X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAppVarna.java;h=b37b374d41390dae50ae4caa0dae5e9ac18bb84e;hb=f6a7e5514230be7ea8c2d4cccb504b4ed95f80ef;hp=7be007ab13e0639635abd141ce1e54c40835df1d;hpb=0f594795fc0aa6f7d795e09203515837049bfc4b;p=jalview.git

diff --git a/src/jalview/gui/AppVarna.java b/src/jalview/gui/AppVarna.java
index 7be007a..b37b374 100644
--- a/src/jalview/gui/AppVarna.java
+++ b/src/jalview/gui/AppVarna.java
@@ -1,13 +1,13 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- * 
+ *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
@@ -73,8 +73,8 @@ public class AppVarna extends JInternalFrame implements
 
   AlignmentPanel ap;
 
-  public AppVarna(SequenceI seq, String strucseq, String struc,
-          String name, AlignmentPanel ap)
+  public AppVarna(String sname, SequenceI seq, String strucseq,
+          String struc, String name, AlignmentPanel ap)
   {
     this.ap = ap;
     ArrayList<RNA> rnaList = new ArrayList<RNA>();
@@ -89,12 +89,12 @@ public class AppVarna extends JInternalFrame implements
     {
       e3.printStackTrace();
     }
-    RNA trim = trimRNA(rna1);
+    RNA trim = trimRNA(rna1, "trimmed " + sname);
     rnaList.add(trim);
     rnaList.add(rna1);
     rnas.put(seq, rna1);
     rnas.put(seq, trim);
-    rna1.setName("consensus_" + rna1.getName());
+    rna1.setName(sname + " (with gaps)");
 
     {
       seqs.put(trim, seq);
@@ -110,7 +110,7 @@ public class AppVarna extends JInternalFrame implements
     vab = new AppVarnaBinding(rnaList);
     // vab = new AppVarnaBinding(seq,struc);
     // System.out.println("Hallo: "+name);
-    this.name = name;
+    this.name = sname + " trimmed to " + name;
     initVarna();
     ssm = ap.getStructureSelectionManager();
     ssm.addStructureViewerListener(this);
@@ -145,10 +145,10 @@ public class AppVarna extends JInternalFrame implements
     return newStr;
   }
 
-  public RNA trimRNA(RNA rna)
+  public RNA trimRNA(RNA rna, String name)
   {
     ShiftList offset = new ShiftList();
-    RNA rnaTrim = new RNA("trim_" + rna.getName());
+    RNA rnaTrim = new RNA(name);
     try
     {
       rnaTrim.setRNA(rna.getSeq(), replaceOddGaps(rna.getStructDBN()));
@@ -333,9 +333,9 @@ public class AppVarna extends JInternalFrame implements
       ShiftList shift = offsets.get(rna);
       if (shift != null)
       {
-   //      System.err.print("Orig pos:"+index);
-         index = shift.shift(index);
-   //      System.err.println("\nFinal pos:"+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);
@@ -392,7 +392,7 @@ public class AppVarna extends JInternalFrame implements
       if (shift != null)
       {
         int i = shift.shift(arg1.getIndex());
- //       System.err.println("shifted "+(arg1.getIndex())+" to "+i);
+        // System.err.println("shifted "+(arg1.getIndex())+" to "+i);
         ssm.mouseOverVamsasSequence(seq, i, this);
       }
       else