2 * Jalview - A Sequence Alignment Editor and Viewer
3 * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
5 * This program is free software; you can redistribute it and/or
6 * modify it under the terms of the GNU General Public License
7 * as published by the Free Software Foundation; either version 2
8 * of the License, or (at your option) any later version.
10 * This program is distributed in the hope that it will be useful,
11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
13 * GNU General Public License for more details.
15 * You should have received a copy of the GNU General Public License
16 * along with this program; if not, write to the Free Software
17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
22 import jalview.schemes.*;
30 import java.util.jar.*;
34 import org.exolab.castor.xml.*;
36 import jalview.schemabinding.version2.*;
47 public class Jalview2XML
53 * This maintains a list of viewports, the key being the
54 * seqSetId. Important to set historyItem and redoList
57 Hashtable viewportsAdded;
59 Hashtable annotationIds = new Hashtable();
61 String uniqueSetSuffix = "";
64 // SAVES SEVERAL ALIGNMENT WINDOWS TO SAME JARFILE
65 public void SaveState(File statefile)
67 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
76 FileOutputStream fos = new FileOutputStream(statefile);
77 JarOutputStream jout = new JarOutputStream(fos);
79 //NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS
80 ////////////////////////////////////////////////////
81 PrintWriter out = new PrintWriter(new OutputStreamWriter(jout,
84 Vector shortNames = new Vector();
87 for (int i = frames.length - 1; i > -1; i--)
89 if (frames[i] instanceof AlignFrame)
91 AlignFrame af = (AlignFrame) frames[i];
93 String shortName = af.getTitle();
95 if (shortName.indexOf(File.separatorChar) > -1)
97 shortName = shortName.substring(shortName.lastIndexOf(
98 File.separatorChar) + 1);
103 while (shortNames.contains(shortName))
105 if (shortName.endsWith("_" + (count - 1)))
107 shortName = shortName.substring(0,
108 shortName.lastIndexOf("_"));
111 shortName = shortName.concat("_" + count);
115 shortNames.addElement(shortName);
117 if (!shortName.endsWith(".xml"))
119 shortName = shortName + ".xml";
122 int ap, apSize= af.alignPanels.size();
123 for (ap = 0; ap < apSize; ap++)
125 AlignmentPanel apanel = (AlignmentPanel) af.alignPanels.
129 apSize == 1 ? shortName : ap+shortName,
140 ex.printStackTrace();
144 // USE THIS METHOD TO SAVE A SINGLE ALIGNMENT WINDOW
145 public boolean SaveAlignment(AlignFrame af, String jarFile,
150 int ap, apSize= af.alignPanels.size();
151 FileOutputStream fos = new FileOutputStream(jarFile);
152 JarOutputStream jout = new JarOutputStream(fos);
153 PrintWriter out = new PrintWriter(new OutputStreamWriter(jout,
155 for( ap=0; ap<apSize; ap++)
157 AlignmentPanel apanel = (AlignmentPanel)af.alignPanels.elementAt(ap);
160 apSize==1?fileName:fileName+ap,
170 ex.printStackTrace();
178 * @param af DOCUMENT ME!
179 * @param timeStamp DOCUMENT ME!
180 * @param fileName DOCUMENT ME!
181 * @param jout DOCUMENT ME!
182 * @param out DOCUMENT ME!
184 public JalviewModel SaveState(AlignmentPanel ap,
186 JarOutputStream jout,
189 if (seqRefIds == null)
190 seqRefIds = new Hashtable();
192 Vector userColours = new Vector();
194 AlignViewport av = ap.av;
196 JalviewModel object = new JalviewModel();
197 object.setVamsasModel(new jalview.schemabinding.version2.VamsasModel());
199 object.setCreationDate(new java.util.Date(System.currentTimeMillis()));
200 object.setVersion(jalview.bin.Cache.getProperty("VERSION"));
202 jalview.datamodel.AlignmentI jal = av.alignment;
206 jal = jal.getHiddenSequences().getFullAlignment();
209 SequenceSet vamsasSet = new SequenceSet();
211 JalviewModelSequence jms = new JalviewModelSequence();
213 vamsasSet.setGapChar(jal.getGapCharacter() + "");
216 Vector pdbfiles = null;
220 jalview.datamodel.SequenceI jds;
221 for (int i = 0; i < jal.getHeight(); i++)
223 jds = jal.getSequenceAt(i);
226 if(seqRefIds.get(id+"")!=null)
232 vamsasSeq = new Sequence();
233 vamsasSeq.setId(id + "");
234 vamsasSeq.setName(jds.getName());
235 vamsasSeq.setSequence(jds.getSequenceAsString());
236 vamsasSeq.setDescription(jds.getDescription());
238 if (jds.getDatasetSequence().getDBRef() != null)
240 jalview.datamodel.DBRefEntry[] dbrefs =
241 jds.getDatasetSequence().getDBRef();
243 for (int d = 0; d < dbrefs.length; d++)
245 DBRef dbref = new DBRef();
246 dbref.setSource(dbrefs[d].getSource());
247 dbref.setVersion(dbrefs[d].getVersion());
248 dbref.setAccessionId(dbrefs[d].getAccessionId());
249 vamsasSeq.addDBRef(dbref);
253 vamsasSet.addSequence(vamsasSeq);
254 seqRefIds.put(id+"", jal.getSequenceAt(i));
258 jseq.setStart(jds.getStart());
259 jseq.setEnd(jds.getEnd());
260 jseq.setColour( av.getSequenceColour(jds).getRGB());
264 if (av.hasHiddenRows)
266 jseq.setHidden(av.alignment.getHiddenSequences().isHidden(jds));
268 if(av.hiddenRepSequences!=null
269 && av.hiddenRepSequences.containsKey(jal.getSequenceAt(i)))
271 jalview.datamodel.SequenceI[] reps =
272 ( (jalview.datamodel.SequenceGroup)
273 av.hiddenRepSequences.get(
274 jal.getSequenceAt(i))).getSequencesInOrder(jal);
276 for(int h=0; h<reps.length; h++)
278 if (reps[h] != jal.getSequenceAt(i))
279 jseq.addHiddenSequences(
280 jal.findIndex(reps[h])
287 if(jds.getDatasetSequence().getSequenceFeatures()!=null)
289 jalview.datamodel.SequenceFeature[] sf
290 = jds.getDatasetSequence().getSequenceFeatures();
292 while(index < sf.length)
294 Features features = new Features();
296 features.setBegin(sf[index].getBegin());
297 features.setEnd(sf[index].getEnd());
298 features.setDescription(sf[index].getDescription());
299 features.setType(sf[index].getType());
300 features.setFeatureGroup(sf[index].getFeatureGroup());
301 features.setScore(sf[index].getScore());
302 if(sf[index].links!=null)
304 for(int l=0; l<sf[index].links.size(); l++)
306 OtherData keyValue = new OtherData();
307 keyValue.setKey("LINK_"+l);
308 keyValue.setValue(sf[index].links.elementAt(l).toString());
309 features.addOtherData(keyValue);
312 if(sf[index].otherDetails!=null)
315 Enumeration keys = sf[index].otherDetails.keys();
316 while(keys.hasMoreElements())
318 key = keys.nextElement().toString();
319 OtherData keyValue = new OtherData();
320 keyValue.setKey( key );
322 sf[index].otherDetails.get(key).toString());
323 features.addOtherData(keyValue);
327 jseq.addFeatures(features);
332 if(jds.getDatasetSequence().getPDBId()!=null)
334 Enumeration en = jds.getDatasetSequence().getPDBId().elements();
335 while(en.hasMoreElements())
337 Pdbids pdb = new Pdbids();
338 jalview.datamodel.PDBEntry entry
339 = (jalview.datamodel.PDBEntry)en.nextElement();
341 pdb.setId(entry.getId());
342 pdb.setType(entry.getType());
345 if(entry.getFile()!=null)
347 pdb.setFile(entry.getFile());
349 pdbfiles = new Vector();
351 if(!pdbfiles.contains(entry.getId()))
353 pdbfiles.addElement(entry.getId());
356 File file = new File(entry.getFile());
357 if(file.exists() && jout!=null)
359 byte[] data = new byte[ (int) file.length()];
360 jout.putNextEntry(new JarEntry(entry.getId()));
361 DataInputStream dis = new DataInputStream(new
362 FileInputStream(file));
365 DataOutputStream dout = new DataOutputStream(jout);
366 dout.write(data, 0, data.length);
372 ex.printStackTrace();
378 if(entry.getProperty()!=null)
380 PdbentryItem item = new PdbentryItem();
381 Hashtable properties = entry.getProperty();
382 Enumeration en2 = properties.keys();
383 while(en2.hasMoreElements())
385 Property prop = new Property();
386 String key = en2.nextElement().toString();
388 prop.setValue( properties.get(key).toString() );
389 item.addProperty(prop);
391 pdb.addPdbentryItem(item);
406 ///////////////////////////////////
407 if (av.currentTree != null)
409 // FIND ANY ASSOCIATED TREES
410 // NOT IMPLEMENTED FOR HEADLESS STATE AT PRESENT
411 if (Desktop.desktop != null)
413 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
415 for (int t = 0; t < frames.length; t++)
417 if (frames[t] instanceof TreePanel)
419 TreePanel tp = (TreePanel) frames[t];
421 if (tp.treeCanvas.av.alignment == jal)
423 Tree tree = new Tree();
424 tree.setTitle(tp.getTitle());
425 tree.setCurrentTree( (av.currentTree == tp.getTree()));
426 tree.setNewick(tp.getTree().toString());
427 tree.setThreshold(tp.treeCanvas.threshold);
429 tree.setFitToWindow(tp.fitToWindow.getState());
430 tree.setFontName(tp.getTreeFont().getName());
431 tree.setFontSize(tp.getTreeFont().getSize());
432 tree.setFontStyle(tp.getTreeFont().getStyle());
433 tree.setMarkUnlinked(tp.placeholdersMenu.getState());
435 tree.setShowBootstrap(tp.bootstrapMenu.getState());
436 tree.setShowDistances(tp.distanceMenu.getState());
438 tree.setHeight(tp.getHeight());
439 tree.setWidth(tp.getWidth());
440 tree.setXpos(tp.getX());
441 tree.setYpos(tp.getY());
451 if (jal.getAlignmentAnnotation() != null)
453 jalview.datamodel.AlignmentAnnotation[] aa = jal.getAlignmentAnnotation();
455 for (int i = 0; i < aa.length; i++)
457 Annotation an = new Annotation();
459 if(aa[i].annotationId!=null)
461 annotationIds.put(aa[i].annotationId, aa[i]);
464 an.setId(aa[i].annotationId);
466 if (aa[i].label.equals("Quality") ||
467 aa[i].label.equals("Conservation") ||
468 aa[i].label.equals("Consensus"))
470 an.setLabel(aa[i].label);
472 vamsasSet.addAnnotation(an);
477 an.setDescription(aa[i].description);
479 if(aa[i].sequenceRef!=null)
481 an.setSequenceRef(aa[i].sequenceRef.getName());
487 an.setGraphType(aa[i].graph);
488 an.setGraphGroup(aa[i].graphGroup);
489 if(aa[i].getThreshold()!=null)
491 ThresholdLine line = new ThresholdLine();
492 line.setLabel(aa[i].getThreshold().label);
493 line.setValue(aa[i].getThreshold().value);
494 line.setColour(aa[i].getThreshold().colour.getRGB());
495 an.setThresholdLine(line);
501 an.setLabel(aa[i].label);
503 AnnotationElement ae;
505 for (int a = 0; a < aa[i].annotations.length; a++)
507 if ((aa[i] == null) || (aa[i].annotations[a] == null))
512 ae = new AnnotationElement();
513 ae.setDescription(aa[i].annotations[a].description);
514 ae.setDisplayCharacter(aa[i].annotations[a].displayCharacter);
515 ae.setValue(aa[i].annotations[a].value);
517 ae.setSecondaryStructure(aa[i].annotations[a].secondaryStructure +
520 if(aa[i].annotations[a].colour!=java.awt.Color.black)
521 ae.setColour(aa[i].annotations[a].colour.getRGB());
523 an.addAnnotationElement(ae);
526 vamsasSet.addAnnotation(an);
531 if (jal.getGroups() != null)
533 JGroup[] groups = new JGroup[jal.getGroups().size()];
535 for (int i = 0; i < groups.length; i++)
537 groups[i] = new JGroup();
539 jalview.datamodel.SequenceGroup sg = (jalview.datamodel.SequenceGroup) jal.getGroups()
541 groups[i].setStart(sg.getStartRes());
542 groups[i].setEnd(sg.getEndRes());
543 groups[i].setName(sg.getName());
546 if (sg.cs.conservationApplied())
548 groups[i].setConsThreshold(sg.cs.getConservationInc());
550 if (sg.cs instanceof jalview.schemes.UserColourScheme)
552 groups[i].setColour(SetUserColourScheme(sg.cs,
558 groups[i].setColour(ColourSchemeProperty.getColourName(sg.
562 else if(sg.cs instanceof jalview.schemes.AnnotationColourGradient)
565 ColourSchemeProperty.getColourName(
566 ( (jalview.schemes.AnnotationColourGradient) sg.cs).getBaseColour()));
568 else if (sg.cs instanceof jalview.schemes.UserColourScheme)
570 groups[i].setColour(SetUserColourScheme(sg.cs, userColours,
575 groups[i].setColour(ColourSchemeProperty.getColourName(
579 groups[i].setPidThreshold(sg.cs.getThreshold());
582 groups[i].setOutlineColour(sg.getOutlineColour().getRGB());
583 groups[i].setDisplayBoxes(sg.getDisplayBoxes());
584 groups[i].setDisplayText(sg.getDisplayText());
585 groups[i].setColourText(sg.getColourText());
586 groups[i].setTextCol1(sg.textColour.getRGB());
587 groups[i].setTextCol2(sg.textColour2.getRGB());
588 groups[i].setTextColThreshold(sg.thresholdTextColour);
590 for (int s = 0; s < sg.getSize(); s++)
592 jalview.datamodel.Sequence seq =
593 (jalview.datamodel.Sequence) sg.getSequenceAt(s);
594 groups[i].addSeq(seq.hashCode());
598 jms.setJGroup(groups);
602 ///////////SAVE VIEWPORT
603 Viewport view = new Viewport();
604 view.setTitle(ap.alignFrame.getTitle());
605 view.setSequenceSetId(av.getSequenceSetId());
606 view.setViewName(av.viewName);
607 view.setGatheredViews(av.gatherViewsHere);
610 if (ap.av.explodedPosition != null)
612 view.setXpos(av.explodedPosition.x);
613 view.setYpos(av.explodedPosition.y);
614 view.setWidth(av.explodedPosition.width);
615 view.setHeight(av.explodedPosition.height);
619 view.setXpos(ap.alignFrame.getBounds().x);
620 view.setYpos(ap.alignFrame.getBounds().y);
621 view.setWidth(ap.alignFrame.getBounds().width);
622 view.setHeight(ap.alignFrame.getBounds().height);
625 view.setStartRes(av.startRes);
626 view.setStartSeq(av.startSeq);
628 if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme)
630 view.setBgColour(SetUserColourScheme(av.getGlobalColourScheme(),
633 else if(av.getGlobalColourScheme() instanceof jalview.schemes.AnnotationColourGradient)
635 jalview.schemes.AnnotationColourGradient acg
636 = (jalview.schemes.AnnotationColourGradient)av.getGlobalColourScheme();
638 AnnotationColours ac = new AnnotationColours();
639 ac.setAboveThreshold(acg.getAboveThreshold());
640 ac.setThreshold(acg.getAnnotationThreshold());
641 ac.setAnnotation(acg.getAnnotation());
642 if(acg.getBaseColour() instanceof jalview.schemes.UserColourScheme)
643 ac.setColourScheme(SetUserColourScheme(acg.getBaseColour(),
646 ac.setColourScheme(ColourSchemeProperty.getColourName(acg.getBaseColour()));
648 ac.setMaxColour(acg.getMaxColour().getRGB());
649 ac.setMinColour(acg.getMinColour().getRGB());
650 view.setAnnotationColours(ac);
651 view.setBgColour("AnnotationColourGradient");
655 view.setBgColour(ColourSchemeProperty.getColourName(
656 av.getGlobalColourScheme()));
659 ColourSchemeI cs = av.getGlobalColourScheme();
663 if (cs.conservationApplied())
665 view.setConsThreshold(cs.getConservationInc());
666 if (cs instanceof jalview.schemes.UserColourScheme)
667 view.setBgColour(SetUserColourScheme(cs, userColours, jms));
670 if (cs instanceof ResidueColourScheme)
672 view.setPidThreshold(cs.getThreshold());
676 view.setConservationSelected(av.getConservationSelected());
677 view.setPidSelected(av.getAbovePIDThreshold());
678 view.setFontName(av.font.getName());
679 view.setFontSize(av.font.getSize());
680 view.setFontStyle(av.font.getStyle());
681 view.setRenderGaps(av.renderGaps);
682 view.setShowAnnotation(av.getShowAnnotation());
683 view.setShowBoxes(av.getShowBoxes());
684 view.setShowColourText(av.getColourText());
685 view.setShowFullId(av.getShowJVSuffix());
686 view.setRightAlignIds(av.rightAlignIds);
687 view.setShowSequenceFeatures(av.showSequenceFeatures);
688 view.setShowText(av.getShowText());
689 view.setWrapAlignment(av.getWrapAlignment());
690 view.setTextCol1(av.textColour.getRGB());
691 view.setTextCol2(av.textColour2.getRGB());
692 view.setTextColThreshold(av.thresholdTextColour);
695 if(av.featuresDisplayed!=null)
697 jalview.schemabinding.version2.FeatureSettings fs
698 = new jalview.schemabinding.version2.FeatureSettings();
700 String [] renderOrder =
701 ap.seqPanel.seqCanvas.getFeatureRenderer().renderOrder;
703 Vector settingsAdded = new Vector();
704 for(int ro=0; ro<renderOrder.length; ro++)
706 Setting setting = new Setting();
707 setting.setType(renderOrder[ro]);
709 ap.seqPanel.seqCanvas.getFeatureRenderer().getColour(renderOrder[ro]).getRGB()
713 av.featuresDisplayed.containsKey(renderOrder[ro])
716 fs.addSetting(setting);
717 settingsAdded.addElement(renderOrder[ro]);
720 //Make sure we save none displayed feature settings
722 ap.seqPanel.seqCanvas.getFeatureRenderer().featureColours.keys();
723 while(en.hasMoreElements())
725 String key = en.nextElement().toString();
726 if(settingsAdded.contains(key))
729 Setting setting = new Setting();
730 setting.setType(key);
732 ap.seqPanel.seqCanvas.getFeatureRenderer().getColour(key).getRGB()
735 setting.setDisplay(false);
737 fs.addSetting(setting);
738 settingsAdded.addElement(key);
741 jms.setFeatureSettings(fs);
745 if(av.hasHiddenColumns)
747 for(int c=0; c<av.getColumnSelection().getHiddenColumns().size(); c++)
749 int [] region = (int[]) av.getColumnSelection().getHiddenColumns().elementAt(c);
750 HiddenColumns hc = new HiddenColumns();
751 hc.setStart(region[0]);
752 hc.setEnd(region[1]);
753 view.addHiddenColumns(hc);
757 jms.addViewport(view);
760 object.setJalviewModelSequence(jms);
761 object.getVamsasModel().addSequenceSet(vamsasSet);
765 //We may not want to right the object to disk,
766 //eg we can copy the alignViewport to a new view object
767 //using save and then load
770 if (!fileName.endsWith(".xml"))
772 fileName = fileName + ".xml";
775 JarEntry entry = new JarEntry(fileName);
776 jout.putNextEntry(entry);
782 ex.printStackTrace();
788 String SetUserColourScheme(jalview.schemes.ColourSchemeI cs,
789 Vector userColours, JalviewModelSequence jms)
792 jalview.schemes.UserColourScheme ucs = (jalview.schemes.UserColourScheme) cs;
794 if (!userColours.contains(ucs))
796 userColours.add(ucs);
798 java.awt.Color[] colours = ucs.getColours();
799 jalview.schemabinding.version2.UserColours uc = new jalview.schemabinding.version2.UserColours();
800 jalview.schemabinding.version2.UserColourScheme jbucs = new jalview.schemabinding.version2.UserColourScheme();
802 for (int i = 0; i < colours.length; i++)
804 jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();
805 col.setName(ResidueProperties.aa[i]);
806 col.setRGB(jalview.util.Format.getHexString(colours[i]));
807 jbucs.addColour(col);
809 if(ucs.getLowerCaseColours()!=null)
811 colours = ucs.getLowerCaseColours();
812 for (int i = 0; i < colours.length; i++)
814 jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();
815 col.setName(ResidueProperties.aa[i].toLowerCase());
816 col.setRGB(jalview.util.Format.getHexString(colours[i]));
817 jbucs.addColour(col);
821 id = "ucs" + userColours.indexOf(ucs);
823 uc.setUserColourScheme(jbucs);
824 jms.addUserColours(uc);
830 jalview.schemes.UserColourScheme GetUserColourScheme(
831 JalviewModelSequence jms, String id)
833 UserColours[] uc = jms.getUserColours();
834 UserColours colours = null;
836 for (int i = 0; i < uc.length; i++)
838 if (uc[i].getId().equals(id))
846 java.awt.Color[] newColours = new java.awt.Color[24];
848 for (int i = 0; i < 24; i++)
850 newColours[i] = new java.awt.Color(Integer.parseInt(
851 colours.getUserColourScheme().getColour(i).getRGB(), 16));
854 jalview.schemes.UserColourScheme ucs =
855 new jalview.schemes.UserColourScheme(newColours);
857 if (colours.getUserColourScheme().getColourCount() > 24)
859 newColours = new java.awt.Color[23];
860 for (int i = 0; i < 23; i++)
862 newColours[i] = new java.awt.Color(Integer.parseInt(
863 colours.getUserColourScheme().getColour(i+24).getRGB(), 16));
865 ucs.setLowerCaseColours(newColours);
875 * @param file DOCUMENT ME!
877 public AlignFrame LoadJalviewAlign(final String file)
879 uniqueSetSuffix = System.currentTimeMillis()%100000 +"";
881 jalview.gui.AlignFrame af = null;
883 seqRefIds = new Hashtable();
884 viewportsAdded = new Hashtable();
886 Vector gatherToThisFrame= new Vector();
890 //UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
893 if (file.startsWith("http://"))
898 JarInputStream jin = null;
899 JarEntry jarentry = null;
906 jin = new JarInputStream(url.openStream());
910 jin = new JarInputStream(new FileInputStream(file));
913 for (int i = 0; i < entryCount; i++)
915 jarentry = jin.getNextJarEntry();
918 if (jarentry != null && jarentry.getName().endsWith(".xml"))
920 InputStreamReader in = new InputStreamReader(jin, "UTF-8");
921 JalviewModel object = new JalviewModel();
923 Unmarshaller unmar = new Unmarshaller(object);
924 unmar.setValidation(false);
925 object = (JalviewModel) unmar.unmarshal( in );
927 af = LoadFromObject(object, file, true);
928 if(af.viewport.gatherViewsHere)
930 gatherToThisFrame.add(af);
934 else if (jarentry != null)
936 //Some other file here.
940 while (jarentry != null);
942 catch(java.net.UnknownHostException ex)
944 ex.printStackTrace();
945 System.err.println("Couldn't locate Jalview XML file : " +
948 javax.swing.SwingUtilities.invokeLater(new Runnable()
952 JOptionPane.showInternalMessageDialog(Desktop.desktop,
953 "Couldn't locate " + file,
955 JOptionPane.WARNING_MESSAGE);
961 //Is Version 1 Jar file?
962 af = new Jalview2XML_V1().LoadJalviewAlign(file);
966 System.out.println("Successfully loaded archive file");
969 ex.printStackTrace();
971 System.err.println("Exception whilst loading jalview XML file : " +
973 javax.swing.SwingUtilities.invokeLater(new Runnable()
978 JOptionPane.showInternalMessageDialog(Desktop.desktop,
979 "Error loading " + file,
980 "Error loading Jalview file",
981 JOptionPane.WARNING_MESSAGE);
985 if (Desktop.instance != null)
986 Desktop.instance.stopLoading();
988 for (int i = 0; i < gatherToThisFrame.size(); i++)
990 Desktop.instance.gatherViews(
991 (AlignFrame) gatherToThisFrame.elementAt(i));
997 String loadPDBFile(String file, String pdbId)
999 System.out.println(file +" "+pdbId);
1002 JarInputStream jin = null;
1004 if (file.startsWith("http://"))
1006 jin = new JarInputStream(new URL(file).openStream());
1010 jin = new JarInputStream(new FileInputStream(file));
1013 JarEntry entry = null;
1016 entry = jin.getNextJarEntry();
1018 while (!entry.getName().equals(pdbId));
1020 BufferedReader in = new BufferedReader(new InputStreamReader(jin));
1021 File outFile = File.createTempFile("jalview_pdb", ".txt");
1022 outFile.deleteOnExit();
1023 PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
1026 while ( (data = in.readLine()) != null)
1031 return outFile.getAbsolutePath();
1034 catch (Exception ex)
1036 ex.printStackTrace();
1043 AlignFrame LoadFromObject(JalviewModel object,
1047 SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);
1048 Sequence[] vamsasSeq = vamsasSet.getSequence();
1050 JalviewModelSequence jms = object.getJalviewModelSequence();
1052 Viewport view = jms.getViewport(0);
1054 //////////////////////////////////
1057 Vector hiddenSeqs = null;
1058 jalview.datamodel.Sequence jseq;
1060 ArrayList tmpseqs = new ArrayList();
1062 boolean multipleView = false;
1064 JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq();
1065 for (int i = 0; i < JSEQ.length; i++)
1067 String seqId = JSEQ[i].getId() + "";
1069 if (seqRefIds.get(seqId) != null)
1071 tmpseqs.add( (jalview.datamodel.Sequence) seqRefIds.get(seqId));
1072 multipleView = true;
1076 jseq = new jalview.datamodel.Sequence(vamsasSeq[i].getName(),
1077 vamsasSeq[i].getSequence());
1078 jseq.setDescription(vamsasSeq[i].getDescription());
1079 jseq.setStart(JSEQ[i].getStart());
1080 jseq.setEnd(JSEQ[i].getEnd());
1081 seqRefIds.put(vamsasSeq[i].getId(), jseq);
1082 tmpseqs.add( jseq );
1087 if (JSEQ[i].getHidden())
1089 if (hiddenSeqs == null)
1090 hiddenSeqs = new Vector();
1093 hiddenSeqs.addElement(
1094 (jalview.datamodel.Sequence) seqRefIds.get(seqId));
1099 ///SequenceFeatures are added to the DatasetSequence,
1100 // so we must create the dataset before loading features
1101 /////////////////////////////////
1104 jalview.datamodel.Sequence[] orderedSeqs = new jalview.datamodel.Sequence[
1107 tmpseqs.toArray(orderedSeqs) ;
1110 jalview.datamodel.Alignment al =
1111 new jalview.datamodel.Alignment(orderedSeqs);
1113 al.setDataset(null);
1114 /////////////////////////////////
1117 Hashtable pdbloaded = new Hashtable();
1120 for (int i = 0; i < vamsasSeq.length; i++)
1122 if (JSEQ[i].getFeaturesCount() > 0)
1124 Features[] features = JSEQ[i].getFeatures();
1125 for (int f = 0; f < features.length; f++)
1127 jalview.datamodel.SequenceFeature sf
1128 = new jalview.datamodel.SequenceFeature(features[f].getType(),
1129 features[f].getDescription(), features[f].getStatus(),
1130 features[f].getBegin(), features[f].getEnd(),
1131 features[f].getFeatureGroup());
1133 sf.setScore(features[f].getScore());
1134 for (int od = 0; od < features[f].getOtherDataCount(); od++)
1136 OtherData keyValue = features[f].getOtherData(od);
1137 if (keyValue.getKey().startsWith("LINK"))
1138 sf.addLink(keyValue.getValue());
1140 sf.setValue(keyValue.getKey(), keyValue.getValue());
1144 al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf);
1147 if (JSEQ[i].getPdbidsCount() > 0)
1149 Pdbids[] ids = JSEQ[i].getPdbids();
1150 for (int p = 0; p < ids.length; p++)
1152 jalview.datamodel.PDBEntry entry = new jalview.datamodel.
1154 entry.setId(ids[p].getId());
1155 entry.setType(ids[p].getType());
1156 if (ids[p].getFile() != null)
1158 if (!pdbloaded.containsKey(ids[p].getFile()))
1160 String tmppdb = loadPDBFile(file, ids[p].getId());
1161 entry.setFile(tmppdb);
1162 pdbloaded.put(ids[p].getId(), tmppdb);
1165 entry.setFile(pdbloaded.get(ids[p].getId()).toString());
1168 al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
1171 if (vamsasSeq[i].getDBRefCount() > 0)
1173 for (int d = 0; d < vamsasSeq[i].getDBRefCount(); d++)
1175 jalview.datamodel.DBRefEntry entry =
1176 new jalview.datamodel.DBRefEntry(
1177 vamsasSeq[i].getDBRef(d).getSource(),
1178 vamsasSeq[i].getDBRef(d).getVersion(),
1179 vamsasSeq[i].getDBRef(d).getAccessionId()
1181 al.getSequenceAt(i).getDatasetSequence().addDBRef(entry);
1189 /////////////////////////////////
1190 //////////////////////////////////
1192 boolean hideQuality = true,
1193 hideConservation = true,
1194 hideConsensus = true;
1196 if (vamsasSet.getAnnotationCount()>0)
1198 Annotation[] an = vamsasSet.getAnnotation();
1200 for (int i = 0; i < an.length; i++)
1202 if (an[i].getLabel().equals("Quality"))
1204 hideQuality = false;
1207 else if(an[i].getLabel().equals("Conservation"))
1209 hideConservation = false;
1212 else if(an[i].getLabel().equals("Consensus"))
1214 hideConsensus = false;
1218 if (an[i].getId() != null
1219 && annotationIds.containsKey(an[i].getId()))
1222 (jalview.datamodel.AlignmentAnnotation)annotationIds.get(an[i].getId())
1228 AnnotationElement[] ae = an[i].getAnnotationElement();
1229 jalview.datamodel.Annotation[] anot = new jalview.datamodel.Annotation[al.getWidth()];
1231 for (int aa = 0; aa < ae.length && aa<anot.length; aa++)
1233 anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(ae[aa].getDisplayCharacter(),
1234 ae[aa].getDescription(),
1235 ae[aa].getSecondaryStructure().length()==0?' ':ae[aa].getSecondaryStructure().charAt(0),
1237 anot[ae[aa].getPosition()].colour = new java.awt.Color( ae[aa].getColour() );
1240 jalview.datamodel.AlignmentAnnotation jaa = null;
1242 if (an[i].getGraph())
1244 jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
1245 an[i].getDescription(), anot, 0, 0,
1246 an[i].getGraphType());
1248 jaa.graphGroup = an[i].getGraphGroup();
1250 if (an[i].getThresholdLine() != null)
1252 jaa.setThreshold(new jalview.datamodel.GraphLine(
1253 an[i].getThresholdLine().getValue(),
1254 an[i].getThresholdLine().getLabel(),
1255 new java.awt.Color(an[i].getThresholdLine().getColour()))
1263 jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
1264 an[i].getDescription(), anot);
1267 if(an[i].getId()!=null)
1269 annotationIds.put(an[i].getId(), jaa);
1270 jaa.annotationId = an[i].getId();
1273 if(an[i].getSequenceRef()!=null)
1275 jaa.createSequenceMapping(
1276 al.findName(an[i].getSequenceRef()), 1, true
1278 al.findName(an[i].getSequenceRef()).addAlignmentAnnotation(jaa);
1281 al.addAnnotation(jaa);
1285 /////////////////////////
1287 if (jms.getJGroupCount() > 0)
1289 JGroup[] groups = jms.getJGroup();
1291 for (int i = 0; i < groups.length; i++)
1293 ColourSchemeI cs = null;
1295 if (groups[i].getColour() != null)
1297 if (groups[i].getColour().startsWith("ucs"))
1299 cs = GetUserColourScheme(jms, groups[i].getColour());
1303 cs = ColourSchemeProperty.getColour(al,
1304 groups[i].getColour());
1308 cs.setThreshold(groups[i].getPidThreshold(), true);
1311 Vector seqs = new Vector();
1313 for (int s = 0; s < groups[i].getSeqCount(); s++)
1315 String seqId = groups[i].getSeq(s)+"";
1316 seqs.addElement((jalview.datamodel.SequenceI) seqRefIds.get(seqId));
1319 jalview.datamodel.SequenceGroup sg = new jalview.datamodel.SequenceGroup(seqs,
1320 groups[i].getName(), cs, groups[i].getDisplayBoxes(),
1321 groups[i].getDisplayText(), groups[i].getColourText(),
1322 groups[i].getStart(), groups[i].getEnd());
1324 sg.setOutlineColour(new java.awt.Color(
1325 groups[i].getOutlineColour()));
1327 sg.textColour = new java.awt.Color(groups[i].getTextCol1());
1328 sg.textColour2 = new java.awt.Color(groups[i].getTextCol2());
1329 sg.thresholdTextColour = groups[i].getTextColThreshold();
1331 if (groups[i].getConsThreshold() != 0)
1333 jalview.analysis.Conservation c = new jalview.analysis.Conservation("All",
1334 ResidueProperties.propHash, 3, sg.getSequences(null), 0,
1337 c.verdict(false, 25);
1338 sg.cs.setConservation(c);
1346 /////////////////////////////////
1349 AlignFrame af = new AlignFrame(al,
1353 af.setFileName(file, "Jalview");
1355 for (int i = 0; i < JSEQ.length; i++)
1357 af.viewport.setSequenceColour(
1358 af.viewport.alignment.getSequenceAt(i),
1360 JSEQ[i].getColour()));
1363 //If we just load in the same jar file again, the sequenceSetId
1364 //will be the same, and we end up with multiple references
1365 //to the same sequenceSet. We must modify this id on load
1366 //so that each load of the file gives a unique id
1367 String uniqueSeqSetId = view.getSequenceSetId()+uniqueSetSuffix;
1369 af.viewport.gatherViewsHere = view.getGatheredViews();
1371 if (view.getSequenceSetId() != null)
1373 jalview.gui.AlignViewport av =
1374 (jalview.gui.AlignViewport)
1375 viewportsAdded.get(uniqueSeqSetId);
1377 af.viewport.sequenceSetID = uniqueSeqSetId;
1381 af.viewport.historyList = av.historyList;
1382 af.viewport.redoList = av.redoList;
1386 viewportsAdded.put(uniqueSeqSetId, af.viewport);
1389 PaintRefresher.Register(af.alignPanel, uniqueSeqSetId);
1391 if(hiddenSeqs!=null)
1393 for(int s=0; s<JSEQ.length; s++)
1395 jalview.datamodel.SequenceGroup hidden =
1396 new jalview.datamodel.SequenceGroup();
1398 for(int r=0; r<JSEQ[s].getHiddenSequencesCount(); r++)
1401 al.getSequenceAt(JSEQ[s].getHiddenSequences(r))
1405 af.viewport.hideRepSequences(al.getSequenceAt(s), hidden);
1408 jalview.datamodel.SequenceI [] hseqs = new
1409 jalview.datamodel.SequenceI[hiddenSeqs.size()];
1411 for(int s=0; s<hiddenSeqs.size(); s++)
1412 hseqs[s] = (jalview.datamodel.SequenceI)hiddenSeqs.elementAt(s);
1414 af.viewport.hideSequence( hseqs );
1419 if((hideConsensus || hideQuality || hideConservation)
1420 && al.getAlignmentAnnotation()!=null)
1422 int hSize = al.getAlignmentAnnotation().length;
1423 for (int h = 0; h < hSize; h++)
1427 al.getAlignmentAnnotation()[h].label.equals("Consensus"))
1430 al.getAlignmentAnnotation()[h].label.equals("Quality"))
1432 (hideConservation &&
1433 al.getAlignmentAnnotation()[h].label.equals("Conservation")))
1435 al.deleteAnnotation(al.getAlignmentAnnotation()[h]);
1440 af.alignPanel.adjustAnnotationHeight();
1443 if(view.getViewName()!=null)
1445 af.viewport.viewName = view.getViewName();
1446 af.setInitialTabVisible();
1448 af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),
1451 af.viewport.setShowAnnotation(view.getShowAnnotation());
1452 af.viewport.setAbovePIDThreshold(view.getPidSelected());
1454 af.viewport.setColourText(view.getShowColourText());
1456 af.viewport.setConservationSelected(view.getConservationSelected());
1457 af.viewport.setShowJVSuffix(view.getShowFullId());
1458 af.viewport.rightAlignIds=view.getRightAlignIds();
1459 af.viewport.setFont(new java.awt.Font(view.getFontName(),
1460 view.getFontStyle(), view.getFontSize()));
1461 af.alignPanel.fontChanged();
1462 af.viewport.setRenderGaps(view.getRenderGaps());
1463 af.viewport.setWrapAlignment(view.getWrapAlignment());
1464 af.alignPanel.setWrapAlignment(view.getWrapAlignment());
1465 af.viewport.setShowAnnotation(view.getShowAnnotation());
1466 af.alignPanel.setAnnotationVisible(view.getShowAnnotation());
1468 af.viewport.setShowBoxes(view.getShowBoxes());
1470 af.viewport.setShowText(view.getShowText());
1472 af.viewport.textColour = new java.awt.Color(view.getTextCol1());
1473 af.viewport.textColour2 = new java.awt.Color(view.getTextCol2());
1474 af.viewport.thresholdTextColour = view.getTextColThreshold();
1476 af.viewport.setStartRes(view.getStartRes());
1477 af.viewport.setStartSeq(view.getStartSeq());
1479 ColourSchemeI cs = null;
1481 if (view.getBgColour() != null)
1483 if (view.getBgColour().startsWith("ucs"))
1485 cs = GetUserColourScheme(jms, view.getBgColour());
1487 else if(view.getBgColour().startsWith("Annotation"))
1489 //int find annotation
1490 for (int i = 0; i < af.viewport.alignment.getAlignmentAnnotation().length; i++)
1492 if (af.viewport.alignment.getAlignmentAnnotation()[i].label.
1493 equals(view.getAnnotationColours().getAnnotation()))
1495 if (af.viewport.alignment.getAlignmentAnnotation()[i].
1496 getThreshold() == null)
1498 af.viewport.alignment.getAlignmentAnnotation()[i].
1500 new jalview.datamodel.GraphLine(
1501 view.getAnnotationColours().getThreshold(),
1502 "Threshold", java.awt.Color.black)
1508 if (view.getAnnotationColours().getColourScheme().equals(
1511 cs = new AnnotationColourGradient(
1512 af.viewport.alignment.getAlignmentAnnotation()[i],
1513 new java.awt.Color(view.getAnnotationColours().
1515 new java.awt.Color(view.getAnnotationColours().
1517 view.getAnnotationColours().getAboveThreshold());
1519 else if (view.getAnnotationColours().getColourScheme().
1522 cs = new AnnotationColourGradient(
1523 af.viewport.alignment.getAlignmentAnnotation()[i],
1524 GetUserColourScheme(jms, view.getAnnotationColours().
1526 view.getAnnotationColours().getAboveThreshold()
1531 cs = new AnnotationColourGradient(
1532 af.viewport.alignment.getAlignmentAnnotation()[i],
1533 ColourSchemeProperty.getColour(al,
1534 view.getAnnotationColours().getColourScheme()),
1535 view.getAnnotationColours().getAboveThreshold()
1539 // Also use these settings for all the groups
1540 if (al.getGroups() != null)
1541 for (int g = 0; g < al.getGroups().size(); g++)
1543 jalview.datamodel.SequenceGroup sg
1544 = (jalview.datamodel.SequenceGroup)al.getGroups().elementAt(g);
1550 /* if (view.getAnnotationColours().getColourScheme().equals("None"))
1552 sg.cs = new AnnotationColourGradient(
1553 af.viewport.alignment.getAlignmentAnnotation()[i],
1554 new java.awt.Color(view.getAnnotationColours().
1556 new java.awt.Color(view.getAnnotationColours().
1558 view.getAnnotationColours().getAboveThreshold());
1562 sg.cs = new AnnotationColourGradient(
1563 af.viewport.alignment.getAlignmentAnnotation()[i],
1565 view.getAnnotationColours().getAboveThreshold()
1579 cs = ColourSchemeProperty.getColour(al, view.getBgColour());
1584 cs.setThreshold(view.getPidThreshold(), true);
1585 cs.setConsensus(af.viewport.hconsensus);
1590 af.viewport.setGlobalColourScheme(cs);
1591 af.viewport.setColourAppliesToAllGroups(false);
1593 if (view.getConservationSelected() && cs!=null)
1595 cs.setConservationInc(view.getConsThreshold());
1598 af.changeColour(cs);
1600 af.viewport.setColourAppliesToAllGroups(true);
1604 if (view.getShowSequenceFeatures())
1606 af.viewport.showSequenceFeatures = true;
1609 if(jms.getFeatureSettings()!=null)
1611 af.viewport.featuresDisplayed = new Hashtable();
1612 String [] renderOrder = new String[jms.getFeatureSettings().getSettingCount()];
1613 for(int fs=0; fs<jms.getFeatureSettings().getSettingCount(); fs++)
1615 Setting setting = jms.getFeatureSettings().getSetting(fs);
1617 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(setting.getType(),
1618 new java.awt.Color(setting.getColour()));
1620 renderOrder[fs] = setting.getType();
1622 if(setting.getDisplay())
1623 af.viewport.featuresDisplayed.put(
1624 setting.getType(), new Integer(setting.getColour()));
1626 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder = renderOrder;
1629 if (view.getHiddenColumnsCount() > 0)
1631 for (int c = 0; c < view.getHiddenColumnsCount(); c++)
1633 af.viewport.hideColumns(
1634 view.getHiddenColumns(c).getStart(),
1635 view.getHiddenColumns(c).getEnd() //+1
1640 af.setMenusFromViewport(af.viewport);
1643 Desktop.addInternalFrame(af, view.getTitle(),
1644 view.getWidth(), view.getHeight());
1647 ///////////////////////////////////////
1648 if (loadTrees && jms.getTreeCount() > 0)
1652 for (int t = 0; t < jms.getTreeCount(); t++)
1655 Tree tree = jms.getTree(t);
1657 TreePanel tp = af.ShowNewickTree(new jalview.io.NewickFile(
1658 tree.getNewick()), tree.getTitle(),
1659 tree.getWidth(), tree.getHeight(),
1660 tree.getXpos(), tree.getYpos());
1662 tp.fitToWindow.setState(tree.getFitToWindow());
1663 tp.fitToWindow_actionPerformed(null);
1665 if(tree.getFontName()!=null)
1666 tp.setTreeFont(new java.awt.Font(tree.getFontName(),
1667 tree.getFontStyle(),
1668 tree.getFontSize()));
1670 tp.setTreeFont(new java.awt.Font(view.getFontName(),
1671 view.getFontStyle(),
1672 tree.getFontSize()));
1674 tp.showPlaceholders(tree.getMarkUnlinked());
1675 tp.showBootstrap(tree.getShowBootstrap());
1676 tp.showDistances(tree.getShowDistances());
1678 tp.treeCanvas.threshold = tree.getThreshold();
1680 if (tree.getCurrentTree())
1681 af.viewport.setCurrentTree(tp.getTree());
1685 catch (Exception ex)
1687 ex.printStackTrace();
1695 public jalview.gui.AlignmentPanel copyAlignPanel(AlignmentPanel ap, boolean keepSeqRefs )
1697 jalview.schemabinding.version2.JalviewModel jm
1698 = SaveState(ap, null, null, null);
1703 jm.getJalviewModelSequence().getViewport(0).setSequenceSetId(null);
1706 uniqueSetSuffix = "";
1708 viewportsAdded = new Hashtable();
1710 AlignFrame af = LoadFromObject(jm, null, false);
1711 af.alignPanels.clear();
1712 af.closeMenuItem_actionPerformed(true);
1714 /* if(ap.av.alignment.getAlignmentAnnotation()!=null)
1716 for(int i=0; i<ap.av.alignment.getAlignmentAnnotation().length; i++)
1718 if(!ap.av.alignment.getAlignmentAnnotation()[i].autoCalculated)
1720 af.alignPanel.av.alignment.getAlignmentAnnotation()[i] =
1721 ap.av.alignment.getAlignmentAnnotation()[i];
1726 return af.alignPanel;