From 8d48cd91b192ef2673b66e9f6eed2425e67a5503 Mon Sep 17 00:00:00 2001
From: edgrif <edgrif>
Date: Sun, 17 Jan 2010 10:29:11 +0000
Subject: [PATCH] fix bug in exon number reporting when revcompd.
---
src/zmapWindow/zmapWindowItemFactory.c | 25 ++++++++++++++-----------
1 file changed, 14 insertions(+), 11 deletions(-)
diff --git a/src/zmapWindow/zmapWindowItemFactory.c b/src/zmapWindow/zmapWindowItemFactory.c
index 58a8f279e..fe3139915 100755
--- a/src/zmapWindow/zmapWindowItemFactory.c
+++ b/src/zmapWindow/zmapWindowItemFactory.c
@@ -28,9 +28,9 @@
*
* Exported functions: See zmapWindowItemFactory.h
* HISTORY:
- * Last edited: Jan 13 13:49 2010 (edgrif)
+ * Last edited: Jan 17 10:28 2010 (edgrif)
* Created: Mon Sep 25 09:09:52 2006 (rds)
- * CVS info: $Id: zmapWindowItemFactory.c,v 1.71 2010-01-14 09:05:42 edgrif Exp $
+ * CVS info: $Id: zmapWindowItemFactory.c,v 1.72 2010-01-17 10:29:11 edgrif Exp $
*-------------------------------------------------------------------
*/
@@ -88,9 +88,11 @@ typedef struct _RunSetStruct
} RunSetStruct ;
-#define GET_SUBPART_INDEX(FEATURE, SUBPART_ARRAY, ARRAY_INDEX) \
- ((FEATURE)->strand == ZMAPSTRAND_FORWARD ? (ARRAY_INDEX) + 1 : (SUBPART_ARRAY)->len - (ARRAY_INDEX))
-
+/* Noddy macro to calculate the index of sub-parts of features like exons, e.g. Exon 1, 2 etc. */
+#define GET_SUBPART_INDEX(REVCOMP, FEATURE, SUBPART_ARRAY, ARRAY_INDEX) \
+ (REVCOMP \
+ ? ((FEATURE)->strand == ZMAPSTRAND_FORWARD ? (SUBPART_ARRAY)->len - (ARRAY_INDEX) : (ARRAY_INDEX) + 1) \
+ : ((FEATURE)->strand == ZMAPSTRAND_FORWARD ? (ARRAY_INDEX) + 1 : (SUBPART_ARRAY)->len - (ARRAY_INDEX)) )
static void copyCheckMethodTable(const ZMapWindowFToIFactoryMethodsStruct *table_in,
@@ -995,7 +997,7 @@ static FooCanvasItem *drawAlignFeature(RunSet run_data, ZMapFeature feature,
ZMapWindowFToIFactory factory = run_data->factory;
ZMapFeatureBlock block = run_data->block;
guint line_width = 0;
-
+ gboolean rev_comped = ((ZMapWindow)(factory->user_data))->revcomped_features ;
if ((!zMapStyleIsShowGaps(style) || !(feature->feature.homol.align)))
{
@@ -1193,7 +1195,7 @@ static FooCanvasItem *drawAlignFeature(RunSet run_data, ZMapFeature feature,
double gap_top, gap_bottom;
gap_data.subpart = ZMAPFEATURE_SUBPART_GAP ;
- gap_data.index = GET_SUBPART_INDEX(feature, feature->feature.homol.align, i) ;
+ gap_data.index = GET_SUBPART_INDEX(rev_comped, feature, feature->feature.homol.align, i) ;
gap_data.start = gap_block.t1;
gap_data.end = gap_block.t2;
#ifdef NO_NEED
@@ -1219,7 +1221,7 @@ 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.index = GET_SUBPART_INDEX(rev_comped, feature, feature->feature.homol.align, i) ;
align_data.start = match_block->t1 ;
align_data.end = match_block->t2 ;
#ifdef NO_NEED
@@ -1245,7 +1247,7 @@ static FooCanvasItem *drawAlignFeature(RunSet run_data, ZMapFeature feature,
ZMapFeatureSubPartSpanStruct align_data;
align_data.subpart = ZMAPFEATURE_SUBPART_MATCH ;
- align_data.index = GET_SUBPART_INDEX(feature, feature->feature.homol.align, 0) ;
+ align_data.index = GET_SUBPART_INDEX(rev_comped, feature, feature->feature.homol.align, 0) ;
align_data.start = first_match_block->t1 ;
align_data.end = first_match_block->t2 ;
#ifdef NO_NEED
@@ -1442,6 +1444,7 @@ static FooCanvasItem *drawTranscriptFeature(RunSet run_data, ZMapFeature featur
double cds_start = 0.0, cds_end = 0.0 ; /* cds_start < cds_end */
double feature_start, feature_end;
double item_left, item_right;
+ gboolean rev_comped = ((ZMapWindow)(factory->user_data))->revcomped_features ;
feature_start = y1;
feature_end = y2;
@@ -1510,7 +1513,7 @@ static FooCanvasItem *drawTranscriptFeature(RunSet run_data, ZMapFeature featur
if (clip_feature_coords(factory, feature, feature_offset, &item_top, &item_bottom))
{
/* set up the item sub feature data */
- intron.index = GET_SUBPART_INDEX(feature, feature->feature.transcript.introns, i) ;
+ intron.index = GET_SUBPART_INDEX(rev_comped, feature, feature->feature.transcript.introns, i) ;
intron.start = intron_span->x1;
intron.end = intron_span->x2;
@@ -1545,7 +1548,7 @@ static FooCanvasItem *drawTranscriptFeature(RunSet run_data, ZMapFeature featur
exon_span = &g_array_index(feature->feature.transcript.exons, ZMapSpanStruct, i);
- item_index = GET_SUBPART_INDEX(feature, feature->feature.transcript.exons, i) ;
+ item_index = GET_SUBPART_INDEX(rev_comped, feature, feature->feature.transcript.exons, i) ;
item_top = exon_span->x1 ;
item_bottom = exon_span->x2 ;
--
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