Merge develop to Release_2_8_3_Branch

[jalview.git] / src / jalview / controller / AlignViewController.java

diff --git a/src/jalview/controller/AlignViewController.java b/src/jalview/controller/AlignViewController.java
index 4d734c7..972b6ab 100644 (file)
--- a/src/jalview/controller/AlignViewController.java
+++ b/src/jalview/controller/AlignViewController.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.
  * 
@@ -79,14 +79,26 @@ public class AlignViewController implements AlignViewControllerI
   @Override
   public boolean makeGroupsFromSelection()
   {
-
-    if (viewport.getSelectionGroup() != null)
+    SequenceGroup sg = viewport.getSelectionGroup();
+    ColumnSelection cs = viewport.getColumnSelection();
+    SequenceGroup[] gps = null;
+    if (sg != null
+            && (cs == null || cs.getSelected() == null || cs.size() == 0))
     {
-      SequenceGroup[] gps = jalview.analysis.Grouping.makeGroupsFrom(
+      gps = jalview.analysis.Grouping.makeGroupsFrom(
               viewport.getSequenceSelection(),
               viewport.getAlignmentView(true).getSequenceStrings(
                       viewport.getGapCharacter()), viewport.getAlignment()
                       .getGroups());
+    } else {
+      if (cs!=null) {
+        gps = jalview.analysis.Grouping.makeGroupsFromCols(
+                (sg == null) ? viewport.getAlignment().getSequencesArray()
+                        : sg.getSequences().toArray(new SequenceI[0]), cs,
+                viewport.getAlignment().getGroups());
+      }
+    }
+    if (gps!=null) {
       viewport.getAlignment().deleteAllGroups();
       viewport.clearSequenceColours();
       viewport.setSelectionGroup(null);
@@ -167,13 +179,7 @@ public class AlignViewController implements AlignViewControllerI
       int tfeat = 0;
       if (sq != null)
       {
-        SequenceI dsq = sq.getDatasetSequence();
-        while (dsq.getDatasetSequence() != null)
-        {
-          dsq = dsq.getDatasetSequence();
-        }
-        ;
-        SequenceFeature[] sf = dsq.getSequenceFeatures();
+        SequenceFeature[] sf = sq.getSequenceFeatures();
         if (sf != null)
         {
           int ist = sq.findIndex(sq.getStart());