package jalview.gui;
import java.util.*;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
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 {
- rna1.setRNA(seq,struc);
+ rna1.setRNA(seq,replaceOddGaps(struc));
} catch (ExceptionUnmatchedClosingParentheses e2) {
e2.printStackTrace();
} catch (ExceptionFileFormatOrSyntax e3) {
//vab = new AppVarnaBinding(seq,struc);
//System.out.println("Hallo: "+name);
this.name=name;
- initVarna();
+ initVarna();
+ ssm = ap.getStructureSelectionManager();
+ ssm.addStructureViewerListener(this);
}
public void initVarna(){
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);
+ //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 String replaceOddGaps(String oldStr){
+ String patternStr = "[^([{<>}])]";
+ String replacementStr = ".";
+ Pattern pattern = Pattern.compile(patternStr);
+ Matcher matcher = pattern.matcher(oldStr);
+ String newStr=matcher.replaceAll(replacementStr);
+ return newStr;
+ }
+
public RNA trimRNA(RNA rna){
RNA rnaTrim = new RNA("trim_"+rna.getName());
try {
- rnaTrim.setRNA(rna.getSeq(),rna.getStructDBN());
+ rnaTrim.setRNA(rna.getSeq(),replaceOddGaps(rna.getStructDBN()));
} catch (ExceptionUnmatchedClosingParentheses e2) {
e2.printStackTrace();
} catch (ExceptionFileFormatOrSyntax e3) {
@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
+
+}
}