bam_tview_curses.c

/*  bam_tview_curses.c -- curses tview implementation.

    Copyright (C) 2008-2015, 2019, 2021 Genome Research Ltd.
    Portions copyright (C) 2013 Pierre Lindenbaum, Institut du Thorax, INSERM U1087, Université de Nantes.

    Author: Heng Li <lh3@sanger.ac.uk>

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:

The above copyright notices and this permission notice shall be included in
all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
DEALINGS IN THE SOFTWARE.  */

#include <config.h>
#include <stdbool.h>

#include "bam_tview.h"

#ifdef HAVE_CURSES

#if defined HAVE_NCURSESW_CURSES_H
#include <ncursesw/curses.h>
#elif defined HAVE_NCURSESW_H
#include <ncursesw.h>
#elif defined HAVE_NCURSES_CURSES_H
#include <ncurses/curses.h>
#elif defined HAVE_NCURSES_H
#include <ncurses.h>
#elif defined HAVE_CURSES_H
#include <curses.h>
#else
// Have the library, but no header file
#warning "Curses header file not found; tview with curses is disabled."
#undef HAVE_CURSES
#endif
#else
#warning "No curses library is available; tview with curses is disabled."
#endif

#ifdef HAVE_CURSES

typedef struct CursesTview {
    tview_t view;
    WINDOW *wgoto, *whelp, *wlistref;
} curses_tview_t;

#define FROM_TV(ptr) ((curses_tview_t*)ptr)

static void curses_destroy(tview_t* base) {
    curses_tview_t* tv=(curses_tview_t*)base;

    delwin(tv->wgoto); delwin(tv->whelp); delwin(tv->wlistref);
    endwin();

    base_tv_destroy(base);

    free(tv);
}

/*
 void (*my_mvprintw)(struct AbstractTview* ,int,int,const char*,...);
    void (*my_)(struct AbstractTview*,int,int,int);
    void (*my_attron)(struct AbstractTview*,int);
    void (*my_attroff)(struct AbstractTview*,int);
    void (*my_clear)(struct AbstractTview*);
    int (*my_colorpair)(struct AbstractTview*,int);
*/

static void curses_mvprintw(struct AbstractTview* tv,int y ,int x,const char* fmt,...) {
    va_list argptr;
    va_start(argptr, fmt);
    if (wmove(stdscr, y, x) != ERR)
        vw_printw(stdscr, fmt, argptr);
    va_end(argptr);
}

static void curses_mvaddch(struct AbstractTview* tv,int y,int x,int ch) {
    mvaddch(y,x,ch);
}

static void curses_attron(struct AbstractTview* tv,int flag) {
    attron(flag);
}

static void curses_attroff(struct AbstractTview* tv,int flag) {
    attroff(flag);
}

static void curses_clear(struct AbstractTview* tv) {
    clear();
}

static int curses_init_colors(int inverse)
{
    if (inverse) {
        init_pair(1, COLOR_WHITE, COLOR_BLUE);
        init_pair(2, COLOR_BLACK, COLOR_GREEN);
        init_pair(3, COLOR_BLACK, COLOR_YELLOW);
        init_pair(4, COLOR_BLACK, COLOR_WHITE);
        init_pair(5, COLOR_BLACK, COLOR_GREEN);
        init_pair(6, COLOR_BLACK, COLOR_CYAN);
        init_pair(7, COLOR_WHITE, COLOR_MAGENTA);
        init_pair(8, COLOR_WHITE, COLOR_RED);
        init_pair(9, COLOR_WHITE, COLOR_BLUE);
    } else {
        init_pair(1, COLOR_BLUE, COLOR_BLACK);
        init_pair(2, COLOR_GREEN, COLOR_BLACK);
        init_pair(3, COLOR_YELLOW, COLOR_BLACK);
        init_pair(4, COLOR_WHITE, COLOR_BLACK);
        init_pair(5, COLOR_GREEN, COLOR_BLACK);
        init_pair(6, COLOR_CYAN, COLOR_BLACK);
        init_pair(7, COLOR_MAGENTA, COLOR_BLACK);
        init_pair(8, COLOR_RED, COLOR_BLACK);
        init_pair(9, COLOR_BLUE, COLOR_BLACK);
    }

    return 0;
}

static int curses_colorpair(struct AbstractTview* tv,int flag) {
    return COLOR_PAIR(flag);
}

static int curses_drawaln(struct AbstractTview* tv, int tid, hts_pos_t pos) {
    return base_draw_aln(tv,  tid, pos);
}

static int tv_win_goto_get_completions(curses_tview_t *tv, char *str,
                                       int **matches, int *matches_size) {


    char **references = tv->view.header->target_name;
    uint32_t *references_lengths = tv->view.header->target_len;
    int num_references = tv->view.header->n_targets;
    int i, num_matches = 0;
    char new_str[TV_MAX_GOTO+1] = {'\0'};
    for (i = 0; i < TV_MAX_GOTO; i++) {
        if (str[i] == ':' || str[i] == '\0') break;
        new_str[i] = str[i];
    }

    size_t l_str = strlen(new_str);
    bool is_different = l_str != strlen(str);

    for (i = 0; i < num_references; i++) {
        char *ref = references[i];
        uint32_t *len = references_lengths + i;
        if (ref == NULL || len == NULL) return -1;
        if (strncmp(ref, new_str, l_str) == 0) {

            // Special case handling if the reference is already selected
            if (is_different && strlen(ref) == l_str) {
                num_matches = 1;
                if (hts_resize(int, num_matches, matches_size, matches, 0) == -1)
                    return -1;
                (*matches)[num_matches-1] = i;

                break;
            } else if (!is_different) {
                num_matches++;

                if (hts_resize(int, num_matches, matches_size, matches, 0) == -1)
                    return -1;

                (*matches)[num_matches-1] = i;

            }
        }
    }

    return num_matches;
}

static void tv_win_listref(curses_tview_t *tv, int* matches, int num_matches,
                           int tab_index, int upper_bound) {
    int i;
    char str[TV_MAX_GOTO+1];
    char **refs = tv->view.header->target_name;
    uint32_t *lengths = tv->view.header->target_len;

    wclear(tv->wlistref);
    wborder(tv->wlistref, '|', '|', '-', '-', '+', '+', '+', '+');

    if (num_matches == 0) {
        mvwprintw(tv->wlistref, 3, 18, "No references found.");
    }

    int offset = upper_bound < TV_MAX_LISTREF ? 0 : upper_bound - TV_MAX_LISTREF;
    int max = num_matches < TV_MAX_LISTREF ? num_matches : TV_MAX_LISTREF;
    for (i = 0; i < max; i++) {
        uint32_t match_idx = matches[i+offset];
        char *ref = refs[match_idx];
        uint32_t len = lengths[match_idx];

        if (tab_index == i+offset) {
            mvwprintw(tv->wlistref, i+1, 1, ">");
        }
        snprintf(str, TV_MAX_GOTO, "%s  length: %d", ref, len);
        mvwprintw(tv->wlistref, i+1, 2, "%s", str);
   }

    if (upper_bound < num_matches) {
        mvwprintw(tv->wlistref, TV_MAX_LISTREF-1, TV_MAX_GOTO+8, "|");
        mvwprintw(tv->wlistref, TV_MAX_LISTREF,   TV_MAX_GOTO+8, "v");
    }
    if (offset > 0) {
        mvwprintw(tv->wlistref, 1, TV_MAX_GOTO+8, "^");
        mvwprintw(tv->wlistref, 2, TV_MAX_GOTO+8, "|");
    }

    wrefresh(tv->wlistref);
}

static void tv_win_goto(curses_tview_t *tv, int *tid, hts_pos_t *pos) {
    char str[TV_MAX_GOTO+1], *p;
    int *matches = NULL;
    int i, l, tab_index = 0, num_matches = 0, matches_size = 0, upper_bound = TV_MAX_LISTREF;
    bool is_tabbing = false;
    tview_t *base=(tview_t*)tv;
    str[0] = '\0';
    wclear(tv->wgoto);
    wborder(tv->wgoto, '|', '|', '-', '-', '+', '+', '+', '+');

    if (tv->view.header->n_targets > *tid) {
        char *ref = tv->view.header->target_name[*tid];
        snprintf(str, TV_MAX_GOTO+1, "%s:%"PRIhts_pos, ref, tv->view.left_pos+1);
    }
    mvwprintw(tv->wgoto, 1, 2, "Goto: %s", str);
    l = strlen(str);

    num_matches = tv_win_goto_get_completions(tv, str, &matches, &matches_size);
    tv_win_listref(tv, matches, num_matches, tab_index, upper_bound);

    for (;;) {
        int invalid = 0;
        int c = wgetch(tv->wgoto);
        wrefresh(tv->wgoto);
        if (c == KEY_BACKSPACE || c == '\010' || c == '\177') {
            if(l > 0) str[--l] = '\0';
        } else if (c == KEY_ENTER || c == '\012' || c == '\015') {
            int _tid = -1;
            hts_pos_t _beg, _end;
            if (str[0] == '=') {
                _beg = strtoll(str+1, &p, 10) - 1;
                if (_beg > 0) {
                    *pos = _beg;
                    free(matches);
                    return;
                }
            } else {
                if (sam_parse_region(base->header, str, &_tid, &_beg, &_end, 0) && _tid >= 0) {
                    *tid = _tid; *pos = _beg;
                    free(matches);
                    return;
                }
            }

            // If we get here, the region string is invalid
            invalid = 1;
        } else if (c == KEY_STAB || c == 9 || c == KEY_UP || c == KEY_DOWN || c == KEY_BTAB) {
            if (is_tabbing) {

                if (c == KEY_UP || c == KEY_BTAB) {
                    tab_index--;
                } else {
                    tab_index++;
                }

                if (tab_index >= num_matches) {
                    tab_index = 0;
                    upper_bound = TV_MAX_LISTREF;
                } else if (tab_index < 0) {
                    tab_index = num_matches == 0 ? 0 : num_matches-1;
                    upper_bound = num_matches == 0 ? TV_MAX_LISTREF : num_matches-1;
                }

                if (num_matches > 0) {
                    if (tab_index >= upper_bound) {
                        upper_bound++;
                    }
                    if (tab_index < upper_bound-TV_MAX_LISTREF) {
                        upper_bound--;
                    }
                }
            } else {
                is_tabbing = true;
            }

            if (num_matches > 0) {
                snprintf(str, TV_MAX_GOTO+1, "%s:", tv->view.header->target_name[matches[tab_index]]);
                l = strlen(str);
            }
        } else if (isgraph(c)) {
            if (l < TV_MAX_GOTO) str[l++] = c;
        } else if (c == '\027') l = 0;
        else if (c == '\033') {
            free(matches);
            return;
        }
        str[l] = '\0';
        for (i = 0; i < TV_MAX_GOTO; ++i) mvwaddch(tv->wgoto, 1, 8 + i, ' ');
        if (invalid) mvwprintw(tv->wgoto, 1, TV_MAX_GOTO - 1, "[Invalid]");
        mvwprintw(tv->wgoto, 1, 8, "%s", str);

        // regenerate completion list if not navigating through them
        if (c != KEY_STAB && c != 9 && c != KEY_DOWN && c != KEY_UP && c!= KEY_BTAB) {
            tab_index = 0;
            upper_bound = TV_MAX_LISTREF;
            num_matches = tv_win_goto_get_completions(tv, str, &matches, &matches_size);
        }

        tv_win_listref(tv, matches, num_matches, tab_index, upper_bound);

    }

    free(matches);
}

static void tv_win_help(curses_tview_t *tv) {
    int r = 1;
    WINDOW *win = tv->whelp;
    wborder(win, '|', '|', '-', '-', '+', '+', '+', '+');
    mvwprintw(win, r++, 2, "        -=-    Help    -=- ");
    r++;
    mvwprintw(win, r++, 2, "?          This window");
    mvwprintw(win, r++, 2, "Arrows     Small scroll movement");
    mvwprintw(win, r++, 2, "h,j,k,l    Small scroll movement");
    mvwprintw(win, r++, 2, "H,J,K,L    Large scroll movement");
    mvwprintw(win, r++, 2, "ctrl-H     Scroll 1k left");
    mvwprintw(win, r++, 2, "ctrl-L     Scroll 1k right");
    mvwprintw(win, r++, 2, "space      Scroll one screen");
    mvwprintw(win, r++, 2, "backspace  Scroll back one screen");
    mvwprintw(win, r++, 2, "g          Go to specific location");
    mvwprintw(win, r++, 2, "m          Color for mapping qual");
    mvwprintw(win, r++, 2, "n          Color for nucleotide");
    mvwprintw(win, r++, 2, "b          Color for base quality");
    mvwprintw(win, r++, 2, "c          Color for cs color");
    mvwprintw(win, r++, 2, "z          Color for cs qual");
    mvwprintw(win, r++, 2, ".          Toggle on/off dot view");
    mvwprintw(win, r++, 2, "s          Toggle on/off ref skip");
    mvwprintw(win, r++, 2, "r          Toggle on/off rd name");
    mvwprintw(win, r++, 2, "N          Turn on nt view");
    mvwprintw(win, r++, 2, "C          Turn on cs view");
    mvwprintw(win, r++, 2, "i          Toggle on/off ins");
    mvwprintw(win, r++, 2, "v          Inverse video");
    mvwprintw(win, r++, 2, "q          Exit");
    r++;
    mvwprintw(win, r++, 2, "Underline:      Secondary or orphan");
    mvwprintw(win, r++, 2, "Blue:    0-9    Green: 10-19");
    mvwprintw(win, r++, 2, "Yellow: 20-29   White: >=30");
    wrefresh(win);
    wgetch(win);
}

static int curses_underline(tview_t* tv) {
    return A_UNDERLINE;
}

static int curses_loop(tview_t* tv) {
    int tid;
    hts_pos_t pos;
    curses_tview_t *CTV=(curses_tview_t *)tv;
    tid = tv->curr_tid; pos = tv->left_pos;
    while (1) {
        int c = getch();
        switch (c) {
            case '?': tv_win_help(CTV); break;
            case '\033':
            case 'q': goto end_loop;
            case '/':
            case 'g': tv_win_goto(CTV, &tid, &pos); break;
            case 'm': tv->color_for = TV_COLOR_MAPQ; break;
            case 'b': tv->color_for = TV_COLOR_BASEQ; break;
            case 'n': tv->color_for = TV_COLOR_NUCL; break;
            case 'c': tv->color_for = TV_COLOR_COL; break;
            case 'z': tv->color_for = TV_COLOR_COLQ; break;
            case 'v': curses_init_colors(tv->inverse = !tv->inverse); break;
            case 's': tv->no_skip = !tv->no_skip; break;
            case 'r': tv->show_name = !tv->show_name; break;
            case KEY_LEFT:
            case 'h': --pos; break;
            case KEY_RIGHT:
            case 'l': ++pos; break;
            case KEY_SLEFT:
            case 'H': pos -= 20; break;
            case KEY_SRIGHT:
            case 'L': pos += 20; break;
            case '.': tv->is_dot = !tv->is_dot; break;
            case 'N': tv->base_for = TV_BASE_NUCL; break;
            case 'C': tv->base_for = TV_BASE_COLOR_SPACE; break;
            case 'i': tv->ins = !tv->ins; break;
            case '\010': pos -= 1000; break;
            case '\014': pos += 1000; break;
            case ' ': pos += tv->mcol; break;
            case KEY_UP:
            case 'j': --tv->row_shift; break;
            case 'J': tv->row_shift -= 20; break;
            case KEY_DOWN:
            case 'k': ++tv->row_shift; break;
            case 'K': tv->row_shift += 20; break;
            case KEY_BACKSPACE:
            case '\177': pos -= tv->mcol; break;
#ifdef KEY_RESIZE
            case KEY_RESIZE: getmaxyx(stdscr, tv->mrow, tv->mcol); break;
#endif
            default: continue;
        }
        if (pos < 0) pos = 0;
        if (tv->row_shift < 0) tv->row_shift = 0;
        tv->my_drawaln(tv, tid, pos);
    }
end_loop:
    return 0;
}

tview_t* curses_tv_init(const char *fn, const char *fn_fa, const char *samples,
                        const htsFormat *fmt) {
    curses_tview_t *tv = (curses_tview_t*)calloc(1, sizeof(curses_tview_t));
    tview_t* base=(tview_t*)tv;
    if(tv==0) {
        fprintf(stderr,"Calloc failed\n");
        return 0;
    }

    base_tv_init(base,fn,fn_fa,NULL,samples,fmt);
    /* initialize callbacks */
#define SET_CALLBACK(fun) base->my_##fun=curses_##fun;
    SET_CALLBACK(destroy);
    SET_CALLBACK(mvprintw);
    SET_CALLBACK(mvaddch);
    SET_CALLBACK(attron);
    SET_CALLBACK(attroff);
    SET_CALLBACK(clear);
    SET_CALLBACK(colorpair);
    SET_CALLBACK(drawaln);
    SET_CALLBACK(loop);
    SET_CALLBACK(underline);
#undef SET_CALLBACK

    initscr();
    keypad(stdscr, TRUE);
    clear();
    noecho();
    cbreak();

    getmaxyx(stdscr, base->mrow, base->mcol);
    tv->wgoto = newwin(3, TV_MAX_GOTO + 10, 10, 5);
    keypad(tv->wgoto, TRUE);
    set_escdelay(0);
    tv->whelp = newwin(30, 40, 5, 5);
    tv->wlistref = newwin(8, TV_MAX_GOTO + 10, 3, 5);

    start_color();
    curses_init_colors(0);
    return base;
}

#else // !HAVE_CURSES

extern tview_t* text_tv_init(const char *fn, const char *fn_fa, const char *fn_idx, const char *samples,
                             const htsFormat *fmt);

tview_t* curses_tv_init(const char *fn, const char *fn_fa, const char *samples,
                        const htsFormat *fmt) {
    return text_tv_init(fn,fn_fa,NULL,samples,fmt);
}

#endif