malacology
/
gde_linux
1
0
Fork 0
Code Issues Pull Requests Projects Releases Wiki Activity
gde_linux/HGL_SRC/DotPlotTool.c

1137 lines
28 KiB
C
Executable File
Raw Permalink Blame History

/********************************
*
* To compile:
*
* cc -o DotPlotTool plot.c HGLfuncs.c Alloc.c ChooseFile.c
* -lxview -lolgx -lX11
*
* Notes: Set canvas width and height to fit the max_width when
* loading a dataset. Change the viewable size by changing
* the viewable_length of the scrollbars.
*
********************************/
#ifndef _GLOBAL_DEFS_H
#include "global_defs.h"
#define _GLOBAL_DEFS_H
#endif
#include <X11/X.h>
#include <X11/Xlib.h>
#include <X11/keysymdef.h>
#include <X11/keysym.h>
#include <xview/xview.h>
#include <xview/canvas.h>
#include <xview/panel.h>
#include <xview/scrollbar.h>
#include <xview/xv_xrect.h>
#include <xview/rect.h>
#include <xview/cms.h>
#include <sys/types.h>
#include <xview/icon.h>
#include <xview/svrimage.h>
#define POS2(array, i, j) (array[2*(i)+(j)])
#define WHITE 0
#define BLACK 8
#define RED 7
#define min_size 1
#define max_size 4
#define min_width 1
#define min_filter 1
#define max_filter 100
#define min_cutoff -7
#define max_cutoff 17
#define mmscore 0 /* WHITE */
#define pmscore 9 /* GREY */
#define mscore 8 /* BLACK */
#define window_size 2
#define margin 50
Frame frame=(Frame)NULL, prop_subframe;
Panel panel_1; /* panel_1 width should change with the size of the
* dataset.
*/
Panel width_panel=(Panel)NULL; /* There is a limitation on the max size of a
* canvas. When loading a large dataset,
* max_width may have to be reduced to fit into
* the canvas. So, width_panel has to be saved
* to allow changes.
*/
Canvas canvas;
Xv_Window paint_win;
Display *display;
GC gc;
Window xwin;
Cms cms;
Scrollbar h_scrollbar, v_scrollbar;
int Xaxis, Yaxis;
int size = 2;
int max_width, width;
int cutoff = 1;
int filter = 1;
int direction = 0; /* both / and \. */
/* 1: \ or direct
-1: / or reversed */
char footnote[256], heading[128];
int drawarea_min_y, drawarea_max_y;
unsigned long *colors;
char clear_mark = 'F', compd = 'N';
Sequence *tSeq;
int tmp_direction, tmp_size,tmp_width,tmp_filter, tmp_cutoff;
char tmp_compd;
int mark_x=0; /* record the x,y of the paint window, */
int mark_y=0; /* not the canvas or the view window. */
int set_offset;/* The offset of the sequences being displayed. */
int AAmatr[256][256];
short plot_bits[] = {
#include "plot.icon"
};
main(argc, argv)
int argc;
char *argv[];
{
int LoadHGLData();
extern exit_proc();
extern size_proc();
extern width_proc();
extern footer_proc();
extern canvas_repaint_proc();
extern Frame load_file();
extern Load();
extern show_prop_frame();
extern dir_proc();
extern compd_proc();
extern ok_proc();
extern filter_proc();
extern cutoff_proc();
extern ToDisplay();
int i, layer, ii, jj, kk, ll;
char GetBase();
Icon icon;
Server_image image;
static Xv_singlecolor cms_colors[] = {
{255, 255, 255}, /* WHITE */
{128, 0, 255}, /* purple */
{0, 0, 128}, /* navy blue */
{0, 0, 255 }, /* blue */
{0, 255, 0}, /* green */
{255, 255, 0}, /* yellow */
{255, 165, 0}, /* orange */
{225, 0, 0}, /* RED */
{0, 0, 0}, /* black */
{192, 192, 192}, /* GREY */
{240, 240, 240},
{210, 210, 210},
{180, 180, 180},
{150, 150, 150},
{120, 120, 120},
{90, 90, 90},
{60,60,60},
{30, 30, 30},
{0, 0, 0}
};
FILE *fp;
Rect *rect;
Panel panel;
int pam;
static char aa[] = {"arndcqeghilkmfpstwyvbzx*"};
static pam120[24][24] = {
/*a r n d c q e g h i l k m f p s t w y v b z x * */
/*a*/ 3,-3,-1, 0,-3,-1, 0, 1,-3,-1,-3,-2,-2,-4, 1, 1, 1,-7,-4, 0, 1, 0,-1,-8,
/*r*/ -3, 6,-1,-3,-4, 1,-3,-4, 1,-2,-4, 2,-1,-5,-1,-1,-2, 1,-5,-3,-1, 0,-2,-8,
/*n*/ -1,-1, 4, 2,-5, 0, 1, 0, 2,-2,-4, 1,-3,-4,-2, 1, 0,-4,-2,-3, 4, 1,-1,-8,
/*d*/ 0,-3, 2, 5,-7, 1, 3, 0, 0,-3,-5,-1,-4,-7,-3, 0,-1,-8,-5,-3, 5, 3,-2,-8,
/*c*/ -3,-4,-5,-7, 9,-7,-7,-4,-4,-3,-7,-7,-6,-6,-4, 0,-3,-8,-1,-3,-4,-6,-4,-8,
/*q*/ -1, 1, 0, 1,-7, 6, 2,-3, 3,-3,-2, 0,-1,-6, 0,-2,-2,-6,-5,-3, 1, 5,-1,-8,
/*e*/ 0,-3, 1, 3,-7, 2, 5,-1,-1,-3,-4,-1,-3,-7,-2,-1,-2,-8,-5,-3, 3, 5,-1,-8,
/*g*/ 1,-4, 0, 0,-4,-3,-1, 5,-4,-4,-5,-3,-4,-5,-2, 1,-1,-8,-6,-2, 1,-1,-2,-8,
/*h*/ -3, 1, 2, 0,-4, 3,-1,-4, 7,-4,-3,-2,-4,-3,-1,-2,-3,-3,-1,-3, 2, 2,-2,-8,
/*i*/ -1,-2,-2,-3,-3,-3,-3,-4,-4, 6, 1,-3, 1, 0,-3,-2, 0,-6,-2, 3,-2,-2,-1,-8,
/*l*/ -3,-4,-4,-5,-7,-2,-4,-5,-3, 1, 5,-4, 3, 0,-3,-4,-3,-3,-2, 1,-3,-2,-2,-8,
/*k*/ -2, 2, 1,-1,-7, 0,-1,-3,-2,-3,-4, 5, 0,-7,-2,-1,-1,-5,-5,-4, 1, 0,-2,-8,
/*m*/ -2,-1,-3,-4,-6,-1,-3,-4,-4, 1, 3, 0, 8,-1,-3,-2,-1,-6,-4, 1,-3,-1,-2,-8,
/*f*/ -4,-5,-4,-7,-6,-6,-7,-5,-3, 0, 0,-7,-1, 8,-5,-3,-4,-1, 4,-3,-4,-5,-3,-8,
/*p*/ 1,-1,-2,-3,-4, 0,-2,-2,-1,-3,-3,-2,-3,-5, 6, 1,-1,-7,-6,-2,-1, 0,-2,-8,
/*s*/ 1,-1, 1, 0, 0,-2,-1, 1,-2,-2,-4,-1,-2,-3, 1, 3, 2,-2,-3,-2, 1, 0,-1,-8,
/*t*/ 1,-2, 0,-1,-3,-2,-2,-1,-3, 0,-3,-1,-1,-4,-1, 2, 4,-6,-3, 0, 1,-1,-1,-8,
/*w*/ -7, 1,-4,-8,-8,-6,-8,-8,-3,-6,-3,-5,-6,-1,-7,-2,-6,12,-2,-8,-5,-6,-5,-8,
/*y*/ -4,-5,-2,-5,-1,-5,-5,-6,-1,-2,-2,-5,-4, 4,-6,-3,-3,-2, 8,-3,-2,-4,-3,-8,
/*v*/ 0,-3,-3,-3,-3,-3,-3,-2,-3, 3, 1,-4, 1,-3,-2,-2, 0,-8,-3, 5,-2,-2,-1,-8,
/*b*/ 1,-1, 4, 5,-4, 1, 3, 1, 2,-2,-3, 1,-3,-4,-1, 1, 1,-5,-2,-2, 6, 4,-1,-8,
/*z*/ 0, 0, 1, 3,-6, 5, 5,-1, 2,-2,-2, 0,-1,-5, 0, 0,-1,-6,-4,-2, 4, 6, 0,-8,
/*x*/ -1,-2,-1,-2,-4,-1,-1,-2,-2,-1,-2,-2,-2,-3,-2,-1,-1,-5,-3,-1,-1, 0,-2,-8,
/***/ -8,-8,-8,-8,-8,-8,-8,-8,-8,-8,-8,-8,-8,-8,-8,-8,-8,-8,-8,-8,-8,-8,-8, 1};
static pam250[24][24] = {
/*a r n d c q e g h i l k m f p s t w y v b z x * */
2,-2, 0, 0,-2, 0, 0, 1,-1,-1,-2,-1,-1,-3, 1, 1, 1,-6,-3, 0, 2, 1, 0,-8,
-2, 6, 0,-1,-4, 1,-1,-3, 2,-2,-3, 3, 0,-4, 0, 0,-1, 2,-4,-2, 1, 2,-1,-8,
0, 0, 2, 2,-4, 1, 1, 0, 2,-2,-3, 1,-2,-3, 0, 1, 0,-4,-2,-2, 4, 3, 0,-8,
0,-1, 2, 4,-5, 2, 3, 1, 1,-2,-4, 0,-3,-6,-1, 0, 0,-7,-4,-2, 5, 4,-1,-8,
-2,-4,-4,-5,12,-5,-5,-3,-3,-2,-6,-5,-5,-4,-3, 0,-2,-8, 0,-2,-3,-4,-3,-8,
0, 1, 1, 2,-5, 4, 2,-1, 3,-2,-2, 1,-1,-5, 0,-1,-1,-5,-4,-2, 3, 5,-1,-8,
0,-1, 1, 3,-5, 2, 4, 0, 1,-2,-3, 0,-2,-5,-1, 0, 0,-7,-4,-2, 4, 5,-1,-8,
1,-3, 0, 1,-3,-1, 0, 5,-2,-3,-4,-2,-3,-5, 0, 1, 0,-7,-5,-1, 2, 1,-1,-8,
-1, 2, 2, 1,-3, 3, 1,-2, 6,-2,-2, 0,-2,-2, 0,-1,-1,-3, 0,-2, 3, 3,-1,-8,
-1,-2,-2,-2,-2,-2,-2,-3,-2, 5, 2,-2, 2, 1,-2,-1, 0,-5,-1, 4,-1,-1,-1,-8,
-2,-3,-3,-4,-6,-2,-3,-4,-2, 2, 6,-3, 4, 2,-3,-3,-2,-2,-1, 2,-2,-1,-1,-8,
-1, 3, 1, 0,-5, 1, 0,-2, 0,-2,-3, 5, 0,-5,-1, 0, 0,-3,-4,-2, 2, 2,-1,-8,
-1, 0,-2,-3,-5,-1,-2,-3,-2, 2, 4, 0, 6, 0,-2,-2,-1,-4,-2, 2,-1, 0,-1,-8,
-3,-4,-3,-6,-4,-5,-5,-5,-2, 1, 2,-5, 0, 9,-5,-3,-3, 0, 7,-1,-3,-4,-2,-8,
1, 0, 0,-1,-3, 0,-1, 0, 0,-2,-3,-1,-2,-5, 6, 1, 0,-6,-5,-1, 1, 1,-1,-8,
1, 0, 1, 0, 0,-1, 0, 1,-1,-1,-3, 0,-2,-3, 1, 2, 1,-2,-3,-1, 2, 1, 0,-8,
1,-1, 0, 0,-2,-1, 0, 0,-1, 0,-2, 0,-1,-3, 0, 1, 3,-5,-3, 0, 2, 1, 0,-8,
-6, 2,-4,-7,-8,-5,-7,-7,-3,-5,-2,-3,-4, 0,-6,-2,-5,17, 0,-6,-4,-4,-4,-8,
-3,-4,-2,-4, 0,-4,-4,-5, 0,-1,-1,-4,-2, 7,-5,-3,-3, 0,10,-2,-2,-3,-2,-8,
0,-2,-2,-2,-2,-2,-2,-1,-2, 4, 2,-2, 2,-1,-1,-1, 0,-6,-2, 4, 0, 0,-1,-8,
2, 1, 4, 5,-3, 3, 4, 2, 3,-1,-2, 2,-1,-3, 1, 2, 2,-4,-2, 0, 6, 5,-1,-8,
1, 2, 3, 4,-4, 5, 5, 1, 3,-1,-1, 2, 0,-4, 1, 1, 1,-4,-3, 0, 5, 6, 0,-8,
0,-1, 0,-1,-3,-1,-1,-1,-1,-1,-1,-1,-1,-2,-1, 0, 0,-4,-2,-1,-1, 0,-1,-8,
-8,-8,-8,-8,-8,-8,-8,-8,-8,-8,-8,-8,-8,-8,-8,-8,-8,-8,-8,-8,-8,-8,-8, 1};
/* malloc_debug(2); */
if(argc == 1)
{
fprintf(stderr, "An input file is required.\n");
fprintf(stderr, "Usage: %s filename [pam120|pam250(If AA seqs)]\n",
argv[0]);
exit(0);
}
set_offset = LoadHGLData(argv[1]);
/* setup comparison AAmatrix. */
for(ii = 0; ii < 256; ii++)
for(jj = 0; jj < 256; jj++)
AAmatr[ii][jj] = -100;
pam = 250;
if(argc > 2)
{
if(strcmp(argv[2], "pam120") == 0)
pam = 120;
else if(strcmp(argv[2], "pam250") != 0)
{
fprintf(stderr, "Incorrect pam name: %s\n", argv[2]);
exit(1);
}
}
for(ii = 0; ii < strlen(aa); ii++)
for(jj = 0; jj < strlen(aa); jj++)
{
AAmatr[aa[ii]][aa[jj]] =
AAmatr[aa[ii]-32][aa[jj]-32] =
AAmatr[aa[ii]][aa[jj]-32] =
AAmatr[aa[ii]-32][aa[jj]] =
(pam==250)?pam250[ii][jj]:pam120[ii][jj];
}
tmp_cutoff = cutoff;
tmp_width = width;
tmp_direction = direction;
tmp_size = size;
tmp_filter = filter;
tmp_compd = compd;
xv_init(XV_INIT_ARGS, argc, argv, NULL);
frame = xv_create(XV_NULL, FRAME,
FRAME_LABEL, heading,
FRAME_SHOW_FOOTER, TRUE,
FRAME_LEFT_FOOTER, "Mouse Location:",
FRAME_RIGHT_FOOTER, footnote,
NULL);
panel_1 = (Panel) xv_create(frame, PANEL,
NULL);
(void) xv_create(panel_1,PANEL_BUTTON,
PANEL_LABEL_STRING, "Properties...",
PANEL_NOTIFY_PROC, show_prop_frame,
NULL);
(void) xv_create(panel_1,PANEL_BUTTON,
PANEL_LABEL_STRING, "Load",
PANEL_NOTIFY_PROC, Load,
NULL);
(void) xv_create(panel_1,PANEL_BUTTON,
PANEL_LABEL_STRING, "Exit",
PANEL_NOTIFY_PROC, exit_proc,
NULL);
window_fit_height(panel_1);
canvas = (Canvas) xv_create(frame, CANVAS,
CANVAS_X_PAINT_WINDOW, TRUE,
CANVAS_REPAINT_PROC, canvas_repaint_proc,
CANVAS_AUTO_CLEAR, FALSE,
CANVAS_AUTO_SHRINK, FALSE,
CANVAS_AUTO_EXPAND, FALSE,
CANVAS_WIDTH, Xaxis*max_width+margin,
CANVAS_HEIGHT,Yaxis*max_width+margin,
XV_WIDTH, MIN(600, Xaxis*width)+margin,
XV_HEIGHT,MIN(400, Yaxis*width)+margin,
WIN_BELOW, panel_1,
CANVAS_RETAINED, FALSE,
NULL);
/*
printf("Canvas_WIDTH=%d _HEIGHT=%d\n",
(int)xv_get(canvas, CANVAS_WIDTH),
(int)xv_get(canvas, CANVAS_HEIGHT));
*/
paint_win = (Xv_Window) canvas_paint_window(canvas);
xv_set(paint_win,
WIN_BIT_GRAVITY, ForgetGravity,
WIN_CONSUME_EVENTS,
MS_LEFT,
NULL,
WIN_EVENT_PROC, footer_proc,
NULL);
h_scrollbar = (Scrollbar) xv_create(canvas, SCROLLBAR,
SCROLLBAR_DIRECTION, SCROLLBAR_HORIZONTAL,
SCROLLBAR_OBJECT_LENGTH, Xaxis*width+margin,
SCROLLBAR_VIEW_START, 0,
NULL);
v_scrollbar = (Scrollbar) xv_create(canvas, SCROLLBAR,
SCROLLBAR_DIRECTION, SCROLLBAR_VERTICAL,
SCROLLBAR_OBJECT_LENGTH, Yaxis*width+margin,
SCROLLBAR_VIEW_START, 0,
NULL);
cms = xv_create((Cms)NULL, CMS,
CMS_SIZE, 19,
CMS_TYPE, XV_DYNAMIC_CMS,
CMS_COLORS, cms_colors,
NULL);
xv_set(canvas, WIN_CMS, cms,
WIN_INHERIT_COLORS, FALSE,
WIN_BACKGROUND_COLOR, WHITE,
NULL);
window_fit(canvas);
prop_subframe = (Frame)xv_create(frame, FRAME_CMD,
FRAME_LABEL, "Properties",
NULL);
panel = (Panel)xv_get(prop_subframe, FRAME_CMD_PANEL);
(void) xv_set(panel, PANEL_LAYOUT, PANEL_VERTICAL,NULL);
(void) xv_create(panel, PANEL_SLIDER,
PANEL_LABEL_STRING, "Dot Size: ",
PANEL_VALUE, size,
PANEL_MIN_VALUE, min_size,
PANEL_MAX_VALUE, max_size,
PANEL_SLIDER_WIDTH, 100,
PANEL_TICKS, 4,
PANEL_NOTIFY_PROC, size_proc,
NULL);
width_panel = xv_create(panel, PANEL_SLIDER,
PANEL_LABEL_STRING, "Dot Width: ",
PANEL_VALUE, width,
PANEL_MIN_VALUE, min_width,
PANEL_MAX_VALUE, max_width,
PANEL_SLIDER_WIDTH, 100,
PANEL_TICKS, 5,
PANEL_NOTIFY_PROC, width_proc,
NULL);
(void) xv_create(panel, PANEL_SLIDER,
PANEL_LABEL_STRING, "Min Match Length: ",
PANEL_VALUE, filter,
PANEL_MIN_VALUE, min_filter,
PANEL_MAX_VALUE, max_filter,
PANEL_SLIDER_WIDTH, 100,
PANEL_TICKS, 5,
PANEL_NOTIFY_PROC, filter_proc,
NULL);
(void)xv_create(panel, PANEL_CHOICE,
PANEL_LABEL_STRING, "Match Direction",
PANEL_CHOICE_STRINGS,
"Direct",
"Reversed",
"Both",
NULL,
PANEL_NOTIFY_PROC, dir_proc,
PANEL_VALUE, 0,
NULL);
(void)xv_create(panel, PANEL_CHOICE,
PANEL_LABEL_STRING, "Complemented(for NN only):",
PANEL_CHOICE_STRINGS, "No", "Yes", NULL,
PANEL_NOTIFY_PROC, compd_proc,
PANEL_VALUE, 0,
NULL);
(void) xv_create(panel, PANEL_SLIDER,
PANEL_LABEL_STRING, "Cutoff PAM250 score(for AA only):",
PANEL_VALUE, cutoff,
PANEL_MIN_VALUE, min_cutoff,
PANEL_MAX_VALUE, max_cutoff,
PANEL_SLIDER_WIDTH, 100,
PANEL_TICKS, 5,
PANEL_NOTIFY_PROC, cutoff_proc,
NULL);
(void)xv_create(panel, PANEL_BUTTON,
PANEL_LABEL_STRING, "OK",
PANEL_NOTIFY_PROC, ok_proc,
NULL);
window_fit(panel);
window_fit(prop_subframe);
colors = (unsigned long *)xv_get(canvas, WIN_X_COLOR_INDICES);
display = (Display *)xv_get(paint_win, XV_DISPLAY);
xwin = (Window)xv_get(paint_win, XV_XID);
gc = DefaultGC(display, DefaultScreen(display));
xv_set(panel_1,XV_WIDTH,MIN(600, Xaxis*width)+margin,NULL);
window_fit(frame);
rect = (Rect *)xv_get(canvas,CANVAS_VIEWABLE_RECT,paint_win);
XClearArea(display, xwin,
rect->r_left, rect->r_top,
rect->r_width, rect->r_height,
0);
image = (Server_image)xv_create((Cms)NULL, SERVER_IMAGE,
XV_WIDTH, 64,
XV_HEIGHT, 64,
SERVER_IMAGE_BITS, plot_bits,
NULL);
icon = (Icon)xv_create(frame, ICON,
ICON_IMAGE, image,
/* ICON_TRANSPARENT, TRUE,*/
WIN_FOREGROUND_COLOR, WHITE,
WIN_BACKGROUND_COLOR, BLACK,
XV_LABEL, "DotPlotTool",
NULL);
xv_set(frame, FRAME_ICON, icon, NULL);
xv_main_loop(frame);
}
int LoadHGLData(name_str)
char *name_str;
{
int iSeq, ii, jj, kk, YY, tmp, cnt_match;
FILE *fp;
if(strcmp(name_str, "") == 0)
return -1;
if((fp = fopen(name_str, "r")) == NULL)
{
fprintf(stderr, "Can't open file %s.\n", name_str);
exit(1);
}
iSeq = 0;
tSeq = (Sequence *)Calloc(2, sizeof(Sequence));
while(iSeq<2 && (ReadRecord(fp, &(tSeq[iSeq]))) != -1)
{
SeqNormal(&(tSeq[iSeq++]));
};
if(iSeq == 1)
{
CopyRecord(&(tSeq[1]), &(tSeq[0]));
iSeq++;
}
fclose(fp);
Xaxis = strlen(tSeq[0].c_elem);
Yaxis = strlen(tSeq[1].c_elem);
max_width = MIN(6, MAX(1, MIN(28000/Xaxis, 28000/Yaxis)));
width = MAX(1, max_width/2);
if(width_panel != (Panel)NULL)
xv_set(width_panel, PANEL_MAX_VALUE, max_width, NULL);
sprintf(heading, "PLOT : %s", name_str);
sprintf(footnote, "X-axis: %s Y-axis: %s ",
(tSeq[0].name[0]!='\0')?tSeq[0].name:tSeq[0].sequence_ID,
(tSeq[1].name[0]!='\0')?tSeq[1].name:tSeq[1].sequence_ID);
if(frame != (Frame)NULL)
{
XClearWindow(display, xwin);
(void)xv_set(canvas,
XV_WIDTH, MIN(600, Xaxis*width)+margin,
XV_HEIGHT,MIN(400, Yaxis*width)+margin,
CANVAS_WIDTH, Xaxis*max_width+margin,
CANVAS_HEIGHT,Yaxis*max_width+margin,
NULL);
xv_set(panel_1,XV_WIDTH,(int)xv_get(canvas,XV_WIDTH),NULL);
window_fit(frame);
xv_set(frame,FRAME_RIGHT_FOOTER, footnote, NULL);
(void)xv_set(h_scrollbar,
SCROLLBAR_OBJECT_LENGTH, Xaxis*width+margin,
SCROLLBAR_VIEW_START, 0,
NULL);
(void)xv_set(v_scrollbar,
SCROLLBAR_OBJECT_LENGTH, Yaxis*width+margin,
SCROLLBAR_VIEW_START, 0,
NULL);
mark_x = mark_y = 0;
canvas_repaint_proc(canvas,paint_win,display, xwin, NULL);
}
}
DrawDot(display, xwin, gc, x, y, size)
Display *display;
Window xwin;
GC gc;
int x, y, size;
{
int ii, jj;
switch(size)
{
case 1:
XDrawPoint(display, xwin, gc, x, y);
break;
case 2:
XDrawLine(display, xwin, gc, x,y+1, x+2,y+1);
XDrawLine(display, xwin, gc, x+1,y, x+1,y+2);
break;
case 3:
XDrawLine(display, xwin, gc, x,y+1, x+3,y+1);
XDrawLine(display, xwin, gc, x,y+2, x+3,y+2);
XDrawLine(display, xwin, gc, x+1,y, x+1,y+3);
XDrawLine(display, xwin, gc, x+2,y, x+2,y+3);
break;
case 4:
XDrawLine(display, xwin, gc, x,y+1, x+4,y+1);
XDrawLine(display, xwin, gc, x,y+2, x+4,y+2);
XDrawLine(display, xwin, gc, x,y+3, x+4,y+3);
XDrawLine(display, xwin, gc, x+1,y, x+1,y+4);
XDrawLine(display, xwin, gc, x+2,y, x+2,y+4);
XDrawLine(display, xwin, gc, x+3,y, x+3,y+4);
break;
default:
fprintf(stderr,
"Dot size %d is not implemented. 2 is used.\n",size);
XDrawLine(display, xwin, gc, x,y+1, x+2,y+1);
XDrawLine(display, xwin, gc, x+1,y, x+1,y+2);
break;
}
}
canvas_repaint_proc(canvas,pw,display, xwin, xrects )
Canvas canvas;
Xv_Window pw;
Display *display;
Window xwin;
Xv_xrectlist *xrects;
{
int y, iSeq, iSeg, i, cnt, head, tail;
XGCValues gc_val;
Rect *rect;
int drawarea_min_x = INT_MAX;
int drawarea_max_x = 0;
int ii, jj, prev_color = -99, tmp_color;
if(xrects == NULL)
{
if(clear_mark == 'F')
{
rect=(Rect *)xv_get(canvas,CANVAS_VIEWABLE_RECT,paint_win);
drawarea_min_y = rect->r_top;
drawarea_max_y = drawarea_min_y + rect->r_height;
}
rect=(Rect *)xv_get(canvas,CANVAS_VIEWABLE_RECT,paint_win);
drawarea_min_x = MAX(0, rect->r_left -1);
drawarea_max_x = rect->r_left + rect->r_width;
/*
printf("min_x=%d max_x=%d min_y=%d max_y=%d\n",
drawarea_min_x,drawarea_max_x,
drawarea_min_y,drawarea_max_y);
*/
for(ii=MAX(drawarea_min_y/width, 0);
ii<MIN(drawarea_max_y/width+1, Yaxis);
ii++)
{
for(jj = MAX(drawarea_min_x/width, 0);
jj<MIN(drawarea_max_x/width+1, Xaxis);
jj++)
{
if((tmp_color=ToDisplay(tSeq, jj, ii)) == WHITE)
continue;
if(tmp_color != prev_color)
{
XSetForeground(display,gc,colors[tmp_color]);
prev_color = tmp_color;
}
DrawDot(display, xwin, gc,
jj * width,
ii * width,
size);
}
}
}
else
{
for(cnt=xrects->count-1; cnt>=0; cnt--)
{
drawarea_min_y = xrects->rect_array[cnt].y;
drawarea_max_y = xrects->rect_array[cnt].y +
xrects->rect_array[cnt].height;
drawarea_min_x = xrects->rect_array[cnt].x;
drawarea_max_x = xrects->rect_array[cnt].x +
xrects->rect_array[cnt].width;
/*
printf("else: min_x=%d max_x=%d min_y=%d max_y=%d\n",
drawarea_min_x,drawarea_max_x,
drawarea_min_y,drawarea_max_y);
*/
for(ii=MAX(drawarea_min_y/width, 0);
ii<MIN(drawarea_max_y/width+1, Yaxis);
ii++)
{
for(jj = MAX(drawarea_min_x/width, 0);
jj<MIN(drawarea_max_x/width+1, Xaxis);
jj++)
{
if((tmp_color=ToDisplay(tSeq, jj, ii)) == WHITE)
continue;
if(tmp_color != prev_color)
{
XSetForeground(display,gc,colors[tmp_color]);
prev_color = tmp_color;
}
DrawDot(display, xwin, gc,
jj * width,
ii * width,
size);
}
}
}
}
/* Draw marker if (mark_x, mark_y) is not the one
* just being deleted.
*/
if(clear_mark == 'F')
{
XSetForeground(display, gc, colors[RED]);
cross(size, mark_x, mark_y);
}
else
clear_mark = 'F';
return XV_OK;
}
/* Find the location of the mouse and print the
* results in the footer of the frame.
*/
footer_proc ( paint_win, event, arg )
Xv_Window paint_win;
Event *event;
Notify_arg arg;
{
char buf[125];
int save_line, i, ii, iSeq, iSeg;
int return_len=10;
char return_str[10];
KeySym keysym;
XEvent *xevent;
int save_mark_x = mark_x;
int save_mark_y = mark_y;
char need_to_paint = 'F';
char loc_name[32];
int loc_col = INT_MAX, ii1, ii2;
char cc1, cc2;
Rect *rect;
if (event_id(event) == LOC_WINENTER)
{
win_set_kbd_focus(canvas, xwin);
}
else if(event_id(event) == LOC_WINEXIT)
{
win_refuse_kbd_focus(canvas);
}
/* else if(event_id(event) == LOC_MOVE) */
if (event_is_down(event) &&
event_action(event)==ACTION_SELECT)
{
mark_x = event_x(event);
mark_y = event_y(event);
need_to_paint = 'T';
if((ii1 = mark_x/width) >= Xaxis)
{
ii1 = Xaxis;
cc1 = ' ';
}
else
cc1 = tSeq[0].c_elem[ii1];
if((ii2 = mark_y/width) >= Yaxis)
{
ii2 = Yaxis;
cc2 = ' ';
}
else
cc2 = tSeq[1].c_elem[ii2];
sprintf(buf,
"Mouse location: X=(%c, %d) Y=(%c, %d) ",
cc1, ii1, cc2, ii2);
xv_set(frame,FRAME_LEFT_FOOTER, buf, NULL);
}
if(need_to_paint == 'T')
{
/**
** clear the old mark.
**/
XSetForeground(display, gc, colors[WHITE]);
cross(size, save_mark_x, save_mark_y);
drawarea_min_y = save_mark_y - 10;
drawarea_max_y = save_mark_y + 15;
clear_mark = 'T';
canvas_repaint_proc(canvas,paint_win,display, xwin, NULL);
/**
** put a new mark.
**/
XSetForeground(display, gc, colors[RED]);
cross(size, mark_x, mark_y);
}
return XV_OK;
}
Load(item,event)
Panel_item item;
Event *event;
{
extern Frame load_file();
(void)load_file(frame,300,150,NULL);
return XV_OK;
}
size_proc(item, i_sz, event)
Panel_item item;
int i_sz;
Event *event;
{
tmp_size = i_sz;
return XV_OK;
}
width_proc(item, i_wd, event)
Panel_item item;
int i_wd;
Event *event;
{
tmp_width = i_wd;
return XV_OK;
}
filter_proc(item, i_fl, event)
Panel_item item;
int i_fl;
Event *event;
{
tmp_filter = i_fl;
return XV_OK;
}
cutoff_proc(item, i_ct, event)
Panel_item item;
int i_ct;
Event *event;
{
tmp_cutoff = i_ct;
return XV_OK;
}
exit_proc(item, event)
Panel_item item;
Event *event;
{
if (event_action(event) == ACTION_SELECT)
{
xv_destroy_safe(frame);
return(XV_OK);
}
else
return(XV_ERROR);
}
show_prop_frame(item, event)
Frame item;
Event *event;
{
xv_set(prop_subframe, XV_SHOW, TRUE, NULL);
}
cross(size, loc_x, loc_y)
int size, loc_x, loc_y;
{
int ii;
if(size == 1)
{
XDrawLine(display,xwin,gc, loc_x-2,loc_y, loc_x+2,loc_y);
XDrawLine(display,xwin,gc, loc_x, loc_y-2,loc_x, loc_y+2);
}
else if(size == 2)
{
for(ii=0; ii<2; ii++)
{
XDrawLine(display,xwin,gc,loc_x-2,loc_y+ii,loc_x+3,loc_y+ii);
XDrawLine(display,xwin,gc,loc_x+ii,loc_y-2,loc_x+ii,loc_y+3);
}
}
else
{
for(ii= -1; ii<2; ii++)
{
XDrawLine(display,xwin,gc,loc_x-4,loc_y+ii,loc_x+4,loc_y+ii);
XDrawLine(display,xwin,gc,loc_x+ii,loc_y-4,loc_x+ii,loc_y+4);
}
}
}
int ScoreMatch(a,b)
char a,b;
{
int i, intc;
char c;
static int tmatr[16] = {'-','a','c','m','g','r','s','v',
't','w','y','h','k','d','b','n'};
static int matr[128] = {
0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0x00,
0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
0x01,0xe,0x02,0x0d,0,0,0x04,0x0b,0,0,0x0c,0,0x03,0x0f,0,0x05,0,0x05,0x06,
0x08,0x08,0x07,0x09,0x00,0xa,0,0,0,0,0,0,0,0x01,0x0e,0x02,0x0d,0,0,0x04,
0x0b,0,0,0x0c,0,0x03,0x0f,0,0x05,0,0x05,0x06,0x08,0x08,0x07,0x09,0x00,0x0a,
0,0,0,0,0x00,0
};
if(a == '-' || b == '-') return(mscore);
if(matr[a] == matr[b]) return(mscore);
intc = matr[a] & matr[b];
if((intc==matr[a]) || (intc==matr[b])) return(pmscore);
return(mmscore);
}
int ToDisplay(tSeq, x, y)
Sequence *tSeq; /* 0 and 1 sequences. */
int x, y; /* axes. */
/* return the color to draw. */
{
int ii, jj, kk, cnt;
char this_score;
char GetBase();
if(strcmp(tSeq[0].type, "PROTEIN") == 0 &&
strcmp(tSeq[1].type, "PROTEIN") == 0)
{
if((this_score=AAmatr[tSeq[0].c_elem[x]][tSeq[1].c_elem[y]])
< cutoff)
return WHITE;
if(direction == 0 || direction == 1)
{
cnt = 1;
for(kk = 1;
cnt < filter &&
kk < filter &&
x - kk >= 0 && y - kk >= 0 &&
AAmatr[tSeq[0].c_elem[x-kk]][tSeq[1].c_elem[y-kk]] >= cutoff;
kk++, cnt++);
for(kk = 1;
cnt < filter &&
kk < filter &&
x + kk < Xaxis && y + kk < Yaxis &&
AAmatr[tSeq[0].c_elem[x+kk]][tSeq[1].c_elem[y+kk]] >= cutoff;
kk++, cnt++);
if(cnt >= filter)
return ((this_score+9)/4+1 +11);
if(direction == 1)
return WHITE;
}
if(direction == 0 || direction == -1)
{
cnt = 1;
for(kk = 1;
cnt < filter &&
kk < filter &&
y + kk < Yaxis && x - kk >= 0 &&
AAmatr[tSeq[0].c_elem[x-kk]][tSeq[1].c_elem[y+kk]] >= cutoff;
kk++, cnt++);
for(kk = 1;
cnt < filter &&
kk < filter &&
y - kk >= 0 && x + kk < Xaxis &&
AAmatr[tSeq[0].c_elem[x+kk]][tSeq[1].c_elem[y-kk]] >= cutoff;
kk++, cnt++);
if(cnt >= filter)
return ((this_score+9)/4+1 +11); /* +11 to use grey scale.*/
return WHITE;
}
}
else if((strcmp(tSeq[0].type, "DNA") == 0 || strcmp(tSeq[0].type, "RNA") == 0) &&
(strcmp(tSeq[1].type, "DNA") == 0 || strcmp(tSeq[1].type, "RNA") == 0))
{
if((this_score=ScoreMatch(tSeq[0].c_elem[x],GetBase(tSeq[1],y)))
== mmscore)
return WHITE;
if(direction == 0 || direction == 1)
{
cnt = 1;
for(kk = 1;
cnt < filter &&
kk < filter &&
x - kk >= 0 && y - kk >= 0 &&
ScoreMatch(tSeq[0].c_elem[x-kk],GetBase(tSeq[1],y-kk))
!= mmscore;
kk++, cnt++);
for(kk = 1;
cnt < filter &&
kk < filter &&
x + kk < Xaxis && y + kk < Yaxis &&
ScoreMatch(tSeq[0].c_elem[x+kk],GetBase(tSeq[1],y+kk))
!= mmscore;
kk++, cnt++);
if(cnt >= filter)
return this_score;
if(direction == 1)
return WHITE;
}
if(direction == 0 || direction == -1)
{
cnt = 1;
for(kk = 1;
cnt < filter &&
kk < filter &&
y + kk < Yaxis && x - kk >= 0 &&
ScoreMatch(tSeq[0].c_elem[x-kk],GetBase(tSeq[1],y+kk))
!= mmscore;
kk++, cnt++);
for(kk = 1;
cnt < filter &&
kk < filter &&
y - kk >= 0 && x + kk < Xaxis &&
ScoreMatch(tSeq[0].c_elem[x+kk],GetBase(tSeq[1],y-kk))
!= mmscore;
kk++, cnt++);
if(cnt >= filter)
return this_score;
return WHITE;
}
}
else
{
fprintf(stderr, "%cCan't plot sequences with types %s vs. %s.\n",
7, tSeq[0].type, tSeq[1].type);
exit(1);
}
}
dir_proc(item, ii, event)
Panel_item item;
int ii;
Event *event;
{
if(ii == 0)
tmp_direction = 1;
else if(ii == 1)
tmp_direction = -1;
else
tmp_direction = 0;
return XV_OK;
}
compd_proc(item, ii, event)
Panel_item item;
int ii;
Event *event;
{
if(ii == 0)
tmp_compd = 'N';
else
tmp_compd = 'Y';
return XV_OK;
}
ok_proc(item, event)
Panel_item item;
Event *event;
{
direction = tmp_direction;
compd = tmp_compd;
size = tmp_size;
filter = tmp_filter;
cutoff = tmp_cutoff;
XClearWindow(display, xwin);
if(tmp_width != width)
{
mark_y = mark_y/width * tmp_width;
mark_x = mark_x/width * tmp_width;
width = tmp_width;
(void)xv_set(h_scrollbar,
SCROLLBAR_OBJECT_LENGTH, Xaxis*width+margin,
SCROLLBAR_VIEW_START,
MIN(MAX(0,mark_x - 100),
MAX(0,Xaxis*width+margin-(int)xv_get(canvas,XV_WIDTH))),
NULL);
(void)xv_set(v_scrollbar,
SCROLLBAR_OBJECT_LENGTH, Yaxis*width+margin,
SCROLLBAR_VIEW_START,
MIN(MAX(0,mark_y - 100),
MAX(0,Yaxis*width+margin-(int)xv_get(canvas, XV_HEIGHT))),
NULL);
}
canvas_repaint_proc(canvas,paint_win,display, xwin, NULL);
return XV_OK;
}
char BaseComp(c)
char c;
{
unsigned char in,out, case_bit;
static int tmatr[16] = {'-','a','c','m','g','r','s','v',
't','w','y','h','k','d','b','n'};
static int matr[128] = {
0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
0,0,0,0x00,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
0,0,0,0,0,0,0,0,0,0,0x01,0x0e,0x02,0x0d,0,0,0x04,0x0b,0,
0,0x0c,0,0x03,0x0f,0,0x05,0,0x05,0x06,0x08,0x08,0x07,0x09,
0x00,0x0a,0,0,0,0,0,0,0,0x01,0x0e,0x02,0x0d,0,0,0x04,0x0b,
0,0,0x0c,0,0x03,0x0f,0,0x05,0,0x05,0x06,0x08,0x08,0x07,
0x09,0x00,0x0a,0,0,0,0,0x00,0
};
/*
* Save Case bit...
*/
case_bit = c & 32;
out = 0;
in = matr[c];
if(in&1)
out|=8;
if(in&2)
out|=4;
if(in&4)
out|=2;
if(in&8)
out|=1;
c = tmatr[out] | case_bit;
return c;
}
char GetBase(tSeq, y)
Sequence tSeq;
int y;
{
if(compd == 'N')
return tSeq.c_elem[y];
if(compd == 'Y')
return BaseComp(tSeq.c_elem[y]);
}
Reference in New Issue View Git Blame Copy Permalink