = map.f;

                //Fast path CommonJS standard dependencies.
                if (depName === "require") {
                    args[i] = handlers.require(name);
                } else if (depName === "exports") {
                    //CommonJS module spec 1.1
                    args[i] = handlers.exports(name);
                    usingExports = true;
                } else if (depName === "module") {
                    //CommonJS module spec 1.1
                    cjsModule = args[i] = handlers.module(name);
                } else if (hasProp(defined, depName) ||
                           hasProp(waiting, depName) ||
                           hasProp(defining, depName)) {
                    args[i] = callDep(depName);
                } else if (map.p) {
                    map.p.load(map.n, makeRequire(relName, true), makeLoad(depName), {});
                    args[i] = defined[depName];
                } else {
                    throw new Error(name + ' missing ' + depName);
                }
            }

            ret = callback.apply(defined[name], args);

            if (name) {
                //If setting exports via "module" is in play,
                //favor that over return value and exports. After that,
                //favor a non-undefined return value over exports use.
                if (cjsModule && cjsModule.exports !== undef &&
                        cjsModule.exports !== defined[name]) {
                    defined[name] = cjsModule.exports;
                } else if (ret !== undef || !usingExports) {
                    //Use the return value from the function.
                    defined[name] = ret;
                }
            }
        } else if (name) {
            //May just be an object definition for the module. Only
            //worry about defining if have a module name.
            defined[name] = callback;
        }
    };

    requirejs = require = req = function (deps, callback, relName, forceSync, alt) {
        if (typeof deps === "string") {
            if (handlers[deps]) {
                //callback in this case is really relName
                return handlers[deps](callback);
            }
            //Just return the module wanted. In this scenario, the
            //deps arg is the module name, and second arg (if passed)
            //is just the relName.
            //Normalize module name, if it contains . or ..
            return callDep(makeMap(deps, callback).f);
        } else if (!deps.splice) {
            //deps is a config object, not an array.
            config = deps;
            if (callback.splice) {
                //callback is an array, which means it is a dependency list.
                //Adjust args if there are dependencies
                deps = callback;
                callback = relName;
                relName = null;
            } else {
                deps = undef;
            }
        }

        //Support require(['a'])
        callback = callback || function () {};

        //If relName is a function, it is an errback handler,
        //so remove it.
        if (typeof relName === 'function') {
            relName = forceSync;
            forceSync = alt;
        }

        //Simulate async callback;
        if (forceSync) {
            main(undef, deps, callback, relName);
        } else {
            //Using a non-zero value because of concern for what old browsers
            //do, and latest browsers "upgrade" to 4 if lower value is used:
            //http://www.whatwg.org/specs/web-apps/current-work/multipage/timers.html#dom-windowtimers-settimeout:
            //If want a value immediately, use require('id') instead -- something
            //that works in almond on the global level, but not guaranteed and
            //unlikely to work in other AMD implementations.
            setTimeout(function () {
                main(undef, deps, callback, relName);
            }, 4);
        }

        return req;
    };

    /**
     * Just drops the config on the floor, but returns req in case
     * the config return value is used.
     */
    req.config = function (cfg) {
        config = cfg;
        if (config.deps) {
            req(config.deps, config.callback);
        }
        return req;
    };

    /**
     * Expose module registry for debugging and tooling
     */
    requirejs._defined = defined;

    define = function (name, deps, callback) {

        //This module may not have dependencies
        if (!deps.splice) {
            //deps is not an array, so probably means
            //an object literal or factory function for
            //the value. Adjust args.
            callback = deps;
            deps = [];
        }

        if (!hasProp(defined, name) && !hasProp(waiting, name)) {
            waiting[name] = [name, deps, callback];
        }
    };

    define.amd = {
        jQuery: true
    };
}());

define("../build/almond", function(){});

/**
 * vkBeautify - javascript plugin to pretty-print or minify text in XML, JSON, CSS and SQL formats.
 *
 * Version - 0.99.00.beta
 * Copyright (c) 2012 Vadim Kiryukhin
 * vkiryukhin @ gmail.com
 * http://www.eslinstructor.net/vkbeautify/
 *
 * Dual licensed under the MIT and GPL licenses:
 *   http://www.opensource.org/licenses/mit-license.php
 *   http://www.gnu.org/licenses/gpl.html
 *
 *   Pretty print
 *
 *        vkbeautify.xml(text [,indent_pattern]);
 *        vkbeautify.json(text [,indent_pattern]);
 *        vkbeautify.css(text [,indent_pattern]);
 *        vkbeautify.sql(text [,indent_pattern]);
 *
 *        @text - String; text to beatufy;
 *        @indent_pattern - Integer | String;
 *                Integer:  number of white spaces;
 *                String:   character string to visualize indentation ( can also be a set of white spaces )
 *   Minify
 *
 *        vkbeautify.xmlmin(text [,preserve_comments]);
 *        vkbeautify.jsonmin(text);
 *        vkbeautify.cssmin(text [,preserve_comments]);
 *        vkbeautify.sqlmin(text);
 *
 *        @text - String; text to minify;
 *        @preserve_comments - Bool; [optional];
 *                Set this flag to true to prevent removing comments from @text ( minxml and mincss functions only. )
 *
 *   Examples:
 *        vkbeautify.xml(text); // pretty print XML
 *        vkbeautify.json(text, 4 ); // pretty print JSON
 *        vkbeautify.css(text, '. . . .'); // pretty print CSS
 *        vkbeautify.sql(text, '----'); // pretty print SQL
 *
 *        vkbeautify.xmlmin(text, true);// minify XML, preserve comments
 *        vkbeautify.jsonmin(text);// minify JSON
 *        vkbeautify.cssmin(text);// minify CSS, remove comments ( default )
 *        vkbeautify.sqlmin(text);// minify SQL
 *
 */

define('lib/vkbeautify',[],function() {

    function createShiftArr(step) {

        var space = '    ';

        if ( isNaN(parseInt(step)) ) {  // argument is string
            space = step;
        } else { // argument is integer
            switch(step) {
            case 1: space = ' '; break;
            case 2: space = '  '; break;
            case 3: space = '   '; break;
            case 4: space = '    '; break;
            case 5: space = '     '; break;
            case 6: space = '      '; break;
            case 7: space = '       '; break;
            case 8: space = '        '; break;
            case 9: space = '         '; break;
            case 10: space = '          '; break;
            case 11: space = '           '; break;
            case 12: space = '            '; break;
            }
        }

        var shift = ['\n']; // array of shifts
        for(ix=0;ix<100;ix++){
            shift.push(shift[ix]+space);
        }
        return shift;
    }

    function vkbeautify(){
        this.step = '    '; // 4 spaces
        this.shift = createShiftArr(this.step);
    };

    vkbeautify.prototype.xml = function(text,step) {

        var ar = text.replace(/>\s{0,}</g,"><")
                .replace(/</g,"~::~<")
                .replace(/\s*xmlns\:/g,"~::~xmlns:")
                .replace(/\s*xmlns\=/g,"~::~xmlns=")
                .split('~::~'),
            len = ar.length,
            inComment = false,
            deep = 0,
            str = '',
            ix = 0,
            shift = step ? createShiftArr(step) : this.shift;

        for(ix=0;ix<len;ix++) {
            // start comment or <![CDATA[...]]> or <!DOCTYPE //
            if(ar[ix].search(/<!/) > -1) {
                str += shift[deep]+ar[ix];
                inComment = true;
                // end comment  or <![CDATA[...]]> //
                if(ar[ix].search(/-->/) > -1 || ar[ix].search(/\]>/) > -1 || ar[ix].search(/!DOCTYPE/) > -1 ) {
                    inComment = false;
                }
            } else
                // end comment  or <![CDATA[...]]> //
                if(ar[ix].search(/-->/) > -1 || ar[ix].search(/\]>/) > -1) {
                    str += ar[ix];
                    inComment = false;
                } else
                    // <elm></elm> //
                    if( /^<\w/.exec(ar[ix-1]) && /^<\/\w/.exec(ar[ix]) &&
                        /^<[\w:\-\.\,]+/.exec(ar[ix-1]) == /^<\/[\w:\-\.\,]+/.exec(ar[ix])[0].replace('/','')) {
                        str += ar[ix];
                        if(!inComment) deep--;
                    } else
                        // <elm> //
                        if(ar[ix].search(/<\w/) > -1 && ar[ix].search(/<\//) == -1 && ar[ix].search(/\/>/) == -1 ) {
                            str = !inComment ? str += shift[deep++]+ar[ix] : str += ar[ix];
                        } else
                            // <elm>...</elm> //
                            if(ar[ix].search(/<\w/) > -1 && ar[ix].search(/<\//) > -1) {
                                str = !inComment ? str += shift[deep]+ar[ix] : str += ar[ix];
                            } else
                                // </elm> //
                                if(ar[ix].search(/<\//) > -1) {
                                    str = !inComment ? str += shift[--deep]+ar[ix] : str += ar[ix];
                                } else
                                    // <elm/> //
                                    if(ar[ix].search(/\/>/) > -1 ) {
                                        str = !inComment ? str += shift[deep]+ar[ix] : str += ar[ix];
                                    } else
                                        // <? xml ... ?> //
                                        if(ar[ix].search(/<\?/) > -1) {
                                            str += shift[deep]+ar[ix];
                                        } else
                                            // xmlns //
                                            if( ar[ix].search(/xmlns\:/) > -1  || ar[ix].search(/xmlns\=/) > -1) {
                                                str += shift[deep]+ar[ix];
                                            }

            else {
                str += ar[ix];
            }
        }

        return  (str[0] == '\n') ? str.slice(1) : str;
    }

    vkbeautify.prototype.json = function(text,step) {

        var step = step ? step : this.step;

        if (typeof JSON === 'undefined' ) return text;

        if ( typeof text === "string" ) return JSON.stringify(JSON.parse(text), null, step);
        if ( typeof text === "object" ) return JSON.stringify(text, null, step);

        return text; // text is not string nor object
    }

    vkbeautify.prototype.css = function(text, step) {

        var ar = text.replace(/\s{1,}/g,' ')
                .replace(/\{/g,"{~::~")
                .replace(/\}/g,"~::~}~::~")
                .replace(/\;/g,";~::~")
                .replace(/\/\*/g,"~::~/*")
                .replace(/\*\//g,"*/~::~")
                .replace(/~::~\s{0,}~::~/g,"~::~")
                .split('~::~'),
            len = ar.length,
            deep = 0,
            str = '',
            ix = 0,
            shift = step ? createShiftArr(step) : this.shift;

        for(ix=0;ix<len;ix++) {

            if( /\{/.exec(ar[ix]))  {
                str += shift[deep++]+ar[ix];
            } else
                if( /\}/.exec(ar[ix]))  {
                    str += shift[--deep]+ar[ix];
                } else
                    if( /\*\\/.exec(ar[ix]))  {
                        str += shift[deep]+ar[ix];
                    }
            else {
                str += shift[deep]+ar[ix];
            }
        }
        return str.replace(/^\n{1,}/,'');
    }

    //----------------------------------------------------------------------------

    function isSubquery(str, parenthesisLevel) {
        return  parenthesisLevel - (str.replace(/\(/g,'').length - str.replace(/\)/g,'').length )
    }

    function split_sql(str, tab) {

        return str.replace(/\s{1,}/g," ")

            .replace(/ AND /ig,"~::~"+tab+tab+"AND ")
            .replace(/ BETWEEN /ig,"~::~"+tab+"BETWEEN ")
            .replace(/ CASE /ig,"~::~"+tab+"CASE ")
            .replace(/ ELSE /ig,"~::~"+tab+"ELSE ")
            .replace(/ END /ig,"~::~"+tab+"END ")
            .replace(/ FROM /ig,"~::~FROM ")
            .replace(/ GROUP\s{1,}BY/ig,"~::~GROUP BY ")
            .replace(/ HAVING /ig,"~::~HAVING ")
        //.replace(/ SET /ig," SET~::~")
            .replace(/ IN /ig," IN ")

            .replace(/ JOIN /ig,"~::~JOIN ")
            .replace(/ CROSS~::~{1,}JOIN /ig,"~::~CROSS JOIN ")
            .replace(/ INNER~::~{1,}JOIN /ig,"~::~INNER JOIN ")
            .replace(/ LEFT~::~{1,}JOIN /ig,"~::~LEFT JOIN ")
            .replace(/ RIGHT~::~{1,}JOIN /ig,"~::~RIGHT JOIN ")

            .replace(/ ON /ig,"~::~"+tab+"ON ")
            .replace(/ OR /ig,"~::~"+tab+tab+"OR ")
            .replace(/ ORDER\s{1,}BY/ig,"~::~ORDER BY ")
            .replace(/ OVER /ig,"~::~"+tab+"OVER ")

            .replace(/\(\s{0,}SELECT /ig,"~::~(SELECT ")
            .replace(/\)\s{0,}SELECT /ig,")~::~SELECT ")

            .replace(/ THEN /ig," THEN~::~"+tab+"")
            .replace(/ UNION /ig,"~::~UNION~::~")
            .replace(/ USING /ig,"~::~USING ")
            .replace(/ WHEN /ig,"~::~"+tab+"WHEN ")
            .replace(/ WHERE /ig,"~::~WHERE ")
            .replace(/ WITH /ig,"~::~WITH ")

        //.replace(/\,\s{0,}\(/ig,",~::~( ")
        //.replace(/\,/ig,",~::~"+tab+tab+"")

            .replace(/ ALL /ig," ALL ")
            .replace(/ AS /ig," AS ")
            .replace(/ ASC /ig," ASC ")
            .replace(/ DESC /ig," DESC ")
            .replace(/ DISTINCT /ig," DISTINCT ")
            .replace(/ EXISTS /ig," EXISTS ")
            .replace(/ NOT /ig," NOT ")
            .replace(/ NULL /ig," NULL ")
            .replace(/ LIKE /ig," LIKE ")
            .replace(/\s{0,}SELECT /ig,"SELECT ")
            .replace(/\s{0,}UPDATE /ig,"UPDATE ")
            .replace(/ SET /ig," SET ")

            .replace(/~::~{1,}/g,"~::~")
            .split('~::~');
    }

    vkbeautify.prototype.sql = function(text,step) {

        var ar_by_quote = text.replace(/\s{1,}/g," ")
                .replace(/\'/ig,"~::~\'")
                .split('~::~'),
            len = ar_by_quote.length,
            ar = [],
            deep = 0,
            tab = this.step,//+this.step,
            inComment = true,
            inQuote = false,
            parenthesisLevel = 0,
            str = '',
            ix = 0,
            shift = step ? createShiftArr(step) : this.shift;;

        for(ix=0;ix<len;ix++) {
            if(ix%2) {
                ar = ar.concat(ar_by_quote[ix]);
            } else {
                ar = ar.concat(split_sql(ar_by_quote[ix], tab) );
            }
        }

        len = ar.length;
        for(ix=0;ix<len;ix++) {

            parenthesisLevel = isSubquery(ar[ix], parenthesisLevel);

            if( /\s{0,}\s{0,}SELECT\s{0,}/.exec(ar[ix]))  {
                ar[ix] = ar[ix].replace(/\,/g,",\n"+tab+tab+"")
            }

            if( /\s{0,}\s{0,}SET\s{0,}/.exec(ar[ix]))  {
                ar[ix] = ar[ix].replace(/\,/g,",\n"+tab+tab+"")
            }

            if( /\s{0,}\(\s{0,}SELECT\s{0,}/.exec(ar[ix]))  {
                deep++;
                str += shift[deep]+ar[ix];
            } else
                if( /\'/.exec(ar[ix]) )  {
                    if(parenthesisLevel<1 && deep) {
                        deep--;
                    }
                    str += ar[ix];
                }
            else  {
                str += shift[deep]+ar[ix];
                if(parenthesisLevel<1 && deep) {
                    deep--;
                }
            }
            var junk = 0;
        }

        str = str.replace(/^\n{1,}/,'').replace(/\n{1,}/g,"\n");
        return str;
    }


    vkbeautify.prototype.xmlmin = function(text, preserveComments) {

        var str = preserveComments ? text
                : text.replace(/\<![ \r\n\t]*(--([^\-]|[\r\n]|-[^\-])*--[ \r\n\t]*)\>/g,"")
                .replace(/[ \r\n\t]{1,}xmlns/g, ' xmlns');
        return  str.replace(/>\s{0,}</g,"><");
    }

    vkbeautify.prototype.jsonmin = function(text) {

        if (typeof JSON === 'undefined' ) return text;

        return JSON.stringify(JSON.parse(text), null, 0);

    }

    vkbeautify.prototype.cssmin = function(text, preserveComments) {

        var str = preserveComments ? text
                : text.replace(/\/\*([^*]|[\r\n]|(\*+([^*/]|[\r\n])))*\*+\//g,"") ;

        return str.replace(/\s{1,}/g,' ')
            .replace(/\{\s{1,}/g,"{")
            .replace(/\}\s{1,}/g,"}")
            .replace(/\;\s{1,}/g,";")
            .replace(/\/\*\s{1,}/g,"/*")
            .replace(/\*\/\s{1,}/g,"*/");
    }

    vkbeautify.prototype.sqlmin = function(text) {
        return text.replace(/\s{1,}/g," ").replace(/\s{1,}\(/,"(").replace(/\s{1,}\)/,")");
    }

    return new vkbeautify();

});

/*! @source http://purl.eligrey.com/github/FileSaver.js/blob/master/FileSaver.js */
var saveAs=saveAs||function(e){if("undefined"==typeof navigator||!/MSIE [1-9]\./.test(navigator.userAgent)){var t=e.document,n=function(){return e.URL||e.webkitURL||e},o=t.createElementNS("http://www.w3.org/1999/xhtml","a"),r="download"in o,i=function(e){var t=new MouseEvent("click");e.dispatchEvent(t)},a=e.webkitRequestFileSystem,c=e.requestFileSystem||a||e.mozRequestFileSystem,u=function(t){(e.setImmediate||e.setTimeout)(function(){throw t},0)},f="application/octet-stream",s=0,d=500,l=function(t){var o=function(){"string"==typeof t?n().revokeObjectURL(t):t.remove()};e.chrome?o():setTimeout(o,d)},v=function(e,t,n){t=[].concat(t);for(var o=t.length;o--;){var r=e["on"+t[o]];if("function"==typeof r)try{r.call(e,n||e)}catch(i){u(i)}}},p=function(e){return/^\s*(?:text\/\S*|application\/xml|\S*\/\S*\+xml)\s*;.*charset\s*=\s*utf-8/i.test(e.type)?new Blob(["",e],{type:e.type}):e},w=function(t,u,d){d||(t=p(t));var w,y,m,S=this,h=t.type,O=!1,R=function(){v(S,"writestart progress write writeend".split(" "))},b=function(){if((O||!w)&&(w=n().createObjectURL(t)),y)y.location.href=w;else{var o=e.open(w,"_blank");void 0==o&&"undefined"!=typeof safari&&(e.location.href=w)}S.readyState=S.DONE,R(),l(w)},g=function(e){return function(){return S.readyState!==S.DONE?e.apply(this,arguments):void 0}},E={create:!0,exclusive:!1};return S.readyState=S.INIT,u||(u="download"),r?(w=n().createObjectURL(t),o.href=w,o.download=u,void setTimeout(function(){i(o),R(),l(w),S.readyState=S.DONE})):(e.chrome&&h&&h!==f&&(m=t.slice||t.webkitSlice,t=m.call(t,0,t.size,f),O=!0),a&&"download"!==u&&(u+=".download"),(h===f||a)&&(y=e),c?(s+=t.size,void c(e.TEMPORARY,s,g(function(e){e.root.getDirectory("saved",E,g(function(e){var n=function(){e.getFile(u,E,g(function(e){e.createWriter(g(function(n){n.onwriteend=function(t){y.location.href=e.toURL(),S.readyState=S.DONE,v(S,"writeend",t),l(e)},n.onerror=function(){var e=n.error;e.code!==e.ABORT_ERR&&b()},"writestart progress write abort".split(" ").forEach(function(e){n["on"+e]=S["on"+e]}),n.write(t),S.abort=function(){n.abort(),S.readyState=S.DONE},S.readyState=S.WRITING}),b)}),b)};e.getFile(u,{create:!1},g(function(e){e.remove(),n()}),g(function(e){e.code===e.NOT_FOUND_ERR?n():b()}))}),b)}),b)):void b())},y=w.prototype,m=function(e,t,n){return new w(e,t,n)};return"undefined"!=typeof navigator&&navigator.msSaveOrOpenBlob?function(e,t,n){return n||(e=p(e)),navigator.msSaveOrOpenBlob(e,t||"download")}:(y.abort=function(){var e=this;e.readyState=e.DONE,v(e,"abort")},y.readyState=y.INIT=0,y.WRITING=1,y.DONE=2,y.error=y.onwritestart=y.onprogress=y.onwrite=y.onabort=y.onerror=y.onwriteend=null,m)}}("undefined"!=typeof self&&self||"undefined"!=typeof window&&window||this.content);"undefined"!=typeof module&&module.exports?module.exports.saveAs=saveAs:"undefined"!=typeof define&&null!==define&&null!=define.amd&&define('lib/FileSaver',[],function(){return saveAs});
/* global define, d3, Blob, XMLSerializer */

define('utils',["lib/vkbeautify", "lib/FileSaver"], function(vkbeautify, saveAs) {
    return { set_options: set_options,
             setup_svg: setup_svg,
             remove_child_nodes: remove_child_nodes,
             load_css: load_css,
             load_files: load_files,
             load_the_file: load_the_file,
             make_class: make_class,
             setup_defs: setup_defs,
             draw_an_object: draw_an_object,
             draw_a_nested_object: draw_a_nested_object,
             make_array: make_array,
             make_array_ref: make_array_ref,
             compare_arrays: compare_arrays,
             array_to_object: array_to_object,
             clone: clone,
             extend: extend,
             unique_concat: unique_concat,
             unique_strings_array: unique_strings_array,
             debounce: debounce,
             object_slice_for_ids: object_slice_for_ids,
             object_slice_for_ids_ref: object_slice_for_ids_ref,
             c_plus_c: c_plus_c,
             c_minus_c: c_minus_c,
             c_times_scalar: c_times_scalar,
             download_json: download_json,
             load_json: load_json,
             load_json_or_csv: load_json_or_csv,
             download_svg: download_svg,
             rotate_coords_recursive: rotate_coords_recursive,
             rotate_coords: rotate_coords,
             get_angle: get_angle,
             to_degrees: to_degrees,
             angle_for_event: angle_for_event,
             distance: distance,
             check_undefined: check_undefined,
             compartmentalize: compartmentalize,
             decompartmentalize: decompartmentalize,
             mean: mean,
             median: median,
             quartiles: quartiles,
             random_characters: random_characters,
             generate_map_id: generate_map_id,
             check_for_parent_tag: check_for_parent_tag,
             name_to_url: name_to_url,
             parse_url_components: parse_url_components };

    // definitions
    function _check_filesaver() {
        /** Check if Blob is available, and alert if it is not. */
        try {
            var isFileSaverSupported = !!new Blob();
        } catch (e) {
            alert("Blob not supported");
        }
    }

    function set_options(options, defaults, must_be_float) {
        if (options === undefined || options === null)
            return defaults;
        var i = -1,
            out = {};
        for (var key in defaults) {
            var has_key = ((key in options) &&
                           (options[key] !== null) &&
                           (options[key] !== undefined));
            var val = (has_key ? options[key] : defaults[key]);
            if (must_be_float && key in must_be_float) {
                val = parseFloat(val);
                if (isNaN(val)) {
                    if (has_key) {
                        console.warn('Bad float for option ' + key);
                        val = parseFloat(defaults[key]);
                        if (isNaN(val)) {
                            console.warn('Bad float for default ' + key);
                            val = null;
                        }
                    } else {
                        console.warn('Bad float for default ' + key);
                        val = null;
                    }
                }
            }
            out[key] = val;
        }
        return out;
    }

    function setup_svg(selection, selection_is_svg, fill_screen) {
        // sub selection places the graph in an existing svg environment
        var add_svg = function(f, s) {
            if (f) {
                d3.select("body").classed('fill-screen-body', true);
                s.classed('fill-screen-div', true);
            }
            var svg = s.append('svg')
                    .attr("class", "escher-svg")
                    .attr('xmlns', "http://www.w3.org/2000/svg");
            return svg;
        };

        // run
        var out;
        // set the selection class
        selection.classed('escher-container', true);
        // make the svg
        if (selection_is_svg) {
            return selection;
        } else if (selection) {
            return add_svg(fill_screen, selection);
        } else {
            throw new Error('No selection');
        }
    }

    function remove_child_nodes(selection) {
        /** Removes all child nodes from a d3 selection

         */
        var node =  selection.node();
        while (node.hasChildNodes()) {
            node.removeChild(node.lastChild);
        }
    }

    function load_css(css_path, callback) {
        var css = "";
        if (css_path) {
            d3.text(css_path, function(error, text) {
                if (error) {
                    console.warn(error);
                }
                css = text;
                callback(css);
            });
        }
        return false;
    };
    function update() {
        return 'omg yes';
    };
    function load_the_file(t, file, callback, value) {
        // if the value is specified, don't even need to do the ajax query
        if (value) {
            if (file) console.warn('File ' + file + ' overridden by value.');
            callback.call(t, null, value, file);
            return;
        }
        if (!file) {
            callback.call(t, "No filename", null, file);
            return;
        }
        if (ends_with(file, 'json'))
            d3.json(file, function(e, d) { callback(e, d, file); });
        else if (ends_with(file, 'css'))
            d3.text(file, function(e, d) { callback(e, d, file); });
        else
            callback.call(t, "Unrecognized file type", null, file);
        return;

        // definitions
        function ends_with(str, suffix) {
            return str.indexOf(suffix, str.length - suffix.length) !== -1;
        }
    }
    function load_files(t, files_to_load, final_callback) {
        // load multiple files asynchronously
        // Takes a list of objects: { file: a_filename.json, callback: a_callback_fn }
        var i = -1, remaining = files_to_load.length, callbacks = {};
        while (++i < files_to_load.length) {
            var this_file = files_to_load[i].file;
            callbacks[this_file] = files_to_load[i].callback;
            load_the_file(t,
                          this_file,
                          function(e, d, file) {
                              callbacks[file].call(t, e, d);
                              if (!--remaining) final_callback.call(t);
                          },
                          files_to_load[i].value);
        }
    }
    // makeClass - By Hubert Kauker (MIT Licensed)
    // original by John Resig (MIT Licensed).
    // http://stackoverflow.com/questions/7892884/simple-class-instantiation
    function make_class(){
        var isInternal;
        var constructor = function(args){
            if ( this instanceof constructor ) {
                if ( typeof this.init == "function" ) {
                    this.init.apply( this, isInternal ? args : arguments );
                }
            } else {
                isInternal = true;
                var instance = new constructor( arguments );
                isInternal = false;
                return instance;
            }
        };
        return constructor;
    }

    function setup_defs(svg, style) {
        // add stylesheet
        svg.select("defs").remove();
        var defs = svg.append("defs");
        // make sure the defs is the first node
        var node = defs.node();
        node.parentNode.insertBefore(node, node.parentNode.firstChild);
        defs.append("style")
            .attr("type", "text/css")
            .text(style);
        return defs;
    }

    function draw_an_object(container_sel, parent_node_selector, children_selector,
                            object, id_key, create_function, update_function,
                            exit_function) {
        /** Run through the d3 data binding steps for an object. Also checks to
         make sure none of the values in the *object* are undefined, and
         ignores those.

         The create_function, update_function, and exit_function CAN modify the
         input data object.

         Arguments
         ---------

         container_sel: A d3 selection containing all objects.

         parent_node_selector: A selector string for a subselection of
         container_sel.

         children_selector: A selector string for each DOM element to bind.

         object: An object to bind to the selection.

         id_key: The key that will be used to store object IDs in the bound data
         points.

         create_function: A function for enter selection.

         update_function: A function for update selection.

         exit_function: A function for exit selection.

         */
        var draw_object = {};
        for (var id in object) {
            if (object[id] === undefined) {
                console.warn('Undefined value for id ' + id + ' in object. Ignoring.');
            } else {
                draw_object[id] = object[id];
            }
        }

        var sel = container_sel.select(parent_node_selector)
                .selectAll(children_selector)
                .data(make_array_ref(draw_object, id_key),
                      function(d) { return d[id_key]; });
        // enter: generate and place reaction
        if (create_function)
            sel.enter().call(create_function);
        // update: update when necessary
        if (update_function)
            sel.call(update_function);
        // exit
        if (exit_function)
            sel.exit().call(exit_function);
    }

    function draw_a_nested_object(container_sel, children_selector, object_data_key,
                                  id_key, create_function, update_function,
                                  exit_function) {
        /** Run through the d3 data binding steps for an object that is nested
         within another element with d3 data.

         The create_function, update_function, and exit_function CAN modify the
         input data object.

         Arguments
         ---------

         container_sel: A d3 selection containing all objects.

         children_selector: A selector string for each DOM element to bind.

         object_data_key: A key for the parent object containing data for the
         new selection.

         id_key: The key that will be used to store object IDs in the bound data
         points.

         create_function: A function for enter selection.

         update_function: A function for update selection.

         exit_function: A function for exit selection.

         */
        var sel = container_sel.selectAll(children_selector)
                .data(function(d) {
                    return make_array_ref(d[object_data_key], id_key);
                }, function(d) { return d[id_key]; });
        // enter: generate and place reaction
        if (create_function)
            sel.enter().call(create_function);
        // update: update when necessary
        if (update_function)
            sel.call(update_function);
        // exit
        if (exit_function)
            sel.exit().call(exit_function);
    }

    function make_array(obj, id_key) { // is this super slow?
        var array = [];
        for (var key in obj) {
            // copy object
            var it = clone(obj[key]);
            // add key as 'id'
            it[id_key] = key;
            // add object to array
            array.push(it);
        }
        return array;
    }

    function make_array_ref(obj, id_key) {
        /** Turn the object into an array, but only by reference. Faster than
         make_array.

         */
        var array = [];
        for (var key in obj) {
            // copy object
            var it = obj[key];
            // add key as 'id'
            it[id_key] = key;
            // add object to array
            array.push(it);
        }
        return array;
    }

    function compare_arrays(a1, a2) {
        /** Compares two simple (not-nested) arrays.

         */
        if (!a1 || !a2) return false;
        if (a1.length != a2.length) return false;
        for (var i = 0, l=a1.length; i < l; i++) {
            if (a1[i] != a2[i]) {
                // Warning - two different object instances will never be equal: {x:20} != {x:20}
                return false;
            }
        }
        return true;
    }

    function array_to_object(arr) {
        /** Convert an array of objects to an object with all keys and values
         that are arrays of the same length as arr. Fills in spaces with null.

         For example, [ { a: 1 }, { b: 2 }] becomes { a: [1, null], b: [null, 2] }.

         */
        // new object
        var obj = {};
        // for each element of the array
        for (var i = 0, l = arr.length; i < l; i++) {
            var column = arr[i],
                keys = Object.keys(column);
            for (var k = 0, nk = keys.length; k < nk; k++) {
                var id = keys[k];
                if (!(id in obj)) {
                    var n = [];
                    // fill spaces with null
                    for (var j = 0; j < l; j++) {
                        n[j] = null;
                    }
                    n[i] = column[id];
                    obj[id] = n;
                } else {
                    obj[id][i] = column[id];
                }
            }
        }
        return obj;
    }

    function clone(obj) {
        // Handles the array and object types, and null or undefined
        if (null == obj || "object" != typeof obj) return obj;
        // Handle Array
        if (obj instanceof Array) {
            var copy = [];
            for (var i = 0, len = obj.length; i < len; i++) {
                copy[i] = clone(obj[i]);
            }
            return copy;
        }
        // Handle Object
        if (obj instanceof Object) {
            var copy = {};
            for (var attr in obj) {
                if (obj.hasOwnProperty(attr)) copy[attr] = clone(obj[attr]);
            }
            return copy;
        }
        throw new Error("Unable to copy obj! Its type isn't supported.");
    }

    function extend(obj1, obj2, overwrite) {
        /** Extends obj1 with keys/values from obj2. Performs the extension
         cautiously, and does not override attributes, unless the overwrite
         argument is true.

         Arguments
         ---------

         obj1: Object to extend

         obj2: Object with which to extend.

         overwrite: (Optional, Default false) Overwrite attributes in obj1.

         */

        if (overwrite === undefined)
            overwrite = false;

        for (var attrname in obj2) {
            if (!(attrname in obj1) || overwrite) // UNIT TEST This
                obj1[attrname] = obj2[attrname];
            else
                throw new Error('Attribute ' + attrname + ' already in object.');
        }
    }

    function unique_concat(arrays) {
        var new_array = [];
        arrays.forEach(function (a) {
            a.forEach(function(x) {
                if (new_array.indexOf(x) < 0)
                    new_array.push(x);
            });
        });
        return new_array;
    }

    function unique_strings_array(arr) {
        /** Return unique values in array of strings.

         http://stackoverflow.com/questions/1960473/unique-values-in-an-array

         */
        var a = [];
        for (var i = 0, l = arr.length; i < l; i++)
            if (a.indexOf(arr[i]) === -1)
                a.push(arr[i]);
        return a;
    }

    function debounce(func, wait, immediate) {
        /** Returns a function, that, as long as it continues to be invoked, will
         not be triggered.

         The function will be called after it stops being called for N
         milliseconds. If `immediate` is passed, trigger the function on the leading
         edge, instead of the trailing.

         */
        var timeout;
        return function() {
            var context = this, args = arguments;
            var later = function() {
                timeout = null;
                if (!immediate) func.apply(context, args);
            };
            var callNow = immediate && !timeout;
            window.clearTimeout(timeout);
            timeout = window.setTimeout(later, wait);
            if (callNow) func.apply(context, args);
        };
    }

    function object_slice_for_ids(obj, ids) {
        /** Return a copy of the object with just the given ids.

         Arguments
         ---------

         obj: An object.

         ids: An array of id strings.

         */
        var subset = {}, i = -1;
        while (++i<ids.length) {
            subset[ids[i]] = clone(obj[ids[i]]);
        }
        if (ids.length != Object.keys(subset).length) {
            console.warn('did not find correct reaction subset');
        }
        return subset;
    }

    function object_slice_for_ids_ref(obj, ids) {
        /** Return a reference of the object with just the given ids. Faster
         than object_slice_for_ids.

         Arguments
         ---------

         obj: An object.

         ids: An array of id strings.

         */
        var subset = {}, i = -1;
        while (++i<ids.length) {
            subset[ids[i]] = obj[ids[i]];
        }
        if (ids.length != Object.keys(subset).length) {
            console.warn('did not find correct reaction subset');
        }
        return subset;
    }

    function c_plus_c(coords1, coords2) {
        if (coords1 === null || coords2 === null ||
            coords1 === undefined || coords2 === undefined)
            return null;
        return { "x": coords1.x + coords2.x,
                 "y": coords1.y + coords2.y };
    }
    function c_minus_c(coords1, coords2) {
        if (coords1 === null || coords2 === null ||
            coords1 === undefined || coords2 === undefined)
            return null;
        return { "x": coords1.x - coords2.x,
                 "y": coords1.y - coords2.y };
    }

    function c_times_scalar(coords, scalar) {
        return { "x": coords.x * scalar,
                 "y": coords.y * scalar };
    }

    function download_json(json, name) {
        /** Download json file in a blob.

         */

        // alert if blob isn't going to work
        _check_filesaver();

        var j = JSON.stringify(json),
            blob = new Blob([j], {type: "application/json"});
        saveAs(blob, name + '.json');
    }

    function load_json(f, callback, pre_fn, failure_fn) {
        /** Try to load the file as JSON.

         Arguments
         ---------

         f: The file path

         callback: A callback function that accepts arguments: error, data.

         pre_fn: (optional) A function to call before loading the data.

         failure_fn: (optional) A function to call if the load fails or is aborted.

         */
        // Check for the various File API support.
        if (!(window.File && window.FileReader && window.FileList && window.Blob))
            callback("The File APIs are not fully supported in this browser.", null);

        var reader = new window.FileReader();
        // Closure to capture the file information.
        reader.onload = function(event) {
            var result = event.target.result,
                data;
            // try JSON
            try {
                data = JSON.parse(result);
            } catch (e) {
                // if it failed, return the error
                callback(e, null);
                return;
            }
            // if successful, return the data
            callback(null, data);
        };
        if (pre_fn !== undefined && pre_fn !== null) {
            try { pre_fn(); }
            catch (e) { console.warn(e); }
        }
        reader.onabort = function(event) {
            try { failure_fn(); }
            catch (e) { console.warn(e); }
        }
        reader.onerror = function(event) {
            try { failure_fn(); }
            catch (e) { console.warn(e); }
        }
        // Read in the image file as a data URL.
        reader.readAsText(f);
    }

    function load_json_or_csv(f, csv_converter, callback, pre_fn, failure_fn,
                              debug_event) {
        /** Try to load the file as JSON or CSV (JSON first).

         Arguments
         ---------

         f: The file path

         csv_converter: A function to convert the CSV output to equivalent JSON.

         callback: A callback function that accepts arguments: error, data.

         pre_fn: (optional) A function to call before loading the data.

         failure_fn: (optional) A function to call if the load fails or is aborted.

         debug_event: (optional) An event, with a string at
         event.target.result, to load as though it was the contents of a
         loaded file.

         */
        // Check for the various File API support.
        if (!(window.File && window.FileReader && window.FileList && window.Blob))
            callback("The File APIs are not fully supported in this browser.", null);

        var reader = new window.FileReader(),
            // Closure to capture the file information.
            onload_function = function(event) {

                var result = event.target.result,
                    data, errors;
                // try JSON
                try {
                    data = JSON.parse(result);
                } catch (e) {
                    errors = 'JSON error: ' + e;

                    // try csv
                    try {
                        data = csv_converter(d3.csv.parseRows(result));
                    } catch (e) {
                        // if both failed, return the errors
                        callback(errors + '\nCSV error: ' + e, null);
                        return;
                    }
                }
                // if successful, return the data
                callback(null, data);
            };
        if (debug_event !== undefined && debug_event !== null) {
            console.warn('Debugging load_json_or_csv');
            return onload_function(debug_event);
        }
        if (pre_fn !== undefined && pre_fn !== null) {
            try { pre_fn(); }
            catch (e) { console.warn(e); }
        }
        reader.onabort = function(event) {
            try { failure_fn(); }
            catch (e) { console.warn(e); }
        };
        reader.onerror = function(event) {
            try { failure_fn(); }
            catch (e) { console.warn(e); }
        };
        // Read in the image file as a data URL.
        reader.onload = onload_function;
        reader.readAsText(f);
    }

    function download_svg(name, svg_sel, do_beautify) {
        /** Download an svg file using FileSaver.js.
         *
         * Arguments
         * ---------
         *
         * name: The filename (without extension).
         *
         * svg_sel: The d3 selection for the SVG element.
         *
         * do_beautify: (Boolean) If true, then beautify the SVG output.
         *
         */

        // alert if blob isn't going to work
        _check_filesaver();

        // make the xml string
        var xml = (new XMLSerializer()).serializeToString(svg_sel.node());
        if (do_beautify) xml = vkbeautify.xml(xml);
        xml = '<?xml version="1.0" encoding="utf-8"?>\n \
            <!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN"\n \
        "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">\n' + xml;

        // save
        var blob = new Blob([xml], {type: "image/svg+xml"});
        saveAs(blob, name + '.svg');
    };

    function rotate_coords_recursive(coords_array, angle, center) {
        var rot = function(c) { return rotate_coords(c, angle, center); };
        return coords_array.map(rot);
    }

    function rotate_coords(c, angle, center) {
        /** Calculates displacement { x: dx, y: dy } based on rotating point c around
         center with angle.

         */
        var dx = Math.cos(-angle) * (c.x - center.x) +
                Math.sin(-angle) * (c.y - center.y)
                + center.x - c.x,
            dy = - Math.sin(-angle) * (c.x - center.x) +
                Math.cos(-angle) * (c.y - center.y)
                + center.y - c.y;
        return { x: dx, y: dy };
    }

    function get_angle(coords) {
        /* Takes an array of 2 coordinate objects {"x": 1, "y": 1}
         *
         * Returns angle between 0 and 2PI.
         */
        var denominator = coords[1].x - coords[0].x,
            numerator = coords[1].y - coords[0].y;
        if (denominator==0 && numerator >= 0) return Math.PI/2;
        else if (denominator==0 && numerator < 0) return 3*Math.PI/2;
        else if (denominator >= 0 && numerator >= 0) return Math.atan(numerator/denominator);
        else if (denominator >= 0) return (Math.atan(numerator/denominator) + 2*Math.PI);
        else return (Math.atan(numerator/denominator) + Math.PI);
    }

    function to_degrees(radians) { return radians*180/Math.PI; }

    function angle_for_event(displacement, point, center) {
        var gamma =  Math.atan2((point.x - center.x), (center.y - point.y)),
            beta = Math.atan2((point.x - center.x + displacement.x),
                              (center.y - point.y - displacement.y)),
            angle = beta - gamma;
        return angle;
    }

    function distance(start, end) { return Math.sqrt(Math.pow(end.y-start.y, 2) + Math.pow(end.x-start.x, 2)); }

    function check_undefined(args, names) {
        /** Report an error if any of the arguments are undefined.

         Call by passing in *arguments* from any function and an array of
         argument names.

         */
        names.map(function(name, i) {
            if (args[i]===undefined) {
                console.error('Argument is undefined: '+String(names[i]));
            }
        });
    }

    function compartmentalize(bigg_id, compartment_id) {
        return bigg_id + '_' + compartment_id;
    }


    // definitions
    function decompartmentalize(id) {
        /** Convert ids to bigg_id and compartment_id.

         */
        var out = no_compartment(id);
        if (out===null) out = [id, null];
        return out;

        // definitions
        function no_compartment(id) {
            /** Returns an array of [bigg_id, compartment id].

             Matches compartment ids with length 1 or 2.

             Return null if no match is found.

             */
            var reg = /(.*)_([a-z0-9]{1,2})$/,
                result = reg.exec(id);
            if (result===null) return null;
            return result.slice(1,3);
        }
    }

    function mean(array) {
        var sum = array.reduce(function(a, b) { return a + b; });
        var avg = sum / array.length;
        return avg;
    }

    function median(array) {
        array.sort(function(a, b) { return a - b; });
        var half = Math.floor(array.length / 2);
        if(array.length % 2 == 1)
            return array[half];
        else
            return (array[half-1] + array[half]) / 2.0;
    }

    function quartiles(array) {
        array.sort(function(a, b) { return a - b; });
        var half = Math.floor(array.length / 2);
        if (array.length == 1)
            return [ array[0], array[0], array[0] ];
        else if (array.length % 2 == 1)
            return [ median(array.slice(0, half)),
                     array[half],
                     median(array.slice(half + 1)) ];
        else
            return [ median(array.slice(0, half)),
                     (array[half-1] + array[half]) / 2.0,
                     median(array.slice(half)) ];
    }

    function random_characters(num) {
        // Thanks to @csharptest.net
        // http://stackoverflow.com/questions/1349404/generate-a-string-of-5-random-characters-in-javascript
        var text = '',
            possible = 'ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz0123456789';
        for (var i = 0; i < num; i++)
            text += possible.charAt(Math.floor(Math.random() * possible.length));
        return text;
    }

    function generate_map_id() {
        return random_characters(12);
    }

    function check_for_parent_tag(el, tag) {
        /** Check that the selection has the given parent tag.

         el: A d3 selection or node.

         tag: A tag name (case insensitive)

         */
        // make sure it is a node
        if (el instanceof Array)
            el = el.node();
        while (el.parentNode !== null) {
            el = el.parentNode;
            if (el.tagName === undefined) continue;
            if (el.tagName.toLowerCase() === tag.toLowerCase())
                return true;
        }
        return false;
    }

    function name_to_url(name, download_url) {
        /** Convert model or map name to url.

         Arguments
         ---------

         name: The short name, e.g. e_coli.iJO1366.central_metabolism.

         download_url: The url to prepend (optional).

         */

        if (download_url !== undefined && download_url !== null) {
            // strip download_url
            download_url = download_url.replace(/^\/|\/$/g, '');
            name = [download_url, name].join('/');
        }
        // strip final path
        return name.replace(/^\/|\/$/g, '') + '.json';
    }

    function parse_url_components(the_window, options) {
        /** Parse the URL and return options based on the URL arguments.

         Arguments
         ---------

         the_window: A reference to the global window.

         options: (optional) an existing options object to which new options
         will be added. Overwrites existing arguments in options.

         Adapted from http://stackoverflow.com/questions/979975/how-to-get-the-value-from-url-parameter

         */
        if (options===undefined) options = {};

        var query = the_window.location.search.substring(1),
            vars = query.split("&");
        for (var i = 0; i < vars.length; i++) {
            var pair = vars[i].split("="),
                val = decodeURIComponent(pair[1]);
            // deal with array options
            if (pair[0].indexOf('[]') == pair[0].length - 2) {
                var o = pair[0].replace('[]', '');
                if (!(o in options))
                    options[o] = [];
                options[o].push(val);
            } else {
                options[pair[0]] = val;
            }
        }
        return options;
    }
});

define('PlacedDiv',['utils'], function(utils) {
    /** A container to position an html div to match the coordinates of a SVG element.

     */

    var PlacedDiv = utils.make_class();
    // instance methods
    PlacedDiv.prototype = { init: init,
                            is_visible: is_visible,
                            place: place,
                            hide: hide };
    return PlacedDiv;

    // definitions
    function init(div, map, displacement) {
        // make the input box
        this.div = div;

        if (displacement===undefined)
            displacement = {x: 0, y: 0};
        this.displacement = displacement;

        this.map = map;
    }

    function is_visible() {
        return this.div.style('display') != 'none';
    }

    function place(coords) {
        /** Position the html div to match the given SVG coordinates.

         */
        // show the input
        this.div.style('display', null);

        // move the new input
        var window_translate = this.map.zoom_container.window_translate,
            window_scale = this.map.zoom_container.window_scale,
            map_size = this.map.get_size(),
            left = Math.max(20,
                            Math.min(map_size.width - 270,
                                     (window_scale * coords.x + window_translate.x - this.displacement.x))),
            top = Math.max(20,
                           Math.min(map_size.height - 40,
                                    (window_scale * coords.y + window_translate.y - this.displacement.y)));
        this.div.style('position', 'absolute')
            .style('display', 'block')
            .style('left', left+'px')
            .style('top', top+'px');
    }
    
    function hide() {
        this.div.style('display', 'none');
    }
});

/**
 * complete.ly 1.0.0
 * MIT Licensing
 * Copyright (c) 2013 Lorenzo Puccetti
 * 
 * This Software shall be used for doing good things, not bad things.
 *
 * Liberally modified by Zachary King (c) 2014.
 * 
 **/

define('lib/complete.ly',[],function() {
    return function(container, config) {
        config = config || {};
        config.fontSize =                       config.fontSize   || '13px';
        config.fontFamily =                     config.fontFamily || 'sans-serif';
        config.promptInnerHTML =                config.promptInnerHTML || ''; 
        config.color =                          config.color || '#333';
        config.hintColor =                      config.hintColor || '#aaa';
        config.backgroundColor =                config.backgroundColor || '#fff';
        config.dropDownBorderColor =            config.dropDownBorderColor || '#aaa';
        config.dropDownZIndex =                 config.dropDownZIndex || '100'; // to ensure we are in front of everybody
        config.dropDownOnHoverBackgroundColor = config.dropDownOnHoverBackgroundColor || '#ddd';
        
        var txtInput = document.createElement('input');
        txtInput.type ='text';
        txtInput.spellcheck = false; 
        txtInput.style.fontSize =        config.fontSize;
        txtInput.style.fontFamily =      config.fontFamily;
        txtInput.style.color =           config.color;
        txtInput.style.backgroundColor = config.backgroundColor;
        txtInput.style.width = '100%';
        txtInput.style.outline = '0';
        txtInput.style.border =  '0';
        txtInput.style.margin =  '0';
        txtInput.style.padding = '0';
        
        var txtHint = txtInput.cloneNode(); 
        txtHint.disabled='';        
        txtHint.style.position = 'absolute';
        txtHint.style.top =  '0';
        txtHint.style.left = '0';
        txtHint.style.borderColor = 'transparent';
        txtHint.style.boxShadow =   'none';
        txtHint.style.color = config.hintColor;
        
        txtInput.style.backgroundColor ='transparent';
        txtInput.style.verticalAlign = 'top';
        txtInput.style.position = 'relative';
        
        var wrapper = document.createElement('div');
        wrapper.style.position = 'relative';
        wrapper.style.outline = '0';
        wrapper.style.border =  '0';
        wrapper.style.margin =  '0';
        wrapper.style.padding = '0';
        
        var prompt = document.createElement('div');
        prompt.style.position = 'absolute';
        prompt.style.outline = '0';
        prompt.style.margin =  '0';
        prompt.style.padding = '0';
        prompt.style.border =  '0';
        prompt.style.fontSize =   config.fontSize;
        prompt.style.fontFamily = config.fontFamily;
        prompt.style.color =           config.color;
        prompt.style.backgroundColor = config.backgroundColor;
        prompt.style.top = '0';
        prompt.style.left = '0';
        prompt.style.overflow = 'hidden';
        prompt.innerHTML = config.promptInnerHTML;
        prompt.style.background = 'transparent';
        if (document.body === undefined) {
            throw 'document.body is undefined. The library was wired up incorrectly.';
        }
        document.body.appendChild(prompt);            
        var w = prompt.getBoundingClientRect().right; // works out the width of the prompt.
        wrapper.appendChild(prompt);
        prompt.style.visibility = 'visible';
        prompt.style.left = '-'+w+'px';
        wrapper.style.marginLeft= w+'px';
        
        wrapper.appendChild(txtHint);
        wrapper.appendChild(txtInput);
        
        var dropDown = document.createElement('div');
        dropDown.style.position = 'absolute';
        dropDown.style.visibility = 'hidden';
        dropDown.style.outline = '0';
        dropDown.style.margin =  '0';
        dropDown.style.padding = '0';  
        dropDown.style.textAlign = 'left';
        dropDown.style.fontSize =   config.fontSize;      
        dropDown.style.fontFamily = config.fontFamily;
        dropDown.style.backgroundColor = config.backgroundColor;
        dropDown.style.zIndex = config.dropDownZIndex; 
        dropDown.style.cursor = 'default';
        dropDown.style.borderStyle = 'solid';
        dropDown.style.borderWidth = '1px';
        dropDown.style.borderColor = config.dropDownBorderColor;
        dropDown.style.overflowX= 'hidden';
        dropDown.style.whiteSpace = 'pre';
        dropDown.style.overflowY = 'scroll';
        
        var createDropDownController = function(elem) {
            var rows = [];
            var ix = 0;
            var oldIndex = -1;
            var current_row = null;
            
            var onMouseOver =  function() { this.style.outline = '1px solid #ddd'; }
            var onMouseOut =   function() { this.style.outline = '0'; }
            var onDblClick =  function(e) {
                e.preventDefault();
                p.onmouseselection(this.id);
            }
            
            var p = {
                hide :  function() { elem.style.visibility = 'hidden'; }, 
                refresh : function(token, options) {
                    elem.style.visibility = 'hidden';
                    ix = 0;
                    elem.innerHTML ='';
                    var vph = (window.innerHeight || document.documentElement.clientHeight);
                    var rect = elem.parentNode.getBoundingClientRect();
                    var distanceToTop = rect.top - 6;                        // heuristic give 6px 
                    var distanceToBottom = vph - rect.bottom -6;  // distance from the browser border.
                    
                    rows = [];
                    for (var i = 0; i < options.length; i++) {
                        // ignore case
                        var found = options[i].matches.filter(function(match) {
                            return match.toLowerCase().indexOf(token.toLowerCase()) == 0;
                        });
                        if (found.length == 0)
                            continue;
                        var divRow = document.createElement('div');
                        divRow.style.color = config.color;
                        divRow.onmouseover = onMouseOver; 
                        divRow.onmouseout =  onMouseOut;
                        // prevent selection for double click
                        divRow.onmousedown = function(e) { e.preventDefault(); };
                        divRow.ondblclick = onDblClick; 
                        divRow.__hint = found[0];
                        divRow.id = options[i].id;
                        divRow.innerHTML = options[i].html;
                        rows.push(divRow);
                        elem.appendChild(divRow);
                        if (rows.length >= rs.display_limit)
                            break;
                    }
                    if (rows.length===0) {
                        return; // nothing to show.
                    }
                    p.highlight(0);
                    
                    // Heuristic (only when the distance to the to top is 4
                    // times more than distance to the bottom
                    if (distanceToTop > distanceToBottom*3) {
                        // we display the dropDown on the top of the input text
                        elem.style.maxHeight =  distanceToTop+'px';  
                        elem.style.top ='';
                        elem.style.bottom ='100%';
                    } else {
                        elem.style.top = '100%';  
                        elem.style.bottom = '';
                        elem.style.maxHeight =  distanceToBottom+'px';
                    }
                    elem.style.visibility = 'visible';
                },
                highlight : function(index) {
                    if (oldIndex !=-1 && rows[oldIndex]) { 
                        rows[oldIndex].style.backgroundColor = config.backgroundColor;
                    }
                    rows[index].style.backgroundColor = config.dropDownOnHoverBackgroundColor; // <-- should be config
                    oldIndex = index;
                    current_row = rows[index];
                },
                // moves the selection either up or down (unless it's not
                // possible) step is either +1 or -1.
                move : function(step) {
                    // nothing to move if there is no dropDown. (this happens if
                    // the user hits escape and then down or up)
                    if (elem.style.visibility === 'hidden')
                        return '';
                    // No circular scrolling
                    if (ix+step === -1 || ix+step === rows.length)
                        return rows[ix].__hint;
                    ix+=step; 
                    p.highlight(ix);
                    return rows[ix].__hint;
                },
                onmouseselection : function() {},
                get_current_row: function () {
                    return current_row;
                }
            };
            return p;
        }
        
        var dropDownController = createDropDownController(dropDown);
        
        dropDownController.onmouseselection = function(id) {
            rs.onEnter(id)
            rs.input.focus();
        }
        
        wrapper.appendChild(dropDown);
        container.appendChild(wrapper);
        
        var spacer,
            // This will contain the leftSide part of the textfield (the bit that
            // was already autocompleted)
            leftSide;         
        
        function calculateWidthForText(text) {
            if (spacer === undefined) { // on first call only.
                spacer = document.createElement('span'); 
                spacer.style.visibility = 'hidden';
                spacer.style.position = 'fixed';
                spacer.style.outline = '0';
                spacer.style.margin =  '0';
                spacer.style.padding = '0';
                spacer.style.border =  '0';
                spacer.style.left = '0';
                spacer.style.whiteSpace = 'pre';
                spacer.style.fontSize =   config.fontSize;
                spacer.style.fontFamily = config.fontFamily;
                spacer.style.fontWeight = 'normal';
                document.body.appendChild(spacer);    
            }        
            
            // Used to encode an HTML string into a plain text.
            // taken from http://stackoverflow.com/questions/1219860/javascript-jquery-html-encoding
            spacer.innerHTML = String(text).replace(/&/g, '&amp;')
                .replace(/"/g, '&quot;')
                .replace(/'/g, '&#39;')
                .replace(/</g, '&lt;')
                .replace(/>/g, '&gt;');
            return spacer.getBoundingClientRect().right;
        }
        
        
        var rs = {
            get_hint :    function(x) { return x; },
            display_limit: 100,
            onArrowDown : function() {},               // defaults to no action.
            onArrowUp :   function() {},               // defaults to no action.
            onEnter :     function() {},               // defaults to no action.
            onTab :       function() {},               // defaults to no action.
            onChange:     function() { rs.repaint() }, // defaults to repainting.
            startFrom:    0,
            options:      [],
            
            // Only to allow easy access to the HTML elements to the final user
            // (possibly for minor customizations)
            wrapper : wrapper,      
            input :  txtInput,      
            hint  :  txtHint,       
            dropDown :  dropDown,
            
            prompt : prompt,
            setText : function(text) {
                txtHint.value = text;
                txtInput.value = text; 
            },
            getText : function() {
                return txtInput.value; 
            },
            hideDropDown : function() {
                dropDownController.hide();
            },
            repaint : function() {
                var text = txtInput.value;
                var startFrom =  rs.startFrom; 
                var options =    rs.options;
                var optionsLength = options.length; 
                
                // breaking text in leftSide and token.
                var token = text.substring(startFrom);
                leftSide =  text.substring(0,startFrom);
                
                // updating the hint. 
                txtHint.value ='';
                for (var i = 0; i < optionsLength; i++) {
                    var found = options[i].matches.filter(function(match) {
                        return match.toLowerCase().indexOf(token.toLowerCase()) == 0;
                    });
                    if (found.length == 0)
                        continue;
                    txtHint.value = rs.get_hint(found[0]);
                    break;
                }
                
                // moving the dropDown and refreshing it.
                dropDown.style.left = calculateWidthForText(leftSide)+'px';
                dropDownController.refresh(token, rs.options);
            }
        };
        
        var registerOnTextChangeOldValue;
        
        // Register a callback function to detect changes to the content of the
        // input-type-text.  Those changes are typically followed by user's
        // action: a key-stroke event but sometimes it might be a mouse click.
        var registerOnTextChange = function(txt, callback) {
            registerOnTextChangeOldValue = txt.value;
            var handler = function() {
                var value = txt.value;
                if (registerOnTextChangeOldValue !== value) {
                    registerOnTextChangeOldValue = value;
                    callback(value);
                }
            };

            // For user's actions, we listen to both input events and key up events
            // It appears that input events are not enough so we defensively listen to key up events too.
            // source: http://help.dottoro.com/ljhxklln.php
            //
            // The cost of listening to three sources should be negligible as the handler will invoke callback function
            // only if the text.value was effectively changed. 
            txt.addEventListener("input",  handler, false);
            txt.addEventListener('keyup',  handler, false);
            txt.addEventListener('change', handler, false);
        };
        
        
        registerOnTextChange(txtInput,function(text) { // note the function needs to be wrapped as API-users will define their onChange
            rs.onChange(text);
            rs.repaint();
        });
        
        
        var keyDownHandler = function(e) {
            e = e || window.event;
            var keyCode = e.keyCode;
            
            if (keyCode == 33) { return; } // page up (do nothing)
            if (keyCode == 34) { return; } // page down (do nothing);

            // right,  end, tab  (autocomplete triggered)
            if (keyCode == 39 || keyCode == 35 || keyCode == 9) {
                // for tabs we need to ensure that we override the default
                // behaviour: move to the next focusable HTML-element
                if (keyCode == 9) {
                    e.preventDefault();
                    e.stopPropagation();
                    if (txtHint.value.length == 0) {
                        // tab was called with no action.
                        rs.onTab(); 
                    }
                }
                // if there is a hint
                if (txtHint.value.length > 0) {
                    txtInput.value = txtHint.value;
                    var hasTextChanged = registerOnTextChangeOldValue != txtInput.value
                    // avoid dropDown to appear again
                    registerOnTextChangeOldValue = txtInput.value; 
                    // for example imagine the array contains the following
                    // words: bee, beef, beetroot. User has hit enter to get
                    // 'bee' it would be prompted with the dropDown again (as
                    // beef and beetroot also match)
                    if (hasTextChanged) {
                        // force it.
                        rs.onChange(txtInput.value);
                    }
                }
                return; 
            }

            if (keyCode == 13) { // enter
                // get current
                var id = dropDownController.get_current_row().id;
                rs.onEnter(id);
                return; 
            }
            
            if (keyCode == 40) { // down
                var m = dropDownController.move(+1);
                if (m == '') { rs.onArrowDown(); }
                txtHint.value = rs.get_hint(m);
                return; 
            } 
            
            if (keyCode == 38 ) { // up
                var m = dropDownController.move(-1);
                if (m == '') { rs.onArrowUp(); }
                txtHint.value = rs.get_hint(m);
                e.preventDefault();
                e.stopPropagation();
                return; 
            }
            
            // it's important to reset the txtHint on key down. Think: user
            // presses a letter (e.g. 'x') and never releases. You get
            // (xxxxxxxxxxxxxxxxx) and you would see still the hint. Reset the
            // txtHint. (it might be updated onKeyUp).
            txtHint.value ='';            
        };
        
        txtInput.addEventListener("keydown",  keyDownHandler, false);
        return rs;
    }
});

define('DirectionArrow',["utils"], function(utils) {
    /** DirectionArrow returns a constructor for an arrow that can be rotated
     and dragged, and supplies its direction.
     */
    var DirectionArrow = utils.make_class();
    DirectionArrow.prototype = { init: init,
                                 set_location: set_location,
                                 set_rotation: set_rotation,
                                 displace_rotation: displace_rotation,
                                 get_rotation: get_rotation,
                                 toggle: toggle,
                                 show: show,
                                 hide: hide,
                                 right: right,
                                 left: left,
                                 up: up,
                                 down: down,
                                 _setup_drag: _setup_drag };
    return DirectionArrow;

    // definitions
    function init(sel) {
        this.arrow_container = sel.append('g')
            .attr('id', 'direction-arrow-container')
            .attr('transform', 'translate(0,0)rotate(0)');
        this.arrow = this.arrow_container.append('path')
            .classed('direction-arrow', true)
            .attr('d', path_for_arrow())
            .style('visibility', 'hidden')
            .attr('transform', 'translate(30,0)scale(2.5)');

        this.sel = sel;
        this.center = { x: 0, y: 0 };

        this._setup_drag();
        this.dragging = false;

        this.is_visible = false;
        this.show();

        // definitions
        function path_for_arrow() {
            return "M0 -5 L0 5 L20 5 L20 10 L30 0 L20 -10 L20 -5 Z";
        }
    }
    function set_location(coords) {
        /** Move the arrow to coords.
         */
        this.center = coords;
        var transform = d3.transform(this.arrow_container.attr('transform'));
        this.arrow_container.attr('transform',
                                  'translate('+coords.x+','+coords.y+')rotate('+transform.rotate+')');
    }
    function set_rotation(rotation) {
        /** Rotate the arrow to rotation.
         */
        var transform = d3.transform(this.arrow_container.attr('transform'));
        this.arrow_container.attr('transform',
                                  'translate('+transform.translate+')rotate('+rotation+')');
    }
    function displace_rotation(d_rotation) {
        /** Displace the arrow rotation by a set amount.
         */
        var transform = d3.transform(this.arrow_container.attr('transform'));
        this.arrow_container.attr('transform',
                                  'translate('+transform.translate+')'+
                                  'rotate('+(transform.rotate+d_rotation)+')');
    }
    function get_rotation() {
        /** Returns the arrow rotation.
         */
        return d3.transform(this.arrow_container.attr('transform')).rotate;
    }
    function toggle(on_off) {
        if (on_off===undefined) this.is_visible = !this.is_visible;
        else this.is_visible = on_off;
        this.arrow.style('visibility', this.is_visible ? 'visible' : 'hidden');
    }
    function show() {
        this.toggle(true);
    }
    function hide() {
        this.toggle(false);
    }
    function right() {
        this.set_rotation(0);
    }
    function down() {
        this.set_rotation(90);
    }
    function left() {
        this.set_rotation(180);
    }
    function up() {
        this.set_rotation(270);
    }
    
    function _setup_drag() {
        var b = d3.behavior.drag()
                .on("dragstart", function(d) {
                    // silence other listeners
                    d3.event.sourceEvent.stopPropagation();
                    this.dragging = true;
                }.bind(this))
                .on("drag.direction_arrow", function(d) {
                    var displacement = { x: d3.event.dx,
                                         y: d3.event.dy },
                        location = { x: d3.mouse(this.sel.node())[0],
                                     y: d3.mouse(this.sel.node())[1] },
                        d_angle = utils.angle_for_event(displacement,
                                                        location,
                                                        this.center);
                    this.displace_rotation(utils.to_degrees(d_angle));
                }.bind(this))
                .on("dragend", function(d) {
                    window.setTimeout(function() {
                        this.dragging = false;
                    }.bind(this), 200);
                }.bind(this));
        this.arrow_container.call(b);
    }
});

define('data_styles',['utils'], function(utils) {
    // globals
    var RETURN_ARG = function(x) { return x; },
        ESCAPE_REG = /([.*+?^=!:${}()|\[\]\/\\])/g,
        EMPTY_LINES = /\n\s*\n/g,
        TRAILING_NEWLINE = /\n\s*(\)*)\s*$/,
        AND_OR = /([\(\) ])(?:and|or)([\)\( ])/ig,
        ALL_PARENS = /[\(\)]/g,
        // capture an expression surrounded by whitespace and a set of parentheses
        EXCESS_PARENS = /\(\s*(\S+)\s*\)/g,
        OR = /\s+or\s+/i,
        AND = /\s+and\s+/i,
        // find ORs
        OR_EXPRESSION = /(^|\()(\s*-?[0-9.]+\s+(?:or\s+-?[0-9.]+\s*)+)(\)|$)/ig,
        // find ANDS, respecting order of operations (and before or)
        AND_EXPRESSION = /(^|\(|or\s)(\s*-?[0-9.]+\s+(?:and\s+-?[0-9.]+\s*)+)(\sor|\)|$)/ig;

    return { import_and_check: import_and_check,
             text_for_data: text_for_data,
             float_for_data: float_for_data,
             reverse_flux_for_data: reverse_flux_for_data,
             gene_string_for_data: gene_string_for_data,
             csv_converter: csv_converter,
             genes_for_gene_reaction_rule: genes_for_gene_reaction_rule,
             evaluate_gene_reaction_rule: evaluate_gene_reaction_rule,
             replace_gene_in_rule: replace_gene_in_rule,
             apply_reaction_data_to_reactions: apply_reaction_data_to_reactions,
             apply_metabolite_data_to_nodes: apply_metabolite_data_to_nodes,
             apply_gene_data_to_reactions: apply_gene_data_to_reactions
           };

    function import_and_check(data, name, all_reactions) {
        /** Convert imported data to a style that can be applied to reactions
         and nodes.

         Arguments
         ---------

         data: The data object.

         name: Either 'reaction_data', 'metabolite_data', or 'gene_data'

         all_reactions: Required for name == 'gene_data'. Must include all
         GPRs for the map and model.

         */

        // check arguments
        if (data===null)
            return null;
        if (['reaction_data', 'metabolite_data', 'gene_data'].indexOf(name) == -1)
            throw new Error('Invalid name argument: ' + name);

        // make array
        if (!(data instanceof Array)) {
            data = [data];
        }
        // check data
        var check = function() {
            if (data===null)
                return null;
            if (data.length==1)
                return null;
            if (data.length==2)
                return null;
            return console.warn('Bad data style: ' + name);
        };
        check();
        data = utils.array_to_object(data);

        if (name == 'gene_data') {
            if (all_reactions === undefined)
                throw new Error('Must pass all_reactions argument for gene_data');
            data = align_gene_data_to_reactions(data, all_reactions);
        }

        return data;

        // definitions
        function align_gene_data_to_reactions(data, reactions) {
            var aligned = {},
                null_val = [null];
            // make an array of nulls as the default
            for (var gene_id in data) {
                null_val = data[gene_id].map(function() { return null; });
                break;
            }
            for (var reaction_id in reactions) {
                var reaction = reactions[reaction_id],
                    bigg_id = reaction.bigg_id,
                    this_gene_data = {};
                // save to aligned

                // get the genes if they aren't already there
                var g = reaction.genes,
                    genes;
                if (typeof g === 'undefined')
                    genes = genes_for_gene_reaction_rule(reaction.gene_reaction_rule);
                else
                    genes = g.map(function(x) { return x.bigg_id; });

                genes.forEach(function(gene_id) {
                    var d = data[gene_id];
                    if (typeof d === 'undefined')
                        d = null_val;
                    this_gene_data[gene_id] = d;
                });
                aligned[bigg_id] = this_gene_data;
            }
            return aligned;
        }
    }

    function float_for_data(d, styles, compare_style) {
        // all null
        if (d === null)
            return null;

        // absolute value
        var take_abs = (styles.indexOf('abs') != -1);

        if (d.length==1) { // 1 set
            // 1 null
            var f = _parse_float_or_null(d[0]);
            if (f === null)
                return null;
            return abs(f, take_abs);
        } else if (d.length==2) { // 2 sets
            // 2 null
            var fs = d.map(_parse_float_or_null);
            if (fs[0] === null || fs[1] === null)
                return null;

            if (compare_style == 'diff') {
                return diff(fs[0], fs[1], take_abs);
            } else if (compare_style == 'fold') {
                return check_finite(fold(fs[0], fs[1], take_abs));
            }
            else if (compare_style == 'log2_fold') {
                return check_finite(log2_fold(fs[0], fs[1], take_abs));
            }
        } else {
            throw new Error('Data array must be of length 1 or 2');
        }
        throw new Error('Bad data compare_style: ' + compare_style);

        // definitions
        function check_finite(x) {
            return isFinite(x) ? x : null;
        }
        function abs(x, take_abs) {
            return take_abs ? Math.abs(x) : x;
        }
        function diff(x, y, take_abs) {
            if (take_abs) return Math.abs(y - x);
            else return y - x;
        }
        function fold(x, y, take_abs) {
            if (x == 0 || y == 0) return null;
            var fold = (y >= x ? y / x : - x / y);
            return take_abs ? Math.abs(fold) : fold;
        }
        function log2_fold(x, y, take_abs) {
            if (x == 0) return null;
            if (y / x < 0) return null;
            var log = Math.log(y / x) / Math.log(2);
            return take_abs ? Math.abs(log) : log;
        }
    }

    function reverse_flux_for_data(d) {
        if (d === null || d[0] === null)
            return false;
        return (d[0] < 0);
    }

    function gene_string_for_data(rule, gene_values, genes, styles,
                                  identifiers_on_map, compare_style) {
        /** Add gene values to the gene_reaction_rule string.

         Arguments
         ---------

         rule: (string) The gene reaction rule.

         gene_values: The values.

         genes: An array of objects specifying the gene bigg_id and name.

         styles: The reaction styles.

         identifiers_on_map: The type of identifiers ('bigg_id' or 'name').

         compare_style: The comparison style.

         Returns
         -------

         A list of objects with {
           bigg_id: The bigg ID.
           name: The name.
           text: The new string with formatted data values.
         }

         The text elements should each appear on a new line.

         */

        var out_text = rule,
            no_data = (gene_values === null),
            // keep track of bigg_id's or names to remove repeats
            genes_found = {};


        genes.forEach(function(g_obj) {
            // get id or name
            var name = g_obj[identifiers_on_map];
            if (typeof name === 'undefined')
                throw new Error('Bad value for identifiers_on_map: ' + identifiers_on_map);
            // remove repeats that may have found their way into genes object
            if (typeof genes_found[name] !== 'undefined')
                return;
            genes_found[name] = true;
            // generate the string
            if (no_data) {
                out_text = replace_gene_in_rule(out_text, g_obj.bigg_id, (name + '\n'));
            } else {
                var d = gene_values[g_obj.bigg_id];
                if (typeof d === 'undefined') d = null;
                var f = float_for_data(d, styles, compare_style),
                    format = (f === null ? RETURN_ARG : d3.format('.3g'));
                if (d.length==1) {
                    out_text = replace_gene_in_rule(out_text, g_obj.bigg_id, (name + ' (' + null_or_d(d[0], format) + ')\n'));
                }
                else if (d.length==2) {
                    // check if they are all text
                    var new_str,
                        any_num = d.reduce(function(c, x) {
                            return c || _parse_float_or_null(x) !== null;
                        }, false);
                    if (any_num) {
                        new_str = (name + ' (' +
                                   null_or_d(d[0], format) + ', ' +
                                   null_or_d(d[1], format) + ': ' +
                                   null_or_d(f, format) +
                                   ')\n');
                    } else {
                        new_str = (name + ' (' +
                                   null_or_d(d[0], format) + ', ' +
                                   null_or_d(d[1], format) + ')\n');
                    }
                    out_text = replace_gene_in_rule(out_text, g_obj.bigg_id, new_str);
                }
            }
        });
        // remove emtpy lines
        out_text = out_text.replace(EMPTY_LINES, '\n')
        // remove trailing newline (with or without parens)
            .replace(TRAILING_NEWLINE, '$1');

        // split by newlines
        var result = out_text.split('\n').map(function(text) {
            for (var i = 0, l = genes.length; i < l; i++) {
                var gene = genes[i];
                if (text.indexOf(gene[identifiers_on_map]) != -1) {
                    return { bigg_id: gene.bigg_id, name: gene.name, text: text };
                    continue;
                }
            }
            // not found, then none
            return { bigg_id: null, name: null, text: text };
        });
        return result;

        // definitions
        function null_or_d(d, format) {
            return d === null ? 'nd' : format(d);
        }
    }

    function text_for_data(d, f) {
        if (d === null)
            return null_or_d(null);
        if (d.length == 1) {
            var format = (f === null ? RETURN_ARG : d3.format('.3g'));
            return null_or_d(d[0], format);
        }
        if (d.length == 2) {
            var format = (f === null ? RETURN_ARG : d3.format('.3g')),
                t = null_or_d(d[0], format);
            t += ', ' + null_or_d(d[1], format);
            t += ': ' + null_or_d(f, format);
            return t;
        }
        return '';

        // definitions
        function null_or_d(d, format) {
            return d === null ? '(nd)' : format(d);
        }
    }

    function csv_converter(csv_rows) {
        /** Convert data from a csv file to json-style data.

         File must include a header row.

         */
        // count rows
        var c = csv_rows[0].length,
            converted = [];
        if (c < 2 || c > 3)
            throw new Error('CSV file must have 2 or 3 columns');
        // set up rows
        for (var i = 1; i < c; i++) {
            converted[i - 1] = {};
        }
        // fill
        csv_rows.slice(1).forEach(function(row) {
            for (var i = 1, l = row.length; i < l; i++) {
                converted[i - 1][row[0]] = row[i];
            }
        });
        return converted;
    }

    function genes_for_gene_reaction_rule(rule) {
        /** Find unique genes in gene_reaction_rule string.

         Arguments
         ---------

         rule: A boolean string containing gene names, parentheses, AND's and
         OR's.

         Returns
         -------

         An array of gene strings.

         */
        var genes = rule
        // remove ANDs and ORs, surrounded by space or parentheses
                .replace(AND_OR, '$1$2')
        // remove parentheses
                .replace(ALL_PARENS, '')
        // split on whitespace
                .split(' ')
                .filter(function(x) { return x != ''; });
        // unique strings
        return utils.unique_strings_array(genes);
    }

    function evaluate_gene_reaction_rule(rule, gene_values, and_method_in_gene_reaction_rule) {
        /** Return a value given the rule and gene_values object.

         Arguments
         ---------

         rule: A boolean string containing gene names, parentheses, AND's and
         OR's.

         gene_values: Object with gene_ids for keys and numbers for values.

         and_method_in_gene_reaction_rule: Either 'mean' or 'min'.

         */

        var null_val = [null],
            l = 1;
        // make an array of nulls as the default
        for (var gene_id in gene_values) {
            null_val = gene_values[gene_id].map(function() { return null; });
            l = null_val.length;
            break;
        }

        if (rule == '') return null_val;

        // for each element in the arrays
        var out = [];
        for (var i = 0; i < l; i++) {
            // get the rule
            var curr_val = rule;

            // put all the numbers into the expression
            var all_null = true;
            for (var gene_id in gene_values) {
                var f = _parse_float_or_null(gene_values[gene_id][i]);
                if (f === null) {
                    f = 0;
                } else {
                    all_null = false;
                }
                curr_val = replace_gene_in_rule(curr_val, gene_id, f);
            }
            if (all_null) {
                out.push(null);
                continue;
            }

            // recursively evaluate
            while (true) {
                // arithemtic expressions
                var new_curr_val = curr_val;

                // take out excessive parentheses
                new_curr_val = new_curr_val.replace(EXCESS_PARENS, ' $1 ');

                // or's
                new_curr_val = new_curr_val.replace(OR_EXPRESSION, function(match, p1, p2, p3) {
                    // sum
                    var nums = p2.split(OR).map(parseFloat),
                        sum = nums.reduce(function(a, b) { return a + b;});
                    return p1 + sum + p3;
                });
                // and's
                new_curr_val = new_curr_val.replace(AND_EXPRESSION, function(match, p1, p2, p3) {
                    // find min
                    var nums = p2.split(AND).map(parseFloat),
                        val = (and_method_in_gene_reaction_rule == 'min' ?
                               Math.min.apply(null, nums) :
                               nums.reduce(function(a, b) { return a + b; }) / nums.length);
                    return p1 + val + p3;
                });
                // break if there is no change
                if (new_curr_val == curr_val)
                    break;
                curr_val = new_curr_val;
            }
            // strict test for number
            var num = Number(curr_val);
            if (isNaN(num)) {
                console.warn('Could not evaluate ' + rule);
                out.push(null);
            } else {
                out.push(num);
            }
        }
        return out;
    }

    function replace_gene_in_rule(rule, gene_id, val) {
        // get the escaped string, with surrounding space or parentheses
        var space_or_par_start = '(^|[\\\s\\\(\\\)])',
            space_or_par_finish = '([\\\s\\\(\\\)]|$)',
            escaped = space_or_par_start + escape_reg_exp(gene_id) + space_or_par_finish;
        return rule.replace(new RegExp(escaped, 'g'),  '$1' + val + '$2');

        // definitions
        function escape_reg_exp(string) {
            return string.replace(ESCAPE_REG, "\\$1");
        }
    }

    function apply_reaction_data_to_reactions(reactions, data, styles, compare_style) {
        /**  Returns True if the scale has changed.

         */

        if (data === null) {
            for (var reaction_id in reactions) {
                var reaction = reactions[reaction_id];
                reaction.data = null;
                reaction.data_string = '';
                for (var segment_id in reaction.segments) {
                    var segment = reaction.segments[segment_id];
                    segment.data = null;
                }
                reaction.gene_string = null;
            }
            return false;
        }

        // apply the datasets to the reactions
        for (var reaction_id in reactions) {
            var reaction = reactions[reaction_id],
                d = (reaction.bigg_id in data ? data[reaction.bigg_id] : null),
                f = float_for_data(d, styles, compare_style),
                r = reverse_flux_for_data(d),
                s = text_for_data(d, f);
            reaction.data = f;
            reaction.data_string = s;
            reaction.reverse_flux = r;
            reaction.gene_string = null;
            // apply to the segments
            for (var segment_id in reaction.segments) {
                var segment = reaction.segments[segment_id];
                segment.data = reaction.data;
                segment.reverse_flux = reaction.reverse_flux;
            }
        }
        return true;
    }

    function apply_metabolite_data_to_nodes(nodes, data, styles, compare_style) {
        /**  Returns True if the scale has changed.

         */
        if (data === null) {
            for (var node_id in nodes) {
                nodes[node_id].data = null;
                nodes[node_id].data_string = '';
            }
            return false;
        }

        // grab the data
        for (var node_id in nodes) {
            var node = nodes[node_id],
                d = (node.bigg_id in data ? data[node.bigg_id] : null),
                f = float_for_data(d, styles, compare_style),
                s = text_for_data(d, f);
            node.data = f;
            node.data_string = s;
        }
        return true;
    }

    function apply_gene_data_to_reactions(reactions, gene_data_obj, styles, identifiers_on_map,
                                          compare_style, and_method_in_gene_reaction_rule) {
        /** Returns true if data is present

         Arguments
         ---------

         reactions: The reactions to update.

         gene_data_obj: The gene data object, with the following style:

         { reaction_id: { gene_id: value } }

         styles:  Gene styles array.

         identifiers_on_map:

         compare_style:

         and_method_in_gene_reaction_rule:

         */

        if (gene_data_obj === null) {
            for (var reaction_id in reactions) {
                var reaction = reactions[reaction_id];
                reaction.data = null;
                reaction.data_string = '';
                reaction.reverse_flux = false;
                for (var segment_id in reaction.segments) {
                    var segment = reaction.segments[segment_id];
                    segment.data = null;
                }
                reaction.gene_string = null;
            }
            return false;
        }

        // get the null val
        var null_val = [null];
        // make an array of nulls as the default
        for (var reaction_id in gene_data_obj) {
            for (var gene_id in gene_data_obj[reaction_id]) {
                null_val = gene_data_obj[reaction_id][gene_id]
                    .map(function() { return null; });
                break;
            }
            break;
        }

        // apply the datasets to the reactions
        for (var reaction_id in reactions) {
            var reaction = reactions[reaction_id],
                rule = reaction.gene_reaction_rule;
            // find the data
            var d, gene_values,
                r_data = gene_data_obj[reaction.bigg_id];
            if (typeof r_data !== 'undefined') {
                gene_values = r_data;
                d = evaluate_gene_reaction_rule(rule, gene_values,
                                                and_method_in_gene_reaction_rule);
            } else {
                gene_values = {};
                d = null_val;
            }
            var f = float_for_data(d, styles, compare_style),
                r = reverse_flux_for_data(d),
                s = text_for_data(d, f);
            reaction.data = f;
            reaction.data_string = s;
            reaction.reverse_flux = r;
            // apply to the segments
            for (var segment_id in reaction.segments) {
                var segment = reaction.segments[segment_id];
                segment.data = reaction.data;
                segment.reverse_flux = reaction.reverse_flux;
            }
            // always update the gene string
            reaction.gene_string = gene_string_for_data(rule,
                                                        gene_values,
                                                        reaction.genes,
                                                        styles,
                                                        identifiers_on_map,
                                                        compare_style);
        }
        return true;
    }

    function _parse_float_or_null(x) {
        // strict number casting
        var f = Number(x);
        // check for null and '', which haven't been caught yet
        return (isNaN(f) || parseFloat(x) != f) ? null : f;
    }
});

define('CobraModel',['utils', 'data_styles'], function(utils, data_styles) {
    /**
     */

    var CobraModel = utils.make_class();
    // class methods
    CobraModel.from_exported_data = from_exported_data;
    CobraModel.from_cobra_json = from_cobra_json;
    CobraModel.build_reaction_string = build_reaction_string;
    // instance methods
    CobraModel.prototype = { init: init,
                             apply_reaction_data: apply_reaction_data,
                             apply_metabolite_data: apply_metabolite_data,
                             apply_gene_data: apply_gene_data,
                             model_for_export: model_for_export };

    return CobraModel;

    // class methods
    function build_reaction_string(stoichiometries, is_reversible) {
        /** Return a reaction string for the given stoichiometries.

         Adapted from cobra.core.Reaction.build_reaction_string().

         Arguments
         ---------

         stoichiometries: An object with metabolites as keys and
         stoichiometries as values.

         is_reversible: Boolean. Whether the reaction is reversible.

         */

        var format = function(number) {
            if (number == 1)
                return "";
            return String(number) + " ";
        };
        var reactant_dict = {},
            product_dict = {},
            reactant_bits = [],
            product_bits = [];
        for (var the_metabolite in stoichiometries) {
            var coefficient = stoichiometries[the_metabolite];
            if (coefficient > 0)
                product_bits.push(format(coefficient) + the_metabolite);
            else
                reactant_bits.push(format(Math.abs(coefficient)) + the_metabolite);
        }
        var reaction_string = reactant_bits.join(' + ');
        if (is_reversible) {
            reaction_string += ' ↔ ';
        } else {
            reaction_string += ' → ';
        }
        reaction_string += product_bits.join(' + ');
        return reaction_string;
    }

    function from_exported_data(data) {
        /** Use data generated by CobraModel.model_for_export() to make a new
         CobraModel object.

         */
        if (!(data.reactions && data.metabolites))
            throw new Error('Bad model data.');

        var model = new CobraModel();
        model.reactions = data.reactions;
        model.metabolites = data.metabolites;
        return model;
    }

    function from_cobra_json(model_data) {
        /** Use a JSON Cobra model exported by COBRApy to make a new CobraModel
         object.

         The COBRA "id" becomes a "bigg_id", and "upper_bound" and "lower_bound"
         bounds become "reversibility".

         Fills out a "genes" list.

         */
        // reactions and metabolites
        if (!(model_data.reactions && model_data.metabolites))
            throw new Error('Bad model data.');

        // make a gene dictionary
        var genes = {};
        for (var i = 0, l = model_data.genes.length; i < l; i++) {
            var r = model_data.genes[i],
                the_id = r.id;
            genes[the_id] = r;
        }

        var model = new CobraModel();

        model.reactions = {};
        for (var i = 0, l = model_data.reactions.length; i<l; i++) {
            var r = model_data.reactions[i],
                the_id = r.id,
                reaction = utils.clone(r);
            delete reaction.id;
            reaction.bigg_id = the_id;
            // add the appropriate genes
            reaction.genes = [];

            // set reversibility
            reaction.reversibility = (reaction.lower_bound < 0 && reaction.upper_bound > 0);
            if (reaction.upper_bound <= 0 && reaction.lower_bound < 0) {
                // reverse stoichiometries
                for (var met_id in reaction.metabolites) {
                    reaction.metabolites[met_id] = -reaction.metabolites[met_id];
                }
            }
            delete reaction.lower_bound;
            delete reaction.upper_bound;

            if ('gene_reaction_rule' in reaction) {
                var gene_ids = data_styles.genes_for_gene_reaction_rule(reaction.gene_reaction_rule);
                gene_ids.forEach(function(gene_id) {
                    if (gene_id in genes) {
                        var gene = utils.clone(genes[gene_id]);
                        // rename id to bigg_id
                        gene.bigg_id = gene.id;
                        delete gene.id;
                        reaction.genes.push(gene);
                    } else {
                        console.warn('Could not find gene for gene_id ' + gene_id);
                    }
                });
            }
            model.reactions[the_id] = reaction;
        }
        model.metabolites = {};
        for (var i=0, l=model_data.metabolites.length; i<l; i++) {
            var r = model_data.metabolites[i],
                the_id = r.id,
                met = utils.clone(r);
            delete met.id;
            met.bigg_id = the_id;
            model.metabolites[the_id] = met;
        }
        return model;
    }

    // instance methods
    function init() {
        this.reactions = {};
        this.metabolites = {};
        this.cofactors = ['atp', 'adp', 'nad', 'nadh', 'nadp', 'nadph', 'gtp',
                          'gdp', 'h', 'coa'];
    }

    function apply_reaction_data(reaction_data, styles, compare_style) {
        /** Apply data to model. This is only used to display options in
         BuildInput.

         apply_reaction_data overrides apply_gene_data.

         */
        data_styles.apply_reaction_data_to_reactions(this.reactions, reaction_data,
                                                     styles, compare_style);
    }

    function apply_metabolite_data(metabolite_data, styles, compare_style) {
        /** Apply data to model. This is only used to display options in
         BuildInput.

         */
        data_styles.apply_metabolite_data_to_nodes(this.metabolites, metabolite_data,
                                                   styles, compare_style);
    }

    function apply_gene_data(gene_data_obj, styles, identifiers_on_map,
                             compare_style, and_method_in_gene_reaction_rule) {
        /** Apply data to model. This is only used to display options in
         BuildInput.

         apply_gene_data overrides apply_reaction_data.

         */
        data_styles.apply_gene_data_to_reactions(this.reactions, gene_data_obj,
                                                 styles, identifiers_on_map,
                                                 compare_style,
                                                 and_method_in_gene_reaction_rule);
    }

    function model_for_export() {
        /** Export a CobraModel object for reloading later.

         This object is not for loading into COBRApy! Export to COBRApy is not
         currently supported.

         */
        return { reactions: this.reactions,
                 metabolites: this.metabolites };
    }
});

define('BuildInput',['utils', 'PlacedDiv', 'lib/complete.ly', 'DirectionArrow', 'CobraModel'], function(utils, PlacedDiv, completely, DirectionArrow, CobraModel) {
    /**
     */

    var BuildInput = utils.make_class();
    // instance methods
    BuildInput.prototype = { init: init,
                             setup_map_callbacks: setup_map_callbacks,
                             setup_zoom_callbacks: setup_zoom_callbacks,
                             is_visible: is_visible,
                             toggle: toggle,
                             show_dropdown: show_dropdown,
                             hide_dropdown: hide_dropdown,
                             place_at_selected: place_at_selected,
                             place: place,
                             reload_at_selected: reload_at_selected,
                             reload: reload,
                             toggle_start_reaction_listener: toggle_start_reaction_listener,
                             hide_target: hide_target,
                             show_target: show_target };

    return BuildInput;

    // definitions
    function init(selection, map, zoom_container, settings) {
        // set up container
        var new_sel = selection.append('div').attr('id', 'rxn-input');
        this.placed_div = PlacedDiv(new_sel, map, {x: 240, y: 0});
        this.placed_div.hide();
        
        // set up complete.ly
        var c = completely(new_sel.node(), { backgroundColor: '#eee' });
        
        d3.select(c.input);
        this.completely = c;
        // close button
        new_sel.append('button').attr('class', "button input-close-button")
            .text("×")
            .on('mousedown', function() { this.hide_dropdown(); }.bind(this));

        // map
        this.map = map;
        // set up the reaction direction arrow
        var default_angle = 90; // degrees
        this.direction_arrow = new DirectionArrow(map.sel);
        this.direction_arrow.set_rotation(default_angle);
        this.setup_map_callbacks(map);
        
        // zoom container
        this.zoom_container = zoom_container;
        this.setup_zoom_callbacks(zoom_container);

        // settings
        this.settings = settings;

        // toggle off
        this.toggle(false);
        this.target_coords = null;
    }

    function setup_map_callbacks(map) {
        // input
        map.callback_manager.set('select_metabolite_with_id.input', function(selected_node, coords) {
            if (this.is_active) this.reload(selected_node, coords, false);
            this.hide_target();
        }.bind(this));
        map.callback_manager.set('select_selectable.input', function(count, selected_node, coords) {
            this.hide_target();
            if (count == 1 && this.is_active && coords) {
                this.reload(selected_node, coords, false);
            } else {
                this.toggle(false);
            }
        }.bind(this)); 
        map.callback_manager.set('deselect_nodes', function() {
            this.direction_arrow.hide();
            this.hide_dropdown();
        }.bind(this));

        // svg export
        map.callback_manager.set('before_svg_export', function() {
            this.direction_arrow.hide();
            this.hide_target();
        }.bind(this));
    }

    function setup_zoom_callbacks(zoom_container) {
        zoom_container.callback_manager.set('zoom.input', function() {
            if (this.is_active) {
                this.place_at_selected();
            }
        }.bind(this));
    }

    function is_visible() {
        return this.placed_div.is_visible();
    }

    function toggle(on_off) {
        if (on_off===undefined) this.is_active = !this.is_active;
        else this.is_active = on_off;
        if (this.is_active) {
            this.toggle_start_reaction_listener(true);
            if (this.target_coords !== null)
                this.show_dropdown(this.target_coords);
            else this.reload_at_selected();
            this.map.set_status('Click on the canvas or an existing metabolite');
            this.direction_arrow.show();
            // escape key
            this.escape = this.map.key_manager
                .add_escape_listener(function() {
                    this.hide_dropdown();
                }.bind(this), 'build_input');
        } else {
            this.toggle_start_reaction_listener(false);
            this.placed_div.hide();
            this.completely.input.blur();
            this.completely.hideDropDown();
            this.map.set_status(null);
            this.direction_arrow.hide();
            if (this.escape) this.escape.clear();
            this.escape = null;
        }
    }
    function show_dropdown(coords) {
        this.placed_div.place(coords);
        this.completely.input.blur();
        this.completely.repaint();
        this.completely.setText("");
        this.completely.input.focus();
    }
    function hide_dropdown() {
        this.placed_div.hide();
        this.completely.hideDropDown();
    }
    function place_at_selected() {
        /** Place autocomplete box at the first selected node.
         
         */

        // get the selected node
        this.map.deselect_text_labels();
        var selected_node = this.map.select_single_node();
        if (selected_node==null) return;
        var coords = { x: selected_node.x, y: selected_node.y };
        this.place(coords);
    }
    function place(coords) {
        this.placed_div.place(coords);
        this.direction_arrow.set_location(coords);
        this.direction_arrow.show();
    }

    function reload_at_selected() {
        /** Reload data for autocomplete box and redraw box at the first
         selected node.
         
         */
        // get the selected node
        this.map.deselect_text_labels();
        var selected_node = this.map.select_single_node();
        if (selected_node==null) return false;
        var coords = { x: selected_node.x, y: selected_node.y };
        // reload the reaction input
        this.reload(selected_node, coords, false);
        return true;
    }
    function reload(selected_node, coords, starting_from_scratch) {
        /** Reload data for autocomplete box and redraw box at the new
         coordinates.
         
         */

        // try finding the selected node
        if (!starting_from_scratch && !selected_node) {
            console.error('No selected node, and not starting from scratch');
            return;
        }

        this.place(coords);

        // blur
        this.completely.input.blur();
        this.completely.repaint(); // put in place()?

        if (this.map.cobra_model===null) {
            this.completely.setText('Cannot add: No model.');
            return;
        }

        // settings
        var show_names = this.settings.get_option('identifiers_on_map') == 'name',
            allow_duplicates = this.settings.get_option('allow_building_duplicate_reactions');

        // Find selected
        var options = [],
            cobra_reactions = this.map.cobra_model.reactions,
            cobra_metabolites = this.map.cobra_model.metabolites,
            reactions = this.map.reactions,
            has_data_on_reactions = this.map.has_data_on_reactions,
            reaction_data = this.map.reaction_data,
            reaction_data_styles = this.map.reaction_data_styles,
            selected_m_name = (selected_node ? (show_names ? selected_node.name : selected_node.bigg_id) : ''),
            bold_mets_in_str = function(str, mets) {
                return str.replace(new RegExp('(^| )(' + mets.join('|') + ')($| )', 'g'),
                                   '$1<b>$2</b>$3');
            };

        // for reactions
        var reaction_suggestions = {};        
        for (var bigg_id in cobra_reactions) {
            var reaction = cobra_reactions[bigg_id],
                reaction_name = reaction.name,
                show_r_name = (show_names ? reaction_name : bigg_id);

            // ignore drawn reactions
            if ((!allow_duplicates) && already_drawn(bigg_id, reactions))
                continue;

            // check segments for match to selected metabolite
            for (var met_bigg_id in reaction.metabolites) {

                // if starting with a selected metabolite, check for that id
                if (starting_from_scratch || met_bigg_id == selected_node.bigg_id) {

                    // don't add suggestions twice
                    if (bigg_id in reaction_suggestions) continue;

                    var met_name = cobra_metabolites[met_bigg_id].name;
                    
                    if (has_data_on_reactions) {
                        options.push({ reaction_data: reaction.data,
                                       html: ('<b>' + show_r_name + '</b>' +
                                              ': ' +
                                              reaction.data_string),
                                       matches: [show_r_name],
                                       id: bigg_id });
                        reaction_suggestions[bigg_id] = true;
                    } else {
                        // get the metabolite names or IDs
                        var mets = {},
                            show_met_names = [];
                        if (show_names) {
                            for (var met_id in reaction.metabolites) {
                                var name = cobra_metabolites[met_id].name;
                                mets[name] = reaction.metabolites[met_id];
                                show_met_names.push(name);
                            }
                        } else {
                            mets = utils.clone(reaction.metabolites);
                            for (var met_id in reaction.metabolites) {
                                show_met_names.push(met_id);
                            }
                        }
                        var key = show_names ? 'name' : 'bigg_id',
                            show_gene_names = reaction.genes.map(function(g_obj) {
                                return g_obj[key];
                            });
                        // get the reaction string
                        var reaction_string = CobraModel.build_reaction_string(mets,
                                                                               reaction.reversibility,
                                                                               reaction.lower_bound,
                                                                               reaction.upper_bound);
                        options.push({ html: ('<b>' + show_r_name + '</b>' +
                                              '\t' +
                                              bold_mets_in_str(reaction_string, [selected_m_name])),
                                       matches: [show_r_name].concat(show_met_names).concat(show_gene_names),
                                       id: bigg_id });
                        reaction_suggestions[bigg_id] = true;
                    }
                }
            }
        }
        
        // Generate the array of reactions to suggest and sort it
        var sort_fn;
        if (has_data_on_reactions) {
            sort_fn = function(x, y) {
                return Math.abs(y.reaction_data) - Math.abs(x.reaction_data);
            };
        } else {
            sort_fn = function(x, y) {
                return (x.html.toLowerCase() < y.html.toLowerCase() ? -1 : 1);
            };
        }
        options = options.sort(sort_fn);
        // set up the box with data, searching for first num results
        var num = 20,
            complete = this.completely;
        complete.options = options;

        // TODO test this behavior
        // if (strings_to_display.length==1) complete.setText(strings_to_display[0]);
        // else complete.setText("");
        complete.setText("");
        
        var direction_arrow = this.direction_arrow,
            check_and_build = function(id) {
                if (id !== null) {
                    // make sure the selected node exists, in case changes were made in the meantime
                    if (starting_from_scratch) {
                        this.map.new_reaction_from_scratch(id,
                                                           coords,
                                                           direction_arrow.get_rotation());
                    } else {
                        if (!(selected_node.node_id in this.map.nodes)) {
                            console.error('Selected node no longer exists');
                            this.hide_dropdown();
                            return;
                        }
                        this.map.new_reaction_for_metabolite(id,
                                                             selected_node.node_id,
                                                             direction_arrow.get_rotation());
                    }
                }
            }.bind(this);
        complete.onEnter = function(id) {
            this.setText("");
            this.onChange("");
            check_and_build(id);
        };
        complete.repaint();
        this.completely.input.focus();

        //definitions
        function already_drawn(bigg_id, reactions) {
            for (var drawn_id in reactions) {
                if (reactions[drawn_id].bigg_id==bigg_id) 
                    return true;
            }
            return false;
        };
    }
    function toggle_start_reaction_listener(on_off) {
        /** Toggle listening for a click to place a new reaction on the canvas.

         */
        if (on_off===undefined)
            this.start_reaction_listener = !this.start_reaction_listener;
        else if (this.start_reaction_listener==on_off)
            return;
        else
            this.start_reaction_listener = on_off;
        
        if (this.start_reaction_listener) {
            this.map.sel.on('click.start_reaction', function(node) {
                // TODO fix this hack
                if (this.direction_arrow.dragging) return;
                // reload the reaction input
                var coords = { x: d3.mouse(node)[0],
                               y: d3.mouse(node)[1] };
                // unselect metabolites
                this.map.deselect_nodes();
                this.map.deselect_text_labels();
                // reload the reaction input
                this.reload(null, coords, true);
                // generate the target symbol
                this.show_target(this.map, coords);
            }.bind(this, this.map.sel.node()));
            this.map.sel.classed('start-reaction-cursor', true);
        } else {
            this.map.sel.on('click.start_reaction', null);
            this.map.sel.classed('start-reaction-cursor', false);
            this.hide_target();
        }
    }

    function hide_target() {
        if (this.target_coords)
            this.map.sel.selectAll('.start-reaction-target').remove();
        this.target_coords = null;
    }
    function show_target(map, coords) {
        var s = map.sel.selectAll('.start-reaction-target').data([12, 5]);
        s.enter().append('circle')
            .classed('start-reaction-target', true)
            .attr('r', function(d) { return d; })
            .style('stroke-width', 4);
        s.style('visibility', 'visible')
            .attr('transform', 'translate('+coords.x+','+coords.y+')');
        this.target_coords = coords;
    }
});

define('CallbackManager',["utils"], function(utils) {
    /** CallbackManager()

     */

    var CallbackManager = utils.make_class();
    CallbackManager.prototype = { init: init,
                                  set: set,
                                  remove: remove,
                                  run: run };

    return CallbackManager;

    function init() {

    }
    function set(name, fn) {
        /** As in d3 callbacks, you can namespace your callbacks after a period:
         
         select_metabolite.direction_arrow
         select_metabolite.input

         Both are called by select_metabolite
         
         */
        if (this.callbacks===undefined) this.callbacks = {};
        if (this.callbacks[name]===undefined) this.callbacks[name] = [];
        this.callbacks[name].push(fn);

        return this;
    }
    function remove(name) {
        /** Remove a callback by name
         
         */
        if (this.callbacks===undefined || Object.keys(this.callbacks).length==0) {
            console.warn('No callbacks to remove');
        }
        delete this.callbacks[name];
        return this;
    }
    function run(name, this_arg) {
        /** Run all callbacks that match the portion of name before the period ('.').

         Arguments
         ---------

         name: The callback name, which can include a tag after a '.' to
         specificy a particular callback.

         this_arg: (Optional, Default: null) The object assigned to `this` in
         the callback.

         */
        if (this.callbacks===undefined) return this;
        if (this_arg===undefined) this_arg = null;
        // pass all but the first (name) argument to the callback
        var pass_args = Array.prototype.slice.call(arguments, 2);
        // look for matching callback names
        for (var a_name in this.callbacks) {
            var split_name = a_name.split('.')[0];
            if (split_name==name) {
                this.callbacks[a_name].forEach(function(fn) {
                    fn.apply(this_arg, pass_args);
                });
            }
        }
        return this;
    }
});

define('ZoomContainer',["utils", "CallbackManager"], function(utils, CallbackManager) {
    /** ZoomContainer

     The zoom behavior is based on this SO question:
     http://stackoverflow.com/questions/18788188/how-to-temporarily-disable-the-zooming-in-d3-js
     */
    var ZoomContainer = utils.make_class();
    ZoomContainer.prototype = { init: init,
                                update_scroll_behavior: update_scroll_behavior,
                                toggle_zoom: toggle_zoom,
                                go_to: go_to,
                                zoom_by: zoom_by,
                                zoom_in: zoom_in,
                                zoom_out: zoom_out,
                                get_size: get_size,
                                translate_off_screen: translate_off_screen,
                                reset: reset };
    return ZoomContainer;

    // definitions
    function init(selection, size_container, scroll_behavior) {
        /** Make a container that will manage panning and zooming.

         selection: A d3 selection of an 'svg' or 'g' node to put the zoom
         container in.

         size_container: A d3 selection of a 'div' node that has defined width
         and height.

         */

        this.zoom_on = true;
        this.initial_zoom = 1.0;
        this.window_translate = {x: 0, y: 0};
        this.window_scale = 1.0;

        // set up the callbacks
        this.callback_manager = new CallbackManager();

        // save the size_container
        this.size_container = size_container;

        // set up the container
        selection.select("#zoom-container").remove();
        var container = selection.append("g")
                .attr("id", "zoom-container");
        this.container = container;
        this.zoomed_sel = container.append("g");
        
        // update the scroll behavior
        this.update_scroll_behavior(scroll_behavior);

        // initialize vars
        this.saved_scale = null;
        this.saved_translate = null;
    }
    
    function update_scroll_behavior(scroll_behavior) {
        // the zoom function and behavior
        var zoom = function(zoom_container, event) {
            if (zoom_container.zoom_on) {
                zoom_container.zoomed_sel.attr("transform", "translate(" + event.translate + ")" +
                                               "scale(" + event.scale + ")");
                zoom_container.window_translate = {'x': event.translate[0],
                                                   'y': event.translate[1]};
                zoom_container.window_scale = event.scale;
                zoom_container.callback_manager.run('zoom');
            }
        };
        // clear all behaviors
        this.container.on("mousewheel.zoom", null)
            .on("DOMMouseScroll.zoom", null) // disables older versions of Firefox
            .on("wheel.zoom", null) // disables newer versions of Firefox
            .on('dblclick.zoom', null)
            .on('mousewheel.escher', wheel_fn)
            .on('DOMMouseScroll.escher', wheel_fn)
            .on('wheel.escher', wheel_fn);
        
        // new zoom
        this.zoom_behavior = d3.behavior.zoom()
            .on("zoom", function() {
                zoom(this, d3.event);
            }.bind(this));
        this.container.call(this.zoom_behavior);    

        // options
        if (scroll_behavior=='none' || scroll_behavior=='pan') {
            this.container.on("mousewheel.zoom", null)
                .on("DOMMouseScroll.zoom", null) // disables older versions of Firefox
                .on("wheel.zoom", null) // disables newer versions of Firefox
                .on('dblclick.zoom', null);
        }
        if (scroll_behavior == 'pan') {
            // Add the wheel listener
            var wheel_fn = function() {
                var ev = d3.event,
                    sensitivity = 0.5;
                // stop scroll in parent elements
                ev.stopPropagation();
                ev.preventDefault();
                ev.returnValue = false;
                // change the location
                this.go_to(this.window_scale,
                           { x: this.window_translate.x -
                             (ev.wheelDeltaX!==undefined ? -ev.wheelDeltaX/1.5 : ev.deltaX) * sensitivity,
                             y: this.window_translate.y -
                             (ev.wheelDeltaY!==undefined ? -ev.wheelDeltaY/1.5 : ev.deltaY) * sensitivity },
                           false);
            }.bind(this);
            this.container.on('mousewheel.escher', wheel_fn);
            this.container.on('DOMMouseScroll.escher', wheel_fn);
            this.container.on('wheel.escher', wheel_fn);
        }
    }

    function toggle_zoom(on_off) {
        /** Toggle the zoom state, and remember zoom when the behavior is off.

         */
        if (on_off===undefined) {
            this.zoom_on = !this.zoom_on;
        } else {
            this.zoom_on = on_off;
        }
        if (this.zoom_on) {
            if (this.saved_scale !== null){
                this.zoom_behavior.scale(this.saved_scale);
                this.saved_scale = null;
            }
            if (this.saved_translate !== null){
                this.zoom_behavior.translate(this.saved_translate);
                this.saved_translate = null;
            }

            // turn on the hand
            this.zoomed_sel
                .classed('cursor-grab', true).classed('cursor-grabbing', false);
            this.zoomed_sel
                .on('mousedown.cursor', function(sel) {
                    sel.classed('cursor-grab', false).classed('cursor-grabbing', true);
                }.bind(null, this.zoomed_sel))
                .on('mouseup.cursor', function(sel) {
                    sel.classed('cursor-grab', true).classed('cursor-grabbing', false);
                }.bind(null, this.zoomed_sel));
        } else {
            if (this.saved_scale === null){
                this.saved_scale = utils.clone(this.zoom_behavior.scale());
            }
            if (this.saved_translate === null){
                this.saved_translate = utils.clone(this.zoom_behavior.translate());
            }

            // turn off the hand
            this.zoomed_sel.style('cursor', null)
                .classed('cursor-grab', false)
                .classed('cursor-grabbing', false);
            this.zoomed_sel.on('mousedown.cursor', null);
            this.zoomed_sel.on('mouseup.cursor', null);
        }
    }

    // functions to scale and translate
    function go_to(scale, translate, show_transition) {
        utils.check_undefined(arguments, ['scale', 'translate']);
        if (show_transition===undefined) show_transition = true;

        if (!scale) throw new Error('Bad scale value');
        if (!translate || !('x' in translate) || !('y' in translate) ||
            isNaN(translate.x) || isNaN(translate.y))
            return console.error('Bad translate value');

        this.zoom_behavior.scale(scale);
        this.window_scale = scale;
        if (this.saved_scale !== null) this.saved_scale = scale;

        var translate_array = [translate.x, translate.y];
        this.zoom_behavior.translate(translate_array);
        this.window_translate = translate;
        if (this.saved_translate !== null) this.saved_translate = translate_array;

        var move_this = (show_transition ?
                         this.zoomed_sel.transition() :
                         this.zoomed_sel);
        move_this.attr('transform',
                       'translate('+this.window_translate.x+','+this.window_translate.y+')'+
                       'scale('+this.window_scale+')');

        this.callback_manager.run('go_to');
        return null;
    }

    function zoom_by(amount) {
        var size = this.get_size(),
            shift = { x: size.width/2 - ((size.width/2 - this.window_translate.x) * amount +
                                         this.window_translate.x),
                      y: size.height/2 - ((size.height/2 - this.window_translate.y) * amount +
                                          this.window_translate.y) };
        this.go_to(this.window_scale*amount,
                   utils.c_plus_c(this.window_translate, shift),
                   true);
    }
    function zoom_in() {
        this.zoom_by(1.5);
    }
    function zoom_out() {
        this.zoom_by(0.667);
    }

    function get_size() {
        return { width: parseInt(this.size_container.style('width'), 10),
                 height: parseInt(this.size_container.style('height'), 10) };
    }

    function translate_off_screen(coords) {
        // shift window if new reaction will draw off the screen
        // TODO BUG not accounting for scale correctly
        var margin = 120, // pixels
            size = this.get_size(),
            current = {'x': {'min': - this.window_translate.x / this.window_scale +
                             margin / this.window_scale,
                             'max': - this.window_translate.x / this.window_scale +
                             (size.width-margin) / this.window_scale },
                       'y': {'min': - this.window_translate.y / this.window_scale +
                             margin / this.window_scale,
                             'max': - this.window_translate.y / this.window_scale +
                             (size.height-margin) / this.window_scale } };
        if (coords.x < current.x.min) {
            this.window_translate.x = this.window_translate.x -
                (coords.x - current.x.min) * this.window_scale;
            this.go_to(this.window_scale, this.window_translate);
        } else if (coords.x > current.x.max) {
            this.window_translate.x = this.window_translate.x -
                (coords.x - current.x.max) * this.window_scale;
            this.go_to(this.window_scale, this.window_translate);
        }
        if (coords.y < current.y.min) {
            this.window_translate.y = this.window_translate.y -
                (coords.y - current.y.min) * this.window_scale;
            this.go_to(this.window_scale, this.window_translate);
        } else if (coords.y > current.y.max) {
            this.window_translate.y = this.window_translate.y -
                (coords.y - current.y.max) * this.window_scale;
            this.go_to(this.window_scale, this.window_translate);
        }
    }
    function reset() {
        this.go_to(1.0, {x: 0.0, y: 0.0});
    }
});

/* global define, d3 */

define('Draw',['utils', 'data_styles', 'CallbackManager'], function(utils, data_styles, CallbackManager) {
    /** Manages creating, updating, and removing objects during d3 data binding.

     Arguments
     ---------

     behavior: An escher.Behavior object.

     settings: An escher.Settings object.

     Callbacks
     ---------

     draw.callback_manager.run('create_membrane', draw, enter_selection);
     draw.callback_manager.run('update_membrane', draw, update_selection);
     draw.callback_manager.run('create_reaction', draw, enter_selection);
     draw.callback_manager.run('update_reaction', draw, update_selection);
     draw.callback_manager.run('create_reaction_label', draw, enter_selection);
     draw.callback_manager.run('update_reaction_label', draw, update_selection);
     draw.callback_manager.run('create_segment', draw, enter_selection);
     draw.callback_manager.run('update_segment', draw, update_selection);
     draw.callback_manager.run('create_bezier', draw, enter_selection);
     draw.callback_manager.run('update_bezier', draw, update_selection);
     draw.callback_manager.run('create_node', draw, enter_selection);
     draw.callback_manager.run('update_node', draw, update_selection);
     draw.callback_manager.run('create_text_label', draw, enter_selection);
     draw.callback_manager.run('update_text_label', draw, update_selection);

     */

    var Draw = utils.make_class();

    // instance methods
    Draw.prototype = { init: init,
                       create_reaction: create_reaction,
                       update_reaction: update_reaction,
                       create_bezier: create_bezier,
                       update_bezier: update_bezier,
                       create_node: create_node,
                       update_node: update_node,
                       create_text_label: create_text_label,
                       update_text_label: update_text_label,
                       create_membrane: create_membrane,
                       update_membrane: update_membrane,
                       create_reaction_label: create_reaction_label,
                       update_reaction_label: update_reaction_label,
                       create_segment: create_segment,
                       update_segment: update_segment
                     };

    return Draw;

    // definitions
    function init(behavior, settings) {
        this.behavior = behavior;
        this.settings = settings;
        this.callback_manager = new CallbackManager();
    }

    function create_membrane(enter_selection) {
        enter_selection.append('rect')
            .attr('class', 'membrane');
        this.callback_manager.run('create_membrane', this, enter_selection);
    }

    function update_membrane(update_selection) {
        update_selection
            .attr('width', function(d){ return d.width; })
            .attr('height', function(d){ return d.height; })
            .attr('transform', function(d){return 'translate('+d.x+','+d.y+')';})
            .style('stroke-width', function(d) { return 10; })
            .attr('rx', function(d){ return 20; })
            .attr('ry', function(d){ return 20; });

        this.callback_manager.run('update_membrane', this, update_selection);
    }

    function create_reaction(enter_selection) {
        // attributes for new reaction group
        enter_selection.append('g')
            .attr('id', function(d) { return 'r'+d.reaction_id; })
            .attr('class', 'reaction')
            .call(this.create_reaction_label.bind(this));

        this.callback_manager.run('create_reaction', this, enter_selection);
        return;
    }

    function update_reaction(update_selection, scale, cobra_model, drawn_nodes,
                             defs, has_data_on_reactions) {
        /** Run on the update selection for reactions.

         Arguments
         ---------

         update_selection: The D3.js update selection.

         scale: A Scale object.

         cobra_model: A CobraModel object.

         drawn_nodes: The nodes object (e.g. Map.nodes).

         defs: The defs object generated by utils.setup_defs() (e.g. Map.defs).

         has_data_on_reactions: Boolean to determine whether data needs to be
         drawn.

         */

        // update reaction label
        update_selection.select('.reaction-label-group')
            .call(function(sel) {
                return this.update_reaction_label(sel, has_data_on_reactions);
            }.bind(this));

        // draw segments
        utils.draw_a_nested_object(update_selection, '.segment-group', 'segments', 'segment_id',
                                   this.create_segment.bind(this),
                                   function(sel) {
                                       return this.update_segment(sel, scale, cobra_model,
                                                                  drawn_nodes, defs,
                                                                  has_data_on_reactions);
                                   }.bind(this),
                                   function(sel) {
                                       sel.remove();
                                   });

        // run the callback
        this.callback_manager.run('update_reaction', this, update_selection);
    }

    function create_reaction_label(enter_selection) {
        /** Draw reaction label for selection.

         */

        var group = enter_selection.append('g')
                .attr('class', 'reaction-label-group');
        group.append('title'); // tooltip
        group.append('text')
            .attr('class', 'reaction-label label');
        group.append('g')
            .attr('class', 'all-genes-label-group');

        this.callback_manager.run('create_reaction_label', this, enter_selection);
    }

    function update_reaction_label(update_selection, has_data_on_reactions) {
        /** Run on the update selection for reaction labels.

         Arguments
         ---------

         update_selection: The D3.js update selection.

         has_data_on_reactions: Boolean to determine whether data needs to be
         drawn.

         */

        var decimal_format = d3.format('.4g'),
            identifiers_on_map = this.settings.get_option('identifiers_on_map'),
            identifiers_in_tooltip = (identifiers_on_map == 'bigg_id' ? 'name' : 'bigg_id'),
            reaction_data_styles = this.settings.get_option('reaction_styles'),
            show_gene_reaction_rules = this.settings.get_option('show_gene_reaction_rules'),
            hide_all_labels = this.settings.get_option('hide_all_labels'),
            gene_font_size = this.settings.get_option('gene_font_size'),
            label_mousedown_fn = this.behavior.label_mousedown,
            label_mouseover_fn = this.behavior.label_mouseover,
            label_mouseout_fn = this.behavior.label_mouseout;

        // label location
        update_selection
            .attr('transform', function(d) {
                return 'translate(' + d.label_x + ',' + d.label_y + ')';
            })
            .call(this.behavior.turn_off_drag)
            .call(this.behavior.reaction_label_drag);

        // update label visibility
        var label = update_selection.select('.reaction-label')
                .attr('visibility', hide_all_labels ? 'hidden' : 'visible');
        if (!hide_all_labels) {
            label
                .text(function(d) {
                    var t = d[identifiers_on_map];
                    if (has_data_on_reactions && reaction_data_styles.indexOf('text') != -1)
                        t += ' ' + d.data_string;
                    return t;
                })
                .on('mousedown', label_mousedown_fn)
                .on('mouseover', label_mouseover_fn)
                .on('mouseout', label_mouseout_fn);

            // tooltip
            update_selection.select('title').text(function(d) {
                return d[identifiers_in_tooltip];
            });
        }
        // gene label
        var all_genes_g = update_selection.select('.all-genes-label-group')
                .selectAll('.gene-label-group')
                .data(function(d) {
                    var show_gene_string = ('gene_string' in d &&
                                            d.gene_string !== null &&
                                            show_gene_reaction_rules &&
                                            (!hide_all_labels) &&
                                            reaction_data_styles.indexOf('text') !== -1),
                        show_gene_reaction_rule = ('gene_reaction_rule' in d &&
                                                   d.gene_reaction_rule !== null &&
                                                   show_gene_reaction_rules &&
                                                   (!hide_all_labels) );
                    if (show_gene_string) {
                        return d.gene_string;
                    } else if (show_gene_reaction_rule) {
                        // make the gene string with no data
                        return data_styles.gene_string_for_data(d.gene_reaction_rule, null,
                                                                d.genes, null, identifiers_on_map,
                                                                null);
                    } else {
                        return [];
                    }
                });
        // enter
        var gene_g = all_genes_g.enter()
                .append('g')
                .attr('class', 'gene-label-group');
        gene_g.append('text')
            .attr('class', 'gene-label')
            .style('font-size', gene_font_size + 'px');
        gene_g.append('title');
        // update
        all_genes_g.attr('transform', function(d, i) {
            return 'translate(0, ' + (gene_font_size * 1.5 * (i + 1)) + ')';
        });
        // update text
        all_genes_g.select('text').text(function(d) {
            return d['text'];
        });
        // update tooltip
        all_genes_g.select('title').text(function(d) {
            return d[identifiers_in_tooltip];
        });
        // exit
        all_genes_g.exit()
            .remove();

        this.callback_manager.run('update_reaction_label', this, update_selection);
    }

    function create_segment(enter_selection) {
        // create segments
        var g = enter_selection
                .append('g')
                .attr('class', 'segment-group')
                .attr('id', function(d) { return 's'+d.segment_id; });

        // create reaction arrow
        g.append('path')
            .attr('class', 'segment');

        g.append('g')
            .attr('class', 'arrowheads');

        g.append('g')
            .attr('class', 'stoichiometry-labels');

        this.callback_manager.run('create_segment', this, enter_selection);
    }

    function update_segment(update_selection, scale, cobra_model,
                            drawn_nodes, defs, has_data_on_reactions) {
        var reaction_data_styles = this.settings.get_option('reaction_styles'),
            should_size = (has_data_on_reactions && reaction_data_styles.indexOf('size') != -1),
            should_color = (has_data_on_reactions && reaction_data_styles.indexOf('color') != -1),
            no_data_size = this.settings.get_option('reaction_no_data_size'),
            no_data_color = this.settings.get_option('reaction_no_data_color');

        // update segment attributes
        var highlight_missing  = this.settings.get_option('highlight_missing'),
            hide_secondary_metabolites = this.settings.get_option('hide_secondary_metabolites'),
            primary_r = this.settings.get_option('primary_metabolite_radius'),
            secondary_r = this.settings.get_option('secondary_metabolite_radius'),
            get_arrow_size = function(data, should_size) {
                var width = 20,
                    height = 13;
                if (should_size) {
                    height = (data === null ? no_data_size : scale.reaction_size(data));
                    // check for nan
                    if (isNaN(height))
                        height = no_data_size;
                    width = height * 2;
                }
                return { width: width, height: height };
            },
            get_disp = function(arrow_size, reversibility, coefficient, node_is_primary) {
                var arrow_height = ((reversibility || coefficient > 0) ?
                                    arrow_size.height :
                                    0),
                    r = node_is_primary ? primary_r : secondary_r;
                return r + arrow_height + 10;
            };
        // update arrows
        update_selection
            .selectAll('.segment')
            .datum(function() {
                return this.parentNode.__data__;
            })
            .style('visibility', function(d) {
                var start = drawn_nodes[d.from_node_id],
                    end = drawn_nodes[d.to_node_id];
                if (hide_secondary_metabolites &&
                    ((end['node_type']=='metabolite' && !end.node_is_primary) ||
                     (start['node_type']=='metabolite' && !start.node_is_primary)))
                    return 'hidden';
                return null;
            })
            .attr('d', function(d) {
                if (d.from_node_id === null || d.to_node_id === null)
                    return null;
                var start = drawn_nodes[d.from_node_id],
                    end = drawn_nodes[d.to_node_id],
                    b1 = d.b1,
                    b2 = d.b2;
                // if metabolite, then displace the arrow
                if (start['node_type'] == 'metabolite') {
                    var arrow_size = get_arrow_size(d.data, should_size),
                        disp = get_disp(arrow_size, d.reversibility,
                                        d.from_node_coefficient,
                                        start.node_is_primary);
                    var direction = (b1 === null) ? end : b1;
                    start = displaced_coords(disp, start, direction, 'start');
                }
                if (end['node_type'] == 'metabolite') {
                    var arrow_size = get_arrow_size(d.data, should_size),
                        disp = get_disp(arrow_size, d.reversibility,
                                        d.to_node_coefficient,
                                        end.node_is_primary);
                    var direction = (b2 === null) ? start : b2;
                    end = displaced_coords(disp, direction, end, 'end');
                }
                var curve = ('M' + start.x + ',' + start.y + ' ');
                if (b1 !== null && b2 !== null) {
                    curve += ('C' + b1.x + ',' + b1.y + ' ' +
                              b2.x + ',' + b2.y + ' ');
                }
                curve += (end.x + ',' + end.y);
                return curve;
            })
            .style('stroke', function(d) {
                var reaction_id = this.parentNode.parentNode.__data__.bigg_id,
                    show_missing = (highlight_missing &&
                                    cobra_model !== null &&
                                    !(reaction_id in cobra_model.reactions));
                if (show_missing) {
                    return 'red';
                }
                if (should_color) {
                    var f = d.data;
                    return f === null ? no_data_color : scale.reaction_color(f);
                }
                return null;
            })
            .style('stroke-width', function(d) {
                if (should_size) {
                    var f = d.data;
                    return f === null ? no_data_size : scale.reaction_size(f);
                } else {
                    return null;
                }
            });

        // new arrowheads
        var arrowheads = update_selection.select('.arrowheads')
                .selectAll('.arrowhead')
                .data(function (d) {
                    var arrowheads = [],
                        start = drawn_nodes[d.from_node_id],
                        b1 = d.b1,
                        end = drawn_nodes[d.to_node_id],
                        b2 = d.b2;
                    // hide_secondary_metabolites option
                    if (hide_secondary_metabolites &&
                        ((end['node_type']=='metabolite' && !end.node_is_primary) ||
                         (start['node_type']=='metabolite' && !start.node_is_primary)))
                        return arrowheads;

                    if (start.node_type == 'metabolite' && (d.reversibility || d.from_node_coefficient > 0)) {
                        var arrow_size = get_arrow_size(d.data, should_size),
                            disp = get_disp(arrow_size, d.reversibility,
                                            d.from_node_coefficient,
                                            start.node_is_primary),
                            direction = (b1 === null) ? end : b1,
                            rotation = utils.to_degrees(utils.get_angle([start, direction])) + 90,
                            loc = displaced_coords(disp, start, direction, 'start');
                        arrowheads.push({ data: d.data,
                                          x: loc.x,
                                          y: loc.y,
                                          size: arrow_size,
                                          rotation: rotation,
                                          show_arrowhead_flux: (((d.from_node_coefficient < 0)==(d.reverse_flux))
                                                                || d.data==0)
                                        });
                    }
                    if (end.node_type == 'metabolite' && (d.reversibility || d.to_node_coefficient > 0)) {
                        var arrow_size = get_arrow_size(d.data, should_size),
                            disp = get_disp(arrow_size, d.reversibility,
                                            d.to_node_coefficient,
                                            end.node_is_primary),
                            direction = (b2 === null) ? start : b2,
                            rotation = utils.to_degrees(utils.get_angle([end, direction])) + 90,
                            loc = displaced_coords(disp, direction, end, 'end');
                        arrowheads.push({ data: d.data,
                                          x: loc.x,
                                          y: loc.y,
                                          size: arrow_size,
                                          rotation: rotation,
                                          show_arrowhead_flux: (((d.to_node_coefficient < 0)==(d.reverse_flux))
                                                                || d.data==0)
                                        });
                    }
                    return arrowheads;
                });
        arrowheads.enter().append('path')
            .classed('arrowhead', true);
        // update arrowheads
        arrowheads.attr('d', function(d) {
            return ('M' + [-d.size.width / 2, 0] +
                    ' L' + [0, d.size.height] +
                    ' L' + [d.size.width / 2, 0] + ' Z');
        }).attr('transform', function(d) {
            return 'translate(' + d.x + ',' + d.y + ')rotate(' + d.rotation + ')';
        }).style('fill', function(d) {
            if (should_color) {
                if (d.show_arrowhead_flux) {
                    // show the flux
                    var f = d.data;
                    return f===null ? no_data_color : scale.reaction_color(f);
                } else {
                    // if the arrowhead is not filled because it is reversed
                    return '#FFFFFF';
                }
            }
            // default fill color
            return null;
        }).style('stroke', function(d) {
            if (should_color) {
                // show the flux color in the stroke whether or not the fill is present
                var f = d.data;
                return f===null ? no_data_color : scale.reaction_color(f);
            }
            // default stroke color
            return null;
        });
        // remove
        arrowheads.exit().remove();

        // new stoichiometry labels
        var stoichiometry_labels = update_selection.select('.stoichiometry-labels')
                .selectAll('.stoichiometry-label')
                .data(function (d) {
                    var labels = [],
                        start = drawn_nodes[d.from_node_id],
                        b1 = d.b1,
                        end = drawn_nodes[d.to_node_id],
                        b2 = d.b2,
                        disp_factor = 1.5;
                    // hide_secondary_metabolites option
                    if (hide_secondary_metabolites &&
                        ((end['node_type']=='metabolite' && !end.node_is_primary) ||
                         (start['node_type']=='metabolite' && !start.node_is_primary)))
                        return labels;

                    if (start.node_type=='metabolite' && (Math.abs(d.from_node_coefficient) != 1)) {
                        var arrow_size = get_arrow_size(d.data, should_size),
                            disp = disp_factor * get_disp(arrow_size, false, 0, end.node_is_primary),
                            direction = (b1 === null) ? end : b1;
                        direction = utils.c_plus_c(direction, utils.rotate_coords(direction, 0.5, start));
                        var loc = displaced_coords(disp, start, direction, 'start');
                        loc = utils.c_plus_c(loc, {x:0, y:7});
                        labels.push({ coefficient: Math.abs(d.from_node_coefficient),
                                      x: loc.x,
                                      y: loc.y,
                                      data: d.data });
                    }
                    if (end.node_type=='metabolite' && (Math.abs(d.to_node_coefficient) != 1)) {
                        var arrow_size = get_arrow_size(d.data, should_size),
                            disp = disp_factor * get_disp(arrow_size, false, 0, end.node_is_primary),
                            direction = (b2 === null) ? start : b2;
                        direction = utils.c_plus_c(direction, utils.rotate_coords(direction, 0.5, end));
                        var loc = displaced_coords(disp, direction, end, 'end');
                        loc = utils.c_plus_c(loc, {x:0, y:7});
                        labels.push({ coefficient: Math.abs(d.to_node_coefficient),
                                      x: loc.x,
                                      y: loc.y,
                                      data: d.data });
                    }
                    return labels;
                });

        // add labels
        stoichiometry_labels.enter()
            .append('text')
            .attr('class', 'stoichiometry-label')
            .attr('text-anchor', 'middle');
        // update stoichiometry_labels
        stoichiometry_labels
            .attr('transform', function(d) {
                return 'translate(' + d.x + ',' + d.y + ')';
            })
            .text(function(d) {
                return d.coefficient;
            })
            .style('fill', function (d) {
                if (should_color) {
                    // show the flux color
                    var f = d.data;
                    return f === null ? no_data_color : scale.reaction_color(f);
                }
                // default segment color
                return null;
            });
        // remove
        stoichiometry_labels.exit().remove();

        this.callback_manager.run('update_segment', this, update_selection);
    }

    function create_bezier(enter_selection) {
        var g = enter_selection.append('g')
                .attr('id', function(d) { return d.bezier_id; })
                .attr('class', function(d) { return 'bezier'; });
        g.append('path')
            .attr('class', 'connect-line');
        g.append('circle')
            .attr('class', function(d) { return 'bezier-circle '+d.bezier; })
            .style('stroke-width', String(1)+'px')
            .attr('r', String(7)+'px');

        this.callback_manager.run('create_bezier', this, enter_selection);
    }

    function update_bezier(update_selection, show_beziers, drag_behavior,
                           mouseover, mouseout, drawn_nodes, drawn_reactions) {
        var hide_secondary_metabolites = this.settings.get_option('hide_secondary_metabolites');

        if (!show_beziers) {
            update_selection.attr('visibility', 'hidden');
            return;
        } else {
            update_selection.attr('visibility', 'visible');
        }

        // hide secondary
        update_selection
            .style('visibility', function(d) {
                var seg_data = drawn_reactions[d.reaction_id].segments[d.segment_id],
                    start = drawn_nodes[seg_data.from_node_id],
                    end = drawn_nodes[seg_data.to_node_id];
                if (hide_secondary_metabolites &&
                    ((end['node_type']=='metabolite' && !end.node_is_primary) ||
                     (start['node_type']=='metabolite' && !start.node_is_primary)))
                    return 'hidden';
                return null;
            });

        // draw bezier points
        update_selection.select('.bezier-circle')
            .call(this.behavior.turn_off_drag)
            .call(drag_behavior)
            .on('mouseover', mouseover)
            .on('mouseout', mouseout)
            .attr('transform', function(d) {
                if (d.x==null || d.y==null) return '';
                return 'translate('+d.x+','+d.y+')';
            });

        // update bezier line
        update_selection
            .select('.connect-line')
            .attr('d', function(d) {
                var node,
                    segment_d = drawn_reactions[d.reaction_id].segments[d.segment_id];
                node = (d.bezier=='b1' ?
                        drawn_nodes[segment_d.from_node_id] :
                        drawn_nodes[segment_d.to_node_id]);
                if (d.x==null || d.y==null || node.x==null || node.y==null)
                    return '';
                return 'M'+d.x+', '+d.y+' '+(node.x)+','+(node.y);
            });

        this.callback_manager.run('update_bezier', this, update_selection);
    }

    function create_node(enter_selection, drawn_nodes, drawn_reactions) {
        /** Run on enter selection for nodes.

         Arguments
         ---------

         enter_selection: The D3.js enter selection.

         drawn_nodes: The nodes object (e.g. Map.nodes).

         drawn_reactions: The reactions object (e.g. Map.reactions).

         */

        // create nodes
        var g = enter_selection
                .append('g')
                .attr('class', 'node')
                .attr('id', function(d) { return 'n'+d.node_id; });

        // create metabolite circle and label
        g.append('circle')
            .attr('class', function(d) {
                var c = 'node-circle';
                if (d.node_type!==null)
                    c += (' ' + d.node_type + '-circle');
                return c;
            });
        // labels
        var metabolite_groups = g.filter(function(d) {
            return d.node_type=='metabolite';
        });
        metabolite_groups.append('text')
            .attr('class', 'node-label label');
        metabolite_groups.append('title'); // tooltip

        this.callback_manager.run('create_node', this, enter_selection);
    }

    function update_node(update_selection, scale, has_data_on_nodes,
                         mousedown_fn, click_fn, mouseover_fn, mouseout_fn,
                         drag_behavior, label_drag_behavior) {
        /** Run on the update selection for nodes.

         Arguments
         ---------

         update_selection: The D3.js update selection.

         scale: A Scale object.

         has_data_on_nodes: Boolean to determine whether data needs to be drawn.

         mousedown_fn: A function to call on mousedown for a node.

         click_fn: A function to call on click for a node.

         mouseover_fn: A function to call on mouseover for a node.

         mouseout_fn: A function to call on mouseout for a node.

         drag_behavior: The D3.js drag behavior object for the nodes.

         label_drag_behavior: The D3.js drag behavior object for the node labels.

         */

        // update circle and label location
        var hide_secondary_metabolites = this.settings.get_option('hide_secondary_metabolites'),
            primary_r = this.settings.get_option('primary_metabolite_radius'),
            secondary_r = this.settings.get_option('secondary_metabolite_radius'),
            marker_r = this.settings.get_option('marker_radius'),
            hide_all_labels = this.settings.get_option('hide_all_labels'),
            identifiers_on_map = this.settings.get_option('identifiers_on_map'),
            identifiers_in_tooltip = (identifiers_on_map == 'bigg_id' ? 'name' : 'bigg_id'),
            metabolite_data_styles = this.settings.get_option('metabolite_styles'),
            no_data_style = { color: this.settings.get_option('metabolite_no_data_color'),
                              size: this.settings.get_option('metabolite_no_data_size') };


        var mg = update_selection
                .select('.node-circle')
                .attr('transform', function(d) {
                    return 'translate('+d.x+','+d.y+')';
                })
                .style('visibility', function(d) {
                    return (hide_secondary_metabolites && !d.node_is_primary) ? 'hidden' : null;
                })
                .attr('r', function(d) {
                    if (d.node_type == 'metabolite') {
                        var should_scale = (has_data_on_nodes &&
                                            metabolite_data_styles.indexOf('size') != -1);
                        if (should_scale) {
                            var f = d.data;
                            return f===null ? no_data_style['size'] : scale.metabolite_size(f);
                        } else {
                            return d.node_is_primary ? primary_r : secondary_r;
                        }
                    }
                    // midmarkers and multimarkers
                    return marker_r;
                })
                .style('fill', function(d) {
                    if (d.node_type=='metabolite') {
                        var should_color_data = (has_data_on_nodes &&
                                                 metabolite_data_styles.indexOf('color') != -1);
                        if (should_color_data) {
                            var f = d.data;
                            return f===null ? no_data_style['color'] : scale.metabolite_color(f);
                        } else {
                            return null;
                        }
                    }
                    // midmarkers and multimarkers
                    return null;
                })
                .call(this.behavior.turn_off_drag)
                .call(drag_behavior)
                .on('mousedown', mousedown_fn)
                .on('click', click_fn)
                .on('mouseover', mouseover_fn)
                .on('mouseout', mouseout_fn);

        // update node label visibility
        var node_label = update_selection
                .select('.node-label')
                .attr('visibility', hide_all_labels ? 'hidden' : 'visible');
        if (!hide_all_labels) {
            node_label
                .style('visibility', function(d) {
                    return (hide_secondary_metabolites && !d.node_is_primary) ? 'hidden' : null;
                })
                .attr('transform', function(d) {
                    return 'translate('+d.label_x+','+d.label_y+')';
                })
                .text(function(d) {
                    var t = d[identifiers_on_map];
                    if (has_data_on_nodes && metabolite_data_styles.indexOf('text') != -1)
                        t += ' ' + d.data_string;
                    return t;
                })
                .call(this.behavior.turn_off_drag)
                .call(label_drag_behavior);

            // tooltip
            update_selection.select('title').text(function(d) {
                return d[identifiers_in_tooltip];
            });
        }

        this.callback_manager.run('update_node', this, update_selection);
    }

    function create_text_label(enter_selection) {
        enter_selection.append('g')
            .attr('id', function(d) { return 'l'+d.text_label_id; })
            .attr('class', 'text-label')
            .append('text')
            .attr('class', 'label');

        this.callback_manager.run('create_text_label', this, enter_selection);
    }

    function update_text_label(update_selection) {
        var mousedown_fn = this.behavior.text_label_mousedown,
            click_fn = this.behavior.text_label_click,
            drag_behavior = this.behavior.selectable_drag,
            turn_off_drag = this.behavior.turn_off_drag;

        update_selection
            .select('.label')
            .text(function(d) { return d.text; })
            .attr('transform', function(d) { return 'translate('+d.x+','+d.y+')';})
            .on('mousedown', mousedown_fn)
            .on('click', click_fn)
            .call(turn_off_drag)
            .call(drag_behavior);

        this.callback_manager.run('update_text_label', this, update_selection);
    }

    function displaced_coords(reaction_arrow_displacement, start, end, displace) {
        utils.check_undefined(arguments, ['reaction_arrow_displacement', 'start', 'end', 'displace']);

        var length = reaction_arrow_displacement,
            hyp = utils.distance(start, end),
            new_x, new_y;
        if (!length || !hyp) console.error('Bad value');
        if (displace=='start') {
            new_x = start.x + length * (end.x - start.x) / hyp,
            new_y = start.y + length * (end.y - start.y) / hyp;
        } else if (displace=='end') {
            new_x = end.x - length * (end.x - start.x) / hyp,
            new_y = end.y - length * (end.y - start.y) / hyp;
        } else { console.error('bad displace value: ' + displace); }
        return {x: new_x, y: new_y};
    }
});

define('build',["utils"], function(utils) {
    return { new_reaction: new_reaction,
             rotate_nodes: rotate_nodes,
             move_node_and_dependents: move_node_and_dependents,
             new_text_label: new_text_label,
             bezier_id_for_segment_id: bezier_id_for_segment_id,
             bezier_ids_for_reaction_ids: bezier_ids_for_reaction_ids,
             new_beziers_for_segments: new_beziers_for_segments,
             new_beziers_for_reactions: new_beziers_for_reactions };
    
    // definitions
    function new_reaction(bigg_id, cobra_reaction, cobra_metabolites,
                          selected_node_id, selected_node,
                          largest_ids, cofactors, angle) {
        /** New reaction.

         angle: clockwise from 'right', in degrees

         */
        
        // rotate the new reaction around the selected metabolite
        // convert to radians
        angle = Math.PI / 180 * angle;

        // generate a new integer id
        var new_reaction_id = String(++largest_ids.reactions);

        // calculate coordinates of reaction
        var selected_node_coords = { x: selected_node.x,
                                     y: selected_node.y };
        
        // rotate main axis around angle with distance
        var reaction_length = 300,
            main_axis = [ selected_node_coords,
                          utils.c_plus_c(selected_node_coords,
                                         {'x': reaction_length, 'y': 0}) ],
            center = { 'x': (main_axis[0].x + main_axis[1].x)/2,  
                       'y': (main_axis[0].y + main_axis[1].y)/2 };
        
        // relative label location
        var label_d;
        if (Math.abs(angle) < Math.PI/4 ||
            Math.abs(angle - Math.PI) < Math.PI/4 ) {
                label_d = { x: -50, y: -40 };
            } else {
                label_d = { x: 30, y: 10 };
            }

        // relative anchor node distance
        var anchor_distance = 20;

        // new reaction structure
        var new_reaction = utils.clone(cobra_reaction);
        utils.extend(new_reaction,
                     { label_x: center.x + label_d.x,
                       label_y: center.y + label_d.y,
                       segments: {} });

        // set primary metabolites and count reactants/products

        // look for the selected metabolite, and record the indices
        var reactant_ranks = [], product_ranks = [], 
            reactant_count = 0, product_count = 0,
            reaction_is_reversed = false;
        for (var met_bigg_id in new_reaction.metabolites) { 
            // make the metabolites into objects
            var metabolite = cobra_metabolites[met_bigg_id],
                coefficient = new_reaction.metabolites[met_bigg_id],
                formula = metabolite.formula,
                new_metabolite = { coefficient: coefficient,
                                   bigg_id: met_bigg_id,
                                   name: metabolite.name };
            if (coefficient < 0) {
                new_metabolite.index = reactant_count;
                // score the metabolites. Infinity == selected, >= 1 == carbon containing
                var carbons = /C([0-9]+)/.exec(formula);
                if (selected_node.bigg_id==new_metabolite.bigg_id) {
                    reactant_ranks.push([new_metabolite.index, Infinity]);
                } else if (carbons && cofactors.indexOf(utils.decompartmentalize(new_metabolite.bigg_id)[0])==-1) {
                    reactant_ranks.push([new_metabolite.index, parseInt(carbons[1])]);
                }
                reactant_count++;
            } else {
                new_metabolite.index = product_count;
                var carbons = /C([0-9]+)/.exec(formula);
                if (selected_node.bigg_id==new_metabolite.bigg_id) {
                    product_ranks.push([new_metabolite.index, Infinity]);
                    reaction_is_reversed = true;
                } else if (carbons && cofactors.indexOf(utils.decompartmentalize(new_metabolite.bigg_id)[0])==-1) {
                    product_ranks.push([new_metabolite.index, parseInt(carbons[1])]);
                }
                product_count++;
            }
            new_reaction.metabolites[met_bigg_id] = new_metabolite;
        }

        // get the rank with the highest score
        var max_rank = function(old, current) { return current[1] > old[1] ? current : old; },
            primary_reactant_index = reactant_ranks.reduce(max_rank, [0,0])[0],
            primary_product_index = product_ranks.reduce(max_rank, [0,0])[0];

        // set primary metabolites, and keep track of the total counts
        for (var met_bigg_id in new_reaction.metabolites) {
            var metabolite = new_reaction.metabolites[met_bigg_id];
            if (metabolite.coefficient < 0) {
                if (metabolite.index==primary_reactant_index) metabolite.is_primary = true;
                metabolite.count = reactant_count + 1;
            } else {
                if (metabolite.index==primary_product_index) metabolite.is_primary = true;
                metabolite.count = product_count + 1;
            }
        }

        // generate anchor nodes
        var new_anchors = {},
            anchors = [ { node_type: 'anchor_reactants',
                          dis: { x: anchor_distance * (reaction_is_reversed ? 1 : -1), y: 0 } },
                        { node_type: 'center',
                          dis: { x: 0, y: 0 } },
                        { node_type: 'anchor_products',
                          dis: { x: anchor_distance * (reaction_is_reversed ? -1 : 1), y: 0 } } ],
            anchor_ids = {};
        anchors.map(function(n) {
            var new_id = String(++largest_ids.nodes),
                general_node_type = (n.node_type=='center' ? 'midmarker' : 'multimarker');
            new_anchors[new_id] = { node_type: general_node_type,
                                    x: center.x + n.dis.x,
                                    y: center.y + n.dis.y,
                                    connected_segments: [],
                                    name: null,
                                    bigg_id: null,
                                    label_x: null,
                                    label_y: null,
                                    node_is_primary: null };
            anchor_ids[n.node_type] = new_id;
        });

        // add the segments, outside to inside
        var new_anchor_groups = [ [ anchor_ids['anchor_reactants'], anchor_ids['center'] ],
                                  [ anchor_ids['anchor_products'],  anchor_ids['center'] ] ];
        new_anchor_groups.map(function(l) {
            var from_id = l[0], to_id = l[1],
                new_segment_id = String(++largest_ids.segments);
            new_reaction.segments[new_segment_id] =  { b1: null,
                                                       b2: null,
                                                       from_node_id: from_id,
                                                       to_node_id: to_id,
                                                       from_node_coefficient: null,
                                                       to_node_coefficient: null,
                                                       reversibility: new_reaction.reversibility,
                                                       data: new_reaction.data,
                                                       reverse_flux: new_reaction.reverse_flux };
            new_anchors[from_id].connected_segments.push({ segment_id: new_segment_id,
                                                           reaction_id: new_reaction_id });
            new_anchors[to_id].connected_segments.push({ segment_id: new_segment_id,
                                                         reaction_id: new_reaction_id });
        });

        // Add the metabolites, keeping track of total reactants and products.
        var new_nodes = new_anchors;
        for (var met_bigg_id in new_reaction.metabolites) {
            var metabolite = new_reaction.metabolites[met_bigg_id],
                primary_index, from_node_id;
            if (metabolite.coefficient < 0) {
                // metabolite.count = reactant_count + 1;
                primary_index = primary_reactant_index;
                from_node_id = anchor_ids['anchor_reactants'];
            } else {
                // metabolite.count = product_count + 1;
                primary_index = primary_product_index;
                from_node_id = anchor_ids['anchor_products'];
            }
            
            // calculate coordinates of metabolite components
            var met_loc = calculate_new_metabolite_coordinates(metabolite,
                                                               primary_index,
                                                               main_axis,
                                                               center,
                                                               reaction_length,
                                                               reaction_is_reversed);

            // if this is the existing metabolite
            if (selected_node.bigg_id==metabolite.bigg_id) {
                var new_segment_id = String(++largest_ids.segments);
                new_reaction.segments[new_segment_id] = { b1: met_loc.b1,
                                                          b2: met_loc.b2,
                                                          from_node_id: from_node_id,
                                                          to_node_id: selected_node_id,
                                                          from_node_coefficient: null,
                                                          to_node_coefficient: metabolite.coefficient,
                                                          reversibility: new_reaction.reversibility,
                                                          data: new_reaction.data,
                                                          reverse_flux: new_reaction.reverse_flux };
                // update the existing node
                selected_node.connected_segments.push({ segment_id: new_segment_id,
                                                        reaction_id: new_reaction_id });
                new_nodes[from_node_id].connected_segments.push({ segment_id: new_segment_id,
                                                                  reaction_id: new_reaction_id });
            } else {
                // save new metabolite
                var new_segment_id = String(++largest_ids.segments),
                    new_node_id = String(++largest_ids.nodes);
                new_reaction.segments[new_segment_id] = { b1: met_loc.b1,
                                                          b2: met_loc.b2,
                                                          from_node_id: from_node_id,
                                                          to_node_id: new_node_id,
                                                          from_node_coefficient: null,
                                                          to_node_coefficient: metabolite.coefficient,
                                                          reversibility: new_reaction.reversibility,
                                                          data: new_reaction.data,
                                                          reverse_flux: new_reaction.reverse_flux };
                // save new node
                new_nodes[new_node_id] = { connected_segments: [{ segment_id: new_segment_id,
                                                                  reaction_id: new_reaction_id }],
                                           x: met_loc.circle.x,
                                           y: met_loc.circle.y,
                                           node_is_primary: Boolean(metabolite.is_primary),
                                           label_x: met_loc.circle.x + label_d.x,
                                           label_y: met_loc.circle.y + label_d.y,
                                           name: metabolite.name,
                                           bigg_id: metabolite.bigg_id,
                                           node_type: 'metabolite' };
                new_nodes[from_node_id].connected_segments.push({ segment_id: new_segment_id,
                                                                  reaction_id: new_reaction_id });
            }
        }

        // now take out the extra reaction details
        var metabolites_array = []
        for (var bigg_id in new_reaction.metabolites) {
            metabolites_array.push({'bigg_id': bigg_id,
                                    'coefficient': new_reaction.metabolites[bigg_id].coefficient});
        }
        new_reaction.metabolites = metabolites_array;    

        // new_reactions object
        var new_reactions = {};
        new_reactions[new_reaction_id] = new_reaction;
        
        // new_beziers object
        var new_beziers = new_beziers_for_reactions(new_reactions);

        // add the selected node for rotation, and return it as a new (updated) node
        new_nodes[selected_node_id] = selected_node;
        rotate_nodes(new_nodes, new_reactions, new_beziers,
                     angle, selected_node_coords);

        return { new_reactions: new_reactions,
                 new_beziers: new_beziers,
                 new_nodes: new_nodes };
    }

    function rotate_nodes(selected_nodes, reactions, beziers, angle, center) {
        /** Rotate the nodes around center.

         selected_nodes: Nodes to rotate.
         reactions: Only updates beziers for these reactions.
         beziers: Also update the bezier points.
         angle: Angle to rotate in radians.
         center: Point to rotate around.

         */
        
        // functions
        var rotate_around = function(coord) {
            if (coord === null)
                return null;
            return utils.rotate_coords(coord, angle, center);
        };

        // recalculate: node
        var updated_node_ids = [], updated_reaction_ids = [];
        for (var node_id in selected_nodes) {
            var node = selected_nodes[node_id],
                // rotation distance
                displacement = rotate_around({ x: node.x, y: node.y }),
                // move the node
                updated = move_node_and_labels(node, reactions,
                                               displacement);
            // move the bezier points
            node.connected_segments.map(function(segment_obj) {
                var reaction = reactions[segment_obj.reaction_id];
                // If the reaction was not passed in the reactions argument, then ignore
                if (reaction === undefined) return;

                // rotate the beziers
                var segment_id = segment_obj.segment_id,
                    segment = reaction.segments[segment_id];
                if (segment.to_node_id==node_id && segment.b2) {
                    var displacement = rotate_around(segment.b2),
                        bez_id = bezier_id_for_segment_id(segment_id, 'b2');
                    segment.b2 = utils.c_plus_c(segment.b2, displacement);
                    beziers[bez_id].x = segment.b2.x;
                    beziers[bez_id].y = segment.b2.y; 
                } else if (segment.from_node_id==node_id && segment.b1) {
                    var displacement = rotate_around(segment.b1),
                        bez_id = bezier_id_for_segment_id(segment_id, 'b1');
                    segment.b1 = utils.c_plus_c(segment.b1, displacement);
                    beziers[bez_id].x = segment.b1.x;
                    beziers[bez_id].y = segment.b1.y; 
                }
            });

            updated_reaction_ids = utils.unique_concat([updated_reaction_ids,
                                                        updated.reaction_ids]);
            updated_node_ids.push(node_id);
        }

        return { node_ids: updated_node_ids,
                 reaction_ids: updated_reaction_ids };
    }
    
    function move_node_and_dependents(node, node_id, reactions, beziers, displacement) {
        /** Move the node and its labels and beziers.

         */
        var updated = move_node_and_labels(node, reactions, displacement);

        // move beziers
        node.connected_segments.map(function(segment_obj) {
            var reaction = reactions[segment_obj.reaction_id];
            // If the reaction was not passed in the reactions argument, then ignore
            if (reaction === undefined) return;

            // update beziers
            var segment_id = segment_obj.segment_id,
                segment = reaction.segments[segment_id];
            [['b1', 'from_node_id'], ['b2', 'to_node_id']].forEach(function(c) {
                var bez = c[0],
                    node = c[1];
                if (segment[node]==node_id && segment[bez]) {
                    segment[bez] = utils.c_plus_c(segment[bez], displacement);
                    var tbez = beziers[bezier_id_for_segment_id(segment_id, bez)];
                    tbez.x = segment[bez].x;
                    tbez.y = segment[bez].y;
                }
            });
            
            // add to list of updated reaction ids if it isn't already there
            if (updated.reaction_ids.indexOf(segment_obj.reaction_id) < 0) {
                updated.reaction_ids.push(segment_obj.reaction_id);
            }
        });
        return updated;
    }

    function move_node_and_labels(node, reactions, displacement) {
        node.x = node.x + displacement.x;
        node.y = node.y + displacement.y;
        
        // recalculate: node label
        node.label_x = node.label_x + displacement.x;
        node.label_y = node.label_y + displacement.y;

        // recalculate: reaction label
        var updated_reaction_ids = [];
        node.connected_segments.map(function(segment_obj) {
            var reaction = reactions[segment_obj.reaction_id];
            // add to list of updated reaction ids if it isn't already there
            if (updated_reaction_ids.indexOf(segment_obj.reaction_id) < 0) {
                updated_reaction_ids.push(segment_obj.reaction_id);

                // update reaction label (but only once per reaction
                if (node.node_type == 'midmarker') {
                    reaction.label_x = reaction.label_x + displacement.x;
                    reaction.label_y = reaction.label_y + displacement.y;
                }
            }
        });
        return { reaction_ids: updated_reaction_ids };
    }

    function calculate_new_metabolite_coordinates(met, primary_index, main_axis, center, dis, is_reversed) {
        /** Calculate metabolite coordinates for a new reaction metabolite.

         */
        // new local coordinate system
        var displacement = main_axis[0],
            main_axis = [utils.c_minus_c(main_axis[0], displacement),
                         utils.c_minus_c(main_axis[1], displacement)],
            center = utils.c_minus_c(center, displacement);
        
        // Curve parameters
        var w = 80,  // distance between reactants and between products
            b1_strength = 0.4,
            b2_strength = 0.25,
            w2 = w*0.7,
            secondary_dis = 40,
            num_slots = Math.min(2, met.count - 1);

        // size and spacing for primary and secondary metabolites
        var ds, draw_at_index, r;
        if (met.is_primary) { // primary
            ds = 20;
        } else { // secondary
            ds = 10;
            // don't use center slot
            if (met.index > primary_index) draw_at_index = met.index - 1;
            else draw_at_index = met.index;
        }

        var de = dis - ds, // distance between ends of line axis
            reaction_axis = [{'x': ds, 'y': 0},
                             {'x': de, 'y': 0}];

        // Define line parameters and axis.
        // Begin with unrotated coordinate system. +y = Down, +x = Right. 
        var end, circle, b1, b2;
        // reactants
        if (((met.coefficient < 0) != is_reversed) && met.is_primary) { // Ali == BADASS
            end = {'x': reaction_axis[0].x,
                   'y': reaction_axis[0].y};
            b1 = {'x': center.x*(1-b1_strength) + reaction_axis[0].x*b1_strength,
                  'y': center.y*(1-b1_strength) + reaction_axis[0].y*b1_strength};
            b2 = {'x': center.x*b2_strength + (end.x)*(1-b2_strength),
                  'y': center.y*b2_strength + (end.y)*(1-b2_strength)},
            circle = {'x': main_axis[0].x,
                      'y': main_axis[0].y};
        } else if ((met.coefficient < 0) != is_reversed) {
            end = {'x': reaction_axis[0].x + secondary_dis,
                   'y': reaction_axis[0].y + (w2*draw_at_index - w2*(num_slots-1)/2)},
            b1 = {'x': center.x*(1-b1_strength) + reaction_axis[0].x*b1_strength,
                  'y': center.y*(1-b1_strength) + reaction_axis[0].y*b1_strength},
            b2 = {'x': center.x*b2_strength + end.x*(1-b2_strength),
                  'y': center.y*b2_strength + end.y*(1-b2_strength)},
            circle = {'x': main_axis[0].x + secondary_dis,
                      'y': main_axis[0].y + (w*draw_at_index - w*(num_slots-1)/2)};
        } else if (((met.coefficient > 0) != is_reversed) && met.is_primary) {        // products
            end = {'x': reaction_axis[1].x,
                   'y': reaction_axis[1].y};
            b1 = {'x': center.x*(1-b1_strength) + reaction_axis[1].x*b1_strength,
                  'y': center.y*(1-b1_strength) + reaction_axis[1].y*b1_strength};
            b2 = {'x': center.x*b2_strength + end.x*(1-b2_strength),
                  'y': center.y*b2_strength + end.y*(1-b2_strength)},
            circle = {'x': main_axis[1].x,
                      'y': main_axis[1].y};
        } else if ((met.coefficient > 0) != is_reversed) {
            end = {'x': reaction_axis[1].x - secondary_dis,
                   'y': reaction_axis[1].y + (w2*draw_at_index - w2*(num_slots-1)/2)},
            b1 = {'x': center.x*(1-b1_strength) + reaction_axis[1].x*b1_strength,
                  'y': center.y*(1-b1_strength) + reaction_axis[1].y*b1_strength};
            b2 = {'x': center.x*b2_strength + end.x*(1-b2_strength),
                  'y': center.y*b2_strength + end.y*(1-b2_strength)},
            circle = {'x': main_axis[1].x - secondary_dis,
                      'y': main_axis[1].y + (w*draw_at_index - w*(num_slots-1)/2)};
        }
        var loc = {};
        loc.b1 = utils.c_plus_c(displacement, b1);
        loc.b2 = utils.c_plus_c(displacement, b2);
        loc.circle = utils.c_plus_c(displacement, circle);
        return loc;
    }

    function new_text_label(largest_ids, text, coords) {
        var new_id = String(++largest_ids.text_labels),
            new_label = { text: text,
                          x: coords.x,
                          y: coords.y };
        return {id: new_id, label: new_label};
    }

    function bezier_id_for_segment_id(segment_id, bez) {
        return segment_id+'_'+bez;
    }

    function bezier_ids_for_reaction_ids(reactions) {
        /** Return an array of beziers ids for the array of reaction ids.

         Arguments
         ---------

         reactions: A reactions object, e.g. a subset of *escher.Map.reactions*.

         */ 
        var bezier_ids = [];
        for (var reaction_id in reactions) {
            var reaction = reactions[reaction_id];

            for (var segment_id in reaction.segments) {
                var segment = reaction.segments[segment_id];

                ['b1', 'b2'].forEach(function(bez) {
                    var seg_bez = segment[bez];
                    if (seg_bez !== null) {
                        bezier_ids.push(bezier_id_for_segment_id(segment_id, bez));
                    }
                });
            }
        }
        return bezier_ids;
    }

    function new_beziers_for_segments(segments, reaction_id) {
        /** Return an object containing beziers for the segments object.

         Arguments
         ---------

         segments: A segments object, e.g. *escher.Map.segments*.

         reaction_id: The reaction id for the segments.

         */
        var beziers = {};
        for (var segment_id in segments) {
            var segment = segments[segment_id];

            ['b1', 'b2'].forEach(function(bez) {
                var seg_bez = segment[bez];
                if (seg_bez !== null) {
                    var bezier_id = bezier_id_for_segment_id(segment_id, bez);
                    beziers[bezier_id] = {
                        bezier: bez,
                        x: seg_bez.x,
                        y: seg_bez.y,
                        reaction_id: reaction_id,
                        segment_id: segment_id
                    };
                }
            });
        }
        return beziers;
    }

    function new_beziers_for_reactions(reactions) {
        /** Return an object containing beziers for the reactions object.

         Arguments
         ---------

         reactions: A reactions object, e.g. *escher.Map.reactions*.

         */
        var beziers = {};
        for (var reaction_id in reactions) {
            var reaction = reactions[reaction_id];

            var these = new_beziers_for_segments(reaction.segments, reaction_id);
            utils.extend(beziers, these);
        }
        return beziers;
    }
});

define('Behavior',["utils", "build"], function(utils, build) {
    /** Defines the set of click and drag behaviors for the map, and keeps track
     of which behaviors are activated. 

     A Behavior instance has the following attributes:

     my_behavior.rotation_drag:

     my_behavior.text_label_mousedown:

     my_behavior.text_label_click:

     my_behavior.selectable_mousedown:

     my_behavior.selectable_click:

     my_behavior.selectable_drag:

     my_behavior.node_mouseover:

     my_behavior.node_mouseout:

     my_behavior.label_mousedown:

     my_behavior.label_mouseover:

     my_behavior.label_mouseout:

     my_behavior.bezier_drag:

     my_behavior.bezier_mouseover:

     my_behavior.bezier_mouseout:

     my_behavior.reaction_label_drag:

     my_behavior.node_label_drag:

     */

    var Behavior = utils.make_class();
    
    // methods
    Behavior.prototype = { init: init,
                           toggle_rotation_mode: toggle_rotation_mode,
                           turn_everything_on: turn_everything_on,
                           turn_everything_off: turn_everything_off,
                           // toggle
                           toggle_selectable_click: toggle_selectable_click,
                           toggle_text_label_edit: toggle_text_label_edit,
                           toggle_selectable_drag: toggle_selectable_drag,
                           toggle_label_drag: toggle_label_drag,
                           toggle_label_mousedown: toggle_label_mousedown,
                           toggle_bezier_drag: toggle_bezier_drag,
                           // util
                           turn_off_drag: turn_off_drag,
                           // get drag behaviors
                           _get_selectable_drag: _get_selectable_drag,
                           _get_bezier_drag: _get_bezier_drag,
                           _get_reaction_label_drag: _get_reaction_label_drag,
                           _get_node_label_drag: _get_node_label_drag,
                           _get_generic_drag: _get_generic_drag,
                           _get_generic_angular_drag: _get_generic_angular_drag };

    return Behavior;

    // definitions
    function init(map, undo_stack) {
        this.map = map;
        this.undo_stack = undo_stack;

        // make an empty function that can be called as a behavior and does nothing
        this.empty_behavior = function() {};

        // rotation mode operates separately from the rest
        this.rotation_mode_enabled = false;
        this.rotation_drag = d3.behavior.drag();

        // behaviors to be applied
        this.selectable_mousedown = null;
        this.text_label_mousedown = null;
        this.text_label_click = null;
        this.selectable_drag = this.empty_behavior;
        this.node_mouseover = null;
        this.node_mouseout = null;
        this.label_mousedown = null;
        this.label_mouseover = null;
        this.label_mouseout = null;
        this.bezier_drag = this.empty_behavior;
        this.bezier_mouseover = null;
        this.bezier_mouseout = null;
        this.reaction_label_drag = this.empty_behavior;
        this.node_label_drag = this.empty_behavior;
        this.turn_everything_on();
    }
    function turn_everything_on() {
        /** Toggle everything except rotation mode and text mode.
         
         */
        this.toggle_selectable_click(true);
        this.toggle_selectable_drag(true);
        this.toggle_label_drag(true);
        this.toggle_label_mousedown(true);
    }
    function turn_everything_off() {
        /** Toggle everything except rotation mode and text mode.

         */
        this.toggle_selectable_click(false);
        this.toggle_selectable_drag(false);
        this.toggle_label_drag(false);
        this.toggle_label_mousedown(false);
    }

    function toggle_rotation_mode(on_off) {
        /** Listen for rotation, and rotate selected nodes.

         */
        if (on_off===undefined) {
            this.rotation_mode_enabled = !this.rotation_mode_enabled;
        } else {
            this.rotation_mode_enabled = on_off;
        }

        var selection_node = this.map.sel.selectAll('.node-circle'),
            selection_background = this.map.sel.selectAll('#canvas');

        if (this.rotation_mode_enabled) {
            this.map.callback_manager.run('start_rotation');
            
            var selected_nodes = this.map.get_selected_nodes();
            if (Object.keys(selected_nodes).length == 0) {
                console.warn('No selected nodes');
                return;
            }
            
            // show center
            this.center = average_location(selected_nodes);
            show_center.call(this);

            // this.set_status('Drag to rotate.');
            var map = this.map,
                selected_node_ids = Object.keys(selected_nodes),
                reactions = this.map.reactions,
                nodes = this.map.nodes,
                beziers = this.map.beziers;

            var start_fn = function(d) {
                // silence other listeners
                d3.event.sourceEvent.stopPropagation();
            },
                drag_fn = function(d, angle, total_angle, center) {
                    var updated = build.rotate_nodes(selected_nodes, reactions,
                                                     beziers, angle, center);
                    map.draw_these_nodes(updated.node_ids);
                    map.draw_these_reactions(updated.reaction_ids);
                },
                end_fn = function(d) {},
                undo_fn = function(d, total_angle, center) {
                    // undo
                    var these_nodes = {};
                    selected_node_ids.forEach(function(id) { 
                        these_nodes[id] = nodes[id];
                    });
                    var updated = build.rotate_nodes(these_nodes, reactions,
                                                     beziers, -total_angle,
                                                     center);
                    map.draw_these_nodes(updated.node_ids);
                    map.draw_these_reactions(updated.reaction_ids);
                },
                redo_fn = function(d, total_angle, center) {
                    // redo
                    var these_nodes = {};
                    selected_node_ids.forEach(function(id) {
                        these_nodes[id] = nodes[id];
                    });
                    var updated = build.rotate_nodes(these_nodes, reactions,
                                                     beziers, total_angle,
                                                     center);
                    map.draw_these_nodes(updated.node_ids);
                    map.draw_these_reactions(updated.reaction_ids);
                },
                center_fn = function() {
                    return this.center;
                }.bind(this);
            this.rotation_drag = this._get_generic_angular_drag(start_fn, drag_fn, end_fn,
                                                                undo_fn, redo_fn, center_fn,
                                                                this.map.sel);
            selection_background.call(this.rotation_drag);
            this.selectable_drag = this.rotation_drag;
        } else {
            // turn off all listeners
            hide_center.call(this);
            selection_node.on('mousedown.center', null);
            selection_background.on('mousedown.center', null);
            selection_background.on('mousedown.drag', null);
            selection_background.on('touchstart.drag', null);
            this.rotation_drag = null;
            this.selectable_drag = null;
        }

        // definitions
        function show_center() {
            var s = this.map.sel.selectAll('#rotation-center')
                    .data([0]),
                enter = s.enter()
                    .append('g').attr('id', 'rotation-center');
            
            enter.append('path').attr('d', 'M-32 0 L32 0')
                .attr('class', 'rotation-center-line');
            enter.append('path').attr('d', 'M0 -32 L0 32')
                .attr('class', 'rotation-center-line');

            s.attr('transform', 'translate('+this.center.x+','+this.center.y+')')
                .attr('visibility', 'visible');

            s.call(d3.behavior.drag()
                   .on('drag', function(sel) {
                       var cur = d3.transform(sel.attr('transform')),
                           new_loc = [d3.event.dx + cur.translate[0],
                                      d3.event.dy + cur.translate[1]];
                       sel.attr('transform', 'translate('+new_loc+')');
                       this.center = { x: new_loc[0], y: new_loc[1] };
                   }.bind(this, s)));
            s.on('mouseover', function() {
                var current = parseFloat(this.selectAll('path').style('stroke-width'));
                this.selectAll('path').style('stroke-width', current * 2 + 'px');
            }.bind(s));
            s.on('mouseout', function() {
                this.selectAll('path').style('stroke-width', null);
            }.bind(s));
        }
        function hide_center(sel) {
            this.map.sel.select('#rotation-center')
                .attr('visibility', 'hidden');
        }
        function average_location(nodes) {
            var xs = [], ys = [];
            for (var node_id in nodes) {
                var node = nodes[node_id];
                if (node.x !== undefined)
                    xs.push(node.x);
                if (node.y !== undefined)
                    ys.push(node.y);
            }
            return { x: utils.mean(xs),
                     y: utils.mean(ys) };
        }       
    }

    function toggle_selectable_click(on_off) {
        /** With no argument, toggle the node click on or off.

         Pass in a boolean argument to set the on/off state.

         */
        if (on_off===undefined) on_off = this.selectable_mousedown==null;
        if (on_off) {
            var map = this.map;
            this.selectable_mousedown = function(d) {
                // stop propogation for the buildinput to work right
                d3.event.stopPropagation();
                // this.parentNode.__data__.was_selected = d3.select(this.parentNode).classed('selected');
                // d3.select(this.parentNode).classed('selected', true);
            };
            this.selectable_click = function(d) {
                // stop propogation for the buildinput to work right
                d3.event.stopPropagation();
                // click suppressed. This DOES have en effect.
                if (d3.event.defaultPrevented) return;
                // turn off the temporary selection so select_selectable
                // works. This is a bit of a hack.
                // if (!this.parentNode.__data__.was_selected)
                //     d3.select(this.parentNode).classed('selected', false); 
                map.select_selectable(this, d);
                // this.parentNode.__data__.was_selected = false;
            };
            this.node_mouseover = function(d) {    
                d3.select(this).style('stroke-width', null);
                var current = parseFloat(d3.select(this).style('stroke-width'));
                if (!d3.select(this.parentNode).classed('selected'))
                    d3.select(this).style('stroke-width', current * 3 + 'px');
            };
            this.node_mouseout = function(d) {
                d3.select(this).style('stroke-width', null);
            };
        } else {
            this.selectable_mousedown = null;
            this.selectable_click = null;
            this.node_mouseover = null;
            this.node_mouseout = null;
            this.map.sel.select('#nodes')
                .selectAll('.node-circle').style('stroke-width', null);
        }
    }

    function toggle_text_label_edit(on_off) {
        /** With no argument, toggle the text edit on mousedown on/off.

         Pass in a boolean argument to set the on/off state.

         The backup state is equal to selectable_mousedown.

         */
        if (on_off===undefined) on_off = this.text_edit_mousedown == null;
        if (on_off) {
            var map = this.map,
                selection = this.selection;
            this.text_label_mousedown = function() {
                if (d3.event.defaultPrevented) return; // mousedown suppressed
                // run the callback
                var coords_a = d3.transform(d3.select(this).attr('transform')).translate,
                    coords = {x: coords_a[0], y: coords_a[1]};
                map.callback_manager.run('edit_text_label', null, d3.select(this), coords);
                d3.event.stopPropagation();
            };
            this.text_label_click = null;
            this.map.sel.select('#text-labels')
                .selectAll('.label')
                .classed('edit-text-cursor', true);
            // add the new-label listener
            this.map.sel.on('mousedown.new_text_label', function(node) {
                // silence other listeners
                d3.event.preventDefault();
                var coords = { x: d3.mouse(node)[0],
                               y: d3.mouse(node)[1] };
                this.map.callback_manager.run('new_text_label', null, coords);
            }.bind(this, this.map.sel.node()));
        } else {
            this.text_label_mousedown = this.selectable_mousedown;
            this.text_label_click = this.selectable_click;
            this.map.sel.select('#text-labels')
                .selectAll('.label')
                .classed('edit-text-cursor', false);
            // remove the new-label listener
            this.map.sel.on('mousedown.new_text_label', null);
            this.map.callback_manager.run('hide_text_label_editor');
        }
    }

    function toggle_selectable_drag(on_off) {
        /** With no argument, toggle the node drag & bezier drag on or off.

         Pass in a boolean argument to set the on/off state.

         */
        if (on_off===undefined) on_off = this.selectable_drag===this.empty_behavior;
        if (on_off) {
            this.selectable_drag = this._get_selectable_drag(this.map, this.undo_stack);
            this.bezier_drag = this._get_bezier_drag(this.map, this.undo_stack);
        } else {
            this.selectable_drag = this.empty_behavior;
            this.bezier_drag = this.empty_behavior;
        }
    }
    function toggle_label_drag(on_off) {
        /** With no argument, toggle the label drag on or off.

         Pass in a boolean argument to set the on/off state.

         */
        if (on_off===undefined) on_off = this.label_drag===this.empty_behavior;
        if (on_off) {
            this.reaction_label_drag = this._get_reaction_label_drag(this.map);
            this.node_label_drag = this._get_node_label_drag(this.map);
        } else {
            this.reaction_label_drag = this.empty_behavior;
            this.node_label_drag = this.empty_behavior;
        }
    }
    
    function toggle_label_mousedown(on_off) {
        /** With no argument, toggle the reaction label mousedown on or off.z

         Arguments
         ---------

         on_off: A boolean argument to set the on/off state.

        */           
        if (on_off===undefined) on_off = this.label_mousedown==null;
        if (on_off) {
            var map = this.map;
            // TODO turn this feature (reaction label selection) back on, but
            // with correct shift key management
            this.label_mousedown = function(d) {
                // if (d3.event.defaultPrevented) return; // mousedown suppressed
                // // select reaction/node
                // d3.select(this.parentNode.parentNode)
                //     .each(function(d) {
                //         var node_ids = {};
                //         for (var seg_id in d.segments) {
                //             ['to_node_id', 'from_node_id'].forEach(function(n) {
                //                 node_ids[d.segments[seg_id][n]] = true;
                //             });
                //         }
                //         map.sel.selectAll('.selected').classed('selected', false);
                //         map.sel.selectAll('.node')
                //             .classed('selected', function(d) {
                //                 return (d.node_id in node_ids);
                //             });
                //     });                            
                // d3.event.stopPropagation();
            };
            this.label_mouseover = function(d) {
                // d3.select(this).style('fill', 'rgb(56, 56, 184)');
            };
            this.label_mouseout = function(d) {
                // d3.select(this).style('fill', null);
            };
        } else {
            this.label_mousedown = null;
            this.label_mouseover = null;
            this.label_mouseout = null;
            this.map.sel.select('.node-label,.reaction-label')
                .style('fill', null);
        }
    }

    function toggle_bezier_drag(on_off) {
        /** With no argument, toggle the bezier drag on or off.

         Pass in a boolean argument to set the on/off state.

         */
        if (on_off===undefined) on_off = this.bezier_drag===this.empty_behavior;
        if (on_off) {
            this.bezier_drag = this._get_bezier_drag(this.map);
            this.bezier_mouseover = function(d) {
                d3.select(this).style('stroke-width', String(3)+'px');
            };
            this.bezier_mouseout = function(d) {
                d3.select(this).style('stroke-width', String(1)+'px');
            };
        } else {
            this.bezier_drag = this.empty_behavior;
            this.bezier_mouseover = null;
            this.bezier_mouseout = null;
        }
    }
    
    function turn_off_drag(sel) {
        sel.on('mousedown.drag', null);
        sel.on('touchstart.drag', null);
    }    

    function _get_selectable_drag(map, undo_stack) {
        /** Drag the selected nodes and text labels.

         */

        // define some variables
        var behavior = d3.behavior.drag(),
            the_timeout = null,
            total_displacement = null,
            // for nodes
            node_ids_to_drag = null,
            reaction_ids = null,
            // for text labels
            text_label_ids_to_drag = null,
            move_label = function(text_label_id, displacement) {
                var text_label = map.text_labels[text_label_id];
                text_label.x = text_label.x + displacement.x;
                text_label.y = text_label.y + displacement.y;
            };

        behavior.on("dragstart", function (d) { 
            // silence other listeners (e.g. nodes BELOW this one)
            d3.event.sourceEvent.stopPropagation();
            // remember the total displacement for later
            // total_displacement = {};
            total_displacement = {x: 0, y: 0};

            // If a text label is selected, the rest is not necessary
            if (d3.select(this).attr('class').indexOf('label') == -1) {           
                // Note that dragstart is called even for a click event
                var data = this.parentNode.__data__,
                    bigg_id = data.bigg_id,
                    node_group = this.parentNode;
                // Move element to back (for the next step to work). Wait 200ms
                // before making the move, becuase otherwise the element will be
                // deleted before the click event gets called, and selection
                // will stop working.
                the_timeout = window.setTimeout(function() {
                    node_group.parentNode.insertBefore(node_group,node_group.parentNode.firstChild);
                }, 200);
                // prepare to combine metabolites
                map.sel.selectAll('.metabolite-circle')
                    .on('mouseover.combine', function(d) {
                        if (d.bigg_id==bigg_id && d.node_id!=data.node_id) {
                            d3.select(this).style('stroke-width', String(12)+'px')
                                .classed('node-to-combine', true);
                        }
                    }).on('mouseout.combine', function(d) {
                        if (d.bigg_id==bigg_id) {
                            map.sel.selectAll('.node-to-combine').style('stroke-width', String(2)+'px')
                                .classed('node-to-combine', false);
                        }
                    });
            }
        });
        behavior.on("drag", function(d) {
            // if this node is not already selected, then select this one and
            // deselect all other nodes. Otherwise, leave the selection alone.
            if (!d3.select(this.parentNode).classed('selected'))
                map.select_selectable(this, d);

            // get the grabbed id
            var grabbed = {};
            if (d3.select(this).attr('class').indexOf('label')==-1) {
                // if it is a node
                grabbed['type'] = 'node';
                grabbed['id'] = this.parentNode.__data__.node_id;
            } else {
                // if it is a text label
                grabbed['type'] = 'label';
                grabbed['id'] = this.__data__.text_label_id;
            }

            var selected_node_ids = map.get_selected_node_ids(),
                selected_text_label_ids = map.get_selected_text_label_ids();
            node_ids_to_drag = []; text_label_ids_to_drag = [];
            // choose the nodes and text labels to drag
            if (grabbed['type']=='node' && 
                selected_node_ids.indexOf(grabbed['id'])==-1) { 
                node_ids_to_drag.push(grabbed['id']);
            } else if (grabbed['type']=='label' && 
                       selected_text_label_ids.indexOf(grabbed['id'])==-1) {
                text_label_ids_to_drag.push(grabbed['id']);
            } else {
                node_ids_to_drag = selected_node_ids;
                text_label_ids_to_drag = selected_text_label_ids;
            }
            reaction_ids = [];
            var displacement = { x: d3.event.dx,
                                 y: d3.event.dy };
            total_displacement = utils.c_plus_c(total_displacement, displacement);
            node_ids_to_drag.forEach(function(node_id) {
                // update data
                var node = map.nodes[node_id],
                    updated = build.move_node_and_dependents(node, node_id,
                                                             map.reactions,
                                                             map.beziers,
                                                             displacement);
                reaction_ids = utils.unique_concat([reaction_ids, updated.reaction_ids]);
                // remember the displacements
                // if (!(node_id in total_displacement))  total_displacement[node_id] = { x: 0, y: 0 };
                // total_displacement[node_id] = utils.c_plus_c(total_displacement[node_id], displacement);
            });
            text_label_ids_to_drag.forEach(function(text_label_id) {
                move_label(text_label_id, displacement);                
                // remember the displacements
                // if (!(node_id in total_displacement))  total_displacement[node_id] = { x: 0, y: 0 };
                // total_displacement[node_id] = utils.c_plus_c(total_displacement[node_id], displacement);
            });
            // draw
            map.draw_these_nodes(node_ids_to_drag);
            map.draw_these_reactions(reaction_ids);
            map.draw_these_text_labels(text_label_ids_to_drag);
        });
        behavior.on("dragend", function() {
            if (node_ids_to_drag===null) {
                // Dragend can be called when drag has not been called. In this,
                // case, do nothing.
                total_displacement = null;
                node_ids_to_drag = null;
                text_label_ids_to_drag = null;
                reaction_ids = null;
                the_timeout = null;
                return;
            }
            // look for mets to combine
            var node_to_combine_array = [];
            map.sel.selectAll('.node-to-combine').each(function(d) {
                node_to_combine_array.push(d.node_id);
            });
            if (node_to_combine_array.length==1) {
                // If a node is ready for it, combine nodes
                var fixed_node_id = node_to_combine_array[0],
                    dragged_node_id = this.parentNode.__data__.node_id,
                    saved_dragged_node = utils.clone(map.nodes[dragged_node_id]),
                    segment_objs_moved_to_combine = combine_nodes_and_draw(fixed_node_id,
                                                                           dragged_node_id);
                undo_stack.push(function() {
                    // undo
                    // put the old node back
                    map.nodes[dragged_node_id] = saved_dragged_node;
                    var fixed_node = map.nodes[fixed_node_id],
                        updated_reactions = [];
                    segment_objs_moved_to_combine.forEach(function(segment_obj) {
                        var segment = map.reactions[segment_obj.reaction_id].segments[segment_obj.segment_id];
                        if (segment.from_node_id==fixed_node_id) {
                            segment.from_node_id = dragged_node_id;
                        } else if (segment.to_node_id==fixed_node_id) {
                            segment.to_node_id = dragged_node_id;
                        } else {
                            console.error('Segment does not connect to fixed node');
                        }
                        // removed this segment_obj from the fixed node
                        fixed_node.connected_segments = fixed_node.connected_segments.filter(function(x) {
                            return !(x.reaction_id==segment_obj.reaction_id && x.segment_id==segment_obj.segment_id);
                        });
                        if (updated_reactions.indexOf(segment_obj.reaction_id)==-1)
                            updated_reactions.push(segment_obj.reaction_id);
                    });
                    map.draw_these_nodes([dragged_node_id]);
                    map.draw_these_reactions(updated_reactions);
                }, function () {
                    // redo
                    combine_nodes_and_draw(fixed_node_id, dragged_node_id);
                });

            } else {
                // otherwise, drag node
                
                // add to undo/redo stack
                // remember the displacement, dragged nodes, and reactions
                var saved_displacement = utils.clone(total_displacement), 
                    // BUG TODO this variable disappears!
                    // Happens sometimes when you drag a node, then delete it, then undo twice
                    saved_node_ids = utils.clone(node_ids_to_drag),
                    saved_text_label_ids = utils.clone(text_label_ids_to_drag),
                    saved_reaction_ids = utils.clone(reaction_ids);
                undo_stack.push(function() {
                    // undo
                    saved_node_ids.forEach(function(node_id) {
                        var node = map.nodes[node_id];
                        build.move_node_and_dependents(node, node_id, map.reactions,
                                                       map.beziers,
                                                       utils.c_times_scalar(saved_displacement, -1));
                    });
                    saved_text_label_ids.forEach(function(text_label_id) {
                        move_label(text_label_id, 
                                   utils.c_times_scalar(saved_displacement, -1));
                    });
                    map.draw_these_nodes(saved_node_ids);
                    map.draw_these_reactions(saved_reaction_ids);
                    map.draw_these_text_labels(saved_text_label_ids);
                }, function () {
                    // redo
                    saved_node_ids.forEach(function(node_id) {
                        var node = map.nodes[node_id];
                        build.move_node_and_dependents(node, node_id, map.reactions,
                                                       map.beziers,
                                                       saved_displacement);
                    });             
                    saved_text_label_ids.forEach(function(text_label_id) {
                        move_label(text_label_id, saved_displacement);
                    });
                    map.draw_these_nodes(saved_node_ids);
                    map.draw_these_reactions(saved_reaction_ids);
                    map.draw_these_text_labels(saved_text_label_ids);
                });
            }

            // stop combining metabolites
            map.sel.selectAll('.metabolite-circle')
                .on('mouseover.combine', null)
                .on('mouseout.combine', null);

            // clear the timeout
            window.clearTimeout(the_timeout);

            // clear the shared variables
            total_displacement = null;
            node_ids_to_drag = null;
            text_label_ids_to_drag = null;
            reaction_ids = null;
            the_timeout = null;
        });
        return behavior;

        // definitions
        function combine_nodes_and_draw(fixed_node_id, dragged_node_id) {
            var dragged_node = map.nodes[dragged_node_id],
                fixed_node = map.nodes[fixed_node_id],
                updated_segment_objs = [];
            dragged_node.connected_segments.forEach(function(segment_obj) {
                // change the segments to reflect
                var segment;
                try {
                    segment = map.reactions[segment_obj.reaction_id].segments[segment_obj.segment_id];
                    if (segment === undefined) throw new Error('undefined segment');
                } catch (e) {
                    console.warn('Could not find connected segment ' + segment_obj.segment_id);
                    return;
                }
                if (segment.from_node_id==dragged_node_id) segment.from_node_id = fixed_node_id;
                else if (segment.to_node_id==dragged_node_id) segment.to_node_id = fixed_node_id;
                else {
                    console.error('Segment does not connect to dragged node');
                    return;
                }
                // moved segment_obj to fixed_node
                fixed_node.connected_segments.push(segment_obj);
                updated_segment_objs.push(utils.clone(segment_obj));
                return;
            });
            // delete the old node
            map.delete_node_data([dragged_node_id]);
            // turn off the class
            map.sel.selectAll('.node-to-combine').classed('node-to-combine', false);
            // draw
            map.draw_everything();
            // return for undo
            return updated_segment_objs;
        }
    }
    function _get_bezier_drag(map) {
        var move_bezier = function(reaction_id, segment_id, bez, bezier_id, displacement) {
            var segment = map.reactions[reaction_id].segments[segment_id];
            segment[bez] = utils.c_plus_c(segment[bez], displacement);
            map.beziers[bezier_id].x = segment[bez].x;
            map.beziers[bezier_id].y = segment[bez].y;
        },
            start_fn = function(d) {
                d.dragging = true;
            },
            drag_fn = function(d, displacement, total_displacement) {
                // draw
                move_bezier(d.reaction_id, d.segment_id, d.bezier, d.bezier_id,
                            displacement);
                map.draw_these_reactions([d.reaction_id], false);
                map.draw_these_beziers([d.bezier_id]);
            },
            end_fn = function(d) {
                d.dragging = false;
            },
            undo_fn = function(d, displacement) {
                move_bezier(d.reaction_id, d.segment_id, d.bezier, d.bezier_id,
                            utils.c_times_scalar(displacement, -1));
                map.draw_these_reactions([d.reaction_id], false);
                map.draw_these_beziers([d.bezier_id]);
            },
            redo_fn = function(d, displacement) {
                move_bezier(d.reaction_id, d.segment_id, d.bezier, d.bezier_id,
                            displacement);
                map.draw_these_reactions([d.reaction_id], false);
                map.draw_these_beziers([d.bezier_id]);
            };
        return this._get_generic_drag(start_fn, drag_fn, end_fn, undo_fn,
                                      redo_fn, this.map.sel);
    }
    function _get_reaction_label_drag(map) {
        var move_label = function(reaction_id, displacement) {
            var reaction = map.reactions[reaction_id];
            reaction.label_x = reaction.label_x + displacement.x;
            reaction.label_y = reaction.label_y + displacement.y;
        },
            start_fn = function(d) {
            },
            drag_fn = function(d, displacement, total_displacement) {
                // draw
                move_label(d.reaction_id, displacement);
                map.draw_these_reactions([d.reaction_id]);
            },
            end_fn = function(d) {
            },
            undo_fn = function(d, displacement) {
                move_label(d.reaction_id, utils.c_times_scalar(displacement, -1));
                map.draw_these_reactions([d.reaction_id]);
            },
            redo_fn = function(d, displacement) {
                move_label(d.reaction_id, displacement);
                map.draw_these_reactions([d.reaction_id]);
            };
        return this._get_generic_drag(start_fn, drag_fn, end_fn, undo_fn,
                                      redo_fn, this.map.sel);
    }
    function _get_node_label_drag(map) {
        var move_label = function(node_id, displacement) {
            var node = map.nodes[node_id];
            node.label_x = node.label_x + displacement.x;
            node.label_y = node.label_y + displacement.y;
        },
            start_fn = function(d) {
            },
            drag_fn = function(d, displacement, total_displacement) {
                // draw
                move_label(d.node_id, displacement);
                map.draw_these_nodes([d.node_id]);
            },
            end_fn = function(d) {
            },
            undo_fn = function(d, displacement) {
                move_label(d.node_id, utils.c_times_scalar(displacement, -1));
                map.draw_these_nodes([d.node_id]);
            },
            redo_fn = function(d, displacement) {
                move_label(d.node_id, displacement);
                map.draw_these_nodes([d.node_id]);
            };
        return this._get_generic_drag(start_fn, drag_fn, end_fn, undo_fn,
                                      redo_fn, this.map.sel);
    }

    function _get_generic_drag(start_fn, drag_fn, end_fn, undo_fn, redo_fn, relative_to_selection) {
        /** Make a generic drag behavior, with undo/redo.

         start_fn: function(d) Called at dragstart.

         drag_fn: function(d, displacement, total_displacement) Called during
         drag.

         end_fn

         undo_fn

         redo_fn

         relative_to_selection: a d3 selection that the locations are calculated against.

         */
        
        // define some variables
        var behavior = d3.behavior.drag(),
            total_displacement,
            undo_stack = this.undo_stack,
            rel = relative_to_selection.node();

        behavior.on("dragstart", function (d) {
            // silence other listeners
            d3.event.sourceEvent.stopPropagation();
            total_displacement = { x: 0, y: 0 };
            start_fn(d);
        });
        behavior.on("drag", function(d) {
            // update data
            var displacement = { x: d3.event.dx,
                                 y: d3.event.dy },
                location = { x: d3.mouse(rel)[0],
                             y: d3.mouse(rel)[1] };

            // remember the displacement
            total_displacement = utils.c_plus_c(total_displacement, displacement);
            drag_fn(d, displacement, total_displacement, location);
        });
        behavior.on("dragend", function(d) {                      
            // add to undo/redo stack
            // remember the displacement, dragged nodes, and reactions
            var saved_d = utils.clone(d),
                saved_displacement = utils.clone(total_displacement), // BUG TODO this variable disappears!
                saved_location = { x: d3.mouse(rel)[0],
                                   y: d3.mouse(rel)[1] };

            undo_stack.push(function() {
                // undo
                undo_fn(saved_d, saved_displacement, saved_location);
            }, function () {
                // redo
                redo_fn(saved_d, saved_displacement, saved_location);
            });
            end_fn(d);
        });
        return behavior;
    }

    function _get_generic_angular_drag(start_fn, drag_fn, end_fn, undo_fn, redo_fn, 
                                       get_center, relative_to_selection) {
        /** Make a generic drag behavior, with undo/redo. Supplies angles in
         place of displacements.

         start_fn: function(d) Called at dragstart.

         drag_fn: function(d, displacement, total_displacement) Called during
         drag.

         end_fn:

         undo_fn:

         redo_fn:

         get_center:

         relative_to_selection: a d3 selection that the locations are calculated against.

         */
        
        // define some variables
        var behavior = d3.behavior.drag(),
            total_angle,
            undo_stack = this.undo_stack,
            rel = relative_to_selection.node();

        behavior.on("dragstart", function (d) {
            // silence other listeners
            d3.event.sourceEvent.stopPropagation();
            total_angle = 0;
            start_fn(d);
        });
        behavior.on("drag", function(d) {
            // update data
            var displacement = { x: d3.event.dx,
                                 y: d3.event.dy },
                location = { x: d3.mouse(rel)[0],
                             y: d3.mouse(rel)[1] },
                center = get_center(),
                angle = utils.angle_for_event(displacement,
                                              location,
                                              center);
            // remember the displacement
            total_angle = total_angle + angle;
            drag_fn(d, angle, total_angle, center);
        });
        behavior.on("dragend", function(d) {                      
            // add to undo/redo stack
            // remember the displacement, dragged nodes, and reactions
            var saved_d = utils.clone(d),
                saved_angle = total_angle,
                saved_center = utils.clone(get_center());

            undo_stack.push(function() {
                // undo
                undo_fn(saved_d, saved_angle, saved_center);
            }, function () {
                // redo
                redo_fn(saved_d, saved_angle, saved_center);
            });
            end_fn(d);
        });
        return behavior;
    }
});

define('Scale',["utils"], function(utils) {
    /** 
     */

    var Scale = utils.make_class();
    Scale.prototype = { init: init,
                        connect_to_settings: connect_to_settings };

    return Scale;

    // definitions
    function init() {
        this.x = d3.scale.linear();
        this.y = d3.scale.linear();
        this.x_size = d3.scale.linear();
        this.y_size = d3.scale.linear();
        this.size = d3.scale.linear();
        this.reaction_color = d3.scale.linear().clamp(true);
        this.reaction_size = d3.scale.linear().clamp(true);
        this.metabolite_color = d3.scale.linear().clamp(true);
        this.metabolite_size = d3.scale.linear().clamp(true);
        this.scale_path = function(path) {
            var x_fn = this.x, y_fn = this.y;
            // TODO: scale arrow width
            var str = d3.format(".2f"),
                path = path.replace(/(M|L)([0-9-.]+),?\s*([0-9-.]+)/g, function (match, p0, p1, p2) {
                    return p0 + [str(x_fn(parseFloat(p1))), str(y_fn(parseFloat(p2)))].join(', ');
                }),
                reg = /C([0-9-.]+),?\s*([0-9-.]+)\s*([0-9-.]+),?\s*([0-9-.]+)\s*([0-9-.]+),?\s*([0-9-.]+)/g;
            path = path.replace(reg, function (match, p1, p2, p3, p4, p5, p6) {
                return 'C'+str(x_fn(parseFloat(p1)))+','+
                    str(y_fn(parseFloat(p2)))+' '+
                    str(x_fn(parseFloat(p3)))+','+
                    str(y_fn(parseFloat(p4)))+' '+
                    [str(x_fn(parseFloat(p5)))+','+str(y_fn(parseFloat(p6)))];
            });
            return path;
        }.bind(this);
        this.scale_decimals = function(path, scale_fn, precision) {
            var str = d3.format("."+String(precision)+"f");
            path = path.replace(/([0-9.]+)/g, function (match, p1) {
                return str(scale_fn(parseFloat(p1)));
            });
            return path;
        };
    }

    function connect_to_settings(settings, map, get_data_statistics) {
        // domains
        var update_reaction = function(s) {
            var out = sort_scale(s, get_data_statistics()['reaction']);
            this.reaction_color.domain(out.domain);
            this.reaction_size.domain(out.domain);
            this.reaction_color.range(out.color_range);
            this.reaction_size.range(out.size_range);
        }.bind(this);
        var update_metabolite = function(s) {
            var out = sort_scale(s, get_data_statistics()['metabolite']);
            this.metabolite_color.domain(out.domain);
            this.metabolite_size.domain(out.domain);
            this.metabolite_color.range(out.color_range);
            this.metabolite_size.range(out.size_range);
        }.bind(this);

        // scale changes
        settings.streams['reaction_scale'].onValue(update_reaction);
        settings.streams['metabolite_scale'].onValue(update_metabolite);
        // stats changes
        map.callback_manager.set('calc_data_stats__reaction', function(changed) {
            if (changed) update_reaction(settings.get_option('reaction_scale'));
        });
        map.callback_manager.set('calc_data_stats__metabolite', function(changed) {
            if (changed) update_metabolite(settings.get_option('metabolite_scale'));
        });
        
        // definitions
        function sort_scale(scale, stats) {
            var sorted = scale.map(function(x) {
                var v;
                if (x.type in stats)
                    v = stats[x.type];
                else if (x.type == 'value')
                    v = x.value;
                else
                    throw new Error('Bad domain type ' + x.type);
                return { v: v,
                         color: x.color,
                         size: x.size };
            }).sort(function(a, b) {
                return a.v - b.v;
            });
            return { domain: sorted.map(function(x) { return x.v; }),
                     color_range: sorted.map(function(x) { return x.color; }),
                     size_range: sorted.map(function(x) { return x.size; }) };
        }
    }
});

define('UndoStack',["utils"], function(utils) {
    /** UndoStack returns a constructor that can be used to store undo info.
     */
    var UndoStack = utils.make_class();
    UndoStack.prototype = { init: init,
                            push: push,
                            undo: undo,
                            redo: redo };
    return UndoStack;

    // definitions
    function init() {
        var stack_size = 40;
        this.stack = Array(stack_size);
        this.current = -1;
        this.oldest = -1;
        this.newest = -1;
        this.end_of_stack = true;
        this.top_of_stack = true;
    }
    function push(undo_fn, redo_fn) {
        this.current = incr(this.current, this.stack.length);
        // var p2 = incr(p1, this.stack.length);
        // change the oldest
        if (this.end_of_stack)
            this.oldest = this.current;
        else if (this.oldest == this.current)
            this.oldest = incr(this.oldest, this.stack.length);
        this.stack[this.current] = { undo: undo_fn, redo: redo_fn };
        this.newest = this.current;

        // top of the stack
        this.top_of_stack = true;
        this.end_of_stack = false;
    }
    function undo() {
        // check that we haven't reached the end
        if (this.end_of_stack) return console.warn('End of stack.');
        // run the lastest stack function
        this.stack[this.current].undo();
        if (this.current == this.oldest) {
            // if the next index is less than the oldest, then the stack is dead
            this.end_of_stack = true;
        } else {
            // reference the next fn
            this.current = decr(this.current, this.stack.length);
        }

        // not at the top of the stack
        this.top_of_stack = false;
    }
    function redo() {
        // check that we haven't reached the end
        if (this.top_of_stack) return console.warn('Top of stack.');

        if (!this.end_of_stack)
            this.current = incr(this.current, this.stack.length);
        this.stack[this.current].redo();

        // if at top of stack
        if (this.current == this.newest)
            this.top_of_stack = true;

        // not at the end of the stack
        this.end_of_stack = false;
    }
    function incr(a, l) {
        return a + 1 > l - 1 ? 0 : a + 1;
    }
    function decr(a, l) {
        return a - 1 < 0 ? l - 1 : a -  1;
    }
});

define('KeyManager',['utils'], function(utils) {
    /** 
     */

    var KeyManager = utils.make_class();
    // static methods
    KeyManager.reset_held_keys = reset_held_keys;
    // instance methods
    KeyManager.prototype = { init: init,
                             update: update,
                             toggle: toggle,
                             add_escape_listener: add_escape_listener,
                             add_enter_listener: add_enter_listener,
                             add_key_listener: add_key_listener };

    return KeyManager;

    // static methods
    function reset_held_keys(h) {
        h.command = false;
        h.control = false;
        h.option = false;
        h.shift = false;
    }
    // instance methods
    function init(unique_map_id, assigned_keys, input_list, ctrl_equals_cmd) {
        /** Assign keys for commands.

         */

        // identify this key manager
        if (unique_map_id===undefined) unique_map_id = null;
        this.unique_string = (unique_map_id === null ? '' : '.' + unique_map_id);        

        if (assigned_keys===undefined) this.assigned_keys = {};
        else this.assigned_keys = assigned_keys;
        if (input_list===undefined) this.input_list = [];
        else this.input_list = input_list;

        if (ctrl_equals_cmd===undefined) ctrl_equals_cmd = true;
        this.ctrl_equals_cmd = ctrl_equals_cmd;

        this.held_keys = {};
        reset_held_keys(this.held_keys);

        this.enabled = true;

        this.update();
    }

    function update() {
        var held_keys = this.held_keys,
            keys = this.assigned_keys,
            self = this;

        var modifier_keys = { command: 91,
                              command_right: 93,
                              control: 17,
                              option: 18,
                              shift: 16 };

        d3.select(window).on('keydown.key_manager' + this.unique_string, null);
        d3.select(window).on('keyup.key_manager' + this.unique_string, null);

        if (!(this.enabled)) return;

        d3.select(window).on('keydown.key_manager' + this.unique_string, function(ctrl_equals_cmd, input_list) {
            var kc = d3.event.keyCode,
                meaningless = true;
            // check the inputs
            var input_visible = false;
            input_list.forEach(function(input) {
                if (input.is_visible()) input_visible = true;
            });
            toggle_modifiers(modifier_keys, held_keys, kc, true);
            for (var key_id in keys) {
                var assigned_key = keys[key_id];
                if (check_key(assigned_key, kc, held_keys, ctrl_equals_cmd)) {
                    meaningless = false;
                    if (!(assigned_key.ignore_with_input && input_visible)) {
                        if (assigned_key.fn) {
                            assigned_key.fn.call(assigned_key.target);
                        } else {
                            console.warn('No function for key');
                        }
                        // prevent browser action
                        d3.event.preventDefault();
                    }
                }
            }
            // Sometimes modifiers get 'stuck', so reset them once in a while.
            // Only do this when a meaningless key is pressed
            for (var k in modifier_keys)
                if (modifier_keys[k] == kc) meaningless = false;
            if (meaningless) 
                reset_held_keys(held_keys);
        }.bind(null, this.ctrl_equals_cmd, this.input_list))
            .on('keyup.key_manager' + this.unique_string, function() {
                toggle_modifiers(modifier_keys, held_keys,
                                 d3.event.keyCode, false);
            });
        function toggle_modifiers(mod, held, kc, on_off) {
            for (var k in mod)
                if (mod[k] == kc)
                    held[k] = on_off;
        }
        function check_key(key, pressed, held, ctrl_equals_cmd) {
            if (key.key != pressed) return false;
            var mod = utils.clone(key.modifiers);
            if (mod === undefined)
                mod = { control: false,
                        command: false,
                        option: false,
                        shift: false };
            for (var k in held) {
                if (ctrl_equals_cmd &&
                    mod['control'] &&
                    (k=='command' || k=='command_right' || k=='control') &&
                    (held['command'] || held['command_right'] || held['control'])) {
                    continue;
                }
                if (mod[k] === undefined) mod[k] = false;
                if (mod[k] != held[k]) return false;
            }
            return true;
        }
    }
    function toggle(on_off) {
        /** Turn the brush on or off

         */
        if (on_off===undefined) on_off = !this.enabled;

        this.enabled = on_off;
        this.update();
    }   
    function add_enter_listener(callback, id) {
        /** Call the callback when the enter key is pressed, then
         unregisters the listener.

         */
        return this.add_key_listener(callback, 13, id);
    }
    function add_escape_listener(callback, id) {
        /** Call the callback when the escape key is pressed, then
         unregisters the listener.

         */
        return this.add_key_listener(callback, 27, id);
    }
    function add_key_listener(callback, kc, id) {
        /** Call the callback when the key is pressed, then unregisters the
         listener.

         */

        var event_name = 'keydown.' + kc;
        if (id !== undefined)
            event_name += ('.' + id);
        event_name += this.unique_string;
        
        var selection = d3.select(window);
        selection.on(event_name, function() {
            if (d3.event.keyCode==kc) {
                callback();
            }
        });
        return {
            clear: function() {
                selection.on(event_name, null);
            }
        };
    }
});

define('Canvas',["utils", "CallbackManager"], function(utils, CallbackManager) {
    /** Defines a canvas that accepts drag/zoom events and can be resized.

     Canvas(selection, x, y, width, height)

     Adapted from http://bl.ocks.org/mccannf/1629464.

     */

    var Canvas = utils.make_class();
    Canvas.prototype = { init: init,
                         toggle_resize: toggle_resize,
                         setup: setup,
                         size_and_location: size_and_location };

    return Canvas;

    function init(selection, size_and_location) {
        this.selection = selection;
        this.x = size_and_location.x;
        this.y = size_and_location.y;
        this.width = size_and_location.width;
        this.height = size_and_location.height;

        // enable by default
        this.resize_enabled = true;

        // set up the callbacks
        this.callback_manager = new CallbackManager();

        this.setup();
    }

    function toggle_resize(on_off) {
        /** Turn the resize on or off

         */
        if (on_off===undefined) on_off = !this.resize_enabled;

        if (on_off) {
            this.selection.selectAll('.drag-rect')
                .style('pointer-events', 'auto');
        } else {
            this.selection.selectAll('.drag-rect')
                .style('pointer-events', 'none');
        }
    }   

    function setup() {  
        var self = this,
            extent = {"x": this.width, "y": this.height},
            dragbar_width = 100,
            mouse_node_mult = 10,
            new_sel = this.selection.append('g')
                .classed('canvas-group', true)
                .data([{x: this.x, y: this.y}]);
        
        var mouse_node = new_sel.append('rect')
                .attr('id', 'mouse-node')
                .attr("width", this.width*mouse_node_mult)
                .attr("height", this.height*mouse_node_mult)
                .attr("transform", "translate("+[self.x - this.width*mouse_node_mult/2,
                                                 self.y - this.height*mouse_node_mult/2]+")")
                .attr('pointer-events', 'all');
        this.mouse_node = mouse_node;
        
        var rect = new_sel.append('rect')
                .attr('id', 'canvas')
                .attr("width", this.width)
                .attr("height", this.height)
                .attr("transform", "translate("+[self.x, self.y]+")");

        var drag_right = d3.behavior.drag()
                .origin(Object)
                .on("dragstart", stop_propagation)
                .on("drag", rdragresize),
            drag_left = d3.behavior.drag()
                .origin(Object)
                .on("dragstart", stop_propagation)
                .on("drag", ldragresize),
            drag_top = d3.behavior.drag()
                .origin(Object)
                .on("dragstart", stop_propagation)
                .on("drag", tdragresize),
            drag_bottom = d3.behavior.drag()
                .origin(Object)
                .on("dragstart", stop_propagation)
                .on("drag", bdragresize);

        var left = new_sel.append("rect")
                .classed('drag-rect', true)
                .attr('transform', function(d) {
                    return 'translate('+[ d.x - (dragbar_width/2),
                                          d.y + (dragbar_width/2) ]+')';
                })
                .attr("height", this.height - dragbar_width)
                .attr("id", "dragleft")
                .attr("width", dragbar_width)
                .attr("cursor", "ew-resize")
                .classed('resize-rect', true)
                .call(drag_left);
        
        var right = new_sel.append("rect")
                .classed('drag-rect', true)
                .attr('transform', function(d) {
                    return 'translate('+[ d.x + self.width - (dragbar_width/2),
                                          d.y + (dragbar_width/2) ]+')';
                })
                .attr("id", "dragright")
                .attr("height", this.height - dragbar_width)
                .attr("width", dragbar_width)
                .attr("cursor", "ew-resize")
                .classed('resize-rect', true)
                .call(drag_right);
        
        var top = new_sel.append("rect")
                .classed('drag-rect', true)
                .attr('transform', function(d) {
                    return 'translate('+[ d.x + (dragbar_width/2),
                                          d.y - (dragbar_width/2) ]+')';
                })
                .attr("height", dragbar_width)
                .attr("id", "dragtop")
                .attr("width", this.width - dragbar_width)
                .attr("cursor", "ns-resize")
                .classed('resize-rect', true)
                .call(drag_top);
        
        var bottom = new_sel.append("rect")
                .classed('drag-rect', true)
                .attr('transform', function(d) {
                    return 'translate('+[ d.x + (dragbar_width/2),
                                          d.y + self.height - (dragbar_width/2) ]+')';
                })
                .attr("id", "dragbottom")
                .attr("height", dragbar_width)
                .attr("width", this.width - dragbar_width)
                .attr("cursor", "ns-resize")
                .classed('resize-rect', true)
                .call(drag_bottom);
        
        // definitions
        function stop_propagation() {
            d3.event.sourceEvent.stopPropagation();
        }
        function transform_string(x, y, current_transform) {
            var tr = d3.transform(current_transform),
                translate = tr.translate;       
            if (x!==null) translate[0] = x;
            if (y!==null) translate[1] = y;
            return 'translate('+translate+')';
        }
        function ldragresize(d) {
            var oldx = d.x; 
            d.x = Math.min(d.x + self.width - (dragbar_width / 2), d3.event.x);
            self.x = d.x;
            self.width = self.width + (oldx - d.x);
            left.attr("transform", function(d) {
                return transform_string(d.x - (dragbar_width / 2), null, left.attr('transform'));
            });
            mouse_node.attr("transform", function(d) {
                return transform_string(d.x, null, mouse_node.attr('transform'));
            }).attr("width", self.width*mouse_node_mult);
            rect.attr("transform", function(d) {
                return transform_string(d.x, null, rect.attr('transform'));
            }).attr("width", self.width);
            top.attr("transform", function(d) {
                return transform_string(d.x + (dragbar_width/2), null, top.attr('transform'));
            }).attr("width", self.width - dragbar_width);
            bottom.attr("transform", function(d) {
                return transform_string(d.x + (dragbar_width/2), null, bottom.attr('transform'));
            }).attr("width", self.width - dragbar_width);

            self.callback_manager.run('resize');
        }

        function rdragresize(d) {
            d3.event.sourceEvent.stopPropagation();
            var dragx = Math.max(d.x + (dragbar_width/2), d.x + self.width + d3.event.dx);
            //recalculate width
            self.width = dragx - d.x;
            //move the right drag handle
            right.attr("transform", function(d) {
                return transform_string(dragx - (dragbar_width/2), null, right.attr('transform'));
            });
            //resize the drag rectangle
            //as we are only resizing from the right, the x coordinate does not need to change
            mouse_node.attr("width", self.width*mouse_node_mult);
            rect.attr("width", self.width);
            top.attr("width", self.width - dragbar_width);
            bottom.attr("width", self.width - dragbar_width);

            self.callback_manager.run('resize');
        }

        function tdragresize(d) {
            d3.event.sourceEvent.stopPropagation();     
            var oldy = d.y; 
            d.y = Math.min(d.y + self.height - (dragbar_width / 2), d3.event.y);
            self.y = d.y;
            self.height = self.height + (oldy - d.y);
            top.attr("transform", function(d) {
                return transform_string(null, d.y - (dragbar_width / 2), top.attr('transform'));
            });
            mouse_node.attr("transform", function(d) {
                return transform_string(null, d.y, mouse_node.attr('transform'));
            }).attr("width", self.height*mouse_node_mult);
            rect.attr("transform", function(d) {
                return transform_string(null, d.y, rect.attr('transform'));
            }).attr("height", self.height);
            left.attr("transform", function(d) {
                return transform_string(null, d.y + (dragbar_width/2), left.attr('transform'));
            }).attr("height", self.height - dragbar_width);
            right.attr("transform", function(d) {
                return transform_string(null, d.y + (dragbar_width/2), right.attr('transform'));
            }).attr("height", self.height - dragbar_width);

            self.callback_manager.run('resize');
        }

        function bdragresize(d) {
            d3.event.sourceEvent.stopPropagation();
            var dragy = Math.max(d.y + (dragbar_width/2), d.y + self.height + d3.event.dy);
            //recalculate width
            self.height = dragy - d.y;
            //move the right drag handle
            bottom.attr("transform", function(d) {
                return transform_string(null, dragy - (dragbar_width/2), bottom.attr('transform'));
            });
            //resize the drag rectangle
            //as we are only resizing from the right, the x coordinate does not need to change
            mouse_node.attr("height", self.height*mouse_node_mult);
            rect.attr("height", self.height);
            left.attr("height", self.height - dragbar_width);
            right.attr("height", self.height - dragbar_width);

            self.callback_manager.run('resize');
        }
    }

    function size_and_location() {
        return { x: this.x,
                 y: this.y,
                 width: this.width,
                 height: this.height };
    }
});

define('SearchIndex',["utils"], function(utils) {
    /** Define an index for searching for reaction and metabolites in the map.

     The index is stored in SearchIndex.index, an object of id/record pairs.

     */

    var SearchIndex = utils.make_class();
    SearchIndex.prototype = { init: init,
                              insert: insert,
                              remove: remove,
                              find: find };

    return SearchIndex;

    // definitions
    function init() {
        this.index = {};
    }

    function insert(id, record, overwrite, check_record) {
        /** Insert a record into the index.

         id: A unique string id.

         record: Records have the form:

         { 'name': '',
         'data': {} }

         Search is performed on substrings of the name.

         overwrite: (Default false) For faster performance, make overwrite true,
         and records will be inserted without checking for an existing record.

         check_record: (Default false) For faster performance, make check_record
         false. If true, records will be checked to make sure they have name and
         data attributes.

         Returns undefined.

         */
        if (!overwrite && (id in this.index))
            throw new Error("id is already in the index");
        if (check_record && !(('name' in record) && ('data' in record)))
            throw new Error("malformed record");
        this.index[id] = record;
    }

    function remove(record_id) {
        /** Remove the matching record.

         Returns true is a record is found, or false if no match is found.

         */
        if (record_id in this.index) {
            delete this.index[record_id];
            return true;
        } else {
            return false;
        }
    }

    function find(substring) {
        /** Find a record that matches the substring.

         Returns an array of data from matching records.

         */

        var re = RegExp(substring, "i"), // ignore case
            matches = [];
        for (var id in this.index) {
            var record = this.index[id];
            if (re.exec(record.name))
                matches.push(record.data);
        }
        return matches;
        
    }
});

(function() {
  var Bacon, BufferingSource, Bus, CompositeUnsubscribe, ConsumingSource, Desc, Dispatcher, End, Error, Event, EventStream, Initial, Next, None, Observable, Property, PropertyDispatcher, Some, Source, UpdateBarrier, addPropertyInitValueToStream, assert, assertArray, assertEventStream, assertFunction, assertNoArguments, assertString, cloneArray, compositeUnsubscribe, containsDuplicateDeps, convertArgsToFunction, describe, end, eventIdCounter, flatMap_, former, idCounter, initial, isArray, isFieldKey, isFunction, isObservable, latterF, liftCallback, makeFunction, makeFunctionArgs, makeFunction_, makeObservable, makeSpawner, next, nop, partiallyApplied, recursionDepth, registerObs, spys, toCombinator, toEvent, toFieldExtractor, toFieldKey, toOption, toSimpleExtractor, withDescription, withMethodCallSupport, _, _ref,
    __slice = [].slice,
    __hasProp = {}.hasOwnProperty,
    __extends = function(child, parent) { for (var key in parent) { if (__hasProp.call(parent, key)) child[key] = parent[key]; } function ctor() { this.constructor = child; } ctor.prototype = parent.prototype; child.prototype = new ctor(); child.__super__ = parent.prototype; return child; },
    __bind = function(fn, me){ return function(){ return fn.apply(me, arguments); }; };

  Bacon = {
    toString: function() {
      return "Bacon";
    }
  };

  Bacon.version = '0.7.12';

  Bacon.fromBinder = function(binder, eventTransformer) {
    if (eventTransformer == null) {
      eventTransformer = _.id;
    }
    return new EventStream(describe(Bacon, "fromBinder", binder, eventTransformer), function(sink) {
      var unbinder;
      return unbinder = binder(function() {
        var args, event, reply, value, _i, _len;
        args = 1 <= arguments.length ? __slice.call(arguments, 0) : [];
        value = eventTransformer.apply(null, args);
        if (!(isArray(value) && _.last(value) instanceof Event)) {
          value = [value];
        }
        reply = Bacon.more;
        for (_i = 0, _len = value.length; _i < _len; _i++) {
          event = value[_i];
          reply = sink(event = toEvent(event));
          if (reply === Bacon.noMore || event.isEnd()) {
            if (unbinder != null) {
              unbinder();
            } else {
              Bacon.scheduler.setTimeout((function() {
                return unbinder();
              }), 0);
            }
            return reply;
          }
        }
        return reply;
      });
    });
  };

  Bacon.$ = {
    asEventStream: function(eventName, selector, eventTransformer) {
      var _ref;
      if (isFunction(selector)) {
        _ref = [selector, null], eventTransformer = _ref[0], selector = _ref[1];
      }
      return withDescription(this.selector || this, "asEventStream", eventName, Bacon.fromBinder((function(_this) {
        return function(handler) {
          _this.on(eventName, selector, handler);
          return function() {
            return _this.off(eventName, selector, handler);
          };
        };
      })(this), eventTransformer));
    }
  };

  if ((_ref = typeof jQuery !== "undefined" && jQuery !== null ? jQuery : typeof Zepto !== "undefined" && Zepto !== null ? Zepto : null) != null) {
    _ref.fn.asEventStream = Bacon.$.asEventStream;
  }

  Bacon.fromEventTarget = function(target, eventName, eventTransformer) {
    var sub, unsub, _ref1, _ref2, _ref3, _ref4;
    sub = (_ref1 = target.addEventListener) != null ? _ref1 : (_ref2 = target.addListener) != null ? _ref2 : target.bind;
    unsub = (_ref3 = target.removeEventListener) != null ? _ref3 : (_ref4 = target.removeListener) != null ? _ref4 : target.unbind;
    return withDescription(Bacon, "fromEventTarget", target, eventName, Bacon.fromBinder(function(handler) {
      sub.call(target, eventName, handler);
      return function() {
        return unsub.call(target, eventName, handler);
      };
    }, eventTransformer));
  };

  Bacon.fromPromise = function(promise, abort) {
    return withDescription(Bacon, "fromPromise", promise, Bacon.fromBinder(function(handler) {
      promise.then(handler, function(e) {
        return handler(new Error(e));
      });
      return function() {
        if (abort) {
          return typeof promise.abort === "function" ? promise.abort() : void 0;
        }
      };
    }, (function(value) {
      return [value, end()];
    })));
  };

  Bacon.noMore = ["<no-more>"];

  Bacon.more = ["<more>"];

  Bacon.later = function(delay, value) {
    return withDescription(Bacon, "later", delay, value, Bacon.sequentially(delay, [value]));
  };

  Bacon.sequentially = function(delay, values) {
    var index;
    index = 0;
    return withDescription(Bacon, "sequentially", delay, values, Bacon.fromPoll(delay, function() {
      var value;
      value = values[index++];
      if (index < values.length) {
        return value;
      } else if (index === values.length) {
        return [value, end()];
      } else {
        return end();
      }
    }));
  };

  Bacon.repeatedly = function(delay, values) {
    var index;
    index = 0;
    return withDescription(Bacon, "repeatedly", delay, values, Bacon.fromPoll(delay, function() {
      return values[index++ % values.length];
    }));
  };

  Bacon.spy = function(spy) {
    return spys.push(spy);
  };

  spys = [];

  registerObs = function(obs) {
    var spy, _i, _len, _results;
    if (spys.length) {
      if (!registerObs.running) {
        try {
          registerObs.running = true;
          _results = [];
          for (_i = 0, _len = spys.length; _i < _len; _i++) {
            spy = spys[_i];
            _results.push(spy(obs));
          }
          return _results;
        } finally {
          delete registerObs.running;
        }
      }
    }
  };

  withMethodCallSupport = function(wrapped) {
    return function() {
      var args, context, f, methodName;
      f = arguments[0], args = 2 <= arguments.length ? __slice.call(arguments, 1) : [];
      if (typeof f === "object" && args.length) {
        context = f;
        methodName = args[0];
        f = function() {
          return context[methodName].apply(context, arguments);
        };
        args = args.slice(1);
      }
      return wrapped.apply(null, [f].concat(__slice.call(args)));
    };
  };

  liftCallback = function(desc, wrapped) {
    return withMethodCallSupport(function() {
      var args, f, stream;
      f = arguments[0], args = 2 <= arguments.length ? __slice.call(arguments, 1) : [];
      stream = partiallyApplied(wrapped, [
        function(values, callback) {
          return f.apply(null, __slice.call(values).concat([callback]));
        }
      ]);
      return withDescription.apply(null, [Bacon, desc, f].concat(__slice.call(args), [Bacon.combineAsArray(args).flatMap(stream)]));
    });
  };

  Bacon.fromCallback = liftCallback("fromCallback", function() {
    var args, f;
    f = arguments[0], args = 2 <= arguments.length ? __slice.call(arguments, 1) : [];
    return Bacon.fromBinder(function(handler) {
      makeFunction(f, args)(handler);
      return nop;
    }, (function(value) {
      return [value, end()];
    }));
  });

  Bacon.fromNodeCallback = liftCallback("fromNodeCallback", function() {
    var args, f;
    f = arguments[0], args = 2 <= arguments.length ? __slice.call(arguments, 1) : [];
    return Bacon.fromBinder(function(handler) {
      makeFunction(f, args)(handler);
      return nop;
    }, function(error, value) {
      if (error) {
        return [new Error(error), end()];
      }
      return [value, end()];
    });
  });

  Bacon.fromPoll = function(delay, poll) {
    return withDescription(Bacon, "fromPoll", delay, poll, Bacon.fromBinder((function(handler) {
      var id;
      id = Bacon.scheduler.setInterval(handler, delay);
      return function() {
        return Bacon.scheduler.clearInterval(id);
      };
    }), poll));
  };

  Bacon.interval = function(delay, value) {
    if (value == null) {
      value = {};
    }
    return withDescription(Bacon, "interval", delay, value, Bacon.fromPoll(delay, function() {
      return next(value);
    }));
  };

  Bacon.constant = function(value) {
    return new Property(describe(Bacon, "constant", value), function(sink) {
      sink(initial(value));
      sink(end());
      return nop;
    });
  };

  Bacon.never = function() {
    return withDescription(Bacon, "never", Bacon.fromArray([]));
  };

  Bacon.once = function(value) {
    return withDescription(Bacon, "once", value, Bacon.fromArray([value]));
  };

  Bacon.fromArray = function(values) {
    assertArray(values);
    values = cloneArray(values);
    return new EventStream(describe(Bacon, "fromArray", values), function(sink) {
      var send, unsubd;
      unsubd = false;
      send = function() {
        var reply, value;
        if (_.empty(values)) {
          return sink(end());
        } else {
          value = values.splice(0, 1)[0];
          reply = sink(toEvent(value));
          if ((reply !== Bacon.noMore) && !unsubd) {
            return send();
          }
        }
      };
      send();
      return function() {
        return unsubd = true;
      };
    });
  };

  Bacon.mergeAll = function() {
    var streams;
    streams = 1 <= arguments.length ? __slice.call(arguments, 0) : [];
    if (isArray(streams[0])) {
      streams = streams[0];
    }
    if (streams.length) {
      return new EventStream(describe.apply(null, [Bacon, "mergeAll"].concat(__slice.call(streams))), function(sink) {
        var ends, sinks, smartSink;
        ends = 0;
        smartSink = function(obs) {
          return function(unsubBoth) {
            return obs.subscribeInternal(function(event) {
              var reply;
              if (event.isEnd()) {
                ends++;
                if (ends === streams.length) {
                  return sink(end());
                } else {
                  return Bacon.more;
                }
              } else {
                reply = sink(event);
                if (reply === Bacon.noMore) {
                  unsubBoth();
                }
                return reply;
              }
            });
          };
        };
        sinks = _.map(smartSink, streams);
        return compositeUnsubscribe.apply(null, sinks);
      });
    } else {
      return Bacon.never();
    }
  };

  Bacon.zipAsArray = function() {
    var streams;
    streams = 1 <= arguments.length ? __slice.call(arguments, 0) : [];
    if (isArray(streams[0])) {
      streams = streams[0];
    }
    return withDescription.apply(null, [Bacon, "zipAsArray"].concat(__slice.call(streams), [Bacon.zipWith(streams, function() {
      var xs;
      xs = 1 <= arguments.length ? __slice.call(arguments, 0) : [];
      return xs;
    })]));
  };

  Bacon.zipWith = function() {
    var f, streams, _ref1;
    f = arguments[0], streams = 2 <= arguments.length ? __slice.call(arguments, 1) : [];
    if (!isFunction(f)) {
      _ref1 = [f, streams[0]], streams = _ref1[0], f = _ref1[1];
    }
    streams = _.map((function(s) {
      return s.toEventStream();
    }), streams);
    return withDescription.apply(null, [Bacon, "zipWith", f].concat(__slice.call(streams), [Bacon.when(streams, f)]));
  };

  Bacon.groupSimultaneous = function() {
    var s, sources, streams;
    streams = 1 <= arguments.length ? __slice.call(arguments, 0) : [];
    if (streams.length === 1 && isArray(streams[0])) {
      streams = streams[0];
    }
    sources = (function() {
      var _i, _len, _results;
      _results = [];
      for (_i = 0, _len = streams.length; _i < _len; _i++) {
        s = streams[_i];
        _results.push(new BufferingSource(s));
      }
      return _results;
    })();
    return withDescription.apply(null, [Bacon, "groupSimultaneous"].concat(__slice.call(streams), [Bacon.when(sources, (function() {
      var xs;
      xs = 1 <= arguments.length ? __slice.call(arguments, 0) : [];
      return xs;
    }))]));
  };

  Bacon.combineAsArray = function() {
    var index, s, sources, stream, streams, _i, _len;
    streams = 1 <= arguments.length ? __slice.call(arguments, 0) : [];
    if (streams.length === 1 && isArray(streams[0])) {
      streams = streams[0];
    }
    for (index = _i = 0, _len = streams.length; _i < _len; index = ++_i) {
      stream = streams[index];
      if (!(isObservable(stream))) {
        streams[index] = Bacon.constant(stream);
      }
    }
    if (streams.length) {
      sources = (function() {
        var _j, _len1, _results;
        _results = [];
        for (_j = 0, _len1 = streams.length; _j < _len1; _j++) {
          s = streams[_j];
          _results.push(new Source(s, true, s.subscribeInternal));
        }
        return _results;
      })();
      return withDescription.apply(null, [Bacon, "combineAsArray"].concat(__slice.call(streams), [Bacon.when(sources, (function() {
        var xs;
        xs = 1 <= arguments.length ? __slice.call(arguments, 0) : [];
        return xs;
      })).toProperty()]));
    } else {
      return Bacon.constant([]);
    }
  };

  Bacon.onValues = function() {
    var f, streams, _i;
    streams = 2 <= arguments.length ? __slice.call(arguments, 0, _i = arguments.length - 1) : (_i = 0, []), f = arguments[_i++];
    return Bacon.combineAsArray(streams).onValues(f);
  };

  Bacon.combineWith = function() {
    var f, streams;
    f = arguments[0], streams = 2 <= arguments.length ? __slice.call(arguments, 1) : [];
    return withDescription.apply(null, [Bacon, "combineWith", f].concat(__slice.call(streams), [Bacon.combineAsArray(streams).map(function(values) {
      return f.apply(null, values);
    })]));
  };

  Bacon.combineTemplate = function(template) {
    var applyStreamValue, combinator, compile, compileTemplate, constantValue, current, funcs, mkContext, setValue, streams;
    funcs = [];
    streams = [];
    current = function(ctxStack) {
      return ctxStack[ctxStack.length - 1];
    };
    setValue = function(ctxStack, key, value) {
      return current(ctxStack)[key] = value;
    };
    applyStreamValue = function(key, index) {
      return function(ctxStack, values) {
        return setValue(ctxStack, key, values[index]);
      };
    };
    constantValue = function(key, value) {
      return function(ctxStack) {
        return setValue(ctxStack, key, value);
      };
    };
    mkContext = function(template) {
      if (isArray(template)) {
        return [];
      } else {
        return {};
      }
    };
    compile = function(key, value) {
      var popContext, pushContext;
      if (isObservable(value)) {
        streams.push(value);
        return funcs.push(applyStreamValue(key, streams.length - 1));
      } else if (value === Object(value) && typeof value !== "function" && !(value instanceof RegExp) && !(value instanceof Date)) {
        pushContext = function(key) {
          return function(ctxStack) {
            var newContext;
            newContext = mkContext(value);
            setValue(ctxStack, key, newContext);
            return ctxStack.push(newContext);
          };
        };
        popContext = function(ctxStack) {
          return ctxStack.pop();
        };
        funcs.push(pushContext(key));
        compileTemplate(value);
        return funcs.push(popContext);
      } else {
        return funcs.push(constantValue(key, value));
      }
    };
    compileTemplate = function(template) {
      return _.each(template, compile);
    };
    compileTemplate(template);
    combinator = function(values) {
      var ctxStack, f, rootContext, _i, _len;
      rootContext = mkContext(template);
      ctxStack = [rootContext];
      for (_i = 0, _len = funcs.length; _i < _len; _i++) {
        f = funcs[_i];
        f(ctxStack, values);
      }
      return rootContext;
    };
    return withDescription(Bacon, "combineTemplate", template, Bacon.combineAsArray(streams).map(combinator));
  };

  Bacon.retry = function(options) {
    var interval, isRetryable, maxRetries, retries, retry, source;
    if (!isFunction(options.source)) {
      throw "'source' option has to be a function";
    }
    source = options.source;
    retries = options.retries || 0;
    maxRetries = options.maxRetries || retries;
    interval = options.interval || function() {
      return 0;
    };
    isRetryable = options.isRetryable || function() {
      return true;
    };
    retry = function(context) {
      var nextAttemptOptions;
      nextAttemptOptions = {
        source: source,
        retries: retries - 1,
        maxRetries: maxRetries,
        interval: interval,
        isRetryable: isRetryable
      };
      return Bacon.later(interval(context)).filter(false).concat(Bacon.retry(nextAttemptOptions));
    };
    return withDescription(Bacon, "retry", options, source().flatMapError(function(e) {
      if (isRetryable(e) && retries > 0) {
        return retry({
          error: e,
          retriesDone: maxRetries - retries
        });
      } else {
        return Bacon.once(new Bacon.Error(e));
      }
    }));
  };

  eventIdCounter = 0;

  Event = (function() {
    function Event() {
      this.id = ++eventIdCounter;
    }

    Event.prototype.isEvent = function() {
      return true;
    };

    Event.prototype.isEnd = function() {
      return false;
    };

    Event.prototype.isInitial = function() {
      return false;
    };

    Event.prototype.isNext = function() {
      return false;
    };

    Event.prototype.isError = function() {
      return false;
    };

    Event.prototype.hasValue = function() {
      return false;
    };

    Event.prototype.filter = function() {
      return true;
    };

    Event.prototype.inspect = function() {
      return this.toString();
    };

    Event.prototype.log = function() {
      return this.toString();
    };

    return Event;

  })();

  Next = (function(_super) {
    __extends(Next, _super);

    function Next(valueF) {
      Next.__super__.constructor.call(this);
      if (isFunction(valueF)) {
        this.value = _.cached(valueF);
      } else {
        this.value = _.always(valueF);
      }
    }

    Next.prototype.isNext = function() {
      return true;
    };

    Next.prototype.hasValue = function() {
      return true;
    };

    Next.prototype.fmap = function(f) {
      var value;
      value = this.value;
      return this.apply(function() {
        return f(value());
      });
    };

    Next.prototype.apply = function(value) {
      return new Next(value);
    };

    Next.prototype.filter = function(f) {
      return f(this.value());
    };

    Next.prototype.toString = function() {
      return _.toString(this.value());
    };

    Next.prototype.log = function() {
      return this.value();
    };

    return Next;

  })(Event);

  Initial = (function(_super) {
    __extends(Initial, _super);

    function Initial() {
      return Initial.__super__.constructor.apply(this, arguments);
    }

    Initial.prototype.isInitial = function() {
      return true;
    };

    Initial.prototype.isNext = function() {
      return false;
    };

    Initial.prototype.apply = function(value) {
      return new Initial(value);
    };

    Initial.prototype.toNext = function() {
      return new Next(this.value);
    };

    return Initial;

  })(Next);

  End = (function(_super) {
    __extends(End, _super);

    function End() {
      return End.__super__.constructor.apply(this, arguments);
    }

    End.prototype.isEnd = function() {
      return true;
    };

    End.prototype.fmap = function() {
      return this;
    };

    End.prototype.apply = function() {
      return this;
    };

    End.prototype.toString = function() {
      return "<end>";
    };

    return End;

  })(Event);

  Error = (function(_super) {
    __extends(Error, _super);

    function Error(error) {
      this.error = error;
    }

    Error.prototype.isError = function() {
      return true;
    };

    Error.prototype.fmap = function() {
      return this;
    };

    Error.prototype.apply = function() {
      return this;
    };

    Error.prototype.toString = function() {
      return "<error> " + _.toString(this.error);
    };

    return Error;

  })(Event);

  idCounter = 0;

  Observable = (function() {
    function Observable(desc) {
      this.flatMapError = __bind(this.flatMapError, this);
      this.id = ++idCounter;
      withDescription(desc, this);
    }

    Observable.prototype.onValue = function() {
      var f;
      f = makeFunctionArgs(arguments);
      return this.subscribe(function(event) {
        if (event.hasValue()) {
          return f(event.value());
        }
      });
    };

    Observable.prototype.onValues = function(f) {
      return this.onValue(function(args) {
        return f.apply(null, args);
      });
    };

    Observable.prototype.onError = function() {
      var f;
      f = makeFunctionArgs(arguments);
      return this.subscribe(function(event) {
        if (event.isError()) {
          return f(event.error);
        }
      });
    };

    Observable.prototype.onEnd = function() {
      var f;
      f = makeFunctionArgs(arguments);
      return this.subscribe(function(event) {
        if (event.isEnd()) {
          return f();
        }
      });
    };

    Observable.prototype.errors = function() {
      return withDescription(this, "errors", this.filter(function() {
        return false;
      }));
    };

    Observable.prototype.filter = function() {
      var args, f;
      f = arguments[0], args = 2 <= arguments.length ? __slice.call(arguments, 1) : [];
      return convertArgsToFunction(this, f, args, function(f) {
        return withDescription(this, "filter", f, this.withHandler(function(event) {
          if (event.filter(f)) {
            return this.push(event);
          } else {
            return Bacon.more;
          }
        }));
      });
    };

    Observable.prototype.takeWhile = function() {
      var args, f;
      f = arguments[0], args = 2 <= arguments.length ? __slice.call(arguments, 1) : [];
      return convertArgsToFunction(this, f, args, function(f) {
        return withDescription(this, "takeWhile", f, this.withHandler(function(event) {
          if (event.filter(f)) {
            return this.push(event);
          } else {
            this.push(end());
            return Bacon.noMore;
          }
        }));
      });
    };

    Observable.prototype.endOnError = function() {
      var args, f;
      f = arguments[0], args = 2 <= arguments.length ? __slice.call(arguments, 1) : [];
      if (f == null) {
        f = true;
      }
      return convertArgsToFunction(this, f, args, function(f) {
        return withDescription(this, "endOnError", this.withHandler(function(event) {
          if (event.isError() && f(event.error)) {
            this.push(event);
            return this.push(end());
          } else {
            return this.push(event);
          }
        }));
      });
    };

    Observable.prototype.take = function(count) {
      if (count <= 0) {
        return Bacon.never();
      }
      return withDescription(this, "take", count, this.withHandler(function(event) {
        if (!event.hasValue()) {
          return this.push(event);
        } else {
          count--;
          if (count > 0) {
            return this.push(event);
          } else {
            if (count === 0) {
              this.push(event);
            }
            this.push(end());
            return Bacon.noMore;
          }
        }
      }));
    };

    Observable.prototype.map = function() {
      var args, p;
      p = arguments[0], args = 2 <= arguments.length ? __slice.call(arguments, 1) : [];
      if (p instanceof Property) {
        return p.sampledBy(this, former);
      } else {
        return convertArgsToFunction(this, p, args, function(f) {
          return withDescription(this, "map", f, this.withHandler(function(event) {
            return this.push(event.fmap(f));
          }));
        });
      }
    };

    Observable.prototype.mapError = function() {
      var f;
      f = makeFunctionArgs(arguments);
      return withDescription(this, "mapError", f, this.withHandler(function(event) {
        if (event.isError()) {
          return this.push(next(f(event.error)));
        } else {
          return this.push(event);
        }
      }));
    };

    Observable.prototype.mapEnd = function() {
      var f;
      f = makeFunctionArgs(arguments);
      return withDescription(this, "mapEnd", f, this.withHandler(function(event) {
        if (event.isEnd()) {
          this.push(next(f(event)));
          this.push(end());
          return Bacon.noMore;
        } else {
          return this.push(event);
        }
      }));
    };

    Observable.prototype.doAction = function() {
      var f;
      f = makeFunctionArgs(arguments);
      return withDescription(this, "doAction", f, this.withHandler(function(event) {
        if (event.hasValue()) {
          f(event.value());
        }
        return this.push(event);
      }));
    };

    Observable.prototype.skip = function(count) {
      return withDescription(this, "skip", count, this.withHandler(function(event) {
        if (!event.hasValue()) {
          return this.push(event);
        } else if (count > 0) {
          count--;
          return Bacon.more;
        } else {
          return this.push(event);
        }
      }));
    };

    Observable.prototype.skipDuplicates = function(isEqual) {
      if (isEqual == null) {
        isEqual = function(a, b) {
          return a === b;
        };
      }
      return withDescription(this, "skipDuplicates", this.withStateMachine(None, function(prev, event) {
        if (!event.hasValue()) {
          return [prev, [event]];
        } else if (event.isInitial() || prev === None || !isEqual(prev.get(), event.value())) {
          return [new Some(event.value()), [event]];
        } else {
          return [prev, []];
        }
      }));
    };

    Observable.prototype.skipErrors = function() {
      return withDescription(this, "skipErrors", this.withHandler(function(event) {
        if (event.isError()) {
          return Bacon.more;
        } else {
          return this.push(event);
        }
      }));
    };

    Observable.prototype.withStateMachine = function(initState, f) {
      var state;
      state = initState;
      return withDescription(this, "withStateMachine", initState, f, this.withHandler(function(event) {
        var fromF, newState, output, outputs, reply, _i, _len;
        fromF = f(state, event);
        newState = fromF[0], outputs = fromF[1];
        state = newState;
        reply = Bacon.more;
        for (_i = 0, _len = outputs.length; _i < _len; _i++) {
          output = outputs[_i];
          reply = this.push(output);
          if (reply === Bacon.noMore) {
            return reply;
          }
        }
        return reply;
      }));
    };

    Observable.prototype.scan = function(seed, f, lazyF) {
      var acc, f_, resultProperty, subscribe;
      f_ = toCombinator(f);
      f = lazyF ? f_ : function(x, y) {
        return f_(x(), y());
      };
      acc = toOption(seed).map(function(x) {
        return _.always(x);
      });
      subscribe = (function(_this) {
        return function(sink) {
          var initSent, reply, sendInit, unsub;
          initSent = false;
          unsub = nop;
          reply = Bacon.more;
          sendInit = function() {
            if (!initSent) {
              return acc.forEach(function(valueF) {
                initSent = true;
                reply = sink(new Initial(valueF));
                if (reply === Bacon.noMore) {
                  unsub();
                  return unsub = nop;
                }
              });
            }
          };
          unsub = _this.subscribeInternal(function(event) {
            var next, prev;
            if (event.hasValue()) {
              if (initSent && event.isInitial()) {
                return Bacon.more;
              } else {
                if (!event.isInitial()) {
                  sendInit();
                }
                initSent = true;
                prev = acc.getOrElse(function() {
                  return void 0;
                });
                next = _.cached(function() {
                  return f(prev, event.value);
                });
                acc = new Some(next);
                return sink(event.apply(next));
              }
            } else {
              if (event.isEnd()) {
                reply = sendInit();
              }
              if (reply !== Bacon.noMore) {
                return sink(event);
              }
            }
          });
          UpdateBarrier.whenDoneWith(resultProperty, sendInit);
          return unsub;
        };
      })(this);
      return resultProperty = new Property(describe(this, "scan", seed, f), subscribe);
    };

    Observable.prototype.fold = function(seed, f) {
      return withDescription(this, "fold", seed, f, this.scan(seed, f).sampledBy(this.filter(false).mapEnd().toProperty()));
    };

    Observable.prototype.zip = function(other, f) {
      if (f == null) {
        f = Array;
      }
      return withDescription(this, "zip", other, Bacon.zipWith([this, other], f));
    };

    Observable.prototype.diff = function(start, f) {
      f = toCombinator(f);
      return withDescription(this, "diff", start, f, this.scan([start], function(prevTuple, next) {
        return [next, f(prevTuple[0], next)];
      }).filter(function(tuple) {
        return tuple.length === 2;
      }).map(function(tuple) {
        return tuple[1];
      }));
    };

    Observable.prototype.flatMap = function() {
      return flatMap_(this, makeSpawner(arguments));
    };

    Observable.prototype.flatMapFirst = function() {
      return flatMap_(this, makeSpawner(arguments), true);
    };

    Observable.prototype.flatMapLatest = function() {
      var f, stream;
      f = makeSpawner(arguments);
      stream = this.toEventStream();
      return withDescription(this, "flatMapLatest", f, stream.flatMap(function(value) {
        return makeObservable(f(value)).takeUntil(stream);
      }));
    };

    Observable.prototype.flatMapError = function(fn) {
      return withDescription(this, "flatMapError", fn, this.mapError(function(err) {
        return new Bacon.Error(err);
      }).flatMap(function(x) {
        if (x instanceof Bacon.Error) {
          return fn(x.error);
        } else {
          return Bacon.once(x);
        }
      }));
    };

    Observable.prototype.not = function() {
      return withDescription(this, "not", this.map(function(x) {
        return !x;
      }));
    };

    Observable.prototype.log = function() {
      var args;
      args = 1 <= arguments.length ? __slice.call(arguments, 0) : [];
      this.subscribe(function(event) {
        return typeof console !== "undefined" && console !== null ? typeof console.log === "function" ? console.log.apply(console, __slice.call(args).concat([event.log()])) : void 0 : void 0;
      });
      return this;
    };

    Observable.prototype.slidingWindow = function(n, minValues) {
      if (minValues == null) {
        minValues = 0;
      }
      return withDescription(this, "slidingWindow", n, minValues, this.scan([], (function(window, value) {
        return window.concat([value]).slice(-n);
      })).filter((function(values) {
        return values.length >= minValues;
      })));
    };

    Observable.prototype.combine = function(other, f) {
      var combinator;
      combinator = toCombinator(f);
      return withDescription(this, "combine", other, f, Bacon.combineAsArray(this, other).map(function(values) {
        return combinator(values[0], values[1]);
      }));
    };

    Observable.prototype.decode = function(cases) {
      return withDescription(this, "decode", cases, this.combine(Bacon.combineTemplate(cases), function(key, values) {
        return values[key];
      }));
    };

    Observable.prototype.awaiting = function(other) {
      return withDescription(this, "awaiting", other, Bacon.groupSimultaneous(this, other).map(function(_arg) {
        var myValues, otherValues;
        myValues = _arg[0], otherValues = _arg[1];
        return otherValues.length === 0;
      }).toProperty(false).skipDuplicates());
    };

    Observable.prototype.name = function(name) {
      this.toString = function() {
        return name;
      };
      return this;
    };

    Observable.prototype.withDescription = function() {
      return describe.apply(null, arguments).apply(this);
    };

    return Observable;

  })();

  Observable.prototype.reduce = Observable.prototype.fold;

  Observable.prototype.assign = Observable.prototype.onValue;

  flatMap_ = function(root, f, firstOnly) {
    return new EventStream(describe(root, "flatMap" + (firstOnly ? "First" : ""), f), function(sink) {
      var checkEnd, composite;
      composite = new CompositeUnsubscribe();
      checkEnd = function(unsub) {
        unsub();
        if (composite.empty()) {
          return sink(end());
        }
      };
      composite.add(function(__, unsubRoot) {
        return root.subscribeInternal(function(event) {
          var child;
          if (event.isEnd()) {
            return checkEnd(unsubRoot);
          } else if (event.isError()) {
            return sink(event);
          } else if (firstOnly && composite.count() > 1) {
            return Bacon.more;
          } else {
            if (composite.unsubscribed) {
              return Bacon.noMore;
            }
            child = makeObservable(f(event.value()));
            return composite.add(function(unsubAll, unsubMe) {
              return child.subscribeInternal(function(event) {
                var reply;
                if (event.isEnd()) {
                  checkEnd(unsubMe);
                  return Bacon.noMore;
                } else {
                  if (event instanceof Initial) {
                    event = event.toNext();
                  }
                  reply = sink(event);
                  if (reply === Bacon.noMore) {
                    unsubAll();
                  }
                  return reply;
                }
              });
            });
          }
        });
      });
      return composite.unsubscribe;
    });
  };

  EventStream = (function(_super) {
    __extends(EventStream, _super);

    function EventStream(desc, subscribe) {
      var dispatcher;
      if (isFunction(desc)) {
        subscribe = desc;
        desc = [];
      }
      EventStream.__super__.constructor.call(this, desc);
      assertFunction(subscribe);
      dispatcher = new Dispatcher(subscribe);
      this.subscribeInternal = dispatcher.subscribe;
      this.subscribe = UpdateBarrier.wrappedSubscribe(this);
      this.hasSubscribers = dispatcher.hasSubscribers;
      registerObs(this);
    }

    EventStream.prototype.delay = function(delay) {
      return withDescription(this, "delay", delay, this.flatMap(function(value) {
        return Bacon.later(delay, value);
      }));
    };

    EventStream.prototype.debounce = function(delay) {
      return withDescription(this, "debounce", delay, this.flatMapLatest(function(value) {
        return Bacon.later(delay, value);
      }));
    };

    EventStream.prototype.debounceImmediate = function(delay) {
      return withDescription(this, "debounceImmediate", delay, this.flatMapFirst(function(value) {
        return Bacon.once(value).concat(Bacon.later(delay).filter(false));
      }));
    };

    EventStream.prototype.throttle = function(delay) {
      return withDescription(this, "throttle", delay, this.bufferWithTime(delay).map(function(values) {
        return values[values.length - 1];
      }));
    };

    EventStream.prototype.bufferWithTime = function(delay) {
      return withDescription(this, "bufferWithTime", delay, this.bufferWithTimeOrCount(delay, Number.MAX_VALUE));
    };

    EventStream.prototype.bufferWithCount = function(count) {
      return withDescription(this, "bufferWithCount", count, this.bufferWithTimeOrCount(void 0, count));
    };

    EventStream.prototype.bufferWithTimeOrCount = function(delay, count) {
      var flushOrSchedule;
      flushOrSchedule = function(buffer) {
        if (buffer.values.length === count) {
          return buffer.flush();
        } else if (delay !== void 0) {
          return buffer.schedule();
        }
      };
      return withDescription(this, "bufferWithTimeOrCount", delay, count, this.buffer(delay, flushOrSchedule, flushOrSchedule));
    };

    EventStream.prototype.buffer = function(delay, onInput, onFlush) {
      var buffer, delayMs, reply;
      if (onInput == null) {
        onInput = (function() {});
      }
      if (onFlush == null) {
        onFlush = (function() {});
      }
      buffer = {
        scheduled: false,
        end: null,
        values: [],
        flush: function() {
          var reply;
          this.scheduled = false;
          if (this.values.length > 0) {
            reply = this.push(next(this.values));
            this.values = [];
            if (this.end != null) {
              return this.push(this.end);
            } else if (reply !== Bacon.noMore) {
              return onFlush(this);
            }
          } else {
            if (this.end != null) {
              return this.push(this.end);
            }
          }
        },
        schedule: function() {
          if (!this.scheduled) {
            this.scheduled = true;
            return delay((function(_this) {
              return function() {
                return _this.flush();
              };
            })(this));
          }
        }
      };
      reply = Bacon.more;
      if (!isFunction(delay)) {
        delayMs = delay;
        delay = function(f) {
          return Bacon.scheduler.setTimeout(f, delayMs);
        };
      }
      return withDescription(this, "buffer", this.withHandler(function(event) {
        buffer.push = this.push;
        if (event.isError()) {
          reply = this.push(event);
        } else if (event.isEnd()) {
          buffer.end = event;
          if (!buffer.scheduled) {
            buffer.flush();
          }
        } else {
          buffer.values.push(event.value());
          onInput(buffer);
        }
        return reply;
      }));
    };

    EventStream.prototype.merge = function(right) {
      var left;
      assertEventStream(right);
      left = this;
      return withDescription(left, "merge", right, Bacon.mergeAll(this, right));
    };

    EventStream.prototype.toProperty = function(initValue) {
      if (arguments.length === 0) {
        initValue = None;
      }
      return withDescription(this, "toProperty", initValue, this.scan(initValue, latterF, true));
    };

    EventStream.prototype.toEventStream = function() {
      return this;
    };

    EventStream.prototype.sampledBy = function(sampler, combinator) {
      return withDescription(this, "sampledBy", sampler, combinator, this.toProperty().sampledBy(sampler, combinator));
    };

    EventStream.prototype.concat = function(right) {
      var left;
      left = this;
      return new EventStream(describe(left, "concat", right), function(sink) {
        var unsubLeft, unsubRight;
        unsubRight = nop;
        unsubLeft = left.subscribeInternal(function(e) {
          if (e.isEnd()) {
            return unsubRight = right.subscribeInternal(sink);
          } else {
            return sink(e);
          }
        });
        return function() {
          unsubLeft();
          return unsubRight();
        };
      });
    };

    EventStream.prototype.takeUntil = function(stopper) {
      var endMarker;
      endMarker = {};
      return withDescription(this, "takeUntil", stopper, Bacon.groupSimultaneous(this.mapEnd(endMarker), stopper.skipErrors()).withHandler(function(event) {
        var data, reply, value, _i, _len, _ref1;
        if (!event.hasValue()) {
          return this.push(event);
        } else {
          _ref1 = event.value(), data = _ref1[0], stopper = _ref1[1];
          if (stopper.length) {
            return this.push(end());
          } else {
            reply = Bacon.more;
            for (_i = 0, _len = data.length; _i < _len; _i++) {
              value = data[_i];
              if (value === endMarker) {
                reply = this.push(end());
              } else {
                reply = this.push(next(value));
              }
            }
            return reply;
          }
        }
      }));
    };

    EventStream.prototype.skipUntil = function(starter) {
      var started;
      started = starter.take(1).map(true).toProperty(false);
      return withDescription(this, "skipUntil", starter, this.filter(started));
    };

    EventStream.prototype.skipWhile = function() {
      var args, f, ok;
      f = arguments[0], args = 2 <= arguments.length ? __slice.call(arguments, 1) : [];
      ok = false;
      return convertArgsToFunction(this, f, args, function(f) {
        return withDescription(this, "skipWhile", f, this.withHandler(function(event) {
          if (ok || !event.hasValue() || !f(event.value())) {
            if (event.hasValue()) {
              ok = true;
            }
            return this.push(event);
          } else {
            return Bacon.more;
          }
        }));
      });
    };

    EventStream.prototype.startWith = function(seed) {
      return withDescription(this, "startWith", seed, Bacon.once(seed).concat(this));
    };

    EventStream.prototype.withHandler = function(handler) {
      var dispatcher;
      dispatcher = new Dispatcher(this.subscribeInternal, handler);
      return new EventStream(describe(this, "withHandler", handler), dispatcher.subscribe);
    };

    return EventStream;

  })(Observable);

  Property = (function(_super) {
    __extends(Property, _super);

    function Property(desc, subscribe, handler) {
      if (isFunction(desc)) {
        handler = subscribe;
        subscribe = desc;
        desc = [];
      }
      Property.__super__.constructor.call(this, desc);
      assertFunction(subscribe);
      if (handler === true) {
        this.subscribeInternal = subscribe;
      } else {
        this.subscribeInternal = new PropertyDispatcher(this, subscribe, handler).subscribe;
      }
      this.subscribe = UpdateBarrier.wrappedSubscribe(this);
      registerObs(this);
    }

    Property.prototype.sampledBy = function(sampler, combinator) {
      var lazy, result, samplerSource, stream, thisSource;
      if (combinator != null) {
        combinator = toCombinator(combinator);
      } else {
        lazy = true;
        combinator = function(f) {
          return f();
        };
      }
      thisSource = new Source(this, false, this.subscribeInternal, lazy);
      samplerSource = new Source(sampler, true, sampler.subscribeInternal, lazy);
      stream = Bacon.when([thisSource, samplerSource], combinator);
      result = sampler instanceof Property ? stream.toProperty() : stream;
      return withDescription(this, "sampledBy", sampler, combinator, result);
    };

    Property.prototype.sample = function(interval) {
      return withDescription(this, "sample", interval, this.sampledBy(Bacon.interval(interval, {})));
    };

    Property.prototype.changes = function() {
      return new EventStream(describe(this, "changes"), (function(_this) {
        return function(sink) {
          return _this.subscribeInternal(function(event) {
            if (!event.isInitial()) {
              return sink(event);
            }
          });
        };
      })(this));
    };

    Property.prototype.withHandler = function(handler) {
      return new Property(describe(this, "withHandler", handler), this.subscribeInternal, handler);
    };

    Property.prototype.toProperty = function() {
      assertNoArguments(arguments);
      return this;
    };

    Property.prototype.toEventStream = function() {
      return new EventStream(describe(this, "toEventStream"), (function(_this) {
        return function(sink) {
          return _this.subscribeInternal(function(event) {
            if (event.isInitial()) {
              event = event.toNext();
            }
            return sink(event);
          });
        };
      })(this));
    };

    Property.prototype.and = function(other) {
      return withDescription(this, "and", other, this.combine(other, function(x, y) {
        return x && y;
      }));
    };

    Property.prototype.or = function(other) {
      return withDescription(this, "or", other, this.combine(other, function(x, y) {
        return x || y;
      }));
    };

    Property.prototype.delay = function(delay) {
      return this.delayChanges("delay", delay, function(changes) {
        return changes.delay(delay);
      });
    };

    Property.prototype.debounce = function(delay) {
      return this.delayChanges("debounce", delay, function(changes) {
        return changes.debounce(delay);
      });
    };

    Property.prototype.throttle = function(delay) {
      return this.delayChanges("throttle", delay, function(changes) {
        return changes.throttle(delay);
      });
    };

    Property.prototype.delayChanges = function() {
      var desc, f, _i;
      desc = 2 <= arguments.length ? __slice.call(arguments, 0, _i = arguments.length - 1) : (_i = 0, []), f = arguments[_i++];
      return withDescription.apply(null, [this].concat(__slice.call(desc), [addPropertyInitValueToStream(this, f(this.changes()))]));
    };

    Property.prototype.takeUntil = function(stopper) {
      var changes;
      changes = this.changes().takeUntil(stopper);
      return withDescription(this, "takeUntil", stopper, addPropertyInitValueToStream(this, changes));
    };

    Property.prototype.startWith = function(value) {
      return withDescription(this, "startWith", value, this.scan(value, function(prev, next) {
        return next;
      }));
    };

    return Property;

  })(Observable);

  convertArgsToFunction = function(obs, f, args, method) {
    var sampled;
    if (f instanceof Property) {
      sampled = f.sampledBy(obs, function(p, s) {
        return [p, s];
      });
      return method.apply(sampled, [
        function(_arg) {
          var p, s;
          p = _arg[0], s = _arg[1];
          return p;
        }
      ]).map(function(_arg) {
        var p, s;
        p = _arg[0], s = _arg[1];
        return s;
      });
    } else {
      f = makeFunction(f, args);
      return method.apply(obs, [f]);
    }
  };

  addPropertyInitValueToStream = function(property, stream) {
    var justInitValue;
    justInitValue = new EventStream(describe(property, "justInitValue"), function(sink) {
      var unsub, value;
      value = null;
      unsub = property.subscribeInternal(function(event) {
        if (event.hasValue()) {
          value = event;
        }
        return Bacon.noMore;
      });
      UpdateBarrier.whenDoneWith(justInitValue, function() {
        if (value != null) {
          sink(value);
        }
        return sink(end());
      });
      return unsub;
    });
    return justInitValue.concat(stream).toProperty();
  };

  Dispatcher = (function() {
    function Dispatcher(subscribe, handleEvent) {
      var done, ended, prevError, pushIt, pushing, queue, removeSub, subscriptions, unsubscribeFromSource, waiters;
      if (subscribe == null) {
        subscribe = function() {
          return nop;
        };
      }
      subscriptions = [];
      queue = [];
      pushing = false;
      ended = false;
      this.hasSubscribers = function() {
        return subscriptions.length > 0;
      };
      prevError = null;
      unsubscribeFromSource = nop;
      removeSub = function(subscription) {
        return subscriptions = _.without(subscription, subscriptions);
      };
      waiters = null;
      done = function() {
        var w, ws, _i, _len, _results;
        if (waiters != null) {
          ws = waiters;
          waiters = null;
          _results = [];
          for (_i = 0, _len = ws.length; _i < _len; _i++) {
            w = ws[_i];
            _results.push(w());
          }
          return _results;
        }
      };
      pushIt = function(event) {
        var reply, sub, success, tmp, _i, _len;
        if (!pushing) {
          if (event === prevError) {
            return;
          }
          if (event.isError()) {
            prevError = event;
          }
          success = false;
          try {
            pushing = true;
            tmp = subscriptions;
            for (_i = 0, _len = tmp.length; _i < _len; _i++) {
              sub = tmp[_i];
              reply = sub.sink(event);
              if (reply === Bacon.noMore || event.isEnd()) {
                removeSub(sub);
              }
            }
            success = true;
          } finally {
            pushing = false;
            if (!success) {
              queue = [];
            }
          }
          success = true;
          while (queue.length) {
            event = queue.shift();
            this.push(event);
          }
          done(event);
          if (this.hasSubscribers()) {
            return Bacon.more;
          } else {
            unsubscribeFromSource();
            return Bacon.noMore;
          }
        } else {
          queue.push(event);
          return Bacon.more;
        }
      };
      this.push = (function(_this) {
        return function(event) {
          return UpdateBarrier.inTransaction(event, _this, pushIt, [event]);
        };
      })(this);
      if (handleEvent == null) {
        handleEvent = function(event) {
          return this.push(event);
        };
      }
      this.handleEvent = (function(_this) {
        return function(event) {
          if (event.isEnd()) {
            ended = true;
          }
          return handleEvent.apply(_this, [event]);
        };
      })(this);
      this.subscribe = (function(_this) {
        return function(sink) {
          var subscription, unsubSrc;
          if (ended) {
            sink(end());
            return nop;
          } else {
            assertFunction(sink);
            subscription = {
              sink: sink
            };
            subscriptions.push(subscription);
            if (subscriptions.length === 1) {
              unsubSrc = subscribe(_this.handleEvent);
              unsubscribeFromSource = function() {
                unsubSrc();
                return unsubscribeFromSource = nop;
              };
            }
            assertFunction(unsubscribeFromSource);
            return function() {
              removeSub(subscription);
              if (!_this.hasSubscribers()) {
                return unsubscribeFromSource();
              }
            };
          }
        };
      })(this);
    }

    return Dispatcher;

  })();

  PropertyDispatcher = (function(_super) {
    __extends(PropertyDispatcher, _super);

    function PropertyDispatcher(p, subscribe, handleEvent) {
      var current, currentValueRootId, ended, push;
      PropertyDispatcher.__super__.constructor.call(this, subscribe, handleEvent);
      current = None;
      currentValueRootId = void 0;
      push = this.push;
      subscribe = this.subscribe;
      ended = false;
      this.push = (function(_this) {
        return function(event) {
          if (event.isEnd()) {
            ended = true;
          }
          if (event.hasValue()) {
            current = new Some(event);
            currentValueRootId = UpdateBarrier.currentEventId();
          }
          return push.apply(_this, [event]);
        };
      })(this);
      this.subscribe = (function(_this) {
        return function(sink) {
          var dispatchingId, initSent, maybeSubSource, reply, valId;
          initSent = false;
          reply = Bacon.more;
          maybeSubSource = function() {
            if (reply === Bacon.noMore) {
              return nop;
            } else if (ended) {
              sink(end());
              return nop;
            } else {
              return subscribe.apply(this, [sink]);
            }
          };
          if (current.isDefined && (_this.hasSubscribers() || ended)) {
            dispatchingId = UpdateBarrier.currentEventId();
            valId = currentValueRootId;
            if (!ended && valId && dispatchingId && dispatchingId !== valId) {
              UpdateBarrier.whenDoneWith(p, function() {
                if (currentValueRootId === valId) {
                  return sink(initial(current.get().value()));
                }
              });
              return maybeSubSource();
            } else {
              UpdateBarrier.inTransaction(void 0, _this, (function() {
                return reply = sink(initial(current.get().value()));
              }), []);
              return maybeSubSource();
            }
          } else {
            return maybeSubSource();
          }
        };
      })(this);
    }

    return PropertyDispatcher;

  })(Dispatcher);

  Bus = (function(_super) {
    __extends(Bus, _super);

    function Bus() {
      var ended, guardedSink, sink, subscribeAll, subscribeInput, subscriptions, unsubAll, unsubscribeInput;
      sink = void 0;
      subscriptions = [];
      ended = false;
      guardedSink = (function(_this) {
        return function(input) {
          return function(event) {
            if (event.isEnd()) {
              unsubscribeInput(input);
              return Bacon.noMore;
            } else {
              return sink(event);
            }
          };
        };
      })(this);
      unsubAll = function() {
        var sub, _i, _len, _results;
        _results = [];
        for (_i = 0, _len = subscriptions.length; _i < _len; _i++) {
          sub = subscriptions[_i];
          _results.push(typeof sub.unsub === "function" ? sub.unsub() : void 0);
        }
        return _results;
      };
      subscribeInput = function(subscription) {
        return subscription.unsub = subscription.input.subscribeInternal(guardedSink(subscription.input));
      };
      unsubscribeInput = function(input) {
        var i, sub, _i, _len;
        for (i = _i = 0, _len = subscriptions.length; _i < _len; i = ++_i) {
          sub = subscriptions[i];
          if (sub.input === input) {
            if (typeof sub.unsub === "function") {
              sub.unsub();
            }
            subscriptions.splice(i, 1);
            return;
          }
        }
      };
      subscribeAll = (function(_this) {
        return function(newSink) {
          var subscription, _i, _len, _ref1;
          sink = newSink;
          _ref1 = cloneArray(subscriptions);
          for (_i = 0, _len = _ref1.length; _i < _len; _i++) {
            subscription = _ref1[_i];
            subscribeInput(subscription);
          }
          return unsubAll;
        };
      })(this);
      Bus.__super__.constructor.call(this, describe(Bacon, "Bus"), subscribeAll);
      this.plug = (function(_this) {
        return function(input) {
          var sub;
          if (ended) {
            return;
          }
          sub = {
            input: input
          };
          subscriptions.push(sub);
          if ((sink != null)) {
            subscribeInput(sub);
          }
          return function() {
            return unsubscribeInput(input);
          };
        };
      })(this);
      this.push = (function(_this) {
        return function(value) {
          return typeof sink === "function" ? sink(next(value)) : void 0;
        };
      })(this);
      this.error = (function(_this) {
        return function(error) {
          return typeof sink === "function" ? sink(new Error(error)) : void 0;
        };
      })(this);
      this.end = (function(_this) {
        return function() {
          ended = true;
          unsubAll();
          return typeof sink === "function" ? sink(end()) : void 0;
        };
      })(this);
    }

    return Bus;

  })(EventStream);

  Source = (function() {
    function Source(obs, sync, subscribe, lazy) {
      this.obs = obs;
      this.sync = sync;
      this.subscribe = subscribe;
      this.lazy = lazy != null ? lazy : false;
      this.queue = [];
      if (this.subscribe == null) {
        this.subscribe = this.obs.subscribeInternal;
      }
      this.toString = this.obs.toString;
    }

    Source.prototype.markEnded = function() {
      return this.ended = true;
    };

    Source.prototype.consume = function() {
      if (this.lazy) {
        return _.always(this.queue[0]);
      } else {
        return this.queue[0];
      }
    };

    Source.prototype.push = function(x) {
      return this.queue = [x];
    };

    Source.prototype.mayHave = function() {
      return true;
    };

    Source.prototype.hasAtLeast = function() {
      return this.queue.length;
    };

    Source.prototype.flatten = true;

    return Source;

  })();

  ConsumingSource = (function(_super) {
    __extends(ConsumingSource, _super);

    function ConsumingSource() {
      return ConsumingSource.__super__.constructor.apply(this, arguments);
    }

    ConsumingSource.prototype.consume = function() {
      return this.queue.shift();
    };

    ConsumingSource.prototype.push = function(x) {
      return this.queue.push(x);
    };

    ConsumingSource.prototype.mayHave = function(c) {
      return !this.ended || this.queue.length >= c;
    };

    ConsumingSource.prototype.hasAtLeast = function(c) {
      return this.queue.length >= c;
    };

    ConsumingSource.prototype.flatten = false;

    return ConsumingSource;

  })(Source);

  BufferingSource = (function(_super) {
    __extends(BufferingSource, _super);

    function BufferingSource(obs) {
      this.obs = obs;
      BufferingSource.__super__.constructor.call(this, this.obs, true, this.obs.subscribeInternal);
    }

    BufferingSource.prototype.consume = function() {
      var values;
      values = this.queue;
      this.queue = [];
      return function() {
        return values;
      };
    };

    BufferingSource.prototype.push = function(x) {
      return this.queue.push(x());
    };

    BufferingSource.prototype.hasAtLeast = function() {
      return true;
    };

    return BufferingSource;

  })(Source);

  Source.isTrigger = function(s) {
    if (s instanceof Source) {
      return s.sync;
    } else {
      return s instanceof EventStream;
    }
  };

  Source.fromObservable = function(s) {
    if (s instanceof Source) {
      return s;
    } else if (s instanceof Property) {
      return new Source(s, false);
    } else {
      return new ConsumingSource(s, true);
    }
  };

  describe = function() {
    var args, context, method;
    context = arguments[0], method = arguments[1], args = 3 <= arguments.length ? __slice.call(arguments, 2) : [];
    if ((context || method) instanceof Desc) {
      return context || method;
    } else {
      return new Desc(context, method, args);
    }
  };

  Desc = (function() {
    function Desc(context, method, args) {
      var collectDeps, dependsOn, findDeps, flatDeps;
      findDeps = function(x) {
        if (isArray(x)) {
          return _.flatMap(findDeps, x);
        } else if (isObservable(x)) {
          return [x];
        } else if (x instanceof Source) {
          return [x.obs];
        } else {
          return [];
        }
      };
      flatDeps = null;
      collectDeps = function(o) {
        var dep, deps, _i, _len, _results;
        deps = o.internalDeps();
        _results = [];
        for (_i = 0, _len = deps.length; _i < _len; _i++) {
          dep = deps[_i];
          flatDeps[dep.id] = true;
          _results.push(collectDeps(dep));
        }
        return _results;
      };
      dependsOn = function(b) {
        if (flatDeps == null) {
          flatDeps = {};
          collectDeps(this);
        }
        return flatDeps[b.id];
      };
      this.apply = function(obs) {
        var deps;
        deps = _.cached((function() {
          return findDeps([context].concat(args));
        }));
        obs.internalDeps = obs.internalDeps || deps;
        obs.dependsOn = dependsOn;
        obs.deps = deps;
        obs.toString = function() {
          return _.toString(context) + "." + _.toString(method) + "(" + _.map(_.toString, args) + ")";
        };
        obs.inspect = function() {
          return obs.toString();
        };
        obs.desc = function() {
          return {
            context: context,
            method: method,
            args: args
          };
        };
        return obs;
      };
    }

    return Desc;

  })();

  withDescription = function() {
    var desc, obs, _i;
    desc = 2 <= arguments.length ? __slice.call(arguments, 0, _i = arguments.length - 1) : (_i = 0, []), obs = arguments[_i++];
    return describe.apply(null, desc).apply(obs);
  };

  Bacon.when = function() {
    var f, i, index, ix, len, needsBarrier, pat, patSources, pats, patterns, resultStream, s, sources, triggerFound, usage, _i, _j, _len, _len1, _ref1;
    patterns = 1 <= arguments.length ? __slice.call(arguments, 0) : [];
    if (patterns.length === 0) {
      return Bacon.never();
    }
    len = patterns.length;
    usage = "when: expecting arguments in the form (Observable+,function)+";
    assert(usage, len % 2 === 0);
    sources = [];
    pats = [];
    i = 0;
    while (i < len) {
      patSources = _.toArray(patterns[i]);
      f = patterns[i + 1];
      pat = {
        f: (isFunction(f) ? f : (function() {
          return f;
        })),
        ixs: []
      };
      triggerFound = false;
      for (_i = 0, _len = patSources.length; _i < _len; _i++) {
        s = patSources[_i];
        index = _.indexOf(sources, s);
        if (!triggerFound) {
          triggerFound = Source.isTrigger(s);
        }
        if (index < 0) {
          sources.push(s);
          index = sources.length - 1;
        }
        _ref1 = pat.ixs;
        for (_j = 0, _len1 = _ref1.length; _j < _len1; _j++) {
          ix = _ref1[_j];
          if (ix.index === index) {
            ix.count++;
          }
        }
        pat.ixs.push({
          index: index,
          count: 1
        });
      }
      assert("At least one EventStream required", triggerFound ||  (!patSources.length));
      if (patSources.length > 0) {
        pats.push(pat);
      }
      i = i + 2;
    }
    if (!sources.length) {
      return Bacon.never();
    }
    sources = _.map(Source.fromObservable, sources);
    needsBarrier = (_.any(sources, function(s) {
      return s.flatten;
    })) && (containsDuplicateDeps(_.map((function(s) {
      return s.obs;
    }), sources)));
    return resultStream = new EventStream(describe.apply(null, [Bacon, "when"].concat(__slice.call(patterns))), function(sink) {
      var cannotMatch, cannotSync, ends, match, nonFlattened, part, triggers;
      triggers = [];
      ends = false;
      match = function(p) {
        var _k, _len2, _ref2;
        _ref2 = p.ixs;
        for (_k = 0, _len2 = _ref2.length; _k < _len2; _k++) {
          i = _ref2[_k];
          if (!sources[i.index].hasAtLeast(i.count)) {
            return false;
          }
        }
        return true;
      };
      cannotSync = function(source) {
        return !source.sync || source.ended;
      };
      cannotMatch = function(p) {
        var _k, _len2, _ref2;
        _ref2 = p.ixs;
        for (_k = 0, _len2 = _ref2.length; _k < _len2; _k++) {
          i = _ref2[_k];
          if (!sources[i.index].mayHave(i.count)) {
            return true;
          }
        }
      };
      nonFlattened = function(trigger) {
        return !trigger.source.flatten;
      };
      part = function(source) {
        return function(unsubAll) {
          var flush, flushLater, flushWhileTriggers;
          flushLater = function() {
            return UpdateBarrier.whenDoneWith(resultStream, flush);
          };
          flushWhileTriggers = function() {
            var functions, p, reply, trigger, _k, _len2;
            if (triggers.length > 0) {
              reply = Bacon.more;
              trigger = triggers.pop();
              for (_k = 0, _len2 = pats.length; _k < _len2; _k++) {
                p = pats[_k];
                if (match(p)) {
                  functions = (function() {
                    var _l, _len3, _ref2, _results;
                    _ref2 = p.ixs;
                    _results = [];
                    for (_l = 0, _len3 = _ref2.length; _l < _len3; _l++) {
                      i = _ref2[_l];
                      _results.push(sources[i.index].consume());
                    }
                    return _results;
                  })();
                  reply = sink(trigger.e.apply(function() {
                    var fun, values;
                    values = (function() {
                      var _l, _len3, _results;
                      _results = [];
                      for (_l = 0, _len3 = functions.length; _l < _len3; _l++) {
                        fun = functions[_l];
                        _results.push(fun());
                      }
                      return _results;
                    })();
                    return p.f.apply(p, values);
                  }));
                  if (triggers.length && needsBarrier) {
                    triggers = _.filter(nonFlattened, triggers);
                  }
                  if (reply === Bacon.noMore) {
                    return reply;
                  } else {
                    return flushWhileTriggers();
                  }
                }
              }
            } else {
              return Bacon.more;
            }
          };
          flush = function() {
            var reply;
            reply = flushWhileTriggers();
            if (ends) {
              ends = false;
              if (_.all(sources, cannotSync) || _.all(pats, cannotMatch)) {
                reply = Bacon.noMore;
                sink(end());
              }
            }
            if (reply === Bacon.noMore) {
              unsubAll();
            }
            return reply;
          };
          return source.subscribe(function(e) {
            var reply;
            if (e.isEnd()) {
              ends = true;
              source.markEnded();
              flushLater();
            } else if (e.isError()) {
              reply = sink(e);
            } else {
              source.push(e.value);
              if (source.sync) {
                triggers.push({
                  source: source,
                  e: e
                });
                if (needsBarrier) {
                  flushLater();
                } else {
                  flush();
                }
              }
            }
            if (reply === Bacon.noMore) {
              unsubAll();
            }
            return reply || Bacon.more;
          });
        };
      };
      return compositeUnsubscribe.apply(null, (function() {
        var _k, _len2, _results;
        _results = [];
        for (_k = 0, _len2 = sources.length; _k < _len2; _k++) {
          s = sources[_k];
          _results.push(part(s));
        }
        return _results;
      })());
    });
  };

  containsDuplicateDeps = function(observables, state) {
    var checkObservable;
    if (state == null) {
      state = [];
    }
    checkObservable = function(obs) {
      var deps;
      if (Bacon._.contains(state, obs)) {
        return true;
      } else {
        deps = obs.internalDeps();
        if (deps.length) {
          state.push(obs);
          return Bacon._.any(deps, checkObservable);
        } else {
          state.push(obs);
          return false;
        }
      }
    };
    return Bacon._.any(observables, checkObservable);
  };

  Bacon.update = function() {
    var i, initial, lateBindFirst, patterns;
    initial = arguments[0], patterns = 2 <= arguments.length ? __slice.call(arguments, 1) : [];
    lateBindFirst = function(f) {
      return function() {
        var args;
        args = 1 <= arguments.length ? __slice.call(arguments, 0) : [];
        return function(i) {
          return f.apply(null, [i].concat(args));
        };
      };
    };
    i = patterns.length - 1;
    while (i > 0) {
      if (!(patterns[i] instanceof Function)) {
        patterns[i] = (function(x) {
          return function() {
            return x;
          };
        })(patterns[i]);
      }
      patterns[i] = lateBindFirst(patterns[i]);
      i = i - 2;
    }
    return withDescription.apply(null, [Bacon, "update", initial].concat(__slice.call(patterns), [Bacon.when.apply(Bacon, patterns).scan(initial, (function(x, f) {
      return f(x);
    }))]));
  };

  compositeUnsubscribe = function() {
    var ss;
    ss = 1 <= arguments.length ? __slice.call(arguments, 0) : [];
    return new CompositeUnsubscribe(ss).unsubscribe;
  };

  CompositeUnsubscribe = (function() {
    function CompositeUnsubscribe(ss) {
      var s, _i, _len;
      if (ss == null) {
        ss = [];
      }
      this.unsubscribe = __bind(this.unsubscribe, this);
      this.unsubscribed = false;
      this.subscriptions = [];
      this.starting = [];
      for (_i = 0, _len = ss.length; _i < _len; _i++) {
        s = ss[_i];
        this.add(s);
      }
    }

    CompositeUnsubscribe.prototype.add = function(subscription) {
      var ended, unsub, unsubMe;
      if (this.unsubscribed) {
        return;
      }
      ended = false;
      unsub = nop;
      this.starting.push(subscription);
      unsubMe = (function(_this) {
        return function() {
          if (_this.unsubscribed) {
            return;
          }
          ended = true;
          _this.remove(unsub);
          return _.remove(subscription, _this.starting);
        };
      })(this);
      unsub = subscription(this.unsubscribe, unsubMe);
      if (!(this.unsubscribed || ended)) {
        this.subscriptions.push(unsub);
      }
      _.remove(subscription, this.starting);
      return unsub;
    };

    CompositeUnsubscribe.prototype.remove = function(unsub) {
      if (this.unsubscribed) {
        return;
      }
      if ((_.remove(unsub, this.subscriptions)) !== void 0) {
        return unsub();
      }
    };

    CompositeUnsubscribe.prototype.unsubscribe = function() {
      var s, _i, _len, _ref1;
      if (this.unsubscribed) {
        return;
      }
      this.unsubscribed = true;
      _ref1 = this.subscriptions;
      for (_i = 0, _len = _ref1.length; _i < _len; _i++) {
        s = _ref1[_i];
        s();
      }
      this.subscriptions = [];
      return this.starting = [];
    };

    CompositeUnsubscribe.prototype.count = function() {
      if (this.unsubscribed) {
        return 0;
      }
      return this.subscriptions.length + this.starting.length;
    };

    CompositeUnsubscribe.prototype.empty = function() {
      return this.count() === 0;
    };

    return CompositeUnsubscribe;

  })();

  Bacon.CompositeUnsubscribe = CompositeUnsubscribe;

  Some = (function() {
    function Some(value) {
      this.value = value;
    }

    Some.prototype.getOrElse = function() {
      return this.value;
    };

    Some.prototype.get = function() {
      return this.value;
    };

    Some.prototype.filter = function(f) {
      if (f(this.value)) {
        return new Some(this.value);
      } else {
        return None;
      }
    };

    Some.prototype.map = function(f) {
      return new Some(f(this.value));
    };

    Some.prototype.forEach = function(f) {
      return f(this.value);
    };

    Some.prototype.isDefined = true;

    Some.prototype.toArray = function() {
      return [this.value];
    };

    Some.prototype.inspect = function() {
      return "Some(" + this.value + ")";
    };

    Some.prototype.toString = function() {
      return this.inspect();
    };

    return Some;

  })();

  None = {
    getOrElse: function(value) {
      return value;
    },
    filter: function() {
      return None;
    },
    map: function() {
      return None;
    },
    forEach: function() {},
    isDefined: false,
    toArray: function() {
      return [];
    },
    inspect: function() {
      return "None";
    },
    toString: function() {
      return this.inspect();
    }
  };

  UpdateBarrier = (function() {
    var afterTransaction, afters, currentEventId, findIndependent, flush, inTransaction, independent, rootEvent, waiters, whenDoneWith, wrappedSubscribe;
    rootEvent = void 0;
    waiters = [];
    afters = [];
    afterTransaction = function(f) {
      if (rootEvent) {
        return afters.push(f);
      } else {
        return f();
      }
    };
    independent = function(waiter) {
      return !_.any(waiters, (function(other) {
        return waiter.obs.dependsOn(other.obs);
      }));
    };
    whenDoneWith = function(obs, f) {
      if (rootEvent) {
        return waiters.push({
          obs: obs,
          f: f
        });
      } else {
        return f();
      }
    };
    findIndependent = function() {
      while (!independent(waiters[0])) {
        waiters.push(waiters.splice(0, 1)[0]);
      }
      return waiters.splice(0, 1)[0];
    };
    flush = function() {
      var _results;
      _results = [];
      while (waiters.length) {
        _results.push(findIndependent().f());
      }
      return _results;
    };
    inTransaction = function(event, context, f, args) {
      var result;
      if (rootEvent) {
        return f.apply(context, args);
      } else {
        rootEvent = event;
        try {
          result = f.apply(context, args);
          flush();
        } finally {
          rootEvent = void 0;
          while (afters.length) {
            f = afters.splice(0, 1)[0];
            f();
          }
        }
        return result;
      }
    };
    currentEventId = function() {
      if (rootEvent) {
        return rootEvent.id;
      } else {
        return void 0;
      }
    };
    wrappedSubscribe = function(obs) {
      return function(sink) {
        var doUnsub, unsub, unsubd;
        unsubd = false;
        doUnsub = function() {};
        unsub = function() {
          unsubd = true;
          return doUnsub();
        };
        if (!unsubd) {
          doUnsub = obs.subscribeInternal(function(event) {
            return afterTransaction(function() {
              var reply;
              if (!unsubd) {
                reply = sink(event);
                if (reply === Bacon.noMore) {
                  return unsub();
                }
              }
            });
          });
        }
        return unsub;
      };
    };
    return {
      whenDoneWith: whenDoneWith,
      inTransaction: inTransaction,
      currentEventId: currentEventId,
      wrappedSubscribe: wrappedSubscribe
    };
  })();

  Bacon.EventStream = EventStream;

  Bacon.Property = Property;

  Bacon.Observable = Observable;

  Bacon.Bus = Bus;

  Bacon.Initial = Initial;

  Bacon.Next = Next;

  Bacon.End = End;

  Bacon.Error = Error;

  nop = function() {};

  latterF = function(_, x) {
    return x();
  };

  former = function(x, _) {
    return x;
  };

  initial = function(value) {
    return new Initial(_.always(value));
  };

  next = function(value) {
    return new Next(_.always(value));
  };

  end = function() {
    return new End();
  };

  toEvent = function(x) {
    if (x instanceof Event) {
      return x;
    } else {
      return next(x);
    }
  };

  cloneArray = function(xs) {
    return xs.slice(0);
  };

  assert = function(message, condition) {
    if (!condition) {
      throw message;
    }
  };

  assertEventStream = function(event) {
    if (!(event instanceof EventStream)) {
      throw "not an EventStream : " + event;
    }
  };

  assertFunction = function(f) {
    return assert("not a function : " + f, isFunction(f));
  };

  isFunction = function(f) {
    return typeof f === "function";
  };

  isArray = function(xs) {
    return xs instanceof Array;
  };

  isObservable = function(x) {
    return x instanceof Observable;
  };

  assertArray = function(xs) {
    if (!isArray(xs)) {
      throw "not an array : " + xs;
    }
  };

  assertNoArguments = function(args) {
    return assert("no arguments supported", args.length === 0);
  };

  assertString = function(x) {
    if (typeof x !== "string") {
      throw "not a string : " + x;
    }
  };

  partiallyApplied = function(f, applied) {
    return function() {
      var args;
      args = 1 <= arguments.length ? __slice.call(arguments, 0) : [];
      return f.apply(null, applied.concat(args));
    };
  };

  makeSpawner = function(args) {
    if (args.length === 1 && isObservable(args[0])) {
      return _.always(args[0]);
    } else {
      return makeFunctionArgs(args);
    }
  };

  makeFunctionArgs = function(args) {
    args = Array.prototype.slice.call(args);
    return makeFunction_.apply(null, args);
  };

  makeFunction_ = withMethodCallSupport(function() {
    var args, f;
    f = arguments[0], args = 2 <= arguments.length ? __slice.call(arguments, 1) : [];
    if (isFunction(f)) {
      if (args.length) {
        return partiallyApplied(f, args);
      } else {
        return f;
      }
    } else if (isFieldKey(f)) {
      return toFieldExtractor(f, args);
    } else {
      return _.always(f);
    }
  });

  makeFunction = function(f, args) {
    return makeFunction_.apply(null, [f].concat(__slice.call(args)));
  };

  makeObservable = function(x) {
    if (isObservable(x)) {
      return x;
    } else {
      return Bacon.once(x);
    }
  };

  isFieldKey = function(f) {
    return (typeof f === "string") && f.length > 1 && f.charAt(0) === ".";
  };

  Bacon.isFieldKey = isFieldKey;

  toFieldExtractor = function(f, args) {
    var partFuncs, parts;
    parts = f.slice(1).split(".");
    partFuncs = _.map(toSimpleExtractor(args), parts);
    return function(value) {
      var _i, _len;
      for (_i = 0, _len = partFuncs.length; _i < _len; _i++) {
        f = partFuncs[_i];
        value = f(value);
      }
      return value;
    };
  };

  toSimpleExtractor = function(args) {
    return function(key) {
      return function(value) {
        var fieldValue;
        if (value == null) {
          return void 0;
        } else {
          fieldValue = value[key];
          if (isFunction(fieldValue)) {
            return fieldValue.apply(value, args);
          } else {
            return fieldValue;
          }
        }
      };
    };
  };

  toFieldKey = function(f) {
    return f.slice(1);
  };

  toCombinator = function(f) {
    var key;
    if (isFunction(f)) {
      return f;
    } else if (isFieldKey(f)) {
      key = toFieldKey(f);
      return function(left, right) {
        return left[key](right);
      };
    } else {
      return assert("not a function or a field key: " + f, false);
    }
  };

  toOption = function(v) {
    if (v instanceof Some || v === None) {
      return v;
    } else {
      return new Some(v);
    }
  };

  _ = {
    indexOf: Array.prototype.indexOf ? function(xs, x) {
      return xs.indexOf(x);
    } : function(xs, x) {
      var i, y, _i, _len;
      for (i = _i = 0, _len = xs.length; _i < _len; i = ++_i) {
        y = xs[i];
        if (x === y) {
          return i;
        }
      }
      return -1;
    },
    indexWhere: function(xs, f) {
      var i, y, _i, _len;
      for (i = _i = 0, _len = xs.length; _i < _len; i = ++_i) {
        y = xs[i];
        if (f(y)) {
          return i;
        }
      }
      return -1;
    },
    head: function(xs) {
      return xs[0];
    },
    always: function(x) {
      return function() {
        return x;
      };
    },
    negate: function(f) {
      return function(x) {
        return !f(x);
      };
    },
    empty: function(xs) {
      return xs.length === 0;
    },
    tail: function(xs) {
      return xs.slice(1, xs.length);
    },
    filter: function(f, xs) {
      var filtered, x, _i, _len;
      filtered = [];
      for (_i = 0, _len = xs.length; _i < _len; _i++) {
        x = xs[_i];
        if (f(x)) {
          filtered.push(x);
        }
      }
      return filtered;
    },
    map: function(f, xs) {
      var x, _i, _len, _results;
      _results = [];
      for (_i = 0, _len = xs.length; _i < _len; _i++) {
        x = xs[_i];
        _results.push(f(x));
      }
      return _results;
    },
    each: function(xs, f) {
      var key, value, _results;
      _results = [];
      for (key in xs) {
        value = xs[key];
        _results.push(f(key, value));
      }
      return _results;
    },
    toArray: function(xs) {
      if (isArray(xs)) {
        return xs;
      } else {
        return [xs];
      }
    },
    contains: function(xs, x) {
      return _.indexOf(xs, x) !== -1;
    },
    id: function(x) {
      return x;
    },
    last: function(xs) {
      return xs[xs.length - 1];
    },
    all: function(xs, f) {
      var x, _i, _len;
      if (f == null) {
        f = _.id;
      }
      for (_i = 0, _len = xs.length; _i < _len; _i++) {
        x = xs[_i];
        if (!f(x)) {
          return false;
        }
      }
      return true;
    },
    any: function(xs, f) {
      var x, _i, _len;
      if (f == null) {
        f = _.id;
      }
      for (_i = 0, _len = xs.length; _i < _len; _i++) {
        x = xs[_i];
        if (f(x)) {
          return true;
        }
      }
      return false;
    },
    without: function(x, xs) {
      return _.filter((function(y) {
        return y !== x;
      }), xs);
    },
    remove: function(x, xs) {
      var i;
      i = _.indexOf(xs, x);
      if (i >= 0) {
        return xs.splice(i, 1);
      }
    },
    fold: function(xs, seed, f) {
      var x, _i, _len;
      for (_i = 0, _len = xs.length; _i < _len; _i++) {
        x = xs[_i];
        seed = f(seed, x);
      }
      return seed;
    },
    flatMap: function(f, xs) {
      return _.fold(xs, [], (function(ys, x) {
        return ys.concat(f(x));
      }));
    },
    cached: function(f) {
      var value;
      value = None;
      return function() {
        if (value === None) {
          value = f();
          f = null;
        }
        return value;
      };
    },
    toString: function(obj) {
      var ex, internals, key, value;
      try {
        recursionDepth++;
        if (obj == null) {
          return "undefined";
        } else if (isFunction(obj)) {
          return "function";
        } else if (isArray(obj)) {
          if (recursionDepth > 5) {
            return "[..]";
          }
          return "[" + _.map(_.toString, obj).toString() + "]";
        } else if (((obj != null ? obj.toString : void 0) != null) && obj.toString !== Object.prototype.toString) {
          return obj.toString();
        } else if (typeof obj === "object") {
          if (recursionDepth > 5) {
            return "{..}";
          }
          internals = (function() {
            var _results;
            _results = [];
            for (key in obj) {
              if (!__hasProp.call(obj, key)) continue;
              value = (function() {
                try {
                  return obj[key];
                } catch (_error) {
                  ex = _error;
                  return ex;
                }
              })();
              _results.push(_.toString(key) + ":" + _.toString(value));
            }
            return _results;
          })();
          return "{" + internals + "}";
        } else {
          return obj;
        }
      } finally {
        recursionDepth--;
      }
    }
  };

  recursionDepth = 0;

  Bacon._ = _;

  Bacon.scheduler = {
    setTimeout: function(f, d) {
      return setTimeout(f, d);
    },
    setInterval: function(f, i) {
      return setInterval(f, i);
    },
    clearInterval: function(id) {
      return clearInterval(id);
    },
    now: function() {
      return new Date().getTime();
    }
  };

  if ((typeof define !== "undefined" && define !== null) && (define.amd != null)) {
    define('lib/bacon',[], function() {
      return Bacon;
    });
    this.Bacon = Bacon;
  } else if (typeof module !== "undefined" && module !== null) {
    module.exports = Bacon;
    Bacon.Bacon = Bacon;
  } else {
    this.Bacon = Bacon;
  }

}).call(this);

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0!==b.maxItems&&a.length>b.maxItems&&(c=this.createError(o.ARRAY_LENGTH_LONG,{length:a.length,maximum:b.maxItems}).prefixWith(null,"maxItems"),this.handleError(c))?c:null},n.prototype.validateArrayUniqueItems=function(a,b){if(b.uniqueItems)for(var c=0;c<a.length;c++)for(var e=c+1;e<a.length;e++)if(d(a[c],a[e])){var f=this.createError(o.ARRAY_UNIQUE,{match1:c,match2:e}).prefixWith(null,"uniqueItems");if(this.handleError(f))return f}return null},n.prototype.validateArrayItems=function(a,b,c){if(void 0===b.items)return null;var d,e;if(Array.isArray(b.items)){for(e=0;e<a.length;e++)if(e<b.items.length){if(d=this.validateAll(a[e],b.items[e],[e],["items",e],c+"/"+e))return d}else if(void 0!==b.additionalItems)if("boolean"==typeof b.additionalItems){if(!b.additionalItems&&(d=this.createError(o.ARRAY_ADDITIONAL_ITEMS,{}).prefixWith(""+e,"additionalItems"),this.handleError(d)))return d}else if(d=this.validateAll(a[e],b.additionalItems,[e],["additionalItems"],c+"/"+e))return d}else for(e=0;e<a.length;e++)if(d=this.validateAll(a[e],b.items,[e],["items"],c+"/"+e))return d;return null},n.prototype.validateObject=function(a,b,c){return"object"!=typeof a||null===a||Array.isArray(a)?null:this.validateObjectMinMaxProperties(a,b,c)||this.validateObjectRequiredProperties(a,b,c)||this.validateObjectProperties(a,b,c)||this.validateObjectDependencies(a,b,c)||null},n.prototype.validateObjectMinMaxProperties=function(a,b){var c,d=Object.keys(a);return void 0!==b.minProperties&&d.length<b.minProperties&&(c=this.createError(o.OBJECT_PROPERTIES_MINIMUM,{propertyCount:d.length,minimum:b.minProperties}).prefixWith(null,"minProperties"),this.handleError(c))?c:void 0!==b.maxProperties&&d.length>b.maxProperties&&(c=this.createError(o.OBJECT_PROPERTIES_MAXIMUM,{propertyCount:d.length,maximum:b.maxProperties}).prefixWith(null,"maxProperties"),this.handleError(c))?c:null},n.prototype.validateObjectRequiredProperties=function(a,b){if(void 0!==b.required)for(var c=0;c<b.required.length;c++){var d=b.required[c];if(void 0===a[d]){var e=this.createError(o.OBJECT_REQUIRED,{key:d}).prefixWith(null,""+c).prefixWith(null,"required");if(this.handleError(e))return e}}return null},n.prototype.validateObjectProperties=function(a,b,c){var d;for(var e in a){var f=c+"/"+e.replace(/~/g,"~0").replace(/\//g,"~1"),g=!1;if(void 0!==b.properties&&void 0!==b.properties[e]&&(g=!0,d=this.validateAll(a[e],b.properties[e],[e],["properties",e],f)))return d;if(void 0!==b.patternProperties)for(var h in b.patternProperties){var i=new RegExp(h);if(i.test(e)&&(g=!0,d=this.validateAll(a[e],b.patternProperties[h],[e],["patternProperties",h],f)))return d}if(g)this.trackUnknownProperties&&(this.knownPropertyPaths[f]=!0,delete this.unknownPropertyPaths[f]);else if(void 0!==b.additionalProperties){if(this.trackUnknownProperties&&(this.knownPropertyPaths[f]=!0,delete this.unknownPropertyPaths[f]),"boolean"==typeof b.additionalProperties){if(!b.additionalProperties&&(d=this.createError(o.OBJECT_ADDITIONAL_PROPERTIES,{}).prefixWith(e,"additionalProperties"),this.handleError(d)))return d}else if(d=this.validateAll(a[e],b.additionalProperties,[e],["additionalProperties"],f))return d}else this.trackUnknownProperties&&!this.knownPropertyPaths[f]&&(this.unknownPropertyPaths[f]=!0)}return null},n.prototype.validateObjectDependencies=function(a,b,c){var d;if(void 0!==b.dependencies)for(var e in b.dependencies)if(void 0!==a[e]){var f=b.dependencies[e];if("string"==typeof f){if(void 0===a[f]&&(d=this.createError(o.OBJECT_DEPENDENCY_KEY,{key:e,missing:f}).prefixWith(null,e).prefixWith(null,"dependencies"),this.handleError(d)))return d}else if(Array.isArray(f))for(var g=0;g<f.length;g++){var h=f[g];if(void 0===a[h]&&(d=this.createError(o.OBJECT_DEPENDENCY_KEY,{key:e,missing:h}).prefixWith(null,""+g).prefixWith(null,e).prefixWith(null,"dependencies"),this.handleError(d)))return d}else if(d=this.validateAll(a,f,[],["dependencies",e],c))return d}return null},n.prototype.validateCombinations=function(a,b,c){return this.validateAllOf(a,b,c)||this.validateAnyOf(a,b,c)||this.validateOneOf(a,b,c)||this.validateNot(a,b,c)||null},n.prototype.validateAllOf=function(a,b,c){if(void 0===b.allOf)return null;for(var d,e=0;e<b.allOf.length;e++){var f=b.allOf[e];if(d=this.validateAll(a,f,[],["allOf",e],c))return d}return null},n.prototype.validateAnyOf=function(a,b,c){if(void 0===b.anyOf)return null;var d,e,f=[],g=this.errors.length;this.trackUnknownProperties&&(d=this.unknownPropertyPaths,e=this.knownPropertyPaths);for(var h=!0,i=0;i<b.anyOf.length;i++){this.trackUnknownProperties&&(this.unknownPropertyPaths={},this.knownPropertyPaths={});var j=b.anyOf[i],k=this.errors.length,l=this.validateAll(a,j,[],["anyOf",i],c);if(null===l&&k===this.errors.length){if(this.errors=this.errors.slice(0,g),this.trackUnknownProperties){for(var m in this.knownPropertyPaths)e[m]=!0,delete d[m];for(var n in this.unknownPropertyPaths)e[n]||(d[n]=!0);h=!1;continue}return null}l&&f.push(l.prefixWith(null,""+i).prefixWith(null,"anyOf"))}return this.trackUnknownProperties&&(this.unknownPropertyPaths=d,this.knownPropertyPaths=e),h?(f=f.concat(this.errors.slice(g)),this.errors=this.errors.slice(0,g),this.createError(o.ANY_OF_MISSING,{},"","/anyOf",f)):void 0},n.prototype.validateOneOf=function(a,b,c){if(void 0===b.oneOf)return null;var d,e,f=null,g=[],h=this.errors.length;this.trackUnknownProperties&&(d=this.unknownPropertyPaths,e=this.knownPropertyPaths);for(var i=0;i<b.oneOf.length;i++){this.trackUnknownProperties&&(this.unknownPropertyPaths={},this.knownPropertyPaths={});var j=b.oneOf[i],k=this.errors.length,l=this.validateAll(a,j,[],["oneOf",i],c);if(null===l&&k===this.errors.length){if(null!==f)return this.errors=this.errors.slice(0,h),this.createError(o.ONE_OF_MULTIPLE,{index1:f,index2:i},"","/oneOf");if(f=i,this.trackUnknownProperties){for(var m in this.knownPropertyPaths)e[m]=!0,delete d[m];for(var n in this.unknownPropertyPaths)e[n]||(d[n]=!0)}}else l&&g.push(l)}return this.trackUnknownProperties&&(this.unknownPropertyPaths=d,this.knownPropertyPaths=e),null===f?(g=g.concat(this.errors.slice(h)),this.errors=this.errors.slice(0,h),this.createError(o.ONE_OF_MISSING,{},"","/oneOf",g)):(this.errors=this.errors.slice(0,h),null)},n.prototype.validateNot=function(a,b,c){if(void 0===b.not)return null;var d,e,f=this.errors.length;this.trackUnknownProperties&&(d=this.unknownPropertyPaths,e=this.knownPropertyPaths,this.unknownPropertyPaths={},this.knownPropertyPaths={});var g=this.validateAll(a,b.not,null,null,c),h=this.errors.slice(f);return this.errors=this.errors.slice(0,f),this.trackUnknownProperties&&(this.unknownPropertyPaths=d,this.knownPropertyPaths=e),null===g&&0===h.length?this.createError(o.NOT_PASSED,{},"","/not"):null},n.prototype.validateHypermedia=function(a,b,d){if(!b.links)return null;for(var e,f=0;f<b.links.length;f++){var g=b.links[f];if("describedby"===g.rel){for(var h=new c(g.href),i=!0,j=0;j<h.varNames.length;j++)if(!(h.varNames[j]in a)){i=!1;break}if(i){var k=h.fillFromObject(a),l={$ref:k};if(e=this.validateAll(a,l,[],["links",f],d))return e}}}};var o={INVALID_TYPE:0,ENUM_MISMATCH:1,ANY_OF_MISSING:10,ONE_OF_MISSING:11,ONE_OF_MULTIPLE:12,NOT_PASSED:13,NUMBER_MULTIPLE_OF:100,NUMBER_MINIMUM:101,NUMBER_MINIMUM_EXCLUSIVE:102,NUMBER_MAXIMUM:103,NUMBER_MAXIMUM_EXCLUSIVE:104,STRING_LENGTH_SHORT:200,STRING_LENGTH_LONG:201,STRING_PATTERN:202,OBJECT_PROPERTIES_MINIMUM:300,OBJECT_PROPERTIES_MAXIMUM:301,OBJECT_REQUIRED:302,OBJECT_ADDITIONAL_PROPERTIES:303,OBJECT_DEPENDENCY_KEY:304,ARRAY_LENGTH_SHORT:400,ARRAY_LENGTH_LONG:401,ARRAY_UNIQUE:402,ARRAY_ADDITIONAL_ITEMS:403,FORMAT_CUSTOM:500,KEYWORD_CUSTOM:501,CIRCULAR_REFERENCE:600,UNKNOWN_PROPERTY:1e3},p={};for(var q in o)p[o[q]]=q;var r={INVALID_TYPE:"Invalid type: {type} (expected {expected})",ENUM_MISMATCH:"No enum match for: {value}",ANY_OF_MISSING:'Data does not match any schemas from "anyOf"',ONE_OF_MISSING:'Data does not match any schemas from "oneOf"',ONE_OF_MULTIPLE:'Data is valid against more than one schema from "oneOf": indices {index1} and {index2}',NOT_PASSED:'Data matches schema from "not"',NUMBER_MULTIPLE_OF:"Value {value} is not a multiple of {multipleOf}",NUMBER_MINIMUM:"Value {value} is less than minimum {minimum}",NUMBER_MINIMUM_EXCLUSIVE:"Value {value} is equal to exclusive minimum {minimum}",NUMBER_MAXIMUM:"Value {value} is greater than maximum {maximum}",NUMBER_MAXIMUM_EXCLUSIVE:"Value {value} is equal to exclusive maximum {maximum}",STRING_LENGTH_SHORT:"String is too short ({length} chars), minimum {minimum}",STRING_LENGTH_LONG:"String is too long ({length} chars), maximum {maximum}",STRING_PATTERN:"String does not match pattern: {pattern}",OBJECT_PROPERTIES_MINIMUM:"Too few properties defined ({propertyCount}), minimum {minimum}",OBJECT_PROPERTIES_MAXIMUM:"Too many properties defined ({propertyCount}), maximum {maximum}",OBJECT_REQUIRED:"Missing required property: {key}",OBJECT_ADDITIONAL_PROPERTIES:"Additional properties not allowed",OBJECT_DEPENDENCY_KEY:"Dependency failed - key must exist: {missing} (due to key: {key})",ARRAY_LENGTH_SHORT:"Array is too short ({length}), minimum {minimum}",ARRAY_LENGTH_LONG:"Array is too long ({length}), maximum {maximum}",ARRAY_UNIQUE:"Array items are not unique (indices {match1} and {match2})",ARRAY_ADDITIONAL_ITEMS:"Additional items not allowed",FORMAT_CUSTOM:"Format validation failed ({message})",KEYWORD_CUSTOM:"Keyword failed: {key} ({message})",CIRCULAR_REFERENCE:"Circular $refs: {urls}",UNKNOWN_PROPERTY:"Unknown property (not in schema)"};i.prototype=Object.create(Error.prototype),i.prototype.constructor=i,i.prototype.name="ValidationError",i.prototype.prefixWith=function(a,b){if(null!==a&&(a=a.replace(/~/g,"~0").replace(/\//g,"~1"),this.dataPath="/"+a+this.dataPath),null!==b&&(b=b.replace(/~/g,"~0").replace(/\//g,"~1"),this.schemaPath="/"+b+this.schemaPath),null!==this.subErrors)for(var c=0;c<this.subErrors.length;c++)this.subErrors[c].prefixWith(a,b);return this};var s={},t=k();return t.addLanguage("en-gb",r),t.tv4=t,t});
/* global define, d3 */

define('Map',['utils', 'Draw', 'Behavior', 'Scale', 'build', 'UndoStack', 'CallbackManager', 'KeyManager', 'Canvas', 'data_styles', 'SearchIndex', 'lib/bacon', 'lib/tv4'], function(utils, Draw, Behavior, Scale, build, UndoStack, CallbackManager, KeyManager, Canvas, data_styles, SearchIndex, bacon, tv4) {
    /** Defines the metabolic map data, and manages drawing and building.

     Arguments
     ---------

     svg: The parent SVG container for the map.

     css:

     selection: A d3 selection for a node to place the map inside.

     selection:

     zoom_container:

     settings:

     cobra_model:

     canvas_size_and_loc:

     enable_search:

     map_name: (Optional, Default: 'new map')

     map_id: (Optional, Default: A string of random characters.)

     map_description: (Optional, Default: '')

     Callbacks
     ---------

     map.callback_manager.run('set_status', null, status);
     map.callback_manager.run('toggle_beziers', null, beziers_enabled);
     map.callback_manager.run('select_metabolite_with_id', null, selected_node, coords);
     map.callback_manager.run('select_selectable', null, node_count, selected_node, coords);
     map.callback_manager.run('deselect_nodes');
     map.callback_manager.run('select_text_label');
     map.callback_manager.run('before_svg_export');
     map.callback_manager.run('after_svg_export');
     map.callback_manager.run('before_convert_map');
     map.callback_manager.run('after_convert_map');
     this.callback_manager.run('calc_data_stats__reaction', null, changed);
     this.callback_manager.run('calc_data_stats__metabolite', null, changed);

     */

    var Map = utils.make_class();
    // class methods
    Map.from_data = from_data;
    // instance methods
    Map.prototype = {
        // setup
        init: init,
        // more setup
        setup_containers: setup_containers,
        reset_containers: reset_containers,
        // appearance
        set_status: set_status,
        clear_map: clear_map,
        // selection
        select_all: select_all,
        select_none: select_none,
        invert_selection: invert_selection,
        select_selectable: select_selectable,
        select_metabolite_with_id: select_metabolite_with_id,
        select_single_node: select_single_node,
        deselect_nodes: deselect_nodes,
        select_text_label: select_text_label,
        deselect_text_labels: deselect_text_labels,
        // build
        new_reaction_from_scratch: new_reaction_from_scratch,
        extend_nodes: extend_nodes,
        extend_reactions: extend_reactions,
        new_reaction_for_metabolite: new_reaction_for_metabolite,
        cycle_primary_node: cycle_primary_node,
        toggle_selected_node_primary: toggle_selected_node_primary,
        new_text_label: new_text_label,
        edit_text_label: edit_text_label,
        // delete
        delete_selected: delete_selected,
        delete_selectable: delete_selectable,
        delete_node_data: delete_node_data,
        delete_segment_data: delete_segment_data,
        delete_reaction_data: delete_reaction_data,
        delete_text_label_data: delete_text_label_data,
        // find
        get_selected_node_ids: get_selected_node_ids,
        get_selected_nodes: get_selected_nodes,
        get_selected_text_label_ids: get_selected_text_label_ids,
        get_selected_text_labels: get_selected_text_labels,
        segments_and_reactions_for_nodes: segments_and_reactions_for_nodes,
        // draw
        draw_everything: draw_everything,
        // draw reactions
        draw_all_reactions: draw_all_reactions,
        draw_these_reactions: draw_these_reactions,
        clear_deleted_reactions: clear_deleted_reactions,
        // draw nodes
        draw_all_nodes: draw_all_nodes,
        draw_these_nodes: draw_these_nodes,
        clear_deleted_nodes: clear_deleted_nodes,
        // draw text_labels
        draw_all_text_labels: draw_all_text_labels,
        draw_these_text_labels: draw_these_text_labels,
        clear_deleted_text_labels: clear_deleted_text_labels,
        // draw beziers
        draw_all_beziers: draw_all_beziers,
        draw_these_beziers: draw_these_beziers,
        clear_deleted_beziers: clear_deleted_beziers,
        toggle_beziers: toggle_beziers,
        hide_beziers: hide_beziers,
        show_beziers: show_beziers,
        // data
        has_cobra_model: has_cobra_model,
        apply_reaction_data_to_map: apply_reaction_data_to_map,
        apply_metabolite_data_to_map: apply_metabolite_data_to_map,
        apply_gene_data_to_map: apply_gene_data_to_map,
        // data statistics
        get_data_statistics: get_data_statistics,
        calc_data_stats: calc_data_stats,
        // zoom
        zoom_extent_nodes: zoom_extent_nodes,
        zoom_extent_canvas: zoom_extent_canvas,
        _zoom_extent: _zoom_extent,
        get_size: get_size,
        zoom_to_reaction: zoom_to_reaction,
        zoom_to_node: zoom_to_node,
        zoom_to_text_label: zoom_to_text_label,
        highlight_reaction: highlight_reaction,
        highlight_node: highlight_node,
        highlight_text_label: highlight_text_label,
        highlight: highlight,
        // io
        save: save,
        map_for_export: map_for_export,
        save_svg: save_svg,
        convert_map: convert_map
    };

    return Map;

    // -------------------------------------------------------------------------
    // setup

    function init(svg, css, selection, zoom_container, settings,
                  cobra_model, canvas_size_and_loc, enable_search,
                  map_name, map_id, map_description) {
        if (canvas_size_and_loc===null) {
            var size = zoom_container.get_size();
            canvas_size_and_loc = {x: -size.width, y: -size.height,
                                   width: size.width*3, height: size.height*3};
        }

        if (map_name === undefined || map_name === null || map_name == '')
            map_name = 'new_map';
        else
            map_name = String(map_name);
        if (map_id === undefined || map_id === null || map_id == '')
            map_id = utils.generate_map_id();
        else
            map_id = String(map_id);
        if (map_description === undefined || map_description === null)
            map_description = '';
        else
            map_description = String(map_description);

        // set up the callbacks
        this.callback_manager = new CallbackManager();

        // set up the defs
        this.svg = svg;
        this.defs = utils.setup_defs(svg, css);

        // make the canvas
        this.canvas = new Canvas(selection, canvas_size_and_loc);

        this.setup_containers(selection);
        this.sel = selection;
        this.zoom_container = zoom_container;

        this.settings = settings;

        // set the model AFTER loading the datasets
        this.cobra_model = cobra_model;

        this.largest_ids = { reactions: -1,
                             nodes: -1,
                             segments: -1,
                             text_labels: -1 };

        // make the scales
        this.scale = new Scale();
        // initialize stats
        this.calc_data_stats('reaction');
        this.calc_data_stats('metabolite');
        this.scale.connect_to_settings(this.settings, this,
                                       get_data_statistics.bind(this));

        // make the undo/redo stack
        this.undo_stack = new UndoStack();

        // make a behavior object
        this.behavior = new Behavior(this, this.undo_stack);

        // draw manager
        this.draw = new Draw(this.behavior, this.settings);

        // make a key manager
        this.key_manager = new KeyManager(this.settings.get_option('unique_map_id'));

        // make the search index
        this.enable_search = enable_search;
        this.search_index = new SearchIndex();

        // map properties
        this.map_name = map_name;
        this.map_id = map_id;
        this.map_description = map_description;

        // deal with the window
        var window_translate = {'x': 0, 'y': 0},
            window_scale = 1;

        // hide beziers
        this.beziers_enabled = false;

        // data
        this.has_data_on_reactions = false;
        this.has_data_on_nodes = false;

        this.nodes = {};
        this.reactions = {};
        this.beziers = {};
        this.text_labels = {};

        // update data with null to populate data-specific attributes
        this.apply_reaction_data_to_map(null);
        this.apply_metabolite_data_to_map(null);
        this.apply_gene_data_to_map(null);

        // rotation mode off
        this.rotation_on = false;

        // validate the JSON file during map export
        this.debug = false;
    };

    // -------------------------------------------------------------------------
    // Import

    function from_data(map_data, svg, css, selection, zoom_container, settings,
                       cobra_model, enable_search) {
        /** Load a json map and add necessary fields for rendering.

         */

        var canvas = map_data[1].canvas,
            map_name = map_data[0].map_name,
            map_id = map_data[0].map_id,
            map_description = (map_data[0].map_description.replace(/(\nLast Modified.*)+$/g, '')
                               + '\nLast Modified ' + Date(Date.now()).toString()),
            map = new Map(svg, css, selection, zoom_container, settings,
                          cobra_model, canvas, enable_search,
                          map_name, map_id, map_description);

        map.reactions = map_data[1].reactions;
        map.nodes = map_data[1].nodes;
        map.text_labels = map_data[1].text_labels;

        for (var n_id in map.nodes) {
            var node = map.nodes[n_id];

            // clear all the connected segments
            node.connected_segments = [];

            //  populate the nodes search index.
            if (enable_search) {
                if (node.node_type!='metabolite') continue;
                map.search_index.insert('n'+n_id, { 'name': node.bigg_id,
                                                    'data': { type: 'metabolite',
                                                              node_id: n_id }});
                map.search_index.insert('n_name'+n_id, { 'name': node.name,
                                                         'data': { type: 'metabolite',
                                                                   node_id: n_id }});
            }
        }

        // Propagate coefficients and reversibility, build the connected
        // segments, add bezier points, and populate the reaction search index.
        for (var r_id in map.reactions) {
            var reaction = map.reactions[r_id];

            // reaction search index
            if (enable_search) {
                map.search_index.insert('r' + r_id,
                                        { 'name': reaction.bigg_id,
                                          'data': { type: 'reaction',
                                                    reaction_id: r_id }});
                map.search_index.insert('r_name' + r_id,
                                        { 'name': reaction.name,
                                          'data': { type: 'reaction',
                                                    reaction_id: r_id }});
                for (var g_id in reaction.genes) {
                    var gene = reaction.genes[g_id];
                    map.search_index.insert('r' + r_id + '_g' + g_id,
                                            { 'name': gene.bigg_id,
                                              'data': { type: 'reaction',
                                                        reaction_id: r_id }});
                    map.search_index.insert('r' + r_id + '_g_name' + g_id,
                                            { 'name': gene.name,
                                              'data': { type: 'reaction',
                                                        reaction_id: r_id }});
                }
            }

            // keep track of any bad segments
            var segments_to_delete = [];
            for (var s_id in reaction.segments) {
                var segment = reaction.segments[s_id];

                // propagate reversibility
                segment.reversibility = reaction.reversibility;

                // if there is an error with to_ or from_ nodes, remove this segment
                if (!(segment.from_node_id in map.nodes) || !(segment.to_node_id in map.nodes)) {
                    console.warn('Bad node references in segment ' + s_id + '. Deleting segment.');
                    segments_to_delete.push(s_id);
                    continue
                }

                var from_node = map.nodes[segment.from_node_id],
                    to_node = map.nodes[segment.to_node_id];

                // propagate coefficients
                reaction.metabolites.forEach(function(met) {
                    if (met.bigg_id==from_node.bigg_id) {
                        segment.from_node_coefficient = met.coefficient;
                    } else if (met.bigg_id==to_node.bigg_id) {
                        segment.to_node_coefficient = met.coefficient;
                    }
                });

                // build connected segments
                [from_node, to_node].forEach(function(node) {
                    node.connected_segments.push({ segment_id: s_id,
                                                   reaction_id: r_id });
                });

                // If the metabolite has no bezier points, then add them.
                var start = map.nodes[segment.from_node_id],
                    end = map.nodes[segment.to_node_id];
                if (start['node_type']=='metabolite' || end['node_type']=='metabolite') {
                    var midpoint = utils.c_plus_c(start, utils.c_times_scalar(utils.c_minus_c(end, start), 0.5));
                    if (segment.b1 === null) segment.b1 = midpoint;
                    if (segment.b2 === null) segment.b2 = midpoint;
                }

            }
            // delete the bad segments
            segments_to_delete.forEach(function(s_id) {
                delete reaction.segments[s_id];
            });
        }

        // add text_labels to the search index
        if (enable_search) {
            for (var label_id in map.text_labels) {
                var label = map.text_labels[label_id];
                map.search_index.insert('l'+label_id, { 'name': label.text,
                                                        'data': { type: 'text_label',
                                                                  text_label_id: label_id }});
            }
        }

        // populate the beziers
        map.beziers = build.new_beziers_for_reactions(map.reactions);

        // get largest ids for adding new reactions, nodes, text labels, and
        // segments
        map.largest_ids.reactions = get_largest_id(map.reactions);
        map.largest_ids.nodes = get_largest_id(map.nodes);
        map.largest_ids.text_labels = get_largest_id(map.text_labels);

        var largest_segment_id = 0;
        for (var id in map.reactions) {
            largest_segment_id = get_largest_id(map.reactions[id].segments,
                                                largest_segment_id);
        }
        map.largest_ids.segments = largest_segment_id;

        // update data with null to populate data-specific attributes
        map.apply_reaction_data_to_map(null);
        map.apply_metabolite_data_to_map(null);
        map.apply_gene_data_to_map(null);

        return map;

        // definitions
        function get_largest_id(obj, current_largest) {
            /** Return the largest integer key in obj, or current_largest, whichever is bigger. */
            if (current_largest===undefined) current_largest = 0;
            if (obj===undefined) return current_largest;
            return Math.max.apply(null, Object.keys(obj).map(function(x) {
                return parseInt(x);
            }).concat([current_largest]));
        }
    }

    // ---------------------------------------------------------------------
    // more setup

    function setup_containers(sel) {
        sel.append('g')
            .attr('id', 'reactions');
        sel.append('g')
            .attr('id', 'nodes');
        sel.append('g')
            .attr('id', 'beziers');
        sel.append('g')
            .attr('id', 'text-labels');
    }
    function reset_containers() {
        this.sel.select('#reactions')
            .selectAll('.reaction')
            .remove();
        this.sel.select('#nodes')
            .selectAll('.node')
            .remove();
        this.sel.select('#beziers')
            .selectAll('.bezier')
            .remove();
        this.sel.select('#text-labels')
            .selectAll('.text-label')
            .remove();
    }

    // -------------------------------------------------------------------------
    // Appearance

    function set_status(status, time) {
        /** Set the status of the map, with an optional expiration
         time. Rendering the status is taken care of by the Builder.

         Arguments
         ---------

         status: The status string.

         time: An optional time, in ms, after which the status is set to ''.

         */

        this.callback_manager.run('set_status', null, status);
        // clear any other timers on the status bar
        window.clearTimeout(this._status_timer);
        this._status_timer = null;

        if (time!==undefined) {
            this._status_timer = window.setTimeout(function() {
                this.callback_manager.run('set_status', null, '');
            }.bind(this), time);
        }
    }
    function clear_map() {
        this.reactions = {};
        this.beziers = {};
        this.nodes = {};
        this.text_labels = {};
        this.map_name = 'new_map';
        this.map_id = utils.generate_map_id();
        this.map_description = '';
        // reaction_data onto existing map reactions
        this.apply_reaction_data_to_map(null);
        this.apply_metabolite_data_to_map(null);
        this.apply_gene_data_to_map(null);
        this.draw_everything();
    }
    function has_cobra_model() {
        return (this.cobra_model !== null);
    }
    function draw_everything() {
        /** Draw the all reactions, nodes, & text labels.

         */
        this.draw_all_reactions(true, true); // also draw beziers
        this.draw_all_nodes(true);
        this.draw_all_text_labels();
    }

    function draw_all_reactions(draw_beziers, clear_deleted) {
        /** Draw all reactions, and clear deleted reactions.

         Arguments
         ---------

         draw_beziers: (Boolean, default True) Whether to also draw the bezier
         control points.

         clear_deleted: (Optional, Default: true) Boolean, if true, then also
         clear deleted nodes.

         */
        if (draw_beziers===undefined) draw_beziers = true;
        if (clear_deleted===undefined) clear_deleted = true;

        // Draw all reactions.
        var reaction_ids = [];
        for (var reaction_id in this.reactions) {
            reaction_ids.push(reaction_id);
        }
        // If draw_beziers is true, just draw them all, rather than deciding
        // which ones to draw.
        this.draw_these_reactions(reaction_ids, false);
        if (draw_beziers && this.beziers_enabled)
            this.draw_all_beziers();

        // Clear all deleted reactions.
        if (clear_deleted)
            this.clear_deleted_reactions(draw_beziers);
    }

    function draw_these_reactions(reaction_ids, draw_beziers) {
        /** Draw specific reactions.

         Does nothing with exit selection. Use clear_deleted_reactions to remove
         reactions from the DOM.

         Arguments
         ---------

         reactions_ids: An array of reaction_ids to update.

         draw_beziers: (Boolean, default True) Whether to also draw the bezier
         control points.

         */
        if (draw_beziers===undefined) draw_beziers = true;

        // find reactions for reaction_ids
        var reaction_subset = utils.object_slice_for_ids_ref(this.reactions,
                                                             reaction_ids);

        // function to update reactions
        var update_fn = function(sel) {
            return this.draw.update_reaction(sel, this.scale, this.cobra_model,
                                             this.nodes, this.defs,
                                             this.has_data_on_reactions);
        }.bind(this);

        // draw the reactions
        utils.draw_an_object(this.sel, '#reactions', '.reaction', reaction_subset,
                             'reaction_id', this.draw.create_reaction.bind(this.draw),
                             update_fn);

        if (draw_beziers) {
            // particular beziers to draw
            var bezier_ids = build.bezier_ids_for_reaction_ids(reaction_subset);
            this.draw_these_beziers(bezier_ids);
        }
    }

    function clear_deleted_reactions(draw_beziers) {
        /** Remove any reactions that are not in *this.reactions*.

         Arguments
         ---------

         draw_beziers: (Boolean, default True) Whether to also clear deleted
         bezier control points.

         */
        if (draw_beziers===undefined) draw_beziers = true;

        // remove deleted reactions and segments
        utils.draw_an_object(this.sel, '#reactions', '.reaction', this.reactions, 'reaction_id',
                             null,
                             clear_deleted_segments,
                             function(sel) { sel.remove(); });

        if (draw_beziers==true)
            this.clear_deleted_beziers();

        // definitions
        function clear_deleted_segments(update_selection) {
            // draw segments
            utils.draw_a_nested_object(update_selection, '.segment-group', 'segments', 'segment_id',
                                       null,
                                       null,
                                       function(sel) { sel.remove(); });
        };
    }

    function draw_all_nodes(clear_deleted) {
        /** Draw all nodes, and clear deleted nodes.

         Arguments
         ---------

         clear_deleted: (Optional, Default: true) Boolean, if true, then also
         clear deleted nodes.

         */
        if (clear_deleted === undefined) clear_deleted = true;

        var node_ids = [];
        for (var node_id in this.nodes) {
            node_ids.push(node_id);
        }
        this.draw_these_nodes(node_ids);

        // clear the deleted nodes
        if (clear_deleted)
            this.clear_deleted_nodes();
    }

    function draw_these_nodes(node_ids) {
        /** Draw specific nodes.

         Does nothing with exit selection. Use clear_deleted_nodes to remove
         nodes from the DOM.

         Arguments
         ---------

         nodes_ids: An array of node_ids to update.

         */
        // find reactions for reaction_ids
        var node_subset = utils.object_slice_for_ids_ref(this.nodes, node_ids);

        // functions to create and update nodes
        var create_fn = function(sel) {
            return this.draw.create_node(sel,
                                         this.nodes,
                                         this.reactions);
        }.bind(this),
            update_fn = function(sel) {
                return this.draw.update_node(sel,
                                             this.scale,
                                             this.has_data_on_nodes,
                                             this.behavior.selectable_mousedown,
                                             this.behavior.selectable_click,
                                             this.behavior.node_mouseover,
                                             this.behavior.node_mouseout,
                                             this.behavior.selectable_drag,
                                             this.behavior.node_label_drag);
            }.bind(this);

        // draw the nodes
        utils.draw_an_object(this.sel, '#nodes', '.node', node_subset, 'node_id',
                             create_fn, update_fn);
    }

    function clear_deleted_nodes() {
        /** Remove any nodes that are not in *this.nodes*.

         */
        // run remove for exit selection
        utils.draw_an_object(this.sel, '#nodes', '.node', this.nodes, 'node_id',
                             null, null, function(sel) { sel.remove(); });
    }

    function draw_all_text_labels() {
        // Draw all text_labels.
        var text_label_ids = [];
        for (var text_label_id in this.text_labels) {
            text_label_ids.push(text_label_id);
        }
        this.draw_these_text_labels(text_label_ids);

        // Clear all deleted text_labels.
        this.clear_deleted_text_labels();
    }

    function draw_these_text_labels(text_label_ids) {
        /** Draw specific text_labels.

         Does nothing with exit selection. Use clear_deleted_text_labels to remove
         text_labels from the DOM.

         Arguments
         ---------

         text_labels_ids: An array of text_label_ids to update.

         */
        // find reactions for reaction_ids
        var text_label_subset = utils.object_slice_for_ids_ref(this.text_labels, text_label_ids);

        // function to update text_labels
        var update_fn = function(sel) {
            return this.draw.update_text_label(sel, this.behavior);;
        }.bind(this);

        // draw the text_labels
        utils.draw_an_object(this.sel, '#text-labels', '.text-label',
                             text_label_subset, 'text_label_id',
                             this.draw.create_text_label.bind(this.draw),
                             update_fn);
    }

    function clear_deleted_text_labels() {
        /** Remove any text_labels that are not in *this.text_labels*.

         */
        // clear deleted
        utils.draw_an_object(this.sel, '#text-labels', '.text-label',
                             this.text_labels, 'text_label_id', null, null,
                             function(sel) { sel.remove(); });
    }

    function draw_all_beziers() {
        /** Draw all beziers, and clear deleted reactions.

         */
        var bezier_ids = [];
        for (var bezier_id in this.beziers) {
            bezier_ids.push(bezier_id);
        }
        this.draw_these_beziers(bezier_ids);

        // clear delete beziers
        this.clear_deleted_beziers();
    }

    function draw_these_beziers(bezier_ids) {
        /** Draw specific beziers.

         Does nothing with exit selection. Use clear_deleted_beziers to remove
         beziers from the DOM.

         Arguments
         ---------

         beziers_ids: An array of bezier_ids to update.

         */
        // find reactions for reaction_ids
        var bezier_subset = utils.object_slice_for_ids_ref(this.beziers, bezier_ids);

        // function to update beziers
        var update_fn = function(sel) {
            return this.draw.update_bezier(sel,
                                           this.beziers_enabled,
                                           this.behavior.bezier_drag,
                                           this.behavior.bezier_mouseover,
                                           this.behavior.bezier_mouseout,
                                           this.nodes,
                                           this.reactions);
        }.bind(this);

        // draw the beziers
        utils.draw_an_object(this.sel, '#beziers', '.bezier', bezier_subset,
                             'bezier_id', this.draw.create_bezier.bind(this.draw),
                             update_fn);
    }

    function clear_deleted_beziers() {
        /** Remove any beziers that are not in *this.beziers*.

         */
        // remove deleted
        utils.draw_an_object(this.sel, '#beziers', '.bezier', this.beziers,
                             'bezier_id', null, null,
                             function(sel) { sel.remove(); });
    }

    function show_beziers() {
        this.toggle_beziers(true);
    }

    function hide_beziers() {
        this.toggle_beziers(false);
    }

    function toggle_beziers(on_off) {
        if (on_off===undefined) this.beziers_enabled = !this.beziers_enabled;
        else this.beziers_enabled = on_off;
        this.draw_all_beziers();
        this.callback_manager.run('toggle_beziers', null, this.beziers_enabled);
    }

    function apply_reaction_data_to_map(data) {
        /**  Returns True if the scale has changed.

         */
        var styles = this.settings.get_option('reaction_styles'),
            compare_style = this.settings.get_option('reaction_compare_style');
        var has_data = data_styles.apply_reaction_data_to_reactions(this.reactions, data,
                                                                    styles, compare_style);
        this.has_data_on_reactions = has_data;

        return this.calc_data_stats('reaction');
    }

    function apply_metabolite_data_to_map(data) {
        /**  Returns True if the scale has changed.

         */
        var styles = this.settings.get_option('metabolite_styles'),
            compare_style = this.settings.get_option('metabolite_compare_style');

        var has_data = data_styles.apply_metabolite_data_to_nodes(this.nodes, data,
                                                                  styles, compare_style);
        this.has_data_on_nodes = has_data;

        return this.calc_data_stats('metabolite');
    }

    function apply_gene_data_to_map(gene_data_obj) {
        /** Returns True if the scale has changed.

         Arguments
         ---------

         gene_data_obj: The gene data object, with the following style:

         { reaction_id: { rule: 'rule_string', genes: { gene_id: value } } }

         */
        var styles = this.settings.get_option('reaction_styles'),
            compare_style = this.settings.get_option('reaction_compare_style'),
            identifiers_on_map = this.settings.get_option('identifiers_on_map'),
            and_method_in_gene_reaction_rule = this.settings.get_option('and_method_in_gene_reaction_rule');

        var has_data = data_styles.apply_gene_data_to_reactions(this.reactions, gene_data_obj,
                                                                styles, identifiers_on_map,
                                                                compare_style,
                                                                and_method_in_gene_reaction_rule);
        this.has_data_on_reactions = has_data;

        return this.calc_data_stats('reaction');
    }

    // ------------------------------------------------
    // Data domains
    function get_data_statistics() {
        return this.data_statistics;
    }

    function calc_data_stats(type) {
        /** Returns True if the stats have changed.

         Arguments
         ---------

         type: Either 'metabolite' or 'reaction'

         */

        if (['reaction', 'metabolite'].indexOf(type) == -1)
            throw new Error('Bad type ' + type);

        // make the data structure
        if (!('data_statistics' in this)) {
            this.data_statistics = {};
            this.data_statistics[type] = {};
        } else if (!(type in this.data_statistics)) {
            this.data_statistics[type] = {};
        }

        var same = true;
        // default min and max
        var vals = [];
        if (type == 'metabolite') {
            for (var node_id in this.nodes) {
                var node = this.nodes[node_id];
                // check number
                if (node.data !== null)
                    vals.push(node.data);
            }
        } else if (type == 'reaction') {
            for (var reaction_id in this.reactions) {
                var reaction = this.reactions[reaction_id];
                // check number
                if (reaction.data !== null)
                    vals.push(reaction.data);
            }
        }

        // calculate these statistics
        var quartiles = utils.quartiles(vals),
            funcs = [['min', on_array(Math.min)],
                     ['max', on_array(Math.max)],
                     ['mean', utils.mean],
                     ['Q1', function() { return quartiles[0]; }],
                     ['median', function() { return quartiles[1]; }],
                     ['Q3', function() { return quartiles[2]; }]];
        funcs.forEach(function(ar) {
            var new_val, name = ar[0];
            if (vals.length == 0) {
                new_val = null;
            } else {
                var fn = ar[1];
                new_val = fn(vals);
            }
            if (new_val != this.data_statistics[type][name])
                same = false;
            this.data_statistics[type][name] = new_val;
        }.bind(this));

        if (type == 'reaction')
            this.callback_manager.run('calc_data_stats__reaction', null, !same);
        else
            this.callback_manager.run('calc_data_stats__metabolite', null, !same);
        return !same;

        // definitions
        function on_array(fn) {
            return function (array) { return fn.apply(null, array); };
        }
    }

    // ---------------------------------------------------------------------
    // Node interaction

    function get_coords_for_node(node_id) {
        var node = this.nodes[node_id],
            coords = {'x': node.x, 'y': node.y};
        return coords;
    }
    function get_selected_node_ids() {
        var selected_node_ids = [];
        this.sel.select('#nodes')
            .selectAll('.selected')
            .each(function(d) { selected_node_ids.push(d.node_id); });
        return selected_node_ids;
    }
    function get_selected_nodes() {
        var selected_nodes = {},
            self = this;
        this.sel.select('#nodes')
            .selectAll('.selected')
            .each(function(d) {
                selected_nodes[d.node_id] = this.nodes[d.node_id];
            }.bind(this));
        return selected_nodes;
    }
    function get_selected_text_label_ids() {
        var selected_text_label_ids = [];
        this.sel.select('#text-labels')
            .selectAll('.selected')
            .each(function(d) { selected_text_label_ids.push(d.text_label_id); });
        return selected_text_label_ids;
    }
    function get_selected_text_labels() {
        var selected_text_labels = {},
            self = this;
        this.sel.select('#text-labels')
            .selectAll('.selected')
            .each(function(d) {
                selected_text_labels[d.text_label_id] = this.text_labels[d.text_label_id];
            }.bind(this));
        return selected_text_labels;
    }

    function select_all() {
        /** Select all nodes and text labels.

         */
        this.sel.selectAll('#nodes,#text-labels')
            .selectAll('.node,.text-label')
            .classed('selected', true);
    }

    function select_none() {
        /** Deselect all nodes and text labels.

         */
        this.sel.selectAll('.selected')
            .classed('selected', false);
    }

    function invert_selection() {
        /** Invert selection of nodes and text labels.

         */
        var selection = this.sel.selectAll('#nodes,#text-labels')
                .selectAll('.node,.text-label');
        selection.classed('selected', function() {
            return !d3.select(this).classed('selected');
        });
    }

    function select_metabolite_with_id(node_id) {
        /** Select a metabolite with the given id, and turn off the reaction
         target.

         */
        // deselect all text labels
        this.deselect_text_labels();

        var node_selection = this.sel.select('#nodes').selectAll('.node'),
            coords,
            selected_node;
        node_selection.classed('selected', function(d) {
            var selected = String(d.node_id) == String(node_id);
            if (selected) {
                selected_node = d;
                coords = { x: d.x, y: d.y };
            }
            return selected;
        });
        this.sel.selectAll('.start-reaction-target').style('visibility', 'hidden');
        this.callback_manager.run('select_metabolite_with_id', null, selected_node, coords);
    }
    function select_selectable(node, d) {
        /** Select a metabolite or text label, and manage the shift key.

         */
        var classable_selection = this.sel.selectAll('#nodes,#text-labels')
                .selectAll('.node,.text-label'),
            shift_key_on = this.key_manager.held_keys.shift,
            classable_node;
        if (d3.select(node).attr('class').indexOf('text-label') == -1) {
            // node
            classable_node = node.parentNode;
        } else {
            // text-label
            classable_node = node;
        }
        // toggle selection
        if (shift_key_on) {
            // toggle this node
            d3.select(classable_node)
                .classed('selected', !d3.select(classable_node).classed('selected'));
        } else {
            // unselect all other nodes, and select this one
            classable_selection.classed('selected', false);
            d3.select(classable_node).classed('selected', true);
        }
        // run the select_metabolite callback
        var selected_nodes = this.sel.select('#nodes').selectAll('.selected'),
            node_count = 0,
            coords,
            selected_node;
        selected_nodes.each(function(d) {
            selected_node = d;
            coords = { x: d.x, y: d.y };
            node_count++;
        });
        this.callback_manager.run('select_selectable', null, node_count, selected_node, coords);
    }
    function select_single_node() {
        /** Unselect all but one selected node, and return the node.

         If no nodes are selected, return null.

         */
        var out = null,
            self = this,
            node_selection = this.sel.select('#nodes').selectAll('.selected');
        node_selection.classed('selected', function(d, i) {
            if (i==0) {
                out = d;
                return true;
            } else {
                return false;
            }
        });
        return out;
    }
    function deselect_nodes() {
        var node_selection = this.sel.select('#nodes').selectAll('.node');
        node_selection.classed('selected', false);
        this.callback_manager.run('deselect_nodes');
    }
    function select_text_label(sel, d) {
        // deselect all nodes
        this.deselect_nodes();
        // find the new selection
        // Ignore shift key and only allow single selection for now
        var text_label_selection = this.sel.select('#text-labels').selectAll('.text-label');
        text_label_selection.classed('selected', function(p) { return d === p; });
        var selected_text_labels = this.sel.select('#text-labels').selectAll('.selected'),
            coords;
        selected_text_labels.each(function(d) {
            coords = { x: d.x, y: d.y };
        });
        this.callback_manager.run('select_text_label');
    }
    function deselect_text_labels() {
        var text_label_selection = this.sel.select('#text-labels').selectAll('.text-label');
        text_label_selection.classed('selected', false);
    }

    // ---------------------------------------------------------------------
    // Delete

    function delete_selected() {
        /** Delete the selected nodes and associated segments and reactions, and selected labels.

         Undoable.

         */
        var selected_nodes = this.get_selected_nodes(),
            selected_text_labels = this.get_selected_text_labels();
        if (Object.keys(selected_nodes).length >= 1 ||
            Object.keys(selected_text_labels).length >= 1)
            this.delete_selectable(selected_nodes, selected_text_labels, true);
    }
    function delete_selectable(selected_nodes, selected_text_labels, should_draw) {
        /** Delete the nodes and associated segments and reactions. Undoable.

         Arguments
         ---------

         selected_nodes: An object that is a subset of map.nodes.

         selected_text_labels: An object that is a subset of map.text_labels.

         should_draw: A boolean argument to determine whether to draw the changes to the map.

         */

        var out = this.segments_and_reactions_for_nodes(selected_nodes),
            segment_objs_w_segments = out.segment_objs_w_segments, // TODO repeated values here
            reactions = out.reactions;

        // copy nodes to undelete
        var saved_nodes = utils.clone(selected_nodes),
            saved_segment_objs_w_segments = utils.clone(segment_objs_w_segments),
            saved_reactions = utils.clone(reactions),
            saved_text_labels = utils.clone(selected_text_labels),
            delete_and_draw = function(nodes, reactions, segment_objs,
                                       selected_text_labels) {
                // delete nodes, segments, and reactions with no segments
                this.delete_node_data(Object.keys(selected_nodes));
                this.delete_segment_data(segment_objs); // also deletes beziers
                this.delete_reaction_data(Object.keys(reactions));
                this.delete_text_label_data(Object.keys(selected_text_labels));

                // apply the reaction and node data
                var changed_r_scale = false,
                    changed_m_scale = false;
                if (this.has_data_on_reactions)
                    changed_r_scale = this.calc_data_stats('reaction');
                if (this.has_data_on_nodes)
                    changed_m_scale = this.calc_data_stats('metabolite');

                // redraw
                if (should_draw) {
                    if (changed_r_scale)
                        this.draw_all_reactions(true, true);
                    else
                        this.clear_deleted_reactions(); // also clears segments and beziers
                    if (changed_m_scale)
                        this.draw_all_nodes(true);
                    else
                        this.clear_deleted_nodes();
                    this.clear_deleted_text_labels();
                }
            }.bind(this);

        // delete
        delete_and_draw(selected_nodes, reactions, segment_objs_w_segments,
                        selected_text_labels);

        // add to undo/redo stack
        this.undo_stack.push(function() {
            // undo
            // redraw the saved nodes, reactions, and segments

            this.extend_nodes(saved_nodes);
            this.extend_reactions(saved_reactions);
            var reaction_ids_to_draw = Object.keys(saved_reactions);
            for (var segment_id in saved_segment_objs_w_segments) {
                var segment_obj = saved_segment_objs_w_segments[segment_id];

                var segment = segment_obj.segment;
                this.reactions[segment_obj.reaction_id]
                    .segments[segment_obj.segment_id] = segment;

                // updated connected nodes
                [segment.from_node_id, segment.to_node_id].forEach(function(node_id) {
                    // not necessary for the deleted nodes
                    if (node_id in saved_nodes) return;
                    var node = this.nodes[node_id];
                    node.connected_segments.push({ reaction_id: segment_obj.reaction_id,
                                                   segment_id: segment_obj.segment_id });
                }.bind(this));

                // extend the beziers
                var seg_id = segment_obj.segment_id,
                    r_id = segment_obj.reaction_id,
                    seg_o = {};
                seg_o[seg_id] = segment_obj.segment;
                utils.extend(this.beziers, build.new_beziers_for_segments(seg_o, r_id));

                if (reaction_ids_to_draw.indexOf(segment_obj.reaction_id)==-1)
                    reaction_ids_to_draw.push(segment_obj.reaction_id);
            }

            // apply the reaction and node data
            // if the scale changes, redraw everything
            if (this.has_data_on_reactions) {
                var scale_changed = this.calc_data_stats('reaction');
                if (scale_changed) this.draw_all_reactions(true, false);
                else this.draw_these_reactions(reaction_ids_to_draw);
            } else {
                if (should_draw) this.draw_these_reactions(reaction_ids_to_draw);
            }
            if (this.has_data_on_nodes) {
                var scale_changed = this.calc_data_stats('metabolite');
                if (should_draw) {
                    if (scale_changed) this.draw_all_nodes(false);
                    else this.draw_these_nodes(Object.keys(saved_nodes));
                }
            } else {
                if (should_draw) this.draw_these_nodes(Object.keys(saved_nodes));
            }

            // redraw the saved text_labels
            utils.extend(this.text_labels, saved_text_labels);
            if (should_draw) this.draw_these_text_labels(Object.keys(saved_text_labels));
            // copy text_labels to re-delete
            selected_text_labels = utils.clone(saved_text_labels);

            // copy nodes to re-delete
            selected_nodes = utils.clone(saved_nodes);
            segment_objs_w_segments = utils.clone(saved_segment_objs_w_segments);
            reactions = utils.clone(saved_reactions);
        }.bind(this), function () {
            // redo
            // clone the nodes and reactions, to redo this action later
            delete_and_draw(selected_nodes, reactions, segment_objs_w_segments,
                            selected_text_labels);
        }.bind(this));
    }

    function delete_node_data(node_ids) {
        /** Delete nodes, and remove from search index.
         */
        node_ids.forEach(function(node_id) {
            if (this.enable_search && this.nodes[node_id].node_type=='metabolite') {
                var found = (this.search_index.remove('n' + node_id)
                             && this.search_index.remove('n_name' + node_id));
                if (!found)
                    console.warn('Could not find deleted metabolite in search index');
            }
            delete this.nodes[node_id];
        }.bind(this));
    }

    function delete_segment_data(segment_objs) {
        /** Delete segments, update connected_segments in nodes, and delete
         bezier points.

         segment_objs: Object with values like { reaction_id: '123', segment_id: '456' }

         */
        for (var segment_id in segment_objs) {
            var segment_obj = segment_objs[segment_id];
            var reaction = this.reactions[segment_obj.reaction_id];

            // segment already deleted
            if (!(segment_obj.segment_id in reaction.segments)) return;

            var segment = reaction.segments[segment_obj.segment_id];
            // updated connected nodes
            [segment.from_node_id, segment.to_node_id].forEach(function(node_id) {
                if (!(node_id in this.nodes)) return;
                var node = this.nodes[node_id];
                node.connected_segments = node.connected_segments.filter(function(so) {
                    return so.segment_id != segment_obj.segment_id;
                });
            }.bind(this));

            // remove beziers
            ['b1', 'b2'].forEach(function(bez) {
                var bez_id = build.bezier_id_for_segment_id(segment_obj.segment_id, bez);
                delete this.beziers[bez_id];
            }.bind(this));

            delete reaction.segments[segment_obj.segment_id];
        }
    }
    function delete_reaction_data(reaction_ids) {
        /** Delete reactions, segments, and beziers, and remove reaction from
         search index.

         */
        reaction_ids.forEach(function(reaction_id) {
            // remove beziers
            var reaction = this.reactions[reaction_id];
            for (var segment_id in reaction.segments) {
                ['b1', 'b2'].forEach(function(bez) {
                    var bez_id = build.bezier_id_for_segment_id(segment_id, bez);
                    delete this.beziers[bez_id];
                }.bind(this));
            }
            // delete reaction
            delete this.reactions[reaction_id];
            // remove from search index
            var found = (this.search_index.remove('r' + reaction_id)
                         && this.search_index.remove('r_name' + reaction_id));
            if (!found)
                console.warn('Could not find deleted reaction ' +
                             reaction_id + ' in search index');
            for (var g_id in reaction.genes) {
                var found = (this.search_index.remove('r' + reaction_id + '_g' + g_id)
                             && this.search_index.remove('r' + reaction_id + '_g_name' + g_id));
                if (!found)
                    console.warn('Could not find deleted gene ' +
                                 g_id + ' in search index');
            }
        }.bind(this));
    }
    function delete_text_label_data(text_label_ids) {
        /** delete text labels for an array of ids
         */
        text_label_ids.forEach(function(text_label_id) {
            // delete label
            delete this.text_labels[text_label_id];
            // remove from search index
            var found = this.search_index.remove('l'+text_label_id);
            if (!found)
                console.warn('Could not find deleted text label in search index');
        }.bind(this));
    }

    // ---------------------------------------------------------------------
    // Building

    function new_reaction_from_scratch(starting_reaction, coords, direction) {
        /** Draw a reaction on a blank canvas.

         starting_reaction: bigg_id for a reaction to draw.
         coords: coordinates to start drawing

         */

        // If there is no cobra model, error
        if (!this.cobra_model) return console.error('No CobraModel. Cannot build new reaction');

        // set reaction coordinates and angle
        // be sure to copy the reaction recursively
        var cobra_reaction = utils.clone(this.cobra_model.reactions[starting_reaction]);

        // create the first node
        for (var metabolite_id in cobra_reaction.metabolites) {
            var coefficient = cobra_reaction.metabolites[metabolite_id],
                metabolite = this.cobra_model.metabolites[metabolite_id];
            if (coefficient < 0) {
                var selected_node_id = String(++this.largest_ids.nodes),
                    label_d = { x: 30, y: 10 },
                    selected_node = { connected_segments: [],
                                      x: coords.x,
                                      y: coords.y,
                                      node_is_primary: true,
                                      label_x: coords.x + label_d.x,
                                      label_y: coords.y + label_d.y,
                                      name: metabolite.name,
                                      bigg_id: metabolite_id,
                                      node_type: 'metabolite' },
                    new_nodes = {};
                new_nodes[selected_node_id] = selected_node;
                break;
            }
        }

        // draw
        extend_and_draw_metabolite.apply(this, [new_nodes, selected_node_id]);

        // clone the nodes and reactions, to redo this action later
        var saved_nodes = utils.clone(new_nodes);

        // draw the reaction
        var out = this.new_reaction_for_metabolite(starting_reaction,
                                                   selected_node_id,
                                                   direction, false),
            reaction_redo = out.redo,
            reaction_undo = out.undo;

        // add to undo/redo stack
        this.undo_stack.push(function() {
            // undo
            // first undo the reaction
            reaction_undo();
            // get the nodes to delete
            this.delete_node_data(Object.keys(new_nodes));
            // save the nodes and reactions again, for redo
            new_nodes = utils.clone(saved_nodes);
            // draw
            this.clear_deleted_nodes();
            // deselect
            this.deselect_nodes();
        }.bind(this), function () {
            // redo
            // clone the nodes and reactions, to redo this action later
            extend_and_draw_metabolite.apply(this, [new_nodes, selected_node_id]);
            // now redo the reaction
            reaction_redo();
        }.bind(this));

        return null;

        // definitions
        function extend_and_draw_metabolite(new_nodes, selected_node_id) {
            this.extend_nodes(new_nodes);
            if (this.has_data_on_nodes) {
                var scale_changed = this.apply_metabolite_data_to_nodes(new_nodes);
                if (scale_changed) this.draw_all_nodes(false);
                else this.draw_these_nodes([selected_node_id]);
            } else {
                this.draw_these_nodes([selected_node_id]);
            }
        }
    }

    function extend_nodes(new_nodes) {
        /** Add new nodes to data and search index.

         */
        if (this.enable_search) {
            for (var node_id in new_nodes) {
                var node = new_nodes[node_id];
                if (node.node_type != 'metabolite')
                    continue;
                this.search_index.insert('n' + node_id,
                                         { 'name': node.bigg_id,
                                           'data': { type: 'metabolite',
                                                     node_id: node_id }});
                this.search_index.insert('n_name' + node_id,
                                         { 'name': node.name,
                                           'data': { type: 'metabolite',
                                                     node_id: node_id }});
            }
        }
        utils.extend(this.nodes, new_nodes);
    }
    function extend_reactions(new_reactions) {
        /** Add new reactions to data and search index.

         */
        if (this.enable_search) {
            for (var r_id in new_reactions) {
                var reaction = new_reactions[r_id];
                this.search_index.insert('r' + r_id, { 'name': reaction.bigg_id,
                                                       'data': { type: 'reaction',
                                                                 reaction_id: r_id }});
                this.search_index.insert('r_name' + r_id, { 'name': reaction.name,
                                                            'data': { type: 'reaction',
                                                                      reaction_id: r_id }});
                for (var g_id in reaction.genes) {
                    var gene = reaction.genes[g_id];
                    this.search_index.insert('r' + r_id + '_g' + g_id,
                                             { 'name': gene.bigg_id,
                                               'data': { type: 'reaction',
                                                         reaction_id: r_id }});
                    this.search_index.insert('r' + r_id + '_g_name' + g_id,
                                             { 'name': gene.name,
                                               'data': { type: 'reaction',
                                                         reaction_id: r_id }});
                }
            }
        }
        utils.extend(this.reactions, new_reactions);
    }

    function new_reaction_for_metabolite(reaction_bigg_id, selected_node_id,
                                         direction, apply_undo_redo) {
        /** Build a new reaction starting with selected_met.

         Undoable

         Arguments
         ---------

         reaction_bigg_id: The BiGG ID of the reaction to draw.

         selected_node_id: The ID of the node to begin drawing with.

         direction: The direction to draw in.

         apply_undo_redo: (Optional, Default: true) If true, then add to the
         undo stack. Otherwise, just return the undo and redo functions.

         Returns
         -------

         { undo: undo_function,
         redo: redo_function }

         */

        // default args
        if (apply_undo_redo === undefined) apply_undo_redo = true;

        // get the metabolite node
        var selected_node = this.nodes[selected_node_id];

        // set reaction coordinates and angle
        // be sure to copy the reaction recursively
        var cobra_reaction = this.cobra_model.reactions[reaction_bigg_id];

        // build the new reaction
        var out = build.new_reaction(reaction_bigg_id, cobra_reaction,
                                     this.cobra_model.metabolites,
                                     selected_node_id,
                                     utils.clone(selected_node),
                                     this.largest_ids,
                                     this.cobra_model.cofactors,
                                     direction),
            new_nodes = out.new_nodes,
            new_reactions = out.new_reactions,
            new_beziers = out.new_beziers;

        // draw
        extend_and_draw_reaction.apply(this, [new_nodes, new_reactions,
                                              new_beziers, selected_node_id]);

        // clone the nodes and reactions, to redo this action later
        var saved_nodes = utils.clone(new_nodes),
            saved_reactions = utils.clone(new_reactions),
            saved_beziers = utils.clone(new_beziers);

        // add to undo/redo stack
        var undo_fn = function() {
            // undo
            // get the nodes to delete
            delete new_nodes[selected_node_id];
            this.delete_node_data(Object.keys(new_nodes));
            this.delete_reaction_data(Object.keys(new_reactions)); // also deletes beziers
            select_metabolite_with_id.apply(this, [selected_node_id]);
            // save the nodes and reactions again, for redo
            new_nodes = utils.clone(saved_nodes);
            new_reactions = utils.clone(saved_reactions);
            new_beziers = utils.clone(saved_beziers);
            // draw
            if (this.has_data_on_reactions) {
                var scale_changed = this.calc_data_stats('reaction');
                if (scale_changed) this.draw_all_reactions(true, true);
                else this.draw_these_reactions(Object.keys(new_reactions));
            } else {
                this.clear_deleted_reactions(true); // also clears segments and beziers
            }
            if (this.has_data_on_nodes) {
                var scale_changed = this.calc_data_stats('metabolite');
                if (scale_changed) this.draw_all_nodes(true);
                else this.draw_these_nodes(Object.keys(new_nodes));
            } else {
                this.clear_deleted_nodes();
            }
        }.bind(this),
            redo_fn = function () {
                // redo
                // clone the nodes and reactions, to redo this action later
                extend_and_draw_reaction.apply(this, [new_nodes, new_reactions,
                                                      new_beziers, selected_node_id]);
            }.bind(this);

        if (apply_undo_redo)
            this.undo_stack.push(undo_fn, redo_fn);

        return { undo: undo_fn,
                 redo: redo_fn };

        // definitions
        function extend_and_draw_reaction(new_nodes, new_reactions, new_beziers,
                                          selected_node_id) {
            this.extend_reactions(new_reactions);
            utils.extend(this.beziers, new_beziers);
            // remove the selected node so it can be updated
            this.delete_node_data([selected_node_id]); // TODO this is a hack. fix
            this.extend_nodes(new_nodes);

            // apply the reaction and node data to the scales
            // if the scale changes, redraw everything
            if (this.has_data_on_reactions) {
                var scale_changed = this.calc_data_stats('reaction');
                if (scale_changed) this.draw_all_reactions(true, false);
                else this.draw_these_reactions(Object.keys(new_reactions));
            } else {
                this.draw_these_reactions(Object.keys(new_reactions));
            }
            if (this.has_data_on_nodes) {
                var scale_changed = this.calc_data_stats('metabolite');
                if (scale_changed) this.draw_all_nodes(false);
                else this.draw_these_nodes(Object.keys(new_nodes));
            } else {
                this.draw_these_nodes(Object.keys(new_nodes));
            }

            // select new primary metabolite
            for (var node_id in new_nodes) {
                var node = new_nodes[node_id];
                if (node.node_is_primary && node_id!=selected_node_id) {
                    this.select_metabolite_with_id(node_id);
                    var new_coords = { x: node.x, y: node.y };
                    if (this.zoom_container)
                        this.zoom_container.translate_off_screen(new_coords);
                }
            }
        }

    }
    function cycle_primary_node() {
        var selected_nodes = this.get_selected_nodes();
        // get the first node
        var node_id = Object.keys(selected_nodes)[0],
            node = selected_nodes[node_id],
            reactions = this.reactions,
            nodes = this.nodes;
        // make the other reactants or products secondary
        // 1. Get the connected anchor nodes for the node
        var connected_anchor_ids = [],
            reactions_to_draw;
        nodes[node_id].connected_segments.forEach(function(segment_info) {
            reactions_to_draw = [segment_info.reaction_id];
            var segment;
            try {
                segment = reactions[segment_info.reaction_id].segments[segment_info.segment_id];
                if (segment === undefined) throw new Error('undefined segment');
            } catch (e) {
                console.warn('Could not find connected segment ' + segment_info.segment_id);
                return;
            }
            connected_anchor_ids.push(segment.from_node_id==node_id ?
                                      segment.to_node_id : segment.from_node_id);
        });
        // can only be connected to one anchor
        if (connected_anchor_ids.length != 1) {
            console.error('Only connected nodes with a single reaction can be selected');
            return;
        }
        var connected_anchor_id = connected_anchor_ids[0];
        // 2. find nodes connected to the anchor that are metabolites
        var related_node_ids = [node_id];
        var segments = [];
        nodes[connected_anchor_id].connected_segments.forEach(function(segment_info) { // deterministic order
            var segment;
            try {
                segment = reactions[segment_info.reaction_id].segments[segment_info.segment_id];
                if (segment === undefined) throw new Error('undefined segment');
            } catch (e) {
                console.warn('Could not find connected segment ' + segment_info.segment_id);
                return;
            }
            var conn_met_id = segment.from_node_id == connected_anchor_id ? segment.to_node_id : segment.from_node_id,
                conn_node = nodes[conn_met_id];
            if (conn_node.node_type == 'metabolite' && conn_met_id != node_id) {
                related_node_ids.push(String(conn_met_id));
            }
        });
        // 3. make sure they only have 1 reaction connection, and check if
        // they match the other selected nodes
        for (var i=0; i<related_node_ids.length; i++) {
            if (nodes[related_node_ids[i]].connected_segments.length > 1) {
                console.error('Only connected nodes with a single reaction can be selected');
                return;
            }
        }
        for (var a_selected_node_id in selected_nodes) {
            if (a_selected_node_id!=node_id && related_node_ids.indexOf(a_selected_node_id) == -1) {
                console.warn('Selected nodes are not on the same reaction');
                return;
            }
        }
        // 4. change the primary node, and change coords, label coords, and beziers
        var nodes_to_draw = [],
            last_i = related_node_ids.length - 1,
            last_node = nodes[related_node_ids[last_i]],
            last_is_primary = last_node.node_is_primary,
            last_coords = { x: last_node.x, y: last_node.y,
                            label_x: last_node.label_x, label_y: last_node.label_y };
        if (last_node.connected_segments.length > 1)
            console.warn('Too many connected segments for node ' + last_node.node_id);
        var last_segment_info = last_node.connected_segments[0], // guaranteed above to have only one
            last_segment;
        try {
            last_segment = reactions[last_segment_info.reaction_id].segments[last_segment_info.segment_id];
            if (last_segment === undefined) throw new Error('undefined segment');
        } catch (e) {
            console.error('Could not find connected segment ' + last_segment_info.segment_id);
            return;
        }
        var last_bezier = { b1: last_segment.b1, b2: last_segment.b2 },
            primary_node_id;
        related_node_ids.forEach(function(related_node_id) {
            var node = nodes[related_node_id],
                this_is_primary = node.node_is_primary,
                these_coords = { x: node.x, y: node.y,
                                 label_x: node.label_x, label_y: node.label_y },
                this_segment_info = node.connected_segments[0],
                this_segment = reactions[this_segment_info.reaction_id].segments[this_segment_info.segment_id],
                this_bezier = { b1: this_segment.b1, b2: this_segment.b2 };
            node.node_is_primary = last_is_primary;
            node.x = last_coords.x; node.y = last_coords.y;
            node.label_x = last_coords.label_x; node.label_y = last_coords.label_y;
            this_segment.b1 = last_bezier.b1; this_segment.b2 = last_bezier.b2;
            last_is_primary = this_is_primary;
            last_coords = these_coords;
            last_bezier = this_bezier;
            if (node.node_is_primary) primary_node_id = related_node_id;
            nodes_to_draw.push(related_node_id);
        });
        // 5. cycle the connected_segments array so the next time, it cycles differently
        var old_connected_segments = nodes[connected_anchor_id].connected_segments,
            last_i = old_connected_segments.length - 1,
            new_connected_segments = [old_connected_segments[last_i]];
        old_connected_segments.forEach(function(segment, i) {
            if (last_i==i) return;
            new_connected_segments.push(segment);
        });
        nodes[connected_anchor_id].connected_segments = new_connected_segments;
        // 6. draw the nodes
        this.draw_these_nodes(nodes_to_draw);
        this.draw_these_reactions(reactions_to_draw);
        // 7. select the primary node
        this.select_metabolite_with_id(primary_node_id);
        return;
    }

    function toggle_selected_node_primary() {
        /** Toggle the primary/secondary status of each selected node.

         Undoable.

         */
        var selected_node_ids = this.get_selected_node_ids(),
            go = function(ids) {
                var nodes_to_draw = {},
                    hide_secondary_metabolites = this.settings.get_option('hide_secondary_metabolites');
                ids.forEach(function(id) {
                    if (!(id in this.nodes)) {
                        console.warn('Could not find node: ' + id);
                        return;
                    }
                    var node = this.nodes[id];
                    if (node.node_type == 'metabolite') {
                        node.node_is_primary = !node.node_is_primary;
                        nodes_to_draw[id] = node;
                    }
                }.bind(this));
                // draw the nodes
                this.draw_these_nodes(Object.keys(nodes_to_draw));
                // draw associated reactions
                if (hide_secondary_metabolites) {
                    var out = this.segments_and_reactions_for_nodes(nodes_to_draw),
                        reaction_ids_to_draw_o = {};
                    for (var id in out.segment_objs_w_segments) {
                        var r_id = out.segment_objs_w_segments[id].reaction_id;
                        reaction_ids_to_draw_o[r_id] = true;
                    }
                    this.draw_these_reactions(Object.keys(reaction_ids_to_draw_o));
                }
            }.bind(this);

        // go
        go(selected_node_ids);

        // add to the undo stack
        this.undo_stack.push(function () {
            go(selected_node_ids);
        }, function () {
            go(selected_node_ids);
        });
    }

    function segments_and_reactions_for_nodes(nodes) {
        /** Get segments and reactions that should be deleted with node deletions

         */
        var segment_objs_w_segments = {},
            these_reactions = {},
            segment_ids_for_reactions = {},
            reactions = this.reactions;
        // for each node
        for (var node_id in nodes) {
            var node = nodes[node_id];
            // find associated segments and reactions
            node.connected_segments.forEach(function(segment_obj) {
                var segment;
                try {
                    segment = reactions[segment_obj.reaction_id].segments[segment_obj.segment_id];
                    if (segment === undefined) throw new Error('undefined segment');
                } catch (e) {
                    console.warn('Could not find connected segments for node');
                    return;
                }
                var segment_obj_w_segment = utils.clone(segment_obj);
                segment_obj_w_segment['segment'] = utils.clone(segment);
                segment_objs_w_segments[segment_obj.segment_id] = segment_obj_w_segment;
                if (!(segment_obj.reaction_id in segment_ids_for_reactions))
                    segment_ids_for_reactions[segment_obj.reaction_id] = [];
                segment_ids_for_reactions[segment_obj.reaction_id].push(segment_obj.segment_id);
            });
        }
        // find the reactions that should be deleted because they have no segments left
        for (var reaction_id in segment_ids_for_reactions) {
            var reaction = reactions[reaction_id],
                these_ids = segment_ids_for_reactions[reaction_id],
                has = true;
            for (var segment_id in reaction.segments) {
                if (these_ids.indexOf(segment_id)==-1) has = false;
            }
            if (has) these_reactions[reaction_id] = reaction;
        }
        return { segment_objs_w_segments: segment_objs_w_segments, reactions: these_reactions };
    }

    function new_text_label(coords, text) {
        // make an label
        var out = build.new_text_label(this.largest_ids, text, coords);
        this.text_labels[out.id] = out.label;
        var sel = this.draw_these_text_labels([out.id]);
        // add to the search index
        this.search_index.insert('l' + out.id, { 'name': text,
                                                 'data': { type: 'text_label',
                                                           text_label_id: out.id }});
        return out.id;
    }

    function edit_text_label(text_label_id, new_value, should_draw) {
        // save old value
        var saved_value = this.text_labels[text_label_id].text,
            edit_and_draw = function(new_val, should_draw) {
                // set the new value
                this.text_labels[text_label_id].text = new_val;
                if (should_draw) this.draw_these_text_labels([text_label_id]);
                // update in the search index
                var record_id = 'l' + text_label_id,
                    found = this.search_index.remove(record_id);
                if (!found)
                    console.warn('Could not find modified text label in search index');
                this.search_index.insert(record_id, { 'name': new_val,
                                                      'data': { type: 'text_label',
                                                                text_label_id: text_label_id }});
            }.bind(this);

        // edit the label
        edit_and_draw(new_value, should_draw);

        // add to undo stack
        this.undo_stack.push(function() {
            edit_and_draw(saved_value, should_draw);
        }, function () {
            edit_and_draw(new_value, should_draw);
        });
    }

    // -------------------------------------------------------------------------
    // Zoom

    function zoom_extent_nodes(margin) {
        /** Zoom to fit all the nodes.

         margin: optional argument to set the margins as a fraction of height.

         Returns error if one is raised.

         */
        this._zoom_extent(margin, 'nodes');
    }
    function zoom_extent_canvas(margin) {
        /** Zoom to fit the canvas.

         margin: optional argument to set the margins as a fraction of height.

         Returns error if one is raised.

         */
        this._zoom_extent(margin, 'canvas');
    }
    function _zoom_extent(margin, mode) {
        /** Zoom to fit all the nodes.

         margin: optional argument to set the margins.
         mode: Values are 'nodes', 'canvas'.

         Returns error if one is raised.

         */

        // optional args
        if (margin===undefined) margin = (mode=='nodes' ? 0.2 : 0);
        if (mode===undefined) mode = 'canvas';

        var new_zoom, new_pos,
            size = this.get_size();
        // scale margin to window size
        margin = margin * size.height;

        if (mode=='nodes') {
            // get the extent of the nodes
            var min = { x: null, y: null }, // TODO make infinity?
                max = { x: null, y: null };
            for (var node_id in this.nodes) {
                var node = this.nodes[node_id];
                if (min.x===null) min.x = node.x;
                if (min.y===null) min.y = node.y;
                if (max.x===null) max.x = node.x;
                if (max.y===null) max.y = node.y;

                min.x = Math.min(min.x, node.x);
                min.y = Math.min(min.y, node.y);
                max.x = Math.max(max.x, node.x);
                max.y = Math.max(max.y, node.y);
            }
            // set the zoom
            new_zoom = Math.min((size.width - margin*2) / (max.x - min.x),
                                (size.height - margin*2) / (max.y - min.y));
            new_pos = { x: - (min.x * new_zoom) + margin + ((size.width - margin*2 - (max.x - min.x)*new_zoom) / 2),
                        y: - (min.y * new_zoom) + margin + ((size.height - margin*2 - (max.y - min.y)*new_zoom) / 2) };
        } else if (mode=='canvas') {
            // center the canvas
            new_zoom =  Math.min((size.width - margin*2) / (this.canvas.width),
                                 (size.height - margin*2) / (this.canvas.height));
            new_pos = { x: - (this.canvas.x * new_zoom) + margin + ((size.width - margin*2 - this.canvas.width*new_zoom) / 2),
                        y: - (this.canvas.y * new_zoom) + margin + ((size.height - margin*2 - this.canvas.height*new_zoom) / 2) };
        } else {
            return console.error('Did not recognize mode');
        }
        this.zoom_container.go_to(new_zoom, new_pos);
        return null;
    }

    function get_size() {
        return this.zoom_container.get_size();
    }

    function zoom_to_reaction(reaction_id) {
        var reaction = this.reactions[reaction_id],
            new_zoom = 0.5,
            size = this.get_size(),
            new_pos = { x: - reaction.label_x * new_zoom + size.width/2,
                        y: - reaction.label_y * new_zoom + size.height/2 };
        this.zoom_container.go_to(new_zoom, new_pos);
    }

    function zoom_to_node(node_id) {
        var node = this.nodes[node_id],
            new_zoom = 0.5,
            size = this.get_size(),
            new_pos = { x: - node.label_x * new_zoom + size.width/2,
                        y: - node.label_y * new_zoom + size.height/2 };
        this.zoom_container.go_to(new_zoom, new_pos);
    }

    function zoom_to_text_label(text_label_id) {
        var text_label = this.text_labels[text_label_id],
            new_zoom = 0.5,
            size = this.get_size(),
            new_pos = { x: - text_label.x * new_zoom + size.width/2,
                        y: - text_label.y * new_zoom + size.height/2 };
        this.zoom_container.go_to(new_zoom, new_pos);
    }

    function highlight_reaction(reaction_id) {
        this.highlight(this.sel.selectAll('#r'+reaction_id).selectAll('text'));
    }

    function highlight_node(node_id) {
        this.highlight(this.sel.selectAll('#n'+node_id).selectAll('text'));
    }

    function highlight_text_label(text_label_id) {
        this.highlight(this.sel.selectAll('#l'+text_label_id).selectAll('text'));
    }

    function highlight(sel) {
        this.sel.selectAll('.highlight')
            .classed('highlight', false);
        if (sel !== null) {
            sel.classed('highlight', true);
        }
    }

    // -------------------------------------------------------------------------
    // IO

    function save() {
        utils.download_json(this.map_for_export(), this.map_name);
    }
    function map_for_export() {
        var out = [{ "map_name": this.map_name,
                     "map_id": this.map_id,
                     "map_description": this.map_description,
                     "homepage": "https://escher.github.io",
                     "schema": "https://escher.github.io/escher/jsonschema/1-0-0#"
                   },
                   { reactions: utils.clone(this.reactions),
                     nodes: utils.clone(this.nodes),
                     text_labels: utils.clone(this.text_labels),
                     canvas: this.canvas.size_and_location() }
                  ];

        // remove extra data
        for (var r_id in out[1].reactions) {
            var reaction = out[1].reactions[r_id],
                new_reaction = {};
            ['name', 'bigg_id','reversibility', 'label_x', 'label_y',
             'gene_reaction_rule', 'genes', 'metabolites'
            ].forEach(function(attr) {
                new_reaction[attr] = reaction[attr];
            });
            new_reaction['segments'] = {};
            for (var s_id in reaction.segments) {
                var segment = reaction.segments[s_id],
                    new_segment = {};
                ['from_node_id', 'to_node_id', 'b1', 'b2'
                ].forEach(function(attr) {
                    new_segment[attr] = segment[attr];
                });
                new_reaction['segments'][s_id] = new_segment;
            }
            out[1].reactions[r_id] = new_reaction;
        }
        for (var n_id in out[1].nodes) {
            var node = out[1].nodes[n_id],
                new_node = {},
                attrs;
            if (node.node_type == 'metabolite') {
                attrs = ['node_type', 'x', 'y', 'bigg_id', 'name', 'label_x', 'label_y',
                         'node_is_primary'];
            } else {
                attrs = ['node_type', 'x', 'y'];
            }
            attrs.forEach(function(attr) {
                new_node[attr] = node[attr];
            });
            out[1].nodes[n_id] = new_node;
        }
        for (var t_id in out[1].text_labels) {
            var text_label = out[1].text_labels[t_id],
                new_text_label = {},
                attrs = ["x", "y", "text"];
            attrs.forEach(function(attr) {
                new_text_label[attr] = text_label[attr];
            });
            out[1].text_labels[t_id] = new_text_label;
        }
        // canvas
        var canvas_el = out[1].canvas,
            new_canvas_el = {},
            attrs = ["x", "y", "width", "height"];
        attrs.forEach(function(attr) {
            new_canvas_el[attr] = canvas_el[attr];
        });
        out[1].canvas = new_canvas_el;

        if (this.debug) {
            d3.json('jsonschema/1-0-0', function(error, schema) {
                if (error) throw new Error(error);
                if (!tv4.validate(out, schema))
                    console.warn(tv4.error);
            });
        }

        return out;
    }
    function save_svg() {
        // run the before callback
        this.callback_manager.run('before_svg_export');

        // turn of zoom and translate so that illustrator likes the map
        var window_scale = this.zoom_container.window_scale,
            window_translate = this.zoom_container.window_translate,
            canvas_size_and_loc = this.canvas.size_and_location(),
            mouse_node_size_and_trans = { w: this.canvas.mouse_node.attr('width'),
                                          h: this.canvas.mouse_node.attr('height'),
                                          transform:  this.canvas.mouse_node.attr('transform')};
        this.zoom_container.go_to(1.0, {x: -canvas_size_and_loc.x, y: -canvas_size_and_loc.y}, false);
        this.svg.attr('width', canvas_size_and_loc.width);
        this.svg.attr('height', canvas_size_and_loc.height);
        this.canvas.mouse_node.attr('width', '0px');
        this.canvas.mouse_node.attr('height', '0px');
        this.canvas.mouse_node.attr('transform', null);
        // hide the segment control points
        var hidden_sel = this.sel.selectAll('.multimarker-circle,.midmarker-circle,#canvas')
                .style('visibility', 'hidden');

        // do the epxort
        utils.download_svg('saved_map', this.svg, true);

        // revert everything
        this.zoom_container.go_to(window_scale, window_translate, false);
        this.svg.attr('width', null);
        this.svg.attr('height', null);
        this.canvas.mouse_node.attr('width', mouse_node_size_and_trans.w);
        this.canvas.mouse_node.attr('height', mouse_node_size_and_trans.h);
        this.canvas.mouse_node.attr('transform', mouse_node_size_and_trans.transform);
        // unhide the segment control points
        hidden_sel.style('visibility', null);

        // run the after callback
        this.callback_manager.run('after_svg_export');
    }

    function convert_map() {
        /** Assign the descriptive names and gene_reaction_rules from the model
         to the map.

         If no map is loaded, then throw an Error.

         If some reactions are not in the model, then warn in the status.

         */
        // run the before callback
        this.callback_manager.run('before_convert_map');

        // check the model
        if (!this.has_cobra_model()) throw Error('No COBRA model loaded.');
        var model = this.cobra_model;

        // ids for reactions and metabolites not found in the model
        var reactions_not_found = {},
            reaction_attrs = ['name', 'gene_reaction_rule', 'genes'],
            met_nodes_not_found = {},
            metabolite_attrs = ['name'],
            found;
        // convert reactions
        for (var reaction_id in this.reactions) {
            var reaction = this.reactions[reaction_id];
            found = false;
            // find in cobra model
            for (var model_reaction_id in model.reactions) {
                var model_reaction = model.reactions[model_reaction_id];
                if (model_reaction.bigg_id == reaction.bigg_id) {
                    reaction_attrs.forEach(function(attr) {
                        reaction[attr] = model_reaction[attr];
                    });
                    found = true;
                }
            }
            if (!found)
                reactions_not_found[reaction_id] = true;
        }
        // convert metabolites
        for (var node_id in this.nodes) {
            var node = this.nodes[node_id];
            // only look at metabolites
            if (node.node_type != 'metabolite') continue;
            found = false;
            // find in cobra model
            for (var model_metabolite_id in model.metabolites) {
                var model_metabolite = model.metabolites[model_metabolite_id];
                if (model_metabolite.bigg_id == node.bigg_id) {
                    metabolite_attrs.forEach(function(attr) {
                        node[attr] = model_metabolite[attr];
                    });
                    found = true;
                }
            }
            if (!found)
                met_nodes_not_found[node_id] = true;
        }

        // status
        var n_reactions_not_found = Object.keys(reactions_not_found).length,
            n_met_nodes_not_found = Object.keys(met_nodes_not_found).length,
            status_delay = 3000;
        if (n_reactions_not_found == 0 &&
            n_met_nodes_not_found == 0) {
            this.set_status('Successfully converted attributes.', status_delay);
        } else if (n_met_nodes_not_found == 0) {
            this.set_status('Converted attributes, but count not find ' + n_reactions_not_found +
                            ' reactions in the model.', status_delay);
            this.settings.set_conditional('highlight_missing', true);
        } else if (n_reactions_not_found == 0) {
            this.set_status('Converted attributes, but count not find ' + n_met_nodes_not_found +
                            ' metabolites in the model.', status_delay);
            this.settings.set_conditional('highlight_missing', true);
        } else {
            this.set_status('Converted attributes, but count not find ' + n_reactions_not_found +
                            ' reactions and ' + n_met_nodes_not_found + ' metabolites in the model.',
                            status_delay);
            this.settings.set_conditional('highlight_missing', true);
        }

        // redraw
        this.draw_everything();

        // run the after callback
        this.callback_manager.run('after_convert_map');
    }
});

define('Brush',["utils"], function(utils) {
    /** Define a brush to select elements in a map.

     Arguments
     ---------

     selection: A d3 selection to place the brush in.

     is_enabled: Whether to turn the brush on.

     map: An instance of escher.Map.

     insert_after: A d3 selector string to choose the svg element that the brush
     will be inserted after. Often a canvas element (e.g. '.canvas-group').

     */

    var Brush = utils.make_class();
    Brush.prototype = { init: init,
                        toggle: toggle,
                        setup_selection_brush: setup_selection_brush };

    return Brush;

    // definitions
    function init(selection, is_enabled, map, insert_after) {
        this.brush_sel = selection.append('g')
            .attr('id', 'brush-container');
        var node = this.brush_sel.node(),
            insert_before_node = selection.select(insert_after).node().nextSibling;
        if (!(node===insert_before_node))
            node.parentNode.insertBefore(node, insert_before_node);
        this.enabled = is_enabled;
        this.map = map;
    };

    function brush_is_enabled() {
        /** Returns a boolean for the on/off status of the brush

         */
        return this.map.sel.select('.brush').empty();
    }
    function toggle(on_off) {
        /** Turn the brush on or off

         */
        if (on_off===undefined) on_off = !this.enabled;

        if (on_off) {
            this.selection_brush = this.setup_selection_brush();
        } else {
            this.brush_sel.selectAll('.brush').remove();
        }
    }   
    function setup_selection_brush() {
        var selection = this.brush_sel, 
            selectable_selection = this.map.sel.selectAll('#nodes,#text-labels'),
            size_and_location = this.map.canvas.size_and_location(),
            width = size_and_location.width,
            height = size_and_location.height,
            x = size_and_location.x,
            y = size_and_location.y;

        // clear existing brush
        selection.selectAll('g').remove();

        var brush_fn = d3.svg.brush()
                .x(d3.scale.identity().domain([x, x+width]))
                .y(d3.scale.identity().domain([y, y+height]))
                .on("brush", function(key_manager) {        
                    var shift_key_on = key_manager.held_keys.shift,
                        extent = d3.event.target.extent(),
                        selection;
                    if (shift_key_on) {
                        // when shift is pressed, ignore the currently selected nodes
                        selection = selectable_selection
                            .selectAll('.node:not(.selected),.text-label:not(.selected)');
                    } else {
                        // otherwise, brush all nodes
                        selection = selectable_selection
                            .selectAll('.node,.text-label');
                    }
                    selection.classed("selected", function(d) { 
                        var sx = d.x, sy = d.y;
                        return extent[0][0] <= sx && sx < extent[1][0]
                            && extent[0][1] <= sy && sy < extent[1][1];
                    });
                }.bind(null, this.map.key_manager))
                .on("brushend", function() {
                    d3.event.target.clear();
                    d3.select(this).call(d3.event.target);
                }),
            brush = selection.append("g")
                .attr("class", "brush")
                .call(brush_fn);

        // turn off the mouse crosshair
        selection.selectAll('.background')
            .classed('cursor-grab', false)
            .classed('cursor-grabbing', false)
            .style('cursor', null);

        return brush;
    }
});

define('ui',["utils", "data_styles"], function(utils, data_styles) {
    return { individual_button: individual_button,
             radio_button_group: radio_button_group,
             button_group: button_group,
             dropdown_menu: dropdown_menu,
             set_json_input_button: set_json_input_button,
             set_json_or_csv_input_button: set_json_or_csv_input_button };

    function individual_button(s, button) {
        var b = s.append('button'),
            c = b.append('span');
        if ('id' in button) b.attr('id', button.id);
        if ('classes' in button) b.attr('class', button.classes);

        // text
        if ('key_text' in button && 'text' in button && button.key_text !== null)
            c.text(button.text + button.key_text);
        else if ('text' in button)
            c.text(button.text);
        
        if ('icon' in button) c.classed(button.icon, true);
        if ('key' in button) set_button(b, button.key);
        // if ('tooltip' in button) 
        b.attr('title', button.tooltip);
    }
    
    function radio_button_group(s) {
        var s2 = s.append('li')
                .attr('class', 'btn-group-vertical')
                .attr('data-toggle', 'buttons');
        return { button: function(button) {
            var b = s2.append("label")
                    .attr("class", "btn btn-default");
            b.append('input').attr('type', 'radio');
            var c = b.append("span");
            if ('id' in button) b.attr('id', button.id);
            
            // text
            if ('key_text' in button && 'text' in button && button.key_text !== null)
                c.text(button.text + button.key_text);
            else if ('text' in button)
                c.text(button.text);

            if ('icon' in button) c.classed(button.icon, true);
            if ('key' in button) set_button(b, button.key);
            if ('tooltip' in button) b.attr('title', button.tooltip);
            return this;
        }};
    }
    
    function button_group(s) {
        var s2 = s.attr('class', 'btn-group-vertical');
        return { button: function(button) {
            var b = s2.append("button")
                    .attr("class", "btn btn-default");
            var c = b.append("span");
            if ('id' in button) b.attr('id', button.id);

            // text
            if ('key_text' in button && 'text' in button && button.key_text !== null)
                c.text(button.text + button.key_text);
            else if ('text' in button)
                c.text(button.text);
            
            if ('icon' in button) c.classed(button.icon, true);
            if ('key' in button) set_button(b, button.key);
            if ('tooltip' in button) b.attr('title', button.tooltip);
            return this;
        }};
    }
    
    function dropdown_menu(s, name, pull_right) {
        if (pull_right === undefined) pull_right = false;
        var s2 = s.append('li')
                .attr('class', 'dropdown');
        s2.append('button').text(name+" ")
            .attr('class', 'btn btn-link btn-sm dropdown-button')
            .attr('data-toggle', 'dropdown')
            .append('b').attr('class', 'caret');
        var ul = s2.append('ul')
                .attr('class', 'dropdown-menu')
                .classed('pull-right', pull_right)
                .attr('role', 'menu')
                .attr('aria-labelledby', 'dLabel');
        return {
            dropdown: s2,
            button: function(button) {
                var li = ul.append("li")
                        .attr('role', 'presentation')
                        .datum(button),
                    link = li.append("a")
                        .attr('href', '#'),
                    icon = link.append('span')
                        .attr('class', 'dropdown-button-icon'),
                    text = link.append('span')
                        .attr('class', 'dropdown-button-text');
                if ('id' in button) li.attr('id', button.id);
                
                // text
                if ('key_text' in button && 'text' in button && button.key_text !== null)
                    text.text(" "+button.text + button.key_text);
                else if ('text' in button)
                    text.text(" "+button.text);

                if ('icon' in button) icon.classed(button.icon, true);
                
                if ('key' in button) {
                    set_button(link, button.key);
                } else if ('input' in button) {
                    var input = button.input,
                        out = (input.accept_csv ?
                               set_json_or_csv_input_button(link, li, input.pre_fn,
                                                            input.fn, input.failure_fn) :
                               set_json_input_button(link, li, input.pre_fn,
                                                     input.fn, input.failure_fn));
                    if ('assign' in input && 'key' in input)
                        input.assign[input.key] = out;
                }
                return this;
            },
            divider: function() {
                ul.append("li")
                    .attr('role', 'presentation')
                    .attr('class', 'divider');
                return this;
            }
        };
    }
    
    function set_button(b, key) {
        b.on("click", function() {
            key.fn.call(key.target);
        });
    }
    
    function set_json_input_button(b, s, pre_fn, post_fn, failure_fn) {
        var input = s.append("input")
                .attr("type", "file")
                .style("display", "none")
                .on("change", function() {
                    utils.load_json(this.files[0],
                                    function(e, d) {
                                        post_fn(e, d);
                                        this.value = "";
                                    }.bind(this),
                                    pre_fn,
                                    failure_fn);
                });
        b.on('click', function(e) {
            input.node().click();
        });
        return function() { input.node().click(); };
    }
    
    function set_json_or_csv_input_button(b, s, pre_fn, post_fn, failure_fn) {
        var input = s.append("input")
                .attr("type", "file")
                .style("display", "none")
                .on("change", function() {
                    utils.load_json_or_csv(this.files[0],
                                           data_styles.csv_converter,
                                           function(e, d) {
                                               post_fn(e, d);
                                               this.value = "";
                                           }.bind(this),
                                           pre_fn,
                                           failure_fn);
                });
        b.on('click', function(e) {
            input.node().click();
        });
        return function() { input.node().click(); };
    }
});


define('SearchBar',["utils", "CallbackManager"], function(utils, CallbackManager) {
    /** 
     */

    var SearchBar = utils.make_class();
    // instance methods
    SearchBar.prototype = { init: init,
                            is_visible: is_visible,
                            toggle: toggle,
                            update: update,
                            next: next,
                            previous: previous };

    return SearchBar;

    // instance methods
    function init(sel, search_index, map) {
        var container = sel.attr('class', 'search-container')
                .style('display', 'none');
        this.input = container.append('input')
            .attr('class', 'search-bar');
        var group = container.append('div').attr('class', 'btn-group btn-group-sm');
        group.append('button')
            .attr("class", "btn btn-default")
            .on('click', this.previous.bind(this))
            .append('span').attr('class', "glyphicon glyphicon-chevron-left");
        group.append('button')
            .attr("class", "btn btn-default")
            .on('click', this.next.bind(this))
            .append('span').attr('class', "glyphicon glyphicon-chevron-right");
        this.counter = container.append('div')
            .attr('class', 'search-counter');
        container.append('button')
            .attr("class", "btn btn-sm btn-default close-button")
            .on('click', function() {
                this.toggle(false);
            }.bind(this))
            .append("span").attr("class",  "glyphicon glyphicon-remove");
        
        this.callback_manager = new CallbackManager();

        this.selection = container;
        this.map = map;
        this.search_index = search_index;

        this.current = 1;
        this.results = null;

        var on_input_fn = function(input) {
            this.current = 1;
            this.results = this.search_index.find(input.value);
            this.update();
        }.bind(this, this.input.node());
        this.input.on('input', utils.debounce(on_input_fn, 200));
    }
    function is_visible() {
        return this.selection.style('display') != 'none';
    }
    function toggle(on_off) {
        if (on_off===undefined) this.is_active = !this.is_active;
        else this.is_active = on_off;

        if (this.is_active) {
            this.selection.style('display', null);
            this.counter.text("");
            this.input.node().value = "";
            this.input.node().focus();
            // escape key
            this.escape = this.map.key_manager
                .add_escape_listener(function() {
                    this.toggle(false);
                }.bind(this), 'settings');
            // enter key
            this.enter = this.map.key_manager
                .add_enter_listener(function() {
                    this.next();
                }.bind(this), 'settings');
            // run the show callback
            this.callback_manager.run('show');
        } else {
            this.map.highlight(null);
            this.selection.style("display", "none");
            this.results = null;
            if (this.escape) this.escape.clear();
            this.escape = null;
            if (this.enter) this.enter.clear();
            this.enter = null;
            // run the hide callback
            this.callback_manager.run('hide');
        }
    }
    function update() {
        if (this.results == null) {
            this.counter.text("");
            this.map.highlight(null);
        } else if (this.results.length == 0) {
            this.counter.text("0 / 0");
            this.map.highlight(null);
        } else {
            this.counter.text(this.current + " / " + this.results.length);
            var r = this.results[this.current - 1];
            if (r.type=='reaction') {           
                this.map.zoom_to_reaction(r.reaction_id);
                this.map.highlight_reaction(r.reaction_id);
            } else if (r.type=='metabolite') {
                this.map.zoom_to_node(r.node_id);
                this.map.highlight_node(r.node_id);
            } else if (r.type=='text_label') {
                this.map.zoom_to_text_label(r.text_label_id);
                this.map.highlight_text_label(r.text_label_id);
            } else {
                throw new Error('Bad search index data type: ' + r.type);
            }
        }
    }
    function next() {
        if (this.results == null) return;
        if (this.current==this.results.length)
            this.current = 1;
        else
            this.current += 1;
        this.update();
    }
    function previous() {
        if (this.results == null) return;
        if (this.current==1)
            this.current = this.results.length;
        else
            this.current -= 1;
        this.update();
    } 
});

define('Settings',["utils", "lib/bacon"], function(utils, bacon) {
    /** A class to manage settings for a Map.

     Arguments
     ---------

     set_option: A function, fn(key), that returns the option value for the
     key.

     get_option: A function, fn(key, value), that sets the option for the key
     and value.

     conditional_options: The options to that are conditionally accepted when
     changed. Changes can be abandoned by calling abandon_changes(), or accepted
     by calling accept_changes().

     */

    var Settings = utils.make_class();
    // instance methods
    Settings.prototype = { init: init,
                           set_conditional: set_conditional,
                           hold_changes: hold_changes,
                           abandon_changes: abandon_changes,
                           accept_changes: accept_changes };

    return Settings;

    // instance methods
    function init(set_option, get_option, conditional_options) {
        this.set_option = set_option;
        this.get_option = get_option;
        
        // manage accepting/abandoning changes
        this.status_bus = new bacon.Bus();

        // force an update of ui components
        this.force_update_bus = new bacon.Bus();

        // modify bacon.observable
        bacon.Observable.prototype.convert_to_conditional_stream = _convert_to_conditional_stream;
        bacon.Observable.prototype.force_update_with_bus = _force_update_with_bus;

        // create the options
        this.busses = {};
        this.streams = {};
        for (var i = 0, l = conditional_options.length; i < l; i++) {
            var name = conditional_options[i],
                out = _create_conditional_setting(name, get_option(name), set_option,
                                                  this.status_bus, this.force_update_bus);
            this.busses[name] = out.bus;
            this.streams[name] = out.stream;
        }
    }
    
    function _convert_to_conditional_stream(status_stream) {
        /** Hold on to event when hold_property is true, and only keep them
         if accept_property is true (when hold_property becomes false).

         */

        // true if hold is pressed
        var is_not_hold_event = status_stream
                .map(function(x) { return x=='hold'; })
                .not()
                .toProperty(true),
            is_not_first_clear = status_stream
                .scan(false, function(c, x) {
                    // first clear only
                    return (c==false && (x=='accepted' || x=='rejected'));
                }).not(),
            is_not_first_hold = status_stream
                .scan(false, function(c, x) {
                    // first clear only
                    return (c==false && x=='hold');
                }).not(),
            combined = bacon.combineAsArray(this, status_stream),
            held = combined
                .scan([], function(c, x) {
                    if (x[1]=='hold') {
                        c.push(x[0]);
                        return c;
                    } else if (x[1]=='accept') {
                        return c;
                    } else if (x[1]=='reject') {
                        return [];
                    } else if (x[1]=='rejected' || x[1]=='accepted') {
                        return [x[0]];
                    } else {
                        throw Error('bad status ' + x[1]);
                    }
                })
        // don't pass in events until the end of a hold
                .filter(is_not_hold_event)
        // ignore the event when clear is passed
                .filter(is_not_first_clear)
        // ignore the event when hold is passed
                .filter(is_not_first_hold)
                .flatMap(function(ar) {
                    return bacon.fromArray(ar);
                }),
            unheld = this.filter(is_not_hold_event);
        return unheld.merge(held);
    }

    function _force_update_with_bus(bus) {        
        return bacon
            .combineAsArray(this, bus.toProperty(false))
            .map(function(t) {
                return t[0];
            });
    }
    
    function _create_conditional_setting(name, initial_value, set_option,
                                         status_bus, force_update_bus) {
        // set up the bus
        var bus = new bacon.Bus();
        // make the event stream
        var stream = bus
        // conditionally accept changes
                .convert_to_conditional_stream(status_bus)
        // force updates
                .force_update_with_bus(force_update_bus);
        
        // get the latest
        stream.onValue(function(v) {
            set_option(name, v);
        });
        
        // push the initial value
        bus.push(initial_value);

        return { bus: bus, stream: stream };
    }

    function set_conditional(name, value) {
        /** Set the value of a conditional setting, one that will only be
         accepted if this.accept_changes() is called.

         Arguments
         ---------

         name: The option name

         value: The new value

         */

        if (!(name in this.busses))
            throw new Error('Invalid setting name');
        this.busses[name].push(value);
    }

    function hold_changes() {
        this.status_bus.push('hold');
    }
    
    function abandon_changes() {
        this.status_bus.push('reject');
        this.status_bus.push('rejected');
        this.force_update_bus.push(true);
    }
    
    function accept_changes() {
        this.status_bus.push('accept');
        this.status_bus.push('accepted');
    }
});


define('ScaleEditor',["utils", "lib/bacon"], function(utils, bacon) {
    /** An interactive UI to edit color and size scales.

     Attributes
     ----------

     sel: A d3 selection.

     type: A type, that should be unique on the page.

     settings: The Settings object.

     */

    var ScaleEditor = utils.make_class();
    // instance methods
    ScaleEditor.prototype = { init: init,
                              update: update,
                              update_no_data: update_no_data,
                              _data_not_loaded: _data_not_loaded };
    return ScaleEditor;

    // instance methods
    function init(sel, type, settings, get_data_statistics) {
        // sels
        var grad_id = 'grad' + type + this.unique_string;
        this.w = 400;
        this.h = 30;
        this.x = 20;
        this.input_width = 90;
        this.input_height = 24;
        var b = sel.append('div')
                .attr('class', 'scale-editor');
        // no data loaded
        this.data_not_loaded = b.append('div')
            .attr('class', 'data-not-loaded')
            .text((type == 'reaction' ? 'Reaction and gene' : 'Metabolite') + ' data not loaded');
        // label
        this.input_label_group = b.append('div')
            .attr('class', 'input-label-group');
        // no data
        var nd = b.append('div')
                .style('top', this.input_height * 3 + 56 + 10 + 'px')
                .attr('class', 'no-data');
        nd.append('span').text('Styles for ' + type + 's with no data')
            .attr('class', 'no-data-heading');
        this.no_data_container = nd.append('div');
        var c = b.append('div')
                .attr('class', 'centered');
        this.add_group = c.append('div');
        this.trash_group = c.append('div')
            .attr('class', 'trash-container');
        var svg = c.append('svg')
                .attr('class', 'scale-svg');
        this.input_group = c.append('div')
            .attr('class', 'input-container');
        this.gradient = svg.append('defs')
            .append('linearGradient')
            .attr('id', grad_id);
        svg.append('rect')
            .attr('class', 'rect')
            .attr('fill', 'url(#' + grad_id + ')')
            .attr('width', this.w + 'px')
            .attr('height', this.h + 'px')
            .attr('x', this.x + 'px'),
        this.pickers_group = svg.append('g');

        // settings
        this.type = type;
        this.settings = settings;
        this.get_data_statistics = get_data_statistics;
        
        var unique_map_id = this.settings.get_option('unique_map_id');
        this.unique_string = (unique_map_id === null ? '' : '.' + unique_map_id);

        // collect data    
        this.no_data = {};
        ['color', 'size'].forEach(function(s) {
            this.no_data[s] = null;
            this.settings.streams[this.type + '_no_data_' + s].onValue(function(val) {
                this.no_data[s] = val;
                this.update_no_data();
            }.bind(this));
        }.bind(this));
        
        this.settings.streams[type + '_scale'].onValue(function(scale) {
            this.scale = scale;
            this.update();
        }.bind(this));
    }

    function update() {
        var scale = this.scale,
            stats = this.get_data_statistics()[this.type],
            bar_w = 14,
            bar_h = 35,
            x_disp = this.x,
            data_not_loaded = this._data_not_loaded();

        // Must have max and min. Otherwise, assume that no data is loaded.
        if (data_not_loaded) {
            scale = [{ type: 'min', 'color': null, 'size': null },
                     { type: 'max', 'color': null, 'size': null }];
            stats = { 'min': 0, 'max': 1 };
        }

        var sc = d3.scale.linear()
                .domain([0, this.w])
                .range([stats.min, stats.max]),
            sc_size = d3.scale.linear()
                .domain([0, this.w])
                .range([0, stats.max - stats.min]);

        // ---------------------------------------------------------------------
        // convenience functions
        var bring_to_front = function(d, i) {
            // bring an input set to the front 
            this.input_group.selectAll('.input-set').each(function(d2) {
                d3.select(this).classed('selected-set', d === d2);
            });
        }.bind(this);
        
        var get_this_val = function(d) {
            return (d.type == 'value') ? d.value : stats[d.type];
        };
        
        var set_scale = function(scale) {
            this.settings.set_conditional(this.type + '_scale', scale);
            this.scale = scale;
            this.update();
        }.bind(this);

        // ---------------------------------------------------------------------
        // make the gradient
        var sorted_domain = scale.map(function(d) {
            return { frac: (get_this_val(d) - stats.min) / (stats.max - stats.min),
                     color: d.color };
        }).filter(function(d) {
            return (d.frac >= 0 && d.frac <= 1.0);
        }).sort(function(a, b) {
            return a.frac - b.frac;
        });
        var stops = this.gradient.selectAll('stop')
                .data(sorted_domain);
        stops.enter()
            .append('stop');
        stops.attr('offset', function(d) {
            return d.frac * 100 + '%';
        }).style('stop-color', function (d) {
            return d.color === null ? '#F1ECFA' : d.color;
        });
        stops.exit().remove();

        // ---------------------------------------------------------------------
        // no data sign

        this.data_not_loaded.style('visibility', (data_not_loaded ? null : 'hidden'));
        
        // ---------------------------------------------------------------------
        // make the pickers
        var pickers = this.pickers_group
                .selectAll('.picker')
                .data(scale);
        // drag 
        var drag = d3.behavior.drag();
        drag.on('drag', function(d, i) {
            // on drag, make it a value type
            if (['value', 'min', 'max'].indexOf(scale[i].type) === -1) {
                // get the current value and set it
                scale[i].value = get_this_val(d);
                scale[i].type = 'value';
            }
            // change the model on drag
            var new_d = scale[i].value + sc_size(d3.event.dx),
                buf = sc_size(bar_w + 2);
            if (new_d > stats.max - buf) new_d = stats.max - buf;
            if (new_d < stats.min + buf) new_d = stats.min + buf;
            // round to 2 decimals
            new_d = Math.floor(new_d * 100.0) / 100.0;
            scale[i].value = new_d;
            this.settings.set_conditional(this.type + '_scale', scale);
            this.scale = scale;
            this.update();
        }.bind(this));
        // enter
        pickers.enter()
            .append('g')
            .attr('class', 'picker')
            .style('cursor', 'pointer')
            .append('rect');
        // update
        pickers.select('rect')
            .attr('x', function(d, i) {
                var val = get_this_val(d),
                    buf = bar_w + 2;
                if (d.type == 'value' && val <= stats.min)
                    return sc.invert(stats.min) - (bar_w / 2) + x_disp - buf;
                if (d.type == 'value' && val >= stats.max)
                    return sc.invert(stats.max) - (bar_w / 2) + x_disp + buf;
                return sc.invert(val) - (bar_w / 2) + x_disp;
            })
            .attr('width', bar_w + 'px')
            .attr('height', bar_h + 'px')
            .call(drag)
            .on('mousedown', bring_to_front);
        // exit
        pickers.exit().remove();

        // ---------------------------------------------------------------------
        // make the delete buttons
        var trashes = this.trash_group.selectAll('span')
                .data(scale);
        // enter
        trashes.enter()
            .append('span');
        // update
        trashes.attr('class', function(d, i) {
            if (d.type == 'min' || d.type == 'max')
                return null;
            return 'trash glyphicon glyphicon-trash';
        }).style('left', function(d) {
            return sc.invert(get_this_val(d)) - (bar_w / 2) + x_disp + 'px';
        }).on('click', function (d, i) {
            if (d.type == 'min' || d.type == 'max')
                return;
            scale = scale.slice(0, i).concat(scale.slice(i + 1));
            this.settings.set_conditional(this.type + '_scale', scale);
            this.scale = scale;
            this.update();
        }.bind(this));
        // exit
        trashes.exit().remove();

        // ---------------------------------------------------------------------
        // make the add button
        var add = this.add_group.selectAll('.add')
                .data(['add']);
        // enter
        add.enter()
            .append('span')
            .attr('class', 'add glyphicon glyphicon-plus');
        // update
        add.on('click', function (d) {
            if (data_not_loaded) return;

            var new_d = (stats.max + stats.min) / 2,
                buf = sc_size(bar_w + 2),
                last_ind = 0;
            // try to make the new point not overlap
            for (var j = 0, l = scale.length; j < l; j++) {
                var th = get_this_val(scale[j]);
                if (Math.abs(th - new_d) < buf) {
                    new_d = new_d + buf;
                    if (new_d > stats.max - buf) new_d = stats.max - buf;
                    if (new_d < stats.min + buf) new_d = stats.min + buf;
                }
                if (new_d > th)
                    last_ind = j;
            }
            // add
            scale.push({ type: 'value',
                         value: new_d,
                         color: scale[last_ind].color,
                         size: scale[last_ind].size });
            set_scale(scale);
        }.bind(this));
        // exit
        add.exit().remove();
        
        // ---------------------------------------------------------------------
        // input labels
        var labels = this.input_label_group.selectAll('.row-label')
                .data(['Value:', 'Color:', 'Size:']);
        // enter
        labels.enter().append('div')
            .attr('class', 'row-label')
            .style('height', this.input_height + 'px')
            .style('line-height', this.input_height + 'px');
        // update
        labels
            .style('top', function(d, i) {
                return 56 + (i * this.input_height) + 'px';
            }.bind(this))
            .text(function(d) { return d; });
        // exit
        labels.exit().remove();
        
        // ---------------------------------------------------------------------
        // inputs
        var inputs = this.input_group.selectAll('.input-set')
                .data(scale);
        
        // enter
        var i = inputs.enter()
                .append('div')
                .attr('class', 'input-set');
        i.append('input')
            .attr('class', 'domain-input')
            .style('width', this.input_width + 'px');
        // type picker
        i.append('select')
            .attr('class', 'domain-type-picker'),
        // color input
        i.append('input')
            .attr('class', 'color-input')
            .style('width', this.input_width + 'px');
        i.append('input')
            .attr('type', 'color')
            .style('visibility', function() {
                // hide the input if the HTML5 color picker is not supported
                return (this.type == 'text') ? 'hidden' : null;
            })
            .attr('class', 'color-picker');
        i.append('input')
            .attr('class', 'size-input')
            .style('width', this.input_width + 'px');
        
        // update
        inputs.style('height', this.input_height * 3 + 'px')
            .style('width', this.input_width + 'px')
            .style('left', function(d) {
                var val = get_this_val(d),
                    buf = bar_w + 2,
                    l;
                if (d.type == 'value' && val <= stats.min)
                    l = sc.invert(stats.min) - (bar_w / 2) + x_disp - buf;
                else if (d.type == 'value' && val >= stats.max)
                    l = sc.invert(stats.max) - (bar_w / 2) + x_disp + buf;
                else
                    l = sc.invert(val) - (bar_w / 2) + x_disp;
                // don't go over the right edge of the bar
                if (l + this.input_width > this.w + this.x)
                    l = l - this.input_width + (bar_w / 2);
                return l + 'px';
            }.bind(this))
            .on('mousedown', bring_to_front);

        var format = d3.format('.4g');
        inputs.select('.domain-input')
            .style('height', this.input_height + 'px')
            .each(function (d, i) {
                if (d.type == 'value') {
                    this.value = get_this_val(d);
                    this.disabled = false;
                } else {
                    this.value = d.type + ' (' + format(get_this_val(d)) + ')';
                    this.disabled = true;
                } 
            }).on('change', function(d, i) {
                var buf = sc_size(bar_w + 2),
                    new_d = parseFloat(this.value);
                scale[i].value = new_d;
                set_scale(scale);
            });
        // update type picker
        var select = inputs.select('.domain-type-picker'),
            // get the function types, except min and max
            stat_types = (['value'].concat(Object.keys(stats))
                          .filter(function(x) {
                              return x != 'min' && x != 'max';
                          })),
            opts = select.selectAll('option').data(stat_types);
        opts.enter().append('option');
        opts.attr('value', function(d) { return d; })
            .text(function(d) { return d; });
        opts.exit().remove();
        select.style('visibility', function(d) {
            return (d.type == 'min' || d.type == 'max') ? 'hidden' : null;
        })
            .style('left', (this.input_width - 20) + 'px')
            .style('width', '20px')
            .each(function (d, i) {
                var sind = 0;
                d3.select(this).selectAll('option').each(function(_, i) {
                    if (this.value == d.type)
                        sind = i;
                });
                this.selectedIndex = sind;
            }).on('change', function(d, i) {
                // set the value to the current location
                if (this.value == 'value')
                    scale[i].value = stats[d.type];
                // switch to the new type
                scale[i].type = this.value;
                // reload
                set_scale(scale);
            });
        // update color input
        inputs.select('.color-input')
            .style('height', this.input_height + 'px')
            .style('top', this.input_height + 'px')
            .each(function (d, i) {
                this.value = (d.color === null ? '' : d.color);
                this.disabled = (d.color === null);
            }).on('change', function(d, i) {
                scale[i].color = this.value;
                set_scale(scale);
            });
        inputs.select('.color-picker')
            .style('left', (this.input_width - this.input_height) + 'px')
            .style('top', this.input_height + 'px')
            .style('width', this.input_height + 'px')
            .style('height', this.input_height + 'px')
            .each(function (d, i) {
                this.value = (d.color === null ? '#dddddd' : d.color);
                this.disabled = (d.color === null);
            }).on('change', function(d, i) {
                scale[i].color = this.value;
                set_scale(scale);
            });
        inputs.select('.size-input')
            .style('height', this.input_height + 'px')
            .style('top', this.input_height * 2 + 'px')
            .each(function (d, i) {
                this.value = (d.size === null ? '' : d.size);
                this.disabled = (d.size === null);
            }).on('change', function(d, i) {
                scale[i].size = parseFloat(this.value);
                set_scale(scale);
            });
        
        // exit
        inputs.exit().remove();
    }
    
    function update_no_data() {
        var no_data = this.no_data,
            data_not_loaded = this._data_not_loaded(),
            label_w = 40;
        
        var ins = this.no_data_container
                .selectAll('.input-group')
                .data([['color', 'Color:'], ['size', 'Size:']]);
        // enter
        var t = ins.enter().append('div')
                .attr('class', 'input-group');
        t.append('span');
        t.append('input');
        t.append('input')
            .attr('type', 'color')
            .style('visibility', function(d) {
                // hide the input if the HTML5 color picker is not supported,
                // or if this is a size box
                return (this.type == 'text' || d[0] != 'color') ? 'hidden' : null;
            })
            .attr('class', 'color-picker');
        // update
        ins.select('span')
            .text(function(d) { return d[1]; })
            .style('height', this.input_height + 'px')
            .style('line-height', this.input_height + 'px')
            .style('left', function(d, i) {
                return ((label_w + this.input_width + 10) * i) + 'px';
            }.bind(this));
        var get_o = function(kind) {
            return this.settings.get_option(this.type + '_no_data_' + kind);
        }.bind(this);
        ins.select('input')
            .style('left', function(d, i) {
                return (label_w + (label_w + this.input_width + 10) * i) + 'px';
            }.bind(this))
            .style('height', this.input_height + 'px')
            .style('width', this.input_width + 'px')
            .each(function(d) {
                // initial value
                this.value = data_not_loaded ? '' : no_data[d[0]];
                this.disabled = data_not_loaded;
            })
            .on('change', function(d) {
                var val = d3.event.target.value;
                if (d[0] == 'size')
                    val = parseFloat(val);
                this.no_data[d[0]] = val;
                this.settings.set_conditional(this.type + '_no_data_' + d[0], val);
                this.update_no_data();
            }.bind(this));
        ins.select('.color-picker')
            .style('left', function(d, i) {
                return ((label_w + this.input_width) * (i + 1) - this.input_height) + 'px';
            }.bind(this))
            .style('width', this.input_height + 'px')
            .style('height', this.input_height + 'px')
            .each(function (d, i) {
                this.value = data_not_loaded ? '#dddddd' : no_data[d[0]];
                this.disabled = data_not_loaded;
            })
            .on('change', function(d, i) {
                var val = d3.event.target.value;
                this.no_data[d[0]] = val;
                this.settings.set_conditional(this.type + '_no_data_' + d[0], val);
                this.update_no_data();
            }.bind(this));
        // exit
        ins.exit().remove();
    }

    function _data_not_loaded() {
        var stats = this.get_data_statistics()[this.type];
        return (stats.max === null || stats.min === null);
    }
});

define('SettingsMenu',["utils", "CallbackManager", "ScaleEditor"], function(utils, CallbackManager, ScaleEditor) {
    /** 
     */

    var SettingsMenu = utils.make_class();
    // instance methods
    SettingsMenu.prototype = { init: init,
                               is_visible: is_visible,
                               toggle: toggle,
                               hold_changes: hold_changes,
                               abandon_changes: abandon_changes,
                               accept_changes: accept_changes,
                               style_gui: style_gui,
                               view_gui: view_gui };

    return SettingsMenu;

    // instance methods
    function init(sel, settings, map, toggle_abs_and_apply_data) {
        this.sel = sel;
        this.settings = settings;
        this.draw = false;
        
        var unique_map_id = this.settings.get_option('unique_map_id');
        this.unique_string = (unique_map_id === null ? '' : '.' + unique_map_id);

        var background = sel.append('div')
                .attr('class', 'settings-box-background')
                .style('display', 'none'),
            container = background.append('div')
                .attr('class', 'settings-box-container')
                .style('display', 'none');

        // done button
        container.append('button')
            .attr("class", "btn btn-sm btn-default settings-button")
            .on('click', function() {
                this.accept_changes();
            }.bind(this))
            .append("span").attr("class",  "glyphicon glyphicon-ok");
        // quit button
        container.append('button')
            .attr("class", "btn btn-sm btn-default settings-button settings-button-close")
            .on('click', function() {
                this.abandon_changes();
            }.bind(this))
            .append("span").attr("class",  "glyphicon glyphicon-remove");

        var box = container.append('div')
                .attr('class', 'settings-box');
        
        // Tip
        box.append('div')
            .text('Tip: Hover over an option to see more details about it.')
            .classed('settings-tip', true);
        box.append('hr');
        
        // view and build
        box.append('div').text('View and build options')
            .attr('class', 'settings-section-heading-large');
        this.view_gui(box.append('div'));
        
        // reactions
        box.append('hr');
        box.append('div')
            .text('Reactions').attr('class', 'settings-section-heading-large');
        var rse = new ScaleEditor(box.append('div'), 'reaction', this.settings,
                                  map.get_data_statistics.bind(map));
        map.callback_manager.set('calc_data_stats__reaction', function(changed) {
            if (changed) {
                rse.update();
                rse.update_no_data();
            }
        });
        box.append('div')
            .text('Reaction or Gene data').attr('class', 'settings-section-heading');
        this.style_gui(box.append('div'), 'reaction', function(on_off) {
            if (toggle_abs_and_apply_data) {
                toggle_abs_and_apply_data('reaction', on_off);
                rse.update();
                rse.update_no_data();
            }
        });

        // metabolite data
        box.append('hr');
        box.append('div').text('Metabolites')
            .attr('class', 'settings-section-heading-large');
        var mse = new ScaleEditor(box.append('div'), 'metabolite', this.settings,
                                  map.get_data_statistics.bind(map));
        map.callback_manager.set('calc_data_stats__metabolite', function(changed) {
            if (changed) {
                mse.update();
                mse.update_no_data();
            }
        });
        box.append('div').text('Metabolite data')
            .attr('class', 'settings-section-heading');
        this.style_gui(box.append('div'), 'metabolite', function(on_off) {
            if (toggle_abs_and_apply_data) {
                toggle_abs_and_apply_data('metabolite', on_off);
                mse.update();
                mse.update_no_data();
            }
        });
        
        this.callback_manager = new CallbackManager();

        this.map = map;
        this.selection = container;
        this.background = background;
    }
    function is_visible() {
        return this.selection.style('display') != 'none';
    }
    function toggle(on_off) {
        if (on_off===undefined) on_off = !this.is_visible();

        if (on_off) {
            // hold changes until accepting/abandoning
            this.hold_changes();
            // show the menu
            this.selection.style("display", "inline-block");
            this.background.style("display", "block");
            this.selection.select('input').node().focus();
            // escape key
            this.escape = this.map.key_manager
                .add_escape_listener(function() {
                    this.abandon_changes();
                }.bind(this), 'settings');
            // enter key
            this.enter = this.map.key_manager
                .add_enter_listener(function() {
                    this.accept_changes();
                }.bind(this), 'settings');
            // run the show callback
            this.callback_manager.run('show');
        } else {
            // draw on finish
            if (this.draw) this.map.draw_everything();
            // hide the menu
            this.selection.style("display", "none");
            this.background.style("display", "none");
            if (this.escape) this.escape.clear();
            if (this.enter) this.enter.clear();
            this.escape = null;
            this.enter = null;
            // run the hide callback
            this.callback_manager.run('hide');
        }
    }
    function hold_changes() {
        this.settings.hold_changes();
    }
    function abandon_changes() {
        this.draw = false;
        this.settings.abandon_changes();
        this.toggle(false);
    }
    function accept_changes() {
        this.sel.selectAll('input').each(function (s) { 
            this.blur();
        });
        this.draw = true;
        this.settings.accept_changes();
        this.toggle(false);
    }
    
    function style_gui(sel, type, abs_callback) {
        /** A UI to edit style.

         */

        var t = sel.append('table').attr('class', 'settings-table'),
            settings = this.settings;

        // styles
        t.append('tr').call(function(r) {
            r.append('td').text('Options:')
                .attr('class', 'options-label')
                .attr('title', ('Options for ' + type + ' data.'));
            var cell = r.append('td');

            var styles = [['Absolute value', 'abs',
                           ('If checked, use the absolute value when ' +
                            'calculating colors and sizes of ' + type + 's on the map')],
                          ['Size', 'size',
                           ('If checked, then size the ' +
                            (type == 'metabolite' ? 'radius of metabolite circles ' : 'thickness of reaction lines ') +
                            'according to the value of the ' + type + ' data')],
                          ['Color', 'color',
                           ('If checked, then color the ' +
                            (type == 'metabolite' ? 'metabolite circles ' : 'reaction lines ') +
                            'according to the value of the ' + type + ' data')],
                          ['Text (Show data in label)', 'text',
                           ('If checked, then show data values in the ' + type + ' ' +
                            'labels')]],
                style_cells = cell.selectAll('.option-group')
                    .data(styles),
                s = style_cells.enter()
                    .append('label')
                    .attr('class', 'option-group');

            // make the checkbox
            var streams = [],
                get_styles = function() {
                    var styles = [];
                    cell.selectAll('input')
                        .each(function(d) { if (this.checked) styles.push(d[1]); });
                    return styles;
                };
            s.append('input').attr('type', 'checkbox')
                .on('change', function(d) {
                    settings.set_conditional(type + '_styles', get_styles());
                    if (d[1] == 'abs')
                        abs_callback(this.checked);
                }).each(function(d) {
                    // subscribe to changes in the model
                    settings.streams[type + '_styles'].onValue(function(ar) {
                        // check the box if the style is present
                        this.checked = (ar.indexOf(d[1]) != -1);
                    }.bind(this));
                });
            s.append('span')
                .text(function(d) { return d[0]; })
                .attr('title', function(d) { return d[2]; });
        });

        // compare_style
        t.append('tr').call(function(r) {
            r.append('td')
                .text('Comparison:')
                .attr('class', 'options-label')
                .attr('title', ('The function that will be used to compare ' +
                                'datasets, when paired data is loaded'));
            var cell = r.append('td')
                    .attr('title', ('The function that will be used to compare ' +
                                    'datasets, when paired data is loaded'));;

            var styles = [['Fold Change', 'fold'],
                          ['Log2(Fold Change)', 'log2_fold'],
                          ['Difference', 'diff']],
                style_cells = cell.selectAll('.option-group')
                    .data(styles),
                s = style_cells.enter()
                    .append('label')
                    .attr('class', 'option-group');
            
            // make the radio
            s.append('input').attr('type', 'radio')
                .attr('name', type + '_compare_style' + this.unique_string)
                .attr('value', function(d) { return d[1]; })
                .on('change', function() {
                    if (this.checked)
                        settings.set_conditional(type + '_compare_style', this.value);
                })
                .each(function() {
                    // subscribe to changes in the model
                    settings.streams[type + '_compare_style'].onValue(function(value) {
                        // check the box for the new value
                        this.checked = (this.value == value);
                    }.bind(this));
                });
            s.append('span')
                .text(function(d) { return d[0]; });

        }.bind(this));

        // gene-specific settings
        if (type=='reaction') {
            var t = sel.append('table').attr('class', 'settings-table')
                    .attr('title', ('The function that will be used to evaluate ' +
                                    'AND connections in gene reaction rules (AND ' +
                                    'connections generally connect components of ' +
                                    'an enzyme complex)'));
            
            // and_method_in_gene_reaction_rule
            t.append('tr').call(function(r) {
                r.append('td')
                    .text('Method for evaluating AND:')
                    .attr('class', 'options-label-wide');
                var cell = r.append('td');

                var styles = [['Mean', 'mean'], ['Min', 'min']],
                    style_cells = cell.selectAll('.option-group')
                        .data(styles),
                    s = style_cells.enter()
                        .append('label')
                        .attr('class', 'option-group');

                // make the radio
                var name = 'and_method_in_gene_reaction_rule';
                s.append('input').attr('type', 'radio')
                    .attr('name', name + this.unique_string)
                    .attr('value', function(d) { return d[1]; })
                    .on('change', function() {
                        if (this.checked)
                            settings.set_conditional(name, this.value);
                    })
                    .each(function() {
                        // subscribe to changes in the model
                        settings.streams[name].onValue(function(value) {
                            // check the box for the new value
                            this.checked = (this.value == value);
                        }.bind(this));
                    });
                s.append('span')
                    .text(function(d) { return d[0]; });
            }.bind(this));

        }
    }
    
    function view_gui(s, option_name, string, options) {

        // columns
        var settings = this.settings;

        var t = s.append('table').attr('class', 'settings-table');
        t.append('tr').call(function(r) {
            // identifiers
            r.attr('title', ('The identifiers that are show in the reaction, ' +
                             'gene, and metabolite labels on the map.'));
            r.append('td').text('Identifiers:')
                .attr('class', 'options-label');
            var cell = r.append('td');

            var options = [['ID\'s', 'bigg_id'], ['Descriptive names', 'name']],
                style_cells = cell.selectAll('.option-group')
                    .data(options),
                s = style_cells.enter()
                    .append('label')
                    .attr('class', 'option-group');

            // make the checkbox
            var name = 'identifiers_on_map';
            s.append('input').attr('type', 'radio')
                .attr('name', name + this.unique_string)
                .attr('value', function(d) { return d[1]; })
                .on('change', function() {
                    if (this.checked)
                        settings.set_conditional(name, this.value);
                })
                .each(function() {
                    // subscribe to changes in the model
                    settings.streams[name].onValue(function(value) {
                        // check the box for the new value
                        this.checked = (this.value == value);
                    }.bind(this));
                });
            s.append('span').text(function(d) { return d[0]; });

        }.bind(this));

        var boolean_options = [
            ['scroll_behavior', 'Scroll to zoom (instead of scroll to pan)',
             ('If checked, then the scroll wheel and trackpad will control zoom ' +
              'rather than pan.'), {'zoom': true, 'pan': false}],
            ['hide_secondary_metabolites', 'Hide secondary metabolites',
             ('If checked, then only the primary metabolites ' +
              'will be displayed.')],
            ['show_gene_reaction_rules', 'Show gene reaction rules',
             ('If checked, then gene reaction rules will be displayed ' +
              'below each reaction label. (Gene reaction rules are always ' +
              'shown when gene data is loaded.)')],
            ['hide_all_labels', 'Hide reaction, gene, and metabolite labels',
             ('If checked, hide all reaction, gene, and metabolite labels')],
            ['allow_building_duplicate_reactions', 'Allow duplicate reactions',
             ('If checked, then allow duplicate reactions during model building.')],
            ['highlight_missing', 'Highlight reactions not in model',
             ('If checked, then highlight in red all the ' +
              'reactions on the map that are not present in ' +
              'the loaded model.')],
        ];
        
        var opts = s.append('div').attr('class', 'settings-container')
                .selectAll('.option-group')
                .data(boolean_options);
        // enter
        var e = opts.enter()
                .append('label')
                .attr('class', 'option-group full-line');
        e.append('input').attr('type', 'checkbox');
        e.append('span');
        // update
        opts.attr('title', function(d) { return d[2]; });
        opts.select('input')
            .on('change', function(d) {
                if (d.length >= 4) { // not a boolean setting
                    for (var key in d[3]) {
                        if (d[3][key] == this.checked) {
                            settings.set_conditional(d[0], key);
                            break;
                        }
                    }
                } else { // boolean setting
                    settings.set_conditional(d[0], this.checked);
                }
            })
            .each(function(d) {
                settings.streams[d[0]].onValue(function(value) {
                    if (d.length >= 4) { // not a boolean setting
                        this.checked = d[3][value];
                    } else { // boolean setting
                        this.checked = value;
                    }
                }.bind(this));
            });
        opts.select('span')
            .text(function(d) { return d[1]; });
        // exit
        opts.exit().remove();
        
        // message about text performance
        s.append('div')
            .style('margin-top', '16px')
            .classed('settings-tip', true)
            .text('Tip: To increase map performance, turn off text boxes (i.e. labels and gene reaction rules).');
    }
});

define('TextEditInput',['utils', 'PlacedDiv', 'build'], function(utils, PlacedDiv, build) {
    /**
     */

    var TextEditInput = utils.make_class();
    // instance methods
    TextEditInput.prototype = { init: init,
                                setup_map_callbacks: setup_map_callbacks,
                                setup_zoom_callbacks: setup_zoom_callbacks,
                                is_visible: is_visible,
                                show: show,
                                hide: hide,
                                _accept_changes: _accept_changes,
                                _add_and_edit: _add_and_edit };

    return TextEditInput;

    // definitions
    function init(selection, map, zoom_container) {
        var div = selection.append('div')
                .attr('id', 'text-edit-input');
        this.placed_div = PlacedDiv(div, map);
        this.placed_div.hide();
        this.input = div.append('input');

        this.map = map;
        this.setup_map_callbacks(map);
        this.zoom_container = zoom_container;
        this.setup_zoom_callbacks(zoom_container);
    }

    function setup_map_callbacks(map) {
        // input
        map.callback_manager.set('edit_text_label.text_edit_input', function(target, coords) {
            this.show(target, coords);
        }.bind(this));

        // new text_label
        map.callback_manager.set('new_text_label.text_edit_input', function(coords) {
            if (this.active_target !== null)
                this._accept_changes(this.active_target.target);
            this.hide();
            this._add_and_edit(coords);
        }.bind(this));
        
        map.callback_manager.set('hide_text_label_editor.text_edit_input', function() {
            this.hide();
        }.bind(this));
    }

    function setup_zoom_callbacks(zoom_container) {
        zoom_container.callback_manager.set('zoom.text_edit_input', function() {
            if (this.active_target)
                this._accept_changes(this.active_target.target);
            this.hide();
        }.bind(this));
        zoom_container.callback_manager.set('go_to.text_edit_input', function() {
            if (this.active_target)
                this._accept_changes(this.active_target.target);
            this.hide();
        }.bind(this));
    }

    function is_visible() {
        return this.placed_div.is_visible();
    }

    function show(target, coords) {
        // save any existing edit
        if (this.active_target) {
            this._accept_changes(this.active_target.target);
        }

        // set the current target
        this.active_target = { target: target,
                               coords: coords };

        // set the new value
        target.each(function(d) {
            this.input.node().value = d.text;
        }.bind(this));

        // place the input
        this.placed_div.place(coords);
        this.input.node().focus();

        // escape key
        this.escape = this.map.key_manager
            .add_escape_listener(function() {
                this._accept_changes(target);
                this.hide();
            }.bind(this));
        // enter key
        this.enter = this.map.key_manager
            .add_enter_listener(function(target) {
                this._accept_changes(target);
                this.hide();
            }.bind(this, target));
    }

    function hide() {
        // hide the input
        this.placed_div.hide();

        // clear the value
        this.input.attr('value', '');
        this.active_target = null;

        // clear escape
        if (this.escape)
            this.escape.clear();
        this.escape = null;
        // clear enter
        if (this.enter)
            this.enter.clear();
        this.enter = null;
        // turn off click listener
        // this.map.sel.on('click.', null);
    }

    function _accept_changes(target) {
        if (this.input.node().value == '') {
            // delete the label
            target.each(function(d) {
                var selected = {};
                selected[d.text_label_id] = this.map.text_labels[d.text_label_id];
                this.map.delete_selectable({}, selected, true);
            }.bind(this));
        } else {
            // set the text
            var text_label_ids = [];
            target.each(function(d) {
                this.map.edit_text_label(d.text_label_id, this.input.node().value, true);
                text_label_ids.push(d.text_label_id);
            }.bind(this));
        }
    }

    function _add_and_edit(coords) {
        // make an empty label
        var text_label_id = this.map.new_text_label(coords, '');
        // apply the cursor to the new label
        var sel = this.map.sel.select('#text-labels').selectAll('.text-label')
                .filter(function(d) { return d.text_label_id == text_label_id; });
        sel.select('text').classed('edit-text-cursor', true);
        this.show(sel, coords);
    }
});

define('QuickJump',['utils'], function(utils) {
    /** A QuickJump menu to move between maps.

     Arguments
     ---------

     sel: The d3 selection of an html node to place the menu inside.

     options: An array of map names to jump to.

     load_callback: A callback function that accepts two arguments: map_name,
     and another callback which returns true or false for success or failure
     (callback purgatory).

     */

    var QuickJump = utils.make_class();
    // instance methods
    QuickJump.prototype = { init: init,
                            reset_selection: reset_selection,
                            replace_state_for_map_name: replace_state_for_map_name };

    return QuickJump;

    // instance methods
    function init(sel, load_callback) {        
        // set up the menu
        var select_sel = sel.append('select')
                .attr('id', 'quick-jump-menu')
                .attr('class', 'form-control'); 
        this.selector = select_sel;

        // get the options to show
        var url_comp = utils.parse_url_components(window),
            current = ('map_name' in url_comp) ? url_comp.map_name : null,
            quick_jump_path = ('quick_jump_path' in url_comp) ? url_comp.quick_jump_path : null,
            options = ('quick_jump' in url_comp) ? url_comp.quick_jump : [],
            default_value = '— Jump to map —',
            view_options = [default_value].concat(options);
        if (current !== null) {
            view_options = view_options.filter(function(o) {
                return o != current;
            });
        }
        
        select_sel.selectAll('option')
            .data(view_options)
            .enter()
            .append('option')
            .text(function(d) {
                // works whether or not a '.' is present
                return d.split('.').slice(-1)[0];
            });
        
        // only show if there are options
        select_sel.style('display', view_options.length > 1 ? 'block' : 'none');

        // on selection
        var change_map = function(map_name) {
            load_callback(map_name, quick_jump_path, function(success) {
                if (success)
                    this.replace_state_for_map_name(map_name);
                else
                    this.reset_selection();
            }.bind(this));
        }.bind(this);
        
        select_sel.on('change', function() {
            // get the new map
            var map_name = this.options[this.selectedIndex].__data__;
            change_map(map_name);
        });
    }

    function reset_selection() {
        this.selector.node().selectedIndex = 0;
    }
    
    function replace_state_for_map_name(map_name) {
        /** Just changes the url to match the new map name. Does not actually
         manage the HTML5 history.

         */
        
        // update the url with the new map
        var url = window.location.href
                .replace(/(map_name=)([^&]+)(&|$)/, '$1' + map_name + '$3');
        window.history.replaceState('Not implemented', '', url);
    }
});

define('Builder',['utils', 'BuildInput', 'ZoomContainer', 'Map', 'CobraModel', 'Brush', 'CallbackManager', 'ui', 'SearchBar', 'Settings', 'SettingsMenu', 'TextEditInput', 'QuickJump', 'data_styles'], function(utils, BuildInput, ZoomContainer, Map, CobraModel, Brush, CallbackManager, ui, SearchBar, Settings, SettingsMenu, TextEditInput, QuickJump, data_styles) {
    /** For documentation of this class, see docs/javascript_api.rst

     */
    var Builder = utils.make_class();
    Builder.prototype = { init: init,
                          load_map: load_map,
                          load_model: load_model,
                          _set_mode: _set_mode,
                          view_mode: view_mode,
                          build_mode: build_mode,
                          brush_mode: brush_mode,
                          zoom_mode: zoom_mode,
                          rotate_mode: rotate_mode,
                          text_mode: text_mode,
                          set_reaction_data: set_reaction_data,
                          set_metabolite_data: set_metabolite_data,
                          set_gene_data: set_gene_data,
                          _update_data: _update_data,
                          _toggle_direction_buttons: _toggle_direction_buttons,
                          _setup_menu: _setup_menu,
                          _setup_simple_zoom_buttons: _setup_simple_zoom_buttons,
                          _setup_status: _setup_status,
                          _setup_quick_jump: _setup_quick_jump,
                          _setup_modes: _setup_modes,
                          _get_keys: _get_keys,
                          _setup_confirm_before_exit: _setup_confirm_before_exit };

    return Builder;

    // definitions
    function init(map_data, model_data, embedded_css, selection, options) {

        // default sel
        if (!selection)
            selection = d3.select('body').append('div');
        if (!options)
            options = {};

        this.map_data = map_data;
        this.model_data = model_data;
        this.embedded_css = embedded_css;
        this.selection = selection;

        // apply this object as data for the selection
        this.selection.datum(this);

        // set defaults
        this.options = utils.set_options(options, {
            // view options
            menu: 'all',
            scroll_behavior: 'pan',
            enable_editing: true,
            enable_keys: true,
            enable_search: true,
            fill_screen: false,
            zoom_to_element: null,
            // map, model, and styles
            starting_reaction: null,
            never_ask_before_quit: false,
            unique_map_id: null,
            primary_metabolite_radius: 20,
            secondary_metabolite_radius: 10,
            marker_radius: 5,
            gene_font_size: 18,
            hide_secondary_metabolites: false,
            show_gene_reaction_rules: false,
            hide_all_labels: false,
            // applied data
            // reaction
            reaction_data: null,
            reaction_styles: ['color', 'size', 'text'],
            reaction_compare_style: 'log2_fold',
            reaction_scale: [{ type: 'min', color: '#c8c8c8', size: 12 },
                             { type: 'median', color: '#9696ff', size: 20 },
                             { type: 'max', color: '#ff0000', size: 25 }],
            reaction_no_data_color: '#dcdcdc',
            reaction_no_data_size: 8,
            // gene
            gene_data: null,
            and_method_in_gene_reaction_rule: 'mean',
            // metabolite
            metabolite_data: null,
            metabolite_styles: ['color', 'size', 'text'],
            metabolite_compare_style: 'log2_fold',
            metabolite_scale: [ { type: 'min', color: '#fffaf0', size: 20 },
                                { type: 'median', color: '#f1c470', size: 30 },
                                { type: 'max', color: '#800000', size: 40 } ],
            metabolite_no_data_color: '#ffffff',
            metabolite_no_data_size: 10,
            // View and build options
            identifiers_on_map: 'bigg_id',
            highlight_missing: false,
            allow_building_duplicate_reactions: false,
            // Callbacks
            first_load_callback: null
        }, {
            primary_metabolite_radius: true,
            secondary_metabolite_radius: true,
            marker_radius: true,
            gene_font_size: true,
            reaction_no_data_size: true,
            metabolite_no_data_size: true
        });

        // check the location
        if (utils.check_for_parent_tag(this.selection, 'svg')) {
            throw new Error('Builder cannot be placed within an svg node '+
                            'becuase UI elements are html-based.');
        }

        // Initialize the settings
        var set_option = function(option, new_value) {
            this.options[option] = new_value;
        }.bind(this),
            get_option = function(option) {
                return this.options[option];
            }.bind(this),
            // the options that are erased when the settings menu is canceled
            conditional_options = ['hide_secondary_metabolites', 'show_gene_reaction_rules',
                                   'hide_all_labels', 'scroll_behavior', 'reaction_styles',
                                   'reaction_compare_style', 'reaction_scale',
                                   'reaction_no_data_color', 'reaction_no_data_size',
                                   'and_method_in_gene_reaction_rule', 'metabolite_styles',
                                   'metabolite_compare_style', 'metabolite_scale',
                                   'metabolite_no_data_color', 'metabolite_no_data_size',
                                   'identifiers_on_map', 'highlight_missing',
                                   'allow_building_duplicate_reactions',];
        this.settings = new Settings(set_option, get_option, conditional_options);

        // check the scales have max and min
        ['reaction_scale', 'metabolite_scale'].forEach(function(name) {
            this.settings.streams[name].onValue(function(val) {
                ['min', 'max'].forEach(function(type) {
                    var has = val.reduce(function(has_found, scale_el) {
                        return has_found || (scale_el.type == type);
                    }, false);
                    if (!has) {
                        val.push({ type: type, color: '#ffffff', size: 10 });
                        this.settings.set_conditional(name, val);
                    }
                }.bind(this));
            }.bind(this));
        }.bind(this));
        // TODO warn about repeated types in the scale

        // set up this callback manager
        this.callback_manager = CallbackManager();
        if (this.options.first_load_callback !== null)
            this.callback_manager.set('first_load', this.options.first_load_callback);

        // load the model, map, and update data in both
        this.load_model(this.model_data, false);
        this.load_map(this.map_data, false);
        this._update_data(true, true);

        // setting callbacks
        // TODO enable atomic updates. Right now, every time
        // the menu closes, everything is drawn.
        this.settings.status_bus
            .onValue(function(x) {
                if (x == 'accepted') {
                    this._update_data(true, true, ['reaction', 'metabolite'], false);
                    if (this.zoom_container !== null) {
                        var new_behavior = this.settings.get_option('scroll_behavior');
                        this.zoom_container.update_scroll_behavior(new_behavior);
                    }
                    if (this.map !== null) {
                        this.map.draw_all_nodes(false);
                        this.map.draw_all_reactions(true, false);
                    }
                }
            }.bind(this));

        this.callback_manager.run('first_load', this);
    }

    // Definitions
    function load_model(model_data, should_update_data) {
        /** For documentation of this function, see docs/javascript_api.rst.

         */
        if (should_update_data === undefined)
            should_update_data = true;

        // Check the cobra model
        if (model_data === null)
            this.cobra_model = null;
        else
            this.cobra_model = CobraModel.from_cobra_json(model_data);

        if (this.map) {
            this.map.cobra_model = this.cobra_model;
            if (should_update_data)
                this._update_data(true, false);
            if (this.settings.get_option('highlight_missing'))
                this.map.draw_all_reactions(false, false);
        }

        this.callback_manager.run('load_model', null, model_data, should_update_data);
    }

    function load_map(map_data, should_update_data) {
        /** For documentation of this function, see docs/javascript_api.rst

         */

        if (should_update_data === undefined)
            should_update_data = true;

        // Begin with some definitions
        var selectable_mousedown_enabled = true,
            shift_key_on = false;

        // remove the old builder
        utils.remove_child_nodes(this.selection);

        // set up the svg
        var svg = utils.setup_svg(this.selection, false,
                                  this.options.fill_screen);

        // se up the zoom container
        this.zoom_container = new ZoomContainer(svg, this.selection,
                                                this.options.scroll_behavior);
        var zoomed_sel = this.zoom_container.zoomed_sel;

        if (map_data!==null) {
            // import map
            this.map = Map.from_data(map_data,
                                     svg,
                                     this.embedded_css,
                                     zoomed_sel,
                                     this.zoom_container,
                                     this.settings,
                                     this.cobra_model,
                                     this.options.enable_search);
            this.zoom_container.reset();
        } else {
            // new map
            this.map = new Map(svg,
                               this.embedded_css,
                               zoomed_sel,
                               this.zoom_container,
                               this.settings,
                               this.cobra_model,
                               null,
                               this.options.enable_search);
        }

        // set the data for the map
        if (should_update_data)
            this._update_data(false, true);

        // set up the reaction input with complete.ly
        this.build_input = BuildInput(this.selection, this.map,
                                      this.zoom_container, this.settings);

        // set up the text edit input
        this.text_edit_input = TextEditInput(this.selection, this.map,
                                             this.zoom_container);

        // set up the Brush
        this.brush = new Brush(zoomed_sel, false, this.map, '.canvas-group');
        this.map.canvas.callback_manager.set('resize', function() {
            this.brush.toggle(true);
        }.bind(this));

        // set up the modes
        this._setup_modes(this.map, this.brush, this.zoom_container);

        var s = this.selection
                .append('div').attr('class', 'search-menu-container')
                .append('div').attr('class', 'search-menu-container-inline'),
            menu_div = s.append('div'),
            search_bar_div = s.append('div'),
            button_div = this.selection.append('div');

        // set up the search bar
        this.search_bar = SearchBar(search_bar_div, this.map.search_index,
                                    this.map);
        // set up the hide callbacks
        this.search_bar.callback_manager.set('show', function() {
            this.settings_bar.toggle(false);
        }.bind(this));

        // set up the settings
        var settings_div = this.selection.append('div');
        this.settings_bar = SettingsMenu(settings_div, this.settings, this.map,
                                         function(type, on_off) {
                                             // temporarily set the abs type, for
                                             // previewing it in the Settings
                                             // menu
                                             var o = this.options[type + '_styles'];
                                             if (on_off && o.indexOf('abs') == -1)
                                                 o.push('abs');
                                             else if (!on_off) {
                                                 var i = o.indexOf('abs');
                                                 if (i != -1)
                                                     this.options[type + '_styles'] = o.slice(0, i).concat(o.slice(i + 1));
                                             }
                                             this._update_data(false, true, type);
                                         }.bind(this));
        this.settings_bar.callback_manager.set('show', function() {
            this.search_bar.toggle(false);
        }.bind(this));

        // set up key manager
        var keys = this._get_keys(this.map, this.zoom_container,
                                  this.search_bar, this.settings_bar,
                                  this.options.enable_editing);
        this.map.key_manager.assigned_keys = keys;
        // tell the key manager about the reaction input and search bar
        this.map.key_manager.input_list = [this.build_input, this.search_bar,
                                           this.settings_bar, this.text_edit_input];
        // make sure the key manager remembers all those changes
        this.map.key_manager.update();
        // turn it on/off
        this.map.key_manager.toggle(this.options.enable_keys);

        // set up menu and status bars
        if (this.options.menu=='all') {
            this._setup_menu(menu_div, button_div, this.map, this.zoom_container, this.map.key_manager, keys,
                             this.options.enable_editing, this.options.enable_keys);
        } else if (this.options.menu=='zoom') {
            this._setup_simple_zoom_buttons(button_div, keys);
        }

        // setup selection box
        if (this.options.zoom_to_element) {
            var type = this.options.zoom_to_element.type,
                element_id = this.options.zoom_to_element.id;
            if (typeof type === 'undefined' || ['reaction', 'node'].indexOf(type) == -1)
                throw new Error('zoom_to_element type must be "reaction" or "node"');
            if (typeof element_id === 'undefined')
                throw new Error('zoom_to_element must include id');
            if (type == 'reaction')
                this.map.zoom_to_reaction(element_id);
            else if (type == 'node')
                this.map.zoom_to_node(element_id);
        } else if (map_data !== null) {
            this.map.zoom_extent_canvas();
        } else {
            if (this.options.starting_reaction !== null && this.cobra_model !== null) {
                // Draw default reaction if no map is provided
                var size = this.zoom_container.get_size();
                var start_coords = { x: size.width / 2,
                                     y: size.height / 4 };
                this.map.new_reaction_from_scratch(this.options.starting_reaction, start_coords, 90);
                this.map.zoom_extent_nodes();
            } else {
                this.map.zoom_extent_canvas();
            }
        }

        // status in both modes
        var status = this._setup_status(this.selection, this.map);

        // set up quick jump
        this._setup_quick_jump(this.selection);

        // start in zoom mode for builder, view mode for viewer
        if (this.options.enable_editing)
            this.zoom_mode();
        else
            this.view_mode();

        // confirm before leaving the page
        if (this.options.enable_editing)
            this._setup_confirm_before_exit();

        // draw
        this.map.draw_everything();
    }

    function _set_mode(mode) {
        this.search_bar.toggle(false);
        // input
        this.build_input.toggle(mode=='build');
        this.build_input.direction_arrow.toggle(mode=='build');
        if (this.options.menu=='all' && this.options.enable_editing)
            this._toggle_direction_buttons(mode=='build');
        // brush
        this.brush.toggle(mode=='brush');
        // zoom
        this.zoom_container.toggle_zoom(mode=='zoom' || mode=='view');
        // resize canvas
        this.map.canvas.toggle_resize(mode=='zoom' || mode=='brush');
        // Behavior. Be careful of the order becuase rotation and
        // toggle_selectable_drag both use Behavior.selectable_drag.
        if (mode == 'rotate') {
            this.map.behavior.toggle_selectable_drag(false); // before toggle_rotation_mode
            this.map.behavior.toggle_rotation_mode(true);
        } else {
            this.map.behavior.toggle_rotation_mode(mode=='rotate'); // before toggle_selectable_drag
            this.map.behavior.toggle_selectable_drag(mode=='brush');
        }
        this.map.behavior.toggle_selectable_click(mode=='build' || mode=='brush');
        this.map.behavior.toggle_label_drag(mode=='brush');
        this.map.behavior.toggle_label_mousedown(mode=='brush');
        this.map.behavior.toggle_text_label_edit(mode=='text');
        this.map.behavior.toggle_bezier_drag(mode=='brush');
        // edit selections
        if (mode=='view' || mode=='text')
            this.map.select_none();
        if (mode=='rotate')
            this.map.deselect_text_labels();
        this.map.draw_everything();
    }

    function view_mode() {
        /** For documentation of this function, see docs/javascript_api.rst.

         */
        this.callback_manager.run('view_mode');
        this._set_mode('view');
    }

    function build_mode() {
        /** For documentation of this function, see docs/javascript_api.rst.

         */
        this.callback_manager.run('build_mode');
        this._set_mode('build');
    }

    function brush_mode() {
        /** For documentation of this function, see docs/javascript_api.rst.

         */
        this.callback_manager.run('brush_mode');
        this._set_mode('brush');
    }

    function zoom_mode() {
        /** For documentation of this function, see docs/javascript_api.rst.

         */
        this.callback_manager.run('zoom_mode');
        this._set_mode('zoom');
    }

    function rotate_mode() {
        /** For documentation of this function, see docs/javascript_api.rst.

         */
        this.callback_manager.run('rotate_mode');
        this._set_mode('rotate');
    }

    function text_mode() {
        /** For documentation of this function, see docs/javascript_api.rst.

         */
        this.callback_manager.run('text_mode');
        this._set_mode('text');
    }

    function set_reaction_data(data) {
        /** For documentation of this function, see docs/javascript_api.rst.

         */
        this.options.reaction_data = data;
        this._update_data(true, true, 'reaction');
        this.map.set_status('');
    }

    function set_gene_data(data, clear_gene_reaction_rules) {
        /** For documentation of this function, see docs/javascript_api.rst.

         */
        if (clear_gene_reaction_rules) // default undefined
            this.settings.set_conditional('show_gene_reaction_rules', false);
        this.options.gene_data = data;
        this._update_data(true, true, 'reaction');
        this.map.set_status('');
    }

    function set_metabolite_data(data) {
        /** For documentation of this function, see docs/javascript_api.rst.

         */
        this.options.metabolite_data = data;
        this._update_data(true, true, 'metabolite');
        this.map.set_status('');
    }

    function _update_data(update_model, update_map, kind, should_draw) {
        /** Set data and settings for the model.

         Arguments
         ---------

         update_model: (Boolean) Update data for the model.

         update_map: (Boolean) Update data for the map.

         kind: (Optional, Default: all) An array defining which data is being
         updated that can include any of: ['reaction', 'metabolite'].

         should_draw: (Optional, Default: true) Whether to redraw the update
         sections of the map.

         */

        // defaults
        if (kind === undefined)
            kind = ['reaction', 'metabolite'];
        if (should_draw === undefined)
            should_draw = true;

        var update_metabolite_data = (kind.indexOf('metabolite') != -1),
            update_reaction_data = (kind.indexOf('reaction') != -1),
            met_data_object,
            reaction_data_object,
            gene_data_object;

        // -------------------
        // First map, and draw

        // metabolite data
        if (update_metabolite_data && update_map && this.map !== null) {
            met_data_object = data_styles.import_and_check(this.options.metabolite_data,
                                                           'metabolite_data');
            this.map.apply_metabolite_data_to_map(met_data_object);
            if (should_draw)
                this.map.draw_all_nodes(false);
        }

        // reaction data
        if (update_reaction_data) {
            if (this.options.reaction_data !== null && update_map && this.map !== null) {
                reaction_data_object = data_styles.import_and_check(this.options.reaction_data,
                                                                    'reaction_data');
                this.map.apply_reaction_data_to_map(reaction_data_object);
                if (should_draw)
                    this.map.draw_all_reactions(false, false);
            } else if (this.options.gene_data !== null && update_map && this.map !== null) {
                gene_data_object = make_gene_data_object(this.options.gene_data,
                                                         this.cobra_model, this.map);
                this.map.apply_gene_data_to_map(gene_data_object);
                if (should_draw)
                    this.map.draw_all_reactions(false, false);
            } else if (update_map && this.map !== null) {
                // clear the data
                this.map.apply_reaction_data_to_map(null);
                if (should_draw)
                    this.map.draw_all_reactions(false, false);
            }
        }

        // ----------------------------------------------------------------
        // Then the model, after drawing. Delay by 5ms so the the map draws
        // first.

        // if this function runs again, cancel the previous model update
        if (this.update_model_timer)
            window.clearTimeout(this.update_model_timer);

        var delay = 5;
        this.update_model_timer = window.setTimeout(function() {

            // metabolite_data
            if (update_metabolite_data && update_model && this.cobra_model !== null) {
                // if we haven't already made this
                if (!met_data_object)
                    met_data_object = data_styles.import_and_check(this.options.metabolite_data,
                                                                   'metabolite_data');
                this.cobra_model.apply_metabolite_data(met_data_object,
                                                       this.options.metabolite_styles,
                                                       this.options.metabolite_compare_style);
            }

            // reaction data
            if (update_reaction_data) {
                if (this.options.reaction_data !== null && update_model && this.cobra_model !== null) {
                    // if we haven't already made this
                    if (!reaction_data_object)
                        reaction_data_object = data_styles.import_and_check(this.options.reaction_data,
                                                                            'reaction_data');
                    this.cobra_model.apply_reaction_data(reaction_data_object,
                                                         this.options.reaction_styles,
                                                         this.options.reaction_compare_style);
                } else if (this.options.gene_data !== null && update_model && this.cobra_model !== null) {
                    if (!gene_data_object)
                        gene_data_object = make_gene_data_object(this.options.gene_data,
                                                                 this.cobra_model, this.map);
                    this.cobra_model.apply_gene_data(gene_data_object,
                                                     this.options.reaction_styles,
                                                     this.options.identifiers_on_map,
                                                     this.options.reaction_compare_style,
                                                     this.options.and_method_in_gene_reaction_rule);
                } else if (update_model && this.cobra_model !== null) {
                    // clear the data
                    this.cobra_model.apply_reaction_data(null,
                                                         this.options.reaction_styles,
                                                         this.options.reaction_compare_style);
                }
            }

            // callback
            this.callback_manager.run('update_data', null, update_model, update_map, kind, should_draw);

        }.bind(this), delay);

        // definitions
        function make_gene_data_object(gene_data, cobra_model, map) {
            var all_reactions = {};
            if (cobra_model !== null)
                utils.extend(all_reactions, cobra_model.reactions);
            // extend, overwrite
            if (map !== null)
                utils.extend(all_reactions, map.reactions, true);

            // this object has reaction keys and values containing associated genes
            return data_styles.import_and_check(gene_data, 'gene_data', all_reactions);
        }
    }

    function _setup_menu(menu_selection, button_selection, map, zoom_container,
                         key_manager, keys, enable_editing, enable_keys) {
        var menu = menu_selection.attr('id', 'menu')
                .append('ul')
                .attr('class', 'nav nav-pills');
        // map dropdown
        ui.dropdown_menu(menu, 'Map')
            .button({ key: keys.save,
                      text: 'Save map JSON',
                      key_text: (enable_keys ? ' (Ctrl+S)' : null) })
            .button({ text: 'Load map JSON',
                      key_text: (enable_keys ? ' (Ctrl+O)' : null),
                      input: { assign: key_manager.assigned_keys.load,
                               key: 'fn',
                               fn: load_map_for_file.bind(this),
                               pre_fn: function() {
                                   map.set_status('Loading map ...');
                               },
                               failure_fn: function() {
                                   map.set_status('');
                               }}
                    })
            .button({ key: keys.save_svg,
                      text: 'Export as SVG',
                      key_text: (enable_keys ? ' (Ctrl+Shift+S)' : null) })
            .button({ key: keys.clear_map,
                      text: 'Clear map' });
        // model dropdown
        var model_menu = ui.dropdown_menu(menu, 'Model')
                .button({ text: 'Load COBRA model JSON',
                          key_text: (enable_keys ? ' (Ctrl+M)' : null),
                          input: { assign: key_manager.assigned_keys.load_model,
                                   key: 'fn',
                                   fn: load_model_for_file.bind(this),
                                   pre_fn: function() {
                                       map.set_status('Loading model ...');
                                   },
                                   failure_fn: function() {
                                       map.set_status('');
                                   } }
                        })
                .button({ id: 'convert_map',
                          key: keys.convert_map,
                          text: 'Update names and gene reaction rules using model' })
                .button({ id: 'clear_model',
                          key: keys.clear_model,
                          text: 'Clear model' });
        // disable the clear and convert buttons
        var disable_model_clear_convert = function() {
            model_menu.dropdown.selectAll('li')
                .classed('escher-disabled', function(d) {
                    if ((d.id == 'clear_model' || d.id == 'convert_map') &&
                        this.cobra_model === null)
                        return true;
                    return null;
                }.bind(this));
        }.bind(this);
        disable_model_clear_convert();
        this.callback_manager.set('load_model', disable_model_clear_convert);

        // data dropdown
        var data_menu = ui.dropdown_menu(menu, 'Data')
                .button({ input: { assign: key_manager.assigned_keys.load_reaction_data,
                                   key: 'fn',
                                   fn: load_reaction_data_for_file.bind(this),
                                   accept_csv: true,
                                   pre_fn: function() {
                                       map.set_status('Loading reaction data ...');
                                   },
                                   failure_fn: function() {
                                       map.set_status('');
                                   }},
                          text: 'Load reaction data' })
                .button({ key: keys.clear_reaction_data,
                          text: 'Clear reaction data' })
                .divider()
                .button({ input: { fn: load_gene_data_for_file.bind(this),
                                   accept_csv: true,
                                   pre_fn: function() {
                                       map.set_status('Loading gene data ...');
                                   },
                                   failure_fn: function() {
                                       map.set_status('');
                                   }},
                          text: 'Load gene data' })
                .button({ key: keys.clear_gene_data,
                          text: 'Clear gene data' })
                .divider()
                .button({ input: { fn: load_metabolite_data_for_file.bind(this),
                                   accept_csv: true,
                                   pre_fn: function() {
                                       map.set_status('Loading metabolite data ...');
                                   },
                                   failure_fn: function() {
                                       map.set_status('');
                                   }},
                          text: 'Load metabolite data' })
                .button({ key: keys.clear_metabolite_data,
                          text: 'Clear metabolite data' });

        // update the buttons
        var disable_clears = function() {
            data_menu.dropdown.selectAll('li')
                .classed('escher-disabled', function(d) {
                    if (!d) return null;
                    if (d.text == 'Clear reaction data' && this.options.reaction_data === null)
                        return true;
                    if (d.text == 'Clear gene data' && this.options.gene_data === null)
                        return true;
                    if (d.text == 'Clear metabolite data' && this.options.metabolite_data === null)
                        return true;
                    return null;
                }.bind(this));
        }.bind(this);
        disable_clears();
        this.callback_manager.set('update_data', disable_clears);

        // edit dropdown
        var edit_menu = ui.dropdown_menu(menu, 'Edit', true);
        if (enable_editing) {
            edit_menu
                .button({ key: keys.zoom_mode,
                          id: 'zoom-mode-menu-button',
                          text: 'Pan mode',
                          key_text: (enable_keys ? ' (Z)' : null) })
                .button({ key: keys.brush_mode,
                          id: 'brush-mode-menu-button',
                          text: 'Select mode',
                          key_text: (enable_keys ? ' (V)' : null) })
                .button({ key: keys.build_mode,
                          id: 'build-mode-menu-button',
                          text: 'Add reaction mode',
                          key_text: (enable_keys ? ' (N)' : null) })
                .button({ key: keys.rotate_mode,
                          id: 'rotate-mode-menu-button',
                          text: 'Rotate mode',
                          key_text: (enable_keys ? ' (R)' : null) })
                .button({ key: keys.text_mode,
                          id: 'text-mode-menu-button',
                          text: 'Text mode',
                          key_text: (enable_keys ? ' (T)' : null) })
                .divider()
                .button({ key: keys.delete,
                          text: 'Delete',
                          key_text: (enable_keys ? ' (Del)' : null) })
                .button({ key: keys.undo,
                          text: 'Undo',
                          key_text: (enable_keys ? ' (Ctrl+Z)' : null) })
                .button({ key: keys.redo,
                          text: 'Redo',
                          key_text: (enable_keys ? ' (Ctrl+Shift+Z)' : null) })
                .button({ key: keys.toggle_primary,
                          text: 'Toggle primary/secondary',
                          key_text: (enable_keys ? ' (P)' : null) })
                .button({ key: keys.cycle_primary,
                          text: 'Rotate reactant locations',
                          key_text: (enable_keys ? ' (C)' : null) })
                .button({ key: keys.select_all,
                          text: 'Select all',
                          key_text: (enable_keys ? ' (Ctrl+A)' : null) })
                .button({ key: keys.select_none,
                          text: 'Select none',
                          key_text: (enable_keys ? ' (Ctrl+Shift+A)' : null) })
                .button({ key: keys.invert_selection,
                          text: 'Invert selection' });
        } else {
            edit_menu.button({ key: keys.view_mode,
                               id: 'view-mode-menu-button',
                               text: 'View mode' });
        }

        // view dropdown
        var view_menu = ui.dropdown_menu(menu, 'View', true)
                .button({ key: keys.zoom_in,
                          text: 'Zoom in',
                          key_text: (enable_keys ? ' (Ctrl and +)' : null) })
                .button({ key: keys.zoom_out,
                          text: 'Zoom out',
                          key_text: (enable_keys ? ' (Ctrl and -)' : null) })
                .button({ key: keys.extent_nodes,
                          text: 'Zoom to nodes',
                          key_text: (enable_keys ? ' (Ctrl+0)' : null) })
                .button({ key: keys.extent_canvas,
                          text: 'Zoom to canvas',
                          key_text: (enable_keys ? ' (Ctrl+1)' : null) })
                .button({ key: keys.search,
                          text: 'Find',
                          key_text: (enable_keys ? ' (Ctrl+F)' : null) });
        if (enable_editing) {
            view_menu.button({ key: keys.toggle_beziers,
                               id: 'bezier-button',
                               text: 'Show control points',
                               key_text: (enable_keys ? ' (B)' : null) });
            map.callback_manager
                .set('toggle_beziers.button', function(on_off) {
                    menu.select('#bezier-button').select('.dropdown-button-text')
                        .text((on_off ? 'Hide' : 'Show') +
                              ' control points' +
                              (enable_keys ? ' (B)' : ''));
                });
        }
        view_menu.divider()
            .button({ key: keys.show_settings,
                      text: 'Settings',
                      key_text: (enable_keys ? ' (Ctrl+,)' : null) });

        // help
        menu.append('a')
            .attr('class', 'help-button')
            .attr('target', '#')
            .attr('href', 'https://escher.readthedocs.org')
            .text('?');

        var button_panel = button_selection.append('ul')
                .attr('class', 'nav nav-pills nav-stacked')
                .attr('id', 'button-panel');

        // buttons
        ui.individual_button(button_panel.append('li'),
                             { key: keys.zoom_in,
                               icon: 'glyphicon glyphicon-plus-sign',
                               classes: 'btn btn-default',
                               tooltip: 'Zoom in',
                               key_text: (enable_keys ? ' (Ctrl and +)' : null) });
        ui.individual_button(button_panel.append('li'),
                             { key: keys.zoom_out,
                               icon: 'glyphicon glyphicon-minus-sign',
                               classes: 'btn btn-default',
                               tooltip: 'Zoom out',
                               key_text: (enable_keys ? ' (Ctrl and -)' : null) });
        ui.individual_button(button_panel.append('li'),
                             { key: keys.extent_canvas,
                               icon: 'glyphicon glyphicon-resize-full',
                               classes: 'btn btn-default',
                               tooltip: 'Zoom to canvas',
                               key_text: (enable_keys ? ' (Ctrl+1)' : null) });

        // mode buttons
        if (enable_editing) {
            ui.radio_button_group(button_panel.append('li'))
                .button({ key: keys.zoom_mode,
                          id: 'zoom-mode-button',
                          icon: 'glyphicon glyphicon-move',
                          tooltip: 'Pan mode',
                          key_text: (enable_keys ? ' (Z)' : null) })
                .button({ key: keys.brush_mode,
                          id: 'brush-mode-button',
                          icon: 'glyphicon glyphicon-hand-up',
                          tooltip: 'Select mode',
                          key_text: (enable_keys ? ' (V)' : null) })
                .button({ key: keys.build_mode,
                          id: 'build-mode-button',
                          icon: 'glyphicon glyphicon-plus',
                          tooltip: 'Add reaction mode',
                          key_text: (enable_keys ? ' (N)' : null) })
                .button({ key: keys.rotate_mode,
                          id: 'rotate-mode-button',
                          icon: 'glyphicon glyphicon-repeat',
                          tooltip: 'Rotate mode',
                          key_text: (enable_keys ? ' (R)' : null) })
                .button({ key: keys.text_mode,
                          id: 'text-mode-button',
                          icon: 'glyphicon glyphicon-font',
                          tooltip: 'Text mode',
                          key_text: (enable_keys ? ' (T)' : null) });

            // arrow buttons
            this.direction_buttons = button_panel.append('li');
            var o = ui.button_group(this.direction_buttons)
                    .button({ key: keys.direction_arrow_left,
                              icon: 'glyphicon glyphicon-arrow-left',
                              tooltip: 'Direction arrow (←)' })
                    .button({ key: keys.direction_arrow_right,
                              icon: 'glyphicon glyphicon-arrow-right',
                              tooltip: 'Direction arrow (→)' })
                    .button({ key: keys.direction_arrow_up,
                              icon: 'glyphicon glyphicon-arrow-up',
                              tooltip: 'Direction arrow (↑)' })
                    .button({ key: keys.direction_arrow_down,
                              icon: 'glyphicon glyphicon-arrow-down',
                              tooltip: 'Direction arrow (↓)' });
        }

        // set up mode callbacks
        var select_button = function(id) {
            // toggle the button
            $(this.selection.node()).find('#' + id)
                .button('toggle');

            // menu buttons
            var ids = ['zoom-mode-menu-button', 'brush-mode-menu-button',
                       'build-mode-menu-button', 'rotate-mode-menu-button',
                       'view-mode-menu-button', 'text-mode-menu-button'];
            ids.forEach(function(this_id) {
                var b_id = this_id.replace('-menu', '');
                this.selection.select('#' + this_id)
                    .select('span')
                    .classed('glyphicon', b_id == id)
                    .classed('glyphicon-ok', b_id == id);
            }.bind(this));
        };
        this.callback_manager.set('zoom_mode', select_button.bind(this, 'zoom-mode-button'));
        this.callback_manager.set('brush_mode', select_button.bind(this, 'brush-mode-button'));
        this.callback_manager.set('build_mode', select_button.bind(this, 'build-mode-button'));
        this.callback_manager.set('rotate_mode', select_button.bind(this, 'rotate-mode-button'));
        this.callback_manager.set('view_mode', select_button.bind(this, 'view-mode-button'));
        this.callback_manager.set('text_mode', select_button.bind(this, 'text-mode-button'));

        // definitions
        function load_map_for_file(error, map_data) {
            /** Load a map. This reloads the whole builder.

             */

            if (error) {
                console.warn(error);
                this.map.set_status('Error loading map: ' + error, 2000);
                return;
            }

            try {
                check_map(map_data);
                this.load_map(map_data);
                this.map.set_status('Loaded map ' + map_data[0].map_name, 3000);
            } catch (e) {
                console.warn(e);
                this.map.set_status('Error loading map: ' + e, 2000);
            }

            // definitions
            function check_map(data) {
                /** Perform a quick check to make sure the map is mostly valid.

                 */

                if (!('map_id' in data[0] && 'reactions' in data[1] &&
                      'nodes' in data[1] && 'canvas' in data[1]))
                    throw new Error('Bad map data.');
            }
        }
        function load_model_for_file(error, data) {
            /** Load a cobra model. Redraws the whole map if the
             highlight_missing option is true.

             */
            if (error) {
                console.warn(error);
                this.map.set_status('Error loading model: ' + error, 2000);
                return;
            }

            try {
                this.load_model(data, true);
                this.build_input.toggle(false);
                if ('id' in data)
                    this.map.set_status('Loaded model ' + data.id, 3000);
                else
                    this.map.set_status('Loaded model (no model id)', 3000);
            } catch (e) {
                console.warn(e);
                this.map.set_status('Error loading model: ' + e, 2000);
            }

        }
        function load_reaction_data_for_file(error, data) {
            if (error) {
                console.warn(error);
                this.map.set_status('Could not parse file as JSON or CSV', 2000);
                return;
            }
            // turn off gene data
            if (data !== null)
                this.set_gene_data(null);

            this.set_reaction_data(data);
        }
        function load_metabolite_data_for_file(error, data) {
            if (error) {
                console.warn(error);
                this.map.set_status('Could not parse file as JSON or CSV', 2000);
                return;
            }
            this.set_metabolite_data(data);
        }
        function load_gene_data_for_file(error, data) {
            if (error) {
                console.warn(error);
                this.map.set_status('Could not parse file as JSON or CSV', 2000);
                return;
            }
            // turn off reaction data
            if (data !== null)
                this.set_reaction_data(null);

            // turn on gene_reaction_rules
            this.settings.set_conditional('show_gene_reaction_rules', true);

            this.set_gene_data(data);
        }
    }

    function _setup_simple_zoom_buttons(button_selection, keys) {
        var button_panel = button_selection.append('div')
                .attr('id', 'simple-button-panel');

        // buttons
        ui.individual_button(button_panel.append('div'),
                             { key: keys.zoom_in,
                               text: '+',
                               classes: 'simple-button',
                               tooltip: 'Zoom in (Ctrl +)' });
        ui.individual_button(button_panel.append('div'),
                             { key: keys.zoom_out,
                               text: '–',
                               classes: 'simple-button',
                               tooltip: 'Zoom out (Ctrl -)' });
        ui.individual_button(button_panel.append('div'),
                             { key: keys.extent_canvas,
                               text: '↔',
                               classes: 'simple-button',
                               tooltip: 'Zoom to canvas (Ctrl 1)' });

    }

    function _toggle_direction_buttons(on_off) {
        if (on_off===undefined)
            on_off = !this.direction_buttons.style('visibility')=='visible';
        this.direction_buttons.style('visibility', on_off ? 'visible' : 'hidden');
    }

    function _setup_status(selection, map) {
        var status_bar = selection.append('div').attr('id', 'status');
        map.callback_manager.set('set_status', function(status) {
            status_bar.text(status);
        });
        return status_bar;
    }

    function _setup_quick_jump(selection) {
        // function to load a map
        var load_fn = function(new_map_name, quick_jump_path, callback) {
            if (this.options.enable_editing && !this.options.never_ask_before_quit) {
                if (!(confirm(('You will lose any unsaved changes.\n\n' +
                               'Are you sure you want to switch maps?')))) {
                    if (callback) callback(false);
                    return;
                }
            }
            this.map.set_status('Loading map ' + new_map_name + ' ...');
            var url = utils.name_to_url(new_map_name, quick_jump_path);
            d3.json(url, function(error, data) {
                if (error) {
                    console.warn('Could not load data: ' + error);
                    if (callback) callback(false);
                }
                // run callback before load_map so the new map has the correct
                // quick_jump menu
                if (callback) callback(true);
                // now reload
                this.load_map(data);
                this.map.set_status('');
            }.bind(this));
        }.bind(this);

        // make the quick jump object
        this.quick_jump = QuickJump(selection, load_fn);
    }

    function _setup_modes(map, brush, zoom_container) {
        // set up zoom+pan and brush modes
        var was_enabled = {};
        map.callback_manager.set('start_rotation', function() {
            was_enabled.brush = brush.enabled;
            brush.toggle(false);
            was_enabled.zoom = zoom_container.zoom_on;
            zoom_container.toggle_zoom(false);
            was_enabled.selectable_mousedown = map.behavior.selectable_mousedown!=null;
            map.behavior.toggle_selectable_click(false);
            was_enabled.label_mousedown = map.behavior.label_mousedown!=null;
            map.behavior.toggle_label_mousedown(false);
        });
        map.callback_manager.set('end_rotation', function() {
            brush.toggle(was_enabled.brush);
            zoom_container.toggle_zoom(was_enabled.zoom);
            map.behavior.toggle_selectable_click(was_enabled.selectable_mousedown);
            map.behavior.toggle_label_mousedown(was_enabled.label_mousedown);
            was_enabled = {};
        });
    }

    function _get_keys(map, zoom_container, search_bar, settings_bar, enable_editing) {
        var keys = {
            save: { key: 83, modifiers: { control: true }, // ctrl-s
                    target: map,
                    fn: map.save },
            save_svg: { key: 83, modifiers: { control: true, shift: true },
                        target: map,
                        fn: map.save_svg },
            load: { key: 79, modifiers: { control: true }, // ctrl-o
                    fn: null }, // defined by button
            convert_map: { fn: this.map.convert_map.bind(this.map) },
            clear_map: { fn: this.map.clear_map.bind(this.map) },
            load_model: { key: 77, modifiers: { control: true }, // ctrl-m
                          fn: null }, // defined by button
            clear_model: { fn: this.load_model.bind(this, null, true) },
            load_reaction_data: { fn: null }, // defined by button
            clear_reaction_data: { target: this,
                                   fn: function() { this.set_reaction_data(null); }},
            load_metabolite_data: { fn: null }, // defined by button
            clear_metabolite_data: { target: this,
                                     fn: function() { this.set_metabolite_data(null); }},
            load_gene_data: { fn: null }, // defined by button
            clear_gene_data: { fn: function() {
                this.set_gene_data(null, true);
            }.bind(this)},
            zoom_in: { key: 187, modifiers: { control: true }, // ctrl +
                       target: zoom_container,
                       fn: zoom_container.zoom_in },
            zoom_out: { key: 189, modifiers: { control: true }, // ctrl -
                        target: zoom_container,
                        fn: zoom_container.zoom_out },
            extent_nodes: { key: 48, modifiers: { control: true }, // ctrl-0
                            target: map,
                            fn: map.zoom_extent_nodes },
            extent_canvas: { key: 49, modifiers: { control: true }, // ctrl-1
                             target: map,
                             fn: map.zoom_extent_canvas },
            search: { key: 70, modifiers: { control: true }, // ctrl-f
                      fn: search_bar.toggle.bind(search_bar, true) },
            view_mode: { fn: this.view_mode.bind(this),
                         ignore_with_input: true },
            show_settings: { key: 188, modifiers: { control: true }, // Ctrl ,
                             fn: settings_bar.toggle.bind(settings_bar) }
        };
        if (enable_editing) {
            utils.extend(keys, {
                build_mode: { key: 78, // n
                              fn: this.build_mode.bind(this),
                              ignore_with_input: true },
                zoom_mode: { key: 90, // z
                             fn: this.zoom_mode.bind(this),
                             ignore_with_input: true },
                brush_mode: { key: 86, // v
                              fn: this.brush_mode.bind(this),
                              ignore_with_input: true },
                rotate_mode: { key: 82, // r
                               fn: this.rotate_mode.bind(this),
                               ignore_with_input: true },
                text_mode: { key: 84, // t
                             fn: this.text_mode.bind(this),
                             ignore_with_input: true },
                toggle_beziers: { key: 66,
                                  target: map,
                                  fn: map.toggle_beziers,
                                  ignore_with_input: true  }, // b
                delete: { key: 8, modifiers: { control: true }, // ctrl-backspace
                          target: map,
                          fn: map.delete_selected,
                          ignore_with_input: true },
                delete_del: { key: 46, modifiers: { control: false }, // Del
                              target: map,
                              fn: map.delete_selected,
                              ignore_with_input: true },
                toggle_primary: { key: 80, // p
                                  target: map,
                                  fn: map.toggle_selected_node_primary,
                                  ignore_with_input: true },
                cycle_primary: { key: 67, // c
                                 target: map,
                                 fn: map.cycle_primary_node,
                                 ignore_with_input: true },
                direction_arrow_right: { key: 39, // right
                                         fn: this.build_input.direction_arrow.right
                                         .bind(this.build_input.direction_arrow),
                                         ignore_with_input: true },
                direction_arrow_down: { key: 40, // down
                                        fn: this.build_input.direction_arrow.down
                                        .bind(this.build_input.direction_arrow),
                                        ignore_with_input: true },
                direction_arrow_left: { key: 37, // left
                                        fn: this.build_input.direction_arrow.left
                                        .bind(this.build_input.direction_arrow),
                                        ignore_with_input: true },
                direction_arrow_up: { key: 38, // up
                                      fn: this.build_input.direction_arrow.up
                                      .bind(this.build_input.direction_arrow),
                                      ignore_with_input: true },
                undo: { key: 90, modifiers: { control: true },
                        target: map.undo_stack,
                        fn: map.undo_stack.undo },
                redo: { key: 90, modifiers: { control: true, shift: true },
                        target: map.undo_stack,
                        fn: map.undo_stack.redo },
                select_all: { key: 65, modifiers: { control: true }, // Ctrl Shift a
                              fn: map.select_all.bind(map) },
                select_none: { key: 65, modifiers: { control: true, shift: true }, // Ctrl Shift a
                               fn: map.select_none.bind(map) },
                invert_selection: { fn: map.invert_selection.bind(map) }
            });
        }
        return keys;
    }

    function _setup_confirm_before_exit() {
        /** Ask if the user wants to exit the page (to avoid unplanned refresh).

         */

        window.onbeforeunload = function(e) {
            // If we haven't been passed the event get the window.event
            e = e || window.event;
            return  (this.options.never_ask_before_quit ? null :
                     'You will lose any unsaved changes.');
        }.bind(this);
    }
});

define('DataMenu',["utils"], function(utils) {
    return function(options) {
        var o = utils.set_options(options, {
            selection: null,
            getdatafiles: null,
            datafiles: null,
            update_callback: null,
            target: null});

        if (o.selection===null)
            throw new Error('No selection provided for DataMenu');

        // setup dropdown menu
        // Append menu if it doesn't exist
        var menu = o.selection.select('.data-menu');
        if (menu.empty()) {
            menu = o.selection.append('div')
                .attr('class','data-menu');
        }
        var select_sel = menu.append('form')
                .append('select').attr('class','dropdown-menu');

        if (o.getdatafiles) {
            if (o.datafiles) {
                console.warn('DataMenu: getdatafiles option overrides datafiles');
            }
            d3.json(o.getdatafiles, function(error, d) {
                // returns json object:  { data: [file0, file1, ...] }
                if (error) {
                    return console.warn(error);
                } else {
                    load_with_files(o.target, d.data, select_sel, o.update_callback, o.selection);
                }
                return null;
            });
        } else if (o.datafiles) {
            load_with_files(o.target, o.datafiles, select_sel, o.update_callback, o.selection);
        } else {
            console.warn('DataMenu: No datafiles given');
        }

        return { update: update };

        // definitions
        function load_with_files(t, files, select_sel, update_callback, selection) {

            //when it changes
            select_sel.node().addEventListener("change", function() {
                load_datafile(t, this.value, selection, update_callback);
            }, false);

            var file = files[0];

            update(files, select_sel);
            load_datafile(t, file, selection, update_callback);
        };
        function load_datafile(t, this_file, selection, callback) {
            utils.load_the_file(t, this_file, function(error, data) {
                if (error) {
                    return console.warn(error);
                    selection.append('error loading');
                    o.data = null;
                } else {
                    o.data = data;
                    if (callback) {
                        callback(data);
                    }
                }
            });
        };

        function update(list, select_sel) {
            // update select element with d3 selection /select_sel/ to have options
            // given by /list/
            // TODO remove paths from file list
            select_sel.selectAll(".menu-option")
                .data(list)
                .enter()
                .append('option')
                .attr('value', function (d) { return d; } )
                .text(function (d) { return d; } );
            // TODO set value to default_filename_index
            select_sel.node().focus();
        };

        function get_data() {
            return o.data;
        };
    };
});

define('static',["utils"], function(utils) {
    return { load_map_model_from_url: load_map_model_from_url };
    
    function load_map_model_from_url(map_download_url, model_download_url,
                                     local_index, options, callback) {
        var opt = utils.parse_url_components(window, options),
            to_load = [],
            load_map = function (fn) { fn(null); },
            load_model = function (fn) { fn(null); };
        if (opt.map_name) {
            var map_path = _get_path('map', opt.map_name,
                                     local_index, map_download_url);
            if (map_path) {
                load_map = function (fn) {
                    d3.json(map_path, function(error, data) {
                        if (error) console.warn(error);
                        fn(data);
                    });
                };
            }
        }
        if (opt.model_name) {
            var model_path = _get_path('model', opt.model_name,
                                       local_index, model_download_url);
            if (model_path) {
                load_model = function (fn) {
                    d3.json(model_path, function(error, data) {
                        if (error) console.warn(error);
                        fn(data);
                    });
                };
            }
        }
        load_map(function(map_data) {
            load_model(function(model_data) {
                callback(map_data, model_data, options);
            });
        });
    }
    
    function _get_path(kind, name, index, url) {
        var match = index[kind+'s'].filter(function(x) {
            return x[kind+'_name'] == name;
        });
        if (match.length == 0)
            throw new Error('Bad ' + kind + ' ' + name);
        return (url + encodeURIComponent(match[0].organism) + 
                '/' + encodeURIComponent(match[0][kind+'_name'])) + '.json';
    }
});

define('main',['Builder', 'Map', 'Behavior', 'KeyManager', 'DataMenu', 'UndoStack', 'CobraModel', 'utils', 'SearchIndex', 'Settings', 'data_styles', 'ui', 'static'],
       function(bu, mp, bh, km, dm, us, cm, ut, si, se, ds, ui, st) {
           return { Builder: bu,
                    Map: mp,
                    Behavior: bh,
                    KeyManager: km,
                    DataMenu: dm,
                    UndoStack: us,
                    CobraModel: cm,
                    utils: ut,
                    SearchIndex: si,
                    Settings: se,
                    data_styles: ds,
                    ui: ui,
                    static: st };
       });

    //The modules for your project will be inlined above
    //this snippet. Ask almond to synchronously require the
    //module value for 'main' here and return it as the
    //value to use for the public API for the built file.
    return require('main');
}));