JAL-2773 add new flag to paintAlignment(updateOverview,updateStructures) and first...

[jalview.git] / src / jalview / gui / TreePanel.java

diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java
index 80f0c73..9403057 100755 (executable)
--- a/src/jalview/gui/TreePanel.java
+++ b/src/jalview/gui/TreePanel.java
@@ -493,7 +493,7 @@ public class TreePanel extends GTreePanel
 
     if (treeCanvas.applyToAllViews)
     {
-      final ArrayList<CommandI> commands = new ArrayList<CommandI>();
+      final ArrayList<CommandI> commands = new ArrayList<>();
       for (AlignmentPanel ap : PaintRefresher
               .getAssociatedPanels(av.getSequenceSetId()))
       {
@@ -550,13 +550,14 @@ public class TreePanel extends GTreePanel
 
   public CommandI sortAlignmentIn(AlignmentPanel ap)
   {
+    // TODO: move to alignment view controller
     AlignmentViewport viewport = ap.av;
     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
     AlignmentSorter.sortByTree(viewport.getAlignment(), tree);
     CommandI undo;
     undo = new OrderCommand("Tree Sort", oldOrder, viewport.getAlignment());
 
-    ap.paintAlignment(true);
+    ap.paintAlignment(true, false);
     return undo;
   }
 
@@ -793,19 +794,17 @@ public class TreePanel extends GTreePanel
             }
             if (newname == null)
             {
-              SequenceFeature sf[] = sq.getSequenceFeatures();
-              for (int i = 0; sf != null && i < sf.length; i++)
+              List<SequenceFeature> features = sq.getFeatures()
+                      .getPositionalFeatures(labelClass);
+              for (SequenceFeature feature : features)
               {
-                if (sf[i].getType().equals(labelClass))
+                if (newname == null)
+                {
+                  newname = feature.getDescription();
+                }
+                else
                 {
-                  if (newname == null)
-                  {
-                    newname = new String(sf[i].getDescription());
-                  }
-                  else
-                  {
-                    newname = newname + "; " + sf[i].getDescription();
-                  }
+                  newname = newname + "; " + feature.getDescription();
                 }
               }
             }