JAL-1687 ignore case when determining if sequence matches consensus

[jalview.git] / src / jalview / io / vamsas / Sequencemapping.java

diff --git a/src/jalview/io/vamsas/Sequencemapping.java b/src/jalview/io/vamsas/Sequencemapping.java
index 6fa49a0..4929a06 100644 (file)
--- a/src/jalview/io/vamsas/Sequencemapping.java
+++ b/src/jalview/io/vamsas/Sequencemapping.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -21,6 +21,7 @@
 package jalview.io.vamsas;
 
 import jalview.datamodel.AlignedCodonFrame;
+import jalview.datamodel.AlignmentI;
 import jalview.datamodel.Mapping;
 import jalview.datamodel.SequenceI;
 import jalview.gui.Desktop;
@@ -325,19 +326,17 @@ public class Sequencemapping extends Rangetype
     }
     // create mapping storage object and make each dataset alignment reference
     // it.
-    jalview.datamodel.AlignmentI dsLoc = (jalview.datamodel.AlignmentI) getvObj2jv(sdloc
-            .getV_parent());
-    jalview.datamodel.AlignmentI dsMap = (jalview.datamodel.AlignmentI) getvObj2jv(sdmap
-            .getV_parent());
-    AlignedCodonFrame afc = new AlignedCodonFrame();
+    AlignmentI dsLoc = (AlignmentI) getvObj2jv(sdloc.getV_parent());
+    AlignmentI dsMap = (AlignmentI) getvObj2jv(sdmap.getV_parent());
+    AlignedCodonFrame acf = new AlignedCodonFrame();
 
     if (dsLoc != null && dsLoc != dsMap)
     {
-      dsLoc.addCodonFrame(afc);
+      dsLoc.addCodonFrame(acf);
     }
     if (dsMap != null)
     {
-      dsMap.addCodonFrame(afc);
+      dsMap.addCodonFrame(acf);
     }
     // create and add the new mapping to (each) dataset's codonFrame
 
@@ -350,24 +349,22 @@ public class Sequencemapping extends Rangetype
         mapping = new jalview.util.MapList(mapping.getToRanges(),
                 mapping.getFromRanges(), mapping.getToRatio(),
                 mapping.getFromRatio());
-        afc.addMap(to, from, mapping);
+        acf.addMap(to, from, mapping);
       }
       else
       {
         mapping = this.parsemapType(sequenceMapping, 3, 1); // correct sense
-        afc.addMap(from, to, mapping);
+        acf.addMap(from, to, mapping);
       }
     }
     else
     {
       mapping = this.parsemapType(sequenceMapping, 1, 1); // correct sense
-      afc.addMap(from, to, mapping);
+      acf.addMap(from, to, mapping);
     }
     bindjvvobj(mapping, sequenceMapping);
     jalview.structure.StructureSelectionManager
-            .getStructureSelectionManager(Desktop.instance).addMappings(
-                    new AlignedCodonFrame[]
-                    { afc });
+            .getStructureSelectionManager(Desktop.instance).addMapping(acf);
     // Try to link up any conjugate database references in the two sequences
     // matchConjugateDBRefs(from, to, mapping);
     // Try to propagate any dbrefs across this mapping.