From 51b45587b808f29be163d100ce08358fb6e90ca1 Mon Sep 17 00:00:00 2001
From: rnc <rnc>
Date: Mon, 28 Jun 2004 14:22:15 +0000
Subject: [PATCH] merged display code with main app, replacing graph calls with
canvas, acedb arrays with g arrays
---
src/zmapWindow/zmapbccol.c | 197 ++++++++++++++++++++-----------------
1 file changed, 107 insertions(+), 90 deletions(-)
diff --git a/src/zmapWindow/zmapbccol.c b/src/zmapWindow/zmapbccol.c
index f6967b1b2..80fc61740 100755
--- a/src/zmapWindow/zmapbccol.c
+++ b/src/zmapWindow/zmapbccol.c
@@ -1,4 +1,4 @@
-/* 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;
}
--
GitLab