X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAppVarna.java;h=70e68eea770bf2fc884f20e8d8988bf8db13fd20;hb=33b4764ff9d75a0e966c3c8b4b7956f54431221f;hp=1a4c7ac76932c1431e2173cec08b9fde26c527ac;hpb=ad20cd92225f2ee8c251d39b00b90555d382a616;p=jalview.git

diff --git a/src/jalview/gui/AppVarna.java b/src/jalview/gui/AppVarna.java
index 1a4c7ac..70e68ee 100644
--- 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;
@@ -64,12 +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);
     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());
     } catch (ExceptionUnmatchedClosingParentheses e2)
     {
       e2.printStackTrace();
@@ -80,6 +102,7 @@ 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)");
@@ -87,7 +110,7 @@ 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,
@@ -100,13 +123,16 @@ public class AppVarna extends JInternalFrame implements
     // System.out.println("Hallo: "+name);
     this.name = sname + " trimmed to " + name;
     initVarna();
+   
     ssm = ap.getStructureSelectionManager();
+    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);
@@ -121,6 +147,7 @@ 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)
@@ -136,6 +163,7 @@ public class AppVarna extends JInternalFrame implements
   public RNA trimRNA(RNA rna, String name)
   {
     ShiftList offset = new ShiftList();
+    
     RNA rnaTrim = new RNA(name);
     try
     {
@@ -398,4 +426,18 @@ public class AppVarna extends JInternalFrame implements
 
   }
 
+  @Override
+  public void onTranslationChanged()
+  {
+    // TODO Auto-generated method stub
+    
+  }
+
+  @Override
+  public void onZoomLevelChanged()
+  {
+    // TODO Auto-generated method stub
+    
+  }
+
 }