--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/PsiCLASS-1.0.2/samtools-0.1.19/bam_tview_curses.c	Fri Mar 26 16:52:45 2021 +0000
@@ -0,0 +1,297 @@
+#undef _HAVE_CURSES
+
+#if _CURSES_LIB == 0
+#elif _CURSES_LIB == 1
+#include <curses.h>
+#ifndef NCURSES_VERSION
+#warning "_CURSES_LIB=1 but NCURSES_VERSION not defined; tview is NOT compiled"
+#else
+#define _HAVE_CURSES
+#endif
+#elif _CURSES_LIB == 2
+#include <xcurses.h>
+#define _HAVE_CURSES
+#else
+#warning "_CURSES_LIB is not 0, 1 or 2; tview is NOT compiled"
+#endif
+
+
+#include "bam_tview.h"
+
+#ifdef _HAVE_CURSES
+
+
+
+typedef struct CursesTview {
+	tview_t view;
+	WINDOW *wgoto, *whelp;
+	} 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);
+	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,...)
+	{
+	unsigned int size=tv->mcol+2;
+	char* str=malloc(size);
+	if(str==0) exit(EXIT_FAILURE);
+	va_list argptr;
+  	va_start(argptr, fmt);
+	vsnprintf(str,size, fmt, argptr);
+	va_end(argptr);
+	mvprintw(y,x,str);
+	free(str);
+	}
+
+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_colorpair(struct AbstractTview* tv,int flag)
+    {
+    return COLOR_PAIR(flag);
+    }
+
+static int curses_drawaln(struct AbstractTview* tv, int tid, int pos)
+    {
+    return base_draw_aln(tv,  tid, pos);
+    }
+
+
+
+static void tv_win_goto(curses_tview_t *tv, int *tid, int *pos)
+	{
+	char str[256], *p;
+	int i, l = 0;
+	tview_t *base=(tview_t*)tv;
+	wborder(tv->wgoto, '|', '|', '-', '-', '+', '+', '+', '+');
+	mvwprintw(tv->wgoto, 1, 2, "Goto: ");
+	for (;;) {
+		int c = wgetch(tv->wgoto);
+		wrefresh(tv->wgoto);
+		if (c == KEY_BACKSPACE || c == '\010' || c == '\177') {
+			if(l > 0) --l;
+		} else if (c == KEY_ENTER || c == '\012' || c == '\015') {
+			int _tid = -1, _beg, _end;
+			if (str[0] == '=') {
+				_beg = strtol(str+1, &p, 10) - 1;
+				if (_beg > 0) {
+					*pos = _beg;
+					return;
+				}
+			} else {
+				bam_parse_region(base->header, str, &_tid, &_beg, &_end);
+				if (_tid >= 0) {
+					*tid = _tid; *pos = _beg;
+					return;
+				}
+			}
+		} else if (isgraph(c)) {
+			if (l < TV_MAX_GOTO) str[l++] = c;
+		} else if (c == '\027') l = 0;
+		else if (c == '\033') return;
+		str[l] = '\0';
+		for (i = 0; i < TV_MAX_GOTO; ++i) mvwaddch(tv->wgoto, 1, 8 + i, ' ');
+		mvwprintw(tv->wgoto, 1, 8, "%s", str);
+	}
+}
+
+
+
+
+static void tv_win_help(curses_tview_t *tv) {
+	int r = 1;
+	tview_t* base=(tview_t*)base;
+	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, "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, 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 '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 KEY_DOWN:
+			case 'k': ++tv->row_shift; break;
+			case KEY_BACKSPACE:
+			case '\177': pos -= tv->mcol; break;
+			case KEY_RESIZE: getmaxyx(stdscr, tv->mrow, tv->mcol); break;
+			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)
+	{
+	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,samples);
+	/* 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);
+	tv->whelp = newwin(29, 40, 5, 5);
+	
+	start_color();
+	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_YELLOW, COLOR_BLACK);
+	init_pair(8, COLOR_RED, COLOR_BLACK);
+	init_pair(9, COLOR_BLUE, COLOR_BLACK);
+	return base;
+	}
+
+
+#else // #ifdef _HAVE_CURSES
+#include <stdio.h>
+#warning "No curses library is available; tview with curses is disabled."
+
+extern tview_t* text_tv_init(const char *fn, const char *fn_fa, const char *samples);
+
+tview_t* curses_tv_init(const char *fn, const char *fn_fa, const char *samples)
+	{
+	return text_tv_init(fn,fn_fa,samples);
+	}
+#endif // #ifdef _HAVE_CURSES
+
+