Further structure accessing feature

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

diff --git a/src/jalview/gui/AppVarna.java b/src/jalview/gui/AppVarna.java
index 3a67e10..d1772c7 100644 (file)
--- a/src/jalview/gui/AppVarna.java
+++ b/src/jalview/gui/AppVarna.java
@@ -38,23 +38,47 @@ public class AppVarna extends JInternalFrame // implements Runnable,SequenceStru
 {
   AppVarnaBinding vab;
 
-  JPanel scriptWindow;
+  JPanel varnaPanel;
+  
+  String name;
 
-  JSplitPane splitPane;
+  //JSplitPane splitPane;
 
   //RenderPanel renderPanel;
 
-  AlignmentPanel ap;
+  //AlignmentPanel ap;
 
-  Vector atomsPicked = new Vector();
+  //Vector atomsPicked = new Vector();
+  
+  public AppVarna(){
+         vab = new AppVarnaBinding(); 
+         initVarna();
+  }
   
-  void initVarna(){
+  public AppVarna(String seq,String struc,String name){
+         vab = new AppVarnaBinding(seq,struc);
+         name=this.name;
+         initVarna();    
+  }
+  
+  public void initVarna(){
+         //TODO: Why is it not possible to include varnaPanel in the AppVarna-Jframe?
          //vab.setFinishedInit(false);
-         //renderPanel = new RenderPanel();
-         // TODO: consider waiting until the structure/view is fully loaded before
-         // displaying
-         //this.getContentPane().add(renderPanel, java.awt.BorderLayout.CENTER);
-         jalview.gui.Desktop.addInternalFrame(this,"test",300,300);
+         varnaPanel=vab.get_varnaPanel();
+         //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);
+  }
+  
+  public void showPanel(boolean show){
+         vab.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
+         vab.pack();
+         vab.setVisible(show);
+           
+         //varnaPanel.setVisible(show);
   }
   
   private boolean _started = false;