Merge branch 'develop' into menard

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

diff --git a/src/jalview/gui/AppVarna.java b/src/jalview/gui/AppVarna.java
index 00670aa..dd570c0 100644 (file)
--- 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 
@@ -23,24 +23,13 @@ import java.util.regex.Pattern;
 import java.awt.*;
 
 import javax.swing.*;
-import javax.swing.event.*;
-
-import java.awt.event.*;
-import java.io.*;
 
-import jalview.api.AlignViewportI;
-import jalview.api.AlignmentViewPanel;
-import jalview.api.SequenceStructureBinding;
 import jalview.bin.Cache;
 import jalview.datamodel.*;
-import jalview.gui.ViewSelectionMenu.ViewSetProvider;
 import jalview.structure.*;
-import jalview.io.*;
-import jalview.schemes.*;
 import jalview.util.ShiftList;
 import fr.orsay.lri.varna.VARNAPanel;
 import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
-import fr.orsay.lri.varna.exceptions.ExceptionNonEqualLength;
 import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
 import fr.orsay.lri.varna.interfaces.InterfaceVARNAListener;
 import fr.orsay.lri.varna.interfaces.InterfaceVARNASelectionListener;
@@ -48,7 +37,6 @@ import fr.orsay.lri.varna.models.BaseList;
 import fr.orsay.lri.varna.models.VARNAConfig;
 import fr.orsay.lri.varna.models.annotations.HighlightRegionAnnotation;
 import fr.orsay.lri.varna.models.rna.ModeleBase;
-import fr.orsay.lri.varna.models.rna.ModeleBaseNucleotide;
 import fr.orsay.lri.varna.models.rna.RNA;
 
 public class AppVarna extends JInternalFrame implements
@@ -73,8 +61,8 @@ public class AppVarna extends JInternalFrame implements
 
   AlignmentPanel ap;
 
-  public AppVarna(String sname, SequenceI seq, String strucseq, String struc,
-          String name, AlignmentPanel ap)
+  public AppVarna(String sname, SequenceI seq, String strucseq,
+          String struc, String name, AlignmentPanel ap)
   {
          System.out.println("je suis là (AppVarna!!");
          System.out.println("1:"+sname);
@@ -100,15 +88,13 @@ public class AppVarna extends JInternalFrame implements
     {
       e3.printStackTrace();
     }
-    
-    RNA trim = trimRNA(rna1, "trimmed "+sname);
+    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)");
+    rna1.setName(sname + " (with gaps)");
 
     {
       seqs.put(trim, seq);
@@ -124,7 +110,7 @@ public class AppVarna extends JInternalFrame implements
     vab = new AppVarnaBinding(rnaList);
     // vab = new AppVarnaBinding(seq,struc);
     // System.out.println("Hallo: "+name);
-    this.name = sname+" trimmed to "+name;
+    this.name = sname + " trimmed to " + name;
     initVarna();
    
     ssm = ap.getStructureSelectionManager();
@@ -352,9 +338,9 @@ 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);
@@ -411,7 +397,7 @@ 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