2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
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
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 import jalview.binding.Annotation;
24 import jalview.binding.AnnotationElement;
25 import jalview.binding.Features;
26 import jalview.binding.JGroup;
27 import jalview.binding.JSeq;
28 import jalview.binding.JalviewModel;
29 import jalview.binding.JalviewModelSequence;
30 import jalview.binding.Pdbids;
31 import jalview.binding.Sequence;
32 import jalview.binding.SequenceSet;
33 import jalview.binding.Setting;
34 import jalview.binding.Tree;
35 import jalview.binding.UserColours;
36 import jalview.binding.Viewport;
37 import jalview.schemes.ColourSchemeI;
38 import jalview.schemes.ColourSchemeProperty;
39 import jalview.schemes.ResidueProperties;
40 import jalview.structure.StructureSelectionManager;
41 import jalview.util.MessageManager;
42 import jalview.util.jarInputStreamProvider;
44 import java.io.InputStreamReader;
45 import java.util.Hashtable;
46 import java.util.Vector;
47 import java.util.jar.JarEntry;
48 import java.util.jar.JarInputStream;
50 import javax.swing.JOptionPane;
52 import jalview.util.MessageManager;
53 import jalview.util.jarInputStreamProvider;
54 import org.exolab.castor.xml.IDResolver;
55 import jalview.viewmodel.seqfeatures.FeatureRendererSettings;
63 public class Jalview2XML_V1
65 boolean raiseGUI = true;
67 public Jalview2XML_V1()
72 public Jalview2XML_V1(boolean raiseGUI)
74 this.raiseGUI = raiseGUI;
77 jalview.schemes.UserColourScheme GetUserColourScheme(
78 JalviewModelSequence jms, String id)
80 UserColours[] uc = jms.getUserColours();
81 UserColours colours = null;
83 for (int i = 0; i < uc.length; i++)
85 if (uc[i].getId().equals(id))
93 int csize = colours.getUserColourScheme().getColourCount();
94 java.awt.Color[] newColours = new java.awt.Color[csize];
96 for (int i = 0; i < csize; i++)
98 newColours[i] = new java.awt.Color(Integer.parseInt(colours
99 .getUserColourScheme().getColour(i).getRGB(), 16));
102 return new jalview.schemes.UserColourScheme(newColours);
111 public AlignFrame LoadJalviewAlign(final jarInputStreamProvider jprovider)
113 final String file = jprovider.getFilename();
114 jalview.gui.AlignFrame af = null;
118 JarInputStream jin = null;
119 JarEntry jarentry = null;
124 jin = jprovider.getJarInputStream();
126 for (int i = 0; i < entryCount; i++)
128 jarentry = jin.getNextJarEntry();
131 class NoDescIDResolver implements IDResolver
133 public Object resolve(String idref)
135 System.out.println(idref + " used");
140 if (jarentry != null)
142 InputStreamReader in = new InputStreamReader(jin, "UTF-8");
143 JalviewModel object = new JalviewModel();
145 object = object.unmarshal(in);
147 af = LoadFromObject(object, file);
150 } while (jarentry != null);
151 } catch (final java.net.UnknownHostException ex)
153 ex.printStackTrace();
156 javax.swing.SwingUtilities.invokeLater(new Runnable()
161 System.err.println("Couldn't locate Jalview XML file : " + ex
163 JOptionPane.showInternalMessageDialog(Desktop.desktop,
164 MessageManager.formatMessage("label.couldnt_locate",
166 { file }), MessageManager
167 .getString("label.url_not_found"),
168 JOptionPane.WARNING_MESSAGE);
173 } catch (Exception ex)
175 System.err.println("Exception whilst loading jalview XML file : ");
176 ex.printStackTrace();
179 javax.swing.SwingUtilities.invokeLater(new Runnable()
184 JOptionPane.showInternalMessageDialog(Desktop.desktop,
185 MessageManager.formatMessage("label.error_loading_file_params", new String[]{file}), MessageManager.getString("label.error_loading_jalview_file"),
186 JOptionPane.WARNING_MESSAGE);
195 AlignFrame LoadFromObject(JalviewModel object, String file)
197 Vector seqids = new Vector();
198 SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);
199 Sequence[] vamsasSeq = vamsasSet.getSequence();
201 JalviewModelSequence jms = object.getJalviewModelSequence();
203 // ////////////////////////////////
205 jalview.datamodel.Sequence[] jseqs = new jalview.datamodel.Sequence[vamsasSeq.length];
206 JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq();
207 for (int i = 0; i < vamsasSeq.length; i++)
209 jseqs[i] = new jalview.datamodel.Sequence(vamsasSeq[i].getName(),
210 vamsasSeq[i].getSequence());
211 jseqs[i].setStart(JSEQ[i].getStart());
212 jseqs[i].setEnd(JSEQ[i].getEnd());
213 seqids.add(jseqs[i]);
216 // /SequenceFeatures are added to the DatasetSequence,
217 // so we must create the dataset before loading features
218 // ///////////////////////////////
219 jalview.datamodel.Alignment al = new jalview.datamodel.Alignment(jseqs);
221 // ///////////////////////////////
223 for (int i = 0; i < vamsasSeq.length; i++)
225 if (JSEQ[i].getFeaturesCount() > 0)
227 Features[] features = JSEQ[i].getFeatures();
228 for (int f = 0; f < features.length; f++)
230 jalview.datamodel.SequenceFeature sf = new jalview.datamodel.SequenceFeature(
231 features[f].getType(), features[f].getDescription(),
232 features[f].getStatus(), features[f].getBegin(),
233 features[f].getEnd(), null);
235 al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf);
238 if (JSEQ[i].getPdbidsCount() > 0)
240 Pdbids[] ids = JSEQ[i].getPdbids();
241 for (int p = 0; p < ids.length; p++)
243 jalview.datamodel.PDBEntry entry = new jalview.datamodel.PDBEntry();
244 entry.setId(ids[p].getId());
245 entry.setType(ids[p].getType());
246 al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
247 StructureSelectionManager.getStructureSelectionManager(
248 Desktop.instance).registerPDBEntry(entry);
254 // ///////////////////////////////
255 // ////////////////////////////////
257 if (vamsasSet.getAnnotation() != null)
259 Annotation[] an = vamsasSet.getAnnotation();
261 for (int i = 0; i < an.length; i++)
263 AnnotationElement[] ae = an[i].getAnnotationElement();
264 jalview.datamodel.Annotation[] anot = new jalview.datamodel.Annotation[al
267 for (int aa = 0; aa < ae.length; aa++)
269 anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(
270 ae[aa].getDisplayCharacter(), ae[aa].getDescription(),
271 ae[aa].getSecondaryStructure().charAt(0),
275 jalview.datamodel.AlignmentAnnotation jaa = null;
277 if (an[i].getGraph())
279 jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
280 an[i].getDescription(), anot, 0, 0,
281 jalview.datamodel.AlignmentAnnotation.BAR_GRAPH);
285 jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
286 an[i].getDescription(), anot);
289 al.addAnnotation(jaa);
293 // ///////////////////////////////
295 Viewport[] views = jms.getViewport();
296 Viewport view = views[0]; // DEAL WITH MULTIPLE VIEWPORTS LATER
298 AlignFrame af = new AlignFrame(al, view.getWidth(), view.getHeight());
300 af.setFileName(file, "Jalview");
302 for (int i = 0; i < JSEQ.length; i++)
304 af.viewport.setSequenceColour(af.viewport.getAlignment()
305 .getSequenceAt(i), new java.awt.Color(JSEQ[i].getColour()));
308 // af.changeColour() );
309 // ///////////////////////
311 if (jms.getJGroupCount() > 0)
313 JGroup[] groups = jms.getJGroup();
315 for (int i = 0; i < groups.length; i++)
317 ColourSchemeI cs = null;
319 if (groups[i].getColour() != null)
321 if (groups[i].getColour().startsWith("ucs"))
323 cs = GetUserColourScheme(jms, groups[i].getColour());
327 cs = ColourSchemeProperty.getColour(al, groups[i].getColour());
332 cs.setThreshold(groups[i].getPidThreshold(), true);
337 Vector seqs = new Vector();
338 int[] ids = groups[i].getSeq();
340 for (int s = 0; s < ids.length; s++)
342 seqs.addElement(seqids
346 jalview.datamodel.SequenceGroup sg = new jalview.datamodel.SequenceGroup(
347 seqs, groups[i].getName(), cs, groups[i].getDisplayBoxes(),
348 groups[i].getDisplayText(), groups[i].getColourText(),
349 groups[i].getStart(), groups[i].getEnd());
351 sg.setOutlineColour(new java.awt.Color(groups[i].getOutlineColour()));
353 if (groups[i].getConsThreshold() != 0)
355 jalview.analysis.Conservation c = new jalview.analysis.Conservation(
356 "All", ResidueProperties.propHash, 3,
357 sg.getSequences(null), 0, sg.getWidth() - 1);
359 c.verdict(false, 25);
360 sg.cs.setConservation(c);
367 af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),
369 af.viewport.setStartRes(view.getStartRes());
370 af.viewport.setStartSeq(view.getStartSeq());
371 af.viewport.setShowAnnotation(view.getShowAnnotation());
372 af.viewport.setAbovePIDThreshold(view.getPidSelected());
373 af.viewport.setColourText(view.getShowColourText());
374 af.viewport.setConservationSelected(view.getConservationSelected());
375 af.viewport.setShowJVSuffix(view.getShowFullId());
376 af.viewport.setFont(new java.awt.Font(view.getFontName(), view
377 .getFontStyle(), view.getFontSize()));
378 af.alignPanel.fontChanged();
380 af.viewport.setRenderGaps(view.getRenderGaps());
381 af.viewport.setWrapAlignment(view.getWrapAlignment());
382 af.alignPanel.setWrapAlignment(view.getWrapAlignment());
383 af.viewport.setShowAnnotation(view.getShowAnnotation());
384 af.alignPanel.setAnnotationVisible(view.getShowAnnotation());
385 af.viewport.setShowBoxes(view.getShowBoxes());
386 af.viewport.setShowText(view.getShowText());
388 ColourSchemeI cs = null;
390 if (view.getBgColour() != null)
392 if (view.getBgColour().startsWith("ucs"))
394 cs = GetUserColourScheme(jms, view.getBgColour());
398 cs = ColourSchemeProperty.getColour(al, view.getBgColour());
403 cs.setThreshold(view.getPidThreshold(), true);
404 cs.setConsensus(af.viewport.getSequenceConsensusHash());
408 af.viewport.setGlobalColourScheme(cs);
409 af.viewport.setColourAppliesToAllGroups(false);
411 if (view.getConservationSelected() && cs != null)
413 cs.setConservationInc(view.getConsThreshold());
416 af.viewport.setColourAppliesToAllGroups(true);
417 af.viewport.setShowSequenceFeatures(view.getShowSequenceFeatures());
419 if (jms.getFeatureSettings() != null)
421 Hashtable featuresDisplayed = new Hashtable();
422 Hashtable featureColours = new Hashtable();
423 String[] renderOrder = new String[jms.getFeatureSettings()
425 for (int fs = 0; fs < jms.getFeatureSettings().getSettingCount(); fs++)
427 Setting setting = jms.getFeatureSettings().getSetting(fs);
430 setting.getType(), new java.awt.Color(setting.getColour()));
432 renderOrder[fs] = setting.getType();
434 if (setting.getDisplay())
436 featuresDisplayed.put(setting.getType(), new Integer(
437 setting.getColour()));
440 FeatureRendererSettings frs = new FeatureRendererSettings(renderOrder, new Hashtable(), featureColours, 1.0f, null);
441 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer().transferSettings(frs);
444 af.setMenusFromViewport(af.viewport);
446 Desktop.addInternalFrame(af, view.getTitle(), view.getWidth(),
450 // /////////////////////////////////////
451 if (jms.getTreeCount() > 0)
455 for (int t = 0; t < jms.getTreeCount(); t++)
458 Tree tree = jms.getTree(t);
460 TreePanel tp = af.ShowNewickTree(
461 new jalview.io.NewickFile(tree.getNewick()),
462 tree.getTitle(), tree.getWidth(), tree.getHeight(),
463 tree.getXpos(), tree.getYpos());
465 tp.fitToWindow.setState(tree.getFitToWindow());
466 tp.fitToWindow_actionPerformed(null);
468 if (tree.getFontName() != null)
470 tp.setTreeFont(new java.awt.Font(tree.getFontName(), tree
471 .getFontStyle(), tree.getFontSize()));
475 tp.setTreeFont(new java.awt.Font(view.getFontName(), view
476 .getFontStyle(), tree.getFontSize()));
479 tp.showPlaceholders(tree.getMarkUnlinked());
480 tp.showBootstrap(tree.getShowBootstrap());
481 tp.showDistances(tree.getShowDistances());
483 tp.treeCanvas.threshold = tree.getThreshold();
485 if (tree.getCurrentTree())
487 af.viewport.setCurrentTree(tp.getTree());
491 } catch (Exception ex)
493 ex.printStackTrace();