2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
3 * Copyright (C) 2014 The Jalview Authors
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/>.
17 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 import java.util.jar.*;
27 import org.exolab.castor.xml.*;
28 import jalview.binding.*;
29 import jalview.schemes.*;
30 import jalview.util.MessageManager;
31 import jalview.util.jarInputStreamProvider;
39 public class Jalview2XML_V1
41 boolean raiseGUI = true;
43 public Jalview2XML_V1()
48 public Jalview2XML_V1(boolean raiseGUI)
50 this.raiseGUI = raiseGUI;
53 jalview.schemes.UserColourScheme GetUserColourScheme(
54 JalviewModelSequence jms, String id)
56 UserColours[] uc = jms.getUserColours();
57 UserColours colours = null;
59 for (int i = 0; i < uc.length; i++)
61 if (uc[i].getId().equals(id))
69 int csize = colours.getUserColourScheme().getColourCount();
70 java.awt.Color[] newColours = new java.awt.Color[csize];
72 for (int i = 0; i < csize; i++)
74 newColours[i] = new java.awt.Color(Integer.parseInt(colours
75 .getUserColourScheme().getColour(i).getRGB(), 16));
78 return new jalview.schemes.UserColourScheme(newColours);
87 public AlignFrame LoadJalviewAlign(final jarInputStreamProvider jprovider)
89 final String file = jprovider.getFilename();
90 jalview.gui.AlignFrame af = null;
94 JarInputStream jin = null;
95 JarEntry jarentry = null;
100 jin = jprovider.getJarInputStream();
102 for (int i = 0; i < entryCount; i++)
104 jarentry = jin.getNextJarEntry();
107 class NoDescIDResolver implements IDResolver
109 public Object resolve(String idref)
111 System.out.println(idref + " used");
116 if (jarentry != null)
118 InputStreamReader in = new InputStreamReader(jin, "UTF-8");
119 JalviewModel object = new JalviewModel();
121 object = (JalviewModel) object.unmarshal(in);
123 af = LoadFromObject(object, file);
126 } while (jarentry != null);
127 } catch (final java.net.UnknownHostException ex)
129 ex.printStackTrace();
132 javax.swing.SwingUtilities.invokeLater(new Runnable()
137 System.err.println("Couldn't locate Jalview XML file : " + ex
139 JOptionPane.showInternalMessageDialog(Desktop.desktop,
140 MessageManager.formatMessage("label.couldnt_locate", new String[]{file}),
141 MessageManager.getString("label.url_not_found"),
142 JOptionPane.WARNING_MESSAGE);
147 } catch (Exception ex)
149 System.err.println("Exception whilst loading jalview XML file : ");
150 ex.printStackTrace();
153 javax.swing.SwingUtilities.invokeLater(new Runnable()
158 JOptionPane.showInternalMessageDialog(Desktop.desktop,
159 "Error loading " + file, "Error loading Jalview file",
160 JOptionPane.WARNING_MESSAGE);
169 AlignFrame LoadFromObject(JalviewModel object, String file)
171 Vector seqids = new Vector();
172 SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);
173 Sequence[] vamsasSeq = vamsasSet.getSequence();
175 JalviewModelSequence jms = object.getJalviewModelSequence();
177 // ////////////////////////////////
179 jalview.datamodel.Sequence[] jseqs = new jalview.datamodel.Sequence[vamsasSeq.length];
180 JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq();
181 for (int i = 0; i < vamsasSeq.length; i++)
183 jseqs[i] = new jalview.datamodel.Sequence(vamsasSeq[i].getName(),
184 vamsasSeq[i].getSequence());
185 jseqs[i].setStart(JSEQ[i].getStart());
186 jseqs[i].setEnd(JSEQ[i].getEnd());
187 seqids.add(jseqs[i]);
190 // /SequenceFeatures are added to the DatasetSequence,
191 // so we must create the dataset before loading features
192 // ///////////////////////////////
193 jalview.datamodel.Alignment al = new jalview.datamodel.Alignment(jseqs);
195 // ///////////////////////////////
197 for (int i = 0; i < vamsasSeq.length; i++)
199 if (JSEQ[i].getFeaturesCount() > 0)
201 Features[] features = JSEQ[i].getFeatures();
202 for (int f = 0; f < features.length; f++)
204 jalview.datamodel.SequenceFeature sf = new jalview.datamodel.SequenceFeature(
205 features[f].getType(), features[f].getDescription(),
206 features[f].getStatus(), features[f].getBegin(),
207 features[f].getEnd(), null);
209 al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf);
212 if (JSEQ[i].getPdbidsCount() > 0)
214 Pdbids[] ids = JSEQ[i].getPdbids();
215 for (int p = 0; p < ids.length; p++)
217 jalview.datamodel.PDBEntry entry = new jalview.datamodel.PDBEntry();
218 entry.setId(ids[p].getId());
219 entry.setType(ids[p].getType());
220 al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
226 // ///////////////////////////////
227 // ////////////////////////////////
229 if (vamsasSet.getAnnotation() != null)
231 Annotation[] an = vamsasSet.getAnnotation();
233 for (int i = 0; i < an.length; i++)
235 AnnotationElement[] ae = an[i].getAnnotationElement();
236 jalview.datamodel.Annotation[] anot = new jalview.datamodel.Annotation[al
239 for (int aa = 0; aa < ae.length; aa++)
241 anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(
242 ae[aa].getDisplayCharacter(), ae[aa].getDescription(),
243 ae[aa].getSecondaryStructure().charAt(0),
247 jalview.datamodel.AlignmentAnnotation jaa = null;
249 if (an[i].getGraph())
251 jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
252 an[i].getDescription(), anot, 0, 0,
253 jalview.datamodel.AlignmentAnnotation.BAR_GRAPH);
257 jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
258 an[i].getDescription(), anot);
261 al.addAnnotation(jaa);
265 // ///////////////////////////////
267 Viewport[] views = jms.getViewport();
268 Viewport view = views[0]; // DEAL WITH MULTIPLE VIEWPORTS LATER
270 AlignFrame af = new AlignFrame(al, view.getWidth(), view.getHeight());
272 af.setFileName(file, "Jalview");
274 for (int i = 0; i < JSEQ.length; i++)
276 af.viewport.setSequenceColour(af.viewport.getAlignment()
277 .getSequenceAt(i), new java.awt.Color(JSEQ[i].getColour()));
280 // af.changeColour() );
281 // ///////////////////////
283 if (jms.getJGroupCount() > 0)
285 JGroup[] groups = jms.getJGroup();
287 for (int i = 0; i < groups.length; i++)
289 ColourSchemeI cs = null;
291 if (groups[i].getColour() != null)
293 if (groups[i].getColour().startsWith("ucs"))
295 cs = GetUserColourScheme(jms, groups[i].getColour());
299 cs = ColourSchemeProperty.getColour(al, groups[i].getColour());
304 cs.setThreshold(groups[i].getPidThreshold(), true);
309 Vector seqs = new Vector();
310 int[] ids = groups[i].getSeq();
312 for (int s = 0; s < ids.length; s++)
314 seqs.addElement((jalview.datamodel.SequenceI) seqids
318 jalview.datamodel.SequenceGroup sg = new jalview.datamodel.SequenceGroup(
319 seqs, groups[i].getName(), cs, groups[i].getDisplayBoxes(),
320 groups[i].getDisplayText(), groups[i].getColourText(),
321 groups[i].getStart(), groups[i].getEnd());
323 sg.setOutlineColour(new java.awt.Color(groups[i].getOutlineColour()));
325 if (groups[i].getConsThreshold() != 0)
327 jalview.analysis.Conservation c = new jalview.analysis.Conservation(
328 "All", ResidueProperties.propHash, 3,
329 sg.getSequences(null), 0, sg.getWidth() - 1);
331 c.verdict(false, 25);
332 sg.cs.setConservation(c);
339 af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),
341 af.viewport.setStartRes(view.getStartRes());
342 af.viewport.setStartSeq(view.getStartSeq());
343 af.viewport.setShowAnnotation(view.getShowAnnotation());
344 af.viewport.setAbovePIDThreshold(view.getPidSelected());
345 af.viewport.setColourText(view.getShowColourText());
346 af.viewport.setConservationSelected(view.getConservationSelected());
347 af.viewport.setShowJVSuffix(view.getShowFullId());
348 af.viewport.setFont(new java.awt.Font(view.getFontName(), view
349 .getFontStyle(), view.getFontSize()));
350 af.alignPanel.fontChanged();
352 af.viewport.setRenderGaps(view.getRenderGaps());
353 af.viewport.setWrapAlignment(view.getWrapAlignment());
354 af.alignPanel.setWrapAlignment(view.getWrapAlignment());
355 af.viewport.setShowAnnotation(view.getShowAnnotation());
356 af.alignPanel.setAnnotationVisible(view.getShowAnnotation());
357 af.viewport.setShowBoxes(view.getShowBoxes());
358 af.viewport.setShowText(view.getShowText());
360 ColourSchemeI cs = null;
362 if (view.getBgColour() != null)
364 if (view.getBgColour().startsWith("ucs"))
366 cs = GetUserColourScheme(jms, view.getBgColour());
370 cs = ColourSchemeProperty.getColour(al, view.getBgColour());
375 cs.setThreshold(view.getPidThreshold(), true);
376 cs.setConsensus(af.viewport.getSequenceConsensusHash());
380 af.viewport.setGlobalColourScheme(cs);
381 af.viewport.setColourAppliesToAllGroups(false);
383 if (view.getConservationSelected() && cs != null)
385 cs.setConservationInc(view.getConsThreshold());
388 af.viewport.setColourAppliesToAllGroups(true);
389 af.viewport.showSequenceFeatures = view.getShowSequenceFeatures();
391 if (jms.getFeatureSettings() != null)
393 af.viewport.featuresDisplayed = new Hashtable();
394 String[] renderOrder = new String[jms.getFeatureSettings()
396 for (int fs = 0; fs < jms.getFeatureSettings().getSettingCount(); fs++)
398 Setting setting = jms.getFeatureSettings().getSetting(fs);
400 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(
401 setting.getType(), new java.awt.Color(setting.getColour()));
403 renderOrder[fs] = setting.getType();
405 if (setting.getDisplay())
407 af.viewport.featuresDisplayed.put(setting.getType(), new Integer(
408 setting.getColour()));
411 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder = renderOrder;
414 af.setMenusFromViewport(af.viewport);
416 Desktop.addInternalFrame(af, view.getTitle(), view.getWidth(),
420 // /////////////////////////////////////
421 if (jms.getTreeCount() > 0)
425 for (int t = 0; t < jms.getTreeCount(); t++)
428 Tree tree = jms.getTree(t);
430 TreePanel tp = af.ShowNewickTree(
431 new jalview.io.NewickFile(tree.getNewick()),
432 tree.getTitle(), tree.getWidth(), tree.getHeight(),
433 tree.getXpos(), tree.getYpos());
435 tp.fitToWindow.setState(tree.getFitToWindow());
436 tp.fitToWindow_actionPerformed(null);
438 if (tree.getFontName() != null)
440 tp.setTreeFont(new java.awt.Font(tree.getFontName(), tree
441 .getFontStyle(), tree.getFontSize()));
445 tp.setTreeFont(new java.awt.Font(view.getFontName(), view
446 .getFontStyle(), tree.getFontSize()));
449 tp.showPlaceholders(tree.getMarkUnlinked());
450 tp.showBootstrap(tree.getShowBootstrap());
451 tp.showDistances(tree.getShowDistances());
453 tp.treeCanvas.threshold = tree.getThreshold();
455 if (tree.getCurrentTree())
457 af.viewport.setCurrentTree(tp.getTree());
461 } catch (Exception ex)
463 ex.printStackTrace();