Merge branch 'develop' into features/JAL-518_justify_seqs_in_region

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

diff --git a/src/jalview/gui/AppVarna.java b/src/jalview/gui/AppVarna.java
index 3a64716..f529316 100644 (file)
--- a/src/jalview/gui/AppVarna.java
+++ b/src/jalview/gui/AppVarna.java
@@ -20,23 +20,6 @@
  */
 package jalview.gui;
 
-import jalview.analysis.AlignSeq;
-import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.ColumnSelection;
-import jalview.datamodel.HiddenColumns;
-import jalview.datamodel.RnaViewerModel;
-import jalview.datamodel.SequenceGroup;
-import jalview.datamodel.SequenceI;
-import jalview.ext.varna.RnaModel;
-import jalview.structure.SecondaryStructureListener;
-import jalview.structure.SelectionListener;
-import jalview.structure.SelectionSource;
-import jalview.structure.StructureSelectionManager;
-import jalview.structure.VamsasSource;
-import jalview.util.Comparison;
-import jalview.util.MessageManager;
-import jalview.util.ShiftList;
-
 import java.awt.BorderLayout;
 import java.awt.Color;
 import java.util.Collection;
@@ -60,6 +43,22 @@ import fr.orsay.lri.varna.models.FullBackup;
 import fr.orsay.lri.varna.models.annotations.HighlightRegionAnnotation;
 import fr.orsay.lri.varna.models.rna.ModeleBase;
 import fr.orsay.lri.varna.models.rna.RNA;
+import jalview.analysis.AlignSeq;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
+import jalview.datamodel.RnaViewerModel;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.ext.varna.RnaModel;
+import jalview.structure.SecondaryStructureListener;
+import jalview.structure.SelectionListener;
+import jalview.structure.SelectionSource;
+import jalview.structure.StructureSelectionManager;
+import jalview.structure.VamsasSource;
+import jalview.util.Comparison;
+import jalview.util.MessageManager;
+import jalview.util.ShiftList;
 
 public class AppVarna extends JInternalFrame
         implements SelectionListener, SecondaryStructureListener,
@@ -216,6 +215,7 @@ public class AppVarna extends JInternalFrame
    */
   protected AppVarna(AlignmentPanel ap)
   {
+    this.setFrameIcon(null);
     this.ap = ap;
     this.viewId = System.currentTimeMillis() + "." + this.hashCode();
     vab = new AppVarnaBinding();
@@ -476,7 +476,8 @@ public class AppVarna extends JInternalFrame
       if (shift != null)
       {
         int i = shift.shift(newBase.getIndex());
-        // System.err.println("shifted "+(arg1.getIndex())+" to "+i);
+        // jalview.bin.Console.errPrintln("shifted "+(arg1.getIndex())+" to
+        // "+i);
         ssm.mouseOverVamsasSequence(seq, i, this);
       }
       else