2 * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
3 * Copyright (C) 2009 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
21 import java.awt.Rectangle;
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 jmol = (AppJmol) frames[f];
583 if (!jmol.pdbentry.getId().equals(entry.getId())
584 && !(entry.getId().length() > 4 && entry.getId()
585 .toLowerCase().startsWith(
586 jmol.pdbentry.getId().toLowerCase())))
588 matchedFile = jmol.pdbentry.getFile(); // record the file so we
589 // can get at it if the ID
590 // match is ambiguous (e.g.
592 StructureState state = new StructureState();
593 state.setVisible(true);
594 state.setXpos(jmol.getX());
595 state.setYpos(jmol.getY());
596 state.setWidth(jmol.getWidth());
597 state.setHeight(jmol.getHeight());
598 state.setViewId(jmol.getViewId());
599 String statestring = jmol.viewer.getStateInfo();
602 state.setContent(statestring.replaceAll("\n", ""));
604 for (int s = 0; s < jmol.sequence.length; s++)
606 if (jal.findIndex(jmol.sequence[s]) > -1)
608 pdb.addStructureState(state);
614 if (matchedFile != null || entry.getFile() != null)
616 if (entry.getFile() != null)
619 matchedFile = entry.getFile();
621 pdb.setFile(matchedFile); // entry.getFile());
622 if (pdbfiles == null)
624 pdbfiles = new Vector();
627 if (!pdbfiles.contains(entry.getId()))
629 pdbfiles.addElement(entry.getId());
632 File file = new File(matchedFile);
633 if (file.exists() && jout != null)
635 byte[] data = new byte[(int) file.length()];
636 jout.putNextEntry(new JarEntry(entry.getId()));
637 DataInputStream dis = new DataInputStream(
638 new FileInputStream(file));
641 DataOutputStream dout = new DataOutputStream(jout);
642 dout.write(data, 0, data.length);
646 } catch (Exception ex)
648 ex.printStackTrace();
654 if (entry.getProperty() != null)
656 PdbentryItem item = new PdbentryItem();
657 Hashtable properties = entry.getProperty();
658 Enumeration en2 = properties.keys();
659 while (en2.hasMoreElements())
661 Property prop = new Property();
662 String key = en2.nextElement().toString();
664 prop.setValue(properties.get(key).toString());
665 item.addProperty(prop);
667 pdb.addPdbentryItem(item);
677 if (av.hasHiddenRows)
682 if (jal.getCodonFrames() != null && jal.getCodonFrames().length > 0)
684 jalview.datamodel.AlignedCodonFrame[] jac = jal.getCodonFrames();
685 for (int i = 0; i < jac.length; i++)
687 AlcodonFrame alc = new AlcodonFrame();
688 vamsasSet.addAlcodonFrame(alc);
689 for (int p = 0; p < jac[i].aaWidth; p++)
691 Alcodon cmap = new Alcodon();
692 if (jac[i].codons[p] != null)
694 // Null codons indicate a gapped column in the translated peptide
696 cmap.setPos1(jac[i].codons[p][0]);
697 cmap.setPos2(jac[i].codons[p][1]);
698 cmap.setPos3(jac[i].codons[p][2]);
700 alc.addAlcodon(cmap);
702 if (jac[i].getProtMappings() != null
703 && jac[i].getProtMappings().length > 0)
705 SequenceI[] dnas = jac[i].getdnaSeqs();
706 jalview.datamodel.Mapping[] pmaps = jac[i].getProtMappings();
707 for (int m = 0; m < pmaps.length; m++)
709 AlcodMap alcmap = new AlcodMap();
710 alcmap.setDnasq(seqHash(dnas[m]));
711 alcmap.setMapping(createVamsasMapping(pmaps[m], dnas[m], null,
713 alc.addAlcodMap(alcmap);
720 // /////////////////////////////////
721 if (av.currentTree != null)
723 // FIND ANY ASSOCIATED TREES
724 // NOT IMPLEMENTED FOR HEADLESS STATE AT PRESENT
725 if (Desktop.desktop != null)
727 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
729 for (int t = 0; t < frames.length; t++)
731 if (frames[t] instanceof TreePanel)
733 TreePanel tp = (TreePanel) frames[t];
735 if (tp.treeCanvas.av.alignment == jal)
737 Tree tree = new Tree();
738 tree.setTitle(tp.getTitle());
739 tree.setCurrentTree((av.currentTree == tp.getTree()));
740 tree.setNewick(tp.getTree().toString());
741 tree.setThreshold(tp.treeCanvas.threshold);
743 tree.setFitToWindow(tp.fitToWindow.getState());
744 tree.setFontName(tp.getTreeFont().getName());
745 tree.setFontSize(tp.getTreeFont().getSize());
746 tree.setFontStyle(tp.getTreeFont().getStyle());
747 tree.setMarkUnlinked(tp.placeholdersMenu.getState());
749 tree.setShowBootstrap(tp.bootstrapMenu.getState());
750 tree.setShowDistances(tp.distanceMenu.getState());
752 tree.setHeight(tp.getHeight());
753 tree.setWidth(tp.getWidth());
754 tree.setXpos(tp.getX());
755 tree.setYpos(tp.getY());
756 tree.setId(makeHashCode(tp, null));
766 * store forward refs from an annotationRow to any groups
768 IdentityHashMap groupRefs = new IdentityHashMap();
769 if (jal.getAlignmentAnnotation() != null)
771 jalview.datamodel.AlignmentAnnotation[] aa = jal
772 .getAlignmentAnnotation();
774 for (int i = 0; i < aa.length; i++)
776 Annotation an = new Annotation();
778 if (aa[i].annotationId != null)
780 annotationIds.put(aa[i].annotationId, aa[i]);
783 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);
801 // make a locally unique String
802 groupRefs.put(aa[i].groupRef, groupIdr = (""+System.currentTimeMillis()+aa[i].groupRef.getName()+groupRefs.size()));
804 an.setGroupRef(groupIdr.toString());
806 if (aa[i] == av.quality || aa[i] == av.conservation
807 || aa[i] == av.consensus || aa[i].autoCalculated)
809 // new way of indicating autocalculated annotation -
810 an.setAutoCalculated(aa[i].autoCalculated);
811 // write a stub for this annotation - indicate presence of autocalc rows
812 an.setLabel(aa[i].label);
814 vamsasSet.addAnnotation(an);
821 an.setGraphType(aa[i].graph);
822 an.setGraphGroup(aa[i].graphGroup);
823 if (aa[i].getThreshold() != null)
825 ThresholdLine line = new ThresholdLine();
826 line.setLabel(aa[i].getThreshold().label);
827 line.setValue(aa[i].getThreshold().value);
828 line.setColour(aa[i].getThreshold().colour.getRGB());
829 an.setThresholdLine(line);
837 an.setLabel(aa[i].label);
838 if (aa[i].hasScore())
840 an.setScore(aa[i].getScore());
842 AnnotationElement ae;
843 if (aa[i].annotations != null)
845 an.setScoreOnly(false);
846 for (int a = 0; a < aa[i].annotations.length; a++)
848 if ((aa[i] == null) || (aa[i].annotations[a] == null))
853 ae = new AnnotationElement();
854 if (aa[i].annotations[a].description != null)
855 ae.setDescription(aa[i].annotations[a].description);
856 if (aa[i].annotations[a].displayCharacter != null)
857 ae.setDisplayCharacter(aa[i].annotations[a].displayCharacter);
859 if (!Float.isNaN(aa[i].annotations[a].value))
860 ae.setValue(aa[i].annotations[a].value);
863 if (aa[i].annotations[a].secondaryStructure != ' '
864 && aa[i].annotations[a].secondaryStructure != '\0')
866 .setSecondaryStructure(aa[i].annotations[a].secondaryStructure
869 if (aa[i].annotations[a].colour != null
870 && aa[i].annotations[a].colour != java.awt.Color.black)
872 ae.setColour(aa[i].annotations[a].colour.getRGB());
875 an.addAnnotationElement(ae);
880 an.setScoreOnly(true);
882 vamsasSet.addAnnotation(an);
886 if (jal.getGroups() != null)
888 JGroup[] groups = new JGroup[jal.getGroups().size()];
890 for (int i = 0; i < groups.length; i++)
892 groups[i] = new JGroup();
894 jalview.datamodel.SequenceGroup sg = (jalview.datamodel.SequenceGroup) jal
895 .getGroups().elementAt(i);
896 groups[i].setStart(sg.getStartRes());
897 groups[i].setEnd(sg.getEndRes());
898 groups[i].setName(sg.getName());
899 if (groupRefs.containsKey(sg)) {
900 // group has references so set it's ID field
901 groups[i].setId(groupRefs.get(sg).toString());
905 if (sg.cs.conservationApplied())
907 groups[i].setConsThreshold(sg.cs.getConservationInc());
909 if (sg.cs instanceof jalview.schemes.UserColourScheme)
911 groups[i].setColour(SetUserColourScheme(sg.cs, userColours,
917 .setColour(ColourSchemeProperty.getColourName(sg.cs));
920 else if (sg.cs instanceof jalview.schemes.AnnotationColourGradient)
923 .setColour(ColourSchemeProperty
924 .getColourName(((jalview.schemes.AnnotationColourGradient) sg.cs)
927 else if (sg.cs instanceof jalview.schemes.UserColourScheme)
930 .setColour(SetUserColourScheme(sg.cs, userColours, jms));
934 groups[i].setColour(ColourSchemeProperty.getColourName(sg.cs));
937 groups[i].setPidThreshold(sg.cs.getThreshold());
940 groups[i].setOutlineColour(sg.getOutlineColour().getRGB());
941 groups[i].setDisplayBoxes(sg.getDisplayBoxes());
942 groups[i].setDisplayText(sg.getDisplayText());
943 groups[i].setColourText(sg.getColourText());
944 groups[i].setTextCol1(sg.textColour.getRGB());
945 groups[i].setTextCol2(sg.textColour2.getRGB());
946 groups[i].setTextColThreshold(sg.thresholdTextColour);
947 groups[i].setShowUnconserved(sg.getShowunconserved());
948 groups[i].setIgnoreGapsinConsensus(sg.getIgnoreGapsConsensus());
949 groups[i].setShowConsensusHistogram(sg.isShowConsensusHistogram());
950 groups[i].setShowSequenceLogo(sg.isShowSequenceLogo());
951 for (int s = 0; s < sg.getSize(); s++)
953 jalview.datamodel.Sequence seq = (jalview.datamodel.Sequence) sg
955 groups[i].addSeq(seqHash(seq));
959 jms.setJGroup(groups);
962 // /////////SAVE VIEWPORT
963 Viewport view = new Viewport();
964 view.setTitle(ap.alignFrame.getTitle());
965 view.setSequenceSetId(makeHashCode(av.getSequenceSetId(), av
966 .getSequenceSetId()));
967 view.setId(av.getViewId());
968 view.setViewName(av.viewName);
969 view.setGatheredViews(av.gatherViewsHere);
971 if (ap.av.explodedPosition != null)
973 view.setXpos(av.explodedPosition.x);
974 view.setYpos(av.explodedPosition.y);
975 view.setWidth(av.explodedPosition.width);
976 view.setHeight(av.explodedPosition.height);
980 view.setXpos(ap.alignFrame.getBounds().x);
981 view.setYpos(ap.alignFrame.getBounds().y);
982 view.setWidth(ap.alignFrame.getBounds().width);
983 view.setHeight(ap.alignFrame.getBounds().height);
986 view.setStartRes(av.startRes);
987 view.setStartSeq(av.startSeq);
989 if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme)
991 view.setBgColour(SetUserColourScheme(av.getGlobalColourScheme(),
994 else if (av.getGlobalColourScheme() instanceof jalview.schemes.AnnotationColourGradient)
996 jalview.schemes.AnnotationColourGradient acg = (jalview.schemes.AnnotationColourGradient) av
997 .getGlobalColourScheme();
999 AnnotationColours ac = new AnnotationColours();
1000 ac.setAboveThreshold(acg.getAboveThreshold());
1001 ac.setThreshold(acg.getAnnotationThreshold());
1002 ac.setAnnotation(acg.getAnnotation());
1003 if (acg.getBaseColour() instanceof jalview.schemes.UserColourScheme)
1005 ac.setColourScheme(SetUserColourScheme(acg.getBaseColour(),
1010 ac.setColourScheme(ColourSchemeProperty.getColourName(acg
1014 ac.setMaxColour(acg.getMaxColour().getRGB());
1015 ac.setMinColour(acg.getMinColour().getRGB());
1016 view.setAnnotationColours(ac);
1017 view.setBgColour("AnnotationColourGradient");
1021 view.setBgColour(ColourSchemeProperty.getColourName(av
1022 .getGlobalColourScheme()));
1025 ColourSchemeI cs = av.getGlobalColourScheme();
1029 if (cs.conservationApplied())
1031 view.setConsThreshold(cs.getConservationInc());
1032 if (cs instanceof jalview.schemes.UserColourScheme)
1034 view.setBgColour(SetUserColourScheme(cs, userColours, jms));
1038 if (cs instanceof ResidueColourScheme)
1040 view.setPidThreshold(cs.getThreshold());
1044 view.setConservationSelected(av.getConservationSelected());
1045 view.setPidSelected(av.getAbovePIDThreshold());
1046 view.setFontName(av.font.getName());
1047 view.setFontSize(av.font.getSize());
1048 view.setFontStyle(av.font.getStyle());
1049 view.setRenderGaps(av.renderGaps);
1050 view.setShowAnnotation(av.getShowAnnotation());
1051 view.setShowBoxes(av.getShowBoxes());
1052 view.setShowColourText(av.getColourText());
1053 view.setShowFullId(av.getShowJVSuffix());
1054 view.setRightAlignIds(av.rightAlignIds);
1055 view.setShowSequenceFeatures(av.showSequenceFeatures);
1056 view.setShowText(av.getShowText());
1057 view.setShowUnconserved(av.getShowUnconserved());
1058 view.setWrapAlignment(av.getWrapAlignment());
1059 view.setTextCol1(av.textColour.getRGB());
1060 view.setTextCol2(av.textColour2.getRGB());
1061 view.setTextColThreshold(av.thresholdTextColour);
1062 view.setShowConsensusHistogram(av.isShowConsensusHistogram());
1063 view.setShowSequenceLogo(av.isShowSequenceLogo());
1064 view.setShowGroupConsensus(av.isShowGroupConsensus());
1065 view.setShowGroupConservation(av.isShowGroupConservation());
1066 view.setShowNPfeatureTooltip(av.isShowNpFeats());
1067 view.setShowDbRefTooltip(av.isShowDbRefs());
1068 view.setFollowHighlight(av.followHighlight);
1069 view.setFollowSelection(av.followSelection);
1070 view.setIgnoreGapsinConsensus(av.getIgnoreGapsConsensus());
1071 if (av.featuresDisplayed != null)
1073 jalview.schemabinding.version2.FeatureSettings fs = new jalview.schemabinding.version2.FeatureSettings();
1075 String[] renderOrder = ap.seqPanel.seqCanvas.getFeatureRenderer().renderOrder;
1077 Vector settingsAdded = new Vector();
1079 GraduatedColor gcol = null;
1080 for (int ro = 0; ro < renderOrder.length; ro++)
1082 gstyle = ap.seqPanel.seqCanvas.getFeatureRenderer().getFeatureStyle(renderOrder[ro]);
1083 Setting setting = new Setting();
1084 setting.setType(renderOrder[ro]);
1085 if (gstyle instanceof GraduatedColor) {
1086 gcol = (GraduatedColor) gstyle;
1087 setting.setColour(gcol.getMaxColor().getRGB());
1088 setting.setMincolour(gcol.getMinColor().getRGB());
1089 setting.setMin(gcol.getMin());
1090 setting.setMax(gcol.getMax());
1091 setting.setColourByLabel(gcol.isColourByLabel());
1092 setting.setAutoScale(gcol.isAutoScale());
1093 setting.setThreshold(gcol.getThresh());
1094 setting.setThreshstate(gcol.getThreshType());
1096 setting.setColour(ap.seqPanel.seqCanvas.getFeatureRenderer() .getColour(renderOrder[ro]).getRGB());
1099 setting.setDisplay(av.featuresDisplayed
1100 .containsKey(renderOrder[ro]));
1101 float rorder = ap.seqPanel.seqCanvas.getFeatureRenderer().getOrder(
1105 setting.setOrder(rorder);
1107 fs.addSetting(setting);
1108 settingsAdded.addElement(renderOrder[ro]);
1111 // Make sure we save none displayed feature settings
1112 Enumeration en = ap.seqPanel.seqCanvas.getFeatureRenderer().featureColours
1114 while (en.hasMoreElements())
1116 String key = en.nextElement().toString();
1117 if (settingsAdded.contains(key))
1122 Setting setting = new Setting();
1123 setting.setType(key);
1124 setting.setColour(ap.seqPanel.seqCanvas.getFeatureRenderer()
1125 .getColour(key).getRGB());
1127 setting.setDisplay(false);
1128 float rorder = ap.seqPanel.seqCanvas.getFeatureRenderer().getOrder(
1132 setting.setOrder(rorder);
1134 fs.addSetting(setting);
1135 settingsAdded.addElement(key);
1137 en = ap.seqPanel.seqCanvas.getFeatureRenderer().featureGroups.keys();
1138 Vector groupsAdded = new Vector();
1139 while (en.hasMoreElements())
1141 String grp = en.nextElement().toString();
1142 if (groupsAdded.contains(grp))
1146 Group g = new Group();
1149 .setDisplay(((Boolean) ap.seqPanel.seqCanvas
1150 .getFeatureRenderer().featureGroups.get(grp))
1153 groupsAdded.addElement(grp);
1155 jms.setFeatureSettings(fs);
1159 if (av.hasHiddenColumns)
1161 if (av.getColumnSelection() == null
1162 || av.getColumnSelection().getHiddenColumns() == null)
1164 warn("REPORT BUG: avoided null columnselection bug (DMAM reported). Please contact Jim about this.");
1168 for (int c = 0; c < av.getColumnSelection().getHiddenColumns()
1171 int[] region = (int[]) av.getColumnSelection().getHiddenColumns()
1173 HiddenColumns hc = new HiddenColumns();
1174 hc.setStart(region[0]);
1175 hc.setEnd(region[1]);
1176 view.addHiddenColumns(hc);
1181 jms.addViewport(view);
1183 object.setJalviewModelSequence(jms);
1184 object.getVamsasModel().addSequenceSet(vamsasSet);
1186 if (jout != null && fileName != null)
1188 // We may not want to write the object to disk,
1189 // eg we can copy the alignViewport to a new view object
1190 // using save and then load
1193 JarEntry entry = new JarEntry(fileName);
1194 jout.putNextEntry(entry);
1195 PrintWriter pout = new PrintWriter(new OutputStreamWriter(jout,
1197 org.exolab.castor.xml.Marshaller marshaller = new org.exolab.castor.xml.Marshaller(
1199 marshaller.marshal(object);
1202 } catch (Exception ex)
1204 // TODO: raise error in GUI if marshalling failed.
1205 ex.printStackTrace();
1212 * External mapping between jalview objects and objects yielding a valid and
1213 * unique object ID string. This is null for normal Jalview project IO, but
1214 * non-null when a jalview project is being read or written as part of a
1217 IdentityHashMap jv2vobj = null;
1220 * Construct a unique ID for jvobj using either existing bindings or if none
1221 * exist, the result of the hashcode call for the object.
1224 * jalview data object
1225 * @return unique ID for referring to jvobj
1227 private String makeHashCode(Object jvobj, String altCode)
1229 if (jv2vobj != null)
1231 Object id = jv2vobj.get(jvobj);
1234 return id.toString();
1236 // check string ID mappings
1237 if (jvids2vobj != null && jvobj instanceof String)
1239 id = jvids2vobj.get(jvobj);
1243 return id.toString();
1245 // give up and warn that something has gone wrong
1246 warn("Cannot find ID for object in external mapping : " + jvobj);
1252 * return local jalview object mapped to ID, if it exists
1256 * @return null or object bound to idcode
1258 private Object retrieveExistingObj(String idcode)
1260 if (idcode != null && vobj2jv != null)
1262 return vobj2jv.get(idcode);
1268 * binding from ID strings from external mapping table to jalview data model
1271 private Hashtable vobj2jv;
1273 private Sequence createVamsasSequence(String id, SequenceI jds)
1275 return createVamsasSequence(true, id, jds, null);
1278 private Sequence createVamsasSequence(boolean recurse, String id,
1279 SequenceI jds, SequenceI parentseq)
1281 Sequence vamsasSeq = new Sequence();
1282 vamsasSeq.setId(id);
1283 vamsasSeq.setName(jds.getName());
1284 vamsasSeq.setSequence(jds.getSequenceAsString());
1285 vamsasSeq.setDescription(jds.getDescription());
1286 jalview.datamodel.DBRefEntry[] dbrefs = null;
1287 if (jds.getDatasetSequence() != null)
1289 vamsasSeq.setDsseqid(seqHash(jds.getDatasetSequence()));
1290 if (jds.getDatasetSequence().getDBRef() != null)
1292 dbrefs = jds.getDatasetSequence().getDBRef();
1297 vamsasSeq.setDsseqid(id); // so we can tell which sequences really are
1298 // dataset sequences only
1299 dbrefs = jds.getDBRef();
1303 for (int d = 0; d < dbrefs.length; d++)
1305 DBRef dbref = new DBRef();
1306 dbref.setSource(dbrefs[d].getSource());
1307 dbref.setVersion(dbrefs[d].getVersion());
1308 dbref.setAccessionId(dbrefs[d].getAccessionId());
1309 if (dbrefs[d].hasMap())
1311 Mapping mp = createVamsasMapping(dbrefs[d].getMap(), parentseq,
1313 dbref.setMapping(mp);
1315 vamsasSeq.addDBRef(dbref);
1321 private Mapping createVamsasMapping(jalview.datamodel.Mapping jmp,
1322 SequenceI parentseq, SequenceI jds, boolean recurse)
1325 if (jmp.getMap() != null)
1329 jalview.util.MapList mlst = jmp.getMap();
1330 int r[] = mlst.getFromRanges();
1331 for (int s = 0; s < r.length; s += 2)
1333 MapListFrom mfrom = new MapListFrom();
1334 mfrom.setStart(r[s]);
1335 mfrom.setEnd(r[s + 1]);
1336 mp.addMapListFrom(mfrom);
1338 r = mlst.getToRanges();
1339 for (int s = 0; s < r.length; s += 2)
1341 MapListTo mto = new MapListTo();
1343 mto.setEnd(r[s + 1]);
1344 mp.addMapListTo(mto);
1346 mp.setMapFromUnit(mlst.getFromRatio());
1347 mp.setMapToUnit(mlst.getToRatio());
1348 if (jmp.getTo() != null)
1350 MappingChoice mpc = new MappingChoice();
1352 && (parentseq != jmp.getTo() || parentseq
1353 .getDatasetSequence() != jmp.getTo()))
1355 mpc.setSequence(createVamsasSequence(false, seqHash(jmp.getTo()),
1361 SequenceI ps = null;
1362 if (parentseq != jmp.getTo()
1363 && parentseq.getDatasetSequence() != jmp.getTo())
1365 // chaining dbref rather than a handshaking one
1366 jmpid = seqHash(ps = jmp.getTo());
1370 jmpid = seqHash(ps = parentseq);
1372 mpc.setDseqFor(jmpid);
1373 if (!seqRefIds.containsKey(mpc.getDseqFor()))
1375 jalview.bin.Cache.log.debug("creatign new DseqFor ID");
1376 seqRefIds.put(mpc.getDseqFor(), ps);
1380 jalview.bin.Cache.log.debug("reusing DseqFor ID");
1383 mp.setMappingChoice(mpc);
1389 String SetUserColourScheme(jalview.schemes.ColourSchemeI cs,
1390 Vector userColours, JalviewModelSequence jms)
1393 jalview.schemes.UserColourScheme ucs = (jalview.schemes.UserColourScheme) cs;
1394 boolean newucs=false;
1395 if (!userColours.contains(ucs))
1397 userColours.add(ucs);
1400 id = "ucs" + userColours.indexOf(ucs);
1402 // actually create the scheme's entry in the XML model
1403 java.awt.Color[] colours = ucs.getColours();
1404 jalview.schemabinding.version2.UserColours uc = new jalview.schemabinding.version2.UserColours();
1405 jalview.schemabinding.version2.UserColourScheme jbucs = new jalview.schemabinding.version2.UserColourScheme();
1407 for (int i = 0; i < colours.length; i++)
1409 jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();
1410 col.setName(ResidueProperties.aa[i]);
1411 col.setRGB(jalview.util.Format.getHexString(colours[i]));
1412 jbucs.addColour(col);
1414 if (ucs.getLowerCaseColours() != null)
1416 colours = ucs.getLowerCaseColours();
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].toLowerCase());
1421 col.setRGB(jalview.util.Format.getHexString(colours[i]));
1422 jbucs.addColour(col);
1427 uc.setUserColourScheme(jbucs);
1428 jms.addUserColours(uc);
1434 jalview.schemes.UserColourScheme GetUserColourScheme(
1435 JalviewModelSequence jms, String id)
1437 UserColours[] uc = jms.getUserColours();
1438 UserColours colours = null;
1440 for (int i = 0; i < uc.length; i++)
1442 if (uc[i].getId().equals(id))
1450 java.awt.Color[] newColours = new java.awt.Color[24];
1452 for (int i = 0; i < 24; i++)
1454 newColours[i] = new java.awt.Color(Integer.parseInt(colours
1455 .getUserColourScheme().getColour(i).getRGB(), 16));
1458 jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(
1461 if (colours.getUserColourScheme().getColourCount() > 24)
1463 newColours = new java.awt.Color[23];
1464 for (int i = 0; i < 23; i++)
1466 newColours[i] = new java.awt.Color(Integer.parseInt(colours
1467 .getUserColourScheme().getColour(i + 24).getRGB(), 16));
1469 ucs.setLowerCaseColours(newColours);
1476 * contains last error message (if any) encountered by XML loader.
1478 String errorMessage = null;
1481 * flag to control whether the Jalview2XML_V1 parser should be deferred to if
1482 * exceptions are raised during project XML parsing
1484 public boolean attemptversion1parse = true;
1487 * Load a jalview project archive from a jar file
1490 * - HTTP URL or filename
1492 public AlignFrame LoadJalviewAlign(final String file)
1495 jalview.gui.AlignFrame af = null;
1499 // UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
1500 // Workaround is to make sure caller implements the JarInputStreamProvider
1502 // so we can re-open the jar input stream for each entry.
1504 jarInputStreamProvider jprovider = createjarInputStreamProvider(file);
1505 af = LoadJalviewAlign(jprovider);
1506 } catch (MalformedURLException e)
1508 errorMessage = "Invalid URL format for '" + file + "'";
1514 private jarInputStreamProvider createjarInputStreamProvider(
1515 final String file) throws MalformedURLException
1518 errorMessage = null;
1519 uniqueSetSuffix = null;
1521 viewportsAdded = null;
1522 frefedSequence = null;
1524 if (file.startsWith("http://"))
1526 url = new URL(file);
1528 final URL _url = url;
1529 return new jarInputStreamProvider()
1532 public JarInputStream getJarInputStream() throws IOException
1536 return new JarInputStream(_url.openStream());
1540 return new JarInputStream(new FileInputStream(file));
1544 public String getFilename()
1552 * Recover jalview session from a jalview project archive. Caller may
1553 * initialise uniqueSetSuffix, seqRefIds, viewportsAdded and frefedSequence
1554 * themselves. Any null fields will be initialised with default values,
1555 * non-null fields are left alone.
1560 public AlignFrame LoadJalviewAlign(final jarInputStreamProvider jprovider)
1562 errorMessage = null;
1563 if (uniqueSetSuffix == null)
1565 uniqueSetSuffix = System.currentTimeMillis() % 100000 + "";
1567 if (seqRefIds == null)
1569 seqRefIds = new Hashtable();
1571 if (viewportsAdded == null)
1573 viewportsAdded = new Hashtable();
1575 if (frefedSequence == null)
1577 frefedSequence = new Vector();
1580 jalview.gui.AlignFrame af = null;
1581 Hashtable gatherToThisFrame = new Hashtable();
1582 final String file = jprovider.getFilename();
1585 JarInputStream jin = null;
1586 JarEntry jarentry = null;
1591 jin = jprovider.getJarInputStream();
1592 for (int i = 0; i < entryCount; i++)
1594 jarentry = jin.getNextJarEntry();
1597 if (jarentry != null && jarentry.getName().endsWith(".xml"))
1599 InputStreamReader in = new InputStreamReader(jin, "UTF-8");
1600 JalviewModel object = new JalviewModel();
1602 Unmarshaller unmar = new Unmarshaller(object);
1603 unmar.setValidation(false);
1604 object = (JalviewModel) unmar.unmarshal(in);
1605 if (true) // !skipViewport(object))
1607 af = LoadFromObject(object, file, true, jprovider);
1608 if (af.viewport.gatherViewsHere)
1610 gatherToThisFrame.put(af.viewport.getSequenceSetId(), af);
1615 else if (jarentry != null)
1617 // Some other file here.
1620 } while (jarentry != null);
1621 resolveFrefedSequences();
1622 } catch (java.io.FileNotFoundException ex)
1624 ex.printStackTrace();
1625 errorMessage = "Couldn't locate Jalview XML file : " + file;
1626 System.err.println("Exception whilst loading jalview XML file : "
1628 } catch (java.net.UnknownHostException ex)
1630 ex.printStackTrace();
1631 errorMessage = "Couldn't locate Jalview XML file : " + file;
1632 System.err.println("Exception whilst loading jalview XML file : "
1634 } catch (Exception ex)
1636 System.err.println("Parsing as Jalview Version 2 file failed.");
1637 ex.printStackTrace(System.err);
1638 if (attemptversion1parse)
1640 // Is Version 1 Jar file?
1643 af = new Jalview2XML_V1(raiseGUI).LoadJalviewAlign(jprovider);
1644 } catch (Exception ex2)
1646 System.err.println("Exception whilst loading as jalviewXMLV1:");
1647 ex2.printStackTrace();
1651 if (Desktop.instance != null)
1653 Desktop.instance.stopLoading();
1657 System.out.println("Successfully loaded archive file");
1660 ex.printStackTrace();
1662 System.err.println("Exception whilst loading jalview XML file : "
1664 } catch (OutOfMemoryError e)
1666 // Don't use the OOM Window here
1667 errorMessage = "Out of memory loading jalview XML file";
1668 System.err.println("Out of memory whilst loading jalview XML file");
1669 e.printStackTrace();
1672 if (Desktop.instance != null)
1674 Desktop.instance.stopLoading();
1677 Enumeration en = gatherToThisFrame.elements();
1678 while (en.hasMoreElements())
1680 Desktop.instance.gatherViews((AlignFrame) en.nextElement());
1682 if (errorMessage != null)
1690 * check errorMessage for a valid error message and raise an error box in the
1691 * GUI or write the current errorMessage to stderr and then clear the error
1694 protected void reportErrors()
1696 reportErrors(false);
1699 protected void reportErrors(final boolean saving)
1701 if (errorMessage != null)
1703 final String finalErrorMessage = errorMessage;
1706 javax.swing.SwingUtilities.invokeLater(new Runnable()
1710 JOptionPane.showInternalMessageDialog(Desktop.desktop,
1711 finalErrorMessage, "Error "
1712 + (saving ? "saving" : "loading")
1713 + " Jalview file", JOptionPane.WARNING_MESSAGE);
1719 System.err.println("Problem loading Jalview file: " + errorMessage);
1722 errorMessage = null;
1725 Hashtable alreadyLoadedPDB;
1728 * when set, local views will be updated from view stored in JalviewXML
1729 * Currently (28th Sep 2008) things will go horribly wrong in vamsas document
1730 * sync if this is set to true.
1732 private boolean updateLocalViews = false;
1734 String loadPDBFile(jarInputStreamProvider jprovider, String pdbId)
1736 if (alreadyLoadedPDB == null)
1737 alreadyLoadedPDB = new Hashtable();
1739 if (alreadyLoadedPDB.containsKey(pdbId))
1740 return alreadyLoadedPDB.get(pdbId).toString();
1744 JarInputStream jin = jprovider.getJarInputStream();
1746 * if (jprovider.startsWith("http://")) { jin = new JarInputStream(new
1747 * URL(jprovider).openStream()); } else { jin = new JarInputStream(new
1748 * FileInputStream(jprovider)); }
1751 JarEntry entry = null;
1754 entry = jin.getNextJarEntry();
1755 } while (entry != null && !entry.getName().equals(pdbId));
1758 BufferedReader in = new BufferedReader(new InputStreamReader(jin));
1759 File outFile = File.createTempFile("jalview_pdb", ".txt");
1760 outFile.deleteOnExit();
1761 PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
1764 while ((data = in.readLine()) != null)
1771 } catch (Exception foo)
1777 alreadyLoadedPDB.put(pdbId, outFile.getAbsolutePath());
1778 return outFile.getAbsolutePath();
1782 warn("Couldn't find PDB file entry in Jalview Jar for " + pdbId);
1784 } catch (Exception ex)
1786 ex.printStackTrace();
1793 * Load alignment frame from jalview XML DOM object
1798 * filename source string
1799 * @param loadTreesAndStructures
1800 * when false only create Viewport
1802 * data source provider
1803 * @return alignment frame created from view stored in DOM
1805 AlignFrame LoadFromObject(JalviewModel object, String file,
1806 boolean loadTreesAndStructures, jarInputStreamProvider jprovider)
1808 SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);
1809 Sequence[] vamsasSeq = vamsasSet.getSequence();
1811 JalviewModelSequence jms = object.getJalviewModelSequence();
1813 Viewport view = jms.getViewport(0);
1814 // ////////////////////////////////
1817 Vector hiddenSeqs = null;
1818 jalview.datamodel.Sequence jseq;
1820 ArrayList tmpseqs = new ArrayList();
1822 boolean multipleView = false;
1824 JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq();
1825 int vi = 0; // counter in vamsasSeq array
1826 for (int i = 0; i < JSEQ.length; i++)
1828 String seqId = JSEQ[i].getId();
1830 if (seqRefIds.get(seqId) != null)
1832 tmpseqs.add((jalview.datamodel.Sequence) seqRefIds.get(seqId));
1833 multipleView = true;
1837 jseq = new jalview.datamodel.Sequence(vamsasSeq[vi].getName(),
1838 vamsasSeq[vi].getSequence());
1839 jseq.setDescription(vamsasSeq[vi].getDescription());
1840 jseq.setStart(JSEQ[i].getStart());
1841 jseq.setEnd(JSEQ[i].getEnd());
1842 jseq.setVamsasId(uniqueSetSuffix + seqId);
1843 seqRefIds.put(vamsasSeq[vi].getId(), jseq);
1848 if (JSEQ[i].getHidden())
1850 if (hiddenSeqs == null)
1852 hiddenSeqs = new Vector();
1855 hiddenSeqs.addElement((jalview.datamodel.Sequence) seqRefIds
1862 // Create the alignment object from the sequence set
1863 // ///////////////////////////////
1864 jalview.datamodel.Sequence[] orderedSeqs = new jalview.datamodel.Sequence[tmpseqs
1867 tmpseqs.toArray(orderedSeqs);
1869 jalview.datamodel.Alignment al = new jalview.datamodel.Alignment(
1872 // / Add the alignment properties
1873 for (int i = 0; i < vamsasSet.getSequenceSetPropertiesCount(); i++)
1875 SequenceSetProperties ssp = vamsasSet.getSequenceSetProperties(i);
1876 al.setProperty(ssp.getKey(), ssp.getValue());
1880 // SequenceFeatures are added to the DatasetSequence,
1881 // so we must create or recover the dataset before loading features
1882 // ///////////////////////////////
1883 if (vamsasSet.getDatasetId() == null || vamsasSet.getDatasetId() == "")
1885 // older jalview projects do not have a dataset id.
1886 al.setDataset(null);
1890 recoverDatasetFor(vamsasSet, al);
1892 // ///////////////////////////////
1894 Hashtable pdbloaded = new Hashtable();
1897 // load sequence features, database references and any associated PDB
1898 // structures for the alignment
1899 for (int i = 0; i < vamsasSeq.length; i++)
1901 if (JSEQ[i].getFeaturesCount() > 0)
1903 Features[] features = JSEQ[i].getFeatures();
1904 for (int f = 0; f < features.length; f++)
1906 jalview.datamodel.SequenceFeature sf = new jalview.datamodel.SequenceFeature(
1907 features[f].getType(), features[f].getDescription(),
1908 features[f].getStatus(), features[f].getBegin(),
1909 features[f].getEnd(), features[f].getFeatureGroup());
1911 sf.setScore(features[f].getScore());
1912 for (int od = 0; od < features[f].getOtherDataCount(); od++)
1914 OtherData keyValue = features[f].getOtherData(od);
1915 if (keyValue.getKey().startsWith("LINK"))
1917 sf.addLink(keyValue.getValue());
1921 sf.setValue(keyValue.getKey(), keyValue.getValue());
1926 al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf);
1929 if (vamsasSeq[i].getDBRefCount() > 0)
1931 addDBRefs(al.getSequenceAt(i).getDatasetSequence(), vamsasSeq[i]);
1933 if (JSEQ[i].getPdbidsCount() > 0)
1935 Pdbids[] ids = JSEQ[i].getPdbids();
1936 for (int p = 0; p < ids.length; p++)
1938 jalview.datamodel.PDBEntry entry = new jalview.datamodel.PDBEntry();
1939 entry.setId(ids[p].getId());
1940 entry.setType(ids[p].getType());
1941 if (ids[p].getFile() != null)
1943 if (!pdbloaded.containsKey(ids[p].getFile()))
1945 entry.setFile(loadPDBFile(jprovider, ids[p].getId()));
1949 entry.setFile(pdbloaded.get(ids[p].getId()).toString());
1953 al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
1957 } // end !multipleview
1959 // ///////////////////////////////
1960 // LOAD SEQUENCE MAPPINGS
1962 if (vamsasSet.getAlcodonFrameCount() > 0)
1964 // TODO Potentially this should only be done once for all views of an
1966 AlcodonFrame[] alc = vamsasSet.getAlcodonFrame();
1967 for (int i = 0; i < alc.length; i++)
1969 jalview.datamodel.AlignedCodonFrame cf = new jalview.datamodel.AlignedCodonFrame(
1970 alc[i].getAlcodonCount());
1971 if (alc[i].getAlcodonCount() > 0)
1973 Alcodon[] alcods = alc[i].getAlcodon();
1974 for (int p = 0; p < cf.codons.length; p++)
1976 if (alcods[p].hasPos1() && alcods[p].hasPos2()
1977 && alcods[p].hasPos3())
1979 // translated codons require three valid positions
1980 cf.codons[p] = new int[3];
1981 cf.codons[p][0] = (int) alcods[p].getPos1();
1982 cf.codons[p][1] = (int) alcods[p].getPos2();
1983 cf.codons[p][2] = (int) alcods[p].getPos3();
1987 cf.codons[p] = null;
1991 if (alc[i].getAlcodMapCount() > 0)
1993 AlcodMap[] maps = alc[i].getAlcodMap();
1994 for (int m = 0; m < maps.length; m++)
1996 SequenceI dnaseq = (SequenceI) seqRefIds
1997 .get(maps[m].getDnasq());
1999 jalview.datamodel.Mapping mapping = null;
2000 // attach to dna sequence reference.
2001 if (maps[m].getMapping() != null)
2003 mapping = addMapping(maps[m].getMapping());
2007 cf.addMap(dnaseq, mapping.getTo(), mapping.getMap());
2012 frefedSequence.add(new Object[]
2013 { maps[m].getDnasq(), cf, mapping });
2017 al.addCodonFrame(cf);
2022 // ////////////////////////////////
2024 boolean hideQuality = true, hideConservation = true, hideConsensus = true;
2026 * store any annotations which forward reference a group's ID
2028 Hashtable groupAnnotRefs = new Hashtable();
2030 if (vamsasSet.getAnnotationCount() > 0)
2032 Annotation[] an = vamsasSet.getAnnotation();
2034 for (int i = 0; i < an.length; i++)
2036 // set visibility for automatic annotation for this view
2037 if (an[i].getLabel().equals("Quality"))
2039 hideQuality = false;
2042 else if (an[i].getLabel().equals("Conservation"))
2044 hideConservation = false;
2047 else if (an[i].getLabel().equals("Consensus"))
2049 hideConsensus = false;
2052 // set visiblity for other annotation in this view
2053 if (an[i].getId() != null
2054 && annotationIds.containsKey(an[i].getId()))
2056 jalview.datamodel.AlignmentAnnotation jda = (jalview.datamodel.AlignmentAnnotation) annotationIds
2057 .get(an[i].getId());
2058 // in principle Visible should always be true for annotation displayed
2059 // in multiple views
2060 if (an[i].hasVisible())
2061 jda.visible = an[i].getVisible();
2063 al.addAnnotation(jda);
2067 // Construct new annotation from model.
2068 AnnotationElement[] ae = an[i].getAnnotationElement();
2069 jalview.datamodel.Annotation[] anot = null;
2071 if (!an[i].getScoreOnly())
2073 anot = new jalview.datamodel.Annotation[al.getWidth()];
2075 for (int aa = 0; aa < ae.length && aa < anot.length; aa++)
2077 if (ae[aa].getPosition() >= anot.length)
2080 anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(
2082 ae[aa].getDisplayCharacter(), ae[aa].getDescription(), (ae[aa]
2083 .getSecondaryStructure() == null || ae[aa]
2084 .getSecondaryStructure().length() == 0) ? ' ' : ae[aa]
2085 .getSecondaryStructure().charAt(0), ae[aa].getValue()
2088 // JBPNote: Consider verifying dataflow for IO of secondary
2089 // structure annotation read from Stockholm files
2090 // this was added to try to ensure that
2091 // if (anot[ae[aa].getPosition()].secondaryStructure>' ')
2093 // anot[ae[aa].getPosition()].displayCharacter = "";
2095 anot[ae[aa].getPosition()].colour = new java.awt.Color(ae[aa]
2099 jalview.datamodel.AlignmentAnnotation jaa = null;
2101 if (an[i].getGraph())
2103 jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
2104 an[i].getDescription(), anot, 0, 0, an[i].getGraphType());
2106 jaa.graphGroup = an[i].getGraphGroup();
2108 if (an[i].getThresholdLine() != null)
2110 jaa.setThreshold(new jalview.datamodel.GraphLine(an[i]
2111 .getThresholdLine().getValue(), an[i]
2112 .getThresholdLine().getLabel(), new java.awt.Color(
2113 an[i].getThresholdLine().getColour())));
2120 jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
2121 an[i].getDescription(), anot);
2123 // register new annotation
2124 if (an[i].getId() != null)
2126 annotationIds.put(an[i].getId(), jaa);
2127 jaa.annotationId = an[i].getId();
2129 // recover sequence association
2130 if (an[i].getSequenceRef() != null)
2132 if (al.findName(an[i].getSequenceRef()) != null)
2134 jaa.createSequenceMapping(al.findName(an[i].getSequenceRef()),
2136 al.findName(an[i].getSequenceRef()).addAlignmentAnnotation(jaa);
2139 // and make a note of any group association
2140 if (an[i].getGroupRef()!=null && an[i].getGroupRef().length()>0)
2142 groupAnnotRefs.put(an[i].getGroupRef(),jaa);
2145 if (an[i].hasScore())
2147 jaa.setScore(an[i].getScore());
2149 if (an[i].hasVisible())
2150 jaa.visible = an[i].getVisible();
2152 if (an[i].hasCentreColLabels())
2153 jaa.centreColLabels = an[i].getCentreColLabels();
2155 if (an[i].hasScaleColLabels())
2157 jaa.scaleColLabel = an[i].getScaleColLabels();
2159 if (an[i].hasAutoCalculated() && an[i].isAutoCalculated())
2161 // newer files have an 'autoCalculated' flag and store calculation state in viewport properties
2162 jaa.autoCalculated = true; // means annotation will be marked for update at end of load.
2164 al.addAnnotation(jaa);
2168 // ///////////////////////
2170 // Create alignment markup and styles for this view
2171 if (jms.getJGroupCount() > 0)
2173 JGroup[] groups = jms.getJGroup();
2175 for (int i = 0; i < groups.length; i++)
2177 ColourSchemeI cs = null;
2179 if (groups[i].getColour() != null)
2181 if (groups[i].getColour().startsWith("ucs"))
2183 cs = GetUserColourScheme(jms, groups[i].getColour());
2187 cs = ColourSchemeProperty.getColour(al, groups[i].getColour());
2192 cs.setThreshold(groups[i].getPidThreshold(), true);
2196 Vector seqs = new Vector();
2198 for (int s = 0; s < groups[i].getSeqCount(); s++)
2200 String seqId = groups[i].getSeq(s) + "";
2201 jalview.datamodel.SequenceI ts = (jalview.datamodel.SequenceI) seqRefIds
2206 seqs.addElement(ts);
2210 if (seqs.size() < 1)
2215 jalview.datamodel.SequenceGroup sg = new jalview.datamodel.SequenceGroup(
2216 seqs, groups[i].getName(), cs, groups[i].getDisplayBoxes(),
2217 groups[i].getDisplayText(), groups[i].getColourText(),
2218 groups[i].getStart(), groups[i].getEnd());
2221 .setOutlineColour(new java.awt.Color(groups[i]
2222 .getOutlineColour()));
2224 sg.textColour = new java.awt.Color(groups[i].getTextCol1());
2225 sg.textColour2 = new java.awt.Color(groups[i].getTextCol2());
2226 sg.setShowunconserved(groups[i].hasShowUnconserved() ? groups[i]
2227 .isShowUnconserved() : false);
2228 sg.thresholdTextColour = groups[i].getTextColThreshold();
2229 if (groups[i].hasShowConsensusHistogram()) {
2230 sg.setShowConsensusHistogram(groups[i].isShowConsensusHistogram());
2232 if (groups[i].hasShowSequenceLogo()) {
2233 sg.setIncludeAllConsSymbols(groups[i].isShowSequenceLogo());
2235 if (groups[i].hasIgnoreGapsinConsensus())
2237 sg.setIgnoreGapsConsensus(groups[i].getIgnoreGapsinConsensus());
2239 if (groups[i].getConsThreshold() != 0)
2241 jalview.analysis.Conservation c = new jalview.analysis.Conservation(
2242 "All", ResidueProperties.propHash, 3, sg
2243 .getSequences(null), 0, sg.getWidth() - 1);
2245 c.verdict(false, 25);
2246 sg.cs.setConservation(c);
2249 if (groups[i].getId()!=null
2250 && groupAnnotRefs.size()>0)
2252 // re-instate unique group/annotation row reference
2253 jalview.datamodel.AlignmentAnnotation jaa = (jalview.datamodel.AlignmentAnnotation) groupAnnotRefs.get(groups[i].getId());
2264 // ///////////////////////////////
2267 // If we just load in the same jar file again, the sequenceSetId
2268 // will be the same, and we end up with multiple references
2269 // to the same sequenceSet. We must modify this id on load
2270 // so that each load of the file gives a unique id
2271 String uniqueSeqSetId = view.getSequenceSetId() + uniqueSetSuffix;
2272 String viewId = (view.getId() == null ? null : view.getId()
2274 AlignFrame af = null;
2275 AlignViewport av = null;
2276 // now check to see if we really need to create a new viewport.
2277 if (multipleView && viewportsAdded.size() == 0)
2279 // We recovered an alignment for which a viewport already exists.
2280 // TODO: fix up any settings necessary for overlaying stored state onto
2281 // state recovered from another document. (may not be necessary).
2282 // we may need a binding from a viewport in memory to one recovered from
2284 // and then recover its containing af to allow the settings to be applied.
2285 // TODO: fix for vamsas demo
2287 .println("About to recover a viewport for existing alignment: Sequence set ID is "
2289 Object seqsetobj = retrieveExistingObj(uniqueSeqSetId);
2290 if (seqsetobj != null)
2292 if (seqsetobj instanceof String)
2294 uniqueSeqSetId = (String) seqsetobj;
2296 .println("Recovered extant sequence set ID mapping for ID : New Sequence set ID is "
2302 .println("Warning : Collision between sequence set ID string and existing jalview object mapping.");
2307 AlignmentPanel ap = null;
2308 boolean isnewview = true;
2311 // Check to see if this alignment already has a view id == viewId
2312 jalview.gui.AlignmentPanel views[] = Desktop
2313 .getAlignmentPanels(uniqueSeqSetId);
2314 if (views != null && views.length > 0)
2316 for (int v = 0; v < views.length; v++)
2318 if (views[v].av.getViewId().equalsIgnoreCase(viewId))
2320 // recover the existing alignpanel, alignframe, viewport
2321 af = views[v].alignFrame;
2324 // TODO: could even skip resetting view settings if we don't want to
2325 // change the local settings from other jalview processes
2334 af = loadViewport(file, JSEQ, hiddenSeqs, al, hideConsensus,
2335 hideQuality, hideConservation, jms, view, uniqueSeqSetId,
2341 // /////////////////////////////////////
2342 if (loadTreesAndStructures && jms.getTreeCount() > 0)
2346 for (int t = 0; t < jms.getTreeCount(); t++)
2349 Tree tree = jms.getTree(t);
2351 TreePanel tp = (TreePanel) retrieveExistingObj(tree.getId());
2354 tp = af.ShowNewickTree(new jalview.io.NewickFile(tree
2355 .getNewick()), tree.getTitle(), tree.getWidth(), tree
2356 .getHeight(), tree.getXpos(), tree.getYpos());
2357 if (tree.getId() != null)
2359 // perhaps bind the tree id to something ?
2364 // update local tree attributes ?
2365 // TODO: should check if tp has been manipulated by user - if so its
2366 // settings shouldn't be modified
2367 tp.setTitle(tree.getTitle());
2368 tp.setBounds(new Rectangle(tree.getXpos(), tree.getYpos(), tree
2369 .getWidth(), tree.getHeight()));
2370 tp.av = av; // af.viewport; // TODO: verify 'associate with all
2373 tp.treeCanvas.av = av; // af.viewport;
2374 tp.treeCanvas.ap = ap; // af.alignPanel;
2379 warn("There was a problem recovering stored Newick tree: \n"
2380 + tree.getNewick());
2384 tp.fitToWindow.setState(tree.getFitToWindow());
2385 tp.fitToWindow_actionPerformed(null);
2387 if (tree.getFontName() != null)
2389 tp.setTreeFont(new java.awt.Font(tree.getFontName(), tree
2390 .getFontStyle(), tree.getFontSize()));
2394 tp.setTreeFont(new java.awt.Font(view.getFontName(), view
2395 .getFontStyle(), tree.getFontSize()));
2398 tp.showPlaceholders(tree.getMarkUnlinked());
2399 tp.showBootstrap(tree.getShowBootstrap());
2400 tp.showDistances(tree.getShowDistances());
2402 tp.treeCanvas.threshold = tree.getThreshold();
2404 if (tree.getCurrentTree())
2406 af.viewport.setCurrentTree(tp.getTree());
2410 } catch (Exception ex)
2412 ex.printStackTrace();
2416 // //LOAD STRUCTURES
2417 if (loadTreesAndStructures)
2419 for (int i = 0; i < JSEQ.length; i++)
2421 if (JSEQ[i].getPdbidsCount() > 0)
2423 Pdbids[] ids = JSEQ[i].getPdbids();
2424 for (int p = 0; p < ids.length; p++)
2426 for (int s = 0; s < ids[p].getStructureStateCount(); s++)
2428 // check to see if we haven't already created this structure view
2429 String sviewid = (ids[p].getStructureState(s).getViewId() == null) ? null
2430 : ids[p].getStructureState(s).getViewId()
2432 jalview.datamodel.PDBEntry jpdb = new jalview.datamodel.PDBEntry();
2433 // Originally : ids[p].getFile()
2434 // : TODO: verify external PDB file recovery still works in normal
2435 // jalview project load
2436 jpdb.setFile(loadPDBFile(jprovider, ids[p].getId()));
2437 jpdb.setId(ids[p].getId());
2439 int x = ids[p].getStructureState(s).getXpos();
2440 int y = ids[p].getStructureState(s).getYpos();
2441 int width = ids[p].getStructureState(s).getWidth();
2442 int height = ids[p].getStructureState(s).getHeight();
2443 AppJmol comp = null;
2444 JInternalFrame[] frames = null;
2449 frames = Desktop.desktop.getAllFrames();
2450 } catch (ArrayIndexOutOfBoundsException e)
2452 // occasional No such child exceptions are thrown here...
2457 } catch (Exception f)
2462 } while (frames == null);
2463 // search for any Jmol windows already open from other
2464 // alignment views that exactly match the stored structure state
2465 for (int f = 0; comp == null && f < frames.length; f++)
2467 if (frames[f] instanceof AppJmol)
2470 && ((AppJmol) frames[f]).getViewId().equals(
2473 // post jalview 2.4 schema includes structure view id
2474 comp = (AppJmol) frames[f];
2476 else if (frames[f].getX() == x && frames[f].getY() == y
2477 && frames[f].getHeight() == height
2478 && frames[f].getWidth() == width)
2480 comp = (AppJmol) frames[f];
2484 // Probably don't need to do this anymore...
2485 // Desktop.desktop.getComponentAt(x, y);
2486 // TODO: NOW: check that this recovers the PDB file correctly.
2487 String pdbFile = loadPDBFile(jprovider, ids[p].getId());
2489 jalview.datamodel.SequenceI[] seq = new jalview.datamodel.SequenceI[]
2490 { (jalview.datamodel.SequenceI) seqRefIds.get(JSEQ[i].getId()
2495 // create a new Jmol window
2496 String state = ids[p].getStructureState(s).getContent();
2497 StringBuffer newFileLoc = null;
2498 if (state.indexOf("load") > -1)
2500 newFileLoc = new StringBuffer(state.substring(0, state
2501 .indexOf("\"", state.indexOf("load")) + 1));
2503 newFileLoc.append(jpdb.getFile());
2504 newFileLoc.append(state.substring(state.indexOf("\"",
2505 state.indexOf("load \"") + 6)));
2510 .println("Ignoring incomplete Jmol state for PDB "
2513 newFileLoc = new StringBuffer(state);
2514 newFileLoc.append("; load \"");
2515 newFileLoc.append(jpdb.getFile());
2516 newFileLoc.append("\";");
2519 if (newFileLoc != null)
2521 new AppJmol(pdbFile, ids[p].getId(), seq, af.alignPanel,
2522 newFileLoc.toString(), new java.awt.Rectangle(x,
2523 y, width, height), sviewid);
2528 // if (comp != null)
2530 // NOTE: if the jalview project is part of a shared session then
2531 // view synchronization should/could be done here.
2533 // add mapping for this sequence to the already open Jmol
2534 // instance (if it doesn't already exist)
2536 StructureSelectionManager.getStructureSelectionManager()
2537 .setMapping(seq, null, pdbFile,
2538 jalview.io.AppletFormatAdapter.FILE);
2540 ((AppJmol) comp).addSequence(seq);
2551 AlignFrame loadViewport(String file, JSeq[] JSEQ, Vector hiddenSeqs,
2552 Alignment al, boolean hideConsensus, boolean hideQuality,
2553 boolean hideConservation, JalviewModelSequence jms,
2554 Viewport view, String uniqueSeqSetId, String viewId)
2556 AlignFrame af = null;
2557 af = new AlignFrame(al, view.getWidth(), view.getHeight(),
2558 uniqueSeqSetId, viewId);
2560 af.setFileName(file, "Jalview");
2562 for (int i = 0; i < JSEQ.length; i++)
2564 af.viewport.setSequenceColour(af.viewport.alignment.getSequenceAt(i),
2565 new java.awt.Color(JSEQ[i].getColour()));
2568 af.viewport.gatherViewsHere = view.getGatheredViews();
2570 if (view.getSequenceSetId() != null)
2572 jalview.gui.AlignViewport av = (jalview.gui.AlignViewport) viewportsAdded
2573 .get(uniqueSeqSetId);
2575 af.viewport.sequenceSetID = uniqueSeqSetId;
2578 // propagate shared settings to this new view
2579 af.viewport.historyList = av.historyList;
2580 af.viewport.redoList = av.redoList;
2584 viewportsAdded.put(uniqueSeqSetId, af.viewport);
2586 // TODO: check if this method can be called repeatedly without
2587 // side-effects if alignpanel already registered.
2588 PaintRefresher.Register(af.alignPanel, uniqueSeqSetId);
2590 // apply Hidden regions to view.
2591 if (hiddenSeqs != null)
2593 for (int s = 0; s < JSEQ.length; s++)
2595 jalview.datamodel.SequenceGroup hidden = new jalview.datamodel.SequenceGroup();
2597 for (int r = 0; r < JSEQ[s].getHiddenSequencesCount(); r++)
2599 hidden.addSequence(al
2600 .getSequenceAt(JSEQ[s].getHiddenSequences(r)), false);
2602 af.viewport.hideRepSequences(al.getSequenceAt(s), hidden);
2605 jalview.datamodel.SequenceI[] hseqs = new jalview.datamodel.SequenceI[hiddenSeqs
2608 for (int s = 0; s < hiddenSeqs.size(); s++)
2610 hseqs[s] = (jalview.datamodel.SequenceI) hiddenSeqs.elementAt(s);
2613 af.viewport.hideSequence(hseqs);
2616 // set visibility of annotation in view
2617 if ((hideConsensus || hideQuality || hideConservation)
2618 && al.getAlignmentAnnotation() != null)
2620 int hSize = al.getAlignmentAnnotation().length;
2621 for (int h = 0; h < hSize; h++)
2623 if ((hideConsensus && al.getAlignmentAnnotation()[h].label
2624 .equals("Consensus"))
2625 || (hideQuality && al.getAlignmentAnnotation()[h].label
2627 || (hideConservation && al.getAlignmentAnnotation()[h].label
2628 .equals("Conservation")))
2630 al.deleteAnnotation(al.getAlignmentAnnotation()[h]);
2635 af.alignPanel.adjustAnnotationHeight();
2637 // recover view properties and display parameters
2638 if (view.getViewName() != null)
2640 af.viewport.viewName = view.getViewName();
2641 af.setInitialTabVisible();
2643 af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(), view
2646 af.viewport.setShowAnnotation(view.getShowAnnotation());
2647 af.viewport.setAbovePIDThreshold(view.getPidSelected());
2649 af.viewport.setColourText(view.getShowColourText());
2651 af.viewport.setConservationSelected(view.getConservationSelected());
2652 af.viewport.setShowJVSuffix(view.getShowFullId());
2653 af.viewport.rightAlignIds = view.getRightAlignIds();
2654 af.viewport.setFont(new java.awt.Font(view.getFontName(), view
2655 .getFontStyle(), view.getFontSize()));
2656 af.alignPanel.fontChanged();
2657 af.viewport.setRenderGaps(view.getRenderGaps());
2658 af.viewport.setWrapAlignment(view.getWrapAlignment());
2659 af.alignPanel.setWrapAlignment(view.getWrapAlignment());
2660 af.viewport.setShowAnnotation(view.getShowAnnotation());
2661 af.alignPanel.setAnnotationVisible(view.getShowAnnotation());
2663 af.viewport.setShowBoxes(view.getShowBoxes());
2665 af.viewport.setShowText(view.getShowText());
2667 af.viewport.textColour = new java.awt.Color(view.getTextCol1());
2668 af.viewport.textColour2 = new java.awt.Color(view.getTextCol2());
2669 af.viewport.thresholdTextColour = view.getTextColThreshold();
2670 af.viewport.setShowUnconserved(view.hasShowUnconserved() ? view
2671 .isShowUnconserved() : false);
2672 af.viewport.setStartRes(view.getStartRes());
2673 af.viewport.setStartSeq(view.getStartSeq());
2675 ColourSchemeI cs = null;
2676 // apply colourschemes
2677 if (view.getBgColour() != null)
2679 if (view.getBgColour().startsWith("ucs"))
2681 cs = GetUserColourScheme(jms, view.getBgColour());
2683 else if (view.getBgColour().startsWith("Annotation"))
2685 // int find annotation
2686 for (int i = 0; i < af.viewport.alignment.getAlignmentAnnotation().length; i++)
2688 if (af.viewport.alignment.getAlignmentAnnotation()[i].label
2689 .equals(view.getAnnotationColours().getAnnotation()))
2691 if (af.viewport.alignment.getAlignmentAnnotation()[i]
2692 .getThreshold() == null)
2694 af.viewport.alignment.getAlignmentAnnotation()[i]
2695 .setThreshold(new jalview.datamodel.GraphLine(view
2696 .getAnnotationColours().getThreshold(),
2697 "Threshold", java.awt.Color.black)
2702 if (view.getAnnotationColours().getColourScheme()
2705 cs = new AnnotationColourGradient(af.viewport.alignment
2706 .getAlignmentAnnotation()[i], new java.awt.Color(view
2707 .getAnnotationColours().getMinColour()),
2708 new java.awt.Color(view.getAnnotationColours()
2709 .getMaxColour()), view.getAnnotationColours()
2710 .getAboveThreshold());
2712 else if (view.getAnnotationColours().getColourScheme()
2715 cs = new AnnotationColourGradient(af.viewport.alignment
2716 .getAlignmentAnnotation()[i], GetUserColourScheme(
2717 jms, view.getAnnotationColours().getColourScheme()),
2718 view.getAnnotationColours().getAboveThreshold());
2722 cs = new AnnotationColourGradient(af.viewport.alignment
2723 .getAlignmentAnnotation()[i], ColourSchemeProperty
2724 .getColour(al, view.getAnnotationColours()
2725 .getColourScheme()), view
2726 .getAnnotationColours().getAboveThreshold());
2729 // Also use these settings for all the groups
2730 if (al.getGroups() != null)
2732 for (int g = 0; g < al.getGroups().size(); g++)
2734 jalview.datamodel.SequenceGroup sg = (jalview.datamodel.SequenceGroup) al
2735 .getGroups().elementAt(g);
2744 * (view.getAnnotationColours().getColourScheme().equals("None"
2745 * )) { sg.cs = new AnnotationColourGradient(
2746 * af.viewport.alignment.getAlignmentAnnotation()[i], new
2747 * java.awt.Color(view.getAnnotationColours(). getMinColour()),
2748 * new java.awt.Color(view.getAnnotationColours().
2750 * view.getAnnotationColours().getAboveThreshold()); } else
2753 sg.cs = new AnnotationColourGradient(
2754 af.viewport.alignment.getAlignmentAnnotation()[i],
2755 sg.cs, view.getAnnotationColours()
2756 .getAboveThreshold());
2769 cs = ColourSchemeProperty.getColour(al, view.getBgColour());
2774 cs.setThreshold(view.getPidThreshold(), true);
2775 cs.setConsensus(af.viewport.hconsensus);
2779 af.viewport.setGlobalColourScheme(cs);
2780 af.viewport.setColourAppliesToAllGroups(false);
2782 if (view.getConservationSelected() && cs != null)
2784 cs.setConservationInc(view.getConsThreshold());
2787 af.changeColour(cs);
2789 af.viewport.setColourAppliesToAllGroups(true);
2791 if (view.getShowSequenceFeatures())
2793 af.viewport.showSequenceFeatures = true;
2795 if (view.hasCentreColumnLabels())
2797 af.viewport.setCentreColumnLabels(view.getCentreColumnLabels());
2799 if (view.hasIgnoreGapsinConsensus())
2801 af.viewport.ignoreGapsInConsensusCalculation=view.getIgnoreGapsinConsensus();
2803 if (view.hasFollowHighlight())
2805 af.viewport.followHighlight = view.getFollowHighlight();
2807 if (view.hasFollowSelection())
2809 af.viewport.followSelection = view.getFollowSelection();
2811 if (view.hasShowConsensusHistogram())
2813 af.viewport.setShowConsensusHistogram(view.getShowConsensusHistogram());
2815 af.viewport.setShowConsensusHistogram(true);
2817 if (view.hasShowSequenceLogo())
2819 af.viewport.setShowSequenceLogo(view.getShowSequenceLogo());
2821 af.viewport.setShowSequenceLogo(false);
2823 if (view.hasShowDbRefTooltip())
2825 af.viewport.setShowDbRefs(view.getShowDbRefTooltip());
2827 if (view.hasShowNPfeatureTooltip())
2829 af.viewport.setShowNpFeats(view.hasShowNPfeatureTooltip());
2831 if (view.hasShowGroupConsensus())
2833 af.viewport.setShowGroupConsensus(view.getShowGroupConsensus());
2835 af.viewport.setShowGroupConsensus(false);
2837 if (view.hasShowGroupConservation())
2839 af.viewport.setShowGroupConservation(view.getShowGroupConservation());
2841 af.viewport.setShowGroupConservation(false);
2844 // recover featre settings
2845 if (jms.getFeatureSettings() != null)
2847 af.viewport.featuresDisplayed = new Hashtable();
2848 String[] renderOrder = new String[jms.getFeatureSettings()
2849 .getSettingCount()];
2850 for (int fs = 0; fs < jms.getFeatureSettings().getSettingCount(); fs++)
2852 Setting setting = jms.getFeatureSettings().getSetting(fs);
2853 if (setting.hasMincolour())
2855 GraduatedColor gc = setting.hasMin() ? new GraduatedColor(new java.awt.Color(setting
2857 new java.awt.Color(setting.getColour()), setting.getMin(), setting.getMax())
2858 : new GraduatedColor(new java.awt.Color(setting
2860 new java.awt.Color(setting.getColour()), 0,1);
2861 if (setting.hasThreshold())
2863 gc.setThresh(setting.getThreshold());
2864 gc.setThreshType(setting.getThreshstate());
2866 gc.setAutoScaled(true); // default
2867 if (setting.hasAutoScale())
2869 gc.setAutoScaled(setting.getAutoScale());
2871 if (setting.hasColourByLabel())
2873 gc.setColourByLabel(setting.getColourByLabel());
2875 // and put in the feature colour table.
2876 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(setting.getType(),gc);
2880 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(
2882 new java.awt.Color(setting.getColour()));
2884 renderOrder[fs] = setting.getType();
2885 if (setting.hasOrder())
2886 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setOrder(
2887 setting.getType(), setting.getOrder());
2889 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setOrder(
2891 fs / jms.getFeatureSettings().getSettingCount());
2892 if (setting.getDisplay())
2894 af.viewport.featuresDisplayed.put(setting.getType(), new Integer(
2895 setting.getColour()));
2898 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder = renderOrder;
2900 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureGroups = fgtable = new Hashtable();
2901 for (int gs = 0; gs < jms.getFeatureSettings().getGroupCount(); gs++)
2903 Group grp = jms.getFeatureSettings().getGroup(gs);
2904 fgtable.put(grp.getName(), new Boolean(grp.getDisplay()));
2908 if (view.getHiddenColumnsCount() > 0)
2910 for (int c = 0; c < view.getHiddenColumnsCount(); c++)
2912 af.viewport.hideColumns(view.getHiddenColumns(c).getStart(), view
2913 .getHiddenColumns(c).getEnd() // +1
2918 af.setMenusFromViewport(af.viewport);
2919 af.alignPanel.updateAnnotation(false); // recompute any autoannotation
2920 // TODO: we don't need to do this if the viewport is aready visible.
2921 Desktop.addInternalFrame(af, view.getTitle(), view.getWidth(), view
2926 Hashtable skipList = null;
2929 * TODO remove this method
2932 * @return AlignFrame bound to sequenceSetId from view, if one exists. private
2933 * AlignFrame getSkippedFrame(Viewport view) { if (skipList==null) {
2934 * throw new Error("Implementation Error. No skipList defined for this
2935 * Jalview2XML instance."); } return (AlignFrame)
2936 * skipList.get(view.getSequenceSetId()); }
2940 * Check if the Jalview view contained in object should be skipped or not.
2943 * @return true if view's sequenceSetId is a key in skipList
2945 private boolean skipViewport(JalviewModel object)
2947 if (skipList == null)
2952 if (skipList.containsKey(id = object.getJalviewModelSequence()
2953 .getViewport()[0].getSequenceSetId()))
2955 if (Cache.log != null && Cache.log.isDebugEnabled())
2957 Cache.log.debug("Skipping seuqence set id " + id);
2964 public void AddToSkipList(AlignFrame af)
2966 if (skipList == null)
2968 skipList = new Hashtable();
2970 skipList.put(af.getViewport().getSequenceSetId(), af);
2973 public void clearSkipList()
2975 if (skipList != null)
2982 private void recoverDatasetFor(SequenceSet vamsasSet, Alignment al)
2984 jalview.datamodel.Alignment ds = getDatasetFor(vamsasSet.getDatasetId());
2985 Vector dseqs = null;
2988 // create a list of new dataset sequences
2989 dseqs = new Vector();
2991 for (int i = 0, iSize = vamsasSet.getSequenceCount(); i < iSize; i++)
2993 Sequence vamsasSeq = vamsasSet.getSequence(i);
2994 ensureJalviewDatasetSequence(vamsasSeq, ds, dseqs);
2996 // create a new dataset
2999 SequenceI[] dsseqs = new SequenceI[dseqs.size()];
3000 dseqs.copyInto(dsseqs);
3001 ds = new jalview.datamodel.Alignment(dsseqs);
3002 debug("Created new dataset " + vamsasSet.getDatasetId()
3003 + " for alignment " + System.identityHashCode(al));
3004 addDatasetRef(vamsasSet.getDatasetId(), ds);
3006 // set the dataset for the newly imported alignment.
3007 if (al.getDataset() == null)
3016 * sequence definition to create/merge dataset sequence for
3020 * vector to add new dataset sequence to
3022 private void ensureJalviewDatasetSequence(Sequence vamsasSeq,
3023 AlignmentI ds, Vector dseqs)
3025 // JBP TODO: Check this is called for AlCodonFrames to support recovery of
3027 jalview.datamodel.Sequence sq = (jalview.datamodel.Sequence) seqRefIds
3028 .get(vamsasSeq.getId());
3029 jalview.datamodel.SequenceI dsq = null;
3030 if (sq != null && sq.getDatasetSequence() != null)
3032 dsq = (jalview.datamodel.SequenceI) sq.getDatasetSequence();
3035 String sqid = vamsasSeq.getDsseqid();
3038 // need to create or add a new dataset sequence reference to this sequence
3041 dsq = (jalview.datamodel.SequenceI) seqRefIds.get(sqid);
3046 // make a new dataset sequence
3047 dsq = sq.createDatasetSequence();
3050 // make up a new dataset reference for this sequence
3051 sqid = seqHash(dsq);
3053 dsq.setVamsasId(uniqueSetSuffix + sqid);
3054 seqRefIds.put(sqid, dsq);
3059 dseqs.addElement(dsq);
3064 ds.addSequence(dsq);
3070 { // make this dataset sequence sq's dataset sequence
3071 sq.setDatasetSequence(dsq);
3075 // TODO: refactor this as a merge dataset sequence function
3076 // now check that sq (the dataset sequence) sequence really is the union of
3077 // all references to it
3078 // boolean pre = sq.getStart() < dsq.getStart();
3079 // boolean post = sq.getEnd() > dsq.getEnd();
3083 StringBuffer sb = new StringBuffer();
3084 String newres = jalview.analysis.AlignSeq.extractGaps(
3085 jalview.util.Comparison.GapChars, sq.getSequenceAsString());
3086 if (!newres.equalsIgnoreCase(dsq.getSequenceAsString())
3087 && newres.length() > dsq.getLength())
3089 // Update with the longer sequence.
3093 * if (pre) { sb.insert(0, newres .substring(0, dsq.getStart() -
3094 * sq.getStart())); dsq.setStart(sq.getStart()); } if (post) {
3095 * sb.append(newres.substring(newres.length() - sq.getEnd() -
3096 * dsq.getEnd())); dsq.setEnd(sq.getEnd()); }
3098 dsq.setSequence(sb.toString());
3100 // TODO: merges will never happen if we 'know' we have the real dataset
3101 // sequence - this should be detected when id==dssid
3102 System.err.println("DEBUG Notice: Merged dataset sequence"); // ("
3103 // + (pre ? "prepended" : "") + " "
3104 // + (post ? "appended" : ""));
3109 java.util.Hashtable datasetIds = null;
3111 java.util.IdentityHashMap dataset2Ids = null;
3113 private Alignment getDatasetFor(String datasetId)
3115 if (datasetIds == null)
3117 datasetIds = new Hashtable();
3120 if (datasetIds.containsKey(datasetId))
3122 return (Alignment) datasetIds.get(datasetId);
3127 private void addDatasetRef(String datasetId, Alignment dataset)
3129 if (datasetIds == null)
3131 datasetIds = new Hashtable();
3133 datasetIds.put(datasetId, dataset);
3137 * make a new dataset ID for this jalview dataset alignment
3142 private String getDatasetIdRef(jalview.datamodel.Alignment dataset)
3144 if (dataset.getDataset() != null)
3146 warn("Serious issue! Dataset Object passed to getDatasetIdRef is not a Jalview DATASET alignment...");
3148 String datasetId = makeHashCode(dataset, null);
3149 if (datasetId == null)
3151 // make a new datasetId and record it
3152 if (dataset2Ids == null)
3154 dataset2Ids = new IdentityHashMap();
3158 datasetId = (String) dataset2Ids.get(dataset);
3160 if (datasetId == null)
3162 datasetId = "ds" + dataset2Ids.size() + 1;
3163 dataset2Ids.put(dataset, datasetId);
3169 private void addDBRefs(SequenceI datasetSequence, Sequence sequence)
3171 for (int d = 0; d < sequence.getDBRefCount(); d++)
3173 DBRef dr = sequence.getDBRef(d);
3174 jalview.datamodel.DBRefEntry entry = new jalview.datamodel.DBRefEntry(
3175 sequence.getDBRef(d).getSource(), sequence.getDBRef(d)
3176 .getVersion(), sequence.getDBRef(d).getAccessionId());
3177 if (dr.getMapping() != null)
3179 entry.setMap(addMapping(dr.getMapping()));
3181 datasetSequence.addDBRef(entry);
3185 private jalview.datamodel.Mapping addMapping(Mapping m)
3187 SequenceI dsto = null;
3188 // Mapping m = dr.getMapping();
3189 int fr[] = new int[m.getMapListFromCount() * 2];
3190 Enumeration f = m.enumerateMapListFrom();
3191 for (int _i = 0; f.hasMoreElements(); _i += 2)
3193 MapListFrom mf = (MapListFrom) f.nextElement();
3194 fr[_i] = mf.getStart();
3195 fr[_i + 1] = mf.getEnd();
3197 int fto[] = new int[m.getMapListToCount() * 2];
3198 f = m.enumerateMapListTo();
3199 for (int _i = 0; f.hasMoreElements(); _i += 2)
3201 MapListTo mf = (MapListTo) f.nextElement();
3202 fto[_i] = mf.getStart();
3203 fto[_i + 1] = mf.getEnd();
3205 jalview.datamodel.Mapping jmap = new jalview.datamodel.Mapping(dsto,
3206 fr, fto, (int) m.getMapFromUnit(), (int) m.getMapToUnit());
3207 if (m.getMappingChoice() != null)
3209 MappingChoice mc = m.getMappingChoice();
3210 if (mc.getDseqFor() != null)
3212 String dsfor = "" + mc.getDseqFor();
3213 if (seqRefIds.containsKey(dsfor))
3218 jmap.setTo((SequenceI) seqRefIds.get(dsfor));
3222 frefedSequence.add(new Object[]
3229 * local sequence definition
3231 Sequence ms = mc.getSequence();
3232 jalview.datamodel.Sequence djs = null;
3233 String sqid = ms.getDsseqid();
3234 if (sqid != null && sqid.length() > 0)
3237 * recover dataset sequence
3239 djs = (jalview.datamodel.Sequence) seqRefIds.get(sqid);
3244 .println("Warning - making up dataset sequence id for DbRef sequence map reference");
3245 sqid = ((Object) ms).toString(); // make up a new hascode for
3246 // undefined dataset sequence hash
3247 // (unlikely to happen)
3253 * make a new dataset sequence and add it to refIds hash
3255 djs = new jalview.datamodel.Sequence(ms.getName(), ms
3257 djs.setStart(jmap.getMap().getToLowest());
3258 djs.setEnd(jmap.getMap().getToHighest());
3259 djs.setVamsasId(uniqueSetSuffix + sqid);
3261 seqRefIds.put(sqid, djs);
3264 jalview.bin.Cache.log.debug("about to recurse on addDBRefs.");
3273 public jalview.gui.AlignmentPanel copyAlignPanel(AlignmentPanel ap,
3274 boolean keepSeqRefs)
3277 jalview.schemabinding.version2.JalviewModel jm = SaveState(ap, null,
3283 jm.getJalviewModelSequence().getViewport(0).setSequenceSetId(null);
3287 uniqueSetSuffix = "";
3288 jm.getJalviewModelSequence().getViewport(0).setId(null); // we don't
3293 if (this.frefedSequence == null)
3295 frefedSequence = new Vector();
3298 viewportsAdded = new Hashtable();
3300 AlignFrame af = LoadFromObject(jm, null, false, null);
3301 af.alignPanels.clear();
3302 af.closeMenuItem_actionPerformed(true);
3305 * if(ap.av.alignment.getAlignmentAnnotation()!=null) { for(int i=0;
3306 * i<ap.av.alignment.getAlignmentAnnotation().length; i++) {
3307 * if(!ap.av.alignment.getAlignmentAnnotation()[i].autoCalculated) {
3308 * af.alignPanel.av.alignment.getAlignmentAnnotation()[i] =
3309 * ap.av.alignment.getAlignmentAnnotation()[i]; } } }
3312 return af.alignPanel;
3316 * flag indicating if hashtables should be cleared on finalization TODO this
3317 * flag may not be necessary
3319 private boolean _cleartables = true;
3321 private Hashtable jvids2vobj;
3326 * @see java.lang.Object#finalize()
3328 protected void finalize() throws Throwable
3330 // really make sure we have no buried refs left.
3335 this.seqRefIds = null;
3336 this.seqsToIds = null;
3340 private void warn(String msg)
3345 private void warn(String msg, Exception e)
3347 if (Cache.log != null)
3351 Cache.log.warn(msg, e);
3355 Cache.log.warn(msg);
3360 System.err.println("Warning: " + msg);
3363 e.printStackTrace();
3368 private void debug(String string)
3370 debug(string, null);
3373 private void debug(String msg, Exception e)
3375 if (Cache.log != null)
3379 Cache.log.debug(msg, e);
3383 Cache.log.debug(msg);
3388 System.err.println("Warning: " + msg);
3391 e.printStackTrace();
3397 * set the object to ID mapping tables used to write/recover objects and XML
3398 * ID strings for the jalview project. If external tables are provided then
3399 * finalize and clearSeqRefs will not clear the tables when the Jalview2XML
3400 * object goes out of scope. - also populates the datasetIds hashtable with
3401 * alignment objects containing dataset sequences
3404 * Map from ID strings to jalview datamodel
3406 * Map from jalview datamodel to ID strings
3410 public void setObjectMappingTables(Hashtable vobj2jv,
3411 IdentityHashMap jv2vobj)
3413 this.jv2vobj = jv2vobj;
3414 this.vobj2jv = vobj2jv;
3415 Iterator ds = jv2vobj.keySet().iterator();
3417 while (ds.hasNext())
3419 Object jvobj = ds.next();
3420 id = jv2vobj.get(jvobj).toString();
3421 if (jvobj instanceof jalview.datamodel.Alignment)
3423 if (((jalview.datamodel.Alignment) jvobj).getDataset() == null)
3425 addDatasetRef(id, (jalview.datamodel.Alignment) jvobj);
3428 else if (jvobj instanceof jalview.datamodel.Sequence)
3430 // register sequence object so the XML parser can recover it.
3431 if (seqRefIds == null)
3433 seqRefIds = new Hashtable();
3435 if (seqsToIds == null)
3437 seqsToIds = new IdentityHashMap();
3439 seqRefIds.put(jv2vobj.get(jvobj).toString(), jvobj);
3440 seqsToIds.put(jvobj, id);
3442 else if (jvobj instanceof jalview.datamodel.AlignmentAnnotation)
3444 if (annotationIds == null)
3446 annotationIds = new Hashtable();
3449 annotationIds.put(anid = jv2vobj.get(jvobj).toString(), jvobj);
3450 jalview.datamodel.AlignmentAnnotation jvann = (jalview.datamodel.AlignmentAnnotation) jvobj;
3451 if (jvann.annotationId == null)
3453 jvann.annotationId = anid;
3455 if (!jvann.annotationId.equals(anid))
3457 // TODO verify that this is the correct behaviour
3458 this.warn("Overriding Annotation ID for " + anid
3459 + " from different id : " + jvann.annotationId);
3460 jvann.annotationId = anid;
3463 else if (jvobj instanceof String)
3465 if (jvids2vobj == null)
3467 jvids2vobj = new Hashtable();
3468 jvids2vobj.put(jvobj, jv2vobj.get(jvobj).toString());
3472 Cache.log.debug("Ignoring " + jvobj.getClass() + " (ID = " + id);
3477 * set the uniqueSetSuffix used to prefix/suffix object IDs for jalview
3478 * objects created from the project archive. If string is null (default for
3479 * construction) then suffix will be set automatically.
3483 public void setUniqueSetSuffix(String string)
3485 uniqueSetSuffix = string;
3490 * uses skipList2 as the skipList for skipping views on sequence sets
3491 * associated with keys in the skipList
3495 public void setSkipList(Hashtable skipList2)
3497 skipList = skipList2;