/*
* Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
* Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* 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 .
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
import jalview.bin.Cache;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.structure.SecondaryStructureListener;
import jalview.structure.SelectionListener;
import jalview.structure.SelectionSource;
import jalview.structure.StructureSelectionManager;
import jalview.structure.VamsasSource;
import jalview.util.ShiftList;
import java.awt.BorderLayout;
import java.awt.Color;
import java.util.ArrayList;
import java.util.Hashtable;
import java.util.Map;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
import javax.swing.JInternalFrame;
import javax.swing.JSplitPane;
import jalview.bin.Cache;
import jalview.util.MessageManager;
import jalview.util.ShiftList;
import fr.orsay.lri.varna.VARNAPanel;
import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
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.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(); }
*/
AlignmentPanel ap;
public AppVarna(String sname, SequenceI seq, String strucseq,
String struc, String name, AlignmentPanel ap)
{
// System.out.println("1:"+sname);
// System.out.println("2:"+seq);
// System.out.println("3:"+strucseq);
// System.out.println("4:"+struc);
// System.out.println("5:"+name);
// System.out.println("6:"+ap);
this.ap = ap;
ArrayList rnaList = new ArrayList();
RNA rna1 = new RNA(name);
try
{
rna1.setRNA(strucseq, replaceOddGaps(struc));
// System.out.println("The sequence is :"+rna1.getSeq());
// System.out.println("The sequence is:"+struc);
// System.out.println("The sequence is:"+replaceOddGaps(struc).toString());
} catch (ExceptionUnmatchedClosingParentheses e2)
{
e2.printStackTrace();
} catch (ExceptionFileFormatOrSyntax e3)
{
e3.printStackTrace();
}
RNA trim = trimRNA(rna1, "trimmed " + sname);
rnaList.add(trim);
rnaList.add(rna1);
rnas.put(seq, rna1);
rnas.put(seq, trim);
rna1.setName(sname + " (with gaps)");
{
seqs.put(trim, seq);
seqs.put(rna1, seq);
/**
* if (false || seq.getStart()!=1) { for (RNA rshift:rnaList) { ShiftList
* shift=offsets.get(rshift); if (shift==null) { offsets.put(rshift,
* shift=new ShiftList());} shift.addShift(1, seq.getStart()-1);
* offsetsInv.put(rshift, shift.getInverse()); } }
**/
}
vab = new AppVarnaBinding(rnaList);
// vab = new AppVarnaBinding(seq,struc);
this.name = sname + " trimmed to " + name;
initVarna();
ssm = ap.getStructureSelectionManager();
// System.out.println(ssm.toString());
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,
MessageManager.formatMessage("label.varna_params", new String[]
{ 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, String name)
{
ShiftList offset = new ShiftList();
RNA rnaTrim = new RNA(name);
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 < 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(offset.shift(ofstart), ofstart - i);
ofstart = -1;
}
}
}
// final gap
if (ofstart > -1)
{
offset.addShift(offset.shift(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;
}
// needs to be many-many
Map seqs = new Hashtable();
Map rnas = 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)
{
clearSelection(null);
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;
}
public void clearSelection(AppVarnaBinding vab)
{
if (_lastRNAhighlighted != null)
{
_lastRNAhighlighted.removeHighlightRegion(_lastHighlight);
if (vab != null)
{
vab.updateSelectedRNA(_lastRNAhighlighted);
}
_lastRNAhighlighted = null;
_lastHighlight = null;
}
}
}
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();
if (seqs.get(rna) == sequence)
{
ShiftList shift = offsets.get(rna);
if (shift != null)
{
// System.err.print("Orig pos:"+index);
index = shift.shift(index);
// System.err.println("\nFinal pos:"+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)
{
if (source != ap.av)
{
// ignore events from anything but our parent alignpanel
// TODO - reuse many-one panel-view system in jmol viewer
return;
}
if (seqsel != null && seqsel.getSize() > 0)
{
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());
// TODO - translate column markings to positions on structure if present.
vab.updateSelectedRNA(rna);
}
else
{
selectionHighlighter.clearSelection(vab);
}
}
@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)
{
int i = shift.shift(arg1.getIndex());
// System.err.println("shifted "+(arg1.getIndex())+" to "+i);
ssm.mouseOverVamsasSequence(seq, i, this);
}
else
{
ssm.mouseOverVamsasSequence(seq, arg1.getIndex(), this);
}
}
}
@Override
public void onSelectionChanged(BaseList arg0, BaseList arg1, BaseList arg2)
{
// TODO translate selected regions in VARNA to a selection on the
// alignpanel.
}
@Override
public void onTranslationChanged()
{
// TODO Auto-generated method stub
}
@Override
public void onZoomLevelChanged()
{
// TODO Auto-generated method stub
}
}