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1 #undef _HAVE_CURSES
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2
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3 #if _CURSES_LIB == 0
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4 #elif _CURSES_LIB == 1
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5 #include <curses.h>
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6 #ifndef NCURSES_VERSION
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7 #warning "_CURSES_LIB=1 but NCURSES_VERSION not defined; tview is NOT compiled"
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8 #else
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9 #define _HAVE_CURSES
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10 #endif
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11 #elif _CURSES_LIB == 2
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12 #include <xcurses.h>
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13 #define _HAVE_CURSES
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14 #else
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15 #warning "_CURSES_LIB is not 0, 1 or 2; tview is NOT compiled"
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16 #endif
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17
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18
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19 #include "bam_tview.h"
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20
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21 #ifdef _HAVE_CURSES
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22
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23
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24
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25 typedef struct CursesTview {
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26 tview_t view;
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27 WINDOW *wgoto, *whelp;
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28 } curses_tview_t;
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29
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30
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31
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32
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33 #define FROM_TV(ptr) ((curses_tview_t*)ptr)
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34
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35 static void curses_destroy(tview_t* base)
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36 {
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37 curses_tview_t* tv=(curses_tview_t*)base;
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38
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39
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40 delwin(tv->wgoto); delwin(tv->whelp);
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41 endwin();
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42
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43 base_tv_destroy(base);
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44
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45 free(tv);
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46 }
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47
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48 /*
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49 void (*my_mvprintw)(struct AbstractTview* ,int,int,const char*,...);
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50 void (*my_)(struct AbstractTview*,int,int,int);
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51 void (*my_attron)(struct AbstractTview*,int);
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52 void (*my_attroff)(struct AbstractTview*,int);
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53 void (*my_clear)(struct AbstractTview*);
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54 int (*my_colorpair)(struct AbstractTview*,int);
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55 */
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56
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57 static void curses_mvprintw(struct AbstractTview* tv,int y ,int x,const char* fmt,...)
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58 {
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59 unsigned int size=tv->mcol+2;
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60 char* str=malloc(size);
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61 if(str==0) exit(EXIT_FAILURE);
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62 va_list argptr;
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63 va_start(argptr, fmt);
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64 vsnprintf(str,size, fmt, argptr);
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65 va_end(argptr);
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66 mvprintw(y,x,str);
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67 free(str);
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68 }
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69
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70 static void curses_mvaddch(struct AbstractTview* tv,int y,int x,int ch)
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71 {
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72 mvaddch(y,x,ch);
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73 }
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74
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75 static void curses_attron(struct AbstractTview* tv,int flag)
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76 {
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77 attron(flag);
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78 }
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79 static void curses_attroff(struct AbstractTview* tv,int flag)
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80 {
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81 attroff(flag);
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82 }
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83 static void curses_clear(struct AbstractTview* tv)
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84 {
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85 clear();
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86 }
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87
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88 static int curses_colorpair(struct AbstractTview* tv,int flag)
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89 {
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90 return COLOR_PAIR(flag);
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91 }
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92
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93 static int curses_drawaln(struct AbstractTview* tv, int tid, int pos)
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94 {
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95 return base_draw_aln(tv, tid, pos);
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96 }
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97
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98
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99
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100 static void tv_win_goto(curses_tview_t *tv, int *tid, int *pos)
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101 {
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102 char str[256], *p;
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103 int i, l = 0;
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104 tview_t *base=(tview_t*)tv;
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105 wborder(tv->wgoto, '|', '|', '-', '-', '+', '+', '+', '+');
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106 mvwprintw(tv->wgoto, 1, 2, "Goto: ");
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107 for (;;) {
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108 int c = wgetch(tv->wgoto);
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109 wrefresh(tv->wgoto);
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110 if (c == KEY_BACKSPACE || c == '\010' || c == '\177') {
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111 if(l > 0) --l;
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112 } else if (c == KEY_ENTER || c == '\012' || c == '\015') {
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113 int _tid = -1, _beg, _end;
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114 if (str[0] == '=') {
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115 _beg = strtol(str+1, &p, 10) - 1;
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116 if (_beg > 0) {
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117 *pos = _beg;
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118 return;
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119 }
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120 } else {
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121 bam_parse_region(base->header, str, &_tid, &_beg, &_end);
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122 if (_tid >= 0) {
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123 *tid = _tid; *pos = _beg;
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124 return;
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125 }
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126 }
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127 } else if (isgraph(c)) {
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128 if (l < TV_MAX_GOTO) str[l++] = c;
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129 } else if (c == '\027') l = 0;
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130 else if (c == '\033') return;
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131 str[l] = '\0';
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132 for (i = 0; i < TV_MAX_GOTO; ++i) mvwaddch(tv->wgoto, 1, 8 + i, ' ');
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133 mvwprintw(tv->wgoto, 1, 8, "%s", str);
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134 }
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135 }
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136
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137
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138
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139
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140 static void tv_win_help(curses_tview_t *tv) {
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141 int r = 1;
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142 tview_t* base=(tview_t*)base;
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143 WINDOW *win = tv->whelp;
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144 wborder(win, '|', '|', '-', '-', '+', '+', '+', '+');
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145 mvwprintw(win, r++, 2, " -=- Help -=- ");
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146 r++;
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147 mvwprintw(win, r++, 2, "? This window");
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148 mvwprintw(win, r++, 2, "Arrows Small scroll movement");
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149 mvwprintw(win, r++, 2, "h,j,k,l Small scroll movement");
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150 mvwprintw(win, r++, 2, "H,J,K,L Large scroll movement");
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151 mvwprintw(win, r++, 2, "ctrl-H Scroll 1k left");
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152 mvwprintw(win, r++, 2, "ctrl-L Scroll 1k right");
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153 mvwprintw(win, r++, 2, "space Scroll one screen");
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154 mvwprintw(win, r++, 2, "backspace Scroll back one screen");
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155 mvwprintw(win, r++, 2, "g Go to specific location");
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156 mvwprintw(win, r++, 2, "m Color for mapping qual");
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157 mvwprintw(win, r++, 2, "n Color for nucleotide");
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158 mvwprintw(win, r++, 2, "b Color for base quality");
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159 mvwprintw(win, r++, 2, "c Color for cs color");
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160 mvwprintw(win, r++, 2, "z Color for cs qual");
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161 mvwprintw(win, r++, 2, ". Toggle on/off dot view");
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162 mvwprintw(win, r++, 2, "s Toggle on/off ref skip");
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163 mvwprintw(win, r++, 2, "r Toggle on/off rd name");
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164 mvwprintw(win, r++, 2, "N Turn on nt view");
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165 mvwprintw(win, r++, 2, "C Turn on cs view");
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166 mvwprintw(win, r++, 2, "i Toggle on/off ins");
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167 mvwprintw(win, r++, 2, "q Exit");
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168 r++;
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169 mvwprintw(win, r++, 2, "Underline: Secondary or orphan");
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170 mvwprintw(win, r++, 2, "Blue: 0-9 Green: 10-19");
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171 mvwprintw(win, r++, 2, "Yellow: 20-29 White: >=30");
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172 wrefresh(win);
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173 wgetch(win);
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174 }
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175
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176 static int curses_underline(tview_t* tv)
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177 {
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178 return A_UNDERLINE;
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179 }
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180
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181 static int curses_loop(tview_t* tv)
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182 {
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183 int tid, pos;
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184 curses_tview_t *CTV=(curses_tview_t *)tv;
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185 tid = tv->curr_tid; pos = tv->left_pos;
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186 while (1) {
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187 int c = getch();
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188 switch (c) {
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189 case '?': tv_win_help(CTV); break;
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190 case '\033':
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191 case 'q': goto end_loop;
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192 case '/':
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193 case 'g': tv_win_goto(CTV, &tid, &pos); break;
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194 case 'm': tv->color_for = TV_COLOR_MAPQ; break;
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195 case 'b': tv->color_for = TV_COLOR_BASEQ; break;
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196 case 'n': tv->color_for = TV_COLOR_NUCL; break;
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197 case 'c': tv->color_for = TV_COLOR_COL; break;
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198 case 'z': tv->color_for = TV_COLOR_COLQ; break;
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199 case 's': tv->no_skip = !tv->no_skip; break;
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200 case 'r': tv->show_name = !tv->show_name; break;
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201 case KEY_LEFT:
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202 case 'h': --pos; break;
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203 case KEY_RIGHT:
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204 case 'l': ++pos; break;
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205 case KEY_SLEFT:
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206 case 'H': pos -= 20; break;
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207 case KEY_SRIGHT:
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208 case 'L': pos += 20; break;
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209 case '.': tv->is_dot = !tv->is_dot; break;
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210 case 'N': tv->base_for = TV_BASE_NUCL; break;
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211 case 'C': tv->base_for = TV_BASE_COLOR_SPACE; break;
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212 case 'i': tv->ins = !tv->ins; break;
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213 case '\010': pos -= 1000; break;
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214 case '\014': pos += 1000; break;
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215 case ' ': pos += tv->mcol; break;
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216 case KEY_UP:
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217 case 'j': --tv->row_shift; break;
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218 case KEY_DOWN:
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219 case 'k': ++tv->row_shift; break;
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220 case KEY_BACKSPACE:
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221 case '\177': pos -= tv->mcol; break;
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222 case KEY_RESIZE: getmaxyx(stdscr, tv->mrow, tv->mcol); break;
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223 default: continue;
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224 }
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225 if (pos < 0) pos = 0;
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226 if (tv->row_shift < 0) tv->row_shift = 0;
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227 tv->my_drawaln(tv, tid, pos);
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228 }
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229 end_loop:
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230 return 0;
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231 }
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232
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233
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234
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235
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236 tview_t* curses_tv_init(const char *fn, const char *fn_fa, const char *samples)
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237 {
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238 curses_tview_t *tv = (curses_tview_t*)calloc(1, sizeof(curses_tview_t));
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239 tview_t* base=(tview_t*)tv;
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240 if(tv==0)
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241 {
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242 fprintf(stderr,"Calloc failed\n");
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243 return 0;
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244 }
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245
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246 base_tv_init(base,fn,fn_fa,samples);
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247 /* initialize callbacks */
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248 #define SET_CALLBACK(fun) base->my_##fun=curses_##fun;
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249 SET_CALLBACK(destroy);
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250 SET_CALLBACK(mvprintw);
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251 SET_CALLBACK(mvaddch);
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252 SET_CALLBACK(attron);
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253 SET_CALLBACK(attroff);
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254 SET_CALLBACK(clear);
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255 SET_CALLBACK(colorpair);
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256 SET_CALLBACK(drawaln);
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257 SET_CALLBACK(loop);
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258 SET_CALLBACK(underline);
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259 #undef SET_CALLBACK
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260
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261 initscr();
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262 keypad(stdscr, TRUE);
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263 clear();
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264 noecho();
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265 cbreak();
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266
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267 getmaxyx(stdscr, base->mrow, base->mcol);
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268 tv->wgoto = newwin(3, TV_MAX_GOTO + 10, 10, 5);
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269 tv->whelp = newwin(29, 40, 5, 5);
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270
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271 start_color();
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272 init_pair(1, COLOR_BLUE, COLOR_BLACK);
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273 init_pair(2, COLOR_GREEN, COLOR_BLACK);
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274 init_pair(3, COLOR_YELLOW, COLOR_BLACK);
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275 init_pair(4, COLOR_WHITE, COLOR_BLACK);
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276 init_pair(5, COLOR_GREEN, COLOR_BLACK);
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277 init_pair(6, COLOR_CYAN, COLOR_BLACK);
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278 init_pair(7, COLOR_YELLOW, COLOR_BLACK);
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279 init_pair(8, COLOR_RED, COLOR_BLACK);
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280 init_pair(9, COLOR_BLUE, COLOR_BLACK);
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281 return base;
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282 }
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283
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284
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285 #else // #ifdef _HAVE_CURSES
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286 #include <stdio.h>
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287 #warning "No curses library is available; tview with curses is disabled."
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288
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289 extern tview_t* text_tv_init(const char *fn, const char *fn_fa, const char *samples);
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290
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291 tview_t* curses_tv_init(const char *fn, const char *fn_fa, const char *samples)
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292 {
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293 return text_tv_init(fn,fn_fa,samples);
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294 }
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295 #endif // #ifdef _HAVE_CURSES
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296
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297
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