Add support RNAML format

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

diff --git a/src/jalview/gui/AppVarna.java b/src/jalview/gui/AppVarna.java
index da6c6e5..00670aa 100644 (file)
--- a/src/jalview/gui/AppVarna.java
+++ b/src/jalview/gui/AppVarna.java
@@ -76,12 +76,23 @@ 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();
@@ -89,17 +100,20 @@ public class AppVarna extends JInternalFrame implements
     {
       e3.printStackTrace();
     }
+    
     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)");
 
     {
       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,
@@ -112,13 +126,16 @@ 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);
@@ -133,6 +150,7 @@ 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)
@@ -148,6 +166,7 @@ public class AppVarna extends JInternalFrame implements
   public RNA trimRNA(RNA rna, String name)
   {
     ShiftList offset = new ShiftList();
+    
     RNA rnaTrim = new RNA(name);
     try
     {