add id of clone that homol matched to.

src/include/ZMap/zmapFeature.h

@@ -25,9 +25,9 @@
  * Description: Data structures describing a sequence feature.
  *              
  * HISTORY:
- * Last edited: Feb 14 14:10 2008 (edgrif)
+ * Last edited: Feb 21 12:49 2008 (edgrif)
  * Created: Fri Jun 11 08:37:19 2004 (edgrif)
- * CVS info:   $Id: zmapFeature.h,v 1.137 2008-02-14 15:11:32 edgrif Exp $
+ * CVS info:   $Id: zmapFeature.h,v 1.138 2008-02-21 15:40:10 edgrif Exp $
  *-------------------------------------------------------------------
  */
 #ifndef ZMAP_FEATURE_H
@@ -333,6 +333,7 @@ typedef struct
 
   int length ;						    /* Length of homol/align etc. */
 
+  GQuark clone_id ;					    /* Clone this match is aligned to. */
 
   /* This is all changing now.... */
   /* Because we don't have a strand in this struct these can be in reverse order, we should NOT do
@@ -356,6 +357,8 @@ typedef struct
 
     unsigned int has_sequence : 1 ;			    /* This homology has sequence in the database. */
 
+    unsigned int has_clone_id : 1 ;			    /* This homol feature is matched to this clone. */
+
   } flags ;
 
 } ZMapHomolStruct, *ZMapHomol ;
@@ -594,6 +597,7 @@ gboolean zMapFeatureAddTranscriptExonIntron(ZMapFeature feature,
 					    ZMapSpanStruct *exon, ZMapSpanStruct *intron) ;
 void zMapFeatureTranscriptExonForeach(ZMapFeature feature, GFunc function, gpointer user_data);
 gboolean zMapFeatureAddAlignmentData(ZMapFeature feature,
+				     GQuark clone_id,
 				     int query_start, int query_end,
 				     ZMapHomolType homol_type,
 				     int query_length,

src/zmapFeature/zmapFeature.c

@@ -27,9 +27,9 @@
  *              
  * Exported functions: See zmapView_P.h
  * HISTORY:
- * Last edited: Feb 20 14:19 2008 (edgrif)
+ * Last edited: Feb 21 12:33 2008 (edgrif)
  * Created: Fri Jul 16 13:05:58 2004 (edgrif)
- * CVS info:   $Id: zmapFeature.c,v 1.87 2008-02-20 14:19:37 edgrif Exp $
+ * CVS info:   $Id: zmapFeature.c,v 1.88 2008-02-21 15:40:10 edgrif Exp $
  *-------------------------------------------------------------------
  */
 
@@ -765,6 +765,7 @@ gboolean zMapFeatureAddSplice(ZMapFeature feature, ZMapBoundaryType boundary)
  * Adds homology data to a feature which may be empty or may already have partial features.
  *  */
 gboolean zMapFeatureAddAlignmentData(ZMapFeature feature,
+				     GQuark clone_id,
 				     int query_start, int query_end,
 				     ZMapHomolType homol_type,
 				     int query_length,
@@ -777,6 +778,12 @@ gboolean zMapFeatureAddAlignmentData(ZMapFeature feature,
 
   zMapAssert(feature && feature->type == ZMAPSTYLE_MODE_ALIGNMENT) ;
 
+  if (clone_id)
+    {
+      feature->feature.homol.flags.has_clone_id = TRUE ;
+      feature->feature.homol.clone_id = clone_id ;
+    }
+
   feature->feature.homol.type = homol_type ;
   feature->feature.homol.strand = query_strand ;
   feature->feature.homol.target_phase = target_phase ;