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.
25 import java.util.jar.*;
29 import org.exolab.castor.xml.*;
30 import jalview.binding.*;
31 import jalview.schemes.*;
32 import jalview.util.MessageManager;
33 import jalview.util.jarInputStreamProvider;
41 public class Jalview2XML_V1
43 boolean raiseGUI = true;
45 public Jalview2XML_V1()
50 public Jalview2XML_V1(boolean raiseGUI)
52 this.raiseGUI = raiseGUI;
55 jalview.schemes.UserColourScheme GetUserColourScheme(
56 JalviewModelSequence jms, String id)
58 UserColours[] uc = jms.getUserColours();
59 UserColours colours = null;
61 for (int i = 0; i < uc.length; i++)
63 if (uc[i].getId().equals(id))
71 int csize = colours.getUserColourScheme().getColourCount();
72 java.awt.Color[] newColours = new java.awt.Color[csize];
74 for (int i = 0; i < csize; i++)
76 newColours[i] = new java.awt.Color(Integer.parseInt(colours
77 .getUserColourScheme().getColour(i).getRGB(), 16));
80 return new jalview.schemes.UserColourScheme(newColours);
89 public AlignFrame LoadJalviewAlign(final jarInputStreamProvider jprovider)
91 final String file = jprovider.getFilename();
92 jalview.gui.AlignFrame af = null;
96 JarInputStream jin = null;
97 JarEntry jarentry = null;
102 jin = jprovider.getJarInputStream();
104 for (int i = 0; i < entryCount; i++)
106 jarentry = jin.getNextJarEntry();
109 class NoDescIDResolver implements IDResolver
111 public Object resolve(String idref)
113 System.out.println(idref + " used");
118 if (jarentry != null)
120 InputStreamReader in = new InputStreamReader(jin, "UTF-8");
121 JalviewModel object = new JalviewModel();
123 object = (JalviewModel) object.unmarshal(in);
125 af = LoadFromObject(object, file);
128 } while (jarentry != null);
129 } catch (final java.net.UnknownHostException ex)
131 ex.printStackTrace();
134 javax.swing.SwingUtilities.invokeLater(new Runnable()
139 System.err.println("Couldn't locate Jalview XML file : " + ex
141 JOptionPane.showInternalMessageDialog(Desktop.desktop,
142 MessageManager.formatMessage("label.couldnt_locate",
144 { file }), MessageManager
145 .getString("label.url_not_found"),
146 JOptionPane.WARNING_MESSAGE);
151 } catch (Exception ex)
153 System.err.println("Exception whilst loading jalview XML file : ");
154 ex.printStackTrace();
157 javax.swing.SwingUtilities.invokeLater(new Runnable()
162 JOptionPane.showInternalMessageDialog(Desktop.desktop,
163 "Error loading " + file, "Error loading Jalview file",
164 JOptionPane.WARNING_MESSAGE);
173 AlignFrame LoadFromObject(JalviewModel object, String file)
175 Vector seqids = new Vector();
176 SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);
177 Sequence[] vamsasSeq = vamsasSet.getSequence();
179 JalviewModelSequence jms = object.getJalviewModelSequence();
181 // ////////////////////////////////
183 jalview.datamodel.Sequence[] jseqs = new jalview.datamodel.Sequence[vamsasSeq.length];
184 JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq();
185 for (int i = 0; i < vamsasSeq.length; i++)
187 jseqs[i] = new jalview.datamodel.Sequence(vamsasSeq[i].getName(),
188 vamsasSeq[i].getSequence());
189 jseqs[i].setStart(JSEQ[i].getStart());
190 jseqs[i].setEnd(JSEQ[i].getEnd());
191 seqids.add(jseqs[i]);
194 // /SequenceFeatures are added to the DatasetSequence,
195 // so we must create the dataset before loading features
196 // ///////////////////////////////
197 jalview.datamodel.Alignment al = new jalview.datamodel.Alignment(jseqs);
199 // ///////////////////////////////
201 for (int i = 0; i < vamsasSeq.length; i++)
203 if (JSEQ[i].getFeaturesCount() > 0)
205 Features[] features = JSEQ[i].getFeatures();
206 for (int f = 0; f < features.length; f++)
208 jalview.datamodel.SequenceFeature sf = new jalview.datamodel.SequenceFeature(
209 features[f].getType(), features[f].getDescription(),
210 features[f].getStatus(), features[f].getBegin(),
211 features[f].getEnd(), null);
213 al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf);
216 if (JSEQ[i].getPdbidsCount() > 0)
218 Pdbids[] ids = JSEQ[i].getPdbids();
219 for (int p = 0; p < ids.length; p++)
221 jalview.datamodel.PDBEntry entry = new jalview.datamodel.PDBEntry();
222 entry.setId(ids[p].getId());
223 entry.setType(ids[p].getType());
224 al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
230 // ///////////////////////////////
231 // ////////////////////////////////
233 if (vamsasSet.getAnnotation() != null)
235 Annotation[] an = vamsasSet.getAnnotation();
237 for (int i = 0; i < an.length; i++)
239 AnnotationElement[] ae = an[i].getAnnotationElement();
240 jalview.datamodel.Annotation[] anot = new jalview.datamodel.Annotation[al
243 for (int aa = 0; aa < ae.length; aa++)
245 anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(
246 ae[aa].getDisplayCharacter(), ae[aa].getDescription(),
247 ae[aa].getSecondaryStructure().charAt(0),
251 jalview.datamodel.AlignmentAnnotation jaa = null;
253 if (an[i].getGraph())
255 jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
256 an[i].getDescription(), anot, 0, 0,
257 jalview.datamodel.AlignmentAnnotation.BAR_GRAPH);
261 jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
262 an[i].getDescription(), anot);
265 al.addAnnotation(jaa);
269 // ///////////////////////////////
271 Viewport[] views = jms.getViewport();
272 Viewport view = views[0]; // DEAL WITH MULTIPLE VIEWPORTS LATER
274 AlignFrame af = new AlignFrame(al, view.getWidth(), view.getHeight());
276 af.setFileName(file, "Jalview");
278 for (int i = 0; i < JSEQ.length; i++)
280 af.viewport.setSequenceColour(af.viewport.getAlignment()
281 .getSequenceAt(i), new java.awt.Color(JSEQ[i].getColour()));
284 // af.changeColour() );
285 // ///////////////////////
287 if (jms.getJGroupCount() > 0)
289 JGroup[] groups = jms.getJGroup();
291 for (int i = 0; i < groups.length; i++)
293 ColourSchemeI cs = null;
295 if (groups[i].getColour() != null)
297 if (groups[i].getColour().startsWith("ucs"))
299 cs = GetUserColourScheme(jms, groups[i].getColour());
303 cs = ColourSchemeProperty.getColour(al, groups[i].getColour());
308 cs.setThreshold(groups[i].getPidThreshold(), true);
313 Vector seqs = new Vector();
314 int[] ids = groups[i].getSeq();
316 for (int s = 0; s < ids.length; s++)
318 seqs.addElement((jalview.datamodel.SequenceI) seqids
322 jalview.datamodel.SequenceGroup sg = new jalview.datamodel.SequenceGroup(
323 seqs, groups[i].getName(), cs, groups[i].getDisplayBoxes(),
324 groups[i].getDisplayText(), groups[i].getColourText(),
325 groups[i].getStart(), groups[i].getEnd());
327 sg.setOutlineColour(new java.awt.Color(groups[i].getOutlineColour()));
329 if (groups[i].getConsThreshold() != 0)
331 jalview.analysis.Conservation c = new jalview.analysis.Conservation(
332 "All", ResidueProperties.propHash, 3,
333 sg.getSequences(null), 0, sg.getWidth() - 1);
335 c.verdict(false, 25);
336 sg.cs.setConservation(c);
343 af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),
345 af.viewport.setStartRes(view.getStartRes());
346 af.viewport.setStartSeq(view.getStartSeq());
347 af.viewport.setShowAnnotation(view.getShowAnnotation());
348 af.viewport.setAbovePIDThreshold(view.getPidSelected());
349 af.viewport.setColourText(view.getShowColourText());
350 af.viewport.setConservationSelected(view.getConservationSelected());
351 af.viewport.setShowJVSuffix(view.getShowFullId());
352 af.viewport.setFont(new java.awt.Font(view.getFontName(), view
353 .getFontStyle(), view.getFontSize()));
354 af.alignPanel.fontChanged();
356 af.viewport.setRenderGaps(view.getRenderGaps());
357 af.viewport.setWrapAlignment(view.getWrapAlignment());
358 af.alignPanel.setWrapAlignment(view.getWrapAlignment());
359 af.viewport.setShowAnnotation(view.getShowAnnotation());
360 af.alignPanel.setAnnotationVisible(view.getShowAnnotation());
361 af.viewport.setShowBoxes(view.getShowBoxes());
362 af.viewport.setShowText(view.getShowText());
364 ColourSchemeI cs = null;
366 if (view.getBgColour() != null)
368 if (view.getBgColour().startsWith("ucs"))
370 cs = GetUserColourScheme(jms, view.getBgColour());
374 cs = ColourSchemeProperty.getColour(al, view.getBgColour());
379 cs.setThreshold(view.getPidThreshold(), true);
380 cs.setConsensus(af.viewport.getSequenceConsensusHash());
384 af.viewport.setGlobalColourScheme(cs);
385 af.viewport.setColourAppliesToAllGroups(false);
387 if (view.getConservationSelected() && cs != null)
389 cs.setConservationInc(view.getConsThreshold());
392 af.viewport.setColourAppliesToAllGroups(true);
393 af.viewport.showSequenceFeatures = view.getShowSequenceFeatures();
395 if (jms.getFeatureSettings() != null)
397 af.viewport.featuresDisplayed = new Hashtable();
398 String[] renderOrder = new String[jms.getFeatureSettings()
400 for (int fs = 0; fs < jms.getFeatureSettings().getSettingCount(); fs++)
402 Setting setting = jms.getFeatureSettings().getSetting(fs);
404 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(
405 setting.getType(), new java.awt.Color(setting.getColour()));
407 renderOrder[fs] = setting.getType();
409 if (setting.getDisplay())
411 af.viewport.featuresDisplayed.put(setting.getType(), new Integer(
412 setting.getColour()));
415 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder = renderOrder;
418 af.setMenusFromViewport(af.viewport);
420 Desktop.addInternalFrame(af, view.getTitle(), view.getWidth(),
424 // /////////////////////////////////////
425 if (jms.getTreeCount() > 0)
429 for (int t = 0; t < jms.getTreeCount(); t++)
432 Tree tree = jms.getTree(t);
434 TreePanel tp = af.ShowNewickTree(
435 new jalview.io.NewickFile(tree.getNewick()),
436 tree.getTitle(), tree.getWidth(), tree.getHeight(),
437 tree.getXpos(), tree.getYpos());
439 tp.fitToWindow.setState(tree.getFitToWindow());
440 tp.fitToWindow_actionPerformed(null);
442 if (tree.getFontName() != null)
444 tp.setTreeFont(new java.awt.Font(tree.getFontName(), tree
445 .getFontStyle(), tree.getFontSize()));
449 tp.setTreeFont(new java.awt.Font(view.getFontName(), view
450 .getFontStyle(), tree.getFontSize()));
453 tp.showPlaceholders(tree.getMarkUnlinked());
454 tp.showBootstrap(tree.getShowBootstrap());
455 tp.showDistances(tree.getShowDistances());
457 tp.treeCanvas.threshold = tree.getThreshold();
459 if (tree.getCurrentTree())
461 af.viewport.setCurrentTree(tp.getTree());
465 } catch (Exception ex)
467 ex.printStackTrace();