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Commit 5da30a44 authored by edgrif's avatar edgrif
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Fix small bugs in cds drawing.

parent 4190fccb
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src/zmapWindow/zmapWindowFeature.c
+ 116
− 43
View file @ 5da30a44
......@@ -28,9 +28,9 @@
*
* Exported functions: See zmapWindow_P.h
* HISTORY:
* Last edited: Jan 16 14:18 2006 (edgrif)
* Last edited: Feb 17 13:53 2006 (edgrif)
* Created: Mon Jan 9 10:25:40 2006 (edgrif)
* CVS info: $Id: zmapWindowFeature.c,v 1.2 2006-01-16 14:19:39 edgrif Exp $
* CVS info: $Id: zmapWindowFeature.c,v 1.3 2006-02-17 13:54:52 edgrif Exp $
*-------------------------------------------------------------------
*/
......@@ -123,6 +123,11 @@ static void removeFeatureLongItems(GList **long_items, FooCanvasItem *feature_it
static void removeLongItemCB(gpointer data, gpointer user_data) ;
static void printItem(gpointer data, gpointer user_data) ;
/* NOTE that we make some assumptions in this code including:
*
......@@ -451,12 +456,26 @@ FooCanvasItem *zmapWindowFeatureDraw(ZMapWindow window, FooCanvasGroup *set_grou
new_feature = top_feature_item ;
}
return new_feature ;
}
static void printItem(gpointer data, gpointer user_data)
{
FooCanvasItem *item = (FooCanvasItem *)data ;
ZMapWindowItemFeatureType type ;
type = GPOINTER_TO_INT(g_object_get_data(G_OBJECT(item), "item_feature_type")) ;
if (type == ITEM_FEATURE_SIMPLE)
printf("found feature simple\n") ;
return ;
}
/* the column_txt_grp need to exist before calling this! */
......@@ -639,7 +658,8 @@ static FooCanvasItem *drawAlignmentFeature(FooCanvasGroup *parent, ZMapFeature f
if(featureClipItemToDraw(feature, &top, &bottom))
continue;
align_data = g_new0(ZMapWindowItemFeatureStruct, 1) ;
align_data = g_new0(ZMapWindowItemFeatureStruct, 1) ;
align_data->subpart = ZMAPFEATURE_SUBPART_MATCH ;
align_data->start = align_span->t1 ;
align_data->end = align_span->t2 ;
......@@ -706,7 +726,9 @@ static FooCanvasItem *drawAlignmentFeature(FooCanvasGroup *parent, ZMapFeature f
box_data = g_new0(ZMapWindowItemFeatureStruct, 1) ;
box_data->start = align_span->t1 ;
box_data->end = prev_align_span->t2 ;
gap_data = g_new0(ZMapWindowItemFeatureStruct, 1) ;
gap_data->subpart = ZMAPFEATURE_SUBPART_GAP ;
gap_data->start = align_span->t1 ;
gap_data->end = prev_align_span->t2 ;
......@@ -719,6 +741,7 @@ static FooCanvasItem *drawAlignmentFeature(FooCanvasGroup *parent, ZMapFeature f
feature->strand);
attachDataToItem(gap_line_box, window, feature, ITEM_FEATURE_BOUNDING_BOX, box_data);
zmapWindowLongItemCheck(window, gap_line_box, bottom, top);
gap_line = zMapDrawAnnotatePolygon(gap_line_box,
ZMAP_ANNOTATE_GAP,
NULL,
......@@ -746,6 +769,7 @@ static FooCanvasItem *drawAlignmentFeature(FooCanvasGroup *parent, ZMapFeature f
/* Finished with the align match */
}
prev_align_span = align_span;
}
......@@ -795,17 +819,23 @@ static FooCanvasItem *drawTranscriptFeature(FooCanvasGroup *parent, ZMapFeature
feature_item = drawparentfeature(parent, feature, feature_start);
feature_group = FOO_CANVAS_GROUP(feature_item);
/* Calculate total offset for for subparts of the feature. */
/* Calculate total offset for subparts of the feature. */
/* We could look @ foo_canavs_group->ypos, but locks us 2 the vertical! */
offset = feature_start + feature_offset ;
/* Set up the cds coords if there is one. */
if(feature->feature.transcript.flags.cds)
{
cds_start = feature->feature.transcript.cds_start;
cds_end = feature->feature.transcript.cds_end;
cds_start = feature->feature.transcript.cds_start ;
cds_end = feature->feature.transcript.cds_end ;
zMapAssert(cds_start < cds_end);
cds_start -= offset;
cds_end -= offset;
/* I think this is correct...???? */
featureClipItemToDraw(feature, &cds_start, &cds_end) ;
zmapWindowSeq2CanOffset(&cds_start, &cds_end, offset) ;
}
/* first we draw the introns, then the exons. Introns will have an invisible
......@@ -832,12 +862,14 @@ static FooCanvasItem *drawTranscriptFeature(FooCanvasGroup *parent, ZMapFeature
bottom = intron_span->x2;
if(featureClipItemToDraw(feature, &top, &bottom))
continue;
continue ;
box_data = g_new0(ZMapWindowItemFeatureStruct, 1) ;
box_data->start = intron_span->x1;
box_data->end = intron_span->x2;
intron_data = g_new0(ZMapWindowItemFeatureStruct, 1) ;
intron_data->subpart = ZMAPFEATURE_SUBPART_INTRON ;
intron_data->start = intron_span->x1;
intron_data->end = intron_span->x2;
......@@ -874,6 +906,7 @@ static FooCanvasItem *drawTranscriptFeature(FooCanvasGroup *parent, ZMapFeature
}
}
if (feature->feature.transcript.exons)
{
for (i = 0; i < feature->feature.transcript.exons->len; i++)
......@@ -891,14 +924,17 @@ static FooCanvasItem *drawTranscriptFeature(FooCanvasGroup *parent, ZMapFeature
if(featureClipItemToDraw(feature, &top, &bottom))
continue;
zmapWindowSeq2CanOffset(&top, &bottom, offset) ;
exon_data = g_new0(ZMapWindowItemFeatureStruct, 1) ;
exon_data->subpart = ZMAPFEATURE_SUBPART_EXON ;
exon_data->start = exon_span->x1;
exon_data->end = exon_span->x2;
exon_data->end = exon_span->x2;
zmapWindowSeq2CanOffset(&top, &bottom, offset);
if(!feature->feature.transcript.flags.cds ||
(feature->feature.transcript.flags.cds &&
(cds_start > bottom)))
if(!feature->feature.transcript.flags.cds
|| (feature->feature.transcript.flags.cds &&
(cds_start > bottom)))
cds_bg = background; /* probably a reverse & cds_end thing here too! */
else
cds_bg = foreground;
......@@ -913,33 +949,69 @@ static FooCanvasItem *drawTranscriptFeature(FooCanvasGroup *parent, ZMapFeature
attachDataToItem(exon_box, window, feature, ITEM_FEATURE_CHILD, exon_data);
zmapWindowLongItemCheck(window, exon_box, top, bottom);
if(feature->feature.transcript.flags.cds &&
(cds_start > top) && (cds_start < bottom))
{
zMapDrawAnnotatePolygon(exon_box,
(feature->strand == ZMAPSTRAND_REVERSE ?
ZMAP_ANNOTATE_UTR_LAST : ZMAP_ANNOTATE_UTR_FIRST),
outline,
background,
cds_start,
feature->strand);
}
if(feature->feature.transcript.flags.cds &&
(cds_end > top) && (cds_end < bottom))
{
zMapDrawAnnotatePolygon(exon_box,
(feature->strand == ZMAPSTRAND_REVERSE ?
ZMAP_ANNOTATE_UTR_FIRST : ZMAP_ANNOTATE_UTR_LAST),
outline,
background,
cds_end,
feature->strand);
}
if (feature->feature.transcript.flags.cds)
{
FooCanvasItem *non_cds_box = NULL ;
int non_start, non_end ;
/* Watch out for the conditions on the start/end here... */
if ((cds_start > top) && (cds_start <= bottom))
{
non_cds_box = zMapDrawAnnotatePolygon(exon_box,
(feature->strand == ZMAPSTRAND_REVERSE ?
ZMAP_ANNOTATE_UTR_LAST
: ZMAP_ANNOTATE_UTR_FIRST),
outline,
background,
cds_start,
feature->strand) ;
if (non_cds_box)
{
non_start = top ;
non_end = top + (cds_start - top) - 1 ;
exon_data = g_new0(ZMapWindowItemFeatureStruct, 1) ;
exon_data->subpart = ZMAPFEATURE_SUBPART_EXON ;
exon_data->start = non_start + offset ;
exon_data->end = non_end + offset ;
attachDataToItem(non_cds_box, window, feature, ITEM_FEATURE_CHILD, exon_data);
zmapWindowLongItemCheck(window, non_cds_box, non_start, non_end) ;
}
}
if ((cds_end >= top) && (cds_end < bottom))
{
non_cds_box = zMapDrawAnnotatePolygon(exon_box,
(feature->strand == ZMAPSTRAND_REVERSE ?
ZMAP_ANNOTATE_UTR_FIRST
: ZMAP_ANNOTATE_UTR_LAST),
outline,
background,
cds_end,
feature->strand) ;
if (non_cds_box)
{
non_start = bottom - (bottom - cds_end) + 1 ;
non_end = bottom ;
exon_data = g_new0(ZMapWindowItemFeatureStruct, 1) ;
exon_data->subpart = ZMAPFEATURE_SUBPART_EXON ;
exon_data->start = non_start + offset ;
exon_data->end = non_end + offset - 1 ; /* - 1 because non_end
calculated from bottom
which covers the last base. */
attachDataToItem(non_cds_box, window, feature, ITEM_FEATURE_CHILD, exon_data);
zmapWindowLongItemCheck(window, non_cds_box, non_start, non_end);
}
}
}
}
}
}
return feature_item ;
......@@ -983,7 +1055,7 @@ static gboolean featureClipItemToDraw(ZMapFeature feature,
if(start_end_crossing & 4)
*end_inout = block_end;
return out_of_block;
return out_of_block ;
}
static void attachDataToItem(FooCanvasItem *feature_item,
......@@ -1118,6 +1190,7 @@ static gboolean canvasItemEventCB(FooCanvasItem *item, GdkEvent *event, gpointer
#ifdef RDS_DONT_INCLUDE
ZMapFeatureTypeStyle type ;
#endif
switch (event->type)
{
case GDK_BUTTON_PRESS:
......@@ -1153,7 +1226,7 @@ static gboolean canvasItemEventCB(FooCanvasItem *item, GdkEvent *event, gpointer
double x = 0.0, y = 0.0 ;
#endif
/* Pass information about the object clicked on back to the application. */
zMapWindowUpdateInfoPanel(window, feature, item);
zMapWindowUpdateInfoPanel(window, feature, real_item) ;
if (but_event->button == 3)
{
......@@ -1480,7 +1553,7 @@ static void itemMenuCB(int menu_item_id, gpointer callback_data)
feature->parent->parent->parent->unique_id,
feature->parent->parent->unique_id,
feature->parent->unique_id,
zmapFeatureLookUpEnum(feature->strand, STRAND_ENUM),
zMapFeatureStrand2Str(feature->strand),
g_quark_from_string("*")) ;
zmapWindowListWindowCreate(menu_data->window, list,
......@@ -1496,7 +1569,7 @@ static void itemMenuCB(int menu_item_id, gpointer callback_data)
feature->parent->parent->parent->unique_id,
feature->parent->parent->unique_id,
feature->parent->unique_id,
zmapFeatureLookUpEnum(feature->strand, STRAND_ENUM),
zMapFeatureStrand2Str(feature->strand),
feature->unique_id);
zmapWindowEditorCreate(menu_data->window, list->data) ;
......
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