Merge branch 'JAL-1403' into develop

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

diff --git a/src/jalview/gui/AppVarna.java b/src/jalview/gui/AppVarna.java
index dd570c0..4bff08c 100644 (file)
--- a/src/jalview/gui/AppVarna.java
+++ b/src/jalview/gui/AppVarna.java
@@ -17,17 +17,28 @@
  */
 package jalview.gui;
 
-import java.util.*;
+import jalview.bin.Cache;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.structure.SecondaryStructureListener;
+import jalview.structure.SelectionListener;
+import jalview.structure.SelectionSource;
+import jalview.structure.StructureSelectionManager;
+import jalview.structure.VamsasSource;
+import jalview.util.ShiftList;
+
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.util.ArrayList;
+import java.util.Hashtable;
+import java.util.Map;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
-import java.awt.*;
 
-import javax.swing.*;
+import javax.swing.JInternalFrame;
+import javax.swing.JSplitPane;
 
-import jalview.bin.Cache;
-import jalview.datamodel.*;
-import jalview.structure.*;
-import jalview.util.ShiftList;
 import fr.orsay.lri.varna.VARNAPanel;
 import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
 import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
@@ -64,23 +75,23 @@ public class AppVarna extends JInternalFrame implements
   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);
-         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);
     try
     {
-    System.out.println("ou ici ?");
+
       rna1.setRNA(strucseq, replaceOddGaps(struc));
-      System.out.println("La séquence est :"+rna1.getSeq());
-      System.out.println("La séquence est :"+struc);
-      System.out.println("La séquence est :"+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();
@@ -109,19 +120,18 @@ 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;
     initVarna();
    
     ssm = ap.getStructureSelectionManager();
-    System.out.println(ssm.toString());
+    //System.out.println(ssm.toString());
     ssm.addStructureViewerListener(this);
     ssm.addSelectionListener(this);
   }
 
   public void initVarna()
   {
-         System.out.println("initialisation VANRA");
+        
     // vab.setFinishedInit(false);
     varnaPanel = vab.get_varnaPanel();
     setBackground(Color.white);
@@ -136,7 +146,7 @@ public class AppVarna extends JInternalFrame implements
             getBounds().width, getBounds().height);
     this.pack();
     showPanel(true);
-    System.out.println("Sortie initialisation VANRA");
+  
   }
 
   public String replaceOddGaps(String oldStr)
@@ -415,4 +425,18 @@ public class AppVarna extends JInternalFrame implements
 
   }
 
+  @Override
+  public void onTranslationChanged()
+  {
+    // TODO Auto-generated method stub
+    
+  }
+
+  @Override
+  public void onZoomLevelChanged()
+  {
+    // TODO Auto-generated method stub
+    
+  }
+
 }