2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
3 * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
11 * Jalview is distributed in the hope that it will be useful, but
12 * WITHOUT ANY WARRANTY; without even the implied warranty
13 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
14 * PURPOSE. See the GNU General Public License for more details.
16 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
21 import java.util.regex.Matcher;
22 import java.util.regex.Pattern;
26 import javax.swing.event.*;
28 import java.awt.event.*;
31 import jalview.api.SequenceStructureBinding;
32 import jalview.bin.Cache;
33 import jalview.datamodel.*;
34 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
35 import jalview.structure.*;
37 import jalview.schemes.*;
38 import jalview.util.ShiftList;
39 import fr.orsay.lri.varna.VARNAPanel;
40 import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
41 import fr.orsay.lri.varna.exceptions.ExceptionNonEqualLength;
42 import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
43 import fr.orsay.lri.varna.interfaces.InterfaceVARNAListener;
44 import fr.orsay.lri.varna.interfaces.InterfaceVARNASelectionListener;
45 import fr.orsay.lri.varna.models.BaseList;
46 import fr.orsay.lri.varna.models.VARNAConfig;
47 import fr.orsay.lri.varna.models.annotations.HighlightRegionAnnotation;
48 import fr.orsay.lri.varna.models.rna.ModeleBase;
49 import fr.orsay.lri.varna.models.rna.ModeleBaseNucleotide;
50 import fr.orsay.lri.varna.models.rna.RNA;
53 public class AppVarna extends JInternalFrame implements InterfaceVARNAListener,SelectionListener, SecondaryStructureListener// implements Runnable,SequenceStructureBinding, ViewSetProvider
54 , InterfaceVARNASelectionListener, VamsasSource
59 VARNAPanel varnaPanel;
63 public StructureSelectionManager ssm;
66 vab = new AppVarnaBinding();
71 public AppVarna(SequenceI seq,String strucseq, String struc,String name,AlignmentPanel ap){
72 ArrayList<RNA> rnaList = new ArrayList<RNA>();
73 RNA rna1 = new RNA(name);
75 rna1.setRNA(strucseq,replaceOddGaps(struc));
76 } catch (ExceptionUnmatchedClosingParentheses e2) {
78 } catch (ExceptionFileFormatOrSyntax e3) {
81 RNA trim=trimRNA(rna1);
84 rna1.setName("consensus_"+rna1.getName());
87 this.seqs.put(trim, seq);
88 this.seqs.put(rna1, seq);
90 vab = new AppVarnaBinding(rnaList);
91 //vab = new AppVarnaBinding(seq,struc);
92 //System.out.println("Hallo: "+name);
95 ssm = ap.getStructureSelectionManager();
96 ssm.addStructureViewerListener(this);
97 ssm.addSelectionListener(this);
100 public void initVarna(){
101 //vab.setFinishedInit(false);
102 varnaPanel=vab.get_varnaPanel();
103 setBackground(Color.white);
104 JSplitPane split = new JSplitPane(JSplitPane.HORIZONTAL_SPLIT,true,vab.getListPanel(),varnaPanel);
105 getContentPane().setLayout(new BorderLayout());
106 getContentPane().add(split, BorderLayout.CENTER);
107 //getContentPane().add(vab.getTools(), BorderLayout.NORTH);
108 varnaPanel.addVARNAListener(this);
109 varnaPanel.addSelectionListener(this);
110 jalview.gui.Desktop.addInternalFrame(this,"VARNA -"+name,getBounds().width, getBounds().height);
115 public String replaceOddGaps(String oldStr){
116 String patternStr = "[^([{<>}])]";
117 String replacementStr = ".";
118 Pattern pattern = Pattern.compile(patternStr);
119 Matcher matcher = pattern.matcher(oldStr);
120 String newStr=matcher.replaceAll(replacementStr);
124 public RNA trimRNA(RNA rna){
125 ShiftList offset=new ShiftList();
126 RNA rnaTrim = new RNA("trim_"+rna.getName());
128 rnaTrim.setRNA(rna.getSeq(),replaceOddGaps(rna.getStructDBN()));
129 } catch (ExceptionUnmatchedClosingParentheses e2) {
130 e2.printStackTrace();
131 } catch (ExceptionFileFormatOrSyntax e3) {
132 e3.printStackTrace();
135 StringBuffer seq=new StringBuffer(rnaTrim.getSeq());
136 StringBuffer struc=new StringBuffer(rnaTrim.getStructDBN());
137 int ofstart=-1,sleng=rnaTrim.getSeq().length();
138 for(int i=0;i<sleng;i++){
139 //TODO: Jalview utility for gap detection java.utils.isGap()
140 //TODO: Switch to jalview rna datamodel
141 if(jalview.util.Comparison.isGap(seq.charAt(i))){
146 if(!rnaTrim.findPair(i).isEmpty()){
147 int m=rnaTrim.findPair(i).get(1);
148 int l=rnaTrim.findPair(i).get(0);
150 struc.replace(m, m+1, "*");
151 struc.replace(l, l+1, "*");
153 struc.replace(i, i+1, "*");
158 offset.addShift(ofstart, ofstart-i);
166 offset.addShift(ofstart, ofstart-sleng);
169 String newSeq=rnaTrim.getSeq().replace("-", "");
170 rnaTrim.getSeq().replace(".", "");
171 String newStruc=struc.toString().replace("*", "");
174 rnaTrim.setRNA(newSeq,newStruc);
175 registerOffset(rnaTrim,offset);
176 } catch (ExceptionUnmatchedClosingParentheses e) {
177 // TODO Auto-generated catch block
179 } catch (ExceptionFileFormatOrSyntax e) {
180 // TODO Auto-generated catch block
185 Map<RNA,SequenceI> seqs=new Hashtable<RNA,SequenceI>();
186 Map<RNA,ShiftList> offsets=new Hashtable<RNA,ShiftList>();
187 Map<RNA,ShiftList> offsetsInv=new Hashtable<RNA,ShiftList>();
188 private void registerOffset(RNA rnaTrim, ShiftList offset)
190 offsets.put(rnaTrim, offset);
191 offsetsInv.put(rnaTrim,offset.getInverse());
194 public void showPanel(boolean show){
195 this.setVisible(show);
198 private boolean _started = false;
206 } catch (OutOfMemoryError oomerror)
208 new OOMWarning("When trying to open the Varna viewer!", oomerror);
209 } catch (Exception ex)
211 Cache.log.error("Couldn't open Varna viewer!", ex);
216 public void onUINewStructure(VARNAConfig v, RNA r) {
221 public void onWarningEmitted(String s) {
222 // TODO Auto-generated method stub
225 private class VarnaHighlighter {
226 private HighlightRegionAnnotation _lastHighlight;
227 private RNA _lastRNAhighlighted=null;
228 public void highlightRegion(RNA rna, int start,int end)
230 if (_lastRNAhighlighted!=null)
232 _lastRNAhighlighted.removeHighlightRegion(_lastHighlight);
234 HighlightRegionAnnotation highlight = new HighlightRegionAnnotation(rna.getBasesBetween(start,end));
235 rna.addHighlightRegion(highlight);
236 _lastHighlight=highlight;
237 _lastRNAhighlighted=rna;
240 public HighlightRegionAnnotation getLastHighlight() {
241 return _lastHighlight;
243 public RNA getLastRNA()
245 return _lastRNAhighlighted;
248 VarnaHighlighter mouseOverHighlighter=new VarnaHighlighter(),
249 selectionHighlighter=new VarnaHighlighter();
251 * If a mouseOver event from the AlignmentPanel
252 * is noticed the currently selected RNA in the
253 * VARNA window is highlighted at the specific position.
254 * To be able to remove it before the next highlight
255 * it is saved in _lastHighlight
258 public void mouseOverSequence(SequenceI sequence, int index) {
259 RNA rna=vab.getSelectedRNA();
260 ShiftList shift=offsets.get(rna);
263 index=shift.shift(index);
265 mouseOverHighlighter.highlightRegion(rna, index, index);
266 vab.updateSelectedRNA(rna);
271 public void onStructureRedrawn()
273 // TODO Auto-generated method stub
278 public void selection(SequenceGroup seqsel, ColumnSelection colsel,
279 SelectionSource source)
281 int start=seqsel.getStartRes(),end=seqsel.getEndRes();
282 RNA rna=vab.getSelectedRNA();
283 ShiftList shift=offsets.get(rna);
286 start=shift.shift(start);
287 end=shift.shift(end);
289 selectionHighlighter.highlightRegion(rna, start, end);
290 selectionHighlighter.getLastHighlight().setOutlineColor(seqsel.getOutlineColour());
291 vab.updateSelectedRNA(rna);
295 public void onHoverChanged(ModeleBase arg0, ModeleBase arg1)
297 RNA rna=vab.getSelectedRNA();
298 ShiftList shift=offsetsInv.get(rna);
299 SequenceI seq=seqs.get(rna);
300 if (arg1!=null && seq!=null)
304 ssm.mouseOverVamsasSequence(seq, seq.findIndex(arg1.getIndex()), this);
306 ssm.mouseOverVamsasSequence(seq, arg1.getIndex(), this);
312 public void onSelectionChanged(BaseList arg0, BaseList arg1, BaseList arg2)
314 // TODO Auto-generated method stub