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 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.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 Runnable,SequenceStructureBinding, ViewSetProvider
+public class AppVarna extends JInternalFrame implements InterfaceVARNAListener,SecondaryStructureListener// implements Runnable,SequenceStructureBinding, ViewSetProvider
{
AppVarnaBinding vab;
- JPanel varnaPanel;
+ VARNAPanel varnaPanel;
- String name;
-
- //JSplitPane splitPane;
-
- //RenderPanel renderPanel;
-
- //AlignmentPanel ap;
-
- //Vector atomsPicked = new Vector();
+ public String name;
- public AppVarna(){
+ public StructureSelectionManager ssm;
+
+ /*public AppVarna(){
vab = new AppVarnaBinding();
initVarna();
- }
+ }*/
- public AppVarna(String seq,String struc,String name){
- vab = new AppVarnaBinding(seq,struc);
- name=this.name;
- initVarna();
+
+
+ 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,replaceOddGaps(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();
+ ssm = ap.getStructureSelectionManager();
+ ssm.addStructureViewerListener(this);
}
public void initVarna(){
- //TODO: Why is it not possible to include varnaPanel in the AppVarna-Jframe?
//vab.setFinishedInit(false);
varnaPanel=vab.get_varnaPanel();
- //varnaPanel.setVisible(true);
- //getContentPane().setLayout(new BorderLayout());
- //getContentPane().add(varnaPanel, BorderLayout.CENTER);
- //setVisible(true);
- //jalview.gui.Desktop.addInternalFrame(this,name,getBounds().width, getBounds().height);
+ 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 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(),replaceOddGaps(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++){
+ //TODO: Jalview utility for gap detection java.utils.isGap()
+ //TODO: Switch to jalview rna datamodel
+ if(seq.substring(i, i+1).compareTo("-")==0 || seq.substring(i, i+1).compareTo(".")==0){
+ if(!rnaTrim.findPair(i).isEmpty()){
+ 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 Auto-generated method stub
+
+}
+
+@Override
+public void onWarningEmitted(String s) {
+ // 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
+
+}
}
git://source.jalview.org / jalview.git / blobdiff