import java.util.*;
import java.awt.*;
+
import javax.swing.*;
import javax.swing.event.*;
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.annotations.HighlightRegionAnnotation;
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 InterfaceVARNAListener// implements Runnable,SequenceStructureBinding, ViewSetProvider
+public class AppVarna extends JInternalFrame implements InterfaceVARNAListener,SecondaryStructureListener// implements Runnable,SequenceStructureBinding, ViewSetProvider
{
AppVarnaBinding vab;
public String name;
+ public StructureSelectionManager ssm;
+
/*public AppVarna(){
vab = new AppVarnaBinding();
initVarna();
}*/
- public AppVarna(String seq,String struc,String name){
+ public AppVarna(String seq,String struc,String name,AlignmentPanel ap){
ArrayList<RNA> rnaList = new ArrayList<RNA>();
RNA rna1 = new RNA(name);
try {
//vab = new AppVarnaBinding(seq,struc);
//System.out.println("Hallo: "+name);
this.name=name;
- initVarna();
+ initVarna();
+ ssm = ap.getStructureSelectionManager();
+ ssm.addStructureViewerListener(this);
}
public void initVarna(){
@Override
public void onUINewStructure(VARNAConfig v, RNA r) {
- //TODO _rnaList.add(v, r,"",true);
// TODO Auto-generated method stub
}
// TODO Auto-generated method stub
}
-
+/**
+ * If a mouseOver event from the AlignmentPanel
+ * is noticed the currently selected RNA in the
+ * VARNA window is highlighted at the specific position.
+ * To be able to remove it before the next highlight
+ * it is saved in _lastHighlight
+ */
+private HighlightRegionAnnotation _lastHighlight;
+@Override
+public void mouseOverSequence(SequenceI sequence, int index) {
+ // TODO Auto-generated method stub
+ RNA rna=vab.getSelectedRNA();
+ rna.removeHighlightRegion(_lastHighlight);
+
+ HighlightRegionAnnotation highlight = new HighlightRegionAnnotation(rna.getBasesBetween(index,index));
+ rna.addHighlightRegion(highlight);
+ _lastHighlight=highlight;
+ vab.updateSelectedRNA(rna);
+}
+
+@Override
+public void mouseOverStructure(int atomIndex, String strInfo) {
+ // TODO Auto-generated method stub
+
+}
}