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Commit 9db60a9b authored by rnc's avatar rnc
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added code to draw features

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src/include/ZMap/zmapWindow.h
+ 4
− 3
View file @ 9db60a9b
......@@ -27,9 +27,9 @@
* window displaying genome data.
*
* HISTORY:
* Last edited: Jul 13 15:49 2004 (edgrif)
* Last edited: Jul 15 10:26 2004 (rnc)
* Created: Thu Jul 24 15:21:56 2003 (edgrif)
* CVS info: $Id: zmapWindow.h,v 1.9 2004-07-14 09:02:38 edgrif Exp $
* CVS info: $Id: zmapWindow.h,v 1.10 2004-07-15 16:27:58 rnc Exp $
*-------------------------------------------------------------------
*/
#ifndef ZMAP_WINDOW_H
......@@ -133,7 +133,8 @@ void zMapRegionFreeDNA (ZMapRegion *region);
void zmapWindowDrawFeatures (ZMapFeatureContext feature_context);
void zmapWindowDrawFeatures (FooCanvas *canvas,
ZMapFeatureContext feature_context);
/* TEST SCAFFOLDING............... */
......
src/zmapControl/zmapControlNavigator.c
+ 5
− 5
View file @ 9db60a9b
......@@ -26,9 +26,9 @@
*
* Exported functions: See zmapControl_P.h
* HISTORY:
* Last edited: Jul 15 15:51 2004 (edgrif)
* Last edited: Jul 15 17:12 2004 (rnc)
* Created: Thu Jul 8 12:54:27 2004 (edgrif)
* CVS info: $Id: zmapControlNavigator.c,v 1.2 2004-07-15 15:06:52 edgrif Exp $
* CVS info: $Id: zmapControlNavigator.c,v 1.3 2004-07-15 16:30:14 rnc Exp $
*-------------------------------------------------------------------
*/
......@@ -141,15 +141,15 @@ void navScale(FooCanvas *canvas, float offset, int start, int end)
for (x = start, count = 1 ; x < end ; x += 10, count++)
{
drawLine(FOO_CANVAS_GROUP(group), offset-5, x, offset, x, "black", 1.0);
zmapDrawLine(FOO_CANVAS_GROUP(group), offset-5, x, offset, x, "black", 1.0);
char text[25];
sprintf(text,"%dk", x);
if (count == 1)
displayText(FOO_CANVAS_GROUP(group), text, offset + 20, x);
zmapDisplayText(FOO_CANVAS_GROUP(group), text, offset + 20, x);
if (count > 9) count = 0;
}
drawLine(FOO_CANVAS_GROUP(group), offset+1, 0, offset+1, end, "black", 1.0);
zmapDrawLine(FOO_CANVAS_GROUP(group), offset+1, 0, offset+1, end, "black", 1.0);
return;
}
......
src/zmapControl/zmapControlWindowButtons.c
+ 12
− 5
View file @ 9db60a9b
......@@ -27,9 +27,9 @@
*
* Exported functions: See zmapControl_P.h
* HISTORY:
* Last edited: Jul 15 15:51 2004 (edgrif)
* Last edited: Jul 15 17:15 2004 (rnc)
* Created: Thu Jul 24 14:36:27 2003 (edgrif)
* CVS info: $Id: zmapControlWindowButtons.c,v 1.9 2004-07-15 15:10:17 edgrif Exp $
* CVS info: $Id: zmapControlWindowButtons.c,v 1.10 2004-07-15 16:31:14 rnc Exp $
*-------------------------------------------------------------------
*/
......@@ -54,7 +54,8 @@ GtkWidget *zmapControlWindowMakeButtons(ZMap zmap)
{
GtkWidget *frame ;
GtkWidget *hbox, *new_button, *load_button, *stop_button, *quit_button,
*hsplit_button, *vsplit_button, *zoomin_button, *zoomout_button ;
*hsplit_button, *vsplit_button, *zoomin_button, *zoomout_button,
*close_button ;
frame = gtk_frame_new(NULL);
gtk_container_border_width(GTK_CONTAINER(frame), 5);
......@@ -97,7 +98,12 @@ GtkWidget *zmapControlWindowMakeButtons(ZMap zmap)
gtk_signal_connect(GTK_OBJECT(zoomout_button), "clicked",
GTK_SIGNAL_FUNC(zoomOutCB), (gpointer)zmap);
gtk_box_pack_start(GTK_BOX(hbox), zoomout_button, FALSE, FALSE, 0) ;
/*
close_button = gtk_button_new_with_label("Close\nPane") ;
gtk_signal_connect(GTK_OBJECT(close_button), "clicked",
GTK_SIGNAL_FUNC(closePane), (gpointer)zmap) ;
gtk_box_pack_start(GTK_BOX(hbox), close_button, FALSE, FALSE, 0) ;
*/
quit_button = gtk_button_new_with_label("Quit") ;
gtk_signal_connect(GTK_OBJECT(quit_button), "clicked",
GTK_SIGNAL_FUNC(quitCB), (gpointer)zmap) ;
......@@ -117,8 +123,9 @@ GtkWidget *zmapControlWindowMakeButtons(ZMap zmap)
/*
* ------------------- Internal functions -------------------
*/
static void testfunc(GQuark key_id, gpointer data, gpointer user_data);
/* These callbacks simple make calls to routines in zmapControl.c, this is because I want all
/* These callbacks simply make calls to routines in zmapControl.c, this is because I want all
* the state handling etc. to be in one file so that its easier to work on. */
static void loadCB(GtkWidget *widget, gpointer cb_data)
{
......
src/zmapControl/zmapControl_P.h
+ 9
− 7
View file @ 9db60a9b
......@@ -25,9 +25,9 @@
* Description: Private header for interface that creates/manages/destroys
* instances of ZMaps.
* HISTORY:
* Last edited: Jul 15 15:52 2004 (edgrif)
* Last edited: Jul 15 17:16 2004 (rnc)
* Created: Thu Jul 24 14:39:06 2003 (edgrif)
* CVS info: $Id: zmapControl_P.h,v 1.6 2004-07-15 15:11:25 edgrif Exp $
* CVS info: $Id: zmapControl_P.h,v 1.7 2004-07-15 16:31:50 rnc Exp $
*-------------------------------------------------------------------
*/
#ifndef ZMAP_CONTROL_P_H
......@@ -58,14 +58,13 @@ typedef enum {
* this top level window there will be one or more zmap "Views". */
typedef struct _ZMapStruct
{
gchar *zmap_id ; /* unique for each zmap.... */
gchar *zmap_id ; /* unique for each zmap.... */
ZmapState state ; /* state of this zmap. */
ZmapState state ;
gboolean firstTime;
GdkAtom zmap_atom ; /* Used for communicating with zmap
windows. */
GdkAtom zmap_atom ; /* Used for communicating with zmap */
void *app_data ; /* Data passed back to all callbacks
registered for this ZMap. */
......@@ -80,9 +79,12 @@ typedef struct _ZMapStruct
/* The navigator. */
GtkWidget *navigator ;
FooCanvas *navcanvas ;
GtkWidget *navHBox, *navVBox;
/* The panes and views. */
// GtkWidget *displayvbox;
// GtkWidget *hbox;
/* I'm not completely sure this is necessary....revisit this later.... */
GtkWidget *pane_vbox ;
......@@ -90,6 +92,7 @@ typedef struct _ZMapStruct
ZMapPane focuspane ;
GNode *panesTree ;
// ZMapView curr_view ;
/* List of views in this zmap. */
GList *view_list ;
......@@ -118,7 +121,6 @@ typedef struct _ZMapPaneStruct
} ZMapPaneStruct ;
/* Functions internal to zmapControl. */
gboolean zmapControlWindowCreate (ZMap zmap) ;
GtkWidget *zmapControlWindowMakeMenuBar(ZMap zmap) ;
......
src/zmapWindow/GFF_scaffold.c
+ 22
− 6
View file @ 9db60a9b
/* Last edited: Jun 25 12:13 2004 (edgrif) */
/* Last edited: Jul 8 12:21 2004 (rnc) */
/* This is a temporary file only to help with testing....it will go once GFF code is combined
* into the threads etc. code proper.... */
......@@ -9,6 +9,7 @@
static ZMapFeatureContext parseGFF(char *filename) ;
static void testfunc(GQuark key_id, gpointer data, gpointer user_data);
ZMapFeatureContext testGetGFF(void)
......@@ -107,11 +108,9 @@ static ZMapFeatureContext parseGFF(char *filename)
/* Try getting the features. */
feature_context = zmapGFFGetFeatures(parser) ;
zMapGFFSetFreeOnDestroy(parser, free_arrays) ;
zMapGFFDestroyParser(parser) ;
if (status == G_IO_STATUS_EOF)
{
if (g_io_channel_shutdown(gff_file, FALSE, &gff_file_err) != G_IO_STATUS_NORMAL)
......@@ -125,11 +124,28 @@ static ZMapFeatureContext parseGFF(char *filename)
printf("Error reading lines from gff file\n") ;
exit(-1) ;
}
}
return feature_context ;
}
static void testfunc(GQuark key_id, gpointer data, gpointer user_data)
{
ZMapFeatureSet zMapFeatureSet = (ZMapFeatureSet)data;
ZMapFeature zMapFeature;
int i;
printf("GFF_scaffold.c; call %s\n", (char*)user_data);
for (i=0; i<zMapFeatureSet->features->len; i++)
{
zMapFeature = &g_array_index(zMapFeatureSet->features, ZMapFeatureStruct, i);
printf("processing %s, x1 is %d, x2 is %d\n", zMapFeature->name, zMapFeature->x1, zMapFeature->x2);
}
return;
}
src/zmapWindow/zmapWindowDrawFeatures.c
+ 154
− 11
View file @ 9db60a9b
......@@ -27,41 +27,184 @@
*
* Exported functions:
* HISTORY:
* Last edited: Jul 2 18:09 2004 (edgrif)
* Last edited: Jul 15 16:02 2004 (rnc)
* Created: Thu Jul 29 10:45:00 2004 (rnc)
* CVS info: $Id: zmapWindowDrawFeatures.c,v 1.2 2004-07-02 18:24:54 edgrif Exp $
* CVS info: $Id: zmapWindowDrawFeatures.c,v 1.3 2004-07-15 16:34:51 rnc Exp $
*-------------------------------------------------------------------
*/
#include <zmapWindow_P.h>
#include <ZMap/zmapDraw.h>
typedef struct _ParamStruct {
FooCanvas *thisCanvas;
int height;
int length;
} ParamStruct;
static void zmapWindowProcessArray(GQuark key_id, gpointer data, gpointer user_data);
static void zmapWindowProcessFeatureSet(GQuark key_id, gpointer data, gpointer user_data);
void zmapWindowDrawFeatures(ZMapFeatureContext feature_context)
void zmapWindowDrawFeatures(FooCanvas *canvas, ZMapFeatureContext feature_context)
{
float column_spacing = 10.0;
float offset = 20.0;
float result;
double x1, x2, y1, y2;
GtkWidget *parent, *label, *vbox, *vscale, *frame;
GtkRequisition req;
ParamStruct params;
int ticks; // number of tickmarks on scale
int scaleUnit = 100; // spacing of tickmarks on scalebar
int seqUnit; // spacing, in bases of tickmarks
int type; // nomial, ie whether in K, M, etc.
int unitType;
int seqPos;
int scalePos;
int height, width;
char cp[20], unitName[] = { 0, 'k', 'M', 'G', 'T', 'P' }, buf[2] ;
GtkWidget *box;
// parent = gtk_widget_get_parent(GTK_WIDGET(canvas));
// gtk_widget_size_request(parent, &req);
foo_canvas_get_scroll_region(canvas, &x1, &y1, &x2, &y2); // for display panel
// gtk_widget_size_request(navHBox, &req); // for navigator
params.thisCanvas = canvas;
params.height = y2 - y1;
params.length = feature_context->sequence_to_parent.c2 - feature_context->sequence_to_parent.c1;
// Draw the navigator vscale
// how many tickmarks do we want?
// ticks = req.height/scaleUnit;
//what is their spacing in bases
// seqUnit = (feature_context->sequence_to_parent.c2 - feature_context->sequence_to_parent.c1)/ticks;
// are we working in K, M, or what?
// for (type = 1, unitType = 0 ;
// seqUnit > 0 && 1000 * type < seqUnit && unitType < 5;
// unitType++, type *= 1000) ;
// round seqUnit sensibly
// seqUnit = ((seqUnit + type/2)/type) * type;
// a vbox to hold all the scale numbers packed in
// vbox = gtk_vbox_new(TRUE, 0);
// gtk_box_pack_start(GTK_BOX(navHBox), vbox, FALSE, FALSE, 0);
// mark up the scale
/* for (scalePos = 0, seqPos = feature_context->sequence_to_parent.c1;
scalePos < req.height;
scalePos += scaleUnit, seqPos += seqUnit)
{
buf[0] = unitName[unitType] ; buf[1] = 0 ;
sprintf (cp, "%d%s", seqPos/type, buf) ;
if (width < strlen (cp))
width = strlen (cp) ;
box = gtk_hbox_new(TRUE, 0);
label = gtk_label_new(cp);
gtk_container_add(GTK_CONTAINER(box), label);
gtk_box_pack_start(GTK_BOX(vbox), box, FALSE, FALSE, 0);
}
*/
// just trying out the vscale in case it's useful
// vscale = gtk_vscale_new_with_range(0, req.height, scaleUnit);
// gtk_box_pack_start(GTK_BOX(navHBox), vscale, FALSE, FALSE, 0);
result = zmapDrawScale(canvas , offset,
feature_context->sequence_to_parent.c1,
feature_context->sequence_to_parent.c2);
if (feature_context)
g_datalist_foreach(&(feature_context->features), zmapWindowProcessArray, &column_spacing);
g_datalist_foreach(&(feature_context->features), zmapWindowProcessFeatureSet, &params);
// gtk_widget_show_all(navHBox);
return;
}
static void zmapWindowProcessArray(GQuark key_id, gpointer data, gpointer user_data)
static void zmapWindowProcessFeatureSet(GQuark key_id, gpointer data, gpointer user_data)
{
ZMapFeatureSet zMapFeatureSet = (ZMapFeatureSet)data;
float *column_spacing = (float*)user_data;
int i;
ZMapFeature zMapFeature;
ZMapSpan zMapSpan, prevSpan;
ZMapAlignBlock *zMapAlign, *prevAlign;
ParamStruct *params = (ParamStruct*)user_data;
int i, j;
double offset = 40.0, column_spacing = 40.0, column_position;
double box_width = 10.0;
FooCanvasItem *group;
int x1, x2, y0, y1, y2;
float middle, line_width = 1.0;
// NB for each column we create a new canvas group, with the initial y coordinate set to
// 5.0 to just drop it a teeny bit from the top of the window. All items live in the group.
for (i = 0; i < zMapFeatureSet->features->len; i++)
{
// printf("processing %s\n", zMapFeatureSet->features->name);
}
column_position = offset + column_spacing;
zMapFeature = &g_array_index(zMapFeatureSet->features, ZMapFeatureStruct, i);
switch (zMapFeature->type)
{
case ZMAPFEATURE_HOMOL: /* type 1 is a homol */
group = foo_canvas_item_new(foo_canvas_root(params->thisCanvas),
foo_canvas_group_get_type(),
"x",(double)column_position,
"y",(double)5.0,
NULL);
zmapDrawBox(group, column_position, (zMapFeature->feature.homol.y1 * params->height / params->length),
column_position + box_width, (zMapFeature->feature.homol.y2 * params->height / params->length),
"black", "green");
break;
case ZMAPFEATURE_TRANSCRIPT: /* type 4 is a transcript */
column_position = offset;
group = foo_canvas_item_new(foo_canvas_root(params->thisCanvas),
foo_canvas_group_get_type(),
"x",(double)column_position,
"y",(double)5.0,
NULL);
for (j = 1; j < zMapFeature->feature.transcript.exons->len; j++)
{
zMapSpan = &g_array_index(zMapFeature->feature.transcript.exons, ZMapSpanStruct, j);
prevSpan = &g_array_index(zMapFeature->feature.transcript.exons, ZMapSpanStruct, j-1);
middle = ((prevSpan->x2 + zMapSpan->x1)/2) * params->height/params->length;
y0 = prevSpan->x1 * params->height/params->length; // y coord of preceding exon
y1 = prevSpan->x2 * params->height/params->length;
y2 = zMapSpan->x1 * params->height/params->length;
// skip this intron if its preceding exon is too small to draw. We use
// y0 and y1 since they are screen coordinates independent of magnification.
// Note this is a kludge which will meet its come-uppance during zooming
// because zooming doesn't revisit this block of code, so tiny exons will
// appear when zoomed, but the intervening introns will be lost forever.
if (y2 > y1 && y0 +2 <= y1)
{
zmapDrawLine(FOO_CANVAS_GROUP(group), column_position + box_width/2, y1,
column_position + box_width, middle, "blue", line_width);
zmapDrawLine(FOO_CANVAS_GROUP(group), column_position + box_width, middle,
column_position + box_width/2, y2, "blue", line_width);
}
}
for (j = 0; j < zMapFeature->feature.transcript.exons->len; j++)
{
zMapSpan = &g_array_index(zMapFeature->feature.transcript.exons, ZMapSpanStruct, j);
zmapDrawBox(group, column_position, (zMapSpan->x1 * params->height / params->length),
column_position + box_width, (zMapSpan->x2 * params->height / params->length),
"black", "blue");
}
break;
default:
break;
}
}
return;
}
/****************** end of file ************************************/
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