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 1a4c7ac..dd570c0 100644 (file)
--- a/src/jalview/gui/AppVarna.java
+++ b/src/jalview/gui/AppVarna.java
@@ -64,12 +64,23 @@ 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 +91,7 @@ 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 +99,7 @@ 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 +112,16 @@ 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 +136,7 @@ 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 +152,7 @@ public class AppVarna extends JInternalFrame implements
   public RNA trimRNA(RNA rna, String name)
   {
     ShiftList offset = new ShiftList();
+    
     RNA rnaTrim = new RNA(name);
     try
     {