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 scriptWindow;
-
- JSplitPane splitPane;
-
- //RenderPanel renderPanel;
-
- AlignmentPanel ap;
-
- Vector atomsPicked = new Vector();
+ VARNAPanel varnaPanel;
- public AppVarna(){
+ String name;
+
+ /*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();
}
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);
- AppVarnaBinding d = new AppVarnaBinding();
- d.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
- d.pack();
- d.setVisible(true);
+ varnaPanel=vab.get_varnaPanel();
+ setBackground(Color.white);
+ getContentPane().setLayout(new BorderLayout());
+ getContentPane().add(varnaPanel, BorderLayout.CENTER);
+
+ varnaPanel.addVARNAListener(this);
+ jalview.gui.Desktop.addInternalFrame(this,name,getBounds().width, getBounds().height);
+ this.pack();
+ this.setVisible(true);
+ //showPanel(true);
+ }
+
+ public void showPanel(boolean show){
+ varnaPanel.setVisible(show);
}
private boolean _started = false;
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
+
+}
}