when changing groups of featurelocs check they are not partial

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@13143 ee4ac58c-ac51-4696-9907-e4b3aa274f04

uk/ac/sanger/artemis/chado/IBatisDAO.java

@@ -878,10 +878,24 @@ public class IBatisDAO extends GmodDAO
         FeatureLoc thisFeatureLoc = (FeatureLoc) featureLocs.get(i);
         int thisSrcFeatureId = 
           thisFeatureLoc.getFeatureBySrcFeatureId().getFeatureId();
+        
         if(srcFeatureId != thisSrcFeatureId)
+        {
+          // check to see if the featureloc fmin/fmax are marked as partial
+          // if they are then ignore as they are likely to be the end of
+          // a contig
+          boolean changed = false;
+          if(!thisFeatureLoc.isFminPartial())
           {
             thisFeatureLoc.setFmin(thisFeatureLoc.getFmin()+diffFmin);
+            changed = true;
+          }
+          if(!thisFeatureLoc.isFmaxPartial())
+          {
             thisFeatureLoc.setFmax(thisFeatureLoc.getFmax()+diffFmax);
+            changed = true;
+          }
+          if(changed)
             sqlMap.update("updateFeatureLoc", thisFeatureLoc);
         }
       }