Merge branch 'docs/2_8_1_Release' into Release_2_8_2_Branch

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

diff --git a/src/jalview/gui/AppVarna.java b/src/jalview/gui/AppVarna.java
index f047199..1d05f29 100644 (file)
--- a/src/jalview/gui/AppVarna.java
+++ b/src/jalview/gui/AppVarna.java
@@ -18,18 +18,32 @@
  */
 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.MessageManager;
 import jalview.util.ShiftList;
+
 import fr.orsay.lri.varna.VARNAPanel;
 import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
 import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
@@ -66,12 +80,23 @@ public class AppVarna extends JInternalFrame implements
   public AppVarna(String sname, SequenceI seq, String strucseq,
           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);
     this.ap = ap;
     ArrayList<RNA> rnaList = new ArrayList<RNA>();
     RNA rna1 = new RNA(name);
     try
     {
+
       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());
     } catch (ExceptionUnmatchedClosingParentheses e2)
     {
       e2.printStackTrace();
@@ -82,6 +107,7 @@ 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)");
@@ -89,7 +115,7 @@ 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,
@@ -99,16 +125,18 @@ 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());
     ssm.addStructureViewerListener(this);
     ssm.addSelectionListener(this);
   }
 
   public void initVarna()
   {
+        
     // vab.setFinishedInit(false);
     varnaPanel = vab.get_varnaPanel();
     setBackground(Color.white);
@@ -123,6 +151,7 @@ public class AppVarna extends JInternalFrame implements
             getBounds().width, getBounds().height);
     this.pack();
     showPanel(true);
+  
   }
 
   public String replaceOddGaps(String oldStr)
@@ -138,6 +167,7 @@ public class AppVarna extends JInternalFrame implements
   public RNA trimRNA(RNA rna, String name)
   {
     ShiftList offset = new ShiftList();
+    
     RNA rnaTrim = new RNA(name);
     try
     {
@@ -400,4 +430,18 @@ public class AppVarna extends JInternalFrame implements
 
   }
 
+  @Override
+  public void onTranslationChanged()
+  {
+    // TODO Auto-generated method stub
+    
+  }
+
+  @Override
+  public void onZoomLevelChanged()
+  {
+    // TODO Auto-generated method stub
+    
+  }
+
 }