JAL-1517 update copyright to version 2.8.2

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

diff --git a/src/jalview/gui/AppVarna.java b/src/jalview/gui/AppVarna.java
index 70e68ee..21f809f 100644 (file)
--- a/src/jalview/gui/AppVarna.java
+++ b/src/jalview/gui/AppVarna.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -14,6 +14,7 @@
  * PURPOSE.  See the GNU General Public License for more details.
  * 
  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.gui;
 
@@ -39,6 +40,10 @@ import java.util.regex.Pattern;
 import javax.swing.JInternalFrame;
 import javax.swing.JSplitPane;
 
+import jalview.bin.Cache;
+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;
@@ -75,23 +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("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);
+
+//       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());
+//      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();
@@ -120,19 +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());
+    //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);
@@ -143,11 +147,11 @@ public class AppVarna extends JInternalFrame implements
     // getContentPane().add(vab.getTools(), BorderLayout.NORTH);
     varnaPanel.addVARNAListener(this);
     varnaPanel.addSelectionListener(this);
-    jalview.gui.Desktop.addInternalFrame(this, "VARNA -" + name,
+    jalview.gui.Desktop.addInternalFrame(this, MessageManager.formatMessage("label.varna_params", new String[]{name}),
             getBounds().width, getBounds().height);
     this.pack();
     showPanel(true);
-    System.out.println("Sortie initialisation VANRA");
+  
   }
 
   public String replaceOddGaps(String oldStr)