2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
3 * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, 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/>.
22 import java.util.jar.*;
26 import org.exolab.castor.xml.*;
27 import jalview.binding.*;
28 import jalview.schemes.*;
29 import jalview.util.jarInputStreamProvider;
37 public class Jalview2XML_V1
39 boolean raiseGUI = true;
41 public Jalview2XML_V1()
46 public Jalview2XML_V1(boolean raiseGUI)
48 this.raiseGUI = raiseGUI;
51 jalview.schemes.UserColourScheme GetUserColourScheme(
52 JalviewModelSequence jms, String id)
54 UserColours[] uc = jms.getUserColours();
55 UserColours colours = null;
57 for (int i = 0; i < uc.length; i++)
59 if (uc[i].getId().equals(id))
67 int csize = colours.getUserColourScheme().getColourCount();
68 java.awt.Color[] newColours = new java.awt.Color[csize];
70 for (int i = 0; i < csize; i++)
72 newColours[i] = new java.awt.Color(Integer.parseInt(colours
73 .getUserColourScheme().getColour(i).getRGB(), 16));
76 return new jalview.schemes.UserColourScheme(newColours);
85 public AlignFrame LoadJalviewAlign(final jarInputStreamProvider jprovider)
87 final String file = jprovider.getFilename();
88 jalview.gui.AlignFrame af = null;
92 JarInputStream jin = null;
93 JarEntry jarentry = null;
98 jin = jprovider.getJarInputStream();
100 for (int i = 0; i < entryCount; i++)
102 jarentry = jin.getNextJarEntry();
105 class NoDescIDResolver implements IDResolver
107 public Object resolve(String idref)
109 System.out.println(idref + " used");
114 if (jarentry != null)
116 InputStreamReader in = new InputStreamReader(jin, "UTF-8");
117 JalviewModel object = new JalviewModel();
119 object = (JalviewModel) object.unmarshal(in);
121 af = LoadFromObject(object, file);
124 } while (jarentry != null);
125 } catch (final java.net.UnknownHostException ex)
127 ex.printStackTrace();
130 javax.swing.SwingUtilities.invokeLater(new Runnable()
135 System.err.println("Couldn't locate Jalview XML file : " + ex
137 JOptionPane.showInternalMessageDialog(Desktop.desktop,
138 "Couldn't locate " + file, "URL not found",
139 JOptionPane.WARNING_MESSAGE);
144 } catch (Exception ex)
146 System.err.println("Exception whilst loading jalview XML file : ");
147 ex.printStackTrace();
150 javax.swing.SwingUtilities.invokeLater(new Runnable()
155 JOptionPane.showInternalMessageDialog(Desktop.desktop,
156 "Error loading " + file, "Error loading Jalview file",
157 JOptionPane.WARNING_MESSAGE);
166 AlignFrame LoadFromObject(JalviewModel object, String file)
168 Vector seqids = new Vector();
169 SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);
170 Sequence[] vamsasSeq = vamsasSet.getSequence();
172 JalviewModelSequence jms = object.getJalviewModelSequence();
174 // ////////////////////////////////
176 jalview.datamodel.Sequence[] jseqs = new jalview.datamodel.Sequence[vamsasSeq.length];
177 JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq();
178 for (int i = 0; i < vamsasSeq.length; i++)
180 jseqs[i] = new jalview.datamodel.Sequence(vamsasSeq[i].getName(),
181 vamsasSeq[i].getSequence());
182 jseqs[i].setStart(JSEQ[i].getStart());
183 jseqs[i].setEnd(JSEQ[i].getEnd());
184 seqids.add(jseqs[i]);
187 // /SequenceFeatures are added to the DatasetSequence,
188 // so we must create the dataset before loading features
189 // ///////////////////////////////
190 jalview.datamodel.Alignment al = new jalview.datamodel.Alignment(jseqs);
192 // ///////////////////////////////
194 for (int i = 0; i < vamsasSeq.length; i++)
196 if (JSEQ[i].getFeaturesCount() > 0)
198 Features[] features = JSEQ[i].getFeatures();
199 for (int f = 0; f < features.length; f++)
201 jalview.datamodel.SequenceFeature sf = new jalview.datamodel.SequenceFeature(
202 features[f].getType(), features[f].getDescription(),
203 features[f].getStatus(), features[f].getBegin(),
204 features[f].getEnd(), null);
206 al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf);
209 if (JSEQ[i].getPdbidsCount() > 0)
211 Pdbids[] ids = JSEQ[i].getPdbids();
212 for (int p = 0; p < ids.length; p++)
214 jalview.datamodel.PDBEntry entry = new jalview.datamodel.PDBEntry();
215 entry.setId(ids[p].getId());
216 entry.setType(ids[p].getType());
217 al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
223 // ///////////////////////////////
224 // ////////////////////////////////
226 if (vamsasSet.getAnnotation() != null)
228 Annotation[] an = vamsasSet.getAnnotation();
230 for (int i = 0; i < an.length; i++)
232 AnnotationElement[] ae = an[i].getAnnotationElement();
233 jalview.datamodel.Annotation[] anot = new jalview.datamodel.Annotation[al
236 for (int aa = 0; aa < ae.length; aa++)
238 anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(
239 ae[aa].getDisplayCharacter(), ae[aa].getDescription(),
240 ae[aa].getSecondaryStructure().charAt(0),
244 jalview.datamodel.AlignmentAnnotation jaa = null;
246 if (an[i].getGraph())
248 jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
249 an[i].getDescription(), anot, 0, 0,
250 jalview.datamodel.AlignmentAnnotation.BAR_GRAPH);
254 jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
255 an[i].getDescription(), anot);
258 al.addAnnotation(jaa);
262 // ///////////////////////////////
264 Viewport[] views = jms.getViewport();
265 Viewport view = views[0]; // DEAL WITH MULTIPLE VIEWPORTS LATER
267 AlignFrame af = new AlignFrame(al, view.getWidth(), view.getHeight());
269 af.setFileName(file, "Jalview");
271 for (int i = 0; i < JSEQ.length; i++)
273 af.viewport.setSequenceColour(af.viewport.getAlignment()
274 .getSequenceAt(i), new java.awt.Color(JSEQ[i].getColour()));
277 // af.changeColour() );
278 // ///////////////////////
280 if (jms.getJGroupCount() > 0)
282 JGroup[] groups = jms.getJGroup();
284 for (int i = 0; i < groups.length; i++)
286 ColourSchemeI cs = null;
288 if (groups[i].getColour() != null)
290 if (groups[i].getColour().startsWith("ucs"))
292 cs = GetUserColourScheme(jms, groups[i].getColour());
296 cs = ColourSchemeProperty.getColour(al, groups[i].getColour());
301 cs.setThreshold(groups[i].getPidThreshold(), true);
306 Vector seqs = new Vector();
307 int[] ids = groups[i].getSeq();
309 for (int s = 0; s < ids.length; s++)
311 seqs.addElement((jalview.datamodel.SequenceI) seqids
315 jalview.datamodel.SequenceGroup sg = new jalview.datamodel.SequenceGroup(
316 seqs, groups[i].getName(), cs, groups[i].getDisplayBoxes(),
317 groups[i].getDisplayText(), groups[i].getColourText(),
318 groups[i].getStart(), groups[i].getEnd());
320 sg.setOutlineColour(new java.awt.Color(groups[i].getOutlineColour()));
322 if (groups[i].getConsThreshold() != 0)
324 jalview.analysis.Conservation c = new jalview.analysis.Conservation(
325 "All", ResidueProperties.propHash, 3,
326 sg.getSequences(null), 0, sg.getWidth() - 1);
328 c.verdict(false, 25);
329 sg.cs.setConservation(c);
336 af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),
338 af.viewport.setStartRes(view.getStartRes());
339 af.viewport.setStartSeq(view.getStartSeq());
340 af.viewport.setShowAnnotation(view.getShowAnnotation());
341 af.viewport.setAbovePIDThreshold(view.getPidSelected());
342 af.viewport.setColourText(view.getShowColourText());
343 af.viewport.setConservationSelected(view.getConservationSelected());
344 af.viewport.setShowJVSuffix(view.getShowFullId());
345 af.viewport.setFont(new java.awt.Font(view.getFontName(), view
346 .getFontStyle(), view.getFontSize()));
347 af.alignPanel.fontChanged();
349 af.viewport.setRenderGaps(view.getRenderGaps());
350 af.viewport.setWrapAlignment(view.getWrapAlignment());
351 af.alignPanel.setWrapAlignment(view.getWrapAlignment());
352 af.viewport.setShowAnnotation(view.getShowAnnotation());
353 af.alignPanel.setAnnotationVisible(view.getShowAnnotation());
354 af.viewport.setShowBoxes(view.getShowBoxes());
355 af.viewport.setShowText(view.getShowText());
357 ColourSchemeI cs = null;
359 if (view.getBgColour() != null)
361 if (view.getBgColour().startsWith("ucs"))
363 cs = GetUserColourScheme(jms, view.getBgColour());
367 cs = ColourSchemeProperty.getColour(al, view.getBgColour());
372 cs.setThreshold(view.getPidThreshold(), true);
373 cs.setConsensus(af.viewport.getSequenceConsensusHash());
377 af.viewport.setGlobalColourScheme(cs);
378 af.viewport.setColourAppliesToAllGroups(false);
380 if (view.getConservationSelected() && cs != null)
382 cs.setConservationInc(view.getConsThreshold());
385 af.viewport.setColourAppliesToAllGroups(true);
386 af.viewport.showSequenceFeatures = view.getShowSequenceFeatures();
388 if (jms.getFeatureSettings() != null)
390 af.viewport.featuresDisplayed = new Hashtable();
391 String[] renderOrder = new String[jms.getFeatureSettings()
393 for (int fs = 0; fs < jms.getFeatureSettings().getSettingCount(); fs++)
395 Setting setting = jms.getFeatureSettings().getSetting(fs);
397 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(
398 setting.getType(), new java.awt.Color(setting.getColour()));
400 renderOrder[fs] = setting.getType();
402 if (setting.getDisplay())
404 af.viewport.featuresDisplayed.put(setting.getType(), new Integer(
405 setting.getColour()));
408 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder = renderOrder;
411 af.setMenusFromViewport(af.viewport);
413 Desktop.addInternalFrame(af, view.getTitle(), view.getWidth(),
417 // /////////////////////////////////////
418 if (jms.getTreeCount() > 0)
422 for (int t = 0; t < jms.getTreeCount(); t++)
425 Tree tree = jms.getTree(t);
427 TreePanel tp = af.ShowNewickTree(
428 new jalview.io.NewickFile(tree.getNewick()),
429 tree.getTitle(), tree.getWidth(), tree.getHeight(),
430 tree.getXpos(), tree.getYpos());
432 tp.fitToWindow.setState(tree.getFitToWindow());
433 tp.fitToWindow_actionPerformed(null);
435 if (tree.getFontName() != null)
437 tp.setTreeFont(new java.awt.Font(tree.getFontName(), tree
438 .getFontStyle(), tree.getFontSize()));
442 tp.setTreeFont(new java.awt.Font(view.getFontName(), view
443 .getFontStyle(), tree.getFontSize()));
446 tp.showPlaceholders(tree.getMarkUnlinked());
447 tp.showBootstrap(tree.getShowBootstrap());
448 tp.showDistances(tree.getShowDistances());
450 tp.treeCanvas.threshold = tree.getThreshold();
452 if (tree.getCurrentTree())
454 af.viewport.setCurrentTree(tp.getTree());
458 } catch (Exception ex)
460 ex.printStackTrace();