X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAppVarna.java;h=524ac82c1779724139ab4a1e6f059fee73891659;hb=ed3945c9051ab14090b5012e4a8ef528df734ddb;hp=d1772c7629bdb3aad3a032131fb7cd990e534656;hpb=8b5356e49064b77364ef8cc0c9af87a59f1e9a0a;p=jalview.git

diff --git a/src/jalview/gui/AppVarna.java b/src/jalview/gui/AppVarna.java
index d1772c7..524ac82 100644
--- a/src/jalview/gui/AppVarna.java
+++ b/src/jalview/gui/AppVarna.java
@@ -32,13 +32,21 @@ import jalview.gui.ViewSelectionMenu.ViewSetProvider;
 import jalview.structure.*;
 import jalview.io.*;
 import jalview.schemes.*;
+import fr.orsay.lri.varna.VARNAPanel;
+import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
+import fr.orsay.lri.varna.exceptions.ExceptionNonEqualLength;
+import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
+import fr.orsay.lri.varna.interfaces.InterfaceVARNAListener;
+import fr.orsay.lri.varna.models.VARNAConfig;
+import fr.orsay.lri.varna.models.rna.RNA;
 
-public class AppVarna extends JInternalFrame // implements Runnable,SequenceStructureBinding, ViewSetProvider
+
+public class AppVarna extends JInternalFrame implements InterfaceVARNAListener// implements Runnable,SequenceStructureBinding, ViewSetProvider
 
 {
   AppVarnaBinding vab;
 
-  JPanel varnaPanel;
+  VARNAPanel varnaPanel;
   
   String name;
 
@@ -50,12 +58,24 @@ public class AppVarna extends JInternalFrame // implements Runnable,SequenceStru
 
   //Vector atomsPicked = new Vector();
   
-  public AppVarna(){
+  /*public AppVarna(){
 	  vab = new AppVarnaBinding(); 
 	  initVarna();
-  }
+  }*/
   
   public AppVarna(String seq,String struc,String name){
+	  ArrayList<RNA> rnaList = new ArrayList<RNA>();
+	  RNA rna1 = new RNA(name);
+	  try {
+		  rna1.setRNA(seq,struc);
+	 } catch (ExceptionUnmatchedClosingParentheses e2) {
+		e2.printStackTrace();
+	  } catch (ExceptionFileFormatOrSyntax e3) {
+		e3.printStackTrace();
+	  }
+	  rnaList.add(rna1);
+	  
+	  //vab = new AppVarnaBinding(rnaList);
 	  vab = new AppVarnaBinding(seq,struc);
 	  name=this.name;
 	  initVarna();	  
@@ -65,20 +85,23 @@ public class AppVarna extends JInternalFrame // implements Runnable,SequenceStru
 	  //TODO: Why is it not possible to include varnaPanel in the AppVarna-Jframe?
 	  //vab.setFinishedInit(false);
 	  varnaPanel=vab.get_varnaPanel();
+	  setBackground(Color.white);
+	  System.out.println("vp: "+vab.get_varnaPanel().getName());
 	  //varnaPanel.setVisible(true);
-	  //getContentPane().setLayout(new BorderLayout());
-	  //getContentPane().add(varnaPanel, BorderLayout.CENTER);
-	  //setVisible(true);
-	  //jalview.gui.Desktop.addInternalFrame(this,name,getBounds().width, getBounds().height);  
-	  showPanel(true);
+	  getContentPane().setLayout(new BorderLayout());
+	  getContentPane().add(varnaPanel, BorderLayout.CENTER);
+	  setVisible(true);
+	  varnaPanel.addVARNAListener(this);
+	  jalview.gui.Desktop.addInternalFrame(this,name,getBounds().width, getBounds().height);  
+	  //showPanel(true);
   }
   
   public void showPanel(boolean show){
-	  vab.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
-	  vab.pack();
-	  vab.setVisible(show);
+	  //vab.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
+	  //vab.pack();
+	  //vab.setVisible(show);
 	    
-	  //varnaPanel.setVisible(show);
+	  varnaPanel.setVisible(show);
   }
   
   private boolean _started = false;
@@ -97,6 +120,25 @@ public class AppVarna extends JInternalFrame // implements Runnable,SequenceStru
         Cache.log.error("Couldn't open Varna viewer!", ex);
       }
   }
+
+@Override
+public void onLayoutChanged() {
+	// TODO Auto-generated method stub
+	
+}
+
+@Override
+public void onUINewStructure(VARNAConfig v, RNA r) {
+	//TODO _rnaList.add(v, r,"",true);
+	// TODO Auto-generated method stub
+	
+}
+
+@Override
+public void onWarningEmitted(String s) {
+	// TODO Auto-generated method stub
+	
+}
   
 
 }