JAL-4227 accept extended WUSS in filter

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

diff --git a/src/jalview/gui/AppVarna.java b/src/jalview/gui/AppVarna.java
index 3a64716..5273aaa 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();
@@ -762,8 +762,9 @@ public class AppVarna extends JInternalFrame
     for (int i = 0; i < bytes.length; i++)
     {
       boolean ok = false;
-      // todo check for ((b >= 'a' && b <= 'z') || (b >= 'A' && b <= 'Z')) if
-      // wanted also
+
+      ok = (bytes[i] >= 'a' && bytes[i] <= 'z') || (bytes[i]>= 'A' && bytes[i] <= 'Z');
+
       for (int j = 0; !ok && (j < PAIRS.length); j++)
       {
         if (bytes[i] == PAIRS[j])