/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
*
* This file is part of Jalview.
*
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 jalview.util.ShiftList;
+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.interfaces.InterfaceVARNASelectionListener;
+import fr.orsay.lri.varna.models.BaseList;
+import fr.orsay.lri.varna.models.VARNAConfig;
+import fr.orsay.lri.varna.models.annotations.HighlightRegionAnnotation;
+import fr.orsay.lri.varna.models.rna.ModeleBase;
+import fr.orsay.lri.varna.models.rna.ModeleBaseNucleotide;
+import fr.orsay.lri.varna.models.rna.RNA;
+
-public class AppVarna extends JInternalFrame // implements Runnable,SequenceStructureBinding, ViewSetProvider
+public class AppVarna extends JInternalFrame implements InterfaceVARNAListener,SelectionListener, SecondaryStructureListener// implements Runnable,SequenceStructureBinding, ViewSetProvider
+, InterfaceVARNASelectionListener, VamsasSource
{
AppVarnaBinding vab;
- JPanel scriptWindow;
-
- JSplitPane splitPane;
+ VARNAPanel varnaPanel;
+
+ public String name;
+
+ public StructureSelectionManager ssm;
+
+ /*public AppVarna(){
+ vab = new AppVarnaBinding();
+ initVarna();
+ }*/
+
+
+ public AppVarna(SequenceI seq,String strucseq, String struc,String name,AlignmentPanel ap){
+ ArrayList<RNA> rnaList = new ArrayList<RNA>();
+ RNA rna1 = new RNA(name);
+ try {
+ rna1.setRNA(strucseq,replaceOddGaps(struc));
+ } catch (ExceptionUnmatchedClosingParentheses e2) {
+ e2.printStackTrace();
+ } catch (ExceptionFileFormatOrSyntax e3) {
+ e3.printStackTrace();
+ }
+ RNA trim=trimRNA(rna1);
+ rnaList.add(trim);
+ rnaList.add(rna1);
+ rna1.setName("consensus_"+rna1.getName());
+
+ {
+ this.seqs.put(trim, seq);
+ this.seqs.put(rna1, seq);
+ }
+ vab = new AppVarnaBinding(rnaList);
+ //vab = new AppVarnaBinding(seq,struc);
+ //System.out.println("Hallo: "+name);
+ this.name=name;
+ initVarna();
+ ssm = ap.getStructureSelectionManager();
+ ssm.addStructureViewerListener(this);
+ ssm.addSelectionListener(this);
+ }
+
+ public void initVarna(){
+ //vab.setFinishedInit(false);
+ 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);
+ varnaPanel.addSelectionListener(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){
+ ShiftList offset=new ShiftList();
+ 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();
+ }
- //RenderPanel renderPanel;
+ StringBuffer seq=new StringBuffer(rnaTrim.getSeq());
+ StringBuffer struc=new StringBuffer(rnaTrim.getStructDBN());
+ int ofstart=-1,sleng=rnaTrim.getSeq().length();
+ for(int i=0;i<sleng;i++){
+ //TODO: Jalview utility for gap detection java.utils.isGap()
+ //TODO: Switch to jalview rna datamodel
+ if(jalview.util.Comparison.isGap(seq.charAt(i))){
+ if (ofstart==-1)
+ {
+ ofstart=i;
+ }
+ 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, "*");
+ }
+ } else {
+ if (ofstart>-1)
+ {
+ offset.addShift(ofstart, ofstart-i);
+ ofstart=-1;
+ }
+ }
+ }
+ // final gap
+ if (ofstart>-1)
+ {
+ offset.addShift(ofstart, ofstart-sleng);
+ ofstart=-1;
+ }
+ String newSeq=rnaTrim.getSeq().replace("-", "");
+ rnaTrim.getSeq().replace(".", "");
+ String newStruc=struc.toString().replace("*", "");
- AlignmentPanel ap;
+ try {
+ rnaTrim.setRNA(newSeq,newStruc);
+ registerOffset(rnaTrim,offset);
+ } catch (ExceptionUnmatchedClosingParentheses e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ } catch (ExceptionFileFormatOrSyntax e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+ return rnaTrim;
+ }
+ Map<RNA,SequenceI> seqs=new Hashtable<RNA,SequenceI>();
+ Map<RNA,ShiftList> offsets=new Hashtable<RNA,ShiftList>();
+ Map<RNA,ShiftList> offsetsInv=new Hashtable<RNA,ShiftList>();
+ private void registerOffset(RNA rnaTrim, ShiftList offset)
+ {
+ offsets.put(rnaTrim, offset);
+ offsetsInv.put(rnaTrim,offset.getInverse());
+ }
- Vector atomsPicked = new Vector();
-
- void initVarna(){
- //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);
+ public void showPanel(boolean show){
+ this.setVisible(show);
}
private boolean _started = false;
Cache.log.error("Couldn't open Varna viewer!", ex);
}
}
+
+@Override
+public void onUINewStructure(VARNAConfig v, RNA r) {
+
+}
+
+@Override
+public void onWarningEmitted(String s) {
+ // TODO Auto-generated method stub
+
+}
+private class VarnaHighlighter {
+ private HighlightRegionAnnotation _lastHighlight;
+ private RNA _lastRNAhighlighted=null;
+ public void highlightRegion(RNA rna, int start,int end)
+ {
+ if (_lastRNAhighlighted!=null)
+ {
+ _lastRNAhighlighted.removeHighlightRegion(_lastHighlight);
+ }
+ HighlightRegionAnnotation highlight = new HighlightRegionAnnotation(rna.getBasesBetween(start,end));
+ rna.addHighlightRegion(highlight);
+ _lastHighlight=highlight;
+ _lastRNAhighlighted=rna;
+
+ }
+ public HighlightRegionAnnotation getLastHighlight() {
+ return _lastHighlight;
+ }
+ public RNA getLastRNA()
+ {
+ return _lastRNAhighlighted;
+ }
+}
+VarnaHighlighter mouseOverHighlighter=new VarnaHighlighter(),
+selectionHighlighter=new VarnaHighlighter();
+/**
+ * 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
+ */
+@Override
+public void mouseOverSequence(SequenceI sequence, int index) {
+ RNA rna=vab.getSelectedRNA();
+ ShiftList shift=offsets.get(rna);
+ if (shift!=null)
+ {
+ index=shift.shift(index);
+ }
+ mouseOverHighlighter.highlightRegion(rna, index, index);
+ vab.updateSelectedRNA(rna);
+}
+
+@Override
+public void mouseOverStructure(int atomIndex, String strInfo) {
+ // TODO Auto-generated method stub
+
+}
+
+@Override
+public void onStructureRedrawn()
+{
+ // TODO Auto-generated method stub
+
+}
+
+@Override
+public void selection(SequenceGroup seqsel, ColumnSelection colsel,
+ SelectionSource source)
+{
+ int start=seqsel.getStartRes(),end=seqsel.getEndRes();
+ RNA rna=vab.getSelectedRNA();
+ ShiftList shift=offsets.get(rna);
+ if (shift!=null)
+ {
+ start=shift.shift(start);
+ end=shift.shift(end);
+ }
+ selectionHighlighter.highlightRegion(rna, start, end);
+ selectionHighlighter.getLastHighlight().setOutlineColor(seqsel.getOutlineColour());
+ vab.updateSelectedRNA(rna);
+}
+
+@Override
+public void onHoverChanged(ModeleBase arg0, ModeleBase arg1)
+{
+ RNA rna=vab.getSelectedRNA();
+ ShiftList shift=offsetsInv.get(rna);
+ SequenceI seq=seqs.get(rna);
+ if (arg1!=null && seq!=null)
+ {
+ if (shift!=null)
+ {
+ ssm.mouseOverVamsasSequence(seq, seq.findIndex(arg1.getIndex()), this);
+ } else {
+ ssm.mouseOverVamsasSequence(seq, arg1.getIndex(), this);
+ }
+ }
+}
+
+@Override
+public void onSelectionChanged(BaseList arg0, BaseList arg1, BaseList arg2)
+{
+ // TODO Auto-generated method stub
+}
+
}
git://source.jalview.org / jalview.git / blobdiff