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.AlignViewportI;
32 import jalview.api.AlignmentViewPanel;
33 import jalview.api.SequenceStructureBinding;
34 import jalview.bin.Cache;
35 import jalview.datamodel.*;
36 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
37 import jalview.structure.*;
39 import jalview.schemes.*;
40 import jalview.util.ShiftList;
41 import fr.orsay.lri.varna.VARNAPanel;
42 import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
43 import fr.orsay.lri.varna.exceptions.ExceptionNonEqualLength;
44 import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
45 import fr.orsay.lri.varna.interfaces.InterfaceVARNAListener;
46 import fr.orsay.lri.varna.interfaces.InterfaceVARNASelectionListener;
47 import fr.orsay.lri.varna.models.BaseList;
48 import fr.orsay.lri.varna.models.VARNAConfig;
49 import fr.orsay.lri.varna.models.annotations.HighlightRegionAnnotation;
50 import fr.orsay.lri.varna.models.rna.ModeleBase;
51 import fr.orsay.lri.varna.models.rna.ModeleBaseNucleotide;
52 import fr.orsay.lri.varna.models.rna.RNA;
54 public class AppVarna extends JInternalFrame implements
55 InterfaceVARNAListener, SelectionListener,
56 SecondaryStructureListener// implements
57 // Runnable,SequenceStructureBinding,
59 , InterfaceVARNASelectionListener, VamsasSource
64 VARNAPanel varnaPanel;
68 public StructureSelectionManager ssm;
71 * public AppVarna(){ vab = new AppVarnaBinding(); initVarna(); }
76 public AppVarna(String sname, SequenceI seq, String strucseq, String struc,
77 String name, AlignmentPanel ap)
79 System.out.println("je suis là (AppVarna!!");
80 System.out.println("1:"+sname);
81 System.out.println("2:"+seq);
82 System.out.println("3:"+strucseq);
83 System.out.println("4:"+struc);
84 System.out.println("5:"+name);
85 System.out.println("6:"+ap);
87 ArrayList<RNA> rnaList = new ArrayList<RNA>();
88 RNA rna1 = new RNA(name);
91 System.out.println("ou ici ?");
92 rna1.setRNA(strucseq, replaceOddGaps(struc));
93 System.out.println("La séquence est :"+rna1.getSeq());
94 System.out.println("La séquence est :"+struc);
95 System.out.println("La séquence est :"+replaceOddGaps(struc).toString());
96 } catch (ExceptionUnmatchedClosingParentheses e2)
99 } catch (ExceptionFileFormatOrSyntax e3)
101 e3.printStackTrace();
104 RNA trim = trimRNA(rna1, "trimmed "+sname);
111 rna1.setName(sname+" (with gaps)");
118 * if (false || seq.getStart()!=1) { for (RNA rshift:rnaList) { ShiftList
119 * shift=offsets.get(rshift); if (shift==null) { offsets.put(rshift,
120 * shift=new ShiftList());} shift.addShift(1, seq.getStart()-1);
121 * offsetsInv.put(rshift, shift.getInverse()); } }
124 vab = new AppVarnaBinding(rnaList);
125 // vab = new AppVarnaBinding(seq,struc);
126 // System.out.println("Hallo: "+name);
127 this.name = sname+" trimmed to "+name;
130 ssm = ap.getStructureSelectionManager();
131 System.out.println(ssm.toString());
132 ssm.addStructureViewerListener(this);
133 ssm.addSelectionListener(this);
136 public void initVarna()
138 System.out.println("initialisation VANRA");
139 // vab.setFinishedInit(false);
140 varnaPanel = vab.get_varnaPanel();
141 setBackground(Color.white);
142 JSplitPane split = new JSplitPane(JSplitPane.HORIZONTAL_SPLIT, true,
143 vab.getListPanel(), varnaPanel);
144 getContentPane().setLayout(new BorderLayout());
145 getContentPane().add(split, BorderLayout.CENTER);
146 // getContentPane().add(vab.getTools(), BorderLayout.NORTH);
147 varnaPanel.addVARNAListener(this);
148 varnaPanel.addSelectionListener(this);
149 jalview.gui.Desktop.addInternalFrame(this, "VARNA -" + name,
150 getBounds().width, getBounds().height);
153 System.out.println("Sortie initialisation VANRA");
156 public String replaceOddGaps(String oldStr)
158 String patternStr = "[^([{<>}])]";
159 String replacementStr = ".";
160 Pattern pattern = Pattern.compile(patternStr);
161 Matcher matcher = pattern.matcher(oldStr);
162 String newStr = matcher.replaceAll(replacementStr);
166 public RNA trimRNA(RNA rna, String name)
168 ShiftList offset = new ShiftList();
170 RNA rnaTrim = new RNA(name);
173 rnaTrim.setRNA(rna.getSeq(), replaceOddGaps(rna.getStructDBN()));
174 } catch (ExceptionUnmatchedClosingParentheses e2)
176 e2.printStackTrace();
177 } catch (ExceptionFileFormatOrSyntax e3)
179 e3.printStackTrace();
182 StringBuffer seq = new StringBuffer(rnaTrim.getSeq());
183 StringBuffer struc = new StringBuffer(rnaTrim.getStructDBN());
184 int ofstart = -1, sleng = rnaTrim.getSeq().length();
185 for (int i = 0; i < sleng; i++)
187 // TODO: Jalview utility for gap detection java.utils.isGap()
188 // TODO: Switch to jalview rna datamodel
189 if (jalview.util.Comparison.isGap(seq.charAt(i)))
195 if (!rnaTrim.findPair(i).isEmpty())
197 int m = rnaTrim.findPair(i).get(1);
198 int l = rnaTrim.findPair(i).get(0);
200 struc.replace(m, m + 1, "*");
201 struc.replace(l, l + 1, "*");
205 struc.replace(i, i + 1, "*");
212 offset.addShift(offset.shift(ofstart), ofstart - i);
220 offset.addShift(offset.shift(ofstart), ofstart - sleng);
223 String newSeq = rnaTrim.getSeq().replace("-", "");
224 rnaTrim.getSeq().replace(".", "");
225 String newStruc = struc.toString().replace("*", "");
229 rnaTrim.setRNA(newSeq, newStruc);
230 registerOffset(rnaTrim, offset);
231 } catch (ExceptionUnmatchedClosingParentheses e)
233 // TODO Auto-generated catch block
235 } catch (ExceptionFileFormatOrSyntax e)
237 // TODO Auto-generated catch block
243 // needs to be many-many
244 Map<RNA, SequenceI> seqs = new Hashtable<RNA, SequenceI>();
246 Map<SequenceI, RNA> rnas = new Hashtable<SequenceI, RNA>();
248 Map<RNA, ShiftList> offsets = new Hashtable<RNA, ShiftList>();
250 Map<RNA, ShiftList> offsetsInv = new Hashtable<RNA, ShiftList>();
252 private void registerOffset(RNA rnaTrim, ShiftList offset)
254 offsets.put(rnaTrim, offset);
255 offsetsInv.put(rnaTrim, offset.getInverse());
258 public void showPanel(boolean show)
260 this.setVisible(show);
263 private boolean _started = false;
272 } catch (OutOfMemoryError oomerror)
274 new OOMWarning("When trying to open the Varna viewer!", oomerror);
275 } catch (Exception ex)
277 Cache.log.error("Couldn't open Varna viewer!", ex);
282 public void onUINewStructure(VARNAConfig v, RNA r)
288 public void onWarningEmitted(String s)
290 // TODO Auto-generated method stub
294 private class VarnaHighlighter
296 private HighlightRegionAnnotation _lastHighlight;
298 private RNA _lastRNAhighlighted = null;
300 public void highlightRegion(RNA rna, int start, int end)
302 clearSelection(null);
303 HighlightRegionAnnotation highlight = new HighlightRegionAnnotation(
304 rna.getBasesBetween(start, end));
305 rna.addHighlightRegion(highlight);
306 _lastHighlight = highlight;
307 _lastRNAhighlighted = rna;
311 public HighlightRegionAnnotation getLastHighlight()
313 return _lastHighlight;
316 public RNA getLastRNA()
318 return _lastRNAhighlighted;
321 public void clearSelection(AppVarnaBinding vab)
323 if (_lastRNAhighlighted != null)
325 _lastRNAhighlighted.removeHighlightRegion(_lastHighlight);
328 vab.updateSelectedRNA(_lastRNAhighlighted);
330 _lastRNAhighlighted = null;
331 _lastHighlight = null;
337 VarnaHighlighter mouseOverHighlighter = new VarnaHighlighter(),
338 selectionHighlighter = new VarnaHighlighter();
341 * If a mouseOver event from the AlignmentPanel is noticed the currently
342 * selected RNA in the VARNA window is highlighted at the specific position.
343 * To be able to remove it before the next highlight it is saved in
347 public void mouseOverSequence(SequenceI sequence, int index)
349 RNA rna = vab.getSelectedRNA();
350 if (seqs.get(rna) == sequence)
352 ShiftList shift = offsets.get(rna);
355 // System.err.print("Orig pos:"+index);
356 index = shift.shift(index);
357 // System.err.println("\nFinal pos:"+index);
359 mouseOverHighlighter.highlightRegion(rna, index, index);
360 vab.updateSelectedRNA(rna);
365 public void onStructureRedrawn()
367 // TODO Auto-generated method stub
372 public void selection(SequenceGroup seqsel, ColumnSelection colsel,
373 SelectionSource source)
377 // ignore events from anything but our parent alignpanel
378 // TODO - reuse many-one panel-view system in jmol viewer
381 if (seqsel != null && seqsel.getSize() > 0)
383 int start = seqsel.getStartRes(), end = seqsel.getEndRes();
384 RNA rna = vab.getSelectedRNA();
385 ShiftList shift = offsets.get(rna);
388 start = shift.shift(start);
389 end = shift.shift(end);
391 selectionHighlighter.highlightRegion(rna, start, end);
392 selectionHighlighter.getLastHighlight().setOutlineColor(
393 seqsel.getOutlineColour());
394 // TODO - translate column markings to positions on structure if present.
395 vab.updateSelectedRNA(rna);
399 selectionHighlighter.clearSelection(vab);
404 public void onHoverChanged(ModeleBase arg0, ModeleBase arg1)
406 RNA rna = vab.getSelectedRNA();
407 ShiftList shift = offsetsInv.get(rna);
408 SequenceI seq = seqs.get(rna);
409 if (arg1 != null && seq != null)
413 int i = shift.shift(arg1.getIndex());
414 // System.err.println("shifted "+(arg1.getIndex())+" to "+i);
415 ssm.mouseOverVamsasSequence(seq, i, this);
419 ssm.mouseOverVamsasSequence(seq, arg1.getIndex(), this);
425 public void onSelectionChanged(BaseList arg0, BaseList arg1, BaseList arg2)
427 // TODO translate selected regions in VARNA to a selection on the