2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ 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.analysis.Conservation;
24 import jalview.api.FeatureColourI;
25 import jalview.binding.Annotation;
26 import jalview.binding.AnnotationElement;
27 import jalview.binding.Features;
28 import jalview.binding.JGroup;
29 import jalview.binding.JSeq;
30 import jalview.binding.JalviewModel;
31 import jalview.binding.JalviewModelSequence;
32 import jalview.binding.Pdbids;
33 import jalview.binding.Sequence;
34 import jalview.binding.SequenceSet;
35 import jalview.binding.Setting;
36 import jalview.binding.Tree;
37 import jalview.binding.UserColours;
38 import jalview.binding.Viewport;
39 import jalview.datamodel.PDBEntry;
40 import jalview.datamodel.SequenceFeature;
41 import jalview.io.FileFormat;
42 import jalview.schemes.ColourSchemeI;
43 import jalview.schemes.ColourSchemeProperty;
44 import jalview.schemes.FeatureColour;
45 import jalview.structure.StructureSelectionManager;
46 import jalview.util.MessageManager;
47 import jalview.util.jarInputStreamProvider;
48 import jalview.viewmodel.seqfeatures.FeatureRendererSettings;
50 import java.io.InputStreamReader;
51 import java.io.Reader;
52 import java.net.UnknownHostException;
53 import java.util.Hashtable;
54 import java.util.Vector;
55 import java.util.jar.JarEntry;
56 import java.util.jar.JarInputStream;
64 public class Jalview2XML_V1
66 boolean raiseGUI = true;
68 public Jalview2XML_V1()
73 public Jalview2XML_V1(boolean raiseGUI)
75 this.raiseGUI = raiseGUI;
78 jalview.schemes.UserColourScheme GetUserColourScheme(
79 JalviewModelSequence jms, String id)
81 UserColours[] uc = jms.getUserColours();
82 UserColours colours = null;
84 for (int i = 0; i < uc.length; i++)
86 if (uc[i].getId().equals(id))
94 int csize = colours.getUserColourScheme().getColourCount();
95 java.awt.Color[] newColours = new java.awt.Color[csize];
97 for (int i = 0; i < csize; i++)
99 newColours[i] = new java.awt.Color(Integer.parseInt(
100 colours.getUserColourScheme().getColour(i).getRGB(), 16));
103 return new jalview.schemes.UserColourScheme(newColours);
112 public AlignFrame LoadJalviewAlign(final jarInputStreamProvider jprovider)
114 final String file = jprovider.getFilename();
115 jalview.gui.AlignFrame af = null;
119 JarInputStream jin = null;
120 JarEntry jarentry = null;
125 jin = jprovider.getJarInputStream();
127 for (int i = 0; i < entryCount; i++)
129 jarentry = jin.getNextJarEntry();
132 if (jarentry != null)
135 if (jarentry.getName().endsWith(".xml"))
137 Reader in = new InputStreamReader(jin, "UTF-8");
138 JalviewModel object = new JalviewModel();
140 object = object.unmarshal(in);
142 af = LoadFromObject(object, file);
146 } while (jarentry != null);
147 } catch (final UnknownHostException ex)
149 ex.printStackTrace();
152 javax.swing.SwingUtilities.invokeLater(new Runnable()
159 "Couldn't locate Jalview XML file : " + ex + "\n");
160 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
161 MessageManager.formatMessage("label.couldnt_locate",
164 MessageManager.getString("label.url_not_found"),
165 JvOptionPane.WARNING_MESSAGE);
170 } catch (Exception ex)
172 System.err.println("Exception whilst loading jalview XML file : ");
173 ex.printStackTrace();
176 javax.swing.SwingUtilities.invokeLater(new Runnable()
182 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
183 MessageManager.formatMessage(
184 "label.error_loading_file_params", new String[]
187 .getString("label.error_loading_jalview_file"),
188 JvOptionPane.WARNING_MESSAGE);
197 AlignFrame LoadFromObject(JalviewModel object, String file)
199 Vector seqids = new Vector();
200 SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);
201 Sequence[] vamsasSeq = vamsasSet.getSequence();
203 JalviewModelSequence jms = object.getJalviewModelSequence();
205 // ////////////////////////////////
207 jalview.datamodel.Sequence[] jseqs = new jalview.datamodel.Sequence[vamsasSeq.length];
208 JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq();
209 for (int i = 0; i < vamsasSeq.length; i++)
211 jseqs[i] = new jalview.datamodel.Sequence(vamsasSeq[i].getName(),
212 vamsasSeq[i].getSequence());
213 jseqs[i].setStart(JSEQ[i].getStart());
214 jseqs[i].setEnd(JSEQ[i].getEnd());
215 seqids.add(jseqs[i]);
218 // /SequenceFeatures are added to the DatasetSequence,
219 // so we must create the dataset before loading features
220 // ///////////////////////////////
221 jalview.datamodel.Alignment al = new jalview.datamodel.Alignment(jseqs);
223 // ///////////////////////////////
225 for (int i = 0; i < vamsasSeq.length; i++)
227 if (JSEQ[i].getFeaturesCount() > 0)
229 Features[] features = JSEQ[i].getFeatures();
230 for (int f = 0; f < features.length; f++)
232 SequenceFeature sf = new SequenceFeature(features[f].getType(),
233 features[f].getDescription(), features[f].getBegin(),
234 features[f].getEnd(), null);
235 sf.setStatus(features[f].getStatus());
236 al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf);
239 if (JSEQ[i].getPdbidsCount() > 0)
241 Pdbids[] ids = JSEQ[i].getPdbids();
242 for (int p = 0; p < ids.length; p++)
244 jalview.datamodel.PDBEntry entry = new jalview.datamodel.PDBEntry();
245 entry.setId(ids[p].getId());
246 if (ids[p].getType() != null)
248 if (ids[p].getType().equalsIgnoreCase("PDB"))
250 entry.setType(PDBEntry.Type.PDB);
254 entry.setType(PDBEntry.Type.FILE);
257 al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
258 StructureSelectionManager
259 .getStructureSelectionManager(Desktop.instance)
260 .registerPDBEntry(entry);
266 // ///////////////////////////////
267 // ////////////////////////////////
269 if (vamsasSet.getAnnotation() != null)
271 Annotation[] an = vamsasSet.getAnnotation();
273 for (int i = 0; i < an.length; i++)
275 AnnotationElement[] ae = an[i].getAnnotationElement();
276 jalview.datamodel.Annotation[] anot = new jalview.datamodel.Annotation[al
279 for (int aa = 0; aa < ae.length; aa++)
281 anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(
282 ae[aa].getDisplayCharacter(), ae[aa].getDescription(),
283 ae[aa].getSecondaryStructure().charAt(0),
287 jalview.datamodel.AlignmentAnnotation jaa = null;
289 if (an[i].getGraph())
291 jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
292 an[i].getDescription(), anot, 0, 0,
293 jalview.datamodel.AlignmentAnnotation.BAR_GRAPH);
297 jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
298 an[i].getDescription(), anot);
301 al.addAnnotation(jaa);
305 // ///////////////////////////////
307 Viewport[] views = jms.getViewport();
308 Viewport view = views[0]; // DEAL WITH MULTIPLE VIEWPORTS LATER
310 AlignFrame af = new AlignFrame(al, view.getWidth(), view.getHeight());
312 af.setFileName(file, FileFormat.Jalview);
314 for (int i = 0; i < JSEQ.length; i++)
316 af.viewport.setSequenceColour(
317 af.viewport.getAlignment().getSequenceAt(i),
318 new java.awt.Color(JSEQ[i].getColour()));
321 // af.changeColour() );
322 // ///////////////////////
324 if (jms.getJGroupCount() > 0)
326 JGroup[] groups = jms.getJGroup();
328 for (int i = 0; i < groups.length; i++)
330 ColourSchemeI cs = null;
332 if (groups[i].getColour() != null)
334 if (groups[i].getColour().startsWith("ucs"))
336 cs = GetUserColourScheme(jms, groups[i].getColour());
340 cs = ColourSchemeProperty.getColourScheme(al,
341 groups[i].getColour());
344 int pidThreshold = groups[i].getPidThreshold();
346 Vector seqs = new Vector();
347 int[] ids = groups[i].getSeq();
349 for (int s = 0; s < ids.length; s++)
351 seqs.addElement(seqids.elementAt(ids[s]));
354 jalview.datamodel.SequenceGroup sg = new jalview.datamodel.SequenceGroup(
355 seqs, groups[i].getName(), cs, groups[i].getDisplayBoxes(),
356 groups[i].getDisplayText(), groups[i].getColourText(),
357 groups[i].getStart(), groups[i].getEnd());
358 sg.getGroupColourScheme().setThreshold(pidThreshold, true);
361 new java.awt.Color(groups[i].getOutlineColour()));
363 if (groups[i].getConsThreshold() != 0)
365 Conservation c = new Conservation("All", sg.getSequences(null), 0,
368 c.verdict(false, 25);
369 sg.cs.setConservation(c);
376 af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),
378 af.viewport.getRanges().setStartRes(view.getStartRes());
379 // startSeq set in af.alignPanel.updateLayout below
380 af.viewport.setShowAnnotation(view.getShowAnnotation());
381 af.viewport.setAbovePIDThreshold(view.getPidSelected());
382 af.viewport.setColourText(view.getShowColourText());
383 af.viewport.setConservationSelected(view.getConservationSelected());
384 af.viewport.setShowJVSuffix(view.getShowFullId());
385 af.viewport.setFont(new java.awt.Font(view.getFontName(),
386 view.getFontStyle(), view.getFontSize()), true);
388 af.viewport.setRenderGaps(view.getRenderGaps());
389 af.viewport.setWrapAlignment(view.getWrapAlignment());
391 af.viewport.setShowAnnotation(view.isShowAnnotation());
392 af.viewport.setShowBoxes(view.getShowBoxes());
393 af.viewport.setShowText(view.getShowText());
395 ColourSchemeI cs = null;
397 if (view.getBgColour() != null)
399 if (view.getBgColour().startsWith("ucs"))
401 cs = GetUserColourScheme(jms, view.getBgColour());
405 cs = ColourSchemeProperty.getColourScheme(al, view.getBgColour());
410 // cs.setThreshold(view.getPidThreshold(), true);
411 // cs.setConsensus(af.viewport.getSequenceConsensusHash());
415 af.viewport.getResidueShading().setThreshold(view.getPidThreshold(),
417 af.viewport.getResidueShading()
418 .setConsensus(af.viewport.getSequenceConsensusHash());
419 af.viewport.setColourAppliesToAllGroups(false);
420 af.alignPanel.updateLayout();
422 if (view.getConservationSelected() && cs != null)
424 af.viewport.getResidueShading()
425 .setConservationInc(view.getConsThreshold());
428 af.viewport.setColourAppliesToAllGroups(true);
429 af.viewport.setShowSequenceFeatures(view.getShowSequenceFeatures());
431 if (jms.getFeatureSettings() != null)
433 Hashtable<String, Integer> featuresDisplayed = new Hashtable<>();
434 Hashtable<String, FeatureColourI> featureColours = new Hashtable<>();
435 String[] renderOrder = new String[jms.getFeatureSettings()
437 for (int fs = 0; fs < jms.getFeatureSettings()
438 .getSettingCount(); fs++)
440 Setting setting = jms.getFeatureSettings().getSetting(fs);
442 featureColours.put(setting.getType(),
443 new FeatureColour(new java.awt.Color(setting.getColour())));
445 renderOrder[fs] = setting.getType();
447 if (setting.getDisplay())
449 featuresDisplayed.put(setting.getType(),
450 new Integer(setting.getColour()));
453 FeatureRendererSettings frs = new FeatureRendererSettings(renderOrder,
454 new Hashtable<String, Boolean>(), featureColours, 1.0f, null,
456 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
457 .transferSettings(frs);
460 af.setMenusFromViewport(af.viewport);
462 Desktop.addInternalFrame(af, view.getTitle(), view.getWidth(),
466 // /////////////////////////////////////
467 if (jms.getTreeCount() > 0)
471 for (int t = 0; t < jms.getTreeCount(); t++)
474 Tree tree = jms.getTree(t);
476 TreePanel tp = af.showNewickTree(
477 new jalview.io.NewickFile(tree.getNewick()),
478 tree.getTitle(), tree.getWidth(), tree.getHeight(),
479 tree.getXpos(), tree.getYpos());
481 tp.fitToWindow.setState(tree.getFitToWindow());
482 tp.fitToWindow_actionPerformed(null);
484 if (tree.getFontName() != null)
486 tp.setTreeFont(new java.awt.Font(tree.getFontName(),
487 tree.getFontStyle(), tree.getFontSize()));
491 tp.setTreeFont(new java.awt.Font(view.getFontName(),
492 view.getFontStyle(), tree.getFontSize()));
495 tp.showPlaceholders(tree.getMarkUnlinked());
496 tp.showBootstrap(tree.getShowBootstrap());
497 tp.showDistances(tree.getShowDistances());
499 tp.treeCanvas.threshold = tree.getThreshold();
501 if (tree.getCurrentTree())
503 af.viewport.setCurrentTree(tp.getTree());
507 } catch (Exception ex)
509 ex.printStackTrace();