2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
3 * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
11 * Jalview is distributed in the hope that it will be useful, but
12 * WITHOUT ANY WARRANTY; without even the implied warranty
13 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
14 * PURPOSE. See the GNU General Public License for more details.
16 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 import java.awt.Rectangle;
22 import java.lang.reflect.InvocationTargetException;
25 import java.util.Map.Entry;
26 import java.util.jar.*;
30 import org.exolab.castor.xml.*;
32 import uk.ac.vamsas.objects.utils.MapList;
33 import jalview.bin.Cache;
34 import jalview.datamodel.Alignment;
35 import jalview.datamodel.AlignmentI;
36 import jalview.datamodel.SequenceI;
37 import jalview.schemabinding.version2.*;
38 import jalview.schemes.*;
39 import jalview.structure.StructureSelectionManager;
40 import jalview.util.jarInputStreamProvider;
43 * Write out the current jalview desktop state as a Jalview XML stream.
45 * Note: the vamsas objects referred to here are primitive versions of the
46 * VAMSAS project schema elements - they are not the same and most likely never
52 public class Jalview2XML
55 * create/return unique hash string for sq
58 * @return new or existing unique string for sq
60 String seqHash(SequenceI sq)
62 if (seqsToIds == null)
66 if (seqsToIds.containsKey(sq))
68 return (String) seqsToIds.get(sq);
72 // create sequential key
73 String key = "sq" + (seqsToIds.size() + 1);
74 key = makeHashCode(sq, key); // check we don't have an external reference
76 seqsToIds.put(sq, key);
85 if (seqRefIds != null)
89 if (seqsToIds != null)
99 warn("clearSeqRefs called when _cleartables was not set. Doing nothing.");
100 // seqRefIds = new Hashtable();
101 // seqsToIds = new IdentityHashMap();
107 if (seqsToIds == null)
109 seqsToIds = new IdentityHashMap();
111 if (seqRefIds == null)
113 seqRefIds = new Hashtable();
118 * SequenceI reference -> XML ID string in jalview XML. Populated as XML reps
119 * of sequence objects are created.
121 java.util.IdentityHashMap seqsToIds = null;
124 * jalview XML Sequence ID to jalview sequence object reference (both dataset
125 * and alignment sequences. Populated as XML reps of sequence objects are
128 java.util.Hashtable seqRefIds = null; // key->SequenceI resolution
130 Vector frefedSequence = null;
132 boolean raiseGUI = true; // whether errors are raised in dialog boxes or not
138 public Jalview2XML(boolean raiseGUI)
140 this.raiseGUI = raiseGUI;
143 public void resolveFrefedSequences()
145 if (frefedSequence.size() > 0)
147 int r = 0, rSize = frefedSequence.size();
150 Object[] ref = (Object[]) frefedSequence.elementAt(r);
153 String sref = (String) ref[0];
154 if (seqRefIds.containsKey(sref))
156 if (ref[1] instanceof jalview.datamodel.Mapping)
158 SequenceI seq = (SequenceI) seqRefIds.get(sref);
159 while (seq.getDatasetSequence() != null)
161 seq = seq.getDatasetSequence();
163 ((jalview.datamodel.Mapping) ref[1]).setTo(seq);
167 if (ref[1] instanceof jalview.datamodel.AlignedCodonFrame)
169 SequenceI seq = (SequenceI) seqRefIds.get(sref);
170 while (seq.getDatasetSequence() != null)
172 seq = seq.getDatasetSequence();
175 && ref[2] instanceof jalview.datamodel.Mapping)
177 jalview.datamodel.Mapping mp = (jalview.datamodel.Mapping) ref[2];
178 ((jalview.datamodel.AlignedCodonFrame) ref[1]).addMap(
179 seq, mp.getTo(), mp.getMap());
184 .println("IMPLEMENTATION ERROR: Unimplemented forward sequence references for AlcodonFrames involving "
185 + ref[2].getClass() + " type objects.");
191 .println("IMPLEMENTATION ERROR: Unimplemented forward sequence references for "
192 + ref[1].getClass() + " type objects.");
195 frefedSequence.remove(r);
201 .println("IMPLEMENTATION WARNING: Unresolved forward reference for hash string "
203 + " with objecttype "
204 + ref[1].getClass());
211 frefedSequence.remove(r);
219 * This maintains a list of viewports, the key being the seqSetId. Important
220 * to set historyItem and redoList for multiple views
222 Hashtable viewportsAdded;
224 Hashtable annotationIds = new Hashtable();
226 String uniqueSetSuffix = "";
229 * List of pdbfiles added to Jar
231 Vector pdbfiles = null;
233 // SAVES SEVERAL ALIGNMENT WINDOWS TO SAME JARFILE
234 public void SaveState(File statefile)
238 FileOutputStream fos = new FileOutputStream(statefile);
239 JarOutputStream jout = new JarOutputStream(fos);
242 } catch (Exception e)
244 // TODO: inform user of the problem - they need to know if their data was
246 if (errorMessage == null)
248 errorMessage = "Couldn't write Jalview Archive to output file '"
249 + statefile + "' - See console error log for details";
253 errorMessage += "(output file was '" + statefile + "')";
261 * Writes a jalview project archive to the given Jar output stream.
265 public void SaveState(JarOutputStream jout)
267 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
277 // NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS
278 // //////////////////////////////////////////////////
279 // NOTE ALSO new PrintWriter must be used for each new JarEntry
280 PrintWriter out = null;
282 Vector shortNames = new Vector();
285 for (int i = frames.length - 1; i > -1; i--)
287 if (frames[i] instanceof AlignFrame)
289 AlignFrame af = (AlignFrame) frames[i];
292 && skipList.containsKey(af.getViewport()
293 .getSequenceSetId()))
298 String shortName = af.getTitle();
300 if (shortName.indexOf(File.separatorChar) > -1)
302 shortName = shortName.substring(shortName
303 .lastIndexOf(File.separatorChar) + 1);
308 while (shortNames.contains(shortName))
310 if (shortName.endsWith("_" + (count - 1)))
312 shortName = shortName
313 .substring(0, shortName.lastIndexOf("_"));
316 shortName = shortName.concat("_" + count);
320 shortNames.addElement(shortName);
322 if (!shortName.endsWith(".xml"))
324 shortName = shortName + ".xml";
327 int ap, apSize = af.alignPanels.size();
328 for (ap = 0; ap < apSize; ap++)
330 AlignmentPanel apanel = (AlignmentPanel) af.alignPanels
332 String fileName = apSize == 1 ? shortName : ap + shortName;
333 if (!fileName.endsWith(".xml"))
335 fileName = fileName + ".xml";
338 SaveState(apanel, fileName, jout);
345 } catch (Exception foo)
350 } catch (Exception ex)
352 // TODO: inform user of the problem - they need to know if their data was
354 if (errorMessage == null)
356 errorMessage = "Couldn't write Jalview Archive - see error output for details";
358 ex.printStackTrace();
362 // USE THIS METHOD TO SAVE A SINGLE ALIGNMENT WINDOW
363 public boolean SaveAlignment(AlignFrame af, String jarFile,
368 int ap, apSize = af.alignPanels.size();
369 FileOutputStream fos = new FileOutputStream(jarFile);
370 JarOutputStream jout = new JarOutputStream(fos);
371 for (ap = 0; ap < apSize; ap++)
373 AlignmentPanel apanel = (AlignmentPanel) af.alignPanels
375 String jfileName = apSize == 1 ? fileName : fileName + ap;
376 if (!jfileName.endsWith(".xml"))
378 jfileName = jfileName + ".xml";
380 SaveState(apanel, jfileName, jout);
386 } catch (Exception foo)
392 } catch (Exception ex)
394 errorMessage = "Couldn't Write alignment view to Jalview Archive - see error output for details";
395 ex.printStackTrace();
401 * create a JalviewModel from an algnment view and marshall it to a
405 * panel to create jalview model for
407 * name of alignment panel written to output stream
413 public JalviewModel SaveState(AlignmentPanel ap, String fileName,
414 JarOutputStream jout)
417 Vector jmolViewIds = new Vector(); //
418 Vector userColours = new Vector();
420 AlignViewport av = ap.av;
422 JalviewModel object = new JalviewModel();
423 object.setVamsasModel(new jalview.schemabinding.version2.VamsasModel());
425 object.setCreationDate(new java.util.Date(System.currentTimeMillis()));
426 object.setVersion(jalview.bin.Cache.getProperty("VERSION"));
428 jalview.datamodel.AlignmentI jal = av.alignment;
430 if (av.hasHiddenRows)
432 jal = jal.getHiddenSequences().getFullAlignment();
435 SequenceSet vamsasSet = new SequenceSet();
437 JalviewModelSequence jms = new JalviewModelSequence();
439 vamsasSet.setGapChar(jal.getGapCharacter() + "");
441 if (jal.getDataset() != null)
443 // dataset id is the dataset's hashcode
444 vamsasSet.setDatasetId(getDatasetIdRef(jal.getDataset()));
446 if (jal.getProperties() != null)
448 Enumeration en = jal.getProperties().keys();
449 while (en.hasMoreElements())
451 String key = en.nextElement().toString();
452 SequenceSetProperties ssp = new SequenceSetProperties();
454 ssp.setValue(jal.getProperties().get(key).toString());
455 vamsasSet.addSequenceSetProperties(ssp);
463 jalview.datamodel.SequenceI jds;
464 for (int i = 0; i < jal.getHeight(); i++)
466 jds = jal.getSequenceAt(i);
469 if (seqRefIds.get(id) != null)
471 // This happens for two reasons: 1. multiple views are being serialised.
472 // 2. the hashCode has collided with another sequence's code. This DOES
473 // HAPPEN! (PF00072.15.stk does this)
474 // JBPNote: Uncomment to debug writing out of files that do not read
475 // back in due to ArrayOutOfBoundExceptions.
476 // System.err.println("vamsasSeq backref: "+id+"");
477 // System.err.println(jds.getName()+"
478 // "+jds.getStart()+"-"+jds.getEnd()+" "+jds.getSequenceAsString());
479 // System.err.println("Hashcode: "+seqHash(jds));
480 // SequenceI rsq = (SequenceI) seqRefIds.get(id + "");
481 // System.err.println(rsq.getName()+"
482 // "+rsq.getStart()+"-"+rsq.getEnd()+" "+rsq.getSequenceAsString());
483 // System.err.println("Hashcode: "+seqHash(rsq));
487 vamsasSeq = createVamsasSequence(id, jds);
488 vamsasSet.addSequence(vamsasSeq);
489 seqRefIds.put(id, jds);
493 jseq.setStart(jds.getStart());
494 jseq.setEnd(jds.getEnd());
495 jseq.setColour(av.getSequenceColour(jds).getRGB());
497 jseq.setId(id); // jseq id should be a string not a number
499 if (av.hasHiddenRows)
501 jseq.setHidden(av.alignment.getHiddenSequences().isHidden(jds));
503 if (av.hiddenRepSequences != null
504 && av.hiddenRepSequences.containsKey(jal.getSequenceAt(i)))
506 jalview.datamodel.SequenceI[] reps = ((jalview.datamodel.SequenceGroup) av.hiddenRepSequences
507 .get(jal.getSequenceAt(i))).getSequencesInOrder(jal);
509 for (int h = 0; h < reps.length; h++)
511 if (reps[h] != jal.getSequenceAt(i))
513 jseq.addHiddenSequences(jal.findIndex(reps[h]));
519 if (jds.getDatasetSequence().getSequenceFeatures() != null)
521 jalview.datamodel.SequenceFeature[] sf = jds.getDatasetSequence()
522 .getSequenceFeatures();
524 while (index < sf.length)
526 Features features = new Features();
528 features.setBegin(sf[index].getBegin());
529 features.setEnd(sf[index].getEnd());
530 features.setDescription(sf[index].getDescription());
531 features.setType(sf[index].getType());
532 features.setFeatureGroup(sf[index].getFeatureGroup());
533 features.setScore(sf[index].getScore());
534 if (sf[index].links != null)
536 for (int l = 0; l < sf[index].links.size(); l++)
538 OtherData keyValue = new OtherData();
539 keyValue.setKey("LINK_" + l);
540 keyValue.setValue(sf[index].links.elementAt(l).toString());
541 features.addOtherData(keyValue);
544 if (sf[index].otherDetails != null)
547 Enumeration keys = sf[index].otherDetails.keys();
548 while (keys.hasMoreElements())
550 key = keys.nextElement().toString();
551 OtherData keyValue = new OtherData();
552 keyValue.setKey(key);
553 keyValue.setValue(sf[index].otherDetails.get(key).toString());
554 features.addOtherData(keyValue);
558 jseq.addFeatures(features);
563 if (jds.getDatasetSequence().getPDBId() != null)
565 Enumeration en = jds.getDatasetSequence().getPDBId().elements();
566 while (en.hasMoreElements())
568 Pdbids pdb = new Pdbids();
569 jalview.datamodel.PDBEntry entry = (jalview.datamodel.PDBEntry) en
572 pdb.setId(entry.getId());
573 pdb.setType(entry.getType());
576 // This must have been loaded, is it still visible?
577 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
578 String matchedFile = null;
579 for (int f = frames.length - 1; f > -1; f--)
581 if (frames[f] instanceof AppJmol)
583 // TODO: revise schema to allow many:one PDB id binding to viewer
584 jmol = (AppJmol) frames[f];
585 for (int peid = 0; peid < jmol.jmb.pdbentry.length; peid++)
587 if (!jmol.jmb.pdbentry[peid].getId().equals(entry.getId())
588 && !(entry.getId().length() > 4 && entry
592 jmol.jmb.pdbentry[peid].getId()
595 if (matchedFile == null)
597 matchedFile = jmol.jmb.pdbentry[peid].getFile();
599 else if (!matchedFile.equals(jmol.jmb.pdbentry[peid]
603 .warn("Probably lost some PDB-Sequence mappings for this structure file (which apparently has same PDB Entry code): "
604 + jmol.jmb.pdbentry[peid].getFile());
608 // can get at it if the ID
609 // match is ambiguous (e.g.
611 String statestring = jmol.jmb.viewer.getStateInfo();
613 for (int smap = 0; smap < jmol.jmb.sequence[peid].length; smap++)
615 if (jal.findIndex(jmol.jmb.sequence[peid][smap]) > -1)
617 StructureState state = new StructureState();
618 state.setVisible(true);
619 state.setXpos(jmol.getX());
620 state.setYpos(jmol.getY());
621 state.setWidth(jmol.getWidth());
622 state.setHeight(jmol.getHeight());
623 state.setViewId(jmol.getViewId());
624 if (!jmolViewIds.contains(state.getViewId()))
626 // Make sure we only store a Jmol state once in each XML
628 jmolViewIds.addElement(state.getViewId());
629 state.setContent(statestring.replaceAll("\n", ""));
633 state.setContent("# duplicate state");
635 pdb.addStructureState(state);
642 if (matchedFile != null || entry.getFile() != null)
644 if (entry.getFile() != null)
647 matchedFile = entry.getFile();
649 pdb.setFile(matchedFile); // entry.getFile());
650 if (pdbfiles == null)
652 pdbfiles = new Vector();
655 if (!pdbfiles.contains(entry.getId()))
657 pdbfiles.addElement(entry.getId());
660 File file = new File(matchedFile);
661 if (file.exists() && jout != null)
663 byte[] data = new byte[(int) file.length()];
664 jout.putNextEntry(new JarEntry(entry.getId()));
665 DataInputStream dis = new DataInputStream(
666 new FileInputStream(file));
669 DataOutputStream dout = new DataOutputStream(jout);
670 dout.write(data, 0, data.length);
674 } catch (Exception ex)
676 ex.printStackTrace();
682 if (entry.getProperty() != null)
684 PdbentryItem item = new PdbentryItem();
685 Hashtable properties = entry.getProperty();
686 Enumeration en2 = properties.keys();
687 while (en2.hasMoreElements())
689 Property prop = new Property();
690 String key = en2.nextElement().toString();
692 prop.setValue(properties.get(key).toString());
693 item.addProperty(prop);
695 pdb.addPdbentryItem(item);
705 if (av.hasHiddenRows)
710 if (jal.getCodonFrames() != null && jal.getCodonFrames().length > 0)
712 jalview.datamodel.AlignedCodonFrame[] jac = jal.getCodonFrames();
713 for (int i = 0; i < jac.length; i++)
715 AlcodonFrame alc = new AlcodonFrame();
716 vamsasSet.addAlcodonFrame(alc);
717 for (int p = 0; p < jac[i].aaWidth; p++)
719 Alcodon cmap = new Alcodon();
720 if (jac[i].codons[p] != null)
722 // Null codons indicate a gapped column in the translated peptide
724 cmap.setPos1(jac[i].codons[p][0]);
725 cmap.setPos2(jac[i].codons[p][1]);
726 cmap.setPos3(jac[i].codons[p][2]);
728 alc.addAlcodon(cmap);
730 if (jac[i].getProtMappings() != null
731 && jac[i].getProtMappings().length > 0)
733 SequenceI[] dnas = jac[i].getdnaSeqs();
734 jalview.datamodel.Mapping[] pmaps = jac[i].getProtMappings();
735 for (int m = 0; m < pmaps.length; m++)
737 AlcodMap alcmap = new AlcodMap();
738 alcmap.setDnasq(seqHash(dnas[m]));
739 alcmap.setMapping(createVamsasMapping(pmaps[m], dnas[m], null,
741 alc.addAlcodMap(alcmap);
748 // /////////////////////////////////
749 if (av.currentTree != null)
751 // FIND ANY ASSOCIATED TREES
752 // NOT IMPLEMENTED FOR HEADLESS STATE AT PRESENT
753 if (Desktop.desktop != null)
755 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
757 for (int t = 0; t < frames.length; t++)
759 if (frames[t] instanceof TreePanel)
761 TreePanel tp = (TreePanel) frames[t];
763 if (tp.treeCanvas.av.alignment == jal)
765 Tree tree = new Tree();
766 tree.setTitle(tp.getTitle());
767 tree.setCurrentTree((av.currentTree == tp.getTree()));
768 tree.setNewick(tp.getTree().toString());
769 tree.setThreshold(tp.treeCanvas.threshold);
771 tree.setFitToWindow(tp.fitToWindow.getState());
772 tree.setFontName(tp.getTreeFont().getName());
773 tree.setFontSize(tp.getTreeFont().getSize());
774 tree.setFontStyle(tp.getTreeFont().getStyle());
775 tree.setMarkUnlinked(tp.placeholdersMenu.getState());
777 tree.setShowBootstrap(tp.bootstrapMenu.getState());
778 tree.setShowDistances(tp.distanceMenu.getState());
780 tree.setHeight(tp.getHeight());
781 tree.setWidth(tp.getWidth());
782 tree.setXpos(tp.getX());
783 tree.setYpos(tp.getY());
784 tree.setId(makeHashCode(tp, null));
794 * store forward refs from an annotationRow to any groups
796 IdentityHashMap groupRefs = new IdentityHashMap();
797 if (jal.getAlignmentAnnotation() != null)
799 jalview.datamodel.AlignmentAnnotation[] aa = jal
800 .getAlignmentAnnotation();
802 for (int i = 0; i < aa.length; i++)
804 Annotation an = new Annotation();
806 if (aa[i].annotationId != null)
808 annotationIds.put(aa[i].annotationId, aa[i]);
811 an.setId(aa[i].annotationId);
813 an.setVisible(aa[i].visible);
815 an.setDescription(aa[i].description);
817 if (aa[i].sequenceRef != null)
819 // TODO later annotation sequenceRef should be the XML ID of the
820 // sequence rather than its display name
821 an.setSequenceRef(aa[i].sequenceRef.getName());
823 if (aa[i].groupRef != null)
825 Object groupIdr = groupRefs.get(aa[i].groupRef);
826 if (groupIdr == null)
828 // make a locally unique String
829 groupRefs.put(aa[i].groupRef,
830 groupIdr = ("" + System.currentTimeMillis()
831 + aa[i].groupRef.getName() + groupRefs.size()));
833 an.setGroupRef(groupIdr.toString());
835 if (aa[i] == av.quality || aa[i] == av.conservation
836 || aa[i] == av.consensus || aa[i].autoCalculated)
838 // new way of indicating autocalculated annotation -
839 an.setAutoCalculated(aa[i].autoCalculated);
840 // write a stub for this annotation - indicate presence of autocalc
842 an.setLabel(aa[i].label);
844 vamsasSet.addAnnotation(an);
851 an.setGraphType(aa[i].graph);
852 an.setGraphGroup(aa[i].graphGroup);
853 if (aa[i].getThreshold() != null)
855 ThresholdLine line = new ThresholdLine();
856 line.setLabel(aa[i].getThreshold().label);
857 line.setValue(aa[i].getThreshold().value);
858 line.setColour(aa[i].getThreshold().colour.getRGB());
859 an.setThresholdLine(line);
867 an.setLabel(aa[i].label);
868 if (aa[i].hasScore())
870 an.setScore(aa[i].getScore());
872 AnnotationElement ae;
873 if (aa[i].annotations != null)
875 an.setScoreOnly(false);
876 for (int a = 0; a < aa[i].annotations.length; a++)
878 if ((aa[i] == null) || (aa[i].annotations[a] == null))
883 ae = new AnnotationElement();
884 if (aa[i].annotations[a].description != null)
885 ae.setDescription(aa[i].annotations[a].description);
886 if (aa[i].annotations[a].displayCharacter != null)
887 ae.setDisplayCharacter(aa[i].annotations[a].displayCharacter);
889 if (!Float.isNaN(aa[i].annotations[a].value))
890 ae.setValue(aa[i].annotations[a].value);
893 if (aa[i].annotations[a].secondaryStructure != ' '
894 && aa[i].annotations[a].secondaryStructure != '\0')
895 ae.setSecondaryStructure(aa[i].annotations[a].secondaryStructure
898 if (aa[i].annotations[a].colour != null
899 && aa[i].annotations[a].colour != java.awt.Color.black)
901 ae.setColour(aa[i].annotations[a].colour.getRGB());
904 an.addAnnotationElement(ae);
909 an.setScoreOnly(true);
911 vamsasSet.addAnnotation(an);
915 if (jal.getGroups() != null)
917 JGroup[] groups = new JGroup[jal.getGroups().size()];
919 for (int i = 0; i < groups.length; i++)
921 groups[i] = new JGroup();
923 jalview.datamodel.SequenceGroup sg = (jalview.datamodel.SequenceGroup) jal
924 .getGroups().elementAt(i);
925 groups[i].setStart(sg.getStartRes());
926 groups[i].setEnd(sg.getEndRes());
927 groups[i].setName(sg.getName());
928 if (groupRefs.containsKey(sg))
930 // group has references so set it's ID field
931 groups[i].setId(groupRefs.get(sg).toString());
935 if (sg.cs.conservationApplied())
937 groups[i].setConsThreshold(sg.cs.getConservationInc());
939 if (sg.cs instanceof jalview.schemes.UserColourScheme)
941 groups[i].setColour(SetUserColourScheme(sg.cs, userColours,
947 .setColour(ColourSchemeProperty.getColourName(sg.cs));
950 else if (sg.cs instanceof jalview.schemes.AnnotationColourGradient)
953 .setColour(ColourSchemeProperty
954 .getColourName(((jalview.schemes.AnnotationColourGradient) sg.cs)
957 else if (sg.cs instanceof jalview.schemes.UserColourScheme)
960 .setColour(SetUserColourScheme(sg.cs, userColours, jms));
964 groups[i].setColour(ColourSchemeProperty.getColourName(sg.cs));
967 groups[i].setPidThreshold(sg.cs.getThreshold());
970 groups[i].setOutlineColour(sg.getOutlineColour().getRGB());
971 groups[i].setDisplayBoxes(sg.getDisplayBoxes());
972 groups[i].setDisplayText(sg.getDisplayText());
973 groups[i].setColourText(sg.getColourText());
974 groups[i].setTextCol1(sg.textColour.getRGB());
975 groups[i].setTextCol2(sg.textColour2.getRGB());
976 groups[i].setTextColThreshold(sg.thresholdTextColour);
977 groups[i].setShowUnconserved(sg.getShowNonconserved());
978 groups[i].setIgnoreGapsinConsensus(sg.getIgnoreGapsConsensus());
979 groups[i].setShowConsensusHistogram(sg.isShowConsensusHistogram());
980 groups[i].setShowSequenceLogo(sg.isShowSequenceLogo());
981 for (int s = 0; s < sg.getSize(); s++)
983 jalview.datamodel.Sequence seq = (jalview.datamodel.Sequence) sg
985 groups[i].addSeq(seqHash(seq));
989 jms.setJGroup(groups);
992 // /////////SAVE VIEWPORT
993 Viewport view = new Viewport();
994 view.setTitle(ap.alignFrame.getTitle());
995 view.setSequenceSetId(makeHashCode(av.getSequenceSetId(),
996 av.getSequenceSetId()));
997 view.setId(av.getViewId());
998 view.setViewName(av.viewName);
999 view.setGatheredViews(av.gatherViewsHere);
1001 if (ap.av.explodedPosition != null)
1003 view.setXpos(av.explodedPosition.x);
1004 view.setYpos(av.explodedPosition.y);
1005 view.setWidth(av.explodedPosition.width);
1006 view.setHeight(av.explodedPosition.height);
1010 view.setXpos(ap.alignFrame.getBounds().x);
1011 view.setYpos(ap.alignFrame.getBounds().y);
1012 view.setWidth(ap.alignFrame.getBounds().width);
1013 view.setHeight(ap.alignFrame.getBounds().height);
1016 view.setStartRes(av.startRes);
1017 view.setStartSeq(av.startSeq);
1019 if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme)
1021 view.setBgColour(SetUserColourScheme(av.getGlobalColourScheme(),
1024 else if (av.getGlobalColourScheme() instanceof jalview.schemes.AnnotationColourGradient)
1026 jalview.schemes.AnnotationColourGradient acg = (jalview.schemes.AnnotationColourGradient) av
1027 .getGlobalColourScheme();
1029 AnnotationColours ac = new AnnotationColours();
1030 ac.setAboveThreshold(acg.getAboveThreshold());
1031 ac.setThreshold(acg.getAnnotationThreshold());
1032 ac.setAnnotation(acg.getAnnotation());
1033 if (acg.getBaseColour() instanceof jalview.schemes.UserColourScheme)
1035 ac.setColourScheme(SetUserColourScheme(acg.getBaseColour(),
1040 ac.setColourScheme(ColourSchemeProperty.getColourName(acg
1044 ac.setMaxColour(acg.getMaxColour().getRGB());
1045 ac.setMinColour(acg.getMinColour().getRGB());
1046 view.setAnnotationColours(ac);
1047 view.setBgColour("AnnotationColourGradient");
1051 view.setBgColour(ColourSchemeProperty.getColourName(av
1052 .getGlobalColourScheme()));
1055 ColourSchemeI cs = av.getGlobalColourScheme();
1059 if (cs.conservationApplied())
1061 view.setConsThreshold(cs.getConservationInc());
1062 if (cs instanceof jalview.schemes.UserColourScheme)
1064 view.setBgColour(SetUserColourScheme(cs, userColours, jms));
1068 if (cs instanceof ResidueColourScheme)
1070 view.setPidThreshold(cs.getThreshold());
1074 view.setConservationSelected(av.getConservationSelected());
1075 view.setPidSelected(av.getAbovePIDThreshold());
1076 view.setFontName(av.font.getName());
1077 view.setFontSize(av.font.getSize());
1078 view.setFontStyle(av.font.getStyle());
1079 view.setRenderGaps(av.renderGaps);
1080 view.setShowAnnotation(av.getShowAnnotation());
1081 view.setShowBoxes(av.getShowBoxes());
1082 view.setShowColourText(av.getColourText());
1083 view.setShowFullId(av.getShowJVSuffix());
1084 view.setRightAlignIds(av.rightAlignIds);
1085 view.setShowSequenceFeatures(av.showSequenceFeatures);
1086 view.setShowText(av.getShowText());
1087 view.setShowUnconserved(av.getShowUnconserved());
1088 view.setWrapAlignment(av.getWrapAlignment());
1089 view.setTextCol1(av.textColour.getRGB());
1090 view.setTextCol2(av.textColour2.getRGB());
1091 view.setTextColThreshold(av.thresholdTextColour);
1092 view.setShowConsensusHistogram(av.isShowConsensusHistogram());
1093 view.setShowSequenceLogo(av.isShowSequenceLogo());
1094 view.setShowGroupConsensus(av.isShowGroupConsensus());
1095 view.setShowGroupConservation(av.isShowGroupConservation());
1096 view.setShowNPfeatureTooltip(av.isShowNpFeats());
1097 view.setShowDbRefTooltip(av.isShowDbRefs());
1098 view.setFollowHighlight(av.followHighlight);
1099 view.setFollowSelection(av.followSelection);
1100 view.setIgnoreGapsinConsensus(av.getIgnoreGapsConsensus());
1101 if (av.featuresDisplayed != null)
1103 jalview.schemabinding.version2.FeatureSettings fs = new jalview.schemabinding.version2.FeatureSettings();
1105 String[] renderOrder = ap.seqPanel.seqCanvas.getFeatureRenderer().renderOrder;
1107 Vector settingsAdded = new Vector();
1108 Object gstyle = null;
1109 GraduatedColor gcol = null;
1110 for (int ro = 0; ro < renderOrder.length; ro++)
1112 gstyle = ap.seqPanel.seqCanvas.getFeatureRenderer()
1113 .getFeatureStyle(renderOrder[ro]);
1114 Setting setting = new Setting();
1115 setting.setType(renderOrder[ro]);
1116 if (gstyle instanceof GraduatedColor)
1118 gcol = (GraduatedColor) gstyle;
1119 setting.setColour(gcol.getMaxColor().getRGB());
1120 setting.setMincolour(gcol.getMinColor().getRGB());
1121 setting.setMin(gcol.getMin());
1122 setting.setMax(gcol.getMax());
1123 setting.setColourByLabel(gcol.isColourByLabel());
1124 setting.setAutoScale(gcol.isAutoScale());
1125 setting.setThreshold(gcol.getThresh());
1126 setting.setThreshstate(gcol.getThreshType());
1130 setting.setColour(ap.seqPanel.seqCanvas.getFeatureRenderer()
1131 .getColour(renderOrder[ro]).getRGB());
1134 setting.setDisplay(av.featuresDisplayed
1135 .containsKey(renderOrder[ro]));
1136 float rorder = ap.seqPanel.seqCanvas.getFeatureRenderer().getOrder(
1140 setting.setOrder(rorder);
1142 fs.addSetting(setting);
1143 settingsAdded.addElement(renderOrder[ro]);
1146 // Make sure we save none displayed feature settings
1147 Enumeration en = ap.seqPanel.seqCanvas.getFeatureRenderer().featureColours
1149 while (en.hasMoreElements())
1151 String key = en.nextElement().toString();
1152 if (settingsAdded.contains(key))
1157 Setting setting = new Setting();
1158 setting.setType(key);
1159 setting.setColour(ap.seqPanel.seqCanvas.getFeatureRenderer()
1160 .getColour(key).getRGB());
1162 setting.setDisplay(false);
1163 float rorder = ap.seqPanel.seqCanvas.getFeatureRenderer().getOrder(
1167 setting.setOrder(rorder);
1169 fs.addSetting(setting);
1170 settingsAdded.addElement(key);
1172 en = ap.seqPanel.seqCanvas.getFeatureRenderer().featureGroups.keys();
1173 Vector groupsAdded = new Vector();
1174 while (en.hasMoreElements())
1176 String grp = en.nextElement().toString();
1177 if (groupsAdded.contains(grp))
1181 Group g = new Group();
1183 g.setDisplay(((Boolean) ap.seqPanel.seqCanvas.getFeatureRenderer().featureGroups
1184 .get(grp)).booleanValue());
1186 groupsAdded.addElement(grp);
1188 jms.setFeatureSettings(fs);
1192 if (av.hasHiddenColumns)
1194 if (av.getColumnSelection() == null
1195 || av.getColumnSelection().getHiddenColumns() == null)
1197 warn("REPORT BUG: avoided null columnselection bug (DMAM reported). Please contact Jim about this.");
1201 for (int c = 0; c < av.getColumnSelection().getHiddenColumns()
1204 int[] region = (int[]) av.getColumnSelection().getHiddenColumns()
1206 HiddenColumns hc = new HiddenColumns();
1207 hc.setStart(region[0]);
1208 hc.setEnd(region[1]);
1209 view.addHiddenColumns(hc);
1214 jms.addViewport(view);
1216 object.setJalviewModelSequence(jms);
1217 object.getVamsasModel().addSequenceSet(vamsasSet);
1219 if (jout != null && fileName != null)
1221 // We may not want to write the object to disk,
1222 // eg we can copy the alignViewport to a new view object
1223 // using save and then load
1226 JarEntry entry = new JarEntry(fileName);
1227 jout.putNextEntry(entry);
1228 PrintWriter pout = new PrintWriter(new OutputStreamWriter(jout,
1230 org.exolab.castor.xml.Marshaller marshaller = new org.exolab.castor.xml.Marshaller(
1232 marshaller.marshal(object);
1235 } catch (Exception ex)
1237 // TODO: raise error in GUI if marshalling failed.
1238 ex.printStackTrace();
1245 * External mapping between jalview objects and objects yielding a valid and
1246 * unique object ID string. This is null for normal Jalview project IO, but
1247 * non-null when a jalview project is being read or written as part of a
1250 IdentityHashMap jv2vobj = null;
1253 * Construct a unique ID for jvobj using either existing bindings or if none
1254 * exist, the result of the hashcode call for the object.
1257 * jalview data object
1258 * @return unique ID for referring to jvobj
1260 private String makeHashCode(Object jvobj, String altCode)
1262 if (jv2vobj != null)
1264 Object id = jv2vobj.get(jvobj);
1267 return id.toString();
1269 // check string ID mappings
1270 if (jvids2vobj != null && jvobj instanceof String)
1272 id = jvids2vobj.get(jvobj);
1276 return id.toString();
1278 // give up and warn that something has gone wrong
1279 warn("Cannot find ID for object in external mapping : " + jvobj);
1285 * return local jalview object mapped to ID, if it exists
1289 * @return null or object bound to idcode
1291 private Object retrieveExistingObj(String idcode)
1293 if (idcode != null && vobj2jv != null)
1295 return vobj2jv.get(idcode);
1301 * binding from ID strings from external mapping table to jalview data model
1304 private Hashtable vobj2jv;
1306 private Sequence createVamsasSequence(String id, SequenceI jds)
1308 return createVamsasSequence(true, id, jds, null);
1311 private Sequence createVamsasSequence(boolean recurse, String id,
1312 SequenceI jds, SequenceI parentseq)
1314 Sequence vamsasSeq = new Sequence();
1315 vamsasSeq.setId(id);
1316 vamsasSeq.setName(jds.getName());
1317 vamsasSeq.setSequence(jds.getSequenceAsString());
1318 vamsasSeq.setDescription(jds.getDescription());
1319 jalview.datamodel.DBRefEntry[] dbrefs = null;
1320 if (jds.getDatasetSequence() != null)
1322 vamsasSeq.setDsseqid(seqHash(jds.getDatasetSequence()));
1323 if (jds.getDatasetSequence().getDBRef() != null)
1325 dbrefs = jds.getDatasetSequence().getDBRef();
1330 vamsasSeq.setDsseqid(id); // so we can tell which sequences really are
1331 // dataset sequences only
1332 dbrefs = jds.getDBRef();
1336 for (int d = 0; d < dbrefs.length; d++)
1338 DBRef dbref = new DBRef();
1339 dbref.setSource(dbrefs[d].getSource());
1340 dbref.setVersion(dbrefs[d].getVersion());
1341 dbref.setAccessionId(dbrefs[d].getAccessionId());
1342 if (dbrefs[d].hasMap())
1344 Mapping mp = createVamsasMapping(dbrefs[d].getMap(), parentseq,
1346 dbref.setMapping(mp);
1348 vamsasSeq.addDBRef(dbref);
1354 private Mapping createVamsasMapping(jalview.datamodel.Mapping jmp,
1355 SequenceI parentseq, SequenceI jds, boolean recurse)
1358 if (jmp.getMap() != null)
1362 jalview.util.MapList mlst = jmp.getMap();
1363 int r[] = mlst.getFromRanges();
1364 for (int s = 0; s < r.length; s += 2)
1366 MapListFrom mfrom = new MapListFrom();
1367 mfrom.setStart(r[s]);
1368 mfrom.setEnd(r[s + 1]);
1369 mp.addMapListFrom(mfrom);
1371 r = mlst.getToRanges();
1372 for (int s = 0; s < r.length; s += 2)
1374 MapListTo mto = new MapListTo();
1376 mto.setEnd(r[s + 1]);
1377 mp.addMapListTo(mto);
1379 mp.setMapFromUnit(mlst.getFromRatio());
1380 mp.setMapToUnit(mlst.getToRatio());
1381 if (jmp.getTo() != null)
1383 MappingChoice mpc = new MappingChoice();
1385 && (parentseq != jmp.getTo() || parentseq
1386 .getDatasetSequence() != jmp.getTo()))
1388 mpc.setSequence(createVamsasSequence(false, seqHash(jmp.getTo()),
1394 SequenceI ps = null;
1395 if (parentseq != jmp.getTo()
1396 && parentseq.getDatasetSequence() != jmp.getTo())
1398 // chaining dbref rather than a handshaking one
1399 jmpid = seqHash(ps = jmp.getTo());
1403 jmpid = seqHash(ps = parentseq);
1405 mpc.setDseqFor(jmpid);
1406 if (!seqRefIds.containsKey(mpc.getDseqFor()))
1408 jalview.bin.Cache.log.debug("creatign new DseqFor ID");
1409 seqRefIds.put(mpc.getDseqFor(), ps);
1413 jalview.bin.Cache.log.debug("reusing DseqFor ID");
1416 mp.setMappingChoice(mpc);
1422 String SetUserColourScheme(jalview.schemes.ColourSchemeI cs,
1423 Vector userColours, JalviewModelSequence jms)
1426 jalview.schemes.UserColourScheme ucs = (jalview.schemes.UserColourScheme) cs;
1427 boolean newucs = false;
1428 if (!userColours.contains(ucs))
1430 userColours.add(ucs);
1433 id = "ucs" + userColours.indexOf(ucs);
1436 // actually create the scheme's entry in the XML model
1437 java.awt.Color[] colours = ucs.getColours();
1438 jalview.schemabinding.version2.UserColours uc = new jalview.schemabinding.version2.UserColours();
1439 jalview.schemabinding.version2.UserColourScheme jbucs = new jalview.schemabinding.version2.UserColourScheme();
1441 for (int i = 0; i < colours.length; i++)
1443 jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();
1444 col.setName(ResidueProperties.aa[i]);
1445 col.setRGB(jalview.util.Format.getHexString(colours[i]));
1446 jbucs.addColour(col);
1448 if (ucs.getLowerCaseColours() != null)
1450 colours = ucs.getLowerCaseColours();
1451 for (int i = 0; i < colours.length; i++)
1453 jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();
1454 col.setName(ResidueProperties.aa[i].toLowerCase());
1455 col.setRGB(jalview.util.Format.getHexString(colours[i]));
1456 jbucs.addColour(col);
1461 uc.setUserColourScheme(jbucs);
1462 jms.addUserColours(uc);
1468 jalview.schemes.UserColourScheme GetUserColourScheme(
1469 JalviewModelSequence jms, String id)
1471 UserColours[] uc = jms.getUserColours();
1472 UserColours colours = null;
1474 for (int i = 0; i < uc.length; i++)
1476 if (uc[i].getId().equals(id))
1484 java.awt.Color[] newColours = new java.awt.Color[24];
1486 for (int i = 0; i < 24; i++)
1488 newColours[i] = new java.awt.Color(Integer.parseInt(colours
1489 .getUserColourScheme().getColour(i).getRGB(), 16));
1492 jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(
1495 if (colours.getUserColourScheme().getColourCount() > 24)
1497 newColours = new java.awt.Color[23];
1498 for (int i = 0; i < 23; i++)
1500 newColours[i] = new java.awt.Color(Integer.parseInt(colours
1501 .getUserColourScheme().getColour(i + 24).getRGB(), 16));
1503 ucs.setLowerCaseColours(newColours);
1510 * contains last error message (if any) encountered by XML loader.
1512 String errorMessage = null;
1515 * flag to control whether the Jalview2XML_V1 parser should be deferred to if
1516 * exceptions are raised during project XML parsing
1518 public boolean attemptversion1parse = true;
1521 * Load a jalview project archive from a jar file
1524 * - HTTP URL or filename
1526 public AlignFrame LoadJalviewAlign(final String file)
1529 jalview.gui.AlignFrame af = null;
1533 // UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
1534 // Workaround is to make sure caller implements the JarInputStreamProvider
1536 // so we can re-open the jar input stream for each entry.
1538 jarInputStreamProvider jprovider = createjarInputStreamProvider(file);
1539 af = LoadJalviewAlign(jprovider);
1540 } catch (MalformedURLException e)
1542 errorMessage = "Invalid URL format for '" + file + "'";
1548 private jarInputStreamProvider createjarInputStreamProvider(
1549 final String file) throws MalformedURLException
1552 errorMessage = null;
1553 uniqueSetSuffix = null;
1555 viewportsAdded = null;
1556 frefedSequence = null;
1558 if (file.startsWith("http://"))
1560 url = new URL(file);
1562 final URL _url = url;
1563 return new jarInputStreamProvider()
1566 public JarInputStream getJarInputStream() throws IOException
1570 return new JarInputStream(_url.openStream());
1574 return new JarInputStream(new FileInputStream(file));
1578 public String getFilename()
1586 * Recover jalview session from a jalview project archive. Caller may
1587 * initialise uniqueSetSuffix, seqRefIds, viewportsAdded and frefedSequence
1588 * themselves. Any null fields will be initialised with default values,
1589 * non-null fields are left alone.
1594 public AlignFrame LoadJalviewAlign(final jarInputStreamProvider jprovider)
1596 errorMessage = null;
1597 if (uniqueSetSuffix == null)
1599 uniqueSetSuffix = System.currentTimeMillis() % 100000 + "";
1601 if (seqRefIds == null)
1603 seqRefIds = new Hashtable();
1605 if (viewportsAdded == null)
1607 viewportsAdded = new Hashtable();
1609 if (frefedSequence == null)
1611 frefedSequence = new Vector();
1614 jalview.gui.AlignFrame af = null;
1615 Hashtable gatherToThisFrame = new Hashtable();
1616 final String file = jprovider.getFilename();
1619 JarInputStream jin = null;
1620 JarEntry jarentry = null;
1625 jin = jprovider.getJarInputStream();
1626 for (int i = 0; i < entryCount; i++)
1628 jarentry = jin.getNextJarEntry();
1631 if (jarentry != null && jarentry.getName().endsWith(".xml"))
1633 InputStreamReader in = new InputStreamReader(jin, "UTF-8");
1634 JalviewModel object = new JalviewModel();
1636 Unmarshaller unmar = new Unmarshaller(object);
1637 unmar.setValidation(false);
1638 object = (JalviewModel) unmar.unmarshal(in);
1639 if (true) // !skipViewport(object))
1641 af = LoadFromObject(object, file, true, jprovider);
1642 if (af.viewport.gatherViewsHere)
1644 gatherToThisFrame.put(af.viewport.getSequenceSetId(), af);
1649 else if (jarentry != null)
1651 // Some other file here.
1654 } while (jarentry != null);
1655 resolveFrefedSequences();
1656 } catch (java.io.FileNotFoundException ex)
1658 ex.printStackTrace();
1659 errorMessage = "Couldn't locate Jalview XML file : " + file;
1660 System.err.println("Exception whilst loading jalview XML file : "
1662 } catch (java.net.UnknownHostException ex)
1664 ex.printStackTrace();
1665 errorMessage = "Couldn't locate Jalview XML file : " + file;
1666 System.err.println("Exception whilst loading jalview XML file : "
1668 } catch (Exception ex)
1670 System.err.println("Parsing as Jalview Version 2 file failed.");
1671 ex.printStackTrace(System.err);
1672 if (attemptversion1parse)
1674 // Is Version 1 Jar file?
1677 af = new Jalview2XML_V1(raiseGUI).LoadJalviewAlign(jprovider);
1678 } catch (Exception ex2)
1680 System.err.println("Exception whilst loading as jalviewXMLV1:");
1681 ex2.printStackTrace();
1685 if (Desktop.instance != null)
1687 Desktop.instance.stopLoading();
1691 System.out.println("Successfully loaded archive file");
1694 ex.printStackTrace();
1696 System.err.println("Exception whilst loading jalview XML file : "
1698 } catch (OutOfMemoryError e)
1700 // Don't use the OOM Window here
1701 errorMessage = "Out of memory loading jalview XML file";
1702 System.err.println("Out of memory whilst loading jalview XML file");
1703 e.printStackTrace();
1706 if (Desktop.instance != null)
1708 Desktop.instance.stopLoading();
1711 Enumeration en = gatherToThisFrame.elements();
1712 while (en.hasMoreElements())
1714 Desktop.instance.gatherViews((AlignFrame) en.nextElement());
1716 if (errorMessage != null)
1724 * check errorMessage for a valid error message and raise an error box in the
1725 * GUI or write the current errorMessage to stderr and then clear the error
1728 protected void reportErrors()
1730 reportErrors(false);
1733 protected void reportErrors(final boolean saving)
1735 if (errorMessage != null)
1737 final String finalErrorMessage = errorMessage;
1740 javax.swing.SwingUtilities.invokeLater(new Runnable()
1744 JOptionPane.showInternalMessageDialog(Desktop.desktop,
1745 finalErrorMessage, "Error "
1746 + (saving ? "saving" : "loading")
1747 + " Jalview file", JOptionPane.WARNING_MESSAGE);
1753 System.err.println("Problem loading Jalview file: " + errorMessage);
1756 errorMessage = null;
1759 Hashtable alreadyLoadedPDB;
1762 * when set, local views will be updated from view stored in JalviewXML
1763 * Currently (28th Sep 2008) things will go horribly wrong in vamsas document
1764 * sync if this is set to true.
1766 private boolean updateLocalViews = false;
1768 String loadPDBFile(jarInputStreamProvider jprovider, String pdbId)
1770 if (alreadyLoadedPDB == null)
1771 alreadyLoadedPDB = new Hashtable();
1773 if (alreadyLoadedPDB.containsKey(pdbId))
1774 return alreadyLoadedPDB.get(pdbId).toString();
1778 JarInputStream jin = jprovider.getJarInputStream();
1780 * if (jprovider.startsWith("http://")) { jin = new JarInputStream(new
1781 * URL(jprovider).openStream()); } else { jin = new JarInputStream(new
1782 * FileInputStream(jprovider)); }
1785 JarEntry entry = null;
1788 entry = jin.getNextJarEntry();
1789 } while (entry != null && !entry.getName().equals(pdbId));
1792 BufferedReader in = new BufferedReader(new InputStreamReader(jin));
1793 File outFile = File.createTempFile("jalview_pdb", ".txt");
1794 outFile.deleteOnExit();
1795 PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
1798 while ((data = in.readLine()) != null)
1805 } catch (Exception foo)
1811 alreadyLoadedPDB.put(pdbId, outFile.getAbsolutePath());
1812 return outFile.getAbsolutePath();
1816 warn("Couldn't find PDB file entry in Jalview Jar for " + pdbId);
1818 } catch (Exception ex)
1820 ex.printStackTrace();
1827 * Load alignment frame from jalview XML DOM object
1832 * filename source string
1833 * @param loadTreesAndStructures
1834 * when false only create Viewport
1836 * data source provider
1837 * @return alignment frame created from view stored in DOM
1839 AlignFrame LoadFromObject(JalviewModel object, String file,
1840 boolean loadTreesAndStructures, jarInputStreamProvider jprovider)
1842 SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);
1843 Sequence[] vamsasSeq = vamsasSet.getSequence();
1845 JalviewModelSequence jms = object.getJalviewModelSequence();
1847 Viewport view = jms.getViewport(0);
1848 // ////////////////////////////////
1851 Vector hiddenSeqs = null;
1852 jalview.datamodel.Sequence jseq;
1854 ArrayList tmpseqs = new ArrayList();
1856 boolean multipleView = false;
1858 JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq();
1859 int vi = 0; // counter in vamsasSeq array
1860 for (int i = 0; i < JSEQ.length; i++)
1862 String seqId = JSEQ[i].getId();
1864 if (seqRefIds.get(seqId) != null)
1866 tmpseqs.add((jalview.datamodel.Sequence) seqRefIds.get(seqId));
1867 multipleView = true;
1871 jseq = new jalview.datamodel.Sequence(vamsasSeq[vi].getName(),
1872 vamsasSeq[vi].getSequence());
1873 jseq.setDescription(vamsasSeq[vi].getDescription());
1874 jseq.setStart(JSEQ[i].getStart());
1875 jseq.setEnd(JSEQ[i].getEnd());
1876 jseq.setVamsasId(uniqueSetSuffix + seqId);
1877 seqRefIds.put(vamsasSeq[vi].getId(), jseq);
1882 if (JSEQ[i].getHidden())
1884 if (hiddenSeqs == null)
1886 hiddenSeqs = new Vector();
1889 hiddenSeqs.addElement((jalview.datamodel.Sequence) seqRefIds
1896 // Create the alignment object from the sequence set
1897 // ///////////////////////////////
1898 jalview.datamodel.Sequence[] orderedSeqs = new jalview.datamodel.Sequence[tmpseqs
1901 tmpseqs.toArray(orderedSeqs);
1903 jalview.datamodel.Alignment al = new jalview.datamodel.Alignment(
1906 // / Add the alignment properties
1907 for (int i = 0; i < vamsasSet.getSequenceSetPropertiesCount(); i++)
1909 SequenceSetProperties ssp = vamsasSet.getSequenceSetProperties(i);
1910 al.setProperty(ssp.getKey(), ssp.getValue());
1914 // SequenceFeatures are added to the DatasetSequence,
1915 // so we must create or recover the dataset before loading features
1916 // ///////////////////////////////
1917 if (vamsasSet.getDatasetId() == null || vamsasSet.getDatasetId() == "")
1919 // older jalview projects do not have a dataset id.
1920 al.setDataset(null);
1924 recoverDatasetFor(vamsasSet, al);
1926 // ///////////////////////////////
1928 Hashtable pdbloaded = new Hashtable();
1931 // load sequence features, database references and any associated PDB
1932 // structures for the alignment
1933 for (int i = 0; i < vamsasSeq.length; i++)
1935 if (JSEQ[i].getFeaturesCount() > 0)
1937 Features[] features = JSEQ[i].getFeatures();
1938 for (int f = 0; f < features.length; f++)
1940 jalview.datamodel.SequenceFeature sf = new jalview.datamodel.SequenceFeature(
1941 features[f].getType(), features[f].getDescription(),
1942 features[f].getStatus(), features[f].getBegin(),
1943 features[f].getEnd(), features[f].getFeatureGroup());
1945 sf.setScore(features[f].getScore());
1946 for (int od = 0; od < features[f].getOtherDataCount(); od++)
1948 OtherData keyValue = features[f].getOtherData(od);
1949 if (keyValue.getKey().startsWith("LINK"))
1951 sf.addLink(keyValue.getValue());
1955 sf.setValue(keyValue.getKey(), keyValue.getValue());
1960 al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf);
1963 if (vamsasSeq[i].getDBRefCount() > 0)
1965 addDBRefs(al.getSequenceAt(i).getDatasetSequence(), vamsasSeq[i]);
1967 if (JSEQ[i].getPdbidsCount() > 0)
1969 Pdbids[] ids = JSEQ[i].getPdbids();
1970 for (int p = 0; p < ids.length; p++)
1972 jalview.datamodel.PDBEntry entry = new jalview.datamodel.PDBEntry();
1973 entry.setId(ids[p].getId());
1974 entry.setType(ids[p].getType());
1975 if (ids[p].getFile() != null)
1977 if (!pdbloaded.containsKey(ids[p].getFile()))
1979 entry.setFile(loadPDBFile(jprovider, ids[p].getId()));
1983 entry.setFile(pdbloaded.get(ids[p].getId()).toString());
1987 al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
1991 } // end !multipleview
1993 // ///////////////////////////////
1994 // LOAD SEQUENCE MAPPINGS
1996 if (vamsasSet.getAlcodonFrameCount() > 0)
1998 // TODO Potentially this should only be done once for all views of an
2000 AlcodonFrame[] alc = vamsasSet.getAlcodonFrame();
2001 for (int i = 0; i < alc.length; i++)
2003 jalview.datamodel.AlignedCodonFrame cf = new jalview.datamodel.AlignedCodonFrame(
2004 alc[i].getAlcodonCount());
2005 if (alc[i].getAlcodonCount() > 0)
2007 Alcodon[] alcods = alc[i].getAlcodon();
2008 for (int p = 0; p < cf.codons.length; p++)
2010 if (alcods[p].hasPos1() && alcods[p].hasPos2()
2011 && alcods[p].hasPos3())
2013 // translated codons require three valid positions
2014 cf.codons[p] = new int[3];
2015 cf.codons[p][0] = (int) alcods[p].getPos1();
2016 cf.codons[p][1] = (int) alcods[p].getPos2();
2017 cf.codons[p][2] = (int) alcods[p].getPos3();
2021 cf.codons[p] = null;
2025 if (alc[i].getAlcodMapCount() > 0)
2027 AlcodMap[] maps = alc[i].getAlcodMap();
2028 for (int m = 0; m < maps.length; m++)
2030 SequenceI dnaseq = (SequenceI) seqRefIds
2031 .get(maps[m].getDnasq());
2033 jalview.datamodel.Mapping mapping = null;
2034 // attach to dna sequence reference.
2035 if (maps[m].getMapping() != null)
2037 mapping = addMapping(maps[m].getMapping());
2041 cf.addMap(dnaseq, mapping.getTo(), mapping.getMap());
2046 frefedSequence.add(new Object[]
2047 { maps[m].getDnasq(), cf, mapping });
2051 al.addCodonFrame(cf);
2056 // ////////////////////////////////
2058 boolean hideQuality = true, hideConservation = true, hideConsensus = true;
2060 * store any annotations which forward reference a group's ID
2062 Hashtable groupAnnotRefs = new Hashtable();
2064 if (vamsasSet.getAnnotationCount() > 0)
2066 Annotation[] an = vamsasSet.getAnnotation();
2068 for (int i = 0; i < an.length; i++)
2070 // set visibility for automatic annotation for this view
2071 if (an[i].getLabel().equals("Quality"))
2073 hideQuality = false;
2076 else if (an[i].getLabel().equals("Conservation"))
2078 hideConservation = false;
2081 else if (an[i].getLabel().equals("Consensus"))
2083 hideConsensus = false;
2086 // set visiblity for other annotation in this view
2087 if (an[i].getId() != null
2088 && annotationIds.containsKey(an[i].getId()))
2090 jalview.datamodel.AlignmentAnnotation jda = (jalview.datamodel.AlignmentAnnotation) annotationIds
2091 .get(an[i].getId());
2092 // in principle Visible should always be true for annotation displayed
2093 // in multiple views
2094 if (an[i].hasVisible())
2095 jda.visible = an[i].getVisible();
2097 al.addAnnotation(jda);
2101 // Construct new annotation from model.
2102 AnnotationElement[] ae = an[i].getAnnotationElement();
2103 jalview.datamodel.Annotation[] anot = null;
2105 if (!an[i].getScoreOnly())
2107 anot = new jalview.datamodel.Annotation[al.getWidth()];
2109 for (int aa = 0; aa < ae.length && aa < anot.length; aa++)
2111 if (ae[aa].getPosition() >= anot.length)
2114 anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(
2116 ae[aa].getDisplayCharacter(), ae[aa].getDescription(),
2117 (ae[aa].getSecondaryStructure() == null || ae[aa]
2118 .getSecondaryStructure().length() == 0) ? ' '
2119 : ae[aa].getSecondaryStructure().charAt(0),
2123 // JBPNote: Consider verifying dataflow for IO of secondary
2124 // structure annotation read from Stockholm files
2125 // this was added to try to ensure that
2126 // if (anot[ae[aa].getPosition()].secondaryStructure>' ')
2128 // anot[ae[aa].getPosition()].displayCharacter = "";
2130 anot[ae[aa].getPosition()].colour = new java.awt.Color(
2131 ae[aa].getColour());
2134 jalview.datamodel.AlignmentAnnotation jaa = null;
2136 if (an[i].getGraph())
2138 jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
2139 an[i].getDescription(), anot, 0, 0, an[i].getGraphType());
2141 jaa.graphGroup = an[i].getGraphGroup();
2143 if (an[i].getThresholdLine() != null)
2145 jaa.setThreshold(new jalview.datamodel.GraphLine(an[i]
2146 .getThresholdLine().getValue(), an[i]
2147 .getThresholdLine().getLabel(), new java.awt.Color(
2148 an[i].getThresholdLine().getColour())));
2155 jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
2156 an[i].getDescription(), anot);
2158 // register new annotation
2159 if (an[i].getId() != null)
2161 annotationIds.put(an[i].getId(), jaa);
2162 jaa.annotationId = an[i].getId();
2164 // recover sequence association
2165 if (an[i].getSequenceRef() != null)
2167 if (al.findName(an[i].getSequenceRef()) != null)
2169 jaa.createSequenceMapping(al.findName(an[i].getSequenceRef()),
2171 al.findName(an[i].getSequenceRef()).addAlignmentAnnotation(jaa);
2174 // and make a note of any group association
2175 if (an[i].getGroupRef() != null && an[i].getGroupRef().length() > 0)
2177 groupAnnotRefs.put(an[i].getGroupRef(), jaa);
2180 if (an[i].hasScore())
2182 jaa.setScore(an[i].getScore());
2184 if (an[i].hasVisible())
2185 jaa.visible = an[i].getVisible();
2187 if (an[i].hasCentreColLabels())
2188 jaa.centreColLabels = an[i].getCentreColLabels();
2190 if (an[i].hasScaleColLabels())
2192 jaa.scaleColLabel = an[i].getScaleColLabels();
2194 if (an[i].hasAutoCalculated() && an[i].isAutoCalculated())
2196 // newer files have an 'autoCalculated' flag and store calculation
2197 // state in viewport properties
2198 jaa.autoCalculated = true; // means annotation will be marked for
2199 // update at end of load.
2201 al.addAnnotation(jaa);
2205 // ///////////////////////
2207 // Create alignment markup and styles for this view
2208 if (jms.getJGroupCount() > 0)
2210 JGroup[] groups = jms.getJGroup();
2212 for (int i = 0; i < groups.length; i++)
2214 ColourSchemeI cs = null;
2216 if (groups[i].getColour() != null)
2218 if (groups[i].getColour().startsWith("ucs"))
2220 cs = GetUserColourScheme(jms, groups[i].getColour());
2224 cs = ColourSchemeProperty.getColour(al, groups[i].getColour());
2229 cs.setThreshold(groups[i].getPidThreshold(), true);
2233 Vector seqs = new Vector();
2235 for (int s = 0; s < groups[i].getSeqCount(); s++)
2237 String seqId = groups[i].getSeq(s) + "";
2238 jalview.datamodel.SequenceI ts = (jalview.datamodel.SequenceI) seqRefIds
2243 seqs.addElement(ts);
2247 if (seqs.size() < 1)
2252 jalview.datamodel.SequenceGroup sg = new jalview.datamodel.SequenceGroup(
2253 seqs, groups[i].getName(), cs, groups[i].getDisplayBoxes(),
2254 groups[i].getDisplayText(), groups[i].getColourText(),
2255 groups[i].getStart(), groups[i].getEnd());
2257 sg.setOutlineColour(new java.awt.Color(groups[i].getOutlineColour()));
2259 sg.textColour = new java.awt.Color(groups[i].getTextCol1());
2260 sg.textColour2 = new java.awt.Color(groups[i].getTextCol2());
2261 sg.setShowNonconserved(groups[i].hasShowUnconserved() ? groups[i]
2262 .isShowUnconserved() : false);
2263 sg.thresholdTextColour = groups[i].getTextColThreshold();
2264 if (groups[i].hasShowConsensusHistogram())
2266 sg.setShowConsensusHistogram(groups[i].isShowConsensusHistogram());
2269 if (groups[i].hasShowSequenceLogo())
2271 sg.setshowSequenceLogo(groups[i].isShowSequenceLogo());
2273 if (groups[i].hasIgnoreGapsinConsensus())
2275 sg.setIgnoreGapsConsensus(groups[i].getIgnoreGapsinConsensus());
2277 if (groups[i].getConsThreshold() != 0)
2279 jalview.analysis.Conservation c = new jalview.analysis.Conservation(
2280 "All", ResidueProperties.propHash, 3,
2281 sg.getSequences(null), 0, sg.getWidth() - 1);
2283 c.verdict(false, 25);
2284 sg.cs.setConservation(c);
2287 if (groups[i].getId() != null && groupAnnotRefs.size() > 0)
2289 // re-instate unique group/annotation row reference
2290 jalview.datamodel.AlignmentAnnotation jaa = (jalview.datamodel.AlignmentAnnotation) groupAnnotRefs
2291 .get(groups[i].getId());
2302 // ///////////////////////////////
2305 // If we just load in the same jar file again, the sequenceSetId
2306 // will be the same, and we end up with multiple references
2307 // to the same sequenceSet. We must modify this id on load
2308 // so that each load of the file gives a unique id
2309 String uniqueSeqSetId = view.getSequenceSetId() + uniqueSetSuffix;
2310 String viewId = (view.getId() == null ? null : view.getId()
2312 AlignFrame af = null;
2313 AlignViewport av = null;
2314 // now check to see if we really need to create a new viewport.
2315 if (multipleView && viewportsAdded.size() == 0)
2317 // We recovered an alignment for which a viewport already exists.
2318 // TODO: fix up any settings necessary for overlaying stored state onto
2319 // state recovered from another document. (may not be necessary).
2320 // we may need a binding from a viewport in memory to one recovered from
2322 // and then recover its containing af to allow the settings to be applied.
2323 // TODO: fix for vamsas demo
2325 .println("About to recover a viewport for existing alignment: Sequence set ID is "
2327 Object seqsetobj = retrieveExistingObj(uniqueSeqSetId);
2328 if (seqsetobj != null)
2330 if (seqsetobj instanceof String)
2332 uniqueSeqSetId = (String) seqsetobj;
2334 .println("Recovered extant sequence set ID mapping for ID : New Sequence set ID is "
2340 .println("Warning : Collision between sequence set ID string and existing jalview object mapping.");
2345 AlignmentPanel ap = null;
2346 boolean isnewview = true;
2349 // Check to see if this alignment already has a view id == viewId
2350 jalview.gui.AlignmentPanel views[] = Desktop
2351 .getAlignmentPanels(uniqueSeqSetId);
2352 if (views != null && views.length > 0)
2354 for (int v = 0; v < views.length; v++)
2356 if (views[v].av.getViewId().equalsIgnoreCase(viewId))
2358 // recover the existing alignpanel, alignframe, viewport
2359 af = views[v].alignFrame;
2362 // TODO: could even skip resetting view settings if we don't want to
2363 // change the local settings from other jalview processes
2372 af = loadViewport(file, JSEQ, hiddenSeqs, al, hideConsensus,
2373 hideQuality, hideConservation, jms, view, uniqueSeqSetId,
2379 // /////////////////////////////////////
2380 if (loadTreesAndStructures && jms.getTreeCount() > 0)
2384 for (int t = 0; t < jms.getTreeCount(); t++)
2387 Tree tree = jms.getTree(t);
2389 TreePanel tp = (TreePanel) retrieveExistingObj(tree.getId());
2392 tp = af.ShowNewickTree(
2393 new jalview.io.NewickFile(tree.getNewick()),
2394 tree.getTitle(), tree.getWidth(), tree.getHeight(),
2395 tree.getXpos(), tree.getYpos());
2396 if (tree.getId() != null)
2398 // perhaps bind the tree id to something ?
2403 // update local tree attributes ?
2404 // TODO: should check if tp has been manipulated by user - if so its
2405 // settings shouldn't be modified
2406 tp.setTitle(tree.getTitle());
2407 tp.setBounds(new Rectangle(tree.getXpos(), tree.getYpos(), tree
2408 .getWidth(), tree.getHeight()));
2409 tp.av = av; // af.viewport; // TODO: verify 'associate with all
2412 tp.treeCanvas.av = av; // af.viewport;
2413 tp.treeCanvas.ap = ap; // af.alignPanel;
2418 warn("There was a problem recovering stored Newick tree: \n"
2419 + tree.getNewick());
2423 tp.fitToWindow.setState(tree.getFitToWindow());
2424 tp.fitToWindow_actionPerformed(null);
2426 if (tree.getFontName() != null)
2428 tp.setTreeFont(new java.awt.Font(tree.getFontName(), tree
2429 .getFontStyle(), tree.getFontSize()));
2433 tp.setTreeFont(new java.awt.Font(view.getFontName(), view
2434 .getFontStyle(), tree.getFontSize()));
2437 tp.showPlaceholders(tree.getMarkUnlinked());
2438 tp.showBootstrap(tree.getShowBootstrap());
2439 tp.showDistances(tree.getShowDistances());
2441 tp.treeCanvas.threshold = tree.getThreshold();
2443 if (tree.getCurrentTree())
2445 af.viewport.setCurrentTree(tp.getTree());
2449 } catch (Exception ex)
2451 ex.printStackTrace();
2455 // //LOAD STRUCTURES
2456 if (loadTreesAndStructures)
2458 // run through all PDB ids on the alignment, and collect mappings between
2459 // jmol view ids and all sequences referring to it
2460 Hashtable<String, Object[]> jmolViewIds = new Hashtable();
2462 for (int i = 0; i < JSEQ.length; i++)
2464 if (JSEQ[i].getPdbidsCount() > 0)
2466 Pdbids[] ids = JSEQ[i].getPdbids();
2467 for (int p = 0; p < ids.length; p++)
2469 for (int s = 0; s < ids[p].getStructureStateCount(); s++)
2471 // check to see if we haven't already created this structure view
2472 String sviewid = (ids[p].getStructureState(s).getViewId() == null) ? null
2473 : ids[p].getStructureState(s).getViewId()
2475 jalview.datamodel.PDBEntry jpdb = new jalview.datamodel.PDBEntry();
2476 // Originally : ids[p].getFile()
2477 // : TODO: verify external PDB file recovery still works in normal
2478 // jalview project load
2479 jpdb.setFile(loadPDBFile(jprovider, ids[p].getId()));
2480 jpdb.setId(ids[p].getId());
2482 int x = ids[p].getStructureState(s).getXpos();
2483 int y = ids[p].getStructureState(s).getYpos();
2484 int width = ids[p].getStructureState(s).getWidth();
2485 int height = ids[p].getStructureState(s).getHeight();
2487 // Probably don't need to do this anymore...
2488 // Desktop.desktop.getComponentAt(x, y);
2489 // TODO: NOW: check that this recovers the PDB file correctly.
2490 String pdbFile = loadPDBFile(jprovider, ids[p].getId());
2491 jalview.datamodel.SequenceI seq = (jalview.datamodel.SequenceI) seqRefIds
2492 .get(JSEQ[i].getId() + "");
2493 if (sviewid == null)
2495 sviewid = "_jalview_pre2_4_" + x + "," + y + "," + width
2498 if (!jmolViewIds.containsKey(sviewid))
2500 jmolViewIds.put(sviewid, new Object[]
2502 { x, y, width, height }, "",
2503 new Hashtable<String, Object[]>() });
2505 // TODO: assemble String[] { pdb files }, String[] { id for each
2506 // file }, orig_fileloc, SequenceI[][] {{ seqs_file 1 }, {
2507 // seqs_file 2}} from hash
2508 Object[] jmoldat = (Object[]) jmolViewIds.get(sviewid);
2509 if (((String) jmoldat[1]).length() < ids[p]
2510 .getStructureState(s).getContent().length())
2513 jmoldat[1] = ids[p].getStructureState(s).getContent();
2516 Object[] seqstrmaps = (Object[]) ((Hashtable) jmoldat[2])
2517 .get(ids[p].getFile());
2518 if (seqstrmaps == null)
2520 ((Hashtable) jmoldat[2]).put(
2521 new File(ids[p].getFile()).toString(),
2522 seqstrmaps = new Object[]
2523 { pdbFile, ids[p].getId(), new Vector(),
2526 if (!((Vector) seqstrmaps[2]).contains(seq))
2528 ((Vector) seqstrmaps[2]).addElement(seq);
2529 // ((Vector)seqstrmaps[3]).addElement(n) : in principle, chains
2530 // should be stored here : do we need to
2531 // TODO: store and recover seq/pdb_id : chain mappings
2539 // Instantiate the associated Jmol views
2540 for (Entry<String, Object[]> entry : jmolViewIds.entrySet())
2542 String sviewid = entry.getKey();
2543 Object[] svattrib = entry.getValue();
2544 int[] geom = (int[]) svattrib[0];
2545 String state = (String) svattrib[1];
2546 Hashtable<String, Object[]> oldFiles = (Hashtable<String, Object[]>) svattrib[2];
2548 int x = geom[0], y = geom[1], width = geom[2], height = geom[3];
2549 // collate the pdbfile -> sequence mappings from this view
2550 Vector<String> pdbfilenames = new Vector<String>();
2551 Vector<SequenceI[]> seqmaps = new Vector<SequenceI[]>();
2552 Vector<String> pdbids = new Vector<String>();
2554 // Search to see if we've already created this Jmol view
2555 AppJmol comp = null;
2556 JInternalFrame[] frames = null;
2561 frames = Desktop.desktop.getAllFrames();
2562 } catch (ArrayIndexOutOfBoundsException e)
2564 // occasional No such child exceptions are thrown here...
2569 } catch (Exception f)
2574 } while (frames == null);
2575 // search for any Jmol windows already open from other
2576 // alignment views that exactly match the stored structure state
2577 for (int f = 0; comp == null && f < frames.length; f++)
2579 if (frames[f] instanceof AppJmol)
2582 && ((AppJmol) frames[f]).getViewId().equals(sviewid))
2584 // post jalview 2.4 schema includes structure view id
2585 comp = (AppJmol) frames[f];
2587 else if (frames[f].getX() == x && frames[f].getY() == y
2588 && frames[f].getHeight() == height
2589 && frames[f].getWidth() == width)
2591 comp = (AppJmol) frames[f];
2598 // create a new Jmol window.
2599 // First parse the Jmol state to translate filenames loaded into the
2600 // view, and record the order in which files are shown in the Jmol
2601 // view, so we can add the sequence mappings in same order.
2602 StringBuffer newFileLoc = null;
2603 int cp = 0, ncp, ecp;
2604 while ((ncp = state.indexOf("load ", cp)) > -1)
2606 if (newFileLoc == null)
2608 newFileLoc = new StringBuffer();
2610 newFileLoc.append(state.substring(cp,
2611 ncp = (state.indexOf("\"", ncp + 1) + 1)));
2612 String oldfilenam = state.substring(ncp,
2613 ecp = state.indexOf("\"", ncp));
2614 // recover the new mapping data for this old filename
2615 // have to normalize filename - since Jmol and jalview do filename
2616 // translation differently.
2617 Object[] filedat = oldFiles.get(new File(oldfilenam)
2619 newFileLoc.append(((String) filedat[0]));
2620 pdbfilenames.addElement((String) filedat[0]);
2621 pdbids.addElement((String) filedat[1]);
2622 seqmaps.addElement((SequenceI[]) ((Vector<SequenceI>) filedat[2])
2623 .toArray(new SequenceI[0]));
2624 newFileLoc.append("\"");
2625 cp = ecp + 1; // advance beyond last \" and set cursor so we can
2626 // look for next file statement.
2630 // just append rest of state
2631 newFileLoc.append(state.substring(cp));
2636 .print("Ignoring incomplete Jmol state for PDB ids: ");
2637 newFileLoc = new StringBuffer(state);
2638 newFileLoc.append("; load append ");
2639 for (String id : oldFiles.keySet())
2641 // add this and any other pdb files that should be present in
2643 Object[] filedat = oldFiles.get(id);
2645 newFileLoc.append(((String) filedat[0]));
2646 pdbfilenames.addElement((String) filedat[0]);
2647 pdbids.addElement((String) filedat[1]);
2648 seqmaps.addElement((SequenceI[]) ((Vector<SequenceI>) filedat[2])
2649 .toArray(new SequenceI[0]));
2650 newFileLoc.append(" \"");
2651 newFileLoc.append((String) filedat[0]);
2652 newFileLoc.append("\"");
2655 newFileLoc.append(";");
2658 if (newFileLoc != null)
2660 int histbug = newFileLoc.indexOf("history = ");
2662 int diff = histbug == -1 ? -1 : newFileLoc.indexOf(";",
2664 String val = (diff == -1) ? null : newFileLoc.substring(
2666 if (val != null && val.length() >= 4)
2668 if (val.contains("e"))
2670 if (val.trim().equals("true"))
2678 newFileLoc.replace(histbug, diff, val);
2681 // TODO: assemble String[] { pdb files }, String[] { id for each
2682 // file }, orig_fileloc, SequenceI[][] {{ seqs_file 1 }, {
2683 // seqs_file 2}} from hash
2684 final String[] pdbf = (String[]) pdbfilenames
2685 .toArray(new String[pdbfilenames.size()]), id = (String[]) pdbids
2686 .toArray(new String[pdbids.size()]);
2687 final SequenceI[][] sq = (SequenceI[][]) seqmaps
2688 .toArray(new SequenceI[seqmaps.size()][]);
2689 final String fileloc = newFileLoc.toString(), vid = sviewid;
2690 final AlignFrame alf = af;
2691 final java.awt.Rectangle rect = new java.awt.Rectangle(x, y,
2695 javax.swing.SwingUtilities.invokeAndWait(new Runnable()
2699 AppJmol sview = null;
2702 sview = new AppJmol(pdbf, id, sq, alf.alignPanel,
2706 } catch (OutOfMemoryError ex)
2708 new OOMWarning("restoring structure view for PDB id "
2709 + id, (OutOfMemoryError) ex.getCause());
2710 if (sview != null && sview.isVisible())
2712 sview.closeViewer();
2713 sview.setVisible(false);
2719 } catch (InvocationTargetException ex)
2721 warn("Unexpected error when opening Jmol view.", ex);
2723 } catch (InterruptedException e)
2725 // e.printStackTrace();
2731 // if (comp != null)
2733 // NOTE: if the jalview project is part of a shared session then
2734 // view synchronization should/could be done here.
2736 // add mapping for sequences in this view to an already open Jmol
2738 for (String id : oldFiles.keySet())
2740 // add this and any other pdb files that should be present in the
2742 Object[] filedat = oldFiles.get(id);
2743 String pdbFile = (String) filedat[0];
2744 SequenceI[] seq = (SequenceI[]) ((Vector<SequenceI>) filedat[2])
2745 .toArray(new SequenceI[0]);
2746 StructureSelectionManager.getStructureSelectionManager()
2747 .setMapping(seq, null, pdbFile,
2748 jalview.io.AppletFormatAdapter.FILE);
2749 ((AppJmol) comp).jmb.addSequenceForStructFile(pdbFile, seq);
2755 // and finally return.
2759 AlignFrame loadViewport(String file, JSeq[] JSEQ, Vector hiddenSeqs,
2760 Alignment al, boolean hideConsensus, boolean hideQuality,
2761 boolean hideConservation, JalviewModelSequence jms,
2762 Viewport view, String uniqueSeqSetId, String viewId)
2764 AlignFrame af = null;
2765 af = new AlignFrame(al, view.getWidth(), view.getHeight(),
2766 uniqueSeqSetId, viewId);
2768 af.setFileName(file, "Jalview");
2770 for (int i = 0; i < JSEQ.length; i++)
2772 af.viewport.setSequenceColour(af.viewport.alignment.getSequenceAt(i),
2773 new java.awt.Color(JSEQ[i].getColour()));
2776 af.viewport.gatherViewsHere = view.getGatheredViews();
2778 if (view.getSequenceSetId() != null)
2780 jalview.gui.AlignViewport av = (jalview.gui.AlignViewport) viewportsAdded
2781 .get(uniqueSeqSetId);
2783 af.viewport.sequenceSetID = uniqueSeqSetId;
2786 // propagate shared settings to this new view
2787 af.viewport.historyList = av.historyList;
2788 af.viewport.redoList = av.redoList;
2792 viewportsAdded.put(uniqueSeqSetId, af.viewport);
2794 // TODO: check if this method can be called repeatedly without
2795 // side-effects if alignpanel already registered.
2796 PaintRefresher.Register(af.alignPanel, uniqueSeqSetId);
2798 // apply Hidden regions to view.
2799 if (hiddenSeqs != null)
2801 for (int s = 0; s < JSEQ.length; s++)
2803 jalview.datamodel.SequenceGroup hidden = new jalview.datamodel.SequenceGroup();
2805 for (int r = 0; r < JSEQ[s].getHiddenSequencesCount(); r++)
2808 al.getSequenceAt(JSEQ[s].getHiddenSequences(r)), false);
2810 af.viewport.hideRepSequences(al.getSequenceAt(s), hidden);
2813 jalview.datamodel.SequenceI[] hseqs = new jalview.datamodel.SequenceI[hiddenSeqs
2816 for (int s = 0; s < hiddenSeqs.size(); s++)
2818 hseqs[s] = (jalview.datamodel.SequenceI) hiddenSeqs.elementAt(s);
2821 af.viewport.hideSequence(hseqs);
2824 // set visibility of annotation in view
2825 if ((hideConsensus || hideQuality || hideConservation)
2826 && al.getAlignmentAnnotation() != null)
2828 int hSize = al.getAlignmentAnnotation().length;
2829 for (int h = 0; h < hSize; h++)
2831 if ((hideConsensus && al.getAlignmentAnnotation()[h].label
2832 .equals("Consensus"))
2833 || (hideQuality && al.getAlignmentAnnotation()[h].label
2835 || (hideConservation && al.getAlignmentAnnotation()[h].label
2836 .equals("Conservation")))
2838 al.deleteAnnotation(al.getAlignmentAnnotation()[h]);
2843 af.alignPanel.adjustAnnotationHeight();
2845 // recover view properties and display parameters
2846 if (view.getViewName() != null)
2848 af.viewport.viewName = view.getViewName();
2849 af.setInitialTabVisible();
2851 af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),
2854 af.viewport.setShowAnnotation(view.getShowAnnotation());
2855 af.viewport.setAbovePIDThreshold(view.getPidSelected());
2857 af.viewport.setColourText(view.getShowColourText());
2859 af.viewport.setConservationSelected(view.getConservationSelected());
2860 af.viewport.setShowJVSuffix(view.getShowFullId());
2861 af.viewport.rightAlignIds = view.getRightAlignIds();
2862 af.viewport.setFont(new java.awt.Font(view.getFontName(), view
2863 .getFontStyle(), view.getFontSize()));
2864 af.alignPanel.fontChanged();
2865 af.viewport.setRenderGaps(view.getRenderGaps());
2866 af.viewport.setWrapAlignment(view.getWrapAlignment());
2867 af.alignPanel.setWrapAlignment(view.getWrapAlignment());
2868 af.viewport.setShowAnnotation(view.getShowAnnotation());
2869 af.alignPanel.setAnnotationVisible(view.getShowAnnotation());
2871 af.viewport.setShowBoxes(view.getShowBoxes());
2873 af.viewport.setShowText(view.getShowText());
2875 af.viewport.textColour = new java.awt.Color(view.getTextCol1());
2876 af.viewport.textColour2 = new java.awt.Color(view.getTextCol2());
2877 af.viewport.thresholdTextColour = view.getTextColThreshold();
2878 af.viewport.setShowUnconserved(view.hasShowUnconserved() ? view
2879 .isShowUnconserved() : false);
2880 af.viewport.setStartRes(view.getStartRes());
2881 af.viewport.setStartSeq(view.getStartSeq());
2883 ColourSchemeI cs = null;
2884 // apply colourschemes
2885 if (view.getBgColour() != null)
2887 if (view.getBgColour().startsWith("ucs"))
2889 cs = GetUserColourScheme(jms, view.getBgColour());
2891 else if (view.getBgColour().startsWith("Annotation"))
2893 // int find annotation
2894 if (af.viewport.alignment.getAlignmentAnnotation() != null)
2896 for (int i = 0; i < af.viewport.alignment
2897 .getAlignmentAnnotation().length; i++)
2899 if (af.viewport.alignment.getAlignmentAnnotation()[i].label
2900 .equals(view.getAnnotationColours().getAnnotation()))
2902 if (af.viewport.alignment.getAlignmentAnnotation()[i]
2903 .getThreshold() == null)
2905 af.viewport.alignment.getAlignmentAnnotation()[i]
2906 .setThreshold(new jalview.datamodel.GraphLine(view
2907 .getAnnotationColours().getThreshold(),
2908 "Threshold", java.awt.Color.black)
2913 if (view.getAnnotationColours().getColourScheme()
2916 cs = new AnnotationColourGradient(
2917 af.viewport.alignment.getAlignmentAnnotation()[i],
2918 new java.awt.Color(view.getAnnotationColours()
2919 .getMinColour()), new java.awt.Color(view
2920 .getAnnotationColours().getMaxColour()),
2921 view.getAnnotationColours().getAboveThreshold());
2923 else if (view.getAnnotationColours().getColourScheme()
2926 cs = new AnnotationColourGradient(
2927 af.viewport.alignment.getAlignmentAnnotation()[i],
2928 GetUserColourScheme(jms, view
2929 .getAnnotationColours().getColourScheme()),
2930 view.getAnnotationColours().getAboveThreshold());
2934 cs = new AnnotationColourGradient(
2935 af.viewport.alignment.getAlignmentAnnotation()[i],
2936 ColourSchemeProperty.getColour(al, view
2937 .getAnnotationColours().getColourScheme()),
2938 view.getAnnotationColours().getAboveThreshold());
2941 // Also use these settings for all the groups
2942 if (al.getGroups() != null)
2944 for (int g = 0; g < al.getGroups().size(); g++)
2946 jalview.datamodel.SequenceGroup sg = (jalview.datamodel.SequenceGroup) al
2947 .getGroups().elementAt(g);
2956 * (view.getAnnotationColours().getColourScheme().equals("None"
2957 * )) { sg.cs = new AnnotationColourGradient(
2958 * af.viewport.alignment.getAlignmentAnnotation()[i], new
2959 * java.awt.Color(view.getAnnotationColours().
2960 * getMinColour()), new
2961 * java.awt.Color(view.getAnnotationColours().
2963 * view.getAnnotationColours().getAboveThreshold()); } else
2966 sg.cs = new AnnotationColourGradient(
2967 af.viewport.alignment.getAlignmentAnnotation()[i],
2968 sg.cs, view.getAnnotationColours()
2969 .getAboveThreshold());
2983 cs = ColourSchemeProperty.getColour(al, view.getBgColour());
2988 cs.setThreshold(view.getPidThreshold(), true);
2989 cs.setConsensus(af.viewport.hconsensus);
2993 af.viewport.setGlobalColourScheme(cs);
2994 af.viewport.setColourAppliesToAllGroups(false);
2996 if (view.getConservationSelected() && cs != null)
2998 cs.setConservationInc(view.getConsThreshold());
3001 af.changeColour(cs);
3003 af.viewport.setColourAppliesToAllGroups(true);
3005 if (view.getShowSequenceFeatures())
3007 af.viewport.showSequenceFeatures = true;
3009 if (view.hasCentreColumnLabels())
3011 af.viewport.setCentreColumnLabels(view.getCentreColumnLabels());
3013 if (view.hasIgnoreGapsinConsensus())
3015 af.viewport.ignoreGapsInConsensusCalculation = view
3016 .getIgnoreGapsinConsensus();
3018 if (view.hasFollowHighlight())
3020 af.viewport.followHighlight = view.getFollowHighlight();
3022 if (view.hasFollowSelection())
3024 af.viewport.followSelection = view.getFollowSelection();
3026 if (view.hasShowConsensusHistogram())
3028 af.viewport.setShowConsensusHistogram(view
3029 .getShowConsensusHistogram());
3033 af.viewport.setShowConsensusHistogram(true);
3035 if (view.hasShowSequenceLogo())
3037 af.viewport.showSequenceLogo = view.getShowSequenceLogo();
3041 af.viewport.showSequenceLogo = false;
3043 if (view.hasShowDbRefTooltip())
3045 af.viewport.setShowDbRefs(view.getShowDbRefTooltip());
3047 if (view.hasShowNPfeatureTooltip())
3049 af.viewport.setShowNpFeats(view.hasShowNPfeatureTooltip());
3051 if (view.hasShowGroupConsensus())
3053 af.viewport.setShowGroupConsensus(view.getShowGroupConsensus());
3057 af.viewport.setShowGroupConsensus(false);
3059 if (view.hasShowGroupConservation())
3061 af.viewport.setShowGroupConservation(view.getShowGroupConservation());
3065 af.viewport.setShowGroupConservation(false);
3068 // recover featre settings
3069 if (jms.getFeatureSettings() != null)
3071 af.viewport.featuresDisplayed = new Hashtable();
3072 String[] renderOrder = new String[jms.getFeatureSettings()
3073 .getSettingCount()];
3074 for (int fs = 0; fs < jms.getFeatureSettings().getSettingCount(); fs++)
3076 Setting setting = jms.getFeatureSettings().getSetting(fs);
3077 if (setting.hasMincolour())
3079 GraduatedColor gc = setting.hasMin() ? new GraduatedColor(
3080 new java.awt.Color(setting.getMincolour()),
3081 new java.awt.Color(setting.getColour()),
3082 setting.getMin(), setting.getMax()) : new GraduatedColor(
3083 new java.awt.Color(setting.getMincolour()),
3084 new java.awt.Color(setting.getColour()), 0, 1);
3085 if (setting.hasThreshold())
3087 gc.setThresh(setting.getThreshold());
3088 gc.setThreshType(setting.getThreshstate());
3090 gc.setAutoScaled(true); // default
3091 if (setting.hasAutoScale())
3093 gc.setAutoScaled(setting.getAutoScale());
3095 if (setting.hasColourByLabel())
3097 gc.setColourByLabel(setting.getColourByLabel());
3099 // and put in the feature colour table.
3100 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(
3101 setting.getType(), gc);
3105 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(
3107 new java.awt.Color(setting.getColour()));
3109 renderOrder[fs] = setting.getType();
3110 if (setting.hasOrder())
3111 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setOrder(
3112 setting.getType(), setting.getOrder());
3114 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setOrder(
3116 fs / jms.getFeatureSettings().getSettingCount());
3117 if (setting.getDisplay())
3119 af.viewport.featuresDisplayed.put(setting.getType(), new Integer(
3120 setting.getColour()));
3123 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder = renderOrder;
3125 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureGroups = fgtable = new Hashtable();
3126 for (int gs = 0; gs < jms.getFeatureSettings().getGroupCount(); gs++)
3128 Group grp = jms.getFeatureSettings().getGroup(gs);
3129 fgtable.put(grp.getName(), new Boolean(grp.getDisplay()));
3133 if (view.getHiddenColumnsCount() > 0)
3135 for (int c = 0; c < view.getHiddenColumnsCount(); c++)
3137 af.viewport.hideColumns(view.getHiddenColumns(c).getStart(), view
3138 .getHiddenColumns(c).getEnd() // +1
3143 af.setMenusFromViewport(af.viewport);
3144 // TODO: we don't need to do this if the viewport is aready visible.
3145 Desktop.addInternalFrame(af, view.getTitle(), view.getWidth(),
3147 af.alignPanel.updateAnnotation(false); // recompute any autoannotation
3151 Hashtable skipList = null;
3154 * TODO remove this method
3157 * @return AlignFrame bound to sequenceSetId from view, if one exists. private
3158 * AlignFrame getSkippedFrame(Viewport view) { if (skipList==null) {
3159 * throw new Error("Implementation Error. No skipList defined for this
3160 * Jalview2XML instance."); } return (AlignFrame)
3161 * skipList.get(view.getSequenceSetId()); }
3165 * Check if the Jalview view contained in object should be skipped or not.
3168 * @return true if view's sequenceSetId is a key in skipList
3170 private boolean skipViewport(JalviewModel object)
3172 if (skipList == null)
3177 if (skipList.containsKey(id = object.getJalviewModelSequence()
3178 .getViewport()[0].getSequenceSetId()))
3180 if (Cache.log != null && Cache.log.isDebugEnabled())
3182 Cache.log.debug("Skipping seuqence set id " + id);
3189 public void AddToSkipList(AlignFrame af)
3191 if (skipList == null)
3193 skipList = new Hashtable();
3195 skipList.put(af.getViewport().getSequenceSetId(), af);
3198 public void clearSkipList()
3200 if (skipList != null)
3207 private void recoverDatasetFor(SequenceSet vamsasSet, Alignment al)
3209 jalview.datamodel.Alignment ds = getDatasetFor(vamsasSet.getDatasetId());
3210 Vector dseqs = null;
3213 // create a list of new dataset sequences
3214 dseqs = new Vector();
3216 for (int i = 0, iSize = vamsasSet.getSequenceCount(); i < iSize; i++)
3218 Sequence vamsasSeq = vamsasSet.getSequence(i);
3219 ensureJalviewDatasetSequence(vamsasSeq, ds, dseqs);
3221 // create a new dataset
3224 SequenceI[] dsseqs = new SequenceI[dseqs.size()];
3225 dseqs.copyInto(dsseqs);
3226 ds = new jalview.datamodel.Alignment(dsseqs);
3227 debug("Created new dataset " + vamsasSet.getDatasetId()
3228 + " for alignment " + System.identityHashCode(al));
3229 addDatasetRef(vamsasSet.getDatasetId(), ds);
3231 // set the dataset for the newly imported alignment.
3232 if (al.getDataset() == null)
3241 * sequence definition to create/merge dataset sequence for
3245 * vector to add new dataset sequence to
3247 private void ensureJalviewDatasetSequence(Sequence vamsasSeq,
3248 AlignmentI ds, Vector dseqs)
3250 // JBP TODO: Check this is called for AlCodonFrames to support recovery of
3252 jalview.datamodel.Sequence sq = (jalview.datamodel.Sequence) seqRefIds
3253 .get(vamsasSeq.getId());
3254 jalview.datamodel.SequenceI dsq = null;
3255 if (sq != null && sq.getDatasetSequence() != null)
3257 dsq = (jalview.datamodel.SequenceI) sq.getDatasetSequence();
3260 String sqid = vamsasSeq.getDsseqid();
3263 // need to create or add a new dataset sequence reference to this sequence
3266 dsq = (jalview.datamodel.SequenceI) seqRefIds.get(sqid);
3271 // make a new dataset sequence
3272 dsq = sq.createDatasetSequence();
3275 // make up a new dataset reference for this sequence
3276 sqid = seqHash(dsq);
3278 dsq.setVamsasId(uniqueSetSuffix + sqid);
3279 seqRefIds.put(sqid, dsq);
3284 dseqs.addElement(dsq);
3289 ds.addSequence(dsq);
3295 { // make this dataset sequence sq's dataset sequence
3296 sq.setDatasetSequence(dsq);
3300 // TODO: refactor this as a merge dataset sequence function
3301 // now check that sq (the dataset sequence) sequence really is the union of
3302 // all references to it
3303 // boolean pre = sq.getStart() < dsq.getStart();
3304 // boolean post = sq.getEnd() > dsq.getEnd();
3308 StringBuffer sb = new StringBuffer();
3309 String newres = jalview.analysis.AlignSeq.extractGaps(
3310 jalview.util.Comparison.GapChars, sq.getSequenceAsString());
3311 if (!newres.equalsIgnoreCase(dsq.getSequenceAsString())
3312 && newres.length() > dsq.getLength())
3314 // Update with the longer sequence.
3318 * if (pre) { sb.insert(0, newres .substring(0, dsq.getStart() -
3319 * sq.getStart())); dsq.setStart(sq.getStart()); } if (post) {
3320 * sb.append(newres.substring(newres.length() - sq.getEnd() -
3321 * dsq.getEnd())); dsq.setEnd(sq.getEnd()); }
3323 dsq.setSequence(sb.toString());
3325 // TODO: merges will never happen if we 'know' we have the real dataset
3326 // sequence - this should be detected when id==dssid
3327 System.err.println("DEBUG Notice: Merged dataset sequence"); // ("
3328 // + (pre ? "prepended" : "") + " "
3329 // + (post ? "appended" : ""));
3334 java.util.Hashtable datasetIds = null;
3336 java.util.IdentityHashMap dataset2Ids = null;
3338 private Alignment getDatasetFor(String datasetId)
3340 if (datasetIds == null)
3342 datasetIds = new Hashtable();
3345 if (datasetIds.containsKey(datasetId))
3347 return (Alignment) datasetIds.get(datasetId);
3352 private void addDatasetRef(String datasetId, Alignment dataset)
3354 if (datasetIds == null)
3356 datasetIds = new Hashtable();
3358 datasetIds.put(datasetId, dataset);
3362 * make a new dataset ID for this jalview dataset alignment
3367 private String getDatasetIdRef(jalview.datamodel.Alignment dataset)
3369 if (dataset.getDataset() != null)
3371 warn("Serious issue! Dataset Object passed to getDatasetIdRef is not a Jalview DATASET alignment...");
3373 String datasetId = makeHashCode(dataset, null);
3374 if (datasetId == null)
3376 // make a new datasetId and record it
3377 if (dataset2Ids == null)
3379 dataset2Ids = new IdentityHashMap();
3383 datasetId = (String) dataset2Ids.get(dataset);
3385 if (datasetId == null)
3387 datasetId = "ds" + dataset2Ids.size() + 1;
3388 dataset2Ids.put(dataset, datasetId);
3394 private void addDBRefs(SequenceI datasetSequence, Sequence sequence)
3396 for (int d = 0; d < sequence.getDBRefCount(); d++)
3398 DBRef dr = sequence.getDBRef(d);
3399 jalview.datamodel.DBRefEntry entry = new jalview.datamodel.DBRefEntry(
3400 sequence.getDBRef(d).getSource(), sequence.getDBRef(d)
3401 .getVersion(), sequence.getDBRef(d).getAccessionId());
3402 if (dr.getMapping() != null)
3404 entry.setMap(addMapping(dr.getMapping()));
3406 datasetSequence.addDBRef(entry);
3410 private jalview.datamodel.Mapping addMapping(Mapping m)
3412 SequenceI dsto = null;
3413 // Mapping m = dr.getMapping();
3414 int fr[] = new int[m.getMapListFromCount() * 2];
3415 Enumeration f = m.enumerateMapListFrom();
3416 for (int _i = 0; f.hasMoreElements(); _i += 2)
3418 MapListFrom mf = (MapListFrom) f.nextElement();
3419 fr[_i] = mf.getStart();
3420 fr[_i + 1] = mf.getEnd();
3422 int fto[] = new int[m.getMapListToCount() * 2];
3423 f = m.enumerateMapListTo();
3424 for (int _i = 0; f.hasMoreElements(); _i += 2)
3426 MapListTo mf = (MapListTo) f.nextElement();
3427 fto[_i] = mf.getStart();
3428 fto[_i + 1] = mf.getEnd();
3430 jalview.datamodel.Mapping jmap = new jalview.datamodel.Mapping(dsto,
3431 fr, fto, (int) m.getMapFromUnit(), (int) m.getMapToUnit());
3432 if (m.getMappingChoice() != null)
3434 MappingChoice mc = m.getMappingChoice();
3435 if (mc.getDseqFor() != null)
3437 String dsfor = "" + mc.getDseqFor();
3438 if (seqRefIds.containsKey(dsfor))
3443 jmap.setTo((SequenceI) seqRefIds.get(dsfor));
3447 frefedSequence.add(new Object[]
3454 * local sequence definition
3456 Sequence ms = mc.getSequence();
3457 jalview.datamodel.Sequence djs = null;
3458 String sqid = ms.getDsseqid();
3459 if (sqid != null && sqid.length() > 0)
3462 * recover dataset sequence
3464 djs = (jalview.datamodel.Sequence) seqRefIds.get(sqid);
3469 .println("Warning - making up dataset sequence id for DbRef sequence map reference");
3470 sqid = ((Object) ms).toString(); // make up a new hascode for
3471 // undefined dataset sequence hash
3472 // (unlikely to happen)
3478 * make a new dataset sequence and add it to refIds hash
3480 djs = new jalview.datamodel.Sequence(ms.getName(),
3482 djs.setStart(jmap.getMap().getToLowest());
3483 djs.setEnd(jmap.getMap().getToHighest());
3484 djs.setVamsasId(uniqueSetSuffix + sqid);
3486 seqRefIds.put(sqid, djs);
3489 jalview.bin.Cache.log.debug("about to recurse on addDBRefs.");
3498 public jalview.gui.AlignmentPanel copyAlignPanel(AlignmentPanel ap,
3499 boolean keepSeqRefs)
3502 jalview.schemabinding.version2.JalviewModel jm = SaveState(ap, null,
3508 jm.getJalviewModelSequence().getViewport(0).setSequenceSetId(null);
3512 uniqueSetSuffix = "";
3513 jm.getJalviewModelSequence().getViewport(0).setId(null); // we don't
3518 if (this.frefedSequence == null)
3520 frefedSequence = new Vector();
3523 viewportsAdded = new Hashtable();
3525 AlignFrame af = LoadFromObject(jm, null, false, null);
3526 af.alignPanels.clear();
3527 af.closeMenuItem_actionPerformed(true);
3530 * if(ap.av.alignment.getAlignmentAnnotation()!=null) { for(int i=0;
3531 * i<ap.av.alignment.getAlignmentAnnotation().length; i++) {
3532 * if(!ap.av.alignment.getAlignmentAnnotation()[i].autoCalculated) {
3533 * af.alignPanel.av.alignment.getAlignmentAnnotation()[i] =
3534 * ap.av.alignment.getAlignmentAnnotation()[i]; } } }
3537 return af.alignPanel;
3541 * flag indicating if hashtables should be cleared on finalization TODO this
3542 * flag may not be necessary
3544 private boolean _cleartables = true;
3546 private Hashtable jvids2vobj;
3551 * @see java.lang.Object#finalize()
3553 protected void finalize() throws Throwable
3555 // really make sure we have no buried refs left.
3560 this.seqRefIds = null;
3561 this.seqsToIds = null;
3565 private void warn(String msg)
3570 private void warn(String msg, Exception e)
3572 if (Cache.log != null)
3576 Cache.log.warn(msg, e);
3580 Cache.log.warn(msg);
3585 System.err.println("Warning: " + msg);
3588 e.printStackTrace();
3593 private void debug(String string)
3595 debug(string, null);
3598 private void debug(String msg, Exception e)
3600 if (Cache.log != null)
3604 Cache.log.debug(msg, e);
3608 Cache.log.debug(msg);
3613 System.err.println("Warning: " + msg);
3616 e.printStackTrace();
3622 * set the object to ID mapping tables used to write/recover objects and XML
3623 * ID strings for the jalview project. If external tables are provided then
3624 * finalize and clearSeqRefs will not clear the tables when the Jalview2XML
3625 * object goes out of scope. - also populates the datasetIds hashtable with
3626 * alignment objects containing dataset sequences
3629 * Map from ID strings to jalview datamodel
3631 * Map from jalview datamodel to ID strings
3635 public void setObjectMappingTables(Hashtable vobj2jv,
3636 IdentityHashMap jv2vobj)
3638 this.jv2vobj = jv2vobj;
3639 this.vobj2jv = vobj2jv;
3640 Iterator ds = jv2vobj.keySet().iterator();
3642 while (ds.hasNext())
3644 Object jvobj = ds.next();
3645 id = jv2vobj.get(jvobj).toString();
3646 if (jvobj instanceof jalview.datamodel.Alignment)
3648 if (((jalview.datamodel.Alignment) jvobj).getDataset() == null)
3650 addDatasetRef(id, (jalview.datamodel.Alignment) jvobj);
3653 else if (jvobj instanceof jalview.datamodel.Sequence)
3655 // register sequence object so the XML parser can recover it.
3656 if (seqRefIds == null)
3658 seqRefIds = new Hashtable();
3660 if (seqsToIds == null)
3662 seqsToIds = new IdentityHashMap();
3664 seqRefIds.put(jv2vobj.get(jvobj).toString(), jvobj);
3665 seqsToIds.put(jvobj, id);
3667 else if (jvobj instanceof jalview.datamodel.AlignmentAnnotation)
3669 if (annotationIds == null)
3671 annotationIds = new Hashtable();
3674 annotationIds.put(anid = jv2vobj.get(jvobj).toString(), jvobj);
3675 jalview.datamodel.AlignmentAnnotation jvann = (jalview.datamodel.AlignmentAnnotation) jvobj;
3676 if (jvann.annotationId == null)
3678 jvann.annotationId = anid;
3680 if (!jvann.annotationId.equals(anid))
3682 // TODO verify that this is the correct behaviour
3683 this.warn("Overriding Annotation ID for " + anid
3684 + " from different id : " + jvann.annotationId);
3685 jvann.annotationId = anid;
3688 else if (jvobj instanceof String)
3690 if (jvids2vobj == null)
3692 jvids2vobj = new Hashtable();
3693 jvids2vobj.put(jvobj, jv2vobj.get(jvobj).toString());
3697 Cache.log.debug("Ignoring " + jvobj.getClass() + " (ID = " + id);
3702 * set the uniqueSetSuffix used to prefix/suffix object IDs for jalview
3703 * objects created from the project archive. If string is null (default for
3704 * construction) then suffix will be set automatically.
3708 public void setUniqueSetSuffix(String string)
3710 uniqueSetSuffix = string;
3715 * uses skipList2 as the skipList for skipping views on sequence sets
3716 * associated with keys in the skipList
3720 public void setSkipList(Hashtable skipList2)
3722 skipList = skipList2;