From 1be78c65c7070d8efe6e6042908edcb988b4376c Mon Sep 17 00:00:00 2001
From: edgrif <edgrif>
Date: Thu, 17 Dec 2009 14:51:22 +0000
Subject: [PATCH] add code to store subpart (exon etc) index to subpart data on
canvas item.
---
src/zmapWindow/zmapWindowItemFactory.c | 166 +++++++++++++++----------
1 file changed, 103 insertions(+), 63 deletions(-)
diff --git a/src/zmapWindow/zmapWindowItemFactory.c b/src/zmapWindow/zmapWindowItemFactory.c
index 9a20e45a5..60f1f9806 100755
--- a/src/zmapWindow/zmapWindowItemFactory.c
+++ b/src/zmapWindow/zmapWindowItemFactory.c
@@ -28,9 +28,9 @@
*
* Exported functions: See zmapWindowItemFactory.h
* HISTORY:
- * Last edited: Nov 30 10:57 2009 (edgrif)
+ * Last edited: Dec 17 14:50 2009 (edgrif)
* Created: Mon Sep 25 09:09:52 2006 (rds)
- * CVS info: $Id: zmapWindowItemFactory.c,v 1.69 2009-12-15 13:49:12 mh17 Exp $
+ * CVS info: $Id: zmapWindowItemFactory.c,v 1.70 2009-12-17 14:51:22 edgrif Exp $
*-------------------------------------------------------------------
*/
@@ -85,7 +85,12 @@ typedef struct _RunSetStruct
ZMapFrame frame;
FooCanvasGroup *container;
FooCanvasItem *canvas_item;
-}RunSetStruct;
+} RunSetStruct ;
+
+
+#define GET_SUBPART_INDEX(FEATURE, SUBPART_ARRAY, ARRAY_INDEX) \
+ ((FEATURE)->strand == ZMAPSTRAND_FORWARD ? (ARRAY_INDEX) + 1 : (SUBPART_ARRAY)->len - (ARRAY_INDEX))
+
static void copyCheckMethodTable(const ZMapWindowFToIFactoryMethodsStruct *table_in,
@@ -167,6 +172,14 @@ static gboolean clip_feature_coords(ZMapWindowFToIFactory factory,
double *start_inout,
double *end_inout);
+static void new_draw_feature_exon(FooCanvasItem *feature_item,
+ double feature_offset,
+ int item_index, double item_top, double item_bottom,
+ double cds_start, double cds_end,
+ double item_right, double line_width,
+ gboolean has_cds) ;
+
+
/*
* Static function tables for drawing features in various ways.
@@ -715,7 +728,7 @@ static FooCanvasItem *drawAssemblyFeature(RunSet run_data, ZMapFeature feature,
canvas_item_position = y1 - feature_offset;
- if(debug_assembly_drawing)
+ if (debug_assembly_drawing)
{
printf("->drawAssemblyFeature(feature=%p, feature_offset=%f, x1=%f, y1=%f, x2=%f, y2=%f)\n",
feature, feature_offset, x1, y1, x2, y2);
@@ -983,11 +996,11 @@ static FooCanvasItem *drawAlignFeature(RunSet run_data, ZMapFeature feature,
ZMapFeatureBlock block = run_data->block;
guint line_width = 0;
- /* If we are here, style should be ok for display. */
- //zMapStyleSetGappedAligns(style, 1.0, 1.0);
+
if ((!zMapStyleIsShowGaps(style) || !(feature->feature.homol.align)))
{
double feature_start, feature_end;
+
feature_start = feature->x1;
feature_end = feature->x2; /* I want this function to find these values */
zmapWindowSeq2CanOffset(&feature_start, &feature_end, feature_offset) ;
@@ -1009,6 +1022,10 @@ static FooCanvasItem *drawAlignFeature(RunSet run_data, ZMapFeature feature,
}
else
{
+ if (zMapLogQuarkIsStr(feature->original_id, "Em:BX410214.1"))
+ printf("found it\n") ;
+
+
/* line width from the factory? Should this be from the style? */
line_width = factory->line_width;
@@ -1027,18 +1044,22 @@ static FooCanvasItem *drawAlignFeature(RunSet run_data, ZMapFeature feature,
feature_start = feature->x1;
feature_end = feature->x2; /* I want this function to find these values */
+
#ifdef DEBUG_COORDS
printf("feature %d -> %d [%d -> %d]\n",
feature->x1, feature->x2,
feature->x1 - feature->x1,
feature->x2 - feature->x1 + 1);
#endif /* DEBUG_COORDS */
+
zmapWindowSeq2CanOffset(&feature_start, &feature_end, feature_offset) ;
+
#ifdef DEBUG_COORDS
printf("feature %f -> %f [%f, %f]\n",
feature_start, feature_end,
feature_start - feature_start, feature_end - feature_start);
#endif /* DEBUG_COORDS */
+
if(!(feature_item = run_data->canvas_item))
{
new_canvas_item = zMapWindowCanvasItemCreate(parent, feature_start, feature, style);
@@ -1172,8 +1193,9 @@ static FooCanvasItem *drawAlignFeature(RunSet run_data, ZMapFeature feature,
double gap_top, gap_bottom;
gap_data.subpart = ZMAPFEATURE_SUBPART_GAP ;
- gap_data.start = gap_block.t1;
- gap_data.end = gap_block.t2;
+ gap_data.index = GET_SUBPART_INDEX(feature, feature->feature.homol.align, i) ;
+ gap_data.start = gap_block.t1;
+ gap_data.end = gap_block.t2;
#ifdef NO_NEED
gap_data->query_start = 0;
gap_data->query_end = 0;
@@ -1197,6 +1219,7 @@ static FooCanvasItem *drawAlignFeature(RunSet run_data, ZMapFeature feature,
}
align_data.subpart = ZMAPFEATURE_SUBPART_MATCH ;
+ align_data.index = GET_SUBPART_INDEX(feature, feature->feature.homol.align, i) ;
align_data.start = match_block->t1 ;
align_data.end = match_block->t2 ;
#ifdef NO_NEED
@@ -1216,12 +1239,13 @@ static FooCanvasItem *drawAlignFeature(RunSet run_data, ZMapFeature feature,
}
- if(first_match_block)
+ if (first_match_block)
{
FooCanvasItem *match;
ZMapFeatureSubPartSpanStruct align_data;
align_data.subpart = ZMAPFEATURE_SUBPART_MATCH ;
+ align_data.index = GET_SUBPART_INDEX(feature, feature->feature.homol.align, 0) ;
align_data.start = first_match_block->t1 ;
align_data.end = first_match_block->t2 ;
#ifdef NO_NEED
@@ -1287,7 +1311,7 @@ static void get_exon_regions(ZMapSpan exon_cds, ZMapSpan utr_one, ZMapSpan utr_t
static void new_draw_feature_exon(FooCanvasItem *feature_item,
double feature_offset,
- double item_top, double item_bottom,
+ int item_index, double item_top, double item_bottom,
double cds_start, double cds_end,
double item_right, double line_width,
gboolean has_cds)
@@ -1304,11 +1328,15 @@ static void new_draw_feature_exon(FooCanvasItem *feature_item,
/* top != feature_offset */
top = (FOO_CANVAS_GROUP(feature_item))->ypos;
- if(has_cds)
- get_exon_regions(®ions[0], ®ions[1], ®ions[2],
- cds_start, cds_end, &first, &last);
- else if(!cdsless_use_utr_colours)
- first = last = cds_idx;
+ if (has_cds)
+ {
+ get_exon_regions(®ions[0], ®ions[1], ®ions[2],
+ cds_start, cds_end, &first, &last);
+ }
+ else if (!cdsless_use_utr_colours)
+ {
+ first = last = cds_idx;
+ }
else
{
int utr_idx = 1;
@@ -1319,11 +1347,13 @@ static void new_draw_feature_exon(FooCanvasItem *feature_item,
canvas_item = ZMAP_CANVAS_ITEM(feature_item);
/* draw the cds [0] over the utr [1,2] */
- for(j = last; j >= first; --j)
+ for (j = last; j >= first; --j)
{
FooCanvasItem *exon_item = NULL;
ZMapFeatureSubPartSpanStruct exon_data;
+ exon_data.index = item_index ;
+
/* actual start will be canvas coord + feature_offset */
exon_data.start = regions[j].x1 + feature_offset;
exon_data.end = regions[j].x2;
@@ -1408,7 +1438,7 @@ static FooCanvasItem *drawTranscriptFeature(RunSet run_data, ZMapFeature featur
FooCanvasGroup *parent = run_data->container;
FooCanvasItem *feature_item = run_data->canvas_item;
ZMapWindowCanvasItem canvas_item;
- gboolean has_cds = FALSE, status = TRUE;
+ gboolean has_cds = FALSE, status = TRUE ;
double cds_start = 0.0, cds_end = 0.0 ; /* cds_start < cds_end */
double feature_start, feature_end;
double item_left, item_right;
@@ -1418,7 +1448,7 @@ static FooCanvasItem *drawTranscriptFeature(RunSet run_data, ZMapFeature featur
zmapWindowSeq2CanOffset(&feature_start, &feature_end, feature_offset) ;
- if(status)
+ if (status)
{
if(!feature_item)
{
@@ -1452,17 +1482,19 @@ static FooCanvasItem *drawTranscriptFeature(RunSet run_data, ZMapFeature featur
item_left = x1;
item_right = x2 - factory->line_width;
- if (status && feature_item &&
- feature->feature.transcript.introns &&
- feature->feature.transcript.exons)
+ if (status && feature_item
+ && feature->feature.transcript.introns && feature->feature.transcript.exons)
{
double line_width = 1.5;
double parent_ypos = 0.0;
- int i;
+ int i, num_parts ;
+
+ /* Note that we do assume here that introns and exons have been sorted for position. */
+
parent_ypos = FOO_CANVAS_GROUP(feature_item)->ypos;
-
- for (i = 0 ; i < feature->feature.transcript.introns->len ; i++)
+ num_parts = feature->feature.transcript.introns->len ;
+ for (i = 0 ; i < num_parts ; i++)
{
ZMapFeatureSubPartSpanStruct intron;
FooCanvasItem *intron_line ;
@@ -1475,60 +1507,65 @@ static FooCanvasItem *drawTranscriptFeature(RunSet run_data, ZMapFeature featur
item_bottom = intron_span->x2;
/* clip the coords to the block, extending end to canvas drawing coords. */
- if(!clip_feature_coords(factory, feature, feature_offset, &item_top, &item_bottom))
- continue;
-
- /* set up the item sub feature data */
- intron.start = intron_span->x1;
- intron.end = intron_span->x2;
-
- if(has_cds)
+ if (clip_feature_coords(factory, feature, feature_offset, &item_top, &item_bottom))
{
- if(!((item_bottom < cds_start) || (item_top > cds_end)))
- intron.subpart = ZMAPFEATURE_SUBPART_INTRON_CDS;
+ /* set up the item sub feature data */
+ intron.index = GET_SUBPART_INDEX(feature, feature->feature.transcript.introns, i) ;
+ intron.start = intron_span->x1;
+ intron.end = intron_span->x2;
+
+ if(has_cds)
+ {
+ if(!((item_bottom < cds_start) || (item_top > cds_end)))
+ intron.subpart = ZMAPFEATURE_SUBPART_INTRON_CDS;
+ else
+ intron.subpart = ZMAPFEATURE_SUBPART_INTRON;
+ }
else
intron.subpart = ZMAPFEATURE_SUBPART_INTRON;
+
+ /* this is a sub item we're drawing _within_ the feature_item,
+ * so we need to zero in its space. new_draw_feature_exon does
+ * this for exons */
+ item_top -= parent_ypos;
+ item_bottom -= parent_ypos;
+
+ /* And draw the item. */
+ intron_line = zMapWindowCanvasItemAddInterval(canvas_item, &intron,
+ item_top, item_bottom,
+ item_left, item_right);
}
- else
- intron.subpart = ZMAPFEATURE_SUBPART_INTRON;
-
- /* this is a sub item we're drawing _within_ the feature_item,
- * so we need to zero in its space. new_draw_feature_exon does
- * this for exons */
- item_top -= parent_ypos;
- item_bottom -= parent_ypos;
-
- /* And draw the item. */
- intron_line = zMapWindowCanvasItemAddInterval(canvas_item, &intron,
- item_top, item_bottom,
- item_left, item_right);
}
- for (i = 0; i < feature->feature.transcript.exons->len; i++)
+ for (i = 0 ; i < feature->feature.transcript.exons->len ; i++)
{
ZMapSpan exon_span ;
+ int item_index ;
double item_top, item_bottom ;
exon_span = &g_array_index(feature->feature.transcript.exons, ZMapSpanStruct, i);
-
- item_top = exon_span->x1;
- item_bottom = exon_span->x2;
-
- /* clip the coords to the block, extending end to canvas drawing coords. */
- if (!clip_feature_coords(factory, feature, feature_offset, &item_top, &item_bottom))
- continue;
- new_draw_feature_exon(feature_item, feature_offset,
- item_top, item_bottom,
- cds_start, cds_end,
- item_right, line_width, has_cds);
+ item_index = GET_SUBPART_INDEX(feature, feature->feature.transcript.exons, i) ;
+ item_top = exon_span->x1 ;
+ item_bottom = exon_span->x2 ;
+
+ /* clip the coords to the block, extending end to canvas drawing coords, only
+ * draw if clip works. */
+ if (clip_feature_coords(factory, feature, feature_offset, &item_top, &item_bottom))
+ {
+ new_draw_feature_exon(feature_item, feature_offset,
+ item_index, item_top, item_bottom,
+ cds_start, cds_end,
+ item_right, line_width, has_cds) ;
+ }
}
}
- else if(status && feature_item)
+ else if (status && feature_item)
{
double item_top, item_bottom;
float line_width = 1.5 ;
-
+ int item_index = 1 ;
+
/* item_top gets feature_offset added and item_bottom gets 1 added,
* as feature_start & feature_end have already been through
* zmapWindowSeq2CanOffset(), but we still need to clip_feature_coords(). */
@@ -1542,7 +1579,7 @@ static FooCanvasItem *drawTranscriptFeature(RunSet run_data, ZMapFeature featur
* with using the simple feature code.. Single exons may have a
* cds */
new_draw_feature_exon(feature_item, feature_offset,
- item_top, item_bottom,
+ item_index, item_top, item_bottom,
cds_start, cds_end,
item_right, line_width, has_cds);
}
@@ -1706,13 +1743,16 @@ static gint canvas_allocate_protein_cb(FooCanvasItem *item,
return buffer_size;
}
+
+
static gint canvas_allocate_dna_cb(FooCanvasItem *item,
- ZMapTextItemDrawData draw_data,
+ ZMapTextDrawData draw_data,
gint max_width,
gint buffer_size,
gpointer user_data)
{
+
buffer_size = zMapWindowTextItemCalculateZoomBufferSize(item, draw_data, buffer_size);
--
GitLab