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Commit 51b45587 authored by rnc's avatar rnc
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merged display code with main app, replacing graph calls with canvas, acedb arrays with g arrays

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src/zmapWindow/zmapbccol.c
+ 107
− 90
View file @ 51b45587
/* Last edited: Apr 15 12:46 2004 (rnc) */
/* Last edited: Jun 22 10:04 2004 (rnc) */
/* file: zmapbccol.c
* Author: Simon Kelley (srk@sanger.ac.uk)
* Copyright (c) Sanger Institute, 2003
......@@ -34,7 +34,8 @@
#include <../acedb/method.h>
#include <../acedb/bump.h>
#include <zmapcontrol.h>
#include <zmapcommon.h>
#include <ZMap/zmapcommon.h>
typedef enum { DEFAULT=0, WIDTH, OFFSET, HIST } BoxColModeType;
......@@ -57,16 +58,17 @@ static void nbcFinalise(void *arg)
{
nbcPrivate *priv = (nbcPrivate *)arg;
if (priv->bump)
bumpDestroy(priv->bump);
// if (priv->bump)
// bumpDestroy(priv->bump);
return;
}
void nbcInit(ZMapPane *pane, ZMapColumn *col)
void nbcInit(ZMapPane pane, ZMapColumn *col)
{
srMeth *meth = srMethodFromID(pane->zMapRegion, col->meth);
nbcPrivate *bc = handleAlloc(nbcFinalise, pane->window->handle,
sizeof(nbcPrivate));
srMeth *meth = srMethodFromID(zMapPaneGetZMapRegion(pane), col->meth);
nbcPrivate *bc = (nbcPrivate*)malloc(sizeof(nbcPrivate));
// nbcPrivate *bc = handleAlloc(nbcFinalise, zMapWindowGetHandle(pane->window),
// sizeof(nbcPrivate));
col->private = bc;
......@@ -215,8 +217,8 @@ static void nbcCalcBox (srMeth *methp, nbcPrivate *bc, float *x1p, float *x2p,
dx = 0.75 ;
xoff = 1 ;
if (bc->bump)
bumpItem (bc->bump, 2, (y2-y1), &xoff, &y1) ;
// if (bc->bump)
// bumpItem (bc->bump, 2, (y2-y1), &xoff, &y1) ;
#if 0
else if (bc->cluster) /* one subcolumn per key */
{
......@@ -239,7 +241,9 @@ static void nbcCalcBox (srMeth *methp, nbcPrivate *bc, float *x1p, float *x2p,
break ;
default:
messcrash("Unknown bc->mode in fMapShowHomol(): %d", bc->mode) ;
//TODO: sort out error handling here
printf("Unknown bc->mode in fMapShowHomol(): %d", bc->mode) ;
exit;
}
......@@ -259,39 +263,50 @@ struct geneSelectData{
int exonNumber;
};
void zMapGeneDraw(ZMapPane *pane, ZMapColumn *col, float *offset, int frame)
void zMapGeneDraw(ZMapPane pane, ZMapColumn *col, float *offset, int frame)
{
ZMapRegion *zMapRegion = pane->zMapRegion;
srMeth *meth = srMethodFromID(zMapRegion, col->meth);
int i, j;
int box;
nbcPrivate *bc = (nbcPrivate *)col->private;
float maxwidth = *offset;
ZMapRegion *zMapRegion = zMapPaneGetZMapRegion(pane);
srMeth *meth = srMethodFromID(zMapRegion, col->meth);
int i, j;
int box;
nbcPrivate *bc = (nbcPrivate *)col->private;
float maxwidth = *offset, width;
FooCanvasItem *group;
char colours[30][10] = { "red", "blue", "pink", "green", "orange", "yellow", "purple", "cyan", "magenta",
"red", "blue", "pink", "green", "orange", "yellow", "purple", "cyan", "magenta",
"red", "blue", "pink", "green", "orange", "yellow", "purple", "cyan", "magenta" };
/* I made these up. Need to find out what meth->colour
equates to */
/* temporary kludge */
if (!zMapRegion) return;
if (meth && (meth->flags & METHOD_BUMPABLE))
bc->bump = bumpCreate(30, 0);
else
// if (meth && (meth->flags & METHOD_BUMPABLE))
// bc->bump = bumpCreate(30, 0);
// else
bc->bump = NULL;
for (i=0; i < arrayMax(zMapRegion->segs); i++)
for (i=0; i < zMapRegionGetSegs(zMapRegion)->len; i++)
{
SEG *seg = arrp(zMapRegion->segs, i, SEG);
SEG *seg = &g_array_index(zMapRegionGetSegs(zMapRegion), SEG, i);
if (seg->method == col->meth &&
seg->type == col->type &&
zmIsOnScreen(pane, seg->x1, seg->x2))
{
Array exons = seg->u.transcript.exons;
float e1, e2, y, x;
GArray *exons = g_array_new(FALSE, FALSE, sizeof(srExon));
float e1, e2, x, y = 0; /* y needs better default */
int xoff = 1;
struct geneSelectData *sd;
if (bc->bump)
bumpItem(bc->bump, 1, seg->x2 - seg->x1, &xoff, &y);
exons = g_array_append_vals(exons,
&seg->u.transcript.exons,
seg->u.transcript.exons.len);
// if (bc->bump)
// bumpItem(bc->bump, 1, seg->x2 - seg->x1, &xoff, &y);
x = *offset + xoff + 30;
x = *offset + xoff;
if (x > maxwidth)
maxwidth = x;
......@@ -300,63 +315,65 @@ void zMapGeneDraw(ZMapPane *pane, ZMapColumn *col, float *offset, int frame)
background on the adjoining intron obscures a little
bit of the next exon. */
for(j = 1; j <arrayMax(exons); j++)
/* make a group to contain the gene */
group = foo_canvas_item_new(FOO_CANVAS_GROUP(zMapPaneGetGroup(pane)),
foo_canvas_group_get_type(),
"x", (double)x,
"y", (double)y ,
NULL);
width = meth->width * 15; /* arbitrary multiplier - needs to be rationalised */
for (j = 1; j < exons->len; j++)
{ /* Intron */
float middle;
e1 = zmScreenCoord(col->pane, array(exons, j-1, srExon).x2);
e2 = zmScreenCoord(col->pane, array(exons, j, srExon).x1);
middle = 0.5 * (e1 + e2);
box = graphBoxStart();
sd = (struct geneSelectData *)
halloc(sizeof(struct geneSelectData), pane->drawHandle);
sd->exonNumber = j;
sd->isIntron = TRUE;
sd->seg = seg;
zmRegBox(pane, box, col, sd);
graphLine(x+0.5, e1, x+0.9, middle);
graphLine(x+0.9, middle, x+0.5, e2);
graphBoxEnd();
graphBoxDraw(box, meth->colour, -1) ;
e1 = zmScreenCoord(col->pane, g_array_index(exons, srExon, j-1).x2);
e2 = zmScreenCoord(col->pane, g_array_index(exons, srExon, j ).x1);
middle = (e1 + e2)/2.0;
/* TODO: if e1 < e2 then it's on the reverse strand so needs different handling */
if (e1 > e2);
drawLine(FOO_CANVAS_GROUP(group), x+(width/2), e1, x+width, middle, colours[meth->colour], 1.0);
drawLine(FOO_CANVAS_GROUP(group), x+width, middle, x+(width/2), e2, colours[meth->colour], 1.0);
}
for (j = 0; j <arrayMax(exons); j++)
for (j = 0; j <exons->len; j++)
{ /* exon */
struct geneSelectData *sd;
e1 = zmScreenCoord(col->pane, array(exons, j, srExon).x1);
e2 = zmScreenCoord(col->pane, array(exons, j, srExon).x2);
sd = (struct geneSelectData *)
halloc(sizeof(struct geneSelectData), pane->drawHandle);
box = graphBoxStart();
sd->exonNumber = j;
sd->isIntron = FALSE;
sd->seg = seg;
e2 = zmScreenCoord(col->pane, array(exons, j, srExon).x2);
zmRegBox(pane, box, col, sd);
graphRectangle(x, e1, x+1, e2);
graphBoxEnd();
graphBoxDraw(box, meth->colour, -1) ;
e1 = zmScreenCoord(col->pane, g_array_index(exons, srExon, j).x1);
e2 = zmScreenCoord(col->pane, g_array_index(exons, srExon, j).x2);
/* if e1 < e2 then it's on the reverse strand so needs different handling */
if (e1 < e2)
drawBox(group, x, e1, x+width, e2, "black", colours[meth->colour]);
else
drawBox(group, x, e2, x+width, e1, "red", colours[meth->colour]);
}
}
}
if (bc->bump)
bumpDestroy (bc->bump);
// if (bc->bump)
// bumpDestroy (bc->bump);
*offset = maxwidth + 2.0 ;
return;
}
void geneSelect(ZMapPane *pane, ZMapColumn *col,
void geneSelect(ZMapPane pane, ZMapColumn *col,
void *arg, int box, double x, double y, BOOL isSelect)
{
struct geneSelectData *sd = (struct geneSelectData *)arg;
SEG *seg = sd->seg;
Array exons = seg->u.transcript.exons;
GArray *exons = g_array_new(FALSE, FALSE, sizeof(srExon));
Coord x1, x2;
char *string;
srMeth *meth = srMethodFromID(pane->zMapRegion, col->meth);
srMeth *meth = srMethodFromID(zMapPaneGetZMapRegion(pane), col->meth);
int colour = WHITE;
exons = g_array_append_vals(exons,
&seg->u.transcript.exons,
seg->u.transcript.exons.len);
if (isSelect)
{
......@@ -364,65 +381,65 @@ void geneSelect(ZMapPane *pane, ZMapColumn *col,
if (sd->isIntron)
{
x1 = arr(exons, sd->exonNumber-1, srExon).x2 + 1 ;
x2 = arr(exons, sd->exonNumber, srExon).x1 - 1 ;
x1 = g_array_index(exons, srExon, sd->exonNumber-1).x2 + 1 ;
x2 = g_array_index(exons, srExon, sd->exonNumber).x1 - 1 ;
}
else
{
x1 = arr(exons, sd->exonNumber, srExon).x1;
x2 = arr(exons, sd->exonNumber, srExon).x2;
x1 = g_array_index(exons, srExon, sd->exonNumber).x1;
x2 = g_array_index(exons, srExon, sd->exonNumber).x2;
}
string = g_strdup_printf("%s [%f] %d %d",
seg->id, seg->score,
zmVisibleCoord(pane->window, x1),
zmVisibleCoord(pane->window, x2));
zmVisibleCoord(zMapPaneGetZMapWindow(pane), x1),
zmVisibleCoord(zMapPaneGetZMapWindow(pane), x2));
gtk_entry_set_text(GTK_ENTRY(pane->window->infoSpace), string);
// gtk_entry_set_text(GTK_ENTRY(pane->window->infoSpace), string);
g_free(string);
}
graphBoxDraw(box, meth->colour, colour);
// graphBoxDraw(box, meth->colour, colour);
return;
}
void zMapFeatureColumn(ZMapPane *pane, ZMapColumn *col, float *offset, int frame)
void zMapFeatureColumn(ZMapPane pane, ZMapColumn *col, float *offset, int frame)
{
ZMapRegion *zMapRegion = pane->zMapRegion;
ZMapRegion *zMapRegion = zMapPaneGetZMapRegion(pane);
srMeth *meth = srMethodFromID(zMapRegion, col->meth);
int i;
nbcPrivate *bc = (nbcPrivate *)col->private;
float maxwidth = *offset;
if (meth->flags & METHOD_BUMPABLE)
bc->bump = bumpCreate(30, 0);
else
// if (meth->flags & METHOD_BUMPABLE)
// bc->bump = bumpCreate(30, 0);
// else
bc->bump = NULL;
for (i=0; i < arrayMax(zMapRegion->segs); i++)
for (i=0; i < zMapRegionGetSegs(zMapRegion)->len; i++)
{
SEG *seg = arrp(zMapRegion->segs, i, SEG);
SEG *seg = &g_array_index(zMapRegionGetSegs(zMapRegion), SEG, i);
if (seg->method == col->meth &&
seg->type == col->type &&
zmIsOnScreen(pane, seg->x1, seg->x2))
{
int box = graphBoxStart();
int box = 0; //graphBoxStart();
float y1, y2, x1, x2;
y1 = zmScreenCoord(col->pane, seg->x1);
y2 = zmScreenCoord(col->pane, seg->x2+1) ;
x1 = *offset;
nbcCalcBox(meth, bc, &x1, &x2, &y1, &y2, seg->score);
graphRectangle(x1, y1, x2, y2);
graphBoxEnd();
graphBoxDraw (box, BLACK, meth->colour) ;
// graphRectangle(x1, y1, x2, y2);
// graphBoxEnd();
// graphBoxDraw (box, BLACK, meth->colour) ;
zmRegBox(pane, box, col, seg);
if (x2 > maxwidth)
maxwidth = x2;
}
}
if (bc->bump)
bumpDestroy (bc->bump);
// if (bc->bump)
// bumpDestroy (bc->bump);
*offset = maxwidth + 0.5 ;
return;
......@@ -430,16 +447,16 @@ void zMapFeatureColumn(ZMapPane *pane, ZMapColumn *col, float *offset, int frame
void nbcSelect(ZMapPane *pane, ZMapColumn *col,
void nbcSelect(ZMapPane pane, ZMapColumn *col,
void *arg, int box, double x, double y, BOOL isSelect)
{
SEG *seg = (SEG *)arg;
char *string = g_strdup_printf("%s [%f] %d %d",
seg->id, seg->score,
zmVisibleCoord(pane->window, seg->x1),
zmVisibleCoord(pane->window, seg->x2));
zmVisibleCoord(zMapPaneGetZMapWindow(pane), seg->x1),
zmVisibleCoord(zMapPaneGetZMapWindow(pane), seg->x2));
gtk_entry_set_text(GTK_ENTRY(pane->window->infoSpace), string);
// gtk_entry_set_text(GTK_ENTRY(pane->window->infoSpace), string);
g_free(string);
return;
}
......
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