X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fcontroller%2FAlignViewController.java;h=972b6ab43282f0ef9e913b452a146ba3ddbfbcae;hb=041905b00ec635c1764f565a22b2ecf762a9a75b;hp=3cf8000969eb2ed46dbf4fd95e014367125d3d99;hpb=770a6a7d91b1f46a7d0372b987f859b35f286ad8;p=jalview.git

diff --git a/src/jalview/controller/AlignViewController.java b/src/jalview/controller/AlignViewController.java
index 3cf8000..972b6ab 100644
--- 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.
  * 
@@ -20,11 +20,6 @@
  */
 package jalview.controller;
 
-import java.awt.Color;
-import java.util.ArrayList;
-import java.util.BitSet;
-import java.util.List;
-
 import jalview.analysis.AlignmentSorter;
 import jalview.api.AlignViewControllerGuiI;
 import jalview.api.AlignViewControllerI;
@@ -33,12 +28,17 @@ import jalview.api.AlignmentViewPanel;
 import jalview.api.FeatureRenderer;
 import jalview.commands.OrderCommand;
 import jalview.datamodel.AlignmentI;
-import jalview.datamodel.AnnotatedCollectionI;
 import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
+import jalview.util.MessageManager;
+
+import java.awt.Color;
+import java.util.ArrayList;
+import java.util.BitSet;
+import java.util.List;
 
 public class AlignViewController implements AlignViewControllerI
 {
@@ -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);
@@ -100,7 +112,9 @@ public class AlignViewController implements AlignViewControllerI
                 (int) (Math.random() * 255), (int) (Math.random() * 255));
         col = col.brighter();
         for (SequenceI sq : gps[g].getSequences(null))
+        {
           viewport.setSequenceColour(sq, col);
+        }
       }
       return true;
     }
@@ -165,13 +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());
@@ -280,16 +288,17 @@ public class AlignViewController implements AlignViewControllerI
       }
       viewport.setColumnSelection(cs);
       alignPanel.paintAlignment(true);
-      avcg.setStatus((toggle ? "Toggled " : "Marked ")
-              + (invert ? (alw - alStart) - bs.cardinality() : bs
-                      .cardinality()) + " columns "
-              + (invert ? "not " : "") + "containing features of type "
-              + featureType + " across " + nseq + " sequence(s)");
+      avcg.setStatus(MessageManager.formatMessage("label.view_controller_toggled_marked",
+    		  new String[]{
+    	  			(toggle ? MessageManager.getString("label.toggled") : MessageManager.getString("label.marked")),
+    	  			(invert ? (Integer.valueOf((alw - alStart) - bs.cardinality()).toString()):(Integer.valueOf(bs.cardinality()).toString())),
+    	  			featureType, Integer.valueOf(nseq).toString()
+      		 	}));
       return true;
     }
     else
     {
-      avcg.setStatus("No features of type " + featureType + " found.");
+      avcg.setStatus(MessageManager.formatMessage("label.no_feature_of_type_found", new String[]{featureType}));
       if (!extendCurrent && cs != null)
       {
         cs.clear();
@@ -299,6 +308,8 @@ public class AlignViewController implements AlignViewControllerI
     }
   }
 
+
+
   @Override
   public void sortAlignmentByFeatureDensity(String[] typ)
   {