jal-842; sequence transmitting to Varna included

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

diff --git a/src/jalview/gui/AppVarna.java b/src/jalview/gui/AppVarna.java
index d0173d0..19b19cd 100644 (file)
--- a/src/jalview/gui/AppVarna.java
+++ b/src/jalview/gui/AppVarna.java
@@ -38,31 +38,39 @@ public class AppVarna extends JInternalFrame // implements Runnable,SequenceStru
 {
   AppVarnaBinding vab;
 
-  JPanel scriptWindow;
+  JPanel varnaPanel;
 
-  JSplitPane splitPane;
+  //JSplitPane splitPane;
 
   //RenderPanel renderPanel;
 
-  AlignmentPanel ap;
+  //AlignmentPanel ap;
 
-  Vector atomsPicked = new Vector();
+  //Vector atomsPicked = new Vector();
   
   public AppVarna(){
+         vab = new AppVarnaBinding(); 
          initVarna();
   }
   
+  public AppVarna(String seq){
+         vab = new AppVarnaBinding(seq);
+         initVarna();    
+  }
+  
   public void initVarna(){
          //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);
-         AppVarnaBinding d = new AppVarnaBinding();
-         d.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
-         d.pack();
-         d.setVisible(true);
+         varnaPanel=vab.vp;
+         this.getContentPane().add(varnaPanel);
+         jalview.gui.Desktop.addInternalFrame(this,"test",200,200);
+         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;