/
index.html
1403 lines (1236 loc) · 42.9 KB
/
index.html
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<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="utf-8" />
<!-- Latest compiled and minified CSS -->
<script src="https://code.jquery.com/jquery.js"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/underscore.js/1.8.3/underscore-min.js"></script>
<link
rel="stylesheet"
href="//maxcdn.bootstrapcdn.com/bootstrap/4.0.0/css/bootstrap.min.css"
integrity="sha384-Gn5384xqQ1aoWXA+058RXPxPg6fy4IWvTNh0E263XmFcJlSAwiGgFAW/dAiS6JXm"
crossorigin="anonymous"
/>
<link
href="//netdna.bootstrapcdn.com/font-awesome/4.0.3/css/font-awesome.css"
rel="stylesheet"
/>
<!-- Optional theme -->
<link
rel="stylesheet"
href="//stackpath.bootstrapcdn.com/bootswatch/4.1.1/spacelab/bootstrap.min.css"
/>
<!-- Latest compiled and minified JavaScript -->
<script
src="//cdnjs.cloudflare.com/ajax/libs/popper.js/1.12.9/umd/popper.min.js"
integrity="sha384-ApNbgh9B+Y1QKtv3Rn7W3mgPxhU9K/ScQsAP7hUibX39j7fakFPskvXusvfa0b4Q"
crossorigin="anonymous"
></script>
<script
src="//maxcdn.bootstrapcdn.com/bootstrap/4.0.0/js/bootstrap.min.js"
integrity="sha384-JZR6Spejh4U02d8jOt6vLEHfe/JQGiRRSQQxSfFWpi1MquVdAyjUar5+76PVCmYl"
crossorigin="anonymous"
></script>
<!-- <meta name="viewport" content="width=device-width, initial-scale=1.0">-->
<script src="//d3js.org/d3.v6.js"></script>
<script src="/dist/phylotree.js"></script>
<link href="phylotree.css" rel="stylesheet" />
<style>
nav {
margin-bottom: 25px;
}
.fa-rotate-45 {
-webkit-transform: rotate(45deg);
-moz-transform: rotate(45deg);
-ms-transform: rotate(45deg);
-o-transform: rotate(45deg);
transform: rotate(45deg);
}
.fa-rotate-135 {
-webkit-transform: rotate(135deg);
-moz-transform: rotate(135deg);
-ms-transform: rotate(135deg);
-o-transform: rotate(135deg);
transform: rotate(135deg);
}
@media (max-width: 1075px) {
.container {
padding-top: 50px;
}
}
.btn {
height: 30px;
}
#toolbar {
display: flex;
justify-content: space-between;
width: 550px;
}
#controls {
position: fixed;
left: 5px;
}
</style>
</head>
<body>
<!--
###############################################################################################################################
-->
<nav class="navbar navbar-expand-lg navbar-light bg-light">
<a class="navbar-brand" href="#">phylotree.js</a>
<!-- Collect the nav links, forms, and other content for toggling -->
<div class="collapse navbar-collapse" id="bs-example-navbar-collapse-1">
<ul class="navbar-nav">
<li class="nav-item dropdown">
<a
href="#"
id="newick-dropdown"
class="nav-link dropdown-toggle"
role="button"
data-toggle="dropdown"
>Newick <b class="caret"></b
></a>
<div class="dropdown-menu">
<a
class="dropdown-item"
href="#"
data-toggle="modal"
data-target="#newick_modal"
>Input Text</a
>
<div class="dropdown-item">
<input id="newick_url" name="newick_url" type="url" placeholder="http://www.example.com">
<button id="newick_url_btn">Get</button>
</div>
<a class="dropdown-item" href="#"
><input type="file" id="newick_file"
/></a>
<div class="dropdown-divider"></div>
<a
class="dropdown-item"
href="#"
data-toggle="modal"
data-target="#newick_export_modal"
>Export</a
>
</div>
</li>
</ul>
<ul class="nav navbar-nav mx-auto">
<li class="nav-item dropdown">
<a
class="nav-link dropdown-toggle"
href="#"
id="navbarDropdown"
role="button"
data-toggle="dropdown"
aria-haspopup="true"
aria-expanded="false"
>
Tag
</a>
<div
class="dropdown-menu"
aria-labelledby="navbarDropdown"
id="selection_name_dropdown"
>
<a id="selection_new" class="dropdown-item" href="#"
>New selection set</a
>
<a id="selection_delete" class="dropdown-item" href="#"
>Delete selection set</a
>
<a id="selection_rename" class="dropdown-item" href="#"
>Rename selection set</a
>
<div class="dropdown-divider"></div>
</div>
</li>
<li>
<form class="form-inline my-2 my-lg-0">
<input
type="text"
id="selection_name_box"
class="form-control mr-sm-2"
value="Foreground"
disabled
size="40"
/>
</form>
</li>
<li id="save_selection_name" style="display:none;" class="my-auto">
<a href="#"
><button id="cancel_selection_button" class="btn btn-info btn-sm">
Cancel
</button></a
>
<a href="#"
><button id="save_selection_button" class="btn btn-info btn-sm">
Save
</button></a
>
</li>
<li class="nav-item dropdown">
<a
class="nav-link dropdown-toggle"
href="#"
id="navbarDropdown"
role="button"
data-toggle="dropdown"
aria-haspopup="true"
aria-expanded="false"
>
Selection
</a>
<div class="dropdown-menu" aria-labelledby="navbarDropdown">
<a id="filter_add" class="dropdown-item" href="#"
>Add filtered nodes to selection</a
>
<a id="filter_remove" class="dropdown-item" href="#"
>Select all but filtered nodes</a
>
<div class="dropdown-divider"></div>
<a id="select_all" class="dropdown-item" href="#">Select all</a>
<a id="select_all_internal" class="dropdown-item" href="#"
>Select all internal nodes</a
>
<a id="select_all_leaves" class="dropdown-item" href="#"
>Select all leaf nodes</a
>
<a id="clear_internal" class="dropdown-item" href="#"
>Clear all internal nodes</a
>
<a id="clear_leaves" class="dropdown-item" href="#"
>Clear all leaves</a
>
<a id="select_none" class="dropdown-item" href="#"
>Clear selection</a
>
<div class="dropdown-divider"></div>
<a id="mp_label" class="dropdown-item" href="#"
>Label internal nodes using maximum parsimony</a
>
<a id="and_label" class="dropdown-item" href="#"
>Label internal nodes using conjunction (AND)</a
>
<a id="or_label" class="dropdown-item" href="#"
>Label internal nodes using disjunction (OR)</a
>
</div>
</li>
</ul>
<ul class="navbar-nav ml-auto">
<li>
<form class="form-inline my-2 my-lg-0">
<input
type="text"
id="branch_filter"
class="form-control mr-sm-2"
placeholder="Filter branches on"
onkeypress="return event.keyCode != 13"
/>
</form>
</li>
</ul>
</div>
<!-- /.container-fluid -->
</nav>
<div class="modal" id="newick_modal" role="dialog">
<div class="modal-dialog" role="document">
<div class="modal-content">
<div class="modal-header">
<h4 class="modal-title">Newick string to render</h4>
<button
type="button"
class="close"
data-dismiss="modal"
aria-hidden="true"
>
×
</button>
</div>
<div class="modal-body" id="newick_body">
<textarea
id="nwk_spec"
autofocus="true"
placeholder=""
style="width: 100%; height: 100%"
rows="20"
selectionStart="1"
selectionEnd="1000"
>
(a : 0.1, (b : 0.11, (c : 0.12, d : 0.13) : 0.14) : 0.15)</textarea
>
</div>
<div class="modal-footer">
<button
type="button"
class="btn btn-primary btn-sm"
id="validate_newick"
>
Display this tree
</button>
</div>
</div>
<!-- /.modal-content -->
</div>
<!-- /.modal-dialog -->
</div>
<!-- /.modal -->
<div class="modal" id="newick_export_modal" role="dialog">
<div class="modal-dialog" role="document">
<div class="modal-content">
<div class="modal-body" id="newick_body">
<textarea
id="nwk_export_spec"
autofocus="true"
placeholder=""
style="width: 100%; height: 100%"
rows="20"
></textarea>
</div>
<div class="modal-footer">
<button
type="button"
class="btn btn-primary btn-sm"
data-dismiss="modal"
>
Close
</button>
</div>
</div>
<!-- /.modal-content -->
</div>
<!-- /.modal-dialog -->
</div>
<!-- /.modal -->
<div class="modal" id="progress_model">
<div class="modal-dialog">
<div class="modal-content">
<div class="modal-header">
<button
type="button"
class="close"
data-dismiss="modal"
aria-hidden="true"
>
×
</button>
<h4 class="modal-title">Task in progress</h4>
</div>
<div class="modal-body" id="progress_model_body"></div>
</div>
<!-- /.modal-content -->
</div>
<!-- /.modal-dialog -->
</div>
<!-- /.modal -->
<div id="controls">
<form id="controls_form" style="width:200px;"></form>
</div>
<div class="container" id="main_display">
<div class="row">
<div class="col-md-8">
<div class="btn-toolbar" role="toolbar" id="toolbar">
<div class="btn-group">
<button
type="button"
class="btn btn-light btn-sm"
data-direction="vertical"
data-amount="1"
title="Expand vertical spacing"
>
<i class="fa fa-arrows-v"></i>
</button>
<button
type="button"
class="btn btn-light btn-sm"
data-direction="vertical"
data-amount="-1"
title="Compress vertical spacing"
>
<i class="fa fa-compress fa-rotate-135"></i>
</button>
<button
type="button"
class="btn btn-light btn-sm"
data-direction="horizontal"
data-amount="1"
title="Expand horizonal spacing"
>
<i class="fa fa-arrows-h"></i>
</button>
<button
type="button"
class="btn btn-light btn-sm"
data-direction="horizontal"
data-amount="-1"
title="Compress horizonal spacing"
>
<i class="fa fa-compress fa-rotate-45"></i>
</button>
<button
type="button"
class="btn btn-light btn-sm"
id="sort_ascending"
title="Sort deepest clades to the bototm"
>
<i class="fa fa-sort-amount-asc"></i>
</button>
<button
type="button"
class="btn btn-light btn-sm"
id="sort_descending"
title="Sort deepsest clades to the top"
>
<i class="fa fa-sort-amount-desc"></i>
</button>
<button
type="button"
class="btn btn-light btn-sm"
id="sort_original"
title="Restore original order"
>
<i class="fa fa-sort"></i>
</button>
<button
type="button"
class="btn btn-light btn-sm"
id="save_image"
title="Save image"
>
<i class="fa fa-picture-o"></i>
</button>
</div>
<div class="btn-group" role="group">
<button
class="btn btn-light btn-sm active phylotree-layout-mode"
data-mode="linear"
>
Linear
</button>
<button
class="btn btn-light btn-sm phylotree-layout-mode"
data-mode="radial"
>
Radial
</button>
</div>
<div class="btn-group" role="group">
<button
class="btn btn-light btn-sm active phylotree-align-toggler"
data-align="left"
>
<i class="fa fa-align-left"></i>
</button>
<button
class="btn btn-light btn-sm phylotree-align-toggler"
data-align="right"
>
<i class="fa fa-align-right"></i>
</button>
</div>
</div>
</div>
<div class="col-md-4">
<label class="pull-right"
><b>Selected</b>
<span class="badge badge-secondary" id="selected_branch_counter"
>0</span
>
<b>branches with current label</b></label
>
</div>
</div>
<div class="row">
<div class="col-md-12">
<div id="tree_container" class="tree-widget"></div>
</div>
</div>
</div>
<!--
###############################################################################################################################
-->
<script>
var phylotree_extensions = new Object();
$("#newick_export_modal").on("show.bs.modal", function(e) {
$('textarea[id$="nwk_export_spec"]').val(
tree.getNewick(function(node) {
var tags = [];
selection_set.forEach(function(d) {
if (node[d]) {
tags.push(d);
}
});
if (tags.length) {
return "{" + tags.join(",") + "}";
}
return "";
})
);
});
$("#newick_file").on("change", function(e) {
var files = e.target.files; // FileList object
if (files.length == 1) {
var f = files[0];
var reader = new FileReader();
reader.onload = function(e) {
var res = e.target.result;
var warning_div = d3
.select("#main_display")
.insert("div", ":first-child");
tree = new phylotree.phylotree(res);
global_tree = tree;
if (!tree["json"]) {
warning_div
.attr("class", "alert alert-danger alert-dismissable")
.html(
"<strong>Newick parser error for file " +
f.name +
": </strong> In file " +
res["error"]
);
} else {
tree.render({
container: "#tree_container",
"draw-size-bubbles": false,
"left-right-spacing": "fixed-step",
"node-styler": node_colorizer,
"edge-styler": edge_colorizer
});
tree.display.selectionLabel(current_selection_name);
tree.display.countHandler(count => {
$("#selected_branch_counter").text(function(d) {
return count[current_selection_name];
});
});
// Get selection set names from parsed newick
if (tree.parsed_tags.length) {
selection_set = tree.parsed_tags;
}
update_selection_names();
$("#newick_modal").modal("hide");
$(tree.display.container).empty();
$(tree.display.container).html(tree.display.show());
}
};
$("#newick-dropdown").dropdown("toggle");
reader.readAsText(f);
}
});
function getNewickFromURL(url) {
d3.text(url).then(res => {
var warning_div = d3
.select("#main_display")
.insert("div", ":first-child");
tree = new phylotree.phylotree(res);
global_tree = tree;
if (!tree["json"]) {
warning_div
.attr("class", "alert alert-danger alert-dismissable")
.html(
"<strong>Newick parser error for file " +
f.name +
": </strong> In file " +
res["error"]
);
} else {
tree.render({
container: "#tree_container",
"draw-size-bubbles": false,
"left-right-spacing": "fixed-step",
"node-styler": node_colorizer,
"edge-styler": edge_colorizer
});
tree.display.selectionLabel(current_selection_name);
tree.display.countHandler(count => {
$("#selected_branch_counter").text(function(d) {
return count[current_selection_name];
});
});
// Get selection set names from parsed newick
if (tree.parsed_tags.length) {
selection_set = tree.parsed_tags;
}
update_selection_names();
$("#newick_modal").modal("hide");
$(tree.display.container).empty();
$(tree.display.container).html(tree.display.show());
}
});
}
$("#newick_url_btn").on("click", function(e) {
let url = $("#newick_url").val();
getNewickFromURL(url);
$("#newick-dropdown").dropdown("toggle");
});
$("#newick_url").on("change", function(e) {
let url = $(e.target).val();
getNewickFromURL(url);
$("#newick-dropdown").dropdown("toggle");
});
$("#display_tree").on("click", function(e) {
tree.options({ branches: "straight" }, true);
});
$("#mp_label").on("click", function(e) {
tree.maxParsimony(true, "Foreground");
});
$("[data-direction]").on("click", function(e) {
var which_function =
$(this).data("direction") == "vertical"
? tree.display.spacing_x.bind(tree.display)
: tree.display.spacing_y.bind(tree.display);
which_function(which_function() + +$(this).data("amount")).update();
});
$(".phylotree-layout-mode").on("click", function(e) {
if (tree.display.radial() != ($(this).data("mode") == "radial")) {
$(".phylotree-layout-mode").toggleClass("active");
tree.display.radial(!tree.display.radial()).update();
}
});
$("#toggle_animation").on("click", function(e) {
var current_mode = $(this).hasClass("active");
$(this).toggleClass("active");
tree.options({ transitions: !current_mode });
});
$(".phylotree-align-toggler").on("click", function(e) {
var button_align = $(this).data("align");
var tree_align = tree.display.options.alignTips;
if (tree_align != button_align) {
tree.display.alignTips(button_align == "right");
$(".phylotree-align-toggler").toggleClass("active");
tree.display.update();
}
});
function sort_nodes(asc) {
tree.resortChildren(function(a, b) {
return (b.height - a.height || b.value - a.value) * (asc ? 1 : -1);
});
}
$("#sort_original").on("click", function(e) {
tree.resortChildren(function(a, b) {
return a["original_child_order"] - b["original_child_order"];
});
});
$("#sort_ascending").on("click", function(e) {
sort_nodes(true);
tree.display.update();
});
$("#sort_descending").on("click", function(e) {
sort_nodes(false);
tree.display.update();
});
$("#and_label").on("click", function(e) {
tree.display.internalLabel(function(d) {
return d.reduce(function(prev, curr) {
return curr[current_selection_name] && prev;
}, true);
}, true);
});
$("#or_label").on("click", function(e) {
tree.display.internalLabel(function(d) {
return d.reduce(function(prev, curr) {
return curr[current_selection_name] || prev;
}, false);
}, true);
});
$("#filter_add").on("click", function(e) {
tree.display
.modifySelection(function(d) {
return d.tag || d[current_selection_name];
})
.modifySelection(
function(d) {
return false;
},
"tag",
false,
false
);
});
$("#filter_remove").on("click", function(e) {
tree.display.modifySelection(function(d) {
return !d.tag;
});
});
$("#select_all").on("click", function(e) {
tree.display.modifySelection(function(d) {
return true;
});
});
$("#select_all_internal").on("click", function(e) {
tree.display.modifySelection(function(d) {
return !tree.isLeafNode(d.target);
});
});
$("#select_all_leaves").on("click", function(e) {
tree.display.modifySelection(function(d) {
return tree.isLeafNode(d.target);
});
});
$("#select_none").on("click", function(e) {
tree.display.modifySelection(function(d) {
return false;
});
});
$("#clear_internal").on("click", function(e) {
tree.display.modifySelection(function(d) {
return tree.isLeafNode(d.target)
? d.target[current_selection_name]
: false;
});
});
$("#clear_leaves").on("click", function(e) {
tree.display.modifySelection(function(d) {
return !tree.isLeafNode(d.target)
? d.target[current_selection_name]
: false;
});
});
$("#display_dengrogram").on("click", function(e) {
tree.display.options({ branches: "step" }, true);
});
$("#branch_filter").on("input propertychange", function(e) {
var filter_value = $(this).val();
var rx = new RegExp(filter_value, "i");
tree.display.modifySelection(n => {
if (!n.target.data.name) {
return false;
}
m = n.target.data.name.search(rx);
return filter_value.length && m != -1;
}, "tag");
});
$("#validate_newick").on("click", function(e) {
let test_string = $('textarea[id$="nwk_spec"]').val();
tree = new phylotree.phylotree(test_string);
global_tree = tree;
if (!tree["json"]) {
var warning_div = d3
.select("#newick_body")
.selectAll("div .alert-danger")
.data([res["error"]]);
warning_div.enter().append("div");
warning_div
.html(function(d) {
return d;
})
.attr("class", "alert-danger");
} else {
tree.render({
container: "#tree_container",
"draw-size-bubbles": false,
"node-styler": node_colorizer,
zoom: false,
"edge-styler": edge_colorizer
});
tree.display.selectionLabel(current_selection_name);
tree.display.countHandler(count => {
$("#selected_branch_counter").text(function(d) {
return count[current_selection_name];
});
});
// Get selection set names from parsed newick
if (tree.parsed_tags.length) {
selection_set = tree.parsed_tags;
}
update_selection_names();
$("#newick_modal").modal("hide");
$(tree.display.container).html(tree.display.show());
}
});
function default_tree_settings() {
tree = phylotree();
tree.branchLength(null);
tree.branchName(null);
tree.display.radial(false).separation(function(a, b) {
return 0;
});
}
function node_colorizer(element, data) {
try {
var count_class = 0;
selection_set.forEach(function(d, i) {
if (data[d]) {
count_class++;
element.style(
"fill",
color_scheme(i),
i == current_selection_id ? "important" : null
);
}
});
if (count_class > 1) {
} else {
if (count_class == 0) {
element.style("fill", null);
}
}
} catch (e) {}
}
function edge_colorizer(element, data) {
try {
var count_class = 0;
selection_set.forEach(function(d, i) {
if (data[d]) {
count_class++;
element.style(
"stroke",
color_scheme(i),
i == current_selection_id ? "important" : null
);
}
});
if (count_class > 1) {
element.classed("branch-multiple", true);
} else if (count_class == 0) {
element.style("stroke", null).classed("branch-multiple", false);
}
} catch (e) {}
}
var valid_id = new RegExp("^[\\w]+$");
$("#selection_name_box").on("input propertychange", function(e) {
var name = $(this).val();
var accept_name =
selection_set.indexOf(name) < 0 && valid_id.exec(name);
d3.select("#save_selection_button").classed(
"disabled",
accept_name ? null : true
);
});
$("#selection_rename").on("click", function(e) {
d3.select("#save_selection_button")
.classed("disabled", true)
.on("click", function(e) {
// save selection handler
var old_selection_name = current_selection_name;
selection_set[current_selection_id] = current_selection_name = $(
"#selection_name_box"
).val();
if (old_selection_name != current_selection_name) {
tree.update_key_name(old_selection_name, current_selection_name);
update_selection_names(current_selection_id);
}
send_click_event_to_menu_objects(
new CustomEvent(selection_menu_element_action, {
detail: ["save", this]
})
);
});
d3.select("#cancel_selection_button")
.classed("disabled", false)
.on("click", function(e) {
// save selection handler
$("#selection_name_box").val(current_selection_name);
send_click_event_to_menu_objects(
new CustomEvent(selection_menu_element_action, {
detail: ["cancel", this]
})
);
});
send_click_event_to_menu_objects(
new CustomEvent(selection_menu_element_action, {
detail: ["rename", this]
})
);
e.preventDefault();
});
$("#selection_delete").on("click", function(e) {
tree.display.updateKeyName(selection_set[current_selection_id], null);
selection_set.splice(current_selection_id, 1);
if (current_selection_id > 0) {
current_selection_id--;
}
current_selection_name = selection_set[current_selection_id];
update_selection_names(current_selection_id);
$("#selection_name_box").val(current_selection_name);
send_click_event_to_menu_objects(
new CustomEvent(selection_menu_element_action, {
detail: ["save", this]
})
);
e.preventDefault();
});
$("#selection_new").on("click", function(e) {
d3.select("#save_selection_button")
.classed("disabled", true)
.on("click", function(e) {
// save selection handler
current_selection_name = $("#selection_name_box").val();
current_selection_id = selection_set.length;
selection_set.push(current_selection_name);
update_selection_names(current_selection_id);
send_click_event_to_menu_objects(
new CustomEvent(selection_menu_element_action, {
detail: ["save", this]
})
);
});
d3.select("#cancel_selection_button")
.classed("disabled", false)
.on("click", function(e) {
// save selection handler
$("#selection_name_box").val(current_selection_name);
send_click_event_to_menu_objects(
new CustomEvent(selection_menu_element_action, {
detail: ["cancel", this]
})
);
});
send_click_event_to_menu_objects(
new CustomEvent(selection_menu_element_action, {
detail: ["new", this]
})