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.ModeleBaseNucleotide;
+import fr.orsay.lri.varna.models.rna.ModeleStyleBP;
+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;
-
- //JSplitPane splitPane;
-
- //RenderPanel renderPanel;
-
- //AlignmentPanel ap;
-
- //Vector atomsPicked = new Vector();
+ VARNAPanel varnaPanel;
- public AppVarna(){
+ public String name;
+
+ /*public AppVarna(){
vab = new AppVarnaBinding();
initVarna();
- }
+ }*/
- public AppVarna(String seq){
- vab = new AppVarnaBinding(seq);
+ 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(trimRNA(rna1));
+ rnaList.add(rna1);
+ rna1.setName("consenus_"+rna1.getName());
+
+
+ vab = new AppVarnaBinding(rnaList);
+ //vab = new AppVarnaBinding(seq,struc);
+ //System.out.println("Hallo: "+name);
+ this.name=name;
initVarna();
}
public void initVarna(){
//vab.setFinishedInit(false);
- varnaPanel=vab.vp;
- this.getContentPane().add(varnaPanel);
- jalview.gui.Desktop.addInternalFrame(this,"test",200,200);
+ varnaPanel=vab.get_varnaPanel();
+ setBackground(Color.white);
+ JSplitPane split = new JSplitPane(JSplitPane.HORIZONTAL_SPLIT,true,vab.getListPanel(),varnaPanel);
+ getContentPane().setLayout(new BorderLayout());
+ getContentPane().add(split, BorderLayout.CENTER);
+ getContentPane().add(vab.getTools(), BorderLayout.NORTH);
+ varnaPanel.addVARNAListener(this);
+ jalview.gui.Desktop.addInternalFrame(this,"VARNA -"+name,getBounds().width, getBounds().height);
+ this.pack();
showPanel(true);
}
+ public RNA trimRNA(RNA rna){
+ RNA rnaTrim = new RNA("trim_"+rna.getName());
+ try {
+ rnaTrim.setRNA(rna.getSeq(),rna.getStructDBN());
+ } catch (ExceptionUnmatchedClosingParentheses e2) {
+ e2.printStackTrace();
+ } catch (ExceptionFileFormatOrSyntax e3) {
+ e3.printStackTrace();
+ }
+
+ StringBuffer seq=new StringBuffer(rnaTrim.getSeq());
+ StringBuffer struc=new StringBuffer(rnaTrim.getStructDBN());
+ for(int i=0;i<rnaTrim.getSeq().length();i++){
+ if(seq.substring(i, i+1).compareTo("-")==0 || seq.substring(i, i+1).compareTo(".")==0){
+ if(!rnaTrim.findPair(i).isEmpty()){
+ System.out.println(rnaTrim.findPair(i));
+ int m=rnaTrim.findPair(i).get(1);
+ int l=rnaTrim.findPair(i).get(0);
+
+ struc.replace(m, m+1, "*");
+ struc.replace(l, l+1, "*");
+ }else{
+ struc.replace(i, i+1, "*");
+ }
+ }
+ }
+
+ String newSeq=rnaTrim.getSeq().replace("-", "");
+ rnaTrim.getSeq().replace(".", "");
+ String newStruc=struc.toString().replace("*", "");
+
+ try {
+ rnaTrim.setRNA(newSeq,newStruc);
+ } catch (ExceptionUnmatchedClosingParentheses e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ } catch (ExceptionFileFormatOrSyntax e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+
+ return rnaTrim;
+ }
+
public void showPanel(boolean show){
- //vab.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
- //vab.pack();
- //vab.setVisible(show);
- varnaPanel.setVisible(show);
+ this.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
+
+}
}