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;
24 import java.util.jar.*;
28 import org.exolab.castor.xml.*;
30 import uk.ac.vamsas.objects.utils.MapList;
31 import jalview.bin.Cache;
32 import jalview.datamodel.Alignment;
33 import jalview.datamodel.AlignmentI;
34 import jalview.datamodel.SequenceI;
35 import jalview.schemabinding.version2.*;
36 import jalview.schemes.*;
37 import jalview.structure.StructureSelectionManager;
38 import jalview.util.jarInputStreamProvider;
41 * Write out the current jalview desktop state as a Jalview XML stream.
43 * Note: the vamsas objects referred to here are primitive versions of the
44 * VAMSAS project schema elements - they are not the same and most likely never
50 public class Jalview2XML
53 * create/return unique hash string for sq
56 * @return new or existing unique string for sq
58 String seqHash(SequenceI sq)
60 if (seqsToIds == null)
64 if (seqsToIds.containsKey(sq))
66 return (String) seqsToIds.get(sq);
70 // create sequential key
71 String key = "sq" + (seqsToIds.size() + 1);
72 key = makeHashCode(sq, key); // check we don't have an external reference
74 seqsToIds.put(sq, key);
83 if (seqRefIds != null)
87 if (seqsToIds != null)
97 warn("clearSeqRefs called when _cleartables was not set. Doing nothing.");
98 // seqRefIds = new Hashtable();
99 // seqsToIds = new IdentityHashMap();
105 if (seqsToIds == null)
107 seqsToIds = new IdentityHashMap();
109 if (seqRefIds == null)
111 seqRefIds = new Hashtable();
116 * SequenceI reference -> XML ID string in jalview XML. Populated as XML reps
117 * of sequence objects are created.
119 java.util.IdentityHashMap seqsToIds = null;
122 * jalview XML Sequence ID to jalview sequence object reference (both dataset
123 * and alignment sequences. Populated as XML reps of sequence objects are
126 java.util.Hashtable seqRefIds = null; // key->SequenceI resolution
128 Vector frefedSequence = null;
130 boolean raiseGUI = true; // whether errors are raised in dialog boxes or not
136 public Jalview2XML(boolean raiseGUI)
138 this.raiseGUI = raiseGUI;
141 public void resolveFrefedSequences()
143 if (frefedSequence.size() > 0)
145 int r = 0, rSize = frefedSequence.size();
148 Object[] ref = (Object[]) frefedSequence.elementAt(r);
151 String sref = (String) ref[0];
152 if (seqRefIds.containsKey(sref))
154 if (ref[1] instanceof jalview.datamodel.Mapping)
156 SequenceI seq = (SequenceI) seqRefIds.get(sref);
157 while (seq.getDatasetSequence() != null)
159 seq = seq.getDatasetSequence();
161 ((jalview.datamodel.Mapping) ref[1]).setTo(seq);
165 if (ref[1] instanceof jalview.datamodel.AlignedCodonFrame)
167 SequenceI seq = (SequenceI) seqRefIds.get(sref);
168 while (seq.getDatasetSequence() != null)
170 seq = seq.getDatasetSequence();
173 && ref[2] instanceof jalview.datamodel.Mapping)
175 jalview.datamodel.Mapping mp = (jalview.datamodel.Mapping) ref[2];
176 ((jalview.datamodel.AlignedCodonFrame) ref[1]).addMap(
177 seq, mp.getTo(), mp.getMap());
182 .println("IMPLEMENTATION ERROR: Unimplemented forward sequence references for AlcodonFrames involving "
183 + ref[2].getClass() + " type objects.");
189 .println("IMPLEMENTATION ERROR: Unimplemented forward sequence references for "
190 + ref[1].getClass() + " type objects.");
193 frefedSequence.remove(r);
199 .println("IMPLEMENTATION WARNING: Unresolved forward reference for hash string "
201 + " with objecttype "
202 + ref[1].getClass());
209 frefedSequence.remove(r);
217 * This maintains a list of viewports, the key being the seqSetId. Important
218 * to set historyItem and redoList for multiple views
220 Hashtable viewportsAdded;
222 Hashtable annotationIds = new Hashtable();
224 String uniqueSetSuffix = "";
227 * List of pdbfiles added to Jar
229 Vector pdbfiles = null;
231 // SAVES SEVERAL ALIGNMENT WINDOWS TO SAME JARFILE
232 public void SaveState(File statefile)
236 FileOutputStream fos = new FileOutputStream(statefile);
237 JarOutputStream jout = new JarOutputStream(fos);
240 } catch (Exception e)
242 // TODO: inform user of the problem - they need to know if their data was
244 if (errorMessage == null)
246 errorMessage = "Couldn't write Jalview Archive to output file '"
247 + statefile + "' - See console error log for details";
251 errorMessage += "(output file was '" + statefile + "')";
259 * Writes a jalview project archive to the given Jar output stream.
263 public void SaveState(JarOutputStream jout)
265 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
275 // NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS
276 // //////////////////////////////////////////////////
277 // NOTE ALSO new PrintWriter must be used for each new JarEntry
278 PrintWriter out = null;
280 Vector shortNames = new Vector();
283 for (int i = frames.length - 1; i > -1; i--)
285 if (frames[i] instanceof AlignFrame)
287 AlignFrame af = (AlignFrame) frames[i];
290 && skipList.containsKey(af.getViewport()
291 .getSequenceSetId()))
296 String shortName = af.getTitle();
298 if (shortName.indexOf(File.separatorChar) > -1)
300 shortName = shortName.substring(shortName
301 .lastIndexOf(File.separatorChar) + 1);
306 while (shortNames.contains(shortName))
308 if (shortName.endsWith("_" + (count - 1)))
310 shortName = shortName
311 .substring(0, shortName.lastIndexOf("_"));
314 shortName = shortName.concat("_" + count);
318 shortNames.addElement(shortName);
320 if (!shortName.endsWith(".xml"))
322 shortName = shortName + ".xml";
325 int ap, apSize = af.alignPanels.size();
326 for (ap = 0; ap < apSize; ap++)
328 AlignmentPanel apanel = (AlignmentPanel) af.alignPanels
330 String fileName = apSize == 1 ? shortName : ap + shortName;
331 if (!fileName.endsWith(".xml"))
333 fileName = fileName + ".xml";
336 SaveState(apanel, fileName, jout);
343 } catch (Exception foo)
348 } catch (Exception ex)
350 // TODO: inform user of the problem - they need to know if their data was
352 if (errorMessage == null)
354 errorMessage = "Couldn't write Jalview Archive - see error output for details";
356 ex.printStackTrace();
360 // USE THIS METHOD TO SAVE A SINGLE ALIGNMENT WINDOW
361 public boolean SaveAlignment(AlignFrame af, String jarFile,
366 int ap, apSize = af.alignPanels.size();
367 FileOutputStream fos = new FileOutputStream(jarFile);
368 JarOutputStream jout = new JarOutputStream(fos);
369 for (ap = 0; ap < apSize; ap++)
371 AlignmentPanel apanel = (AlignmentPanel) af.alignPanels
373 String jfileName = apSize == 1 ? fileName : fileName + ap;
374 if (!jfileName.endsWith(".xml"))
376 jfileName = jfileName + ".xml";
378 SaveState(apanel, jfileName, jout);
384 } catch (Exception foo)
390 } catch (Exception ex)
392 errorMessage = "Couldn't Write alignment view to Jalview Archive - see error output for details";
393 ex.printStackTrace();
399 * create a JalviewModel from an algnment view and marshall it to a
403 * panel to create jalview model for
405 * name of alignment panel written to output stream
411 public JalviewModel SaveState(AlignmentPanel ap, String fileName,
412 JarOutputStream jout)
416 Vector userColours = new Vector();
418 AlignViewport av = ap.av;
420 JalviewModel object = new JalviewModel();
421 object.setVamsasModel(new jalview.schemabinding.version2.VamsasModel());
423 object.setCreationDate(new java.util.Date(System.currentTimeMillis()));
424 object.setVersion(jalview.bin.Cache.getProperty("VERSION"));
426 jalview.datamodel.AlignmentI jal = av.alignment;
428 if (av.hasHiddenRows)
430 jal = jal.getHiddenSequences().getFullAlignment();
433 SequenceSet vamsasSet = new SequenceSet();
435 JalviewModelSequence jms = new JalviewModelSequence();
437 vamsasSet.setGapChar(jal.getGapCharacter() + "");
439 if (jal.getDataset() != null)
441 // dataset id is the dataset's hashcode
442 vamsasSet.setDatasetId(getDatasetIdRef(jal.getDataset()));
444 if (jal.getProperties() != null)
446 Enumeration en = jal.getProperties().keys();
447 while (en.hasMoreElements())
449 String key = en.nextElement().toString();
450 SequenceSetProperties ssp = new SequenceSetProperties();
452 ssp.setValue(jal.getProperties().get(key).toString());
453 vamsasSet.addSequenceSetProperties(ssp);
461 jalview.datamodel.SequenceI jds;
462 for (int i = 0; i < jal.getHeight(); i++)
464 jds = jal.getSequenceAt(i);
467 if (seqRefIds.get(id) != null)
469 // This happens for two reasons: 1. multiple views are being serialised.
470 // 2. the hashCode has collided with another sequence's code. This DOES
471 // HAPPEN! (PF00072.15.stk does this)
472 // JBPNote: Uncomment to debug writing out of files that do not read
473 // back in due to ArrayOutOfBoundExceptions.
474 // System.err.println("vamsasSeq backref: "+id+"");
475 // System.err.println(jds.getName()+"
476 // "+jds.getStart()+"-"+jds.getEnd()+" "+jds.getSequenceAsString());
477 // System.err.println("Hashcode: "+seqHash(jds));
478 // SequenceI rsq = (SequenceI) seqRefIds.get(id + "");
479 // System.err.println(rsq.getName()+"
480 // "+rsq.getStart()+"-"+rsq.getEnd()+" "+rsq.getSequenceAsString());
481 // System.err.println("Hashcode: "+seqHash(rsq));
485 vamsasSeq = createVamsasSequence(id, jds);
486 vamsasSet.addSequence(vamsasSeq);
487 seqRefIds.put(id, jds);
491 jseq.setStart(jds.getStart());
492 jseq.setEnd(jds.getEnd());
493 jseq.setColour(av.getSequenceColour(jds).getRGB());
495 jseq.setId(id); // jseq id should be a string not a number
497 if (av.hasHiddenRows)
499 jseq.setHidden(av.alignment.getHiddenSequences().isHidden(jds));
501 if (av.hiddenRepSequences != null
502 && av.hiddenRepSequences.containsKey(jal.getSequenceAt(i)))
504 jalview.datamodel.SequenceI[] reps = ((jalview.datamodel.SequenceGroup) av.hiddenRepSequences
505 .get(jal.getSequenceAt(i))).getSequencesInOrder(jal);
507 for (int h = 0; h < reps.length; h++)
509 if (reps[h] != jal.getSequenceAt(i))
511 jseq.addHiddenSequences(jal.findIndex(reps[h]));
517 if (jds.getDatasetSequence().getSequenceFeatures() != null)
519 jalview.datamodel.SequenceFeature[] sf = jds.getDatasetSequence()
520 .getSequenceFeatures();
522 while (index < sf.length)
524 Features features = new Features();
526 features.setBegin(sf[index].getBegin());
527 features.setEnd(sf[index].getEnd());
528 features.setDescription(sf[index].getDescription());
529 features.setType(sf[index].getType());
530 features.setFeatureGroup(sf[index].getFeatureGroup());
531 features.setScore(sf[index].getScore());
532 if (sf[index].links != null)
534 for (int l = 0; l < sf[index].links.size(); l++)
536 OtherData keyValue = new OtherData();
537 keyValue.setKey("LINK_" + l);
538 keyValue.setValue(sf[index].links.elementAt(l).toString());
539 features.addOtherData(keyValue);
542 if (sf[index].otherDetails != null)
545 Enumeration keys = sf[index].otherDetails.keys();
546 while (keys.hasMoreElements())
548 key = keys.nextElement().toString();
549 OtherData keyValue = new OtherData();
550 keyValue.setKey(key);
551 keyValue.setValue(sf[index].otherDetails.get(key).toString());
552 features.addOtherData(keyValue);
556 jseq.addFeatures(features);
561 if (jds.getDatasetSequence().getPDBId() != null)
563 Enumeration en = jds.getDatasetSequence().getPDBId().elements();
564 while (en.hasMoreElements())
566 Pdbids pdb = new Pdbids();
567 jalview.datamodel.PDBEntry entry = (jalview.datamodel.PDBEntry) en
570 pdb.setId(entry.getId());
571 pdb.setType(entry.getType());
574 // This must have been loaded, is it still visible?
575 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
576 String matchedFile = null;
577 for (int f = frames.length - 1; f > -1; f--)
579 if (frames[f] instanceof AppJmol)
581 jmol = (AppJmol) frames[f];
582 if (!jmol.pdbentry.getId().equals(entry.getId())
583 && !(entry.getId().length() > 4 && entry.getId()
584 .toLowerCase().startsWith(
585 jmol.pdbentry.getId().toLowerCase())))
587 matchedFile = jmol.pdbentry.getFile(); // record the file so we
588 // can get at it if the ID
589 // match is ambiguous (e.g.
591 StructureState state = new StructureState();
592 state.setVisible(true);
593 state.setXpos(jmol.getX());
594 state.setYpos(jmol.getY());
595 state.setWidth(jmol.getWidth());
596 state.setHeight(jmol.getHeight());
597 state.setViewId(jmol.getViewId());
598 String statestring = jmol.viewer.getStateInfo();
601 state.setContent(statestring.replaceAll("\n", ""));
603 for (int s = 0; s < jmol.sequence.length; s++)
605 if (jal.findIndex(jmol.sequence[s]) > -1)
607 pdb.addStructureState(state);
613 if (matchedFile != null || entry.getFile() != null)
615 if (entry.getFile() != null)
618 matchedFile = entry.getFile();
620 pdb.setFile(matchedFile); // entry.getFile());
621 if (pdbfiles == null)
623 pdbfiles = new Vector();
626 if (!pdbfiles.contains(entry.getId()))
628 pdbfiles.addElement(entry.getId());
631 File file = new File(matchedFile);
632 if (file.exists() && jout != null)
634 byte[] data = new byte[(int) file.length()];
635 jout.putNextEntry(new JarEntry(entry.getId()));
636 DataInputStream dis = new DataInputStream(
637 new FileInputStream(file));
640 DataOutputStream dout = new DataOutputStream(jout);
641 dout.write(data, 0, data.length);
645 } catch (Exception ex)
647 ex.printStackTrace();
653 if (entry.getProperty() != null)
655 PdbentryItem item = new PdbentryItem();
656 Hashtable properties = entry.getProperty();
657 Enumeration en2 = properties.keys();
658 while (en2.hasMoreElements())
660 Property prop = new Property();
661 String key = en2.nextElement().toString();
663 prop.setValue(properties.get(key).toString());
664 item.addProperty(prop);
666 pdb.addPdbentryItem(item);
676 if (av.hasHiddenRows)
681 if (jal.getCodonFrames() != null && jal.getCodonFrames().length > 0)
683 jalview.datamodel.AlignedCodonFrame[] jac = jal.getCodonFrames();
684 for (int i = 0; i < jac.length; i++)
686 AlcodonFrame alc = new AlcodonFrame();
687 vamsasSet.addAlcodonFrame(alc);
688 for (int p = 0; p < jac[i].aaWidth; p++)
690 Alcodon cmap = new Alcodon();
691 if (jac[i].codons[p] != null)
693 // Null codons indicate a gapped column in the translated peptide
695 cmap.setPos1(jac[i].codons[p][0]);
696 cmap.setPos2(jac[i].codons[p][1]);
697 cmap.setPos3(jac[i].codons[p][2]);
699 alc.addAlcodon(cmap);
701 if (jac[i].getProtMappings() != null
702 && jac[i].getProtMappings().length > 0)
704 SequenceI[] dnas = jac[i].getdnaSeqs();
705 jalview.datamodel.Mapping[] pmaps = jac[i].getProtMappings();
706 for (int m = 0; m < pmaps.length; m++)
708 AlcodMap alcmap = new AlcodMap();
709 alcmap.setDnasq(seqHash(dnas[m]));
710 alcmap.setMapping(createVamsasMapping(pmaps[m], dnas[m], null,
712 alc.addAlcodMap(alcmap);
719 // /////////////////////////////////
720 if (av.currentTree != null)
722 // FIND ANY ASSOCIATED TREES
723 // NOT IMPLEMENTED FOR HEADLESS STATE AT PRESENT
724 if (Desktop.desktop != null)
726 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
728 for (int t = 0; t < frames.length; t++)
730 if (frames[t] instanceof TreePanel)
732 TreePanel tp = (TreePanel) frames[t];
734 if (tp.treeCanvas.av.alignment == jal)
736 Tree tree = new Tree();
737 tree.setTitle(tp.getTitle());
738 tree.setCurrentTree((av.currentTree == tp.getTree()));
739 tree.setNewick(tp.getTree().toString());
740 tree.setThreshold(tp.treeCanvas.threshold);
742 tree.setFitToWindow(tp.fitToWindow.getState());
743 tree.setFontName(tp.getTreeFont().getName());
744 tree.setFontSize(tp.getTreeFont().getSize());
745 tree.setFontStyle(tp.getTreeFont().getStyle());
746 tree.setMarkUnlinked(tp.placeholdersMenu.getState());
748 tree.setShowBootstrap(tp.bootstrapMenu.getState());
749 tree.setShowDistances(tp.distanceMenu.getState());
751 tree.setHeight(tp.getHeight());
752 tree.setWidth(tp.getWidth());
753 tree.setXpos(tp.getX());
754 tree.setYpos(tp.getY());
755 tree.setId(makeHashCode(tp, null));
765 * store forward refs from an annotationRow to any groups
767 IdentityHashMap groupRefs = new IdentityHashMap();
768 if (jal.getAlignmentAnnotation() != null)
770 jalview.datamodel.AlignmentAnnotation[] aa = jal
771 .getAlignmentAnnotation();
773 for (int i = 0; i < aa.length; i++)
775 Annotation an = new Annotation();
777 if (aa[i].annotationId != null)
779 annotationIds.put(aa[i].annotationId, aa[i]);
782 an.setId(aa[i].annotationId);
784 an.setVisible(aa[i].visible);
786 an.setDescription(aa[i].description);
788 if (aa[i].sequenceRef != null)
790 // TODO later annotation sequenceRef should be the XML ID of the
791 // sequence rather than its display name
792 an.setSequenceRef(aa[i].sequenceRef.getName());
794 if (aa[i].groupRef != null)
796 Object groupIdr = groupRefs.get(aa[i].groupRef);
797 if (groupIdr == null)
799 // make a locally unique String
800 groupRefs.put(aa[i].groupRef,
801 groupIdr = ("" + System.currentTimeMillis()
802 + 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
813 an.setLabel(aa[i].label);
815 vamsasSet.addAnnotation(an);
822 an.setGraphType(aa[i].graph);
823 an.setGraphGroup(aa[i].graphGroup);
824 if (aa[i].getThreshold() != null)
826 ThresholdLine line = new ThresholdLine();
827 line.setLabel(aa[i].getThreshold().label);
828 line.setValue(aa[i].getThreshold().value);
829 line.setColour(aa[i].getThreshold().colour.getRGB());
830 an.setThresholdLine(line);
838 an.setLabel(aa[i].label);
839 if (aa[i].hasScore())
841 an.setScore(aa[i].getScore());
843 AnnotationElement ae;
844 if (aa[i].annotations != null)
846 an.setScoreOnly(false);
847 for (int a = 0; a < aa[i].annotations.length; a++)
849 if ((aa[i] == null) || (aa[i].annotations[a] == null))
854 ae = new AnnotationElement();
855 if (aa[i].annotations[a].description != null)
856 ae.setDescription(aa[i].annotations[a].description);
857 if (aa[i].annotations[a].displayCharacter != null)
858 ae.setDisplayCharacter(aa[i].annotations[a].displayCharacter);
860 if (!Float.isNaN(aa[i].annotations[a].value))
861 ae.setValue(aa[i].annotations[a].value);
864 if (aa[i].annotations[a].secondaryStructure != ' '
865 && aa[i].annotations[a].secondaryStructure != '\0')
867 .setSecondaryStructure(aa[i].annotations[a].secondaryStructure
870 if (aa[i].annotations[a].colour != null
871 && aa[i].annotations[a].colour != java.awt.Color.black)
873 ae.setColour(aa[i].annotations[a].colour.getRGB());
876 an.addAnnotationElement(ae);
881 an.setScoreOnly(true);
883 vamsasSet.addAnnotation(an);
887 if (jal.getGroups() != null)
889 JGroup[] groups = new JGroup[jal.getGroups().size()];
891 for (int i = 0; i < groups.length; i++)
893 groups[i] = new JGroup();
895 jalview.datamodel.SequenceGroup sg = (jalview.datamodel.SequenceGroup) jal
896 .getGroups().elementAt(i);
897 groups[i].setStart(sg.getStartRes());
898 groups[i].setEnd(sg.getEndRes());
899 groups[i].setName(sg.getName());
900 if (groupRefs.containsKey(sg))
902 // group has references so set it's ID field
903 groups[i].setId(groupRefs.get(sg).toString());
907 if (sg.cs.conservationApplied())
909 groups[i].setConsThreshold(sg.cs.getConservationInc());
911 if (sg.cs instanceof jalview.schemes.UserColourScheme)
913 groups[i].setColour(SetUserColourScheme(sg.cs, userColours,
919 .setColour(ColourSchemeProperty.getColourName(sg.cs));
922 else if (sg.cs instanceof jalview.schemes.AnnotationColourGradient)
925 .setColour(ColourSchemeProperty
926 .getColourName(((jalview.schemes.AnnotationColourGradient) sg.cs)
929 else if (sg.cs instanceof jalview.schemes.UserColourScheme)
932 .setColour(SetUserColourScheme(sg.cs, userColours, jms));
936 groups[i].setColour(ColourSchemeProperty.getColourName(sg.cs));
939 groups[i].setPidThreshold(sg.cs.getThreshold());
942 groups[i].setOutlineColour(sg.getOutlineColour().getRGB());
943 groups[i].setDisplayBoxes(sg.getDisplayBoxes());
944 groups[i].setDisplayText(sg.getDisplayText());
945 groups[i].setColourText(sg.getColourText());
946 groups[i].setTextCol1(sg.textColour.getRGB());
947 groups[i].setTextCol2(sg.textColour2.getRGB());
948 groups[i].setTextColThreshold(sg.thresholdTextColour);
949 groups[i].setShowUnconserved(sg.getShowNonconserved());
950 groups[i].setIgnoreGapsinConsensus(sg.getIgnoreGapsConsensus());
951 groups[i].setShowConsensusHistogram(sg.isShowConsensusHistogram());
952 groups[i].setShowSequenceLogo(sg.isShowSequenceLogo());
953 for (int s = 0; s < sg.getSize(); s++)
955 jalview.datamodel.Sequence seq = (jalview.datamodel.Sequence) sg
957 groups[i].addSeq(seqHash(seq));
961 jms.setJGroup(groups);
964 // /////////SAVE VIEWPORT
965 Viewport view = new Viewport();
966 view.setTitle(ap.alignFrame.getTitle());
967 view.setSequenceSetId(makeHashCode(av.getSequenceSetId(), av
968 .getSequenceSetId()));
969 view.setId(av.getViewId());
970 view.setViewName(av.viewName);
971 view.setGatheredViews(av.gatherViewsHere);
973 if (ap.av.explodedPosition != null)
975 view.setXpos(av.explodedPosition.x);
976 view.setYpos(av.explodedPosition.y);
977 view.setWidth(av.explodedPosition.width);
978 view.setHeight(av.explodedPosition.height);
982 view.setXpos(ap.alignFrame.getBounds().x);
983 view.setYpos(ap.alignFrame.getBounds().y);
984 view.setWidth(ap.alignFrame.getBounds().width);
985 view.setHeight(ap.alignFrame.getBounds().height);
988 view.setStartRes(av.startRes);
989 view.setStartSeq(av.startSeq);
991 if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme)
993 view.setBgColour(SetUserColourScheme(av.getGlobalColourScheme(),
996 else if (av.getGlobalColourScheme() instanceof jalview.schemes.AnnotationColourGradient)
998 jalview.schemes.AnnotationColourGradient acg = (jalview.schemes.AnnotationColourGradient) av
999 .getGlobalColourScheme();
1001 AnnotationColours ac = new AnnotationColours();
1002 ac.setAboveThreshold(acg.getAboveThreshold());
1003 ac.setThreshold(acg.getAnnotationThreshold());
1004 ac.setAnnotation(acg.getAnnotation());
1005 if (acg.getBaseColour() instanceof jalview.schemes.UserColourScheme)
1007 ac.setColourScheme(SetUserColourScheme(acg.getBaseColour(),
1012 ac.setColourScheme(ColourSchemeProperty.getColourName(acg
1016 ac.setMaxColour(acg.getMaxColour().getRGB());
1017 ac.setMinColour(acg.getMinColour().getRGB());
1018 view.setAnnotationColours(ac);
1019 view.setBgColour("AnnotationColourGradient");
1023 view.setBgColour(ColourSchemeProperty.getColourName(av
1024 .getGlobalColourScheme()));
1027 ColourSchemeI cs = av.getGlobalColourScheme();
1031 if (cs.conservationApplied())
1033 view.setConsThreshold(cs.getConservationInc());
1034 if (cs instanceof jalview.schemes.UserColourScheme)
1036 view.setBgColour(SetUserColourScheme(cs, userColours, jms));
1040 if (cs instanceof ResidueColourScheme)
1042 view.setPidThreshold(cs.getThreshold());
1046 view.setConservationSelected(av.getConservationSelected());
1047 view.setPidSelected(av.getAbovePIDThreshold());
1048 view.setFontName(av.font.getName());
1049 view.setFontSize(av.font.getSize());
1050 view.setFontStyle(av.font.getStyle());
1051 view.setRenderGaps(av.renderGaps);
1052 view.setShowAnnotation(av.getShowAnnotation());
1053 view.setShowBoxes(av.getShowBoxes());
1054 view.setShowColourText(av.getColourText());
1055 view.setShowFullId(av.getShowJVSuffix());
1056 view.setRightAlignIds(av.rightAlignIds);
1057 view.setShowSequenceFeatures(av.showSequenceFeatures);
1058 view.setShowText(av.getShowText());
1059 view.setShowUnconserved(av.getShowUnconserved());
1060 view.setWrapAlignment(av.getWrapAlignment());
1061 view.setTextCol1(av.textColour.getRGB());
1062 view.setTextCol2(av.textColour2.getRGB());
1063 view.setTextColThreshold(av.thresholdTextColour);
1064 view.setShowConsensusHistogram(av.isShowConsensusHistogram());
1065 view.setShowSequenceLogo(av.isShowSequenceLogo());
1066 view.setShowGroupConsensus(av.isShowGroupConsensus());
1067 view.setShowGroupConservation(av.isShowGroupConservation());
1068 view.setShowNPfeatureTooltip(av.isShowNpFeats());
1069 view.setShowDbRefTooltip(av.isShowDbRefs());
1070 view.setFollowHighlight(av.followHighlight);
1071 view.setFollowSelection(av.followSelection);
1072 view.setIgnoreGapsinConsensus(av.getIgnoreGapsConsensus());
1073 if (av.featuresDisplayed != null)
1075 jalview.schemabinding.version2.FeatureSettings fs = new jalview.schemabinding.version2.FeatureSettings();
1077 String[] renderOrder = ap.seqPanel.seqCanvas.getFeatureRenderer().renderOrder;
1079 Vector settingsAdded = new Vector();
1080 Object gstyle = null;
1081 GraduatedColor gcol = null;
1082 for (int ro = 0; ro < renderOrder.length; ro++)
1084 gstyle = ap.seqPanel.seqCanvas.getFeatureRenderer()
1085 .getFeatureStyle(renderOrder[ro]);
1086 Setting setting = new Setting();
1087 setting.setType(renderOrder[ro]);
1088 if (gstyle instanceof GraduatedColor)
1090 gcol = (GraduatedColor) gstyle;
1091 setting.setColour(gcol.getMaxColor().getRGB());
1092 setting.setMincolour(gcol.getMinColor().getRGB());
1093 setting.setMin(gcol.getMin());
1094 setting.setMax(gcol.getMax());
1095 setting.setColourByLabel(gcol.isColourByLabel());
1096 setting.setAutoScale(gcol.isAutoScale());
1097 setting.setThreshold(gcol.getThresh());
1098 setting.setThreshstate(gcol.getThreshType());
1102 setting.setColour(ap.seqPanel.seqCanvas.getFeatureRenderer()
1103 .getColour(renderOrder[ro]).getRGB());
1106 setting.setDisplay(av.featuresDisplayed
1107 .containsKey(renderOrder[ro]));
1108 float rorder = ap.seqPanel.seqCanvas.getFeatureRenderer().getOrder(
1112 setting.setOrder(rorder);
1114 fs.addSetting(setting);
1115 settingsAdded.addElement(renderOrder[ro]);
1118 // Make sure we save none displayed feature settings
1119 Enumeration en = ap.seqPanel.seqCanvas.getFeatureRenderer().featureColours
1121 while (en.hasMoreElements())
1123 String key = en.nextElement().toString();
1124 if (settingsAdded.contains(key))
1129 Setting setting = new Setting();
1130 setting.setType(key);
1131 setting.setColour(ap.seqPanel.seqCanvas.getFeatureRenderer()
1132 .getColour(key).getRGB());
1134 setting.setDisplay(false);
1135 float rorder = ap.seqPanel.seqCanvas.getFeatureRenderer().getOrder(
1139 setting.setOrder(rorder);
1141 fs.addSetting(setting);
1142 settingsAdded.addElement(key);
1144 en = ap.seqPanel.seqCanvas.getFeatureRenderer().featureGroups.keys();
1145 Vector groupsAdded = new Vector();
1146 while (en.hasMoreElements())
1148 String grp = en.nextElement().toString();
1149 if (groupsAdded.contains(grp))
1153 Group g = new Group();
1156 .setDisplay(((Boolean) ap.seqPanel.seqCanvas
1157 .getFeatureRenderer().featureGroups.get(grp))
1160 groupsAdded.addElement(grp);
1162 jms.setFeatureSettings(fs);
1166 if (av.hasHiddenColumns)
1168 if (av.getColumnSelection() == null
1169 || av.getColumnSelection().getHiddenColumns() == null)
1171 warn("REPORT BUG: avoided null columnselection bug (DMAM reported). Please contact Jim about this.");
1175 for (int c = 0; c < av.getColumnSelection().getHiddenColumns()
1178 int[] region = (int[]) av.getColumnSelection().getHiddenColumns()
1180 HiddenColumns hc = new HiddenColumns();
1181 hc.setStart(region[0]);
1182 hc.setEnd(region[1]);
1183 view.addHiddenColumns(hc);
1188 jms.addViewport(view);
1190 object.setJalviewModelSequence(jms);
1191 object.getVamsasModel().addSequenceSet(vamsasSet);
1193 if (jout != null && fileName != null)
1195 // We may not want to write the object to disk,
1196 // eg we can copy the alignViewport to a new view object
1197 // using save and then load
1200 JarEntry entry = new JarEntry(fileName);
1201 jout.putNextEntry(entry);
1202 PrintWriter pout = new PrintWriter(new OutputStreamWriter(jout,
1204 org.exolab.castor.xml.Marshaller marshaller = new org.exolab.castor.xml.Marshaller(
1206 marshaller.marshal(object);
1209 } catch (Exception ex)
1211 // TODO: raise error in GUI if marshalling failed.
1212 ex.printStackTrace();
1219 * External mapping between jalview objects and objects yielding a valid and
1220 * unique object ID string. This is null for normal Jalview project IO, but
1221 * non-null when a jalview project is being read or written as part of a
1224 IdentityHashMap jv2vobj = null;
1227 * Construct a unique ID for jvobj using either existing bindings or if none
1228 * exist, the result of the hashcode call for the object.
1231 * jalview data object
1232 * @return unique ID for referring to jvobj
1234 private String makeHashCode(Object jvobj, String altCode)
1236 if (jv2vobj != null)
1238 Object id = jv2vobj.get(jvobj);
1241 return id.toString();
1243 // check string ID mappings
1244 if (jvids2vobj != null && jvobj instanceof String)
1246 id = jvids2vobj.get(jvobj);
1250 return id.toString();
1252 // give up and warn that something has gone wrong
1253 warn("Cannot find ID for object in external mapping : " + jvobj);
1259 * return local jalview object mapped to ID, if it exists
1263 * @return null or object bound to idcode
1265 private Object retrieveExistingObj(String idcode)
1267 if (idcode != null && vobj2jv != null)
1269 return vobj2jv.get(idcode);
1275 * binding from ID strings from external mapping table to jalview data model
1278 private Hashtable vobj2jv;
1280 private Sequence createVamsasSequence(String id, SequenceI jds)
1282 return createVamsasSequence(true, id, jds, null);
1285 private Sequence createVamsasSequence(boolean recurse, String id,
1286 SequenceI jds, SequenceI parentseq)
1288 Sequence vamsasSeq = new Sequence();
1289 vamsasSeq.setId(id);
1290 vamsasSeq.setName(jds.getName());
1291 vamsasSeq.setSequence(jds.getSequenceAsString());
1292 vamsasSeq.setDescription(jds.getDescription());
1293 jalview.datamodel.DBRefEntry[] dbrefs = null;
1294 if (jds.getDatasetSequence() != null)
1296 vamsasSeq.setDsseqid(seqHash(jds.getDatasetSequence()));
1297 if (jds.getDatasetSequence().getDBRef() != null)
1299 dbrefs = jds.getDatasetSequence().getDBRef();
1304 vamsasSeq.setDsseqid(id); // so we can tell which sequences really are
1305 // dataset sequences only
1306 dbrefs = jds.getDBRef();
1310 for (int d = 0; d < dbrefs.length; d++)
1312 DBRef dbref = new DBRef();
1313 dbref.setSource(dbrefs[d].getSource());
1314 dbref.setVersion(dbrefs[d].getVersion());
1315 dbref.setAccessionId(dbrefs[d].getAccessionId());
1316 if (dbrefs[d].hasMap())
1318 Mapping mp = createVamsasMapping(dbrefs[d].getMap(), parentseq,
1320 dbref.setMapping(mp);
1322 vamsasSeq.addDBRef(dbref);
1328 private Mapping createVamsasMapping(jalview.datamodel.Mapping jmp,
1329 SequenceI parentseq, SequenceI jds, boolean recurse)
1332 if (jmp.getMap() != null)
1336 jalview.util.MapList mlst = jmp.getMap();
1337 int r[] = mlst.getFromRanges();
1338 for (int s = 0; s < r.length; s += 2)
1340 MapListFrom mfrom = new MapListFrom();
1341 mfrom.setStart(r[s]);
1342 mfrom.setEnd(r[s + 1]);
1343 mp.addMapListFrom(mfrom);
1345 r = mlst.getToRanges();
1346 for (int s = 0; s < r.length; s += 2)
1348 MapListTo mto = new MapListTo();
1350 mto.setEnd(r[s + 1]);
1351 mp.addMapListTo(mto);
1353 mp.setMapFromUnit(mlst.getFromRatio());
1354 mp.setMapToUnit(mlst.getToRatio());
1355 if (jmp.getTo() != null)
1357 MappingChoice mpc = new MappingChoice();
1359 && (parentseq != jmp.getTo() || parentseq
1360 .getDatasetSequence() != jmp.getTo()))
1362 mpc.setSequence(createVamsasSequence(false, seqHash(jmp.getTo()),
1368 SequenceI ps = null;
1369 if (parentseq != jmp.getTo()
1370 && parentseq.getDatasetSequence() != jmp.getTo())
1372 // chaining dbref rather than a handshaking one
1373 jmpid = seqHash(ps = jmp.getTo());
1377 jmpid = seqHash(ps = parentseq);
1379 mpc.setDseqFor(jmpid);
1380 if (!seqRefIds.containsKey(mpc.getDseqFor()))
1382 jalview.bin.Cache.log.debug("creatign new DseqFor ID");
1383 seqRefIds.put(mpc.getDseqFor(), ps);
1387 jalview.bin.Cache.log.debug("reusing DseqFor ID");
1390 mp.setMappingChoice(mpc);
1396 String SetUserColourScheme(jalview.schemes.ColourSchemeI cs,
1397 Vector userColours, JalviewModelSequence jms)
1400 jalview.schemes.UserColourScheme ucs = (jalview.schemes.UserColourScheme) cs;
1401 boolean newucs = false;
1402 if (!userColours.contains(ucs))
1404 userColours.add(ucs);
1407 id = "ucs" + userColours.indexOf(ucs);
1410 // actually create the scheme's entry in the XML model
1411 java.awt.Color[] colours = ucs.getColours();
1412 jalview.schemabinding.version2.UserColours uc = new jalview.schemabinding.version2.UserColours();
1413 jalview.schemabinding.version2.UserColourScheme jbucs = new jalview.schemabinding.version2.UserColourScheme();
1415 for (int i = 0; i < colours.length; i++)
1417 jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();
1418 col.setName(ResidueProperties.aa[i]);
1419 col.setRGB(jalview.util.Format.getHexString(colours[i]));
1420 jbucs.addColour(col);
1422 if (ucs.getLowerCaseColours() != null)
1424 colours = ucs.getLowerCaseColours();
1425 for (int i = 0; i < colours.length; i++)
1427 jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();
1428 col.setName(ResidueProperties.aa[i].toLowerCase());
1429 col.setRGB(jalview.util.Format.getHexString(colours[i]));
1430 jbucs.addColour(col);
1435 uc.setUserColourScheme(jbucs);
1436 jms.addUserColours(uc);
1442 jalview.schemes.UserColourScheme GetUserColourScheme(
1443 JalviewModelSequence jms, String id)
1445 UserColours[] uc = jms.getUserColours();
1446 UserColours colours = null;
1448 for (int i = 0; i < uc.length; i++)
1450 if (uc[i].getId().equals(id))
1458 java.awt.Color[] newColours = new java.awt.Color[24];
1460 for (int i = 0; i < 24; i++)
1462 newColours[i] = new java.awt.Color(Integer.parseInt(colours
1463 .getUserColourScheme().getColour(i).getRGB(), 16));
1466 jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(
1469 if (colours.getUserColourScheme().getColourCount() > 24)
1471 newColours = new java.awt.Color[23];
1472 for (int i = 0; i < 23; i++)
1474 newColours[i] = new java.awt.Color(Integer.parseInt(colours
1475 .getUserColourScheme().getColour(i + 24).getRGB(), 16));
1477 ucs.setLowerCaseColours(newColours);
1484 * contains last error message (if any) encountered by XML loader.
1486 String errorMessage = null;
1489 * flag to control whether the Jalview2XML_V1 parser should be deferred to if
1490 * exceptions are raised during project XML parsing
1492 public boolean attemptversion1parse = true;
1495 * Load a jalview project archive from a jar file
1498 * - HTTP URL or filename
1500 public AlignFrame LoadJalviewAlign(final String file)
1503 jalview.gui.AlignFrame af = null;
1507 // UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
1508 // Workaround is to make sure caller implements the JarInputStreamProvider
1510 // so we can re-open the jar input stream for each entry.
1512 jarInputStreamProvider jprovider = createjarInputStreamProvider(file);
1513 af = LoadJalviewAlign(jprovider);
1514 } catch (MalformedURLException e)
1516 errorMessage = "Invalid URL format for '" + file + "'";
1522 private jarInputStreamProvider createjarInputStreamProvider(
1523 final String file) throws MalformedURLException
1526 errorMessage = null;
1527 uniqueSetSuffix = null;
1529 viewportsAdded = null;
1530 frefedSequence = null;
1532 if (file.startsWith("http://"))
1534 url = new URL(file);
1536 final URL _url = url;
1537 return new jarInputStreamProvider()
1540 public JarInputStream getJarInputStream() throws IOException
1544 return new JarInputStream(_url.openStream());
1548 return new JarInputStream(new FileInputStream(file));
1552 public String getFilename()
1560 * Recover jalview session from a jalview project archive. Caller may
1561 * initialise uniqueSetSuffix, seqRefIds, viewportsAdded and frefedSequence
1562 * themselves. Any null fields will be initialised with default values,
1563 * non-null fields are left alone.
1568 public AlignFrame LoadJalviewAlign(final jarInputStreamProvider jprovider)
1570 errorMessage = null;
1571 if (uniqueSetSuffix == null)
1573 uniqueSetSuffix = System.currentTimeMillis() % 100000 + "";
1575 if (seqRefIds == null)
1577 seqRefIds = new Hashtable();
1579 if (viewportsAdded == null)
1581 viewportsAdded = new Hashtable();
1583 if (frefedSequence == null)
1585 frefedSequence = new Vector();
1588 jalview.gui.AlignFrame af = null;
1589 Hashtable gatherToThisFrame = new Hashtable();
1590 final String file = jprovider.getFilename();
1593 JarInputStream jin = null;
1594 JarEntry jarentry = null;
1599 jin = jprovider.getJarInputStream();
1600 for (int i = 0; i < entryCount; i++)
1602 jarentry = jin.getNextJarEntry();
1605 if (jarentry != null && jarentry.getName().endsWith(".xml"))
1607 InputStreamReader in = new InputStreamReader(jin, "UTF-8");
1608 JalviewModel object = new JalviewModel();
1610 Unmarshaller unmar = new Unmarshaller(object);
1611 unmar.setValidation(false);
1612 object = (JalviewModel) unmar.unmarshal(in);
1613 if (true) // !skipViewport(object))
1615 af = LoadFromObject(object, file, true, jprovider);
1616 if (af.viewport.gatherViewsHere)
1618 gatherToThisFrame.put(af.viewport.getSequenceSetId(), af);
1623 else if (jarentry != null)
1625 // Some other file here.
1628 } while (jarentry != null);
1629 resolveFrefedSequences();
1630 } catch (java.io.FileNotFoundException ex)
1632 ex.printStackTrace();
1633 errorMessage = "Couldn't locate Jalview XML file : " + file;
1634 System.err.println("Exception whilst loading jalview XML file : "
1636 } catch (java.net.UnknownHostException ex)
1638 ex.printStackTrace();
1639 errorMessage = "Couldn't locate Jalview XML file : " + file;
1640 System.err.println("Exception whilst loading jalview XML file : "
1642 } catch (Exception ex)
1644 System.err.println("Parsing as Jalview Version 2 file failed.");
1645 ex.printStackTrace(System.err);
1646 if (attemptversion1parse)
1648 // Is Version 1 Jar file?
1651 af = new Jalview2XML_V1(raiseGUI).LoadJalviewAlign(jprovider);
1652 } catch (Exception ex2)
1654 System.err.println("Exception whilst loading as jalviewXMLV1:");
1655 ex2.printStackTrace();
1659 if (Desktop.instance != null)
1661 Desktop.instance.stopLoading();
1665 System.out.println("Successfully loaded archive file");
1668 ex.printStackTrace();
1670 System.err.println("Exception whilst loading jalview XML file : "
1672 } catch (OutOfMemoryError e)
1674 // Don't use the OOM Window here
1675 errorMessage = "Out of memory loading jalview XML file";
1676 System.err.println("Out of memory whilst loading jalview XML file");
1677 e.printStackTrace();
1680 if (Desktop.instance != null)
1682 Desktop.instance.stopLoading();
1685 Enumeration en = gatherToThisFrame.elements();
1686 while (en.hasMoreElements())
1688 Desktop.instance.gatherViews((AlignFrame) en.nextElement());
1690 if (errorMessage != null)
1698 * check errorMessage for a valid error message and raise an error box in the
1699 * GUI or write the current errorMessage to stderr and then clear the error
1702 protected void reportErrors()
1704 reportErrors(false);
1707 protected void reportErrors(final boolean saving)
1709 if (errorMessage != null)
1711 final String finalErrorMessage = errorMessage;
1714 javax.swing.SwingUtilities.invokeLater(new Runnable()
1718 JOptionPane.showInternalMessageDialog(Desktop.desktop,
1719 finalErrorMessage, "Error "
1720 + (saving ? "saving" : "loading")
1721 + " Jalview file", JOptionPane.WARNING_MESSAGE);
1727 System.err.println("Problem loading Jalview file: " + errorMessage);
1730 errorMessage = null;
1733 Hashtable alreadyLoadedPDB;
1736 * when set, local views will be updated from view stored in JalviewXML
1737 * Currently (28th Sep 2008) things will go horribly wrong in vamsas document
1738 * sync if this is set to true.
1740 private boolean updateLocalViews = false;
1742 String loadPDBFile(jarInputStreamProvider jprovider, String pdbId)
1744 if (alreadyLoadedPDB == null)
1745 alreadyLoadedPDB = new Hashtable();
1747 if (alreadyLoadedPDB.containsKey(pdbId))
1748 return alreadyLoadedPDB.get(pdbId).toString();
1752 JarInputStream jin = jprovider.getJarInputStream();
1754 * if (jprovider.startsWith("http://")) { jin = new JarInputStream(new
1755 * URL(jprovider).openStream()); } else { jin = new JarInputStream(new
1756 * FileInputStream(jprovider)); }
1759 JarEntry entry = null;
1762 entry = jin.getNextJarEntry();
1763 } while (entry != null && !entry.getName().equals(pdbId));
1766 BufferedReader in = new BufferedReader(new InputStreamReader(jin));
1767 File outFile = File.createTempFile("jalview_pdb", ".txt");
1768 outFile.deleteOnExit();
1769 PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
1772 while ((data = in.readLine()) != null)
1779 } catch (Exception foo)
1785 alreadyLoadedPDB.put(pdbId, outFile.getAbsolutePath());
1786 return outFile.getAbsolutePath();
1790 warn("Couldn't find PDB file entry in Jalview Jar for " + pdbId);
1792 } catch (Exception ex)
1794 ex.printStackTrace();
1801 * Load alignment frame from jalview XML DOM object
1806 * filename source string
1807 * @param loadTreesAndStructures
1808 * when false only create Viewport
1810 * data source provider
1811 * @return alignment frame created from view stored in DOM
1813 AlignFrame LoadFromObject(JalviewModel object, String file,
1814 boolean loadTreesAndStructures, jarInputStreamProvider jprovider)
1816 SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);
1817 Sequence[] vamsasSeq = vamsasSet.getSequence();
1819 JalviewModelSequence jms = object.getJalviewModelSequence();
1821 Viewport view = jms.getViewport(0);
1822 // ////////////////////////////////
1825 Vector hiddenSeqs = null;
1826 jalview.datamodel.Sequence jseq;
1828 ArrayList tmpseqs = new ArrayList();
1830 boolean multipleView = false;
1832 JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq();
1833 int vi = 0; // counter in vamsasSeq array
1834 for (int i = 0; i < JSEQ.length; i++)
1836 String seqId = JSEQ[i].getId();
1838 if (seqRefIds.get(seqId) != null)
1840 tmpseqs.add((jalview.datamodel.Sequence) seqRefIds.get(seqId));
1841 multipleView = true;
1845 jseq = new jalview.datamodel.Sequence(vamsasSeq[vi].getName(),
1846 vamsasSeq[vi].getSequence());
1847 jseq.setDescription(vamsasSeq[vi].getDescription());
1848 jseq.setStart(JSEQ[i].getStart());
1849 jseq.setEnd(JSEQ[i].getEnd());
1850 jseq.setVamsasId(uniqueSetSuffix + seqId);
1851 seqRefIds.put(vamsasSeq[vi].getId(), jseq);
1856 if (JSEQ[i].getHidden())
1858 if (hiddenSeqs == null)
1860 hiddenSeqs = new Vector();
1863 hiddenSeqs.addElement((jalview.datamodel.Sequence) seqRefIds
1870 // Create the alignment object from the sequence set
1871 // ///////////////////////////////
1872 jalview.datamodel.Sequence[] orderedSeqs = new jalview.datamodel.Sequence[tmpseqs
1875 tmpseqs.toArray(orderedSeqs);
1877 jalview.datamodel.Alignment al = new jalview.datamodel.Alignment(
1880 // / Add the alignment properties
1881 for (int i = 0; i < vamsasSet.getSequenceSetPropertiesCount(); i++)
1883 SequenceSetProperties ssp = vamsasSet.getSequenceSetProperties(i);
1884 al.setProperty(ssp.getKey(), ssp.getValue());
1888 // SequenceFeatures are added to the DatasetSequence,
1889 // so we must create or recover the dataset before loading features
1890 // ///////////////////////////////
1891 if (vamsasSet.getDatasetId() == null || vamsasSet.getDatasetId() == "")
1893 // older jalview projects do not have a dataset id.
1894 al.setDataset(null);
1898 recoverDatasetFor(vamsasSet, al);
1900 // ///////////////////////////////
1902 Hashtable pdbloaded = new Hashtable();
1905 // load sequence features, database references and any associated PDB
1906 // structures for the alignment
1907 for (int i = 0; i < vamsasSeq.length; i++)
1909 if (JSEQ[i].getFeaturesCount() > 0)
1911 Features[] features = JSEQ[i].getFeatures();
1912 for (int f = 0; f < features.length; f++)
1914 jalview.datamodel.SequenceFeature sf = new jalview.datamodel.SequenceFeature(
1915 features[f].getType(), features[f].getDescription(),
1916 features[f].getStatus(), features[f].getBegin(),
1917 features[f].getEnd(), features[f].getFeatureGroup());
1919 sf.setScore(features[f].getScore());
1920 for (int od = 0; od < features[f].getOtherDataCount(); od++)
1922 OtherData keyValue = features[f].getOtherData(od);
1923 if (keyValue.getKey().startsWith("LINK"))
1925 sf.addLink(keyValue.getValue());
1929 sf.setValue(keyValue.getKey(), keyValue.getValue());
1934 al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf);
1937 if (vamsasSeq[i].getDBRefCount() > 0)
1939 addDBRefs(al.getSequenceAt(i).getDatasetSequence(), vamsasSeq[i]);
1941 if (JSEQ[i].getPdbidsCount() > 0)
1943 Pdbids[] ids = JSEQ[i].getPdbids();
1944 for (int p = 0; p < ids.length; p++)
1946 jalview.datamodel.PDBEntry entry = new jalview.datamodel.PDBEntry();
1947 entry.setId(ids[p].getId());
1948 entry.setType(ids[p].getType());
1949 if (ids[p].getFile() != null)
1951 if (!pdbloaded.containsKey(ids[p].getFile()))
1953 entry.setFile(loadPDBFile(jprovider, ids[p].getId()));
1957 entry.setFile(pdbloaded.get(ids[p].getId()).toString());
1961 al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
1965 } // end !multipleview
1967 // ///////////////////////////////
1968 // LOAD SEQUENCE MAPPINGS
1970 if (vamsasSet.getAlcodonFrameCount() > 0)
1972 // TODO Potentially this should only be done once for all views of an
1974 AlcodonFrame[] alc = vamsasSet.getAlcodonFrame();
1975 for (int i = 0; i < alc.length; i++)
1977 jalview.datamodel.AlignedCodonFrame cf = new jalview.datamodel.AlignedCodonFrame(
1978 alc[i].getAlcodonCount());
1979 if (alc[i].getAlcodonCount() > 0)
1981 Alcodon[] alcods = alc[i].getAlcodon();
1982 for (int p = 0; p < cf.codons.length; p++)
1984 if (alcods[p].hasPos1() && alcods[p].hasPos2()
1985 && alcods[p].hasPos3())
1987 // translated codons require three valid positions
1988 cf.codons[p] = new int[3];
1989 cf.codons[p][0] = (int) alcods[p].getPos1();
1990 cf.codons[p][1] = (int) alcods[p].getPos2();
1991 cf.codons[p][2] = (int) alcods[p].getPos3();
1995 cf.codons[p] = null;
1999 if (alc[i].getAlcodMapCount() > 0)
2001 AlcodMap[] maps = alc[i].getAlcodMap();
2002 for (int m = 0; m < maps.length; m++)
2004 SequenceI dnaseq = (SequenceI) seqRefIds
2005 .get(maps[m].getDnasq());
2007 jalview.datamodel.Mapping mapping = null;
2008 // attach to dna sequence reference.
2009 if (maps[m].getMapping() != null)
2011 mapping = addMapping(maps[m].getMapping());
2015 cf.addMap(dnaseq, mapping.getTo(), mapping.getMap());
2020 frefedSequence.add(new Object[]
2021 { maps[m].getDnasq(), cf, mapping });
2025 al.addCodonFrame(cf);
2030 // ////////////////////////////////
2032 boolean hideQuality = true, hideConservation = true, hideConsensus = true;
2034 * store any annotations which forward reference a group's ID
2036 Hashtable groupAnnotRefs = new Hashtable();
2038 if (vamsasSet.getAnnotationCount() > 0)
2040 Annotation[] an = vamsasSet.getAnnotation();
2042 for (int i = 0; i < an.length; i++)
2044 // set visibility for automatic annotation for this view
2045 if (an[i].getLabel().equals("Quality"))
2047 hideQuality = false;
2050 else if (an[i].getLabel().equals("Conservation"))
2052 hideConservation = false;
2055 else if (an[i].getLabel().equals("Consensus"))
2057 hideConsensus = false;
2060 // set visiblity for other annotation in this view
2061 if (an[i].getId() != null
2062 && annotationIds.containsKey(an[i].getId()))
2064 jalview.datamodel.AlignmentAnnotation jda = (jalview.datamodel.AlignmentAnnotation) annotationIds
2065 .get(an[i].getId());
2066 // in principle Visible should always be true for annotation displayed
2067 // in multiple views
2068 if (an[i].hasVisible())
2069 jda.visible = an[i].getVisible();
2071 al.addAnnotation(jda);
2075 // Construct new annotation from model.
2076 AnnotationElement[] ae = an[i].getAnnotationElement();
2077 jalview.datamodel.Annotation[] anot = null;
2079 if (!an[i].getScoreOnly())
2081 anot = new jalview.datamodel.Annotation[al.getWidth()];
2083 for (int aa = 0; aa < ae.length && aa < anot.length; aa++)
2085 if (ae[aa].getPosition() >= anot.length)
2088 anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(
2090 ae[aa].getDisplayCharacter(), ae[aa].getDescription(), (ae[aa]
2091 .getSecondaryStructure() == null || ae[aa]
2092 .getSecondaryStructure().length() == 0) ? ' ' : ae[aa]
2093 .getSecondaryStructure().charAt(0), ae[aa].getValue()
2096 // JBPNote: Consider verifying dataflow for IO of secondary
2097 // structure annotation read from Stockholm files
2098 // this was added to try to ensure that
2099 // if (anot[ae[aa].getPosition()].secondaryStructure>' ')
2101 // anot[ae[aa].getPosition()].displayCharacter = "";
2103 anot[ae[aa].getPosition()].colour = new java.awt.Color(ae[aa]
2107 jalview.datamodel.AlignmentAnnotation jaa = null;
2109 if (an[i].getGraph())
2111 jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
2112 an[i].getDescription(), anot, 0, 0, an[i].getGraphType());
2114 jaa.graphGroup = an[i].getGraphGroup();
2116 if (an[i].getThresholdLine() != null)
2118 jaa.setThreshold(new jalview.datamodel.GraphLine(an[i]
2119 .getThresholdLine().getValue(), an[i]
2120 .getThresholdLine().getLabel(), new java.awt.Color(
2121 an[i].getThresholdLine().getColour())));
2128 jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
2129 an[i].getDescription(), anot);
2131 // register new annotation
2132 if (an[i].getId() != null)
2134 annotationIds.put(an[i].getId(), jaa);
2135 jaa.annotationId = an[i].getId();
2137 // recover sequence association
2138 if (an[i].getSequenceRef() != null)
2140 if (al.findName(an[i].getSequenceRef()) != null)
2142 jaa.createSequenceMapping(al.findName(an[i].getSequenceRef()),
2144 al.findName(an[i].getSequenceRef()).addAlignmentAnnotation(jaa);
2147 // and make a note of any group association
2148 if (an[i].getGroupRef() != null && an[i].getGroupRef().length() > 0)
2150 groupAnnotRefs.put(an[i].getGroupRef(), jaa);
2153 if (an[i].hasScore())
2155 jaa.setScore(an[i].getScore());
2157 if (an[i].hasVisible())
2158 jaa.visible = an[i].getVisible();
2160 if (an[i].hasCentreColLabels())
2161 jaa.centreColLabels = an[i].getCentreColLabels();
2163 if (an[i].hasScaleColLabels())
2165 jaa.scaleColLabel = an[i].getScaleColLabels();
2167 if (an[i].hasAutoCalculated() && an[i].isAutoCalculated())
2169 // newer files have an 'autoCalculated' flag and store calculation
2170 // state in viewport properties
2171 jaa.autoCalculated = true; // means annotation will be marked for
2172 // update at end of load.
2174 al.addAnnotation(jaa);
2178 // ///////////////////////
2180 // Create alignment markup and styles for this view
2181 if (jms.getJGroupCount() > 0)
2183 JGroup[] groups = jms.getJGroup();
2185 for (int i = 0; i < groups.length; i++)
2187 ColourSchemeI cs = null;
2189 if (groups[i].getColour() != null)
2191 if (groups[i].getColour().startsWith("ucs"))
2193 cs = GetUserColourScheme(jms, groups[i].getColour());
2197 cs = ColourSchemeProperty.getColour(al, groups[i].getColour());
2202 cs.setThreshold(groups[i].getPidThreshold(), true);
2206 Vector seqs = new Vector();
2208 for (int s = 0; s < groups[i].getSeqCount(); s++)
2210 String seqId = groups[i].getSeq(s) + "";
2211 jalview.datamodel.SequenceI ts = (jalview.datamodel.SequenceI) seqRefIds
2216 seqs.addElement(ts);
2220 if (seqs.size() < 1)
2225 jalview.datamodel.SequenceGroup sg = new jalview.datamodel.SequenceGroup(
2226 seqs, groups[i].getName(), cs, groups[i].getDisplayBoxes(),
2227 groups[i].getDisplayText(), groups[i].getColourText(),
2228 groups[i].getStart(), groups[i].getEnd());
2231 .setOutlineColour(new java.awt.Color(groups[i]
2232 .getOutlineColour()));
2234 sg.textColour = new java.awt.Color(groups[i].getTextCol1());
2235 sg.textColour2 = new java.awt.Color(groups[i].getTextCol2());
2236 sg.setShowNonconserved(groups[i].hasShowUnconserved() ? groups[i]
2237 .isShowUnconserved() : false);
2238 sg.thresholdTextColour = groups[i].getTextColThreshold();
2239 if (groups[i].hasShowConsensusHistogram())
2242 .setShowConsensusHistogram(groups[i]
2243 .isShowConsensusHistogram());
2246 if (groups[i].hasShowSequenceLogo())
2248 sg.setIncludeAllConsSymbols(groups[i].isShowSequenceLogo());
2250 if (groups[i].hasIgnoreGapsinConsensus())
2252 sg.setIgnoreGapsConsensus(groups[i].getIgnoreGapsinConsensus());
2254 if (groups[i].getConsThreshold() != 0)
2256 jalview.analysis.Conservation c = new jalview.analysis.Conservation(
2257 "All", ResidueProperties.propHash, 3, sg
2258 .getSequences(null), 0, sg.getWidth() - 1);
2260 c.verdict(false, 25);
2261 sg.cs.setConservation(c);
2264 if (groups[i].getId() != null && groupAnnotRefs.size() > 0)
2266 // re-instate unique group/annotation row reference
2267 jalview.datamodel.AlignmentAnnotation jaa = (jalview.datamodel.AlignmentAnnotation) groupAnnotRefs
2268 .get(groups[i].getId());
2279 // ///////////////////////////////
2282 // If we just load in the same jar file again, the sequenceSetId
2283 // will be the same, and we end up with multiple references
2284 // to the same sequenceSet. We must modify this id on load
2285 // so that each load of the file gives a unique id
2286 String uniqueSeqSetId = view.getSequenceSetId() + uniqueSetSuffix;
2287 String viewId = (view.getId() == null ? null : view.getId()
2289 AlignFrame af = null;
2290 AlignViewport av = null;
2291 // now check to see if we really need to create a new viewport.
2292 if (multipleView && viewportsAdded.size() == 0)
2294 // We recovered an alignment for which a viewport already exists.
2295 // TODO: fix up any settings necessary for overlaying stored state onto
2296 // state recovered from another document. (may not be necessary).
2297 // we may need a binding from a viewport in memory to one recovered from
2299 // and then recover its containing af to allow the settings to be applied.
2300 // TODO: fix for vamsas demo
2302 .println("About to recover a viewport for existing alignment: Sequence set ID is "
2304 Object seqsetobj = retrieveExistingObj(uniqueSeqSetId);
2305 if (seqsetobj != null)
2307 if (seqsetobj instanceof String)
2309 uniqueSeqSetId = (String) seqsetobj;
2311 .println("Recovered extant sequence set ID mapping for ID : New Sequence set ID is "
2317 .println("Warning : Collision between sequence set ID string and existing jalview object mapping.");
2322 AlignmentPanel ap = null;
2323 boolean isnewview = true;
2326 // Check to see if this alignment already has a view id == viewId
2327 jalview.gui.AlignmentPanel views[] = Desktop
2328 .getAlignmentPanels(uniqueSeqSetId);
2329 if (views != null && views.length > 0)
2331 for (int v = 0; v < views.length; v++)
2333 if (views[v].av.getViewId().equalsIgnoreCase(viewId))
2335 // recover the existing alignpanel, alignframe, viewport
2336 af = views[v].alignFrame;
2339 // TODO: could even skip resetting view settings if we don't want to
2340 // change the local settings from other jalview processes
2349 af = loadViewport(file, JSEQ, hiddenSeqs, al, hideConsensus,
2350 hideQuality, hideConservation, jms, view, uniqueSeqSetId,
2356 // /////////////////////////////////////
2357 if (loadTreesAndStructures && jms.getTreeCount() > 0)
2361 for (int t = 0; t < jms.getTreeCount(); t++)
2364 Tree tree = jms.getTree(t);
2366 TreePanel tp = (TreePanel) retrieveExistingObj(tree.getId());
2369 tp = af.ShowNewickTree(new jalview.io.NewickFile(tree
2370 .getNewick()), tree.getTitle(), tree.getWidth(), tree
2371 .getHeight(), tree.getXpos(), tree.getYpos());
2372 if (tree.getId() != null)
2374 // perhaps bind the tree id to something ?
2379 // update local tree attributes ?
2380 // TODO: should check if tp has been manipulated by user - if so its
2381 // settings shouldn't be modified
2382 tp.setTitle(tree.getTitle());
2383 tp.setBounds(new Rectangle(tree.getXpos(), tree.getYpos(), tree
2384 .getWidth(), tree.getHeight()));
2385 tp.av = av; // af.viewport; // TODO: verify 'associate with all
2388 tp.treeCanvas.av = av; // af.viewport;
2389 tp.treeCanvas.ap = ap; // af.alignPanel;
2394 warn("There was a problem recovering stored Newick tree: \n"
2395 + tree.getNewick());
2399 tp.fitToWindow.setState(tree.getFitToWindow());
2400 tp.fitToWindow_actionPerformed(null);
2402 if (tree.getFontName() != null)
2404 tp.setTreeFont(new java.awt.Font(tree.getFontName(), tree
2405 .getFontStyle(), tree.getFontSize()));
2409 tp.setTreeFont(new java.awt.Font(view.getFontName(), view
2410 .getFontStyle(), tree.getFontSize()));
2413 tp.showPlaceholders(tree.getMarkUnlinked());
2414 tp.showBootstrap(tree.getShowBootstrap());
2415 tp.showDistances(tree.getShowDistances());
2417 tp.treeCanvas.threshold = tree.getThreshold();
2419 if (tree.getCurrentTree())
2421 af.viewport.setCurrentTree(tp.getTree());
2425 } catch (Exception ex)
2427 ex.printStackTrace();
2431 // //LOAD STRUCTURES
2432 if (loadTreesAndStructures)
2434 for (int i = 0; i < JSEQ.length; i++)
2436 if (JSEQ[i].getPdbidsCount() > 0)
2438 Pdbids[] ids = JSEQ[i].getPdbids();
2439 for (int p = 0; p < ids.length; p++)
2441 for (int s = 0; s < ids[p].getStructureStateCount(); s++)
2443 // check to see if we haven't already created this structure view
2444 String sviewid = (ids[p].getStructureState(s).getViewId() == null) ? null
2445 : ids[p].getStructureState(s).getViewId()
2447 jalview.datamodel.PDBEntry jpdb = new jalview.datamodel.PDBEntry();
2448 // Originally : ids[p].getFile()
2449 // : TODO: verify external PDB file recovery still works in normal
2450 // jalview project load
2451 jpdb.setFile(loadPDBFile(jprovider, ids[p].getId()));
2452 jpdb.setId(ids[p].getId());
2454 int x = ids[p].getStructureState(s).getXpos();
2455 int y = ids[p].getStructureState(s).getYpos();
2456 int width = ids[p].getStructureState(s).getWidth();
2457 int height = ids[p].getStructureState(s).getHeight();
2458 AppJmol comp = null;
2459 JInternalFrame[] frames = null;
2464 frames = Desktop.desktop.getAllFrames();
2465 } catch (ArrayIndexOutOfBoundsException e)
2467 // occasional No such child exceptions are thrown here...
2472 } catch (Exception f)
2477 } while (frames == null);
2478 // search for any Jmol windows already open from other
2479 // alignment views that exactly match the stored structure state
2480 for (int f = 0; comp == null && f < frames.length; f++)
2482 if (frames[f] instanceof AppJmol)
2485 && ((AppJmol) frames[f]).getViewId().equals(
2488 // post jalview 2.4 schema includes structure view id
2489 comp = (AppJmol) frames[f];
2491 else if (frames[f].getX() == x && frames[f].getY() == y
2492 && frames[f].getHeight() == height
2493 && frames[f].getWidth() == width)
2495 comp = (AppJmol) frames[f];
2499 // Probably don't need to do this anymore...
2500 // Desktop.desktop.getComponentAt(x, y);
2501 // TODO: NOW: check that this recovers the PDB file correctly.
2502 String pdbFile = loadPDBFile(jprovider, ids[p].getId());
2504 jalview.datamodel.SequenceI[] seq = new jalview.datamodel.SequenceI[]
2505 { (jalview.datamodel.SequenceI) seqRefIds.get(JSEQ[i].getId()
2510 // create a new Jmol window
2511 String state = ids[p].getStructureState(s).getContent();
2512 StringBuffer newFileLoc = null;
2513 if (state.indexOf("load") > -1)
2515 newFileLoc = new StringBuffer(state.substring(0, state
2516 .indexOf("\"", state.indexOf("load")) + 1));
2518 newFileLoc.append(jpdb.getFile());
2519 newFileLoc.append(state.substring(state.indexOf("\"",
2520 state.indexOf("load \"") + 6)));
2525 .println("Ignoring incomplete Jmol state for PDB "
2528 newFileLoc = new StringBuffer(state);
2529 newFileLoc.append("; load \"");
2530 newFileLoc.append(jpdb.getFile());
2531 newFileLoc.append("\";");
2534 if (newFileLoc != null)
2536 new AppJmol(pdbFile, ids[p].getId(), seq, af.alignPanel,
2537 newFileLoc.toString(), new java.awt.Rectangle(x,
2538 y, width, height), sviewid);
2543 // if (comp != null)
2545 // NOTE: if the jalview project is part of a shared session then
2546 // view synchronization should/could be done here.
2548 // add mapping for this sequence to the already open Jmol
2549 // instance (if it doesn't already exist)
2551 StructureSelectionManager.getStructureSelectionManager()
2552 .setMapping(seq, null, pdbFile,
2553 jalview.io.AppletFormatAdapter.FILE);
2555 ((AppJmol) comp).addSequence(seq);
2566 AlignFrame loadViewport(String file, JSeq[] JSEQ, Vector hiddenSeqs,
2567 Alignment al, boolean hideConsensus, boolean hideQuality,
2568 boolean hideConservation, JalviewModelSequence jms,
2569 Viewport view, String uniqueSeqSetId, String viewId)
2571 AlignFrame af = null;
2572 af = new AlignFrame(al, view.getWidth(), view.getHeight(),
2573 uniqueSeqSetId, viewId);
2575 af.setFileName(file, "Jalview");
2577 for (int i = 0; i < JSEQ.length; i++)
2579 af.viewport.setSequenceColour(af.viewport.alignment.getSequenceAt(i),
2580 new java.awt.Color(JSEQ[i].getColour()));
2583 af.viewport.gatherViewsHere = view.getGatheredViews();
2585 if (view.getSequenceSetId() != null)
2587 jalview.gui.AlignViewport av = (jalview.gui.AlignViewport) viewportsAdded
2588 .get(uniqueSeqSetId);
2590 af.viewport.sequenceSetID = uniqueSeqSetId;
2593 // propagate shared settings to this new view
2594 af.viewport.historyList = av.historyList;
2595 af.viewport.redoList = av.redoList;
2599 viewportsAdded.put(uniqueSeqSetId, af.viewport);
2601 // TODO: check if this method can be called repeatedly without
2602 // side-effects if alignpanel already registered.
2603 PaintRefresher.Register(af.alignPanel, uniqueSeqSetId);
2605 // apply Hidden regions to view.
2606 if (hiddenSeqs != null)
2608 for (int s = 0; s < JSEQ.length; s++)
2610 jalview.datamodel.SequenceGroup hidden = new jalview.datamodel.SequenceGroup();
2612 for (int r = 0; r < JSEQ[s].getHiddenSequencesCount(); r++)
2614 hidden.addSequence(al
2615 .getSequenceAt(JSEQ[s].getHiddenSequences(r)), false);
2617 af.viewport.hideRepSequences(al.getSequenceAt(s), hidden);
2620 jalview.datamodel.SequenceI[] hseqs = new jalview.datamodel.SequenceI[hiddenSeqs
2623 for (int s = 0; s < hiddenSeqs.size(); s++)
2625 hseqs[s] = (jalview.datamodel.SequenceI) hiddenSeqs.elementAt(s);
2628 af.viewport.hideSequence(hseqs);
2631 // set visibility of annotation in view
2632 if ((hideConsensus || hideQuality || hideConservation)
2633 && al.getAlignmentAnnotation() != null)
2635 int hSize = al.getAlignmentAnnotation().length;
2636 for (int h = 0; h < hSize; h++)
2638 if ((hideConsensus && al.getAlignmentAnnotation()[h].label
2639 .equals("Consensus"))
2640 || (hideQuality && al.getAlignmentAnnotation()[h].label
2642 || (hideConservation && al.getAlignmentAnnotation()[h].label
2643 .equals("Conservation")))
2645 al.deleteAnnotation(al.getAlignmentAnnotation()[h]);
2650 af.alignPanel.adjustAnnotationHeight();
2652 // recover view properties and display parameters
2653 if (view.getViewName() != null)
2655 af.viewport.viewName = view.getViewName();
2656 af.setInitialTabVisible();
2658 af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(), view
2661 af.viewport.setShowAnnotation(view.getShowAnnotation());
2662 af.viewport.setAbovePIDThreshold(view.getPidSelected());
2664 af.viewport.setColourText(view.getShowColourText());
2666 af.viewport.setConservationSelected(view.getConservationSelected());
2667 af.viewport.setShowJVSuffix(view.getShowFullId());
2668 af.viewport.rightAlignIds = view.getRightAlignIds();
2669 af.viewport.setFont(new java.awt.Font(view.getFontName(), view
2670 .getFontStyle(), view.getFontSize()));
2671 af.alignPanel.fontChanged();
2672 af.viewport.setRenderGaps(view.getRenderGaps());
2673 af.viewport.setWrapAlignment(view.getWrapAlignment());
2674 af.alignPanel.setWrapAlignment(view.getWrapAlignment());
2675 af.viewport.setShowAnnotation(view.getShowAnnotation());
2676 af.alignPanel.setAnnotationVisible(view.getShowAnnotation());
2678 af.viewport.setShowBoxes(view.getShowBoxes());
2680 af.viewport.setShowText(view.getShowText());
2682 af.viewport.textColour = new java.awt.Color(view.getTextCol1());
2683 af.viewport.textColour2 = new java.awt.Color(view.getTextCol2());
2684 af.viewport.thresholdTextColour = view.getTextColThreshold();
2685 af.viewport.setShowUnconserved(view.hasShowUnconserved() ? view
2686 .isShowUnconserved() : false);
2687 af.viewport.setStartRes(view.getStartRes());
2688 af.viewport.setStartSeq(view.getStartSeq());
2690 ColourSchemeI cs = null;
2691 // apply colourschemes
2692 if (view.getBgColour() != null)
2694 if (view.getBgColour().startsWith("ucs"))
2696 cs = GetUserColourScheme(jms, view.getBgColour());
2698 else if (view.getBgColour().startsWith("Annotation"))
2700 // int find annotation
2701 if (af.viewport.alignment.getAlignmentAnnotation() != null)
2703 for (int i = 0; i < af.viewport.alignment
2704 .getAlignmentAnnotation().length; i++)
2706 if (af.viewport.alignment.getAlignmentAnnotation()[i].label
2707 .equals(view.getAnnotationColours().getAnnotation()))
2709 if (af.viewport.alignment.getAlignmentAnnotation()[i]
2710 .getThreshold() == null)
2712 af.viewport.alignment.getAlignmentAnnotation()[i]
2713 .setThreshold(new jalview.datamodel.GraphLine(view
2714 .getAnnotationColours().getThreshold(),
2715 "Threshold", java.awt.Color.black)
2720 if (view.getAnnotationColours().getColourScheme().equals(
2723 cs = new AnnotationColourGradient(af.viewport.alignment
2724 .getAlignmentAnnotation()[i], new java.awt.Color(
2725 view.getAnnotationColours().getMinColour()),
2726 new java.awt.Color(view.getAnnotationColours()
2727 .getMaxColour()), view
2728 .getAnnotationColours().getAboveThreshold());
2730 else if (view.getAnnotationColours().getColourScheme()
2733 cs = new AnnotationColourGradient(af.viewport.alignment
2734 .getAlignmentAnnotation()[i],
2735 GetUserColourScheme(jms, view
2736 .getAnnotationColours().getColourScheme()),
2737 view.getAnnotationColours().getAboveThreshold());
2741 cs = new AnnotationColourGradient(af.viewport.alignment
2742 .getAlignmentAnnotation()[i], ColourSchemeProperty
2743 .getColour(al, view.getAnnotationColours()
2744 .getColourScheme()), view
2745 .getAnnotationColours().getAboveThreshold());
2748 // Also use these settings for all the groups
2749 if (al.getGroups() != null)
2751 for (int g = 0; g < al.getGroups().size(); g++)
2753 jalview.datamodel.SequenceGroup sg = (jalview.datamodel.SequenceGroup) al
2754 .getGroups().elementAt(g);
2763 * (view.getAnnotationColours().getColourScheme().equals("None"
2764 * )) { sg.cs = new AnnotationColourGradient(
2765 * af.viewport.alignment.getAlignmentAnnotation()[i], new
2766 * java.awt.Color(view.getAnnotationColours().
2767 * getMinColour()), new
2768 * java.awt.Color(view.getAnnotationColours().
2770 * view.getAnnotationColours().getAboveThreshold()); } else
2773 sg.cs = new AnnotationColourGradient(
2774 af.viewport.alignment.getAlignmentAnnotation()[i],
2775 sg.cs, view.getAnnotationColours()
2776 .getAboveThreshold());
2790 cs = ColourSchemeProperty.getColour(al, view.getBgColour());
2795 cs.setThreshold(view.getPidThreshold(), true);
2796 cs.setConsensus(af.viewport.hconsensus);
2800 af.viewport.setGlobalColourScheme(cs);
2801 af.viewport.setColourAppliesToAllGroups(false);
2803 if (view.getConservationSelected() && cs != null)
2805 cs.setConservationInc(view.getConsThreshold());
2808 af.changeColour(cs);
2810 af.viewport.setColourAppliesToAllGroups(true);
2812 if (view.getShowSequenceFeatures())
2814 af.viewport.showSequenceFeatures = true;
2816 if (view.hasCentreColumnLabels())
2818 af.viewport.setCentreColumnLabels(view.getCentreColumnLabels());
2820 if (view.hasIgnoreGapsinConsensus())
2822 af.viewport.ignoreGapsInConsensusCalculation = view
2823 .getIgnoreGapsinConsensus();
2825 if (view.hasFollowHighlight())
2827 af.viewport.followHighlight = view.getFollowHighlight();
2829 if (view.hasFollowSelection())
2831 af.viewport.followSelection = view.getFollowSelection();
2833 if (view.hasShowConsensusHistogram())
2835 af.viewport.setShowConsensusHistogram(view
2836 .getShowConsensusHistogram());
2840 af.viewport.setShowConsensusHistogram(true);
2842 if (view.hasShowSequenceLogo())
2844 af.viewport.setShowSequenceLogo(view.getShowSequenceLogo());
2848 af.viewport.setShowSequenceLogo(false);
2850 if (view.hasShowDbRefTooltip())
2852 af.viewport.setShowDbRefs(view.getShowDbRefTooltip());
2854 if (view.hasShowNPfeatureTooltip())
2856 af.viewport.setShowNpFeats(view.hasShowNPfeatureTooltip());
2858 if (view.hasShowGroupConsensus())
2860 af.viewport.setShowGroupConsensus(view.getShowGroupConsensus());
2864 af.viewport.setShowGroupConsensus(false);
2866 if (view.hasShowGroupConservation())
2868 af.viewport.setShowGroupConservation(view.getShowGroupConservation());
2872 af.viewport.setShowGroupConservation(false);
2875 // recover featre settings
2876 if (jms.getFeatureSettings() != null)
2878 af.viewport.featuresDisplayed = new Hashtable();
2879 String[] renderOrder = new String[jms.getFeatureSettings()
2880 .getSettingCount()];
2881 for (int fs = 0; fs < jms.getFeatureSettings().getSettingCount(); fs++)
2883 Setting setting = jms.getFeatureSettings().getSetting(fs);
2884 if (setting.hasMincolour())
2886 GraduatedColor gc = setting.hasMin() ? new GraduatedColor(
2887 new java.awt.Color(setting.getMincolour()),
2888 new java.awt.Color(setting.getColour()),
2889 setting.getMin(), setting.getMax()) : new GraduatedColor(
2890 new java.awt.Color(setting.getMincolour()),
2891 new java.awt.Color(setting.getColour()), 0, 1);
2892 if (setting.hasThreshold())
2894 gc.setThresh(setting.getThreshold());
2895 gc.setThreshType(setting.getThreshstate());
2897 gc.setAutoScaled(true); // default
2898 if (setting.hasAutoScale())
2900 gc.setAutoScaled(setting.getAutoScale());
2902 if (setting.hasColourByLabel())
2904 gc.setColourByLabel(setting.getColourByLabel());
2906 // and put in the feature colour table.
2907 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(
2908 setting.getType(), gc);
2912 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(
2914 new java.awt.Color(setting.getColour()));
2916 renderOrder[fs] = setting.getType();
2917 if (setting.hasOrder())
2918 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setOrder(
2919 setting.getType(), setting.getOrder());
2921 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setOrder(
2923 fs / jms.getFeatureSettings().getSettingCount());
2924 if (setting.getDisplay())
2926 af.viewport.featuresDisplayed.put(setting.getType(), new Integer(
2927 setting.getColour()));
2930 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder = renderOrder;
2932 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureGroups = fgtable = new Hashtable();
2933 for (int gs = 0; gs < jms.getFeatureSettings().getGroupCount(); gs++)
2935 Group grp = jms.getFeatureSettings().getGroup(gs);
2936 fgtable.put(grp.getName(), new Boolean(grp.getDisplay()));
2940 if (view.getHiddenColumnsCount() > 0)
2942 for (int c = 0; c < view.getHiddenColumnsCount(); c++)
2944 af.viewport.hideColumns(view.getHiddenColumns(c).getStart(), view
2945 .getHiddenColumns(c).getEnd() // +1
2950 af.setMenusFromViewport(af.viewport);
2951 // TODO: we don't need to do this if the viewport is aready visible.
2952 Desktop.addInternalFrame(af, view.getTitle(), view.getWidth(), view
2954 af.alignPanel.updateAnnotation(false); // recompute any autoannotation
2958 Hashtable skipList = null;
2961 * TODO remove this method
2964 * @return AlignFrame bound to sequenceSetId from view, if one exists. private
2965 * AlignFrame getSkippedFrame(Viewport view) { if (skipList==null) {
2966 * throw new Error("Implementation Error. No skipList defined for this
2967 * Jalview2XML instance."); } return (AlignFrame)
2968 * skipList.get(view.getSequenceSetId()); }
2972 * Check if the Jalview view contained in object should be skipped or not.
2975 * @return true if view's sequenceSetId is a key in skipList
2977 private boolean skipViewport(JalviewModel object)
2979 if (skipList == null)
2984 if (skipList.containsKey(id = object.getJalviewModelSequence()
2985 .getViewport()[0].getSequenceSetId()))
2987 if (Cache.log != null && Cache.log.isDebugEnabled())
2989 Cache.log.debug("Skipping seuqence set id " + id);
2996 public void AddToSkipList(AlignFrame af)
2998 if (skipList == null)
3000 skipList = new Hashtable();
3002 skipList.put(af.getViewport().getSequenceSetId(), af);
3005 public void clearSkipList()
3007 if (skipList != null)
3014 private void recoverDatasetFor(SequenceSet vamsasSet, Alignment al)
3016 jalview.datamodel.Alignment ds = getDatasetFor(vamsasSet.getDatasetId());
3017 Vector dseqs = null;
3020 // create a list of new dataset sequences
3021 dseqs = new Vector();
3023 for (int i = 0, iSize = vamsasSet.getSequenceCount(); i < iSize; i++)
3025 Sequence vamsasSeq = vamsasSet.getSequence(i);
3026 ensureJalviewDatasetSequence(vamsasSeq, ds, dseqs);
3028 // create a new dataset
3031 SequenceI[] dsseqs = new SequenceI[dseqs.size()];
3032 dseqs.copyInto(dsseqs);
3033 ds = new jalview.datamodel.Alignment(dsseqs);
3034 debug("Created new dataset " + vamsasSet.getDatasetId()
3035 + " for alignment " + System.identityHashCode(al));
3036 addDatasetRef(vamsasSet.getDatasetId(), ds);
3038 // set the dataset for the newly imported alignment.
3039 if (al.getDataset() == null)
3048 * sequence definition to create/merge dataset sequence for
3052 * vector to add new dataset sequence to
3054 private void ensureJalviewDatasetSequence(Sequence vamsasSeq,
3055 AlignmentI ds, Vector dseqs)
3057 // JBP TODO: Check this is called for AlCodonFrames to support recovery of
3059 jalview.datamodel.Sequence sq = (jalview.datamodel.Sequence) seqRefIds
3060 .get(vamsasSeq.getId());
3061 jalview.datamodel.SequenceI dsq = null;
3062 if (sq != null && sq.getDatasetSequence() != null)
3064 dsq = (jalview.datamodel.SequenceI) sq.getDatasetSequence();
3067 String sqid = vamsasSeq.getDsseqid();
3070 // need to create or add a new dataset sequence reference to this sequence
3073 dsq = (jalview.datamodel.SequenceI) seqRefIds.get(sqid);
3078 // make a new dataset sequence
3079 dsq = sq.createDatasetSequence();
3082 // make up a new dataset reference for this sequence
3083 sqid = seqHash(dsq);
3085 dsq.setVamsasId(uniqueSetSuffix + sqid);
3086 seqRefIds.put(sqid, dsq);
3091 dseqs.addElement(dsq);
3096 ds.addSequence(dsq);
3102 { // make this dataset sequence sq's dataset sequence
3103 sq.setDatasetSequence(dsq);
3107 // TODO: refactor this as a merge dataset sequence function
3108 // now check that sq (the dataset sequence) sequence really is the union of
3109 // all references to it
3110 // boolean pre = sq.getStart() < dsq.getStart();
3111 // boolean post = sq.getEnd() > dsq.getEnd();
3115 StringBuffer sb = new StringBuffer();
3116 String newres = jalview.analysis.AlignSeq.extractGaps(
3117 jalview.util.Comparison.GapChars, sq.getSequenceAsString());
3118 if (!newres.equalsIgnoreCase(dsq.getSequenceAsString())
3119 && newres.length() > dsq.getLength())
3121 // Update with the longer sequence.
3125 * if (pre) { sb.insert(0, newres .substring(0, dsq.getStart() -
3126 * sq.getStart())); dsq.setStart(sq.getStart()); } if (post) {
3127 * sb.append(newres.substring(newres.length() - sq.getEnd() -
3128 * dsq.getEnd())); dsq.setEnd(sq.getEnd()); }
3130 dsq.setSequence(sb.toString());
3132 // TODO: merges will never happen if we 'know' we have the real dataset
3133 // sequence - this should be detected when id==dssid
3134 System.err.println("DEBUG Notice: Merged dataset sequence"); // ("
3135 // + (pre ? "prepended" : "") + " "
3136 // + (post ? "appended" : ""));
3141 java.util.Hashtable datasetIds = null;
3143 java.util.IdentityHashMap dataset2Ids = null;
3145 private Alignment getDatasetFor(String datasetId)
3147 if (datasetIds == null)
3149 datasetIds = new Hashtable();
3152 if (datasetIds.containsKey(datasetId))
3154 return (Alignment) datasetIds.get(datasetId);
3159 private void addDatasetRef(String datasetId, Alignment dataset)
3161 if (datasetIds == null)
3163 datasetIds = new Hashtable();
3165 datasetIds.put(datasetId, dataset);
3169 * make a new dataset ID for this jalview dataset alignment
3174 private String getDatasetIdRef(jalview.datamodel.Alignment dataset)
3176 if (dataset.getDataset() != null)
3178 warn("Serious issue! Dataset Object passed to getDatasetIdRef is not a Jalview DATASET alignment...");
3180 String datasetId = makeHashCode(dataset, null);
3181 if (datasetId == null)
3183 // make a new datasetId and record it
3184 if (dataset2Ids == null)
3186 dataset2Ids = new IdentityHashMap();
3190 datasetId = (String) dataset2Ids.get(dataset);
3192 if (datasetId == null)
3194 datasetId = "ds" + dataset2Ids.size() + 1;
3195 dataset2Ids.put(dataset, datasetId);
3201 private void addDBRefs(SequenceI datasetSequence, Sequence sequence)
3203 for (int d = 0; d < sequence.getDBRefCount(); d++)
3205 DBRef dr = sequence.getDBRef(d);
3206 jalview.datamodel.DBRefEntry entry = new jalview.datamodel.DBRefEntry(
3207 sequence.getDBRef(d).getSource(), sequence.getDBRef(d)
3208 .getVersion(), sequence.getDBRef(d).getAccessionId());
3209 if (dr.getMapping() != null)
3211 entry.setMap(addMapping(dr.getMapping()));
3213 datasetSequence.addDBRef(entry);
3217 private jalview.datamodel.Mapping addMapping(Mapping m)
3219 SequenceI dsto = null;
3220 // Mapping m = dr.getMapping();
3221 int fr[] = new int[m.getMapListFromCount() * 2];
3222 Enumeration f = m.enumerateMapListFrom();
3223 for (int _i = 0; f.hasMoreElements(); _i += 2)
3225 MapListFrom mf = (MapListFrom) f.nextElement();
3226 fr[_i] = mf.getStart();
3227 fr[_i + 1] = mf.getEnd();
3229 int fto[] = new int[m.getMapListToCount() * 2];
3230 f = m.enumerateMapListTo();
3231 for (int _i = 0; f.hasMoreElements(); _i += 2)
3233 MapListTo mf = (MapListTo) f.nextElement();
3234 fto[_i] = mf.getStart();
3235 fto[_i + 1] = mf.getEnd();
3237 jalview.datamodel.Mapping jmap = new jalview.datamodel.Mapping(dsto,
3238 fr, fto, (int) m.getMapFromUnit(), (int) m.getMapToUnit());
3239 if (m.getMappingChoice() != null)
3241 MappingChoice mc = m.getMappingChoice();
3242 if (mc.getDseqFor() != null)
3244 String dsfor = "" + mc.getDseqFor();
3245 if (seqRefIds.containsKey(dsfor))
3250 jmap.setTo((SequenceI) seqRefIds.get(dsfor));
3254 frefedSequence.add(new Object[]
3261 * local sequence definition
3263 Sequence ms = mc.getSequence();
3264 jalview.datamodel.Sequence djs = null;
3265 String sqid = ms.getDsseqid();
3266 if (sqid != null && sqid.length() > 0)
3269 * recover dataset sequence
3271 djs = (jalview.datamodel.Sequence) seqRefIds.get(sqid);
3276 .println("Warning - making up dataset sequence id for DbRef sequence map reference");
3277 sqid = ((Object) ms).toString(); // make up a new hascode for
3278 // undefined dataset sequence hash
3279 // (unlikely to happen)
3285 * make a new dataset sequence and add it to refIds hash
3287 djs = new jalview.datamodel.Sequence(ms.getName(), ms
3289 djs.setStart(jmap.getMap().getToLowest());
3290 djs.setEnd(jmap.getMap().getToHighest());
3291 djs.setVamsasId(uniqueSetSuffix + sqid);
3293 seqRefIds.put(sqid, djs);
3296 jalview.bin.Cache.log.debug("about to recurse on addDBRefs.");
3305 public jalview.gui.AlignmentPanel copyAlignPanel(AlignmentPanel ap,
3306 boolean keepSeqRefs)
3309 jalview.schemabinding.version2.JalviewModel jm = SaveState(ap, null,
3315 jm.getJalviewModelSequence().getViewport(0).setSequenceSetId(null);
3319 uniqueSetSuffix = "";
3320 jm.getJalviewModelSequence().getViewport(0).setId(null); // we don't
3325 if (this.frefedSequence == null)
3327 frefedSequence = new Vector();
3330 viewportsAdded = new Hashtable();
3332 AlignFrame af = LoadFromObject(jm, null, false, null);
3333 af.alignPanels.clear();
3334 af.closeMenuItem_actionPerformed(true);
3337 * if(ap.av.alignment.getAlignmentAnnotation()!=null) { for(int i=0;
3338 * i<ap.av.alignment.getAlignmentAnnotation().length; i++) {
3339 * if(!ap.av.alignment.getAlignmentAnnotation()[i].autoCalculated) {
3340 * af.alignPanel.av.alignment.getAlignmentAnnotation()[i] =
3341 * ap.av.alignment.getAlignmentAnnotation()[i]; } } }
3344 return af.alignPanel;
3348 * flag indicating if hashtables should be cleared on finalization TODO this
3349 * flag may not be necessary
3351 private boolean _cleartables = true;
3353 private Hashtable jvids2vobj;
3358 * @see java.lang.Object#finalize()
3360 protected void finalize() throws Throwable
3362 // really make sure we have no buried refs left.
3367 this.seqRefIds = null;
3368 this.seqsToIds = null;
3372 private void warn(String msg)
3377 private void warn(String msg, Exception e)
3379 if (Cache.log != null)
3383 Cache.log.warn(msg, e);
3387 Cache.log.warn(msg);
3392 System.err.println("Warning: " + msg);
3395 e.printStackTrace();
3400 private void debug(String string)
3402 debug(string, null);
3405 private void debug(String msg, Exception e)
3407 if (Cache.log != null)
3411 Cache.log.debug(msg, e);
3415 Cache.log.debug(msg);
3420 System.err.println("Warning: " + msg);
3423 e.printStackTrace();
3429 * set the object to ID mapping tables used to write/recover objects and XML
3430 * ID strings for the jalview project. If external tables are provided then
3431 * finalize and clearSeqRefs will not clear the tables when the Jalview2XML
3432 * object goes out of scope. - also populates the datasetIds hashtable with
3433 * alignment objects containing dataset sequences
3436 * Map from ID strings to jalview datamodel
3438 * Map from jalview datamodel to ID strings
3442 public void setObjectMappingTables(Hashtable vobj2jv,
3443 IdentityHashMap jv2vobj)
3445 this.jv2vobj = jv2vobj;
3446 this.vobj2jv = vobj2jv;
3447 Iterator ds = jv2vobj.keySet().iterator();
3449 while (ds.hasNext())
3451 Object jvobj = ds.next();
3452 id = jv2vobj.get(jvobj).toString();
3453 if (jvobj instanceof jalview.datamodel.Alignment)
3455 if (((jalview.datamodel.Alignment) jvobj).getDataset() == null)
3457 addDatasetRef(id, (jalview.datamodel.Alignment) jvobj);
3460 else if (jvobj instanceof jalview.datamodel.Sequence)
3462 // register sequence object so the XML parser can recover it.
3463 if (seqRefIds == null)
3465 seqRefIds = new Hashtable();
3467 if (seqsToIds == null)
3469 seqsToIds = new IdentityHashMap();
3471 seqRefIds.put(jv2vobj.get(jvobj).toString(), jvobj);
3472 seqsToIds.put(jvobj, id);
3474 else if (jvobj instanceof jalview.datamodel.AlignmentAnnotation)
3476 if (annotationIds == null)
3478 annotationIds = new Hashtable();
3481 annotationIds.put(anid = jv2vobj.get(jvobj).toString(), jvobj);
3482 jalview.datamodel.AlignmentAnnotation jvann = (jalview.datamodel.AlignmentAnnotation) jvobj;
3483 if (jvann.annotationId == null)
3485 jvann.annotationId = anid;
3487 if (!jvann.annotationId.equals(anid))
3489 // TODO verify that this is the correct behaviour
3490 this.warn("Overriding Annotation ID for " + anid
3491 + " from different id : " + jvann.annotationId);
3492 jvann.annotationId = anid;
3495 else if (jvobj instanceof String)
3497 if (jvids2vobj == null)
3499 jvids2vobj = new Hashtable();
3500 jvids2vobj.put(jvobj, jv2vobj.get(jvobj).toString());
3504 Cache.log.debug("Ignoring " + jvobj.getClass() + " (ID = " + id);
3509 * set the uniqueSetSuffix used to prefix/suffix object IDs for jalview
3510 * objects created from the project archive. If string is null (default for
3511 * construction) then suffix will be set automatically.
3515 public void setUniqueSetSuffix(String string)
3517 uniqueSetSuffix = string;
3522 * uses skipList2 as the skipList for skipping views on sequence sets
3523 * associated with keys in the skipList
3527 public void setSkipList(Hashtable skipList2)
3529 skipList = skipList2;