Merge branch 'Release_2_8_2b1_Branch'

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

diff --git a/src/jalview/gui/AppVarna.java b/src/jalview/gui/AppVarna.java
index d9795f0..014e6eb 100644 (file)
--- a/src/jalview/gui/AppVarna.java
+++ b/src/jalview/gui/AppVarna.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
@@ -83,12 +83,12 @@ public class AppVarna extends JInternalFrame implements
           String struc, String name, AlignmentPanel ap)
   {
 
-//       System.out.println("1:"+sname);
-//       System.out.println("2:"+seq);
-//       System.out.println("3:"+strucseq);
-//       System.out.println("4:"+struc);
-//       System.out.println("5:"+name);
-//       System.out.println("6:"+ap);
+    // System.out.println("1:"+sname);
+    // System.out.println("2:"+seq);
+    // System.out.println("3:"+strucseq);
+    // System.out.println("4:"+struc);
+    // System.out.println("5:"+name);
+    // System.out.println("6:"+ap);
     this.ap = ap;
     ArrayList<RNA> rnaList = new ArrayList<RNA>();
     RNA rna1 = new RNA(name);
@@ -96,9 +96,9 @@ public class AppVarna extends JInternalFrame implements
     {
 
       rna1.setRNA(strucseq, replaceOddGaps(struc));
-//      System.out.println("The sequence is :"+rna1.getSeq());
-//      System.out.println("The sequence is:"+struc);
-//      System.out.println("The sequence is:"+replaceOddGaps(struc).toString());
+      // System.out.println("The sequence is :"+rna1.getSeq());
+      // System.out.println("The sequence is:"+struc);
+      // System.out.println("The sequence is:"+replaceOddGaps(struc).toString());
     } catch (ExceptionUnmatchedClosingParentheses e2)
     {
       e2.printStackTrace();
@@ -109,7 +109,7 @@ public class AppVarna extends JInternalFrame implements
     RNA trim = trimRNA(rna1, "trimmed " + sname);
     rnaList.add(trim);
     rnaList.add(rna1);
-    
+
     rnas.put(seq, rna1);
     rnas.put(seq, trim);
     rna1.setName(sname + " (with gaps)");
@@ -117,7 +117,7 @@ public class AppVarna extends JInternalFrame implements
     {
       seqs.put(trim, seq);
       seqs.put(rna1, seq);
-      
+
       /**
        * if (false || seq.getStart()!=1) { for (RNA rshift:rnaList) { ShiftList
        * shift=offsets.get(rshift); if (shift==null) { offsets.put(rshift,
@@ -129,16 +129,16 @@ public class AppVarna extends JInternalFrame implements
     // vab = new AppVarnaBinding(seq,struc);
     this.name = sname + " trimmed to " + name;
     initVarna();
-   
+
     ssm = ap.getStructureSelectionManager();
-    //System.out.println(ssm.toString());
+    // System.out.println(ssm.toString());
     ssm.addStructureViewerListener(this);
     ssm.addSelectionListener(this);
   }
 
   public void initVarna()
   {
-        
+
     // vab.setFinishedInit(false);
     varnaPanel = vab.get_varnaPanel();
     setBackground(Color.white);
@@ -149,11 +149,12 @@ public class AppVarna extends JInternalFrame implements
     // getContentPane().add(vab.getTools(), BorderLayout.NORTH);
     varnaPanel.addVARNAListener(this);
     varnaPanel.addSelectionListener(this);
-    jalview.gui.Desktop.addInternalFrame(this, MessageManager.formatMessage("label.varna_params", new String[]{name}),
-            getBounds().width, getBounds().height);
+    jalview.gui.Desktop.addInternalFrame(this,
+            MessageManager.formatMessage("label.varna_params", new String[]
+            { name }), getBounds().width, getBounds().height);
     this.pack();
     showPanel(true);
-  
+
   }
 
   public String replaceOddGaps(String oldStr)
@@ -169,7 +170,7 @@ public class AppVarna extends JInternalFrame implements
   public RNA trimRNA(RNA rna, String name)
   {
     ShiftList offset = new ShiftList();
-    
+
     RNA rnaTrim = new RNA(name);
     try
     {
@@ -436,14 +437,14 @@ public class AppVarna extends JInternalFrame implements
   public void onTranslationChanged()
   {
     // TODO Auto-generated method stub
-    
+
   }
 
   @Override
   public void onZoomLevelChanged()
   {
     // TODO Auto-generated method stub
-    
+
   }
 
 }