Fix up the three frame func so it will reuse existing pep features and redo...

Fix up the three frame func so it will reuse existing pep features and redo their sequence for revcomping

src/zmapFeature/zmapFeatureUtils.c

@@ -26,9 +26,9 @@
  *              
  * Exported functions: See ZMap/zmapFeature.h
  * HISTORY:
- * Last edited: Mar  2 11:50 2007 (rds)
+ * Last edited: Mar 13 13:48 2007 (edgrif)
  * Created: Tue Nov 2 2004 (rnc)
- * CVS info:   $Id: zmapFeatureUtils.c,v 1.46 2007-03-02 14:57:21 rds Exp $
+ * CVS info:   $Id: zmapFeatureUtils.c,v 1.47 2007-03-13 16:12:36 edgrif Exp $
  *-------------------------------------------------------------------
  */
 
@@ -668,35 +668,49 @@ ZMapFeature zMapFeatureCopy(ZMapFeature feature)
 }
 
 
+/* Creates the three reading frame translations for a piece of dna. Note that the function
+ * will create the three frame set and a feature for each translation if they don't
+ * already exist. If they do exist, the existing translation text is simply replaced
+ * with a new translation (e.g. after a revcomp the translation must be redone).
+ * 
+ * This must be done on a per block basis as each block has its own dna. */
 gboolean zMapFeatureBlockThreeFrameTranslation(ZMapFeatureBlock block, ZMapFeatureSet *set_out)
 {
+  gboolean result = FALSE ;
   ZMapFeatureSet feature_set = NULL;
   ZMapFeatureTypeStyle style = NULL;
   ZMapFeatureContext context = NULL;
   GQuark style_id = 0, feature_set_id = 0;
-  gboolean still_good = FALSE, created = FALSE;
+  gboolean new_set = FALSE ;
 
   feature_set_id = zMapFeatureSetCreateID(ZMAP_FIXED_STYLE_3FT_NAME);
-  style_id       = zMapStyleCreateID(ZMAP_FIXED_STYLE_3FT_NAME);
-
-  if(block->sequence.length)
-    still_good = TRUE;
+  style_id = zMapStyleCreateID(ZMAP_FIXED_STYLE_3FT_NAME);
 
-  if(!(context = (ZMapFeatureContext)(zMapFeatureGetParentGroup((ZMapFeatureAny)block, 
-                                                                ZMAPFEATURE_STRUCT_CONTEXT))))
-    still_good = FALSE;
+  if (block->sequence.length)
+    result = TRUE;
 
-  if((feature_set = (ZMapFeatureSet)(g_datalist_id_get_data(&(block->feature_sets), feature_set_id))))
-    still_good = FALSE;         /* We've already got one */
+  if (!(context = (ZMapFeatureContext)(zMapFeatureGetParentGroup((ZMapFeatureAny)block, ZMAPFEATURE_STRUCT_CONTEXT))))
+    result = FALSE;
 
-  if (still_good && (style = zMapFindStyle(context->styles, style_id)) != NULL)
+  /* If we don't have a 3 frame feature set then make one. */
+  if (result)
     {
-      feature_set = zMapFeatureSetCreate(ZMAP_FIXED_STYLE_3FT_NAME, NULL);
-      feature_set->style = style;
-      created = TRUE;
+      if (!(feature_set = (ZMapFeatureSet)(g_datalist_id_get_data(&(block->feature_sets), feature_set_id))))
+	{
+	  if ((style = zMapFindStyle(context->styles, style_id)) != NULL)
+	    {
+	      feature_set = zMapFeatureSetCreate(ZMAP_FIXED_STYLE_3FT_NAME, NULL);
+	      feature_set->style = style;
+	      new_set = TRUE ;
+	    }
+	  else
+	    result = FALSE;
+	}
+      else
+	style = feature_set->style ;
     }
 
-  if(still_good && feature_set)
+  if (result && feature_set)
     {
       int i, frame_offset;
       char *seq = NULL, *f_name = NULL, *s_name;
@@ -709,33 +723,46 @@ gboolean zMapFeatureBlockThreeFrameTranslation(ZMapFeatureBlock block, ZMapFeatu
 
       frame_offset = 0 - ZMAPFRAME_0; /* set this up ! */
 
-      for(i = ZMAPFRAME_0; seq && *seq && i <= ZMAPFRAME_2; i++, seq++)
+      for (i = ZMAPFRAME_0; seq && *seq && i <= ZMAPFRAME_2; i++, seq++)
         {
-          threeft = zMapFeatureCreateEmpty();
-
-          f_name = g_strdup_printf("%s_frame_%d",
+	  f_name = g_strdup_printf("%s_frame_%d",
 				   g_quark_to_string(feature_set_id),
 				   i);
 
           pep = zMapPeptideCreateSafely(NULL, NULL, seq, NULL, FALSE);
-          
-          threeft->text = g_strdup(zMapPeptideSequence(pep));
-          
-          zMapFeatureAddStandardData(threeft, f_name, f_name,
-                                     s_name, "sequence",
-                                     ZMAPFEATURE_PEP_SEQUENCE, style,
-                                     i, zMapPeptideLength(pep) * 3 + i,
-                                     FALSE, 0.0,
-                                     ZMAPSTRAND_NONE, ZMAPPHASE_NONE);
-
-          zMapFeatureSetAddFeature(feature_set, threeft);
+
+	  /* For a new feature set we create new features, otherwise we simply replace the translation. */
+	  if (new_set)
+	    {
+	      threeft = zMapFeatureCreateEmpty();
+
+	      zMapFeatureAddStandardData(threeft, f_name, f_name,
+					 s_name, "sequence",
+					 ZMAPFEATURE_PEP_SEQUENCE, style,
+					 i, zMapPeptideLength(pep) * 3 + i,
+					 FALSE, 0.0,
+					 ZMAPSTRAND_NONE, ZMAPPHASE_NONE);
+
+	      zMapFeatureSetAddFeature(feature_set, threeft);
+	    }
+	  else
+	    {
+	      threeft = zMapFeatureSetGetFeatureByID(feature_set, g_quark_from_string(f_name)) ;
+	      zMapAssert(threeft) ;
+
+	      g_free(threeft->text) ;
+	    }
+
+          threeft->text = g_strdup(zMapPeptideSequence(pep)) ;
+
+	  zMapPeptideDestroy(pep) ;
         }
     }
 
-  if(set_out)
+  if (set_out)
     *set_out = feature_set;
 
-  return created;
+  return result ;
 }