From e58d5a56b3f3595be8427e1a8f9e78f3cc2a74c2 Mon Sep 17 00:00:00 2001
From: edgrif <edgrif>
Date: Wed, 18 Aug 2010 09:16:53 +0000
Subject: [PATCH] add function to test whether an alignment is gapped.
---
src/include/ZMap/zmapFeature.h | 5 +++--
src/zmapFeature/zmapFeature.c | 33 +++++++++++++++++++++++++++++++--
2 files changed, 34 insertions(+), 4 deletions(-)
diff --git a/src/include/ZMap/zmapFeature.h b/src/include/ZMap/zmapFeature.h
index 792107b96..f16a85996 100755
--- a/src/include/ZMap/zmapFeature.h
+++ b/src/include/ZMap/zmapFeature.h
@@ -25,9 +25,9 @@
* Description: Data structures describing a sequence feature.
*
* HISTORY:
- * Last edited: Aug 11 09:47 2010 (edgrif)
+ * Last edited: Aug 17 08:35 2010 (edgrif)
* Created: Fri Jun 11 08:37:19 2004 (edgrif)
- * CVS info: $Id: zmapFeature.h,v 1.178 2010-08-11 08:47:36 edgrif Exp $
+ * CVS info: $Id: zmapFeature.h,v 1.179 2010-08-18 09:16:53 edgrif Exp $
*-------------------------------------------------------------------
*/
#ifndef ZMAP_FEATURE_H
@@ -782,6 +782,7 @@ gboolean zMapFeatureAddAlignmentData(ZMapFeature feature,
ZMapPhase target_phase,
GArray *gaps, unsigned int align_error,
gboolean has_local_sequence) ;
+gboolean zMapFeatureAlignmentIsGapped(ZMapFeature feature) ;
gboolean zMapFeatureAddAssemblyPathData(ZMapFeature feature,
int length, ZMapStrand strand, GArray *path) ;
gboolean zMapFeatureSetCoords(ZMapStrand strand, int *start, int *end,
diff --git a/src/zmapFeature/zmapFeature.c b/src/zmapFeature/zmapFeature.c
index 0f35b3e59..894ef1517 100755
--- a/src/zmapFeature/zmapFeature.c
+++ b/src/zmapFeature/zmapFeature.c
@@ -28,9 +28,9 @@
*
* Exported functions: See zmapView_P.h
* HISTORY:
- * Last edited: Aug 5 15:01 2010 (edgrif)
+ * Last edited: Aug 17 08:42 2010 (edgrif)
* Created: Fri Jul 16 13:05:58 2004 (edgrif)
- * CVS info: $Id: zmapFeature.c,v 1.132 2010-08-09 09:04:30 edgrif Exp $
+ * CVS info: $Id: zmapFeature.c,v 1.133 2010-08-18 09:16:53 edgrif Exp $
*-------------------------------------------------------------------
*/
@@ -832,6 +832,35 @@ gboolean zMapFeatureAddAlignmentData(ZMapFeature feature,
return result ;
}
+/* Returns TRUE if alignment is gapped, FALSE otherwise. NOTE that sometimes
+ * we are passed data for an alignment feature which must represent a gapped
+ * alignment but we are not passed the gap data. This test all this. */
+gboolean zMapFeatureAlignmentIsGapped(ZMapFeature feature)
+{
+ gboolean result = FALSE ;
+
+ zMapAssert(zMapFeatureIsValidFull(feature, ZMAPFEATURE_STRUCT_FEATURE)) ;
+
+ if (feature->type == ZMAPSTYLE_MODE_ALIGNMENT)
+ {
+ int ref_length, match_length ;
+
+ ref_length = (feature->x2 - feature->x1) + 1 ;
+
+ match_length = (feature->feature.homol.y2 - feature->feature.homol.y1) + 1 ;
+ if (feature->feature.homol.type != ZMAPHOMOL_N_HOMOL)
+ match_length *= 3 ;
+
+ if (ref_length != match_length)
+ result = TRUE ;
+ }
+
+ return result ;
+}
+
+
+
+
/*!
* Adds assembly path data to a feature.
* */
--
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