2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
3 * Copyright (C) 2010 J Procter, AM Waterhouse, 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/>.
20 import java.awt.Rectangle;
22 import java.lang.reflect.InvocationTargetException;
25 import java.util.jar.*;
29 import org.exolab.castor.xml.*;
31 import uk.ac.vamsas.objects.utils.MapList;
32 import jalview.bin.Cache;
33 import jalview.datamodel.Alignment;
34 import jalview.datamodel.AlignmentI;
35 import jalview.datamodel.SequenceI;
36 import jalview.schemabinding.version2.*;
37 import jalview.schemes.*;
38 import jalview.structure.StructureSelectionManager;
39 import jalview.util.jarInputStreamProvider;
42 * Write out the current jalview desktop state as a Jalview XML stream.
44 * Note: the vamsas objects referred to here are primitive versions of the
45 * VAMSAS project schema elements - they are not the same and most likely never
51 public class Jalview2XML
54 * create/return unique hash string for sq
57 * @return new or existing unique string for sq
59 String seqHash(SequenceI sq)
61 if (seqsToIds == null)
65 if (seqsToIds.containsKey(sq))
67 return (String) seqsToIds.get(sq);
71 // create sequential key
72 String key = "sq" + (seqsToIds.size() + 1);
73 key = makeHashCode(sq, key); // check we don't have an external reference
75 seqsToIds.put(sq, key);
84 if (seqRefIds != null)
88 if (seqsToIds != null)
98 warn("clearSeqRefs called when _cleartables was not set. Doing nothing.");
99 // seqRefIds = new Hashtable();
100 // seqsToIds = new IdentityHashMap();
106 if (seqsToIds == null)
108 seqsToIds = new IdentityHashMap();
110 if (seqRefIds == null)
112 seqRefIds = new Hashtable();
117 * SequenceI reference -> XML ID string in jalview XML. Populated as XML reps
118 * of sequence objects are created.
120 java.util.IdentityHashMap seqsToIds = null;
123 * jalview XML Sequence ID to jalview sequence object reference (both dataset
124 * and alignment sequences. Populated as XML reps of sequence objects are
127 java.util.Hashtable seqRefIds = null; // key->SequenceI resolution
129 Vector frefedSequence = null;
131 boolean raiseGUI = true; // whether errors are raised in dialog boxes or not
137 public Jalview2XML(boolean raiseGUI)
139 this.raiseGUI = raiseGUI;
142 public void resolveFrefedSequences()
144 if (frefedSequence.size() > 0)
146 int r = 0, rSize = frefedSequence.size();
149 Object[] ref = (Object[]) frefedSequence.elementAt(r);
152 String sref = (String) ref[0];
153 if (seqRefIds.containsKey(sref))
155 if (ref[1] instanceof jalview.datamodel.Mapping)
157 SequenceI seq = (SequenceI) seqRefIds.get(sref);
158 while (seq.getDatasetSequence() != null)
160 seq = seq.getDatasetSequence();
162 ((jalview.datamodel.Mapping) ref[1]).setTo(seq);
166 if (ref[1] instanceof jalview.datamodel.AlignedCodonFrame)
168 SequenceI seq = (SequenceI) seqRefIds.get(sref);
169 while (seq.getDatasetSequence() != null)
171 seq = seq.getDatasetSequence();
174 && ref[2] instanceof jalview.datamodel.Mapping)
176 jalview.datamodel.Mapping mp = (jalview.datamodel.Mapping) ref[2];
177 ((jalview.datamodel.AlignedCodonFrame) ref[1]).addMap(
178 seq, mp.getTo(), mp.getMap());
183 .println("IMPLEMENTATION ERROR: Unimplemented forward sequence references for AlcodonFrames involving "
184 + ref[2].getClass() + " type objects.");
190 .println("IMPLEMENTATION ERROR: Unimplemented forward sequence references for "
191 + ref[1].getClass() + " type objects.");
194 frefedSequence.remove(r);
200 .println("IMPLEMENTATION WARNING: Unresolved forward reference for hash string "
202 + " with objecttype "
203 + ref[1].getClass());
210 frefedSequence.remove(r);
218 * This maintains a list of viewports, the key being the seqSetId. Important
219 * to set historyItem and redoList for multiple views
221 Hashtable viewportsAdded;
223 Hashtable annotationIds = new Hashtable();
225 String uniqueSetSuffix = "";
228 * List of pdbfiles added to Jar
230 Vector pdbfiles = null;
232 // SAVES SEVERAL ALIGNMENT WINDOWS TO SAME JARFILE
233 public void SaveState(File statefile)
237 FileOutputStream fos = new FileOutputStream(statefile);
238 JarOutputStream jout = new JarOutputStream(fos);
241 } catch (Exception e)
243 // TODO: inform user of the problem - they need to know if their data was
245 if (errorMessage == null)
247 errorMessage = "Couldn't write Jalview Archive to output file '"
248 + statefile + "' - See console error log for details";
252 errorMessage += "(output file was '" + statefile + "')";
260 * Writes a jalview project archive to the given Jar output stream.
264 public void SaveState(JarOutputStream jout)
266 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
276 // NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS
277 // //////////////////////////////////////////////////
278 // NOTE ALSO new PrintWriter must be used for each new JarEntry
279 PrintWriter out = null;
281 Vector shortNames = new Vector();
284 for (int i = frames.length - 1; i > -1; i--)
286 if (frames[i] instanceof AlignFrame)
288 AlignFrame af = (AlignFrame) frames[i];
291 && skipList.containsKey(af.getViewport()
292 .getSequenceSetId()))
297 String shortName = af.getTitle();
299 if (shortName.indexOf(File.separatorChar) > -1)
301 shortName = shortName.substring(shortName
302 .lastIndexOf(File.separatorChar) + 1);
307 while (shortNames.contains(shortName))
309 if (shortName.endsWith("_" + (count - 1)))
311 shortName = shortName
312 .substring(0, shortName.lastIndexOf("_"));
315 shortName = shortName.concat("_" + count);
319 shortNames.addElement(shortName);
321 if (!shortName.endsWith(".xml"))
323 shortName = shortName + ".xml";
326 int ap, apSize = af.alignPanels.size();
327 for (ap = 0; ap < apSize; ap++)
329 AlignmentPanel apanel = (AlignmentPanel) af.alignPanels
331 String fileName = apSize == 1 ? shortName : ap + shortName;
332 if (!fileName.endsWith(".xml"))
334 fileName = fileName + ".xml";
337 SaveState(apanel, fileName, jout);
344 } catch (Exception foo)
349 } catch (Exception ex)
351 // TODO: inform user of the problem - they need to know if their data was
353 if (errorMessage == null)
355 errorMessage = "Couldn't write Jalview Archive - see error output for details";
357 ex.printStackTrace();
361 // USE THIS METHOD TO SAVE A SINGLE ALIGNMENT WINDOW
362 public boolean SaveAlignment(AlignFrame af, String jarFile,
367 int ap, apSize = af.alignPanels.size();
368 FileOutputStream fos = new FileOutputStream(jarFile);
369 JarOutputStream jout = new JarOutputStream(fos);
370 for (ap = 0; ap < apSize; ap++)
372 AlignmentPanel apanel = (AlignmentPanel) af.alignPanels
374 String jfileName = apSize == 1 ? fileName : fileName + ap;
375 if (!jfileName.endsWith(".xml"))
377 jfileName = jfileName + ".xml";
379 SaveState(apanel, jfileName, jout);
385 } catch (Exception foo)
391 } catch (Exception ex)
393 errorMessage = "Couldn't Write alignment view to Jalview Archive - see error output for details";
394 ex.printStackTrace();
400 * create a JalviewModel from an algnment view and marshall it to a
404 * panel to create jalview model for
406 * name of alignment panel written to output stream
412 public JalviewModel SaveState(AlignmentPanel ap, String fileName,
413 JarOutputStream jout)
417 Vector userColours = new Vector();
419 AlignViewport av = ap.av;
421 JalviewModel object = new JalviewModel();
422 object.setVamsasModel(new jalview.schemabinding.version2.VamsasModel());
424 object.setCreationDate(new java.util.Date(System.currentTimeMillis()));
425 object.setVersion(jalview.bin.Cache.getProperty("VERSION"));
427 jalview.datamodel.AlignmentI jal = av.alignment;
429 if (av.hasHiddenRows)
431 jal = jal.getHiddenSequences().getFullAlignment();
434 SequenceSet vamsasSet = new SequenceSet();
436 JalviewModelSequence jms = new JalviewModelSequence();
438 vamsasSet.setGapChar(jal.getGapCharacter() + "");
440 if (jal.getDataset() != null)
442 // dataset id is the dataset's hashcode
443 vamsasSet.setDatasetId(getDatasetIdRef(jal.getDataset()));
445 if (jal.getProperties() != null)
447 Enumeration en = jal.getProperties().keys();
448 while (en.hasMoreElements())
450 String key = en.nextElement().toString();
451 SequenceSetProperties ssp = new SequenceSetProperties();
453 ssp.setValue(jal.getProperties().get(key).toString());
454 vamsasSet.addSequenceSetProperties(ssp);
462 jalview.datamodel.SequenceI jds;
463 for (int i = 0; i < jal.getHeight(); i++)
465 jds = jal.getSequenceAt(i);
468 if (seqRefIds.get(id) != null)
470 // This happens for two reasons: 1. multiple views are being serialised.
471 // 2. the hashCode has collided with another sequence's code. This DOES
472 // HAPPEN! (PF00072.15.stk does this)
473 // JBPNote: Uncomment to debug writing out of files that do not read
474 // back in due to ArrayOutOfBoundExceptions.
475 // System.err.println("vamsasSeq backref: "+id+"");
476 // System.err.println(jds.getName()+"
477 // "+jds.getStart()+"-"+jds.getEnd()+" "+jds.getSequenceAsString());
478 // System.err.println("Hashcode: "+seqHash(jds));
479 // SequenceI rsq = (SequenceI) seqRefIds.get(id + "");
480 // System.err.println(rsq.getName()+"
481 // "+rsq.getStart()+"-"+rsq.getEnd()+" "+rsq.getSequenceAsString());
482 // System.err.println("Hashcode: "+seqHash(rsq));
486 vamsasSeq = createVamsasSequence(id, jds);
487 vamsasSet.addSequence(vamsasSeq);
488 seqRefIds.put(id, jds);
492 jseq.setStart(jds.getStart());
493 jseq.setEnd(jds.getEnd());
494 jseq.setColour(av.getSequenceColour(jds).getRGB());
496 jseq.setId(id); // jseq id should be a string not a number
498 if (av.hasHiddenRows)
500 jseq.setHidden(av.alignment.getHiddenSequences().isHidden(jds));
502 if (av.hiddenRepSequences != null
503 && av.hiddenRepSequences.containsKey(jal.getSequenceAt(i)))
505 jalview.datamodel.SequenceI[] reps = ((jalview.datamodel.SequenceGroup) av.hiddenRepSequences
506 .get(jal.getSequenceAt(i))).getSequencesInOrder(jal);
508 for (int h = 0; h < reps.length; h++)
510 if (reps[h] != jal.getSequenceAt(i))
512 jseq.addHiddenSequences(jal.findIndex(reps[h]));
518 if (jds.getDatasetSequence().getSequenceFeatures() != null)
520 jalview.datamodel.SequenceFeature[] sf = jds.getDatasetSequence()
521 .getSequenceFeatures();
523 while (index < sf.length)
525 Features features = new Features();
527 features.setBegin(sf[index].getBegin());
528 features.setEnd(sf[index].getEnd());
529 features.setDescription(sf[index].getDescription());
530 features.setType(sf[index].getType());
531 features.setFeatureGroup(sf[index].getFeatureGroup());
532 features.setScore(sf[index].getScore());
533 if (sf[index].links != null)
535 for (int l = 0; l < sf[index].links.size(); l++)
537 OtherData keyValue = new OtherData();
538 keyValue.setKey("LINK_" + l);
539 keyValue.setValue(sf[index].links.elementAt(l).toString());
540 features.addOtherData(keyValue);
543 if (sf[index].otherDetails != null)
546 Enumeration keys = sf[index].otherDetails.keys();
547 while (keys.hasMoreElements())
549 key = keys.nextElement().toString();
550 OtherData keyValue = new OtherData();
551 keyValue.setKey(key);
552 keyValue.setValue(sf[index].otherDetails.get(key).toString());
553 features.addOtherData(keyValue);
557 jseq.addFeatures(features);
562 if (jds.getDatasetSequence().getPDBId() != null)
564 Enumeration en = jds.getDatasetSequence().getPDBId().elements();
565 while (en.hasMoreElements())
567 Pdbids pdb = new Pdbids();
568 jalview.datamodel.PDBEntry entry = (jalview.datamodel.PDBEntry) en
571 pdb.setId(entry.getId());
572 pdb.setType(entry.getType());
575 // This must have been loaded, is it still visible?
576 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
577 String matchedFile = null;
578 for (int f = frames.length - 1; f > -1; f--)
580 if (frames[f] instanceof AppJmol)
582 // TODO: revise schema to allow many:one PDB id binding to viewer
583 jmol = (AppJmol) frames[f];
584 if (!jmol.jmb.pdbentry[0].getId().equals(entry.getId())
585 && !(entry.getId().length() > 4 && entry.getId()
586 .toLowerCase().startsWith(
587 jmol.jmb.pdbentry[0].getId().toLowerCase())))
589 matchedFile = jmol.jmb.pdbentry[0].getFile(); // record the file so we
590 // can get at it if the ID
591 // match is ambiguous (e.g.
593 StructureState state = new StructureState();
594 state.setVisible(true);
595 state.setXpos(jmol.getX());
596 state.setYpos(jmol.getY());
597 state.setWidth(jmol.getWidth());
598 state.setHeight(jmol.getHeight());
599 state.setViewId(jmol.getViewId());
600 String statestring = jmol.jmb.viewer.getStateInfo();
603 state.setContent(statestring.replaceAll("\n", ""));
605 for (int s = 0; s < jmol.jmb.sequence.length; s++)
607 if (jal.findIndex(jmol.jmb.sequence[s]) > -1)
609 pdb.addStructureState(state);
615 if (matchedFile != null || entry.getFile() != null)
617 if (entry.getFile() != null)
620 matchedFile = entry.getFile();
622 pdb.setFile(matchedFile); // entry.getFile());
623 if (pdbfiles == null)
625 pdbfiles = new Vector();
628 if (!pdbfiles.contains(entry.getId()))
630 pdbfiles.addElement(entry.getId());
633 File file = new File(matchedFile);
634 if (file.exists() && jout != null)
636 byte[] data = new byte[(int) file.length()];
637 jout.putNextEntry(new JarEntry(entry.getId()));
638 DataInputStream dis = new DataInputStream(
639 new FileInputStream(file));
642 DataOutputStream dout = new DataOutputStream(jout);
643 dout.write(data, 0, data.length);
647 } catch (Exception ex)
649 ex.printStackTrace();
655 if (entry.getProperty() != null)
657 PdbentryItem item = new PdbentryItem();
658 Hashtable properties = entry.getProperty();
659 Enumeration en2 = properties.keys();
660 while (en2.hasMoreElements())
662 Property prop = new Property();
663 String key = en2.nextElement().toString();
665 prop.setValue(properties.get(key).toString());
666 item.addProperty(prop);
668 pdb.addPdbentryItem(item);
678 if (av.hasHiddenRows)
683 if (jal.getCodonFrames() != null && jal.getCodonFrames().length > 0)
685 jalview.datamodel.AlignedCodonFrame[] jac = jal.getCodonFrames();
686 for (int i = 0; i < jac.length; i++)
688 AlcodonFrame alc = new AlcodonFrame();
689 vamsasSet.addAlcodonFrame(alc);
690 for (int p = 0; p < jac[i].aaWidth; p++)
692 Alcodon cmap = new Alcodon();
693 if (jac[i].codons[p] != null)
695 // Null codons indicate a gapped column in the translated peptide
697 cmap.setPos1(jac[i].codons[p][0]);
698 cmap.setPos2(jac[i].codons[p][1]);
699 cmap.setPos3(jac[i].codons[p][2]);
701 alc.addAlcodon(cmap);
703 if (jac[i].getProtMappings() != null
704 && jac[i].getProtMappings().length > 0)
706 SequenceI[] dnas = jac[i].getdnaSeqs();
707 jalview.datamodel.Mapping[] pmaps = jac[i].getProtMappings();
708 for (int m = 0; m < pmaps.length; m++)
710 AlcodMap alcmap = new AlcodMap();
711 alcmap.setDnasq(seqHash(dnas[m]));
712 alcmap.setMapping(createVamsasMapping(pmaps[m], dnas[m], null,
714 alc.addAlcodMap(alcmap);
721 // /////////////////////////////////
722 if (av.currentTree != null)
724 // FIND ANY ASSOCIATED TREES
725 // NOT IMPLEMENTED FOR HEADLESS STATE AT PRESENT
726 if (Desktop.desktop != null)
728 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
730 for (int t = 0; t < frames.length; t++)
732 if (frames[t] instanceof TreePanel)
734 TreePanel tp = (TreePanel) frames[t];
736 if (tp.treeCanvas.av.alignment == jal)
738 Tree tree = new Tree();
739 tree.setTitle(tp.getTitle());
740 tree.setCurrentTree((av.currentTree == tp.getTree()));
741 tree.setNewick(tp.getTree().toString());
742 tree.setThreshold(tp.treeCanvas.threshold);
744 tree.setFitToWindow(tp.fitToWindow.getState());
745 tree.setFontName(tp.getTreeFont().getName());
746 tree.setFontSize(tp.getTreeFont().getSize());
747 tree.setFontStyle(tp.getTreeFont().getStyle());
748 tree.setMarkUnlinked(tp.placeholdersMenu.getState());
750 tree.setShowBootstrap(tp.bootstrapMenu.getState());
751 tree.setShowDistances(tp.distanceMenu.getState());
753 tree.setHeight(tp.getHeight());
754 tree.setWidth(tp.getWidth());
755 tree.setXpos(tp.getX());
756 tree.setYpos(tp.getY());
757 tree.setId(makeHashCode(tp, null));
767 * store forward refs from an annotationRow to any groups
769 IdentityHashMap groupRefs = new IdentityHashMap();
770 if (jal.getAlignmentAnnotation() != null)
772 jalview.datamodel.AlignmentAnnotation[] aa = jal
773 .getAlignmentAnnotation();
775 for (int i = 0; i < aa.length; i++)
777 Annotation an = new Annotation();
779 if (aa[i].annotationId != null)
781 annotationIds.put(aa[i].annotationId, aa[i]);
784 an.setId(aa[i].annotationId);
786 an.setVisible(aa[i].visible);
788 an.setDescription(aa[i].description);
790 if (aa[i].sequenceRef != null)
792 // TODO later annotation sequenceRef should be the XML ID of the
793 // sequence rather than its display name
794 an.setSequenceRef(aa[i].sequenceRef.getName());
796 if (aa[i].groupRef != null)
798 Object groupIdr = groupRefs.get(aa[i].groupRef);
799 if (groupIdr == null)
801 // make a locally unique String
802 groupRefs.put(aa[i].groupRef,
803 groupIdr = ("" + System.currentTimeMillis()
804 + aa[i].groupRef.getName() + groupRefs.size()));
806 an.setGroupRef(groupIdr.toString());
808 if (aa[i] == av.quality || aa[i] == av.conservation
809 || aa[i] == av.consensus || aa[i].autoCalculated)
811 // new way of indicating autocalculated annotation -
812 an.setAutoCalculated(aa[i].autoCalculated);
813 // write a stub for this annotation - indicate presence of autocalc
815 an.setLabel(aa[i].label);
817 vamsasSet.addAnnotation(an);
824 an.setGraphType(aa[i].graph);
825 an.setGraphGroup(aa[i].graphGroup);
826 if (aa[i].getThreshold() != null)
828 ThresholdLine line = new ThresholdLine();
829 line.setLabel(aa[i].getThreshold().label);
830 line.setValue(aa[i].getThreshold().value);
831 line.setColour(aa[i].getThreshold().colour.getRGB());
832 an.setThresholdLine(line);
840 an.setLabel(aa[i].label);
841 if (aa[i].hasScore())
843 an.setScore(aa[i].getScore());
845 AnnotationElement ae;
846 if (aa[i].annotations != null)
848 an.setScoreOnly(false);
849 for (int a = 0; a < aa[i].annotations.length; a++)
851 if ((aa[i] == null) || (aa[i].annotations[a] == null))
856 ae = new AnnotationElement();
857 if (aa[i].annotations[a].description != null)
858 ae.setDescription(aa[i].annotations[a].description);
859 if (aa[i].annotations[a].displayCharacter != null)
860 ae.setDisplayCharacter(aa[i].annotations[a].displayCharacter);
862 if (!Float.isNaN(aa[i].annotations[a].value))
863 ae.setValue(aa[i].annotations[a].value);
866 if (aa[i].annotations[a].secondaryStructure != ' '
867 && aa[i].annotations[a].secondaryStructure != '\0')
869 .setSecondaryStructure(aa[i].annotations[a].secondaryStructure
872 if (aa[i].annotations[a].colour != null
873 && aa[i].annotations[a].colour != java.awt.Color.black)
875 ae.setColour(aa[i].annotations[a].colour.getRGB());
878 an.addAnnotationElement(ae);
883 an.setScoreOnly(true);
885 vamsasSet.addAnnotation(an);
889 if (jal.getGroups() != null)
891 JGroup[] groups = new JGroup[jal.getGroups().size()];
893 for (int i = 0; i < groups.length; i++)
895 groups[i] = new JGroup();
897 jalview.datamodel.SequenceGroup sg = (jalview.datamodel.SequenceGroup) jal
898 .getGroups().elementAt(i);
899 groups[i].setStart(sg.getStartRes());
900 groups[i].setEnd(sg.getEndRes());
901 groups[i].setName(sg.getName());
902 if (groupRefs.containsKey(sg))
904 // group has references so set it's ID field
905 groups[i].setId(groupRefs.get(sg).toString());
909 if (sg.cs.conservationApplied())
911 groups[i].setConsThreshold(sg.cs.getConservationInc());
913 if (sg.cs instanceof jalview.schemes.UserColourScheme)
915 groups[i].setColour(SetUserColourScheme(sg.cs, userColours,
921 .setColour(ColourSchemeProperty.getColourName(sg.cs));
924 else if (sg.cs instanceof jalview.schemes.AnnotationColourGradient)
927 .setColour(ColourSchemeProperty
928 .getColourName(((jalview.schemes.AnnotationColourGradient) sg.cs)
931 else if (sg.cs instanceof jalview.schemes.UserColourScheme)
934 .setColour(SetUserColourScheme(sg.cs, userColours, jms));
938 groups[i].setColour(ColourSchemeProperty.getColourName(sg.cs));
941 groups[i].setPidThreshold(sg.cs.getThreshold());
944 groups[i].setOutlineColour(sg.getOutlineColour().getRGB());
945 groups[i].setDisplayBoxes(sg.getDisplayBoxes());
946 groups[i].setDisplayText(sg.getDisplayText());
947 groups[i].setColourText(sg.getColourText());
948 groups[i].setTextCol1(sg.textColour.getRGB());
949 groups[i].setTextCol2(sg.textColour2.getRGB());
950 groups[i].setTextColThreshold(sg.thresholdTextColour);
951 groups[i].setShowUnconserved(sg.getShowNonconserved());
952 groups[i].setIgnoreGapsinConsensus(sg.getIgnoreGapsConsensus());
953 groups[i].setShowConsensusHistogram(sg.isShowConsensusHistogram());
954 groups[i].setShowSequenceLogo(sg.isShowSequenceLogo());
955 for (int s = 0; s < sg.getSize(); s++)
957 jalview.datamodel.Sequence seq = (jalview.datamodel.Sequence) sg
959 groups[i].addSeq(seqHash(seq));
963 jms.setJGroup(groups);
966 // /////////SAVE VIEWPORT
967 Viewport view = new Viewport();
968 view.setTitle(ap.alignFrame.getTitle());
969 view.setSequenceSetId(makeHashCode(av.getSequenceSetId(), av
970 .getSequenceSetId()));
971 view.setId(av.getViewId());
972 view.setViewName(av.viewName);
973 view.setGatheredViews(av.gatherViewsHere);
975 if (ap.av.explodedPosition != null)
977 view.setXpos(av.explodedPosition.x);
978 view.setYpos(av.explodedPosition.y);
979 view.setWidth(av.explodedPosition.width);
980 view.setHeight(av.explodedPosition.height);
984 view.setXpos(ap.alignFrame.getBounds().x);
985 view.setYpos(ap.alignFrame.getBounds().y);
986 view.setWidth(ap.alignFrame.getBounds().width);
987 view.setHeight(ap.alignFrame.getBounds().height);
990 view.setStartRes(av.startRes);
991 view.setStartSeq(av.startSeq);
993 if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme)
995 view.setBgColour(SetUserColourScheme(av.getGlobalColourScheme(),
998 else if (av.getGlobalColourScheme() instanceof jalview.schemes.AnnotationColourGradient)
1000 jalview.schemes.AnnotationColourGradient acg = (jalview.schemes.AnnotationColourGradient) av
1001 .getGlobalColourScheme();
1003 AnnotationColours ac = new AnnotationColours();
1004 ac.setAboveThreshold(acg.getAboveThreshold());
1005 ac.setThreshold(acg.getAnnotationThreshold());
1006 ac.setAnnotation(acg.getAnnotation());
1007 if (acg.getBaseColour() instanceof jalview.schemes.UserColourScheme)
1009 ac.setColourScheme(SetUserColourScheme(acg.getBaseColour(),
1014 ac.setColourScheme(ColourSchemeProperty.getColourName(acg
1018 ac.setMaxColour(acg.getMaxColour().getRGB());
1019 ac.setMinColour(acg.getMinColour().getRGB());
1020 view.setAnnotationColours(ac);
1021 view.setBgColour("AnnotationColourGradient");
1025 view.setBgColour(ColourSchemeProperty.getColourName(av
1026 .getGlobalColourScheme()));
1029 ColourSchemeI cs = av.getGlobalColourScheme();
1033 if (cs.conservationApplied())
1035 view.setConsThreshold(cs.getConservationInc());
1036 if (cs instanceof jalview.schemes.UserColourScheme)
1038 view.setBgColour(SetUserColourScheme(cs, userColours, jms));
1042 if (cs instanceof ResidueColourScheme)
1044 view.setPidThreshold(cs.getThreshold());
1048 view.setConservationSelected(av.getConservationSelected());
1049 view.setPidSelected(av.getAbovePIDThreshold());
1050 view.setFontName(av.font.getName());
1051 view.setFontSize(av.font.getSize());
1052 view.setFontStyle(av.font.getStyle());
1053 view.setRenderGaps(av.renderGaps);
1054 view.setShowAnnotation(av.getShowAnnotation());
1055 view.setShowBoxes(av.getShowBoxes());
1056 view.setShowColourText(av.getColourText());
1057 view.setShowFullId(av.getShowJVSuffix());
1058 view.setRightAlignIds(av.rightAlignIds);
1059 view.setShowSequenceFeatures(av.showSequenceFeatures);
1060 view.setShowText(av.getShowText());
1061 view.setShowUnconserved(av.getShowUnconserved());
1062 view.setWrapAlignment(av.getWrapAlignment());
1063 view.setTextCol1(av.textColour.getRGB());
1064 view.setTextCol2(av.textColour2.getRGB());
1065 view.setTextColThreshold(av.thresholdTextColour);
1066 view.setShowConsensusHistogram(av.isShowConsensusHistogram());
1067 view.setShowSequenceLogo(av.isShowSequenceLogo());
1068 view.setShowGroupConsensus(av.isShowGroupConsensus());
1069 view.setShowGroupConservation(av.isShowGroupConservation());
1070 view.setShowNPfeatureTooltip(av.isShowNpFeats());
1071 view.setShowDbRefTooltip(av.isShowDbRefs());
1072 view.setFollowHighlight(av.followHighlight);
1073 view.setFollowSelection(av.followSelection);
1074 view.setIgnoreGapsinConsensus(av.getIgnoreGapsConsensus());
1075 if (av.featuresDisplayed != null)
1077 jalview.schemabinding.version2.FeatureSettings fs = new jalview.schemabinding.version2.FeatureSettings();
1079 String[] renderOrder = ap.seqPanel.seqCanvas.getFeatureRenderer().renderOrder;
1081 Vector settingsAdded = new Vector();
1082 Object gstyle = null;
1083 GraduatedColor gcol = null;
1084 for (int ro = 0; ro < renderOrder.length; ro++)
1086 gstyle = ap.seqPanel.seqCanvas.getFeatureRenderer()
1087 .getFeatureStyle(renderOrder[ro]);
1088 Setting setting = new Setting();
1089 setting.setType(renderOrder[ro]);
1090 if (gstyle instanceof GraduatedColor)
1092 gcol = (GraduatedColor) gstyle;
1093 setting.setColour(gcol.getMaxColor().getRGB());
1094 setting.setMincolour(gcol.getMinColor().getRGB());
1095 setting.setMin(gcol.getMin());
1096 setting.setMax(gcol.getMax());
1097 setting.setColourByLabel(gcol.isColourByLabel());
1098 setting.setAutoScale(gcol.isAutoScale());
1099 setting.setThreshold(gcol.getThresh());
1100 setting.setThreshstate(gcol.getThreshType());
1104 setting.setColour(ap.seqPanel.seqCanvas.getFeatureRenderer()
1105 .getColour(renderOrder[ro]).getRGB());
1108 setting.setDisplay(av.featuresDisplayed
1109 .containsKey(renderOrder[ro]));
1110 float rorder = ap.seqPanel.seqCanvas.getFeatureRenderer().getOrder(
1114 setting.setOrder(rorder);
1116 fs.addSetting(setting);
1117 settingsAdded.addElement(renderOrder[ro]);
1120 // Make sure we save none displayed feature settings
1121 Enumeration en = ap.seqPanel.seqCanvas.getFeatureRenderer().featureColours
1123 while (en.hasMoreElements())
1125 String key = en.nextElement().toString();
1126 if (settingsAdded.contains(key))
1131 Setting setting = new Setting();
1132 setting.setType(key);
1133 setting.setColour(ap.seqPanel.seqCanvas.getFeatureRenderer()
1134 .getColour(key).getRGB());
1136 setting.setDisplay(false);
1137 float rorder = ap.seqPanel.seqCanvas.getFeatureRenderer().getOrder(
1141 setting.setOrder(rorder);
1143 fs.addSetting(setting);
1144 settingsAdded.addElement(key);
1146 en = ap.seqPanel.seqCanvas.getFeatureRenderer().featureGroups.keys();
1147 Vector groupsAdded = new Vector();
1148 while (en.hasMoreElements())
1150 String grp = en.nextElement().toString();
1151 if (groupsAdded.contains(grp))
1155 Group g = new Group();
1158 .setDisplay(((Boolean) ap.seqPanel.seqCanvas
1159 .getFeatureRenderer().featureGroups.get(grp))
1162 groupsAdded.addElement(grp);
1164 jms.setFeatureSettings(fs);
1168 if (av.hasHiddenColumns)
1170 if (av.getColumnSelection() == null
1171 || av.getColumnSelection().getHiddenColumns() == null)
1173 warn("REPORT BUG: avoided null columnselection bug (DMAM reported). Please contact Jim about this.");
1177 for (int c = 0; c < av.getColumnSelection().getHiddenColumns()
1180 int[] region = (int[]) av.getColumnSelection().getHiddenColumns()
1182 HiddenColumns hc = new HiddenColumns();
1183 hc.setStart(region[0]);
1184 hc.setEnd(region[1]);
1185 view.addHiddenColumns(hc);
1190 jms.addViewport(view);
1192 object.setJalviewModelSequence(jms);
1193 object.getVamsasModel().addSequenceSet(vamsasSet);
1195 if (jout != null && fileName != null)
1197 // We may not want to write the object to disk,
1198 // eg we can copy the alignViewport to a new view object
1199 // using save and then load
1202 JarEntry entry = new JarEntry(fileName);
1203 jout.putNextEntry(entry);
1204 PrintWriter pout = new PrintWriter(new OutputStreamWriter(jout,
1206 org.exolab.castor.xml.Marshaller marshaller = new org.exolab.castor.xml.Marshaller(
1208 marshaller.marshal(object);
1211 } catch (Exception ex)
1213 // TODO: raise error in GUI if marshalling failed.
1214 ex.printStackTrace();
1221 * External mapping between jalview objects and objects yielding a valid and
1222 * unique object ID string. This is null for normal Jalview project IO, but
1223 * non-null when a jalview project is being read or written as part of a
1226 IdentityHashMap jv2vobj = null;
1229 * Construct a unique ID for jvobj using either existing bindings or if none
1230 * exist, the result of the hashcode call for the object.
1233 * jalview data object
1234 * @return unique ID for referring to jvobj
1236 private String makeHashCode(Object jvobj, String altCode)
1238 if (jv2vobj != null)
1240 Object id = jv2vobj.get(jvobj);
1243 return id.toString();
1245 // check string ID mappings
1246 if (jvids2vobj != null && jvobj instanceof String)
1248 id = jvids2vobj.get(jvobj);
1252 return id.toString();
1254 // give up and warn that something has gone wrong
1255 warn("Cannot find ID for object in external mapping : " + jvobj);
1261 * return local jalview object mapped to ID, if it exists
1265 * @return null or object bound to idcode
1267 private Object retrieveExistingObj(String idcode)
1269 if (idcode != null && vobj2jv != null)
1271 return vobj2jv.get(idcode);
1277 * binding from ID strings from external mapping table to jalview data model
1280 private Hashtable vobj2jv;
1282 private Sequence createVamsasSequence(String id, SequenceI jds)
1284 return createVamsasSequence(true, id, jds, null);
1287 private Sequence createVamsasSequence(boolean recurse, String id,
1288 SequenceI jds, SequenceI parentseq)
1290 Sequence vamsasSeq = new Sequence();
1291 vamsasSeq.setId(id);
1292 vamsasSeq.setName(jds.getName());
1293 vamsasSeq.setSequence(jds.getSequenceAsString());
1294 vamsasSeq.setDescription(jds.getDescription());
1295 jalview.datamodel.DBRefEntry[] dbrefs = null;
1296 if (jds.getDatasetSequence() != null)
1298 vamsasSeq.setDsseqid(seqHash(jds.getDatasetSequence()));
1299 if (jds.getDatasetSequence().getDBRef() != null)
1301 dbrefs = jds.getDatasetSequence().getDBRef();
1306 vamsasSeq.setDsseqid(id); // so we can tell which sequences really are
1307 // dataset sequences only
1308 dbrefs = jds.getDBRef();
1312 for (int d = 0; d < dbrefs.length; d++)
1314 DBRef dbref = new DBRef();
1315 dbref.setSource(dbrefs[d].getSource());
1316 dbref.setVersion(dbrefs[d].getVersion());
1317 dbref.setAccessionId(dbrefs[d].getAccessionId());
1318 if (dbrefs[d].hasMap())
1320 Mapping mp = createVamsasMapping(dbrefs[d].getMap(), parentseq,
1322 dbref.setMapping(mp);
1324 vamsasSeq.addDBRef(dbref);
1330 private Mapping createVamsasMapping(jalview.datamodel.Mapping jmp,
1331 SequenceI parentseq, SequenceI jds, boolean recurse)
1334 if (jmp.getMap() != null)
1338 jalview.util.MapList mlst = jmp.getMap();
1339 int r[] = mlst.getFromRanges();
1340 for (int s = 0; s < r.length; s += 2)
1342 MapListFrom mfrom = new MapListFrom();
1343 mfrom.setStart(r[s]);
1344 mfrom.setEnd(r[s + 1]);
1345 mp.addMapListFrom(mfrom);
1347 r = mlst.getToRanges();
1348 for (int s = 0; s < r.length; s += 2)
1350 MapListTo mto = new MapListTo();
1352 mto.setEnd(r[s + 1]);
1353 mp.addMapListTo(mto);
1355 mp.setMapFromUnit(mlst.getFromRatio());
1356 mp.setMapToUnit(mlst.getToRatio());
1357 if (jmp.getTo() != null)
1359 MappingChoice mpc = new MappingChoice();
1361 && (parentseq != jmp.getTo() || parentseq
1362 .getDatasetSequence() != jmp.getTo()))
1364 mpc.setSequence(createVamsasSequence(false, seqHash(jmp.getTo()),
1370 SequenceI ps = null;
1371 if (parentseq != jmp.getTo()
1372 && parentseq.getDatasetSequence() != jmp.getTo())
1374 // chaining dbref rather than a handshaking one
1375 jmpid = seqHash(ps = jmp.getTo());
1379 jmpid = seqHash(ps = parentseq);
1381 mpc.setDseqFor(jmpid);
1382 if (!seqRefIds.containsKey(mpc.getDseqFor()))
1384 jalview.bin.Cache.log.debug("creatign new DseqFor ID");
1385 seqRefIds.put(mpc.getDseqFor(), ps);
1389 jalview.bin.Cache.log.debug("reusing DseqFor ID");
1392 mp.setMappingChoice(mpc);
1398 String SetUserColourScheme(jalview.schemes.ColourSchemeI cs,
1399 Vector userColours, JalviewModelSequence jms)
1402 jalview.schemes.UserColourScheme ucs = (jalview.schemes.UserColourScheme) cs;
1403 boolean newucs = false;
1404 if (!userColours.contains(ucs))
1406 userColours.add(ucs);
1409 id = "ucs" + userColours.indexOf(ucs);
1412 // actually create the scheme's entry in the XML model
1413 java.awt.Color[] colours = ucs.getColours();
1414 jalview.schemabinding.version2.UserColours uc = new jalview.schemabinding.version2.UserColours();
1415 jalview.schemabinding.version2.UserColourScheme jbucs = new jalview.schemabinding.version2.UserColourScheme();
1417 for (int i = 0; i < colours.length; i++)
1419 jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();
1420 col.setName(ResidueProperties.aa[i]);
1421 col.setRGB(jalview.util.Format.getHexString(colours[i]));
1422 jbucs.addColour(col);
1424 if (ucs.getLowerCaseColours() != null)
1426 colours = ucs.getLowerCaseColours();
1427 for (int i = 0; i < colours.length; i++)
1429 jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();
1430 col.setName(ResidueProperties.aa[i].toLowerCase());
1431 col.setRGB(jalview.util.Format.getHexString(colours[i]));
1432 jbucs.addColour(col);
1437 uc.setUserColourScheme(jbucs);
1438 jms.addUserColours(uc);
1444 jalview.schemes.UserColourScheme GetUserColourScheme(
1445 JalviewModelSequence jms, String id)
1447 UserColours[] uc = jms.getUserColours();
1448 UserColours colours = null;
1450 for (int i = 0; i < uc.length; i++)
1452 if (uc[i].getId().equals(id))
1460 java.awt.Color[] newColours = new java.awt.Color[24];
1462 for (int i = 0; i < 24; i++)
1464 newColours[i] = new java.awt.Color(Integer.parseInt(colours
1465 .getUserColourScheme().getColour(i).getRGB(), 16));
1468 jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(
1471 if (colours.getUserColourScheme().getColourCount() > 24)
1473 newColours = new java.awt.Color[23];
1474 for (int i = 0; i < 23; i++)
1476 newColours[i] = new java.awt.Color(Integer.parseInt(colours
1477 .getUserColourScheme().getColour(i + 24).getRGB(), 16));
1479 ucs.setLowerCaseColours(newColours);
1486 * contains last error message (if any) encountered by XML loader.
1488 String errorMessage = null;
1491 * flag to control whether the Jalview2XML_V1 parser should be deferred to if
1492 * exceptions are raised during project XML parsing
1494 public boolean attemptversion1parse = true;
1497 * Load a jalview project archive from a jar file
1500 * - HTTP URL or filename
1502 public AlignFrame LoadJalviewAlign(final String file)
1505 jalview.gui.AlignFrame af = null;
1509 // UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
1510 // Workaround is to make sure caller implements the JarInputStreamProvider
1512 // so we can re-open the jar input stream for each entry.
1514 jarInputStreamProvider jprovider = createjarInputStreamProvider(file);
1515 af = LoadJalviewAlign(jprovider);
1516 } catch (MalformedURLException e)
1518 errorMessage = "Invalid URL format for '" + file + "'";
1524 private jarInputStreamProvider createjarInputStreamProvider(
1525 final String file) throws MalformedURLException
1528 errorMessage = null;
1529 uniqueSetSuffix = null;
1531 viewportsAdded = null;
1532 frefedSequence = null;
1534 if (file.startsWith("http://"))
1536 url = new URL(file);
1538 final URL _url = url;
1539 return new jarInputStreamProvider()
1542 public JarInputStream getJarInputStream() throws IOException
1546 return new JarInputStream(_url.openStream());
1550 return new JarInputStream(new FileInputStream(file));
1554 public String getFilename()
1562 * Recover jalview session from a jalview project archive. Caller may
1563 * initialise uniqueSetSuffix, seqRefIds, viewportsAdded and frefedSequence
1564 * themselves. Any null fields will be initialised with default values,
1565 * non-null fields are left alone.
1570 public AlignFrame LoadJalviewAlign(final jarInputStreamProvider jprovider)
1572 errorMessage = null;
1573 if (uniqueSetSuffix == null)
1575 uniqueSetSuffix = System.currentTimeMillis() % 100000 + "";
1577 if (seqRefIds == null)
1579 seqRefIds = new Hashtable();
1581 if (viewportsAdded == null)
1583 viewportsAdded = new Hashtable();
1585 if (frefedSequence == null)
1587 frefedSequence = new Vector();
1590 jalview.gui.AlignFrame af = null;
1591 Hashtable gatherToThisFrame = new Hashtable();
1592 final String file = jprovider.getFilename();
1595 JarInputStream jin = null;
1596 JarEntry jarentry = null;
1601 jin = jprovider.getJarInputStream();
1602 for (int i = 0; i < entryCount; i++)
1604 jarentry = jin.getNextJarEntry();
1607 if (jarentry != null && jarentry.getName().endsWith(".xml"))
1609 InputStreamReader in = new InputStreamReader(jin, "UTF-8");
1610 JalviewModel object = new JalviewModel();
1612 Unmarshaller unmar = new Unmarshaller(object);
1613 unmar.setValidation(false);
1614 object = (JalviewModel) unmar.unmarshal(in);
1615 if (true) // !skipViewport(object))
1617 af = LoadFromObject(object, file, true, jprovider);
1618 if (af.viewport.gatherViewsHere)
1620 gatherToThisFrame.put(af.viewport.getSequenceSetId(), af);
1625 else if (jarentry != null)
1627 // Some other file here.
1630 } while (jarentry != null);
1631 resolveFrefedSequences();
1632 } catch (java.io.FileNotFoundException ex)
1634 ex.printStackTrace();
1635 errorMessage = "Couldn't locate Jalview XML file : " + file;
1636 System.err.println("Exception whilst loading jalview XML file : "
1638 } catch (java.net.UnknownHostException ex)
1640 ex.printStackTrace();
1641 errorMessage = "Couldn't locate Jalview XML file : " + file;
1642 System.err.println("Exception whilst loading jalview XML file : "
1644 } catch (Exception ex)
1646 System.err.println("Parsing as Jalview Version 2 file failed.");
1647 ex.printStackTrace(System.err);
1648 if (attemptversion1parse)
1650 // Is Version 1 Jar file?
1653 af = new Jalview2XML_V1(raiseGUI).LoadJalviewAlign(jprovider);
1654 } catch (Exception ex2)
1656 System.err.println("Exception whilst loading as jalviewXMLV1:");
1657 ex2.printStackTrace();
1661 if (Desktop.instance != null)
1663 Desktop.instance.stopLoading();
1667 System.out.println("Successfully loaded archive file");
1670 ex.printStackTrace();
1672 System.err.println("Exception whilst loading jalview XML file : "
1674 } catch (OutOfMemoryError e)
1676 // Don't use the OOM Window here
1677 errorMessage = "Out of memory loading jalview XML file";
1678 System.err.println("Out of memory whilst loading jalview XML file");
1679 e.printStackTrace();
1682 if (Desktop.instance != null)
1684 Desktop.instance.stopLoading();
1687 Enumeration en = gatherToThisFrame.elements();
1688 while (en.hasMoreElements())
1690 Desktop.instance.gatherViews((AlignFrame) en.nextElement());
1692 if (errorMessage != null)
1700 * check errorMessage for a valid error message and raise an error box in the
1701 * GUI or write the current errorMessage to stderr and then clear the error
1704 protected void reportErrors()
1706 reportErrors(false);
1709 protected void reportErrors(final boolean saving)
1711 if (errorMessage != null)
1713 final String finalErrorMessage = errorMessage;
1716 javax.swing.SwingUtilities.invokeLater(new Runnable()
1720 JOptionPane.showInternalMessageDialog(Desktop.desktop,
1721 finalErrorMessage, "Error "
1722 + (saving ? "saving" : "loading")
1723 + " Jalview file", JOptionPane.WARNING_MESSAGE);
1729 System.err.println("Problem loading Jalview file: " + errorMessage);
1732 errorMessage = null;
1735 Hashtable alreadyLoadedPDB;
1738 * when set, local views will be updated from view stored in JalviewXML
1739 * Currently (28th Sep 2008) things will go horribly wrong in vamsas document
1740 * sync if this is set to true.
1742 private boolean updateLocalViews = false;
1744 String loadPDBFile(jarInputStreamProvider jprovider, String pdbId)
1746 if (alreadyLoadedPDB == null)
1747 alreadyLoadedPDB = new Hashtable();
1749 if (alreadyLoadedPDB.containsKey(pdbId))
1750 return alreadyLoadedPDB.get(pdbId).toString();
1754 JarInputStream jin = jprovider.getJarInputStream();
1756 * if (jprovider.startsWith("http://")) { jin = new JarInputStream(new
1757 * URL(jprovider).openStream()); } else { jin = new JarInputStream(new
1758 * FileInputStream(jprovider)); }
1761 JarEntry entry = null;
1764 entry = jin.getNextJarEntry();
1765 } while (entry != null && !entry.getName().equals(pdbId));
1768 BufferedReader in = new BufferedReader(new InputStreamReader(jin));
1769 File outFile = File.createTempFile("jalview_pdb", ".txt");
1770 outFile.deleteOnExit();
1771 PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
1774 while ((data = in.readLine()) != null)
1781 } catch (Exception foo)
1787 alreadyLoadedPDB.put(pdbId, outFile.getAbsolutePath());
1788 return outFile.getAbsolutePath();
1792 warn("Couldn't find PDB file entry in Jalview Jar for " + pdbId);
1794 } catch (Exception ex)
1796 ex.printStackTrace();
1803 * Load alignment frame from jalview XML DOM object
1808 * filename source string
1809 * @param loadTreesAndStructures
1810 * when false only create Viewport
1812 * data source provider
1813 * @return alignment frame created from view stored in DOM
1815 AlignFrame LoadFromObject(JalviewModel object, String file,
1816 boolean loadTreesAndStructures, jarInputStreamProvider jprovider)
1818 SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);
1819 Sequence[] vamsasSeq = vamsasSet.getSequence();
1821 JalviewModelSequence jms = object.getJalviewModelSequence();
1823 Viewport view = jms.getViewport(0);
1824 // ////////////////////////////////
1827 Vector hiddenSeqs = null;
1828 jalview.datamodel.Sequence jseq;
1830 ArrayList tmpseqs = new ArrayList();
1832 boolean multipleView = false;
1834 JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq();
1835 int vi = 0; // counter in vamsasSeq array
1836 for (int i = 0; i < JSEQ.length; i++)
1838 String seqId = JSEQ[i].getId();
1840 if (seqRefIds.get(seqId) != null)
1842 tmpseqs.add((jalview.datamodel.Sequence) seqRefIds.get(seqId));
1843 multipleView = true;
1847 jseq = new jalview.datamodel.Sequence(vamsasSeq[vi].getName(),
1848 vamsasSeq[vi].getSequence());
1849 jseq.setDescription(vamsasSeq[vi].getDescription());
1850 jseq.setStart(JSEQ[i].getStart());
1851 jseq.setEnd(JSEQ[i].getEnd());
1852 jseq.setVamsasId(uniqueSetSuffix + seqId);
1853 seqRefIds.put(vamsasSeq[vi].getId(), jseq);
1858 if (JSEQ[i].getHidden())
1860 if (hiddenSeqs == null)
1862 hiddenSeqs = new Vector();
1865 hiddenSeqs.addElement((jalview.datamodel.Sequence) seqRefIds
1872 // Create the alignment object from the sequence set
1873 // ///////////////////////////////
1874 jalview.datamodel.Sequence[] orderedSeqs = new jalview.datamodel.Sequence[tmpseqs
1877 tmpseqs.toArray(orderedSeqs);
1879 jalview.datamodel.Alignment al = new jalview.datamodel.Alignment(
1882 // / Add the alignment properties
1883 for (int i = 0; i < vamsasSet.getSequenceSetPropertiesCount(); i++)
1885 SequenceSetProperties ssp = vamsasSet.getSequenceSetProperties(i);
1886 al.setProperty(ssp.getKey(), ssp.getValue());
1890 // SequenceFeatures are added to the DatasetSequence,
1891 // so we must create or recover the dataset before loading features
1892 // ///////////////////////////////
1893 if (vamsasSet.getDatasetId() == null || vamsasSet.getDatasetId() == "")
1895 // older jalview projects do not have a dataset id.
1896 al.setDataset(null);
1900 recoverDatasetFor(vamsasSet, al);
1902 // ///////////////////////////////
1904 Hashtable pdbloaded = new Hashtable();
1907 // load sequence features, database references and any associated PDB
1908 // structures for the alignment
1909 for (int i = 0; i < vamsasSeq.length; i++)
1911 if (JSEQ[i].getFeaturesCount() > 0)
1913 Features[] features = JSEQ[i].getFeatures();
1914 for (int f = 0; f < features.length; f++)
1916 jalview.datamodel.SequenceFeature sf = new jalview.datamodel.SequenceFeature(
1917 features[f].getType(), features[f].getDescription(),
1918 features[f].getStatus(), features[f].getBegin(),
1919 features[f].getEnd(), features[f].getFeatureGroup());
1921 sf.setScore(features[f].getScore());
1922 for (int od = 0; od < features[f].getOtherDataCount(); od++)
1924 OtherData keyValue = features[f].getOtherData(od);
1925 if (keyValue.getKey().startsWith("LINK"))
1927 sf.addLink(keyValue.getValue());
1931 sf.setValue(keyValue.getKey(), keyValue.getValue());
1936 al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf);
1939 if (vamsasSeq[i].getDBRefCount() > 0)
1941 addDBRefs(al.getSequenceAt(i).getDatasetSequence(), vamsasSeq[i]);
1943 if (JSEQ[i].getPdbidsCount() > 0)
1945 Pdbids[] ids = JSEQ[i].getPdbids();
1946 for (int p = 0; p < ids.length; p++)
1948 jalview.datamodel.PDBEntry entry = new jalview.datamodel.PDBEntry();
1949 entry.setId(ids[p].getId());
1950 entry.setType(ids[p].getType());
1951 if (ids[p].getFile() != null)
1953 if (!pdbloaded.containsKey(ids[p].getFile()))
1955 entry.setFile(loadPDBFile(jprovider, ids[p].getId()));
1959 entry.setFile(pdbloaded.get(ids[p].getId()).toString());
1963 al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
1967 } // end !multipleview
1969 // ///////////////////////////////
1970 // LOAD SEQUENCE MAPPINGS
1972 if (vamsasSet.getAlcodonFrameCount() > 0)
1974 // TODO Potentially this should only be done once for all views of an
1976 AlcodonFrame[] alc = vamsasSet.getAlcodonFrame();
1977 for (int i = 0; i < alc.length; i++)
1979 jalview.datamodel.AlignedCodonFrame cf = new jalview.datamodel.AlignedCodonFrame(
1980 alc[i].getAlcodonCount());
1981 if (alc[i].getAlcodonCount() > 0)
1983 Alcodon[] alcods = alc[i].getAlcodon();
1984 for (int p = 0; p < cf.codons.length; p++)
1986 if (alcods[p].hasPos1() && alcods[p].hasPos2()
1987 && alcods[p].hasPos3())
1989 // translated codons require three valid positions
1990 cf.codons[p] = new int[3];
1991 cf.codons[p][0] = (int) alcods[p].getPos1();
1992 cf.codons[p][1] = (int) alcods[p].getPos2();
1993 cf.codons[p][2] = (int) alcods[p].getPos3();
1997 cf.codons[p] = null;
2001 if (alc[i].getAlcodMapCount() > 0)
2003 AlcodMap[] maps = alc[i].getAlcodMap();
2004 for (int m = 0; m < maps.length; m++)
2006 SequenceI dnaseq = (SequenceI) seqRefIds
2007 .get(maps[m].getDnasq());
2009 jalview.datamodel.Mapping mapping = null;
2010 // attach to dna sequence reference.
2011 if (maps[m].getMapping() != null)
2013 mapping = addMapping(maps[m].getMapping());
2017 cf.addMap(dnaseq, mapping.getTo(), mapping.getMap());
2022 frefedSequence.add(new Object[]
2023 { maps[m].getDnasq(), cf, mapping });
2027 al.addCodonFrame(cf);
2032 // ////////////////////////////////
2034 boolean hideQuality = true, hideConservation = true, hideConsensus = true;
2036 * store any annotations which forward reference a group's ID
2038 Hashtable groupAnnotRefs = new Hashtable();
2040 if (vamsasSet.getAnnotationCount() > 0)
2042 Annotation[] an = vamsasSet.getAnnotation();
2044 for (int i = 0; i < an.length; i++)
2046 // set visibility for automatic annotation for this view
2047 if (an[i].getLabel().equals("Quality"))
2049 hideQuality = false;
2052 else if (an[i].getLabel().equals("Conservation"))
2054 hideConservation = false;
2057 else if (an[i].getLabel().equals("Consensus"))
2059 hideConsensus = false;
2062 // set visiblity for other annotation in this view
2063 if (an[i].getId() != null
2064 && annotationIds.containsKey(an[i].getId()))
2066 jalview.datamodel.AlignmentAnnotation jda = (jalview.datamodel.AlignmentAnnotation) annotationIds
2067 .get(an[i].getId());
2068 // in principle Visible should always be true for annotation displayed
2069 // in multiple views
2070 if (an[i].hasVisible())
2071 jda.visible = an[i].getVisible();
2073 al.addAnnotation(jda);
2077 // Construct new annotation from model.
2078 AnnotationElement[] ae = an[i].getAnnotationElement();
2079 jalview.datamodel.Annotation[] anot = null;
2081 if (!an[i].getScoreOnly())
2083 anot = new jalview.datamodel.Annotation[al.getWidth()];
2085 for (int aa = 0; aa < ae.length && aa < anot.length; aa++)
2087 if (ae[aa].getPosition() >= anot.length)
2090 anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(
2092 ae[aa].getDisplayCharacter(), ae[aa].getDescription(), (ae[aa]
2093 .getSecondaryStructure() == null || ae[aa]
2094 .getSecondaryStructure().length() == 0) ? ' ' : ae[aa]
2095 .getSecondaryStructure().charAt(0), ae[aa].getValue()
2098 // JBPNote: Consider verifying dataflow for IO of secondary
2099 // structure annotation read from Stockholm files
2100 // this was added to try to ensure that
2101 // if (anot[ae[aa].getPosition()].secondaryStructure>' ')
2103 // anot[ae[aa].getPosition()].displayCharacter = "";
2105 anot[ae[aa].getPosition()].colour = new java.awt.Color(ae[aa]
2109 jalview.datamodel.AlignmentAnnotation jaa = null;
2111 if (an[i].getGraph())
2113 jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
2114 an[i].getDescription(), anot, 0, 0, an[i].getGraphType());
2116 jaa.graphGroup = an[i].getGraphGroup();
2118 if (an[i].getThresholdLine() != null)
2120 jaa.setThreshold(new jalview.datamodel.GraphLine(an[i]
2121 .getThresholdLine().getValue(), an[i]
2122 .getThresholdLine().getLabel(), new java.awt.Color(
2123 an[i].getThresholdLine().getColour())));
2130 jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
2131 an[i].getDescription(), anot);
2133 // register new annotation
2134 if (an[i].getId() != null)
2136 annotationIds.put(an[i].getId(), jaa);
2137 jaa.annotationId = an[i].getId();
2139 // recover sequence association
2140 if (an[i].getSequenceRef() != null)
2142 if (al.findName(an[i].getSequenceRef()) != null)
2144 jaa.createSequenceMapping(al.findName(an[i].getSequenceRef()),
2146 al.findName(an[i].getSequenceRef()).addAlignmentAnnotation(jaa);
2149 // and make a note of any group association
2150 if (an[i].getGroupRef() != null && an[i].getGroupRef().length() > 0)
2152 groupAnnotRefs.put(an[i].getGroupRef(), jaa);
2155 if (an[i].hasScore())
2157 jaa.setScore(an[i].getScore());
2159 if (an[i].hasVisible())
2160 jaa.visible = an[i].getVisible();
2162 if (an[i].hasCentreColLabels())
2163 jaa.centreColLabels = an[i].getCentreColLabels();
2165 if (an[i].hasScaleColLabels())
2167 jaa.scaleColLabel = an[i].getScaleColLabels();
2169 if (an[i].hasAutoCalculated() && an[i].isAutoCalculated())
2171 // newer files have an 'autoCalculated' flag and store calculation
2172 // state in viewport properties
2173 jaa.autoCalculated = true; // means annotation will be marked for
2174 // update at end of load.
2176 al.addAnnotation(jaa);
2180 // ///////////////////////
2182 // Create alignment markup and styles for this view
2183 if (jms.getJGroupCount() > 0)
2185 JGroup[] groups = jms.getJGroup();
2187 for (int i = 0; i < groups.length; i++)
2189 ColourSchemeI cs = null;
2191 if (groups[i].getColour() != null)
2193 if (groups[i].getColour().startsWith("ucs"))
2195 cs = GetUserColourScheme(jms, groups[i].getColour());
2199 cs = ColourSchemeProperty.getColour(al, groups[i].getColour());
2204 cs.setThreshold(groups[i].getPidThreshold(), true);
2208 Vector seqs = new Vector();
2210 for (int s = 0; s < groups[i].getSeqCount(); s++)
2212 String seqId = groups[i].getSeq(s) + "";
2213 jalview.datamodel.SequenceI ts = (jalview.datamodel.SequenceI) seqRefIds
2218 seqs.addElement(ts);
2222 if (seqs.size() < 1)
2227 jalview.datamodel.SequenceGroup sg = new jalview.datamodel.SequenceGroup(
2228 seqs, groups[i].getName(), cs, groups[i].getDisplayBoxes(),
2229 groups[i].getDisplayText(), groups[i].getColourText(),
2230 groups[i].getStart(), groups[i].getEnd());
2233 .setOutlineColour(new java.awt.Color(groups[i]
2234 .getOutlineColour()));
2236 sg.textColour = new java.awt.Color(groups[i].getTextCol1());
2237 sg.textColour2 = new java.awt.Color(groups[i].getTextCol2());
2238 sg.setShowNonconserved(groups[i].hasShowUnconserved() ? groups[i]
2239 .isShowUnconserved() : false);
2240 sg.thresholdTextColour = groups[i].getTextColThreshold();
2241 if (groups[i].hasShowConsensusHistogram())
2244 .setShowConsensusHistogram(groups[i]
2245 .isShowConsensusHistogram());
2248 if (groups[i].hasShowSequenceLogo())
2250 sg.setshowSequenceLogo(groups[i].isShowSequenceLogo());
2252 if (groups[i].hasIgnoreGapsinConsensus())
2254 sg.setIgnoreGapsConsensus(groups[i].getIgnoreGapsinConsensus());
2256 if (groups[i].getConsThreshold() != 0)
2258 jalview.analysis.Conservation c = new jalview.analysis.Conservation(
2259 "All", ResidueProperties.propHash, 3, sg
2260 .getSequences(null), 0, sg.getWidth() - 1);
2262 c.verdict(false, 25);
2263 sg.cs.setConservation(c);
2266 if (groups[i].getId() != null && groupAnnotRefs.size() > 0)
2268 // re-instate unique group/annotation row reference
2269 jalview.datamodel.AlignmentAnnotation jaa = (jalview.datamodel.AlignmentAnnotation) groupAnnotRefs
2270 .get(groups[i].getId());
2281 // ///////////////////////////////
2284 // If we just load in the same jar file again, the sequenceSetId
2285 // will be the same, and we end up with multiple references
2286 // to the same sequenceSet. We must modify this id on load
2287 // so that each load of the file gives a unique id
2288 String uniqueSeqSetId = view.getSequenceSetId() + uniqueSetSuffix;
2289 String viewId = (view.getId() == null ? null : view.getId()
2291 AlignFrame af = null;
2292 AlignViewport av = null;
2293 // now check to see if we really need to create a new viewport.
2294 if (multipleView && viewportsAdded.size() == 0)
2296 // We recovered an alignment for which a viewport already exists.
2297 // TODO: fix up any settings necessary for overlaying stored state onto
2298 // state recovered from another document. (may not be necessary).
2299 // we may need a binding from a viewport in memory to one recovered from
2301 // and then recover its containing af to allow the settings to be applied.
2302 // TODO: fix for vamsas demo
2304 .println("About to recover a viewport for existing alignment: Sequence set ID is "
2306 Object seqsetobj = retrieveExistingObj(uniqueSeqSetId);
2307 if (seqsetobj != null)
2309 if (seqsetobj instanceof String)
2311 uniqueSeqSetId = (String) seqsetobj;
2313 .println("Recovered extant sequence set ID mapping for ID : New Sequence set ID is "
2319 .println("Warning : Collision between sequence set ID string and existing jalview object mapping.");
2324 AlignmentPanel ap = null;
2325 boolean isnewview = true;
2328 // Check to see if this alignment already has a view id == viewId
2329 jalview.gui.AlignmentPanel views[] = Desktop
2330 .getAlignmentPanels(uniqueSeqSetId);
2331 if (views != null && views.length > 0)
2333 for (int v = 0; v < views.length; v++)
2335 if (views[v].av.getViewId().equalsIgnoreCase(viewId))
2337 // recover the existing alignpanel, alignframe, viewport
2338 af = views[v].alignFrame;
2341 // TODO: could even skip resetting view settings if we don't want to
2342 // change the local settings from other jalview processes
2351 af = loadViewport(file, JSEQ, hiddenSeqs, al, hideConsensus,
2352 hideQuality, hideConservation, jms, view, uniqueSeqSetId,
2358 // /////////////////////////////////////
2359 if (loadTreesAndStructures && jms.getTreeCount() > 0)
2363 for (int t = 0; t < jms.getTreeCount(); t++)
2366 Tree tree = jms.getTree(t);
2368 TreePanel tp = (TreePanel) retrieveExistingObj(tree.getId());
2371 tp = af.ShowNewickTree(new jalview.io.NewickFile(tree
2372 .getNewick()), tree.getTitle(), tree.getWidth(), tree
2373 .getHeight(), tree.getXpos(), tree.getYpos());
2374 if (tree.getId() != null)
2376 // perhaps bind the tree id to something ?
2381 // update local tree attributes ?
2382 // TODO: should check if tp has been manipulated by user - if so its
2383 // settings shouldn't be modified
2384 tp.setTitle(tree.getTitle());
2385 tp.setBounds(new Rectangle(tree.getXpos(), tree.getYpos(), tree
2386 .getWidth(), tree.getHeight()));
2387 tp.av = av; // af.viewport; // TODO: verify 'associate with all
2390 tp.treeCanvas.av = av; // af.viewport;
2391 tp.treeCanvas.ap = ap; // af.alignPanel;
2396 warn("There was a problem recovering stored Newick tree: \n"
2397 + tree.getNewick());
2401 tp.fitToWindow.setState(tree.getFitToWindow());
2402 tp.fitToWindow_actionPerformed(null);
2404 if (tree.getFontName() != null)
2406 tp.setTreeFont(new java.awt.Font(tree.getFontName(), tree
2407 .getFontStyle(), tree.getFontSize()));
2411 tp.setTreeFont(new java.awt.Font(view.getFontName(), view
2412 .getFontStyle(), tree.getFontSize()));
2415 tp.showPlaceholders(tree.getMarkUnlinked());
2416 tp.showBootstrap(tree.getShowBootstrap());
2417 tp.showDistances(tree.getShowDistances());
2419 tp.treeCanvas.threshold = tree.getThreshold();
2421 if (tree.getCurrentTree())
2423 af.viewport.setCurrentTree(tp.getTree());
2427 } catch (Exception ex)
2429 ex.printStackTrace();
2433 // //LOAD STRUCTURES
2434 if (loadTreesAndStructures)
2436 for (int i = 0; i < JSEQ.length; i++)
2438 if (JSEQ[i].getPdbidsCount() > 0)
2440 Pdbids[] ids = JSEQ[i].getPdbids();
2441 for (int p = 0; p < ids.length; p++)
2443 for (int s = 0; s < ids[p].getStructureStateCount(); s++)
2445 // check to see if we haven't already created this structure view
2446 String sviewid = (ids[p].getStructureState(s).getViewId() == null) ? null
2447 : ids[p].getStructureState(s).getViewId()
2449 jalview.datamodel.PDBEntry jpdb = new jalview.datamodel.PDBEntry();
2450 // Originally : ids[p].getFile()
2451 // : TODO: verify external PDB file recovery still works in normal
2452 // jalview project load
2453 jpdb.setFile(loadPDBFile(jprovider, ids[p].getId()));
2454 jpdb.setId(ids[p].getId());
2456 int x = ids[p].getStructureState(s).getXpos();
2457 int y = ids[p].getStructureState(s).getYpos();
2458 int width = ids[p].getStructureState(s).getWidth();
2459 int height = ids[p].getStructureState(s).getHeight();
2460 AppJmol comp = null;
2461 JInternalFrame[] frames = null;
2466 frames = Desktop.desktop.getAllFrames();
2467 } catch (ArrayIndexOutOfBoundsException e)
2469 // occasional No such child exceptions are thrown here...
2474 } catch (Exception f)
2479 } while (frames == null);
2480 // search for any Jmol windows already open from other
2481 // alignment views that exactly match the stored structure state
2482 for (int f = 0; comp == null && f < frames.length; f++)
2484 if (frames[f] instanceof AppJmol)
2487 && ((AppJmol) frames[f]).getViewId().equals(
2490 // post jalview 2.4 schema includes structure view id
2491 comp = (AppJmol) frames[f];
2493 else if (frames[f].getX() == x && frames[f].getY() == y
2494 && frames[f].getHeight() == height
2495 && frames[f].getWidth() == width)
2497 comp = (AppJmol) frames[f];
2501 // Probably don't need to do this anymore...
2502 // Desktop.desktop.getComponentAt(x, y);
2503 // TODO: NOW: check that this recovers the PDB file correctly.
2504 String pdbFile = loadPDBFile(jprovider, ids[p].getId());
2506 jalview.datamodel.SequenceI[] seq = new jalview.datamodel.SequenceI[]
2507 { (jalview.datamodel.SequenceI) seqRefIds.get(JSEQ[i].getId()
2512 // create a new Jmol window
2513 String state = ids[p].getStructureState(s).getContent();
2514 StringBuffer newFileLoc = null;
2516 if ((cp=state.indexOf("load ")) > -1)
2518 newFileLoc = new StringBuffer(state.substring(0, (cp=state
2519 .indexOf("\"", cp+1)+1)));
2521 newFileLoc.append(jpdb.getFile());
2522 newFileLoc.append(state.substring(state.indexOf("\"",
2528 .println("Ignoring incomplete Jmol state for PDB "
2531 newFileLoc = new StringBuffer(state);
2532 newFileLoc.append("; load \"");
2533 newFileLoc.append(jpdb.getFile());
2534 newFileLoc.append("\";");
2537 if (newFileLoc != null)
2539 int histbug = newFileLoc.indexOf("history = ");
2541 int diff = histbug==-1 ? -1 : newFileLoc.indexOf(";",histbug);
2542 String val = (diff==-1) ? null : newFileLoc.substring(histbug,diff);
2543 if (val!=null && val.length()>=4)
2545 if (val.contains("e")) {
2546 if (val.trim().equals("true")) {
2551 newFileLoc.replace(histbug, diff, val);
2554 final String pdbf=pdbFile, id=ids[p].getId(), fileloc=newFileLoc.toString(),vid=sviewid;
2555 final SequenceI[] sq=seq;
2556 final AlignFrame alf = af;
2557 final java.awt.Rectangle rect = new java.awt.Rectangle(x,
2560 javax.swing.SwingUtilities.invokeAndWait(new Runnable() {
2562 new AppJmol(pdbf, id, sq, alf.alignPanel,
2563 fileloc, rect, vid);
2567 catch (InvocationTargetException ex)
2569 System.err.println("Unexpected error when opening Jmol view.");
2570 ex.printStackTrace();
2571 } catch (InterruptedException e)
2573 // e.printStackTrace();
2579 // if (comp != null)
2581 // NOTE: if the jalview project is part of a shared session then
2582 // view synchronization should/could be done here.
2584 // add mapping for this sequence to the already open Jmol
2585 // instance (if it doesn't already exist)
2587 StructureSelectionManager.getStructureSelectionManager()
2588 .setMapping(seq, null, pdbFile,
2589 jalview.io.AppletFormatAdapter.FILE);
2591 ((AppJmol) comp).jmb.addSequence(seq);
2602 AlignFrame loadViewport(String file, JSeq[] JSEQ, Vector hiddenSeqs,
2603 Alignment al, boolean hideConsensus, boolean hideQuality,
2604 boolean hideConservation, JalviewModelSequence jms,
2605 Viewport view, String uniqueSeqSetId, String viewId)
2607 AlignFrame af = null;
2608 af = new AlignFrame(al, view.getWidth(), view.getHeight(),
2609 uniqueSeqSetId, viewId);
2611 af.setFileName(file, "Jalview");
2613 for (int i = 0; i < JSEQ.length; i++)
2615 af.viewport.setSequenceColour(af.viewport.alignment.getSequenceAt(i),
2616 new java.awt.Color(JSEQ[i].getColour()));
2619 af.viewport.gatherViewsHere = view.getGatheredViews();
2621 if (view.getSequenceSetId() != null)
2623 jalview.gui.AlignViewport av = (jalview.gui.AlignViewport) viewportsAdded
2624 .get(uniqueSeqSetId);
2626 af.viewport.sequenceSetID = uniqueSeqSetId;
2629 // propagate shared settings to this new view
2630 af.viewport.historyList = av.historyList;
2631 af.viewport.redoList = av.redoList;
2635 viewportsAdded.put(uniqueSeqSetId, af.viewport);
2637 // TODO: check if this method can be called repeatedly without
2638 // side-effects if alignpanel already registered.
2639 PaintRefresher.Register(af.alignPanel, uniqueSeqSetId);
2641 // apply Hidden regions to view.
2642 if (hiddenSeqs != null)
2644 for (int s = 0; s < JSEQ.length; s++)
2646 jalview.datamodel.SequenceGroup hidden = new jalview.datamodel.SequenceGroup();
2648 for (int r = 0; r < JSEQ[s].getHiddenSequencesCount(); r++)
2650 hidden.addSequence(al
2651 .getSequenceAt(JSEQ[s].getHiddenSequences(r)), false);
2653 af.viewport.hideRepSequences(al.getSequenceAt(s), hidden);
2656 jalview.datamodel.SequenceI[] hseqs = new jalview.datamodel.SequenceI[hiddenSeqs
2659 for (int s = 0; s < hiddenSeqs.size(); s++)
2661 hseqs[s] = (jalview.datamodel.SequenceI) hiddenSeqs.elementAt(s);
2664 af.viewport.hideSequence(hseqs);
2667 // set visibility of annotation in view
2668 if ((hideConsensus || hideQuality || hideConservation)
2669 && al.getAlignmentAnnotation() != null)
2671 int hSize = al.getAlignmentAnnotation().length;
2672 for (int h = 0; h < hSize; h++)
2674 if ((hideConsensus && al.getAlignmentAnnotation()[h].label
2675 .equals("Consensus"))
2676 || (hideQuality && al.getAlignmentAnnotation()[h].label
2678 || (hideConservation && al.getAlignmentAnnotation()[h].label
2679 .equals("Conservation")))
2681 al.deleteAnnotation(al.getAlignmentAnnotation()[h]);
2686 af.alignPanel.adjustAnnotationHeight();
2688 // recover view properties and display parameters
2689 if (view.getViewName() != null)
2691 af.viewport.viewName = view.getViewName();
2692 af.setInitialTabVisible();
2694 af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(), view
2697 af.viewport.setShowAnnotation(view.getShowAnnotation());
2698 af.viewport.setAbovePIDThreshold(view.getPidSelected());
2700 af.viewport.setColourText(view.getShowColourText());
2702 af.viewport.setConservationSelected(view.getConservationSelected());
2703 af.viewport.setShowJVSuffix(view.getShowFullId());
2704 af.viewport.rightAlignIds = view.getRightAlignIds();
2705 af.viewport.setFont(new java.awt.Font(view.getFontName(), view
2706 .getFontStyle(), view.getFontSize()));
2707 af.alignPanel.fontChanged();
2708 af.viewport.setRenderGaps(view.getRenderGaps());
2709 af.viewport.setWrapAlignment(view.getWrapAlignment());
2710 af.alignPanel.setWrapAlignment(view.getWrapAlignment());
2711 af.viewport.setShowAnnotation(view.getShowAnnotation());
2712 af.alignPanel.setAnnotationVisible(view.getShowAnnotation());
2714 af.viewport.setShowBoxes(view.getShowBoxes());
2716 af.viewport.setShowText(view.getShowText());
2718 af.viewport.textColour = new java.awt.Color(view.getTextCol1());
2719 af.viewport.textColour2 = new java.awt.Color(view.getTextCol2());
2720 af.viewport.thresholdTextColour = view.getTextColThreshold();
2721 af.viewport.setShowUnconserved(view.hasShowUnconserved() ? view
2722 .isShowUnconserved() : false);
2723 af.viewport.setStartRes(view.getStartRes());
2724 af.viewport.setStartSeq(view.getStartSeq());
2726 ColourSchemeI cs = null;
2727 // apply colourschemes
2728 if (view.getBgColour() != null)
2730 if (view.getBgColour().startsWith("ucs"))
2732 cs = GetUserColourScheme(jms, view.getBgColour());
2734 else if (view.getBgColour().startsWith("Annotation"))
2736 // int find annotation
2737 if (af.viewport.alignment.getAlignmentAnnotation() != null)
2739 for (int i = 0; i < af.viewport.alignment
2740 .getAlignmentAnnotation().length; i++)
2742 if (af.viewport.alignment.getAlignmentAnnotation()[i].label
2743 .equals(view.getAnnotationColours().getAnnotation()))
2745 if (af.viewport.alignment.getAlignmentAnnotation()[i]
2746 .getThreshold() == null)
2748 af.viewport.alignment.getAlignmentAnnotation()[i]
2749 .setThreshold(new jalview.datamodel.GraphLine(view
2750 .getAnnotationColours().getThreshold(),
2751 "Threshold", java.awt.Color.black)
2756 if (view.getAnnotationColours().getColourScheme().equals(
2759 cs = new AnnotationColourGradient(af.viewport.alignment
2760 .getAlignmentAnnotation()[i], new java.awt.Color(
2761 view.getAnnotationColours().getMinColour()),
2762 new java.awt.Color(view.getAnnotationColours()
2763 .getMaxColour()), view
2764 .getAnnotationColours().getAboveThreshold());
2766 else if (view.getAnnotationColours().getColourScheme()
2769 cs = new AnnotationColourGradient(af.viewport.alignment
2770 .getAlignmentAnnotation()[i],
2771 GetUserColourScheme(jms, view
2772 .getAnnotationColours().getColourScheme()),
2773 view.getAnnotationColours().getAboveThreshold());
2777 cs = new AnnotationColourGradient(af.viewport.alignment
2778 .getAlignmentAnnotation()[i], ColourSchemeProperty
2779 .getColour(al, view.getAnnotationColours()
2780 .getColourScheme()), view
2781 .getAnnotationColours().getAboveThreshold());
2784 // Also use these settings for all the groups
2785 if (al.getGroups() != null)
2787 for (int g = 0; g < al.getGroups().size(); g++)
2789 jalview.datamodel.SequenceGroup sg = (jalview.datamodel.SequenceGroup) al
2790 .getGroups().elementAt(g);
2799 * (view.getAnnotationColours().getColourScheme().equals("None"
2800 * )) { sg.cs = new AnnotationColourGradient(
2801 * af.viewport.alignment.getAlignmentAnnotation()[i], new
2802 * java.awt.Color(view.getAnnotationColours().
2803 * getMinColour()), new
2804 * java.awt.Color(view.getAnnotationColours().
2806 * view.getAnnotationColours().getAboveThreshold()); } else
2809 sg.cs = new AnnotationColourGradient(
2810 af.viewport.alignment.getAlignmentAnnotation()[i],
2811 sg.cs, view.getAnnotationColours()
2812 .getAboveThreshold());
2826 cs = ColourSchemeProperty.getColour(al, view.getBgColour());
2831 cs.setThreshold(view.getPidThreshold(), true);
2832 cs.setConsensus(af.viewport.hconsensus);
2836 af.viewport.setGlobalColourScheme(cs);
2837 af.viewport.setColourAppliesToAllGroups(false);
2839 if (view.getConservationSelected() && cs != null)
2841 cs.setConservationInc(view.getConsThreshold());
2844 af.changeColour(cs);
2846 af.viewport.setColourAppliesToAllGroups(true);
2848 if (view.getShowSequenceFeatures())
2850 af.viewport.showSequenceFeatures = true;
2852 if (view.hasCentreColumnLabels())
2854 af.viewport.setCentreColumnLabels(view.getCentreColumnLabels());
2856 if (view.hasIgnoreGapsinConsensus())
2858 af.viewport.ignoreGapsInConsensusCalculation = view
2859 .getIgnoreGapsinConsensus();
2861 if (view.hasFollowHighlight())
2863 af.viewport.followHighlight = view.getFollowHighlight();
2865 if (view.hasFollowSelection())
2867 af.viewport.followSelection = view.getFollowSelection();
2869 if (view.hasShowConsensusHistogram())
2871 af.viewport.setShowConsensusHistogram(view
2872 .getShowConsensusHistogram());
2876 af.viewport.setShowConsensusHistogram(true);
2878 if (view.hasShowSequenceLogo())
2880 af.viewport.showSequenceLogo = view.getShowSequenceLogo();
2884 af.viewport.showSequenceLogo = false;
2886 if (view.hasShowDbRefTooltip())
2888 af.viewport.setShowDbRefs(view.getShowDbRefTooltip());
2890 if (view.hasShowNPfeatureTooltip())
2892 af.viewport.setShowNpFeats(view.hasShowNPfeatureTooltip());
2894 if (view.hasShowGroupConsensus())
2896 af.viewport.setShowGroupConsensus(view.getShowGroupConsensus());
2900 af.viewport.setShowGroupConsensus(false);
2902 if (view.hasShowGroupConservation())
2904 af.viewport.setShowGroupConservation(view.getShowGroupConservation());
2908 af.viewport.setShowGroupConservation(false);
2911 // recover featre settings
2912 if (jms.getFeatureSettings() != null)
2914 af.viewport.featuresDisplayed = new Hashtable();
2915 String[] renderOrder = new String[jms.getFeatureSettings()
2916 .getSettingCount()];
2917 for (int fs = 0; fs < jms.getFeatureSettings().getSettingCount(); fs++)
2919 Setting setting = jms.getFeatureSettings().getSetting(fs);
2920 if (setting.hasMincolour())
2922 GraduatedColor gc = setting.hasMin() ? new GraduatedColor(
2923 new java.awt.Color(setting.getMincolour()),
2924 new java.awt.Color(setting.getColour()),
2925 setting.getMin(), setting.getMax()) : new GraduatedColor(
2926 new java.awt.Color(setting.getMincolour()),
2927 new java.awt.Color(setting.getColour()), 0, 1);
2928 if (setting.hasThreshold())
2930 gc.setThresh(setting.getThreshold());
2931 gc.setThreshType(setting.getThreshstate());
2933 gc.setAutoScaled(true); // default
2934 if (setting.hasAutoScale())
2936 gc.setAutoScaled(setting.getAutoScale());
2938 if (setting.hasColourByLabel())
2940 gc.setColourByLabel(setting.getColourByLabel());
2942 // and put in the feature colour table.
2943 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(
2944 setting.getType(), gc);
2948 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(
2950 new java.awt.Color(setting.getColour()));
2952 renderOrder[fs] = setting.getType();
2953 if (setting.hasOrder())
2954 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setOrder(
2955 setting.getType(), setting.getOrder());
2957 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setOrder(
2959 fs / jms.getFeatureSettings().getSettingCount());
2960 if (setting.getDisplay())
2962 af.viewport.featuresDisplayed.put(setting.getType(), new Integer(
2963 setting.getColour()));
2966 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder = renderOrder;
2968 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureGroups = fgtable = new Hashtable();
2969 for (int gs = 0; gs < jms.getFeatureSettings().getGroupCount(); gs++)
2971 Group grp = jms.getFeatureSettings().getGroup(gs);
2972 fgtable.put(grp.getName(), new Boolean(grp.getDisplay()));
2976 if (view.getHiddenColumnsCount() > 0)
2978 for (int c = 0; c < view.getHiddenColumnsCount(); c++)
2980 af.viewport.hideColumns(view.getHiddenColumns(c).getStart(), view
2981 .getHiddenColumns(c).getEnd() // +1
2986 af.setMenusFromViewport(af.viewport);
2987 // TODO: we don't need to do this if the viewport is aready visible.
2988 Desktop.addInternalFrame(af, view.getTitle(), view.getWidth(), view
2990 af.alignPanel.updateAnnotation(false); // recompute any autoannotation
2994 Hashtable skipList = null;
2997 * TODO remove this method
3000 * @return AlignFrame bound to sequenceSetId from view, if one exists. private
3001 * AlignFrame getSkippedFrame(Viewport view) { if (skipList==null) {
3002 * throw new Error("Implementation Error. No skipList defined for this
3003 * Jalview2XML instance."); } return (AlignFrame)
3004 * skipList.get(view.getSequenceSetId()); }
3008 * Check if the Jalview view contained in object should be skipped or not.
3011 * @return true if view's sequenceSetId is a key in skipList
3013 private boolean skipViewport(JalviewModel object)
3015 if (skipList == null)
3020 if (skipList.containsKey(id = object.getJalviewModelSequence()
3021 .getViewport()[0].getSequenceSetId()))
3023 if (Cache.log != null && Cache.log.isDebugEnabled())
3025 Cache.log.debug("Skipping seuqence set id " + id);
3032 public void AddToSkipList(AlignFrame af)
3034 if (skipList == null)
3036 skipList = new Hashtable();
3038 skipList.put(af.getViewport().getSequenceSetId(), af);
3041 public void clearSkipList()
3043 if (skipList != null)
3050 private void recoverDatasetFor(SequenceSet vamsasSet, Alignment al)
3052 jalview.datamodel.Alignment ds = getDatasetFor(vamsasSet.getDatasetId());
3053 Vector dseqs = null;
3056 // create a list of new dataset sequences
3057 dseqs = new Vector();
3059 for (int i = 0, iSize = vamsasSet.getSequenceCount(); i < iSize; i++)
3061 Sequence vamsasSeq = vamsasSet.getSequence(i);
3062 ensureJalviewDatasetSequence(vamsasSeq, ds, dseqs);
3064 // create a new dataset
3067 SequenceI[] dsseqs = new SequenceI[dseqs.size()];
3068 dseqs.copyInto(dsseqs);
3069 ds = new jalview.datamodel.Alignment(dsseqs);
3070 debug("Created new dataset " + vamsasSet.getDatasetId()
3071 + " for alignment " + System.identityHashCode(al));
3072 addDatasetRef(vamsasSet.getDatasetId(), ds);
3074 // set the dataset for the newly imported alignment.
3075 if (al.getDataset() == null)
3084 * sequence definition to create/merge dataset sequence for
3088 * vector to add new dataset sequence to
3090 private void ensureJalviewDatasetSequence(Sequence vamsasSeq,
3091 AlignmentI ds, Vector dseqs)
3093 // JBP TODO: Check this is called for AlCodonFrames to support recovery of
3095 jalview.datamodel.Sequence sq = (jalview.datamodel.Sequence) seqRefIds
3096 .get(vamsasSeq.getId());
3097 jalview.datamodel.SequenceI dsq = null;
3098 if (sq != null && sq.getDatasetSequence() != null)
3100 dsq = (jalview.datamodel.SequenceI) sq.getDatasetSequence();
3103 String sqid = vamsasSeq.getDsseqid();
3106 // need to create or add a new dataset sequence reference to this sequence
3109 dsq = (jalview.datamodel.SequenceI) seqRefIds.get(sqid);
3114 // make a new dataset sequence
3115 dsq = sq.createDatasetSequence();
3118 // make up a new dataset reference for this sequence
3119 sqid = seqHash(dsq);
3121 dsq.setVamsasId(uniqueSetSuffix + sqid);
3122 seqRefIds.put(sqid, dsq);
3127 dseqs.addElement(dsq);
3132 ds.addSequence(dsq);
3138 { // make this dataset sequence sq's dataset sequence
3139 sq.setDatasetSequence(dsq);
3143 // TODO: refactor this as a merge dataset sequence function
3144 // now check that sq (the dataset sequence) sequence really is the union of
3145 // all references to it
3146 // boolean pre = sq.getStart() < dsq.getStart();
3147 // boolean post = sq.getEnd() > dsq.getEnd();
3151 StringBuffer sb = new StringBuffer();
3152 String newres = jalview.analysis.AlignSeq.extractGaps(
3153 jalview.util.Comparison.GapChars, sq.getSequenceAsString());
3154 if (!newres.equalsIgnoreCase(dsq.getSequenceAsString())
3155 && newres.length() > dsq.getLength())
3157 // Update with the longer sequence.
3161 * if (pre) { sb.insert(0, newres .substring(0, dsq.getStart() -
3162 * sq.getStart())); dsq.setStart(sq.getStart()); } if (post) {
3163 * sb.append(newres.substring(newres.length() - sq.getEnd() -
3164 * dsq.getEnd())); dsq.setEnd(sq.getEnd()); }
3166 dsq.setSequence(sb.toString());
3168 // TODO: merges will never happen if we 'know' we have the real dataset
3169 // sequence - this should be detected when id==dssid
3170 System.err.println("DEBUG Notice: Merged dataset sequence"); // ("
3171 // + (pre ? "prepended" : "") + " "
3172 // + (post ? "appended" : ""));
3177 java.util.Hashtable datasetIds = null;
3179 java.util.IdentityHashMap dataset2Ids = null;
3181 private Alignment getDatasetFor(String datasetId)
3183 if (datasetIds == null)
3185 datasetIds = new Hashtable();
3188 if (datasetIds.containsKey(datasetId))
3190 return (Alignment) datasetIds.get(datasetId);
3195 private void addDatasetRef(String datasetId, Alignment dataset)
3197 if (datasetIds == null)
3199 datasetIds = new Hashtable();
3201 datasetIds.put(datasetId, dataset);
3205 * make a new dataset ID for this jalview dataset alignment
3210 private String getDatasetIdRef(jalview.datamodel.Alignment dataset)
3212 if (dataset.getDataset() != null)
3214 warn("Serious issue! Dataset Object passed to getDatasetIdRef is not a Jalview DATASET alignment...");
3216 String datasetId = makeHashCode(dataset, null);
3217 if (datasetId == null)
3219 // make a new datasetId and record it
3220 if (dataset2Ids == null)
3222 dataset2Ids = new IdentityHashMap();
3226 datasetId = (String) dataset2Ids.get(dataset);
3228 if (datasetId == null)
3230 datasetId = "ds" + dataset2Ids.size() + 1;
3231 dataset2Ids.put(dataset, datasetId);
3237 private void addDBRefs(SequenceI datasetSequence, Sequence sequence)
3239 for (int d = 0; d < sequence.getDBRefCount(); d++)
3241 DBRef dr = sequence.getDBRef(d);
3242 jalview.datamodel.DBRefEntry entry = new jalview.datamodel.DBRefEntry(
3243 sequence.getDBRef(d).getSource(), sequence.getDBRef(d)
3244 .getVersion(), sequence.getDBRef(d).getAccessionId());
3245 if (dr.getMapping() != null)
3247 entry.setMap(addMapping(dr.getMapping()));
3249 datasetSequence.addDBRef(entry);
3253 private jalview.datamodel.Mapping addMapping(Mapping m)
3255 SequenceI dsto = null;
3256 // Mapping m = dr.getMapping();
3257 int fr[] = new int[m.getMapListFromCount() * 2];
3258 Enumeration f = m.enumerateMapListFrom();
3259 for (int _i = 0; f.hasMoreElements(); _i += 2)
3261 MapListFrom mf = (MapListFrom) f.nextElement();
3262 fr[_i] = mf.getStart();
3263 fr[_i + 1] = mf.getEnd();
3265 int fto[] = new int[m.getMapListToCount() * 2];
3266 f = m.enumerateMapListTo();
3267 for (int _i = 0; f.hasMoreElements(); _i += 2)
3269 MapListTo mf = (MapListTo) f.nextElement();
3270 fto[_i] = mf.getStart();
3271 fto[_i + 1] = mf.getEnd();
3273 jalview.datamodel.Mapping jmap = new jalview.datamodel.Mapping(dsto,
3274 fr, fto, (int) m.getMapFromUnit(), (int) m.getMapToUnit());
3275 if (m.getMappingChoice() != null)
3277 MappingChoice mc = m.getMappingChoice();
3278 if (mc.getDseqFor() != null)
3280 String dsfor = "" + mc.getDseqFor();
3281 if (seqRefIds.containsKey(dsfor))
3286 jmap.setTo((SequenceI) seqRefIds.get(dsfor));
3290 frefedSequence.add(new Object[]
3297 * local sequence definition
3299 Sequence ms = mc.getSequence();
3300 jalview.datamodel.Sequence djs = null;
3301 String sqid = ms.getDsseqid();
3302 if (sqid != null && sqid.length() > 0)
3305 * recover dataset sequence
3307 djs = (jalview.datamodel.Sequence) seqRefIds.get(sqid);
3312 .println("Warning - making up dataset sequence id for DbRef sequence map reference");
3313 sqid = ((Object) ms).toString(); // make up a new hascode for
3314 // undefined dataset sequence hash
3315 // (unlikely to happen)
3321 * make a new dataset sequence and add it to refIds hash
3323 djs = new jalview.datamodel.Sequence(ms.getName(), ms
3325 djs.setStart(jmap.getMap().getToLowest());
3326 djs.setEnd(jmap.getMap().getToHighest());
3327 djs.setVamsasId(uniqueSetSuffix + sqid);
3329 seqRefIds.put(sqid, djs);
3332 jalview.bin.Cache.log.debug("about to recurse on addDBRefs.");
3341 public jalview.gui.AlignmentPanel copyAlignPanel(AlignmentPanel ap,
3342 boolean keepSeqRefs)
3345 jalview.schemabinding.version2.JalviewModel jm = SaveState(ap, null,
3351 jm.getJalviewModelSequence().getViewport(0).setSequenceSetId(null);
3355 uniqueSetSuffix = "";
3356 jm.getJalviewModelSequence().getViewport(0).setId(null); // we don't
3361 if (this.frefedSequence == null)
3363 frefedSequence = new Vector();
3366 viewportsAdded = new Hashtable();
3368 AlignFrame af = LoadFromObject(jm, null, false, null);
3369 af.alignPanels.clear();
3370 af.closeMenuItem_actionPerformed(true);
3373 * if(ap.av.alignment.getAlignmentAnnotation()!=null) { for(int i=0;
3374 * i<ap.av.alignment.getAlignmentAnnotation().length; i++) {
3375 * if(!ap.av.alignment.getAlignmentAnnotation()[i].autoCalculated) {
3376 * af.alignPanel.av.alignment.getAlignmentAnnotation()[i] =
3377 * ap.av.alignment.getAlignmentAnnotation()[i]; } } }
3380 return af.alignPanel;
3384 * flag indicating if hashtables should be cleared on finalization TODO this
3385 * flag may not be necessary
3387 private boolean _cleartables = true;
3389 private Hashtable jvids2vobj;
3394 * @see java.lang.Object#finalize()
3396 protected void finalize() throws Throwable
3398 // really make sure we have no buried refs left.
3403 this.seqRefIds = null;
3404 this.seqsToIds = null;
3408 private void warn(String msg)
3413 private void warn(String msg, Exception e)
3415 if (Cache.log != null)
3419 Cache.log.warn(msg, e);
3423 Cache.log.warn(msg);
3428 System.err.println("Warning: " + msg);
3431 e.printStackTrace();
3436 private void debug(String string)
3438 debug(string, null);
3441 private void debug(String msg, Exception e)
3443 if (Cache.log != null)
3447 Cache.log.debug(msg, e);
3451 Cache.log.debug(msg);
3456 System.err.println("Warning: " + msg);
3459 e.printStackTrace();
3465 * set the object to ID mapping tables used to write/recover objects and XML
3466 * ID strings for the jalview project. If external tables are provided then
3467 * finalize and clearSeqRefs will not clear the tables when the Jalview2XML
3468 * object goes out of scope. - also populates the datasetIds hashtable with
3469 * alignment objects containing dataset sequences
3472 * Map from ID strings to jalview datamodel
3474 * Map from jalview datamodel to ID strings
3478 public void setObjectMappingTables(Hashtable vobj2jv,
3479 IdentityHashMap jv2vobj)
3481 this.jv2vobj = jv2vobj;
3482 this.vobj2jv = vobj2jv;
3483 Iterator ds = jv2vobj.keySet().iterator();
3485 while (ds.hasNext())
3487 Object jvobj = ds.next();
3488 id = jv2vobj.get(jvobj).toString();
3489 if (jvobj instanceof jalview.datamodel.Alignment)
3491 if (((jalview.datamodel.Alignment) jvobj).getDataset() == null)
3493 addDatasetRef(id, (jalview.datamodel.Alignment) jvobj);
3496 else if (jvobj instanceof jalview.datamodel.Sequence)
3498 // register sequence object so the XML parser can recover it.
3499 if (seqRefIds == null)
3501 seqRefIds = new Hashtable();
3503 if (seqsToIds == null)
3505 seqsToIds = new IdentityHashMap();
3507 seqRefIds.put(jv2vobj.get(jvobj).toString(), jvobj);
3508 seqsToIds.put(jvobj, id);
3510 else if (jvobj instanceof jalview.datamodel.AlignmentAnnotation)
3512 if (annotationIds == null)
3514 annotationIds = new Hashtable();
3517 annotationIds.put(anid = jv2vobj.get(jvobj).toString(), jvobj);
3518 jalview.datamodel.AlignmentAnnotation jvann = (jalview.datamodel.AlignmentAnnotation) jvobj;
3519 if (jvann.annotationId == null)
3521 jvann.annotationId = anid;
3523 if (!jvann.annotationId.equals(anid))
3525 // TODO verify that this is the correct behaviour
3526 this.warn("Overriding Annotation ID for " + anid
3527 + " from different id : " + jvann.annotationId);
3528 jvann.annotationId = anid;
3531 else if (jvobj instanceof String)
3533 if (jvids2vobj == null)
3535 jvids2vobj = new Hashtable();
3536 jvids2vobj.put(jvobj, jv2vobj.get(jvobj).toString());
3540 Cache.log.debug("Ignoring " + jvobj.getClass() + " (ID = " + id);
3545 * set the uniqueSetSuffix used to prefix/suffix object IDs for jalview
3546 * objects created from the project archive. If string is null (default for
3547 * construction) then suffix will be set automatically.
3551 public void setUniqueSetSuffix(String string)
3553 uniqueSetSuffix = string;
3558 * uses skipList2 as the skipList for skipping views on sequence sets
3559 * associated with keys in the skipList
3563 public void setSkipList(Hashtable skipList2)
3565 skipList = skipList2;