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;
43 import jalview.viewmodel.seqfeatures.FeatureRendererSettings;
45 import java.io.InputStreamReader;
46 import java.util.Hashtable;
47 import java.util.Vector;
48 import java.util.jar.JarEntry;
49 import java.util.jar.JarInputStream;
51 import javax.swing.JOptionPane;
53 import org.exolab.castor.xml.IDResolver;
61 public class Jalview2XML_V1
63 boolean raiseGUI = true;
65 public Jalview2XML_V1()
70 public Jalview2XML_V1(boolean raiseGUI)
72 this.raiseGUI = raiseGUI;
75 jalview.schemes.UserColourScheme GetUserColourScheme(
76 JalviewModelSequence jms, String id)
78 UserColours[] uc = jms.getUserColours();
79 UserColours colours = null;
81 for (int i = 0; i < uc.length; i++)
83 if (uc[i].getId().equals(id))
91 int csize = colours.getUserColourScheme().getColourCount();
92 java.awt.Color[] newColours = new java.awt.Color[csize];
94 for (int i = 0; i < csize; i++)
96 newColours[i] = new java.awt.Color(Integer.parseInt(colours
97 .getUserColourScheme().getColour(i).getRGB(), 16));
100 return new jalview.schemes.UserColourScheme(newColours);
109 public AlignFrame LoadJalviewAlign(final jarInputStreamProvider jprovider)
111 final String file = jprovider.getFilename();
112 jalview.gui.AlignFrame af = null;
116 JarInputStream jin = null;
117 JarEntry jarentry = null;
122 jin = jprovider.getJarInputStream();
124 for (int i = 0; i < entryCount; i++)
126 jarentry = jin.getNextJarEntry();
129 class NoDescIDResolver implements IDResolver
131 public Object resolve(String idref)
133 System.out.println(idref + " used");
138 if (jarentry != null)
140 InputStreamReader in = new InputStreamReader(jin, "UTF-8");
141 JalviewModel object = new JalviewModel();
143 object = object.unmarshal(in);
145 af = LoadFromObject(object, file);
148 } while (jarentry != null);
149 } catch (final java.net.UnknownHostException ex)
151 ex.printStackTrace();
154 javax.swing.SwingUtilities.invokeLater(new Runnable()
159 System.err.println("Couldn't locate Jalview XML file : " + ex
161 JOptionPane.showInternalMessageDialog(Desktop.desktop,
162 MessageManager.formatMessage("label.couldnt_locate",
164 { file }), MessageManager
165 .getString("label.url_not_found"),
166 JOptionPane.WARNING_MESSAGE);
171 } catch (Exception ex)
173 System.err.println("Exception whilst loading jalview XML file : ");
174 ex.printStackTrace();
177 javax.swing.SwingUtilities.invokeLater(new Runnable()
182 JOptionPane.showInternalMessageDialog(Desktop.desktop,
183 MessageManager.formatMessage("label.error_loading_file_params", new String[]{file}), MessageManager.getString("label.error_loading_jalview_file"),
184 JOptionPane.WARNING_MESSAGE);
193 AlignFrame LoadFromObject(JalviewModel object, String file)
195 Vector seqids = new Vector();
196 SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);
197 Sequence[] vamsasSeq = vamsasSet.getSequence();
199 JalviewModelSequence jms = object.getJalviewModelSequence();
201 // ////////////////////////////////
203 jalview.datamodel.Sequence[] jseqs = new jalview.datamodel.Sequence[vamsasSeq.length];
204 JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq();
205 for (int i = 0; i < vamsasSeq.length; i++)
207 jseqs[i] = new jalview.datamodel.Sequence(vamsasSeq[i].getName(),
208 vamsasSeq[i].getSequence());
209 jseqs[i].setStart(JSEQ[i].getStart());
210 jseqs[i].setEnd(JSEQ[i].getEnd());
211 seqids.add(jseqs[i]);
214 // /SequenceFeatures are added to the DatasetSequence,
215 // so we must create the dataset before loading features
216 // ///////////////////////////////
217 jalview.datamodel.Alignment al = new jalview.datamodel.Alignment(jseqs);
219 // ///////////////////////////////
221 for (int i = 0; i < vamsasSeq.length; i++)
223 if (JSEQ[i].getFeaturesCount() > 0)
225 Features[] features = JSEQ[i].getFeatures();
226 for (int f = 0; f < features.length; f++)
228 jalview.datamodel.SequenceFeature sf = new jalview.datamodel.SequenceFeature(
229 features[f].getType(), features[f].getDescription(),
230 features[f].getStatus(), features[f].getBegin(),
231 features[f].getEnd(), null);
233 al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf);
236 if (JSEQ[i].getPdbidsCount() > 0)
238 Pdbids[] ids = JSEQ[i].getPdbids();
239 for (int p = 0; p < ids.length; p++)
241 jalview.datamodel.PDBEntry entry = new jalview.datamodel.PDBEntry();
242 entry.setId(ids[p].getId());
243 entry.setType(ids[p].getType());
244 al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
245 StructureSelectionManager.getStructureSelectionManager(
246 Desktop.instance).registerPDBEntry(entry);
252 // ///////////////////////////////
253 // ////////////////////////////////
255 if (vamsasSet.getAnnotation() != null)
257 Annotation[] an = vamsasSet.getAnnotation();
259 for (int i = 0; i < an.length; i++)
261 AnnotationElement[] ae = an[i].getAnnotationElement();
262 jalview.datamodel.Annotation[] anot = new jalview.datamodel.Annotation[al
265 for (int aa = 0; aa < ae.length; aa++)
267 anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(
268 ae[aa].getDisplayCharacter(), ae[aa].getDescription(),
269 ae[aa].getSecondaryStructure().charAt(0),
273 jalview.datamodel.AlignmentAnnotation jaa = null;
275 if (an[i].getGraph())
277 jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
278 an[i].getDescription(), anot, 0, 0,
279 jalview.datamodel.AlignmentAnnotation.BAR_GRAPH);
283 jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
284 an[i].getDescription(), anot);
287 al.addAnnotation(jaa);
291 // ///////////////////////////////
293 Viewport[] views = jms.getViewport();
294 Viewport view = views[0]; // DEAL WITH MULTIPLE VIEWPORTS LATER
296 AlignFrame af = new AlignFrame(al, view.getWidth(), view.getHeight());
298 af.setFileName(file, "Jalview");
300 for (int i = 0; i < JSEQ.length; i++)
302 af.viewport.setSequenceColour(af.viewport.getAlignment()
303 .getSequenceAt(i), new java.awt.Color(JSEQ[i].getColour()));
306 // af.changeColour() );
307 // ///////////////////////
309 if (jms.getJGroupCount() > 0)
311 JGroup[] groups = jms.getJGroup();
313 for (int i = 0; i < groups.length; i++)
315 ColourSchemeI cs = null;
317 if (groups[i].getColour() != null)
319 if (groups[i].getColour().startsWith("ucs"))
321 cs = GetUserColourScheme(jms, groups[i].getColour());
325 cs = ColourSchemeProperty.getColour(al, groups[i].getColour());
330 cs.setThreshold(groups[i].getPidThreshold(), true);
335 Vector seqs = new Vector();
336 int[] ids = groups[i].getSeq();
338 for (int s = 0; s < ids.length; s++)
340 seqs.addElement(seqids
344 jalview.datamodel.SequenceGroup sg = new jalview.datamodel.SequenceGroup(
345 seqs, groups[i].getName(), cs, groups[i].getDisplayBoxes(),
346 groups[i].getDisplayText(), groups[i].getColourText(),
347 groups[i].getStart(), groups[i].getEnd());
349 sg.setOutlineColour(new java.awt.Color(groups[i].getOutlineColour()));
351 if (groups[i].getConsThreshold() != 0)
353 jalview.analysis.Conservation c = new jalview.analysis.Conservation(
354 "All", ResidueProperties.propHash, 3,
355 sg.getSequences(null), 0, sg.getWidth() - 1);
357 c.verdict(false, 25);
358 sg.cs.setConservation(c);
365 af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),
367 af.viewport.setStartRes(view.getStartRes());
368 af.viewport.setStartSeq(view.getStartSeq());
369 af.viewport.setShowAnnotation(view.getShowAnnotation());
370 af.viewport.setAbovePIDThreshold(view.getPidSelected());
371 af.viewport.setColourText(view.getShowColourText());
372 af.viewport.setConservationSelected(view.getConservationSelected());
373 af.viewport.setShowJVSuffix(view.getShowFullId());
374 af.viewport.setFont(new java.awt.Font(view.getFontName(), view
375 .getFontStyle(), view.getFontSize()));
376 af.alignPanel.fontChanged();
378 af.viewport.setRenderGaps(view.getRenderGaps());
379 af.viewport.setWrapAlignment(view.getWrapAlignment());
380 af.alignPanel.setWrapAlignment(view.getWrapAlignment());
381 af.viewport.setShowAnnotation(view.getShowAnnotation());
382 af.alignPanel.setAnnotationVisible(view.getShowAnnotation());
383 af.viewport.setShowBoxes(view.getShowBoxes());
384 af.viewport.setShowText(view.getShowText());
386 ColourSchemeI cs = null;
388 if (view.getBgColour() != null)
390 if (view.getBgColour().startsWith("ucs"))
392 cs = GetUserColourScheme(jms, view.getBgColour());
396 cs = ColourSchemeProperty.getColour(al, view.getBgColour());
401 cs.setThreshold(view.getPidThreshold(), true);
402 cs.setConsensus(af.viewport.getSequenceConsensusHash());
406 af.viewport.setGlobalColourScheme(cs);
407 af.viewport.setColourAppliesToAllGroups(false);
409 if (view.getConservationSelected() && cs != null)
411 cs.setConservationInc(view.getConsThreshold());
414 af.viewport.setColourAppliesToAllGroups(true);
415 af.viewport.setShowSequenceFeatures(view.getShowSequenceFeatures());
417 if (jms.getFeatureSettings() != null)
419 Hashtable featuresDisplayed = new Hashtable();
420 Hashtable featureColours = new Hashtable();
421 String[] renderOrder = new String[jms.getFeatureSettings()
423 for (int fs = 0; fs < jms.getFeatureSettings().getSettingCount(); fs++)
425 Setting setting = jms.getFeatureSettings().getSetting(fs);
428 setting.getType(), new java.awt.Color(setting.getColour()));
430 renderOrder[fs] = setting.getType();
432 if (setting.getDisplay())
434 featuresDisplayed.put(setting.getType(), new Integer(
435 setting.getColour()));
438 FeatureRendererSettings frs = new FeatureRendererSettings(renderOrder, new Hashtable(), featureColours, 1.0f, null);
439 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer().transferSettings(frs);
442 af.setMenusFromViewport(af.viewport);
444 Desktop.addInternalFrame(af, view.getTitle(), view.getWidth(),
448 // /////////////////////////////////////
449 if (jms.getTreeCount() > 0)
453 for (int t = 0; t < jms.getTreeCount(); t++)
456 Tree tree = jms.getTree(t);
458 TreePanel tp = af.ShowNewickTree(
459 new jalview.io.NewickFile(tree.getNewick()),
460 tree.getTitle(), tree.getWidth(), tree.getHeight(),
461 tree.getXpos(), tree.getYpos());
463 tp.fitToWindow.setState(tree.getFitToWindow());
464 tp.fitToWindow_actionPerformed(null);
466 if (tree.getFontName() != null)
468 tp.setTreeFont(new java.awt.Font(tree.getFontName(), tree
469 .getFontStyle(), tree.getFontSize()));
473 tp.setTreeFont(new java.awt.Font(view.getFontName(), view
474 .getFontStyle(), tree.getFontSize()));
477 tp.showPlaceholders(tree.getMarkUnlinked());
478 tp.showBootstrap(tree.getShowBootstrap());
479 tp.showDistances(tree.getShowDistances());
481 tp.treeCanvas.threshold = tree.getThreshold();
483 if (tree.getCurrentTree())
485 af.viewport.setCurrentTree(tp.getTree());
489 } catch (Exception ex)
491 ex.printStackTrace();