X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAppVarna.java;h=5273aaa703cc5006913525d2f6c60a749478049d;hb=0590202f01c201d5e0dc0be25024b0a9ad2dd3de;hp=1bbe8d80ac6e21a17bd2f8b7e4fc9227cb5a930c;hpb=3d0101179759ef157b088ea135423cd909512d9f;p=jalview.git

diff --git a/src/jalview/gui/AppVarna.java b/src/jalview/gui/AppVarna.java
index 1bbe8d8..5273aaa 100644
--- 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,
@@ -120,6 +119,15 @@ public class AppVarna extends JInternalFrame
       }
     }
 
+    /**
+     * highlight a region from start to end (inclusive) on rna
+     * 
+     * @param rna
+     * @param start
+     *          - first base pair index (from 0)
+     * @param end
+     *          - last base pair index (from 0)
+     */
     public void highlightRegion(RNA rna, int start, int end)
     {
       clearLastSelection();
@@ -207,6 +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();
@@ -397,7 +406,8 @@ public class AppVarna extends JInternalFrame
     RnaModel rnaModel = models.get(rna);
     if (rnaModel.seq == sequence)
     {
-      int highlightPos = rnaModel.gapped ? index : position - 1;
+      int highlightPos = rnaModel.gapped ? index
+              : position - sequence.getStart();
       mouseOverHighlighter.highlightRegion(rna, highlightPos, highlightPos);
       vab.updateSelectedRNA(rna);
     }
@@ -418,15 +428,28 @@ public class AppVarna extends JInternalFrame
     {
       return;
     }
-    if (seqsel != null && seqsel.getSize() > 0)
+
+    RnaModel rnaModel = models.get(rna);
+
+    if (seqsel != null && seqsel.getSize() > 0
+            && seqsel.contains(rnaModel.seq))
     {
       int start = seqsel.getStartRes(), end = seqsel.getEndRes();
-      ShiftList shift = offsets.get(rna);
-      if (shift != null)
+      if (rnaModel.gapped)
+      {
+        ShiftList shift = offsets.get(rna);
+        if (shift != null)
+        {
+          start = shift.shift(start);
+          end = shift.shift(end);
+        }
+      }
+      else
       {
-        start = shift.shift(start);
-        end = shift.shift(end);
+        start = rnaModel.seq.findPosition(start) - rnaModel.seq.getStart();
+        end = rnaModel.seq.findPosition(end) - rnaModel.seq.getStart();
       }
+
       selectionHighlighter.highlightRegion(rna, start, end);
       selectionHighlighter.getLastHighlight()
               .setOutlineColor(seqsel.getOutlineColour());
@@ -628,11 +651,10 @@ public class AppVarna extends JInternalFrame
     ShiftList offset = new ShiftList();
     int ofstart = -1;
     int sleng = seq.getLength();
-    char[] seqChars = seq.getSequence();
 
     for (int i = 0; i < sleng; i++)
     {
-      if (Comparison.isGap(seqChars[i]))
+      if (Comparison.isGap(seq.getCharAt(i)))
       {
         if (ofstart == -1)
         {
@@ -740,8 +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])