last version stay many bugs ..

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

diff --git a/src/jalview/gui/AppVarna.java b/src/jalview/gui/AppVarna.java
index dd970f6..00670aa 100644 (file)
--- a/src/jalview/gui/AppVarna.java
+++ b/src/jalview/gui/AppVarna.java
@@ -73,32 +73,35 @@ public class AppVarna extends JInternalFrame implements
 
   AlignmentPanel ap;
 
-  public AppVarna(String sname, SequenceI seq, String strucseq, RNA struc,
+  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>();
-    System.out.println(struc);
-    RNA rna1 = new RNA(struc);
-    rna1.setName(name);
-    rna1.restrictTo(strucseq);
-    /*try
+    RNA rna1 = new RNA(name);
+    try
     {
-      System.err.println(struc + "->" + replaceOddGaps(struc));
+    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();
     } catch (ExceptionFileFormatOrSyntax e3)
     {
       e3.printStackTrace();
-    }*/
+    }
     
     RNA trim = trimRNA(rna1, "trimmed "+sname);
-    //TODO: Use RNA.selectTo instead...
     rnaList.add(trim);
     rnaList.add(rna1);
     
@@ -132,7 +135,7 @@ public class AppVarna extends JInternalFrame implements
 
   public void initVarna()
   {
-         
+         System.out.println("initialisation VANRA");
     // vab.setFinishedInit(false);
     varnaPanel = vab.get_varnaPanel();
     setBackground(Color.white);
@@ -147,7 +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)