(JAL-942) more tweaking mapping between 2-struct and seqs

diff --git a/src/jalview/gui/AppVarna.java b/src/jalview/gui/AppVarna.java
index 06de21f..cbb3f95 100644 (file)
--- a/src/jalview/gui/AppVarna.java
+++ b/src/jalview/gui/AppVarna.java
@@ -190,7 +190,7 @@ public class AppVarna extends JInternalFrame implements
       {
         if (ofstart > -1)
         {
-          offset.addShift(ofstart, ofstart - i);
+          offset.addShift(offset.shift(ofstart), ofstart - i);
           ofstart = -1;
         }
       }
@@ -198,7 +198,7 @@ public class AppVarna extends JInternalFrame implements
     // final gap
     if (ofstart > -1)
     {
-      offset.addShift(ofstart, ofstart - sleng);
+      offset.addShift(offset.shift(ofstart), ofstart - sleng);
       ofstart = -1;
     }
     String newSeq = rnaTrim.getSeq().replace("-", "");
@@ -327,12 +327,14 @@ public class AppVarna extends JInternalFrame implements
   public void mouseOverSequence(SequenceI sequence, int index)
   {
     RNA rna = vab.getSelectedRNA();
-    if (rnas.get(sequence) == rna)
+    if (seqs.get(rna) == sequence)
     {
       ShiftList shift = offsets.get(rna);
       if (shift != null)
       {
-        index = shift.shift(index);
+   //      System.err.print("Orig pos:"+index);
+         index = shift.shift(index);
+   //      System.err.println("\nFinal pos:"+index);
       }
       mouseOverHighlighter.highlightRegion(rna, index, index);
       vab.updateSelectedRNA(rna);
@@ -388,9 +390,9 @@ public class AppVarna extends JInternalFrame implements
     {
       if (shift != null)
       {
-        int i=shift.shift(arg1.getIndex());
-        ssm.mouseOverVamsasSequence(seq,
-                i, this);
+        int i = shift.shift(arg1.getIndex());
+ //       System.err.println("shifted "+(arg1.getIndex())+" to "+i);
+        ssm.mouseOverVamsasSequence(seq, i, this);
       }
       else
       {