X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAppVarna.java;h=4fe9ac2139d4a41bf3446fa6e735cd22dd60683e;hb=5c33de4092732a61c2bc4ab3cb76b773752ad37a;hp=daa0beae83ad0ce9234a17f1531d9284e5b672c1;hpb=8f3cf5f09e970ac6e5d9032c03ec29f69fb4b356;p=jalview.git
diff --git a/src/jalview/gui/AppVarna.java b/src/jalview/gui/AppVarna.java
index daa0bea..4fe9ac2 100644
--- a/src/jalview/gui/AppVarna.java
+++ b/src/jalview/gui/AppVarna.java
@@ -1,44 +1,53 @@
/*
- * 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
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 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.
- *
+ * 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 .
+ * 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 java.util.*;
+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 java.awt.*;
-
-import javax.swing.*;
-import javax.swing.event.*;
-import java.awt.event.*;
-import java.io.*;
+import javax.swing.JInternalFrame;
+import javax.swing.JSplitPane;
-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.MessageManager;
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;
@@ -46,279 +55,396 @@ 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
+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){
+
+ /*
+ * 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));
- } catch (ExceptionUnmatchedClosingParentheses e2) {
+ 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) {
+ } catch (ExceptionFileFormatOrSyntax e3)
+ {
e3.printStackTrace();
}
- RNA trim=trimRNA(rna1);
- rnaList.add(trim);
+ RNA trim = trimRNA(rna1, "trimmed " + sname);
+ rnaList.add(trim);
rnaList.add(rna1);
- rna1.setName("consensus_"+rna1.getName());
-
+
+ rnas.put(seq, rna1);
+ rnas.put(seq, trim);
+ rna1.setName(sname + " (with gaps)");
+
{
- this.seqs.put(trim, seq);
- this.seqs.put(rna1, seq);
+ 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);
- //System.out.println("Hallo: "+name);
- this.name=name;
+ // 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,"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)
+
+ public void initVarna()
{
- offsets.put(rnaTrim, offset);
- offsetsInv.put(rnaTrim,offset.getInverse());
+
+ // 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 void showPanel(boolean show){
- this.setVisible(show);
+ 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;
}
-
- private boolean _started = false;
- public void run(){
- _started = true;
-
- try
- {
- initVarna();
- } catch (OutOfMemoryError oomerror)
+ 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)))
{
- new OOMWarning("When trying to open the Varna viewer!", oomerror);
- } catch (Exception ex)
+ 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
{
- Cache.log.error("Couldn't open Varna viewer!", ex);
+ 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;
}
-@Override
-public void onUINewStructure(VARNAConfig v, RNA r) {
-
-}
+ // needs to be many-many
+ Map seqs = new Hashtable();
-@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)
+ Map rnas = new Hashtable();
+
+ Map offsets = new Hashtable();
+
+ Map offsetsInv = new Hashtable();
+
+ private void registerOffset(RNA rnaTrim, ShiftList offset)
{
- if (_lastRNAhighlighted!=null)
+ 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)
{
- _lastRNAhighlighted.removeHighlightRegion(_lastHighlight);
+
}
- HighlightRegionAnnotation highlight = new HighlightRegionAnnotation(rna.getBasesBetween(start,end));
- rna.addHighlightRegion(highlight);
- _lastHighlight=highlight;
- _lastRNAhighlighted=rna;
+
+ @Override
+ public void onWarningEmitted(String s)
+ {
+ // TODO Auto-generated method stub
}
- public HighlightRegionAnnotation getLastHighlight() {
- return _lastHighlight;
+
+ 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;
+
+ }
+ }
}
- public RNA getLastRNA()
+
+ 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)
{
- return _lastRNAhighlighted;
+ 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);
+ }
}
-}
-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 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)
+ @Override
+ public void selection(SequenceGroup seqsel, ColumnSelection colsel,
+ SelectionSource source)
{
- start=shift.shift(start);
- end=shift.shift(end);
+ 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);
+ }
}
- 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)
+ @Override
+ public void onHoverChanged(ModeleBase arg0, ModeleBase arg1)
{
- if (shift!=null)
+ RNA rna = vab.getSelectedRNA();
+ ShiftList shift = offsetsInv.get(rna);
+ SequenceI seq = seqs.get(rna);
+ if (arg1 != null && seq != null)
{
- ssm.mouseOverVamsasSequence(seq, seq.findIndex(arg1.getIndex()), this);
- } else {
- ssm.mouseOverVamsasSequence(seq, arg1.getIndex(), this);
+ 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 Auto-generated method stub
-
-}
+ @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
+
+ }
}