/*
- * 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 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.ModeleStyleBP;
import fr.orsay.lri.varna.models.rna.RNA;
-public class AppVarna extends JInternalFrame implements InterfaceVARNAListener,SecondaryStructureListener// implements Runnable,SequenceStructureBinding, ViewSetProvider
+public class AppVarna extends JInternalFrame implements InterfaceVARNAListener,SelectionListener, SecondaryStructureListener// implements Runnable,SequenceStructureBinding, ViewSetProvider
+, InterfaceVARNASelectionListener, VamsasSource
{
AppVarnaBinding vab;
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,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 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);
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);
+ 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(),rna.getStructDBN());
+ rnaTrim.setRNA(rna.getSeq(),replaceOddGaps(rna.getStructDBN()));
} catch (ExceptionUnmatchedClosingParentheses e2) {
e2.printStackTrace();
} catch (ExceptionFileFormatOrSyntax e3) {
StringBuffer seq=new StringBuffer(rnaTrim.getSeq());
StringBuffer struc=new StringBuffer(rnaTrim.getStructDBN());
- for(int i=0;i<rnaTrim.getSeq().length();i++){
+ 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(seq.substring(i, i+1).compareTo("-")==0 || seq.substring(i, i+1).compareTo(".")==0){
+ 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);
}else{
struc.replace(i, i+1, "*");
}
+ } else {
+ if (ofstart>-1)
+ {
+ offset.addShift(ofstart, ofstart-i);
+ ofstart=-1;
+ }
}
- }
-
- String newSeq=rnaTrim.getSeq().replace("-", "");
+ }
+ // 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("*", "");
try {
rnaTrim.setRNA(newSeq,newStruc);
+ registerOffset(rnaTrim,offset);
} catch (ExceptionUnmatchedClosingParentheses e) {
// TODO Auto-generated catch block
e.printStackTrace();
// 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());
+ }
public void showPanel(boolean show){
this.setVisible(show);
}
@Override
-public void onLayoutChanged() {
- // TODO Auto-generated method stub
-
-}
-
-@Override
public void onUINewStructure(VARNAConfig v, RNA r) {
- // TODO Auto-generated method stub
-
+
}
@Override
// 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
* 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;
+ 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 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
+
+}
+
+
}