/*
* 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.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see .
*/
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 java.awt.event.*;
import java.io.*;
import jalview.api.SequenceStructureBinding;
import jalview.bin.Cache;
import jalview.datamodel.*;
import jalview.gui.ViewSelectionMenu.ViewSetProvider;
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 InterfaceVARNAListener,SelectionListener, SecondaryStructureListener// implements Runnable,SequenceStructureBinding, ViewSetProvider
, InterfaceVARNASelectionListener, VamsasSource
{
AppVarnaBinding vab;
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 rnaList = new ArrayList();
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();
}
StringBuffer seq=new StringBuffer(rnaTrim.getSeq());
StringBuffer struc=new StringBuffer(rnaTrim.getStructDBN());
int ofstart=-1,sleng=rnaTrim.getSeq().length();
for(int i=0;i-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("*", "");
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 seqs=new Hashtable();
Map offsets=new Hashtable();
Map offsetsInv=new Hashtable();
private void registerOffset(RNA rnaTrim, ShiftList offset)
{
offsets.put(rnaTrim, offset);
offsetsInv.put(rnaTrim,offset.getInverse());
}
public void showPanel(boolean show){
this.setVisible(show);
}
private boolean _started = false;
public void run(){
_started = true;
try
{
initVarna();
} catch (OutOfMemoryError oomerror)
{
new OOMWarning("When trying to open the Varna viewer!", oomerror);
} catch (Exception ex)
{
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 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
}
}