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)
80 ArrayList<RNA> rnaList = new ArrayList<RNA>();
81 RNA rna1 = new RNA(name);
84 rna1.setRNA(strucseq, replaceOddGaps(struc));
85 } catch (ExceptionUnmatchedClosingParentheses e2)
88 } catch (ExceptionFileFormatOrSyntax e3)
92 RNA trim = trimRNA(rna1, "trimmed "+sname);
97 rna1.setName(sname+" (with gaps)");
104 * if (false || seq.getStart()!=1) { for (RNA rshift:rnaList) { ShiftList
105 * shift=offsets.get(rshift); if (shift==null) { offsets.put(rshift,
106 * shift=new ShiftList());} shift.addShift(1, seq.getStart()-1);
107 * offsetsInv.put(rshift, shift.getInverse()); } }
110 vab = new AppVarnaBinding(rnaList);
111 // vab = new AppVarnaBinding(seq,struc);
112 // System.out.println("Hallo: "+name);
113 this.name = sname+" trimmed to "+name;
115 ssm = ap.getStructureSelectionManager();
116 ssm.addStructureViewerListener(this);
117 ssm.addSelectionListener(this);
120 public void initVarna()
122 // vab.setFinishedInit(false);
123 varnaPanel = vab.get_varnaPanel();
124 setBackground(Color.white);
125 JSplitPane split = new JSplitPane(JSplitPane.HORIZONTAL_SPLIT, true,
126 vab.getListPanel(), varnaPanel);
127 getContentPane().setLayout(new BorderLayout());
128 getContentPane().add(split, BorderLayout.CENTER);
129 // getContentPane().add(vab.getTools(), BorderLayout.NORTH);
130 varnaPanel.addVARNAListener(this);
131 varnaPanel.addSelectionListener(this);
132 jalview.gui.Desktop.addInternalFrame(this, "VARNA -" + name,
133 getBounds().width, getBounds().height);
138 public String replaceOddGaps(String oldStr)
140 String patternStr = "[^([{<>}])]";
141 String replacementStr = ".";
142 Pattern pattern = Pattern.compile(patternStr);
143 Matcher matcher = pattern.matcher(oldStr);
144 String newStr = matcher.replaceAll(replacementStr);
148 public RNA trimRNA(RNA rna, String name)
150 ShiftList offset = new ShiftList();
151 RNA rnaTrim = new RNA(name);
154 rnaTrim.setRNA(rna.getSeq(), replaceOddGaps(rna.getStructDBN()));
155 } catch (ExceptionUnmatchedClosingParentheses e2)
157 e2.printStackTrace();
158 } catch (ExceptionFileFormatOrSyntax e3)
160 e3.printStackTrace();
163 StringBuffer seq = new StringBuffer(rnaTrim.getSeq());
164 StringBuffer struc = new StringBuffer(rnaTrim.getStructDBN());
165 int ofstart = -1, sleng = rnaTrim.getSeq().length();
166 for (int i = 0; i < sleng; i++)
168 // TODO: Jalview utility for gap detection java.utils.isGap()
169 // TODO: Switch to jalview rna datamodel
170 if (jalview.util.Comparison.isGap(seq.charAt(i)))
176 if (!rnaTrim.findPair(i).isEmpty())
178 int m = rnaTrim.findPair(i).get(1);
179 int l = rnaTrim.findPair(i).get(0);
181 struc.replace(m, m + 1, "*");
182 struc.replace(l, l + 1, "*");
186 struc.replace(i, i + 1, "*");
193 offset.addShift(offset.shift(ofstart), ofstart - i);
201 offset.addShift(offset.shift(ofstart), ofstart - sleng);
204 String newSeq = rnaTrim.getSeq().replace("-", "");
205 rnaTrim.getSeq().replace(".", "");
206 String newStruc = struc.toString().replace("*", "");
210 rnaTrim.setRNA(newSeq, newStruc);
211 registerOffset(rnaTrim, offset);
212 } catch (ExceptionUnmatchedClosingParentheses e)
214 // TODO Auto-generated catch block
216 } catch (ExceptionFileFormatOrSyntax e)
218 // TODO Auto-generated catch block
224 // needs to be many-many
225 Map<RNA, SequenceI> seqs = new Hashtable<RNA, SequenceI>();
227 Map<SequenceI, RNA> rnas = new Hashtable<SequenceI, RNA>();
229 Map<RNA, ShiftList> offsets = new Hashtable<RNA, ShiftList>();
231 Map<RNA, ShiftList> offsetsInv = new Hashtable<RNA, ShiftList>();
233 private void registerOffset(RNA rnaTrim, ShiftList offset)
235 offsets.put(rnaTrim, offset);
236 offsetsInv.put(rnaTrim, offset.getInverse());
239 public void showPanel(boolean show)
241 this.setVisible(show);
244 private boolean _started = false;
253 } catch (OutOfMemoryError oomerror)
255 new OOMWarning("When trying to open the Varna viewer!", oomerror);
256 } catch (Exception ex)
258 Cache.log.error("Couldn't open Varna viewer!", ex);
263 public void onUINewStructure(VARNAConfig v, RNA r)
269 public void onWarningEmitted(String s)
271 // TODO Auto-generated method stub
275 private class VarnaHighlighter
277 private HighlightRegionAnnotation _lastHighlight;
279 private RNA _lastRNAhighlighted = null;
281 public void highlightRegion(RNA rna, int start, int end)
283 clearSelection(null);
284 HighlightRegionAnnotation highlight = new HighlightRegionAnnotation(
285 rna.getBasesBetween(start, end));
286 rna.addHighlightRegion(highlight);
287 _lastHighlight = highlight;
288 _lastRNAhighlighted = rna;
292 public HighlightRegionAnnotation getLastHighlight()
294 return _lastHighlight;
297 public RNA getLastRNA()
299 return _lastRNAhighlighted;
302 public void clearSelection(AppVarnaBinding vab)
304 if (_lastRNAhighlighted != null)
306 _lastRNAhighlighted.removeHighlightRegion(_lastHighlight);
309 vab.updateSelectedRNA(_lastRNAhighlighted);
311 _lastRNAhighlighted = null;
312 _lastHighlight = null;
318 VarnaHighlighter mouseOverHighlighter = new VarnaHighlighter(),
319 selectionHighlighter = new VarnaHighlighter();
322 * If a mouseOver event from the AlignmentPanel is noticed the currently
323 * selected RNA in the VARNA window is highlighted at the specific position.
324 * To be able to remove it before the next highlight it is saved in
328 public void mouseOverSequence(SequenceI sequence, int index)
330 RNA rna = vab.getSelectedRNA();
331 if (seqs.get(rna) == sequence)
333 ShiftList shift = offsets.get(rna);
336 // System.err.print("Orig pos:"+index);
337 index = shift.shift(index);
338 // System.err.println("\nFinal pos:"+index);
340 mouseOverHighlighter.highlightRegion(rna, index, index);
341 vab.updateSelectedRNA(rna);
346 public void onStructureRedrawn()
348 // TODO Auto-generated method stub
353 public void selection(SequenceGroup seqsel, ColumnSelection colsel,
354 SelectionSource source)
358 // ignore events from anything but our parent alignpanel
359 // TODO - reuse many-one panel-view system in jmol viewer
362 if (seqsel != null && seqsel.getSize() > 0)
364 int start = seqsel.getStartRes(), end = seqsel.getEndRes();
365 RNA rna = vab.getSelectedRNA();
366 ShiftList shift = offsets.get(rna);
369 start = shift.shift(start);
370 end = shift.shift(end);
372 selectionHighlighter.highlightRegion(rna, start, end);
373 selectionHighlighter.getLastHighlight().setOutlineColor(
374 seqsel.getOutlineColour());
375 // TODO - translate column markings to positions on structure if present.
376 vab.updateSelectedRNA(rna);
380 selectionHighlighter.clearSelection(vab);
385 public void onHoverChanged(ModeleBase arg0, ModeleBase arg1)
387 RNA rna = vab.getSelectedRNA();
388 ShiftList shift = offsetsInv.get(rna);
389 SequenceI seq = seqs.get(rna);
390 if (arg1 != null && seq != null)
394 int i = shift.shift(arg1.getIndex());
395 // System.err.println("shifted "+(arg1.getIndex())+" to "+i);
396 ssm.mouseOverVamsasSequence(seq, i, this);
400 ssm.mouseOverVamsasSequence(seq, arg1.getIndex(), this);
406 public void onSelectionChanged(BaseList arg0, BaseList arg1, BaseList arg2)
408 // TODO translate selected regions in VARNA to a selection on the