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 jmol = (AppJmol) frames[f];
584 for (int peid = 0; peid < jmol.jmb.pdbentry.length; peid++)
586 if (!jmol.jmb.pdbentry[peid].getId().equals(entry.getId())
587 && !(entry.getId().length() > 4 && entry
591 jmol.jmb.pdbentry[peid].getId()
594 if (matchedFile == null)
596 matchedFile = jmol.jmb.pdbentry[peid].getFile();
598 else if (!matchedFile.equals(jmol.jmb.pdbentry[peid]
602 .warn("Probably lost some PDB-Sequence mappings for this structure file (which apparently has same PDB Entry code): "
603 + jmol.jmb.pdbentry[peid].getFile());
607 // can get at it if the ID
608 // match is ambiguous (e.g.
610 String statestring = jmol.jmb.viewer.getStateInfo();
612 for (int smap = 0; smap < jmol.jmb.sequence[peid].length; smap++)
614 if (jal.findIndex(jmol.jmb.sequence[peid][smap]) > -1)
616 StructureState state = new StructureState();
617 state.setVisible(true);
618 state.setXpos(jmol.getX());
619 state.setYpos(jmol.getY());
620 state.setWidth(jmol.getWidth());
621 state.setHeight(jmol.getHeight());
622 state.setViewId(jmol.getViewId());
623 state.setAlignwithAlignPanel(jmol.isUsedforaligment(ap));
624 state.setColourwithAlignPanel(jmol
625 .isUsedforcolourby(ap));
626 if (!jmolViewIds.contains(state.getViewId()))
628 // Make sure we only store a Jmol state once in each XML
630 jmolViewIds.addElement(state.getViewId());
631 state.setContent(statestring.replaceAll("\n", ""));
635 state.setContent("# duplicate state");
637 pdb.addStructureState(state);
644 if (matchedFile != null || entry.getFile() != null)
646 if (entry.getFile() != null)
649 matchedFile = entry.getFile();
651 pdb.setFile(matchedFile); // entry.getFile());
652 if (pdbfiles == null)
654 pdbfiles = new Vector();
657 if (!pdbfiles.contains(entry.getId()))
659 pdbfiles.addElement(entry.getId());
662 File file = new File(matchedFile);
663 if (file.exists() && jout != null)
665 byte[] data = new byte[(int) file.length()];
666 jout.putNextEntry(new JarEntry(entry.getId()));
667 DataInputStream dis = new DataInputStream(
668 new FileInputStream(file));
671 DataOutputStream dout = new DataOutputStream(jout);
672 dout.write(data, 0, data.length);
676 } catch (Exception ex)
678 ex.printStackTrace();
684 if (entry.getProperty() != null)
686 PdbentryItem item = new PdbentryItem();
687 Hashtable properties = entry.getProperty();
688 Enumeration en2 = properties.keys();
689 while (en2.hasMoreElements())
691 Property prop = new Property();
692 String key = en2.nextElement().toString();
694 prop.setValue(properties.get(key).toString());
695 item.addProperty(prop);
697 pdb.addPdbentryItem(item);
707 if (av.hasHiddenRows)
712 if (jal.getCodonFrames() != null && jal.getCodonFrames().length > 0)
714 jalview.datamodel.AlignedCodonFrame[] jac = jal.getCodonFrames();
715 for (int i = 0; i < jac.length; i++)
717 AlcodonFrame alc = new AlcodonFrame();
718 vamsasSet.addAlcodonFrame(alc);
719 for (int p = 0; p < jac[i].aaWidth; p++)
721 Alcodon cmap = new Alcodon();
722 if (jac[i].codons[p] != null)
724 // Null codons indicate a gapped column in the translated peptide
726 cmap.setPos1(jac[i].codons[p][0]);
727 cmap.setPos2(jac[i].codons[p][1]);
728 cmap.setPos3(jac[i].codons[p][2]);
730 alc.addAlcodon(cmap);
732 if (jac[i].getProtMappings() != null
733 && jac[i].getProtMappings().length > 0)
735 SequenceI[] dnas = jac[i].getdnaSeqs();
736 jalview.datamodel.Mapping[] pmaps = jac[i].getProtMappings();
737 for (int m = 0; m < pmaps.length; m++)
739 AlcodMap alcmap = new AlcodMap();
740 alcmap.setDnasq(seqHash(dnas[m]));
741 alcmap.setMapping(createVamsasMapping(pmaps[m], dnas[m], null,
743 alc.addAlcodMap(alcmap);
750 // /////////////////////////////////
751 if (av.currentTree != null)
753 // FIND ANY ASSOCIATED TREES
754 // NOT IMPLEMENTED FOR HEADLESS STATE AT PRESENT
755 if (Desktop.desktop != null)
757 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
759 for (int t = 0; t < frames.length; t++)
761 if (frames[t] instanceof TreePanel)
763 TreePanel tp = (TreePanel) frames[t];
765 if (tp.treeCanvas.av.alignment == jal)
767 Tree tree = new Tree();
768 tree.setTitle(tp.getTitle());
769 tree.setCurrentTree((av.currentTree == tp.getTree()));
770 tree.setNewick(tp.getTree().toString());
771 tree.setThreshold(tp.treeCanvas.threshold);
773 tree.setFitToWindow(tp.fitToWindow.getState());
774 tree.setFontName(tp.getTreeFont().getName());
775 tree.setFontSize(tp.getTreeFont().getSize());
776 tree.setFontStyle(tp.getTreeFont().getStyle());
777 tree.setMarkUnlinked(tp.placeholdersMenu.getState());
779 tree.setShowBootstrap(tp.bootstrapMenu.getState());
780 tree.setShowDistances(tp.distanceMenu.getState());
782 tree.setHeight(tp.getHeight());
783 tree.setWidth(tp.getWidth());
784 tree.setXpos(tp.getX());
785 tree.setYpos(tp.getY());
786 tree.setId(makeHashCode(tp, null));
796 * store forward refs from an annotationRow to any groups
798 IdentityHashMap groupRefs = new IdentityHashMap();
799 if (jal.getAlignmentAnnotation() != null)
801 jalview.datamodel.AlignmentAnnotation[] aa = jal
802 .getAlignmentAnnotation();
804 for (int i = 0; i < aa.length; i++)
806 Annotation an = new Annotation();
808 if (aa[i].annotationId != null)
810 annotationIds.put(aa[i].annotationId, aa[i]);
813 an.setId(aa[i].annotationId);
815 an.setVisible(aa[i].visible);
817 an.setDescription(aa[i].description);
819 if (aa[i].sequenceRef != null)
821 // TODO later annotation sequenceRef should be the XML ID of the
822 // sequence rather than its display name
823 an.setSequenceRef(aa[i].sequenceRef.getName());
825 if (aa[i].groupRef != null)
827 Object groupIdr = groupRefs.get(aa[i].groupRef);
828 if (groupIdr == null)
830 // make a locally unique String
831 groupRefs.put(aa[i].groupRef,
832 groupIdr = ("" + System.currentTimeMillis()
833 + aa[i].groupRef.getName() + groupRefs.size()));
835 an.setGroupRef(groupIdr.toString());
837 if (aa[i] == av.quality || aa[i] == av.conservation
838 || aa[i] == av.consensus || aa[i].autoCalculated)
840 // new way of indicating autocalculated annotation -
841 an.setAutoCalculated(aa[i].autoCalculated);
842 // write a stub for this annotation - indicate presence of autocalc
844 an.setLabel(aa[i].label);
846 vamsasSet.addAnnotation(an);
853 an.setGraphType(aa[i].graph);
854 an.setGraphGroup(aa[i].graphGroup);
855 if (aa[i].getThreshold() != null)
857 ThresholdLine line = new ThresholdLine();
858 line.setLabel(aa[i].getThreshold().label);
859 line.setValue(aa[i].getThreshold().value);
860 line.setColour(aa[i].getThreshold().colour.getRGB());
861 an.setThresholdLine(line);
869 an.setLabel(aa[i].label);
870 if (aa[i].hasScore())
872 an.setScore(aa[i].getScore());
874 AnnotationElement ae;
875 if (aa[i].annotations != null)
877 an.setScoreOnly(false);
878 for (int a = 0; a < aa[i].annotations.length; a++)
880 if ((aa[i] == null) || (aa[i].annotations[a] == null))
885 ae = new AnnotationElement();
886 if (aa[i].annotations[a].description != null)
887 ae.setDescription(aa[i].annotations[a].description);
888 if (aa[i].annotations[a].displayCharacter != null)
889 ae.setDisplayCharacter(aa[i].annotations[a].displayCharacter);
891 if (!Float.isNaN(aa[i].annotations[a].value))
892 ae.setValue(aa[i].annotations[a].value);
895 if (aa[i].annotations[a].secondaryStructure != ' '
896 && aa[i].annotations[a].secondaryStructure != '\0')
897 ae.setSecondaryStructure(aa[i].annotations[a].secondaryStructure
900 if (aa[i].annotations[a].colour != null
901 && aa[i].annotations[a].colour != java.awt.Color.black)
903 ae.setColour(aa[i].annotations[a].colour.getRGB());
906 an.addAnnotationElement(ae);
911 an.setScoreOnly(true);
913 vamsasSet.addAnnotation(an);
917 if (jal.getGroups() != null)
919 JGroup[] groups = new JGroup[jal.getGroups().size()];
921 for (int i = 0; i < groups.length; i++)
923 groups[i] = new JGroup();
925 jalview.datamodel.SequenceGroup sg = (jalview.datamodel.SequenceGroup) jal
926 .getGroups().elementAt(i);
927 groups[i].setStart(sg.getStartRes());
928 groups[i].setEnd(sg.getEndRes());
929 groups[i].setName(sg.getName());
930 if (groupRefs.containsKey(sg))
932 // group has references so set it's ID field
933 groups[i].setId(groupRefs.get(sg).toString());
937 if (sg.cs.conservationApplied())
939 groups[i].setConsThreshold(sg.cs.getConservationInc());
941 if (sg.cs instanceof jalview.schemes.UserColourScheme)
943 groups[i].setColour(SetUserColourScheme(sg.cs, userColours,
949 .setColour(ColourSchemeProperty.getColourName(sg.cs));
952 else if (sg.cs instanceof jalview.schemes.AnnotationColourGradient)
955 .setColour(ColourSchemeProperty
956 .getColourName(((jalview.schemes.AnnotationColourGradient) sg.cs)
959 else if (sg.cs instanceof jalview.schemes.UserColourScheme)
962 .setColour(SetUserColourScheme(sg.cs, userColours, jms));
966 groups[i].setColour(ColourSchemeProperty.getColourName(sg.cs));
969 groups[i].setPidThreshold(sg.cs.getThreshold());
972 groups[i].setOutlineColour(sg.getOutlineColour().getRGB());
973 groups[i].setDisplayBoxes(sg.getDisplayBoxes());
974 groups[i].setDisplayText(sg.getDisplayText());
975 groups[i].setColourText(sg.getColourText());
976 groups[i].setTextCol1(sg.textColour.getRGB());
977 groups[i].setTextCol2(sg.textColour2.getRGB());
978 groups[i].setTextColThreshold(sg.thresholdTextColour);
979 groups[i].setShowUnconserved(sg.getShowNonconserved());
980 groups[i].setIgnoreGapsinConsensus(sg.getIgnoreGapsConsensus());
981 groups[i].setShowConsensusHistogram(sg.isShowConsensusHistogram());
982 groups[i].setShowSequenceLogo(sg.isShowSequenceLogo());
983 for (int s = 0; s < sg.getSize(); s++)
985 jalview.datamodel.Sequence seq = (jalview.datamodel.Sequence) sg
987 groups[i].addSeq(seqHash(seq));
991 jms.setJGroup(groups);
994 // /////////SAVE VIEWPORT
995 Viewport view = new Viewport();
996 view.setTitle(ap.alignFrame.getTitle());
997 view.setSequenceSetId(makeHashCode(av.getSequenceSetId(),
998 av.getSequenceSetId()));
999 view.setId(av.getViewId());
1000 view.setViewName(av.viewName);
1001 view.setGatheredViews(av.gatherViewsHere);
1003 if (ap.av.explodedPosition != null)
1005 view.setXpos(av.explodedPosition.x);
1006 view.setYpos(av.explodedPosition.y);
1007 view.setWidth(av.explodedPosition.width);
1008 view.setHeight(av.explodedPosition.height);
1012 view.setXpos(ap.alignFrame.getBounds().x);
1013 view.setYpos(ap.alignFrame.getBounds().y);
1014 view.setWidth(ap.alignFrame.getBounds().width);
1015 view.setHeight(ap.alignFrame.getBounds().height);
1018 view.setStartRes(av.startRes);
1019 view.setStartSeq(av.startSeq);
1021 if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme)
1023 view.setBgColour(SetUserColourScheme(av.getGlobalColourScheme(),
1026 else if (av.getGlobalColourScheme() instanceof jalview.schemes.AnnotationColourGradient)
1028 jalview.schemes.AnnotationColourGradient acg = (jalview.schemes.AnnotationColourGradient) av
1029 .getGlobalColourScheme();
1031 AnnotationColours ac = new AnnotationColours();
1032 ac.setAboveThreshold(acg.getAboveThreshold());
1033 ac.setThreshold(acg.getAnnotationThreshold());
1034 ac.setAnnotation(acg.getAnnotation());
1035 if (acg.getBaseColour() instanceof jalview.schemes.UserColourScheme)
1037 ac.setColourScheme(SetUserColourScheme(acg.getBaseColour(),
1042 ac.setColourScheme(ColourSchemeProperty.getColourName(acg
1046 ac.setMaxColour(acg.getMaxColour().getRGB());
1047 ac.setMinColour(acg.getMinColour().getRGB());
1048 view.setAnnotationColours(ac);
1049 view.setBgColour("AnnotationColourGradient");
1053 view.setBgColour(ColourSchemeProperty.getColourName(av
1054 .getGlobalColourScheme()));
1057 ColourSchemeI cs = av.getGlobalColourScheme();
1061 if (cs.conservationApplied())
1063 view.setConsThreshold(cs.getConservationInc());
1064 if (cs instanceof jalview.schemes.UserColourScheme)
1066 view.setBgColour(SetUserColourScheme(cs, userColours, jms));
1070 if (cs instanceof ResidueColourScheme)
1072 view.setPidThreshold(cs.getThreshold());
1076 view.setConservationSelected(av.getConservationSelected());
1077 view.setPidSelected(av.getAbovePIDThreshold());
1078 view.setFontName(av.font.getName());
1079 view.setFontSize(av.font.getSize());
1080 view.setFontStyle(av.font.getStyle());
1081 view.setRenderGaps(av.renderGaps);
1082 view.setShowAnnotation(av.getShowAnnotation());
1083 view.setShowBoxes(av.getShowBoxes());
1084 view.setShowColourText(av.getColourText());
1085 view.setShowFullId(av.getShowJVSuffix());
1086 view.setRightAlignIds(av.rightAlignIds);
1087 view.setShowSequenceFeatures(av.showSequenceFeatures);
1088 view.setShowText(av.getShowText());
1089 view.setShowUnconserved(av.getShowUnconserved());
1090 view.setWrapAlignment(av.getWrapAlignment());
1091 view.setTextCol1(av.textColour.getRGB());
1092 view.setTextCol2(av.textColour2.getRGB());
1093 view.setTextColThreshold(av.thresholdTextColour);
1094 view.setShowConsensusHistogram(av.isShowConsensusHistogram());
1095 view.setShowSequenceLogo(av.isShowSequenceLogo());
1096 view.setShowGroupConsensus(av.isShowGroupConsensus());
1097 view.setShowGroupConservation(av.isShowGroupConservation());
1098 view.setShowNPfeatureTooltip(av.isShowNpFeats());
1099 view.setShowDbRefTooltip(av.isShowDbRefs());
1100 view.setFollowHighlight(av.followHighlight);
1101 view.setFollowSelection(av.followSelection);
1102 view.setIgnoreGapsinConsensus(av.getIgnoreGapsConsensus());
1103 if (av.featuresDisplayed != null)
1105 jalview.schemabinding.version2.FeatureSettings fs = new jalview.schemabinding.version2.FeatureSettings();
1107 String[] renderOrder = ap.seqPanel.seqCanvas.getFeatureRenderer().renderOrder;
1109 Vector settingsAdded = new Vector();
1110 Object gstyle = null;
1111 GraduatedColor gcol = null;
1112 for (int ro = 0; ro < renderOrder.length; ro++)
1114 gstyle = ap.seqPanel.seqCanvas.getFeatureRenderer()
1115 .getFeatureStyle(renderOrder[ro]);
1116 Setting setting = new Setting();
1117 setting.setType(renderOrder[ro]);
1118 if (gstyle instanceof GraduatedColor)
1120 gcol = (GraduatedColor) gstyle;
1121 setting.setColour(gcol.getMaxColor().getRGB());
1122 setting.setMincolour(gcol.getMinColor().getRGB());
1123 setting.setMin(gcol.getMin());
1124 setting.setMax(gcol.getMax());
1125 setting.setColourByLabel(gcol.isColourByLabel());
1126 setting.setAutoScale(gcol.isAutoScale());
1127 setting.setThreshold(gcol.getThresh());
1128 setting.setThreshstate(gcol.getThreshType());
1132 setting.setColour(ap.seqPanel.seqCanvas.getFeatureRenderer()
1133 .getColour(renderOrder[ro]).getRGB());
1136 setting.setDisplay(av.featuresDisplayed
1137 .containsKey(renderOrder[ro]));
1138 float rorder = ap.seqPanel.seqCanvas.getFeatureRenderer().getOrder(
1142 setting.setOrder(rorder);
1144 fs.addSetting(setting);
1145 settingsAdded.addElement(renderOrder[ro]);
1148 // Make sure we save none displayed feature settings
1149 Enumeration en = ap.seqPanel.seqCanvas.getFeatureRenderer().featureColours
1151 while (en.hasMoreElements())
1153 String key = en.nextElement().toString();
1154 if (settingsAdded.contains(key))
1159 Setting setting = new Setting();
1160 setting.setType(key);
1161 setting.setColour(ap.seqPanel.seqCanvas.getFeatureRenderer()
1162 .getColour(key).getRGB());
1164 setting.setDisplay(false);
1165 float rorder = ap.seqPanel.seqCanvas.getFeatureRenderer().getOrder(
1169 setting.setOrder(rorder);
1171 fs.addSetting(setting);
1172 settingsAdded.addElement(key);
1174 en = ap.seqPanel.seqCanvas.getFeatureRenderer().featureGroups.keys();
1175 Vector groupsAdded = new Vector();
1176 while (en.hasMoreElements())
1178 String grp = en.nextElement().toString();
1179 if (groupsAdded.contains(grp))
1183 Group g = new Group();
1185 g.setDisplay(((Boolean) ap.seqPanel.seqCanvas.getFeatureRenderer().featureGroups
1186 .get(grp)).booleanValue());
1188 groupsAdded.addElement(grp);
1190 jms.setFeatureSettings(fs);
1194 if (av.hasHiddenColumns)
1196 if (av.getColumnSelection() == null
1197 || av.getColumnSelection().getHiddenColumns() == null)
1199 warn("REPORT BUG: avoided null columnselection bug (DMAM reported). Please contact Jim about this.");
1203 for (int c = 0; c < av.getColumnSelection().getHiddenColumns()
1206 int[] region = (int[]) av.getColumnSelection().getHiddenColumns()
1208 HiddenColumns hc = new HiddenColumns();
1209 hc.setStart(region[0]);
1210 hc.setEnd(region[1]);
1211 view.addHiddenColumns(hc);
1216 jms.addViewport(view);
1218 object.setJalviewModelSequence(jms);
1219 object.getVamsasModel().addSequenceSet(vamsasSet);
1221 if (jout != null && fileName != null)
1223 // We may not want to write the object to disk,
1224 // eg we can copy the alignViewport to a new view object
1225 // using save and then load
1228 JarEntry entry = new JarEntry(fileName);
1229 jout.putNextEntry(entry);
1230 PrintWriter pout = new PrintWriter(new OutputStreamWriter(jout,
1232 org.exolab.castor.xml.Marshaller marshaller = new org.exolab.castor.xml.Marshaller(
1234 marshaller.marshal(object);
1237 } catch (Exception ex)
1239 // TODO: raise error in GUI if marshalling failed.
1240 ex.printStackTrace();
1247 * External mapping between jalview objects and objects yielding a valid and
1248 * unique object ID string. This is null for normal Jalview project IO, but
1249 * non-null when a jalview project is being read or written as part of a
1252 IdentityHashMap jv2vobj = null;
1255 * Construct a unique ID for jvobj using either existing bindings or if none
1256 * exist, the result of the hashcode call for the object.
1259 * jalview data object
1260 * @return unique ID for referring to jvobj
1262 private String makeHashCode(Object jvobj, String altCode)
1264 if (jv2vobj != null)
1266 Object id = jv2vobj.get(jvobj);
1269 return id.toString();
1271 // check string ID mappings
1272 if (jvids2vobj != null && jvobj instanceof String)
1274 id = jvids2vobj.get(jvobj);
1278 return id.toString();
1280 // give up and warn that something has gone wrong
1281 warn("Cannot find ID for object in external mapping : " + jvobj);
1287 * return local jalview object mapped to ID, if it exists
1291 * @return null or object bound to idcode
1293 private Object retrieveExistingObj(String idcode)
1295 if (idcode != null && vobj2jv != null)
1297 return vobj2jv.get(idcode);
1303 * binding from ID strings from external mapping table to jalview data model
1306 private Hashtable vobj2jv;
1308 private Sequence createVamsasSequence(String id, SequenceI jds)
1310 return createVamsasSequence(true, id, jds, null);
1313 private Sequence createVamsasSequence(boolean recurse, String id,
1314 SequenceI jds, SequenceI parentseq)
1316 Sequence vamsasSeq = new Sequence();
1317 vamsasSeq.setId(id);
1318 vamsasSeq.setName(jds.getName());
1319 vamsasSeq.setSequence(jds.getSequenceAsString());
1320 vamsasSeq.setDescription(jds.getDescription());
1321 jalview.datamodel.DBRefEntry[] dbrefs = null;
1322 if (jds.getDatasetSequence() != null)
1324 vamsasSeq.setDsseqid(seqHash(jds.getDatasetSequence()));
1325 if (jds.getDatasetSequence().getDBRef() != null)
1327 dbrefs = jds.getDatasetSequence().getDBRef();
1332 vamsasSeq.setDsseqid(id); // so we can tell which sequences really are
1333 // dataset sequences only
1334 dbrefs = jds.getDBRef();
1338 for (int d = 0; d < dbrefs.length; d++)
1340 DBRef dbref = new DBRef();
1341 dbref.setSource(dbrefs[d].getSource());
1342 dbref.setVersion(dbrefs[d].getVersion());
1343 dbref.setAccessionId(dbrefs[d].getAccessionId());
1344 if (dbrefs[d].hasMap())
1346 Mapping mp = createVamsasMapping(dbrefs[d].getMap(), parentseq,
1348 dbref.setMapping(mp);
1350 vamsasSeq.addDBRef(dbref);
1356 private Mapping createVamsasMapping(jalview.datamodel.Mapping jmp,
1357 SequenceI parentseq, SequenceI jds, boolean recurse)
1360 if (jmp.getMap() != null)
1364 jalview.util.MapList mlst = jmp.getMap();
1365 int r[] = mlst.getFromRanges();
1366 for (int s = 0; s < r.length; s += 2)
1368 MapListFrom mfrom = new MapListFrom();
1369 mfrom.setStart(r[s]);
1370 mfrom.setEnd(r[s + 1]);
1371 mp.addMapListFrom(mfrom);
1373 r = mlst.getToRanges();
1374 for (int s = 0; s < r.length; s += 2)
1376 MapListTo mto = new MapListTo();
1378 mto.setEnd(r[s + 1]);
1379 mp.addMapListTo(mto);
1381 mp.setMapFromUnit(mlst.getFromRatio());
1382 mp.setMapToUnit(mlst.getToRatio());
1383 if (jmp.getTo() != null)
1385 MappingChoice mpc = new MappingChoice();
1387 && (parentseq != jmp.getTo() || parentseq
1388 .getDatasetSequence() != jmp.getTo()))
1390 mpc.setSequence(createVamsasSequence(false, seqHash(jmp.getTo()),
1396 SequenceI ps = null;
1397 if (parentseq != jmp.getTo()
1398 && parentseq.getDatasetSequence() != jmp.getTo())
1400 // chaining dbref rather than a handshaking one
1401 jmpid = seqHash(ps = jmp.getTo());
1405 jmpid = seqHash(ps = parentseq);
1407 mpc.setDseqFor(jmpid);
1408 if (!seqRefIds.containsKey(mpc.getDseqFor()))
1410 jalview.bin.Cache.log.debug("creatign new DseqFor ID");
1411 seqRefIds.put(mpc.getDseqFor(), ps);
1415 jalview.bin.Cache.log.debug("reusing DseqFor ID");
1418 mp.setMappingChoice(mpc);
1424 String SetUserColourScheme(jalview.schemes.ColourSchemeI cs,
1425 Vector userColours, JalviewModelSequence jms)
1428 jalview.schemes.UserColourScheme ucs = (jalview.schemes.UserColourScheme) cs;
1429 boolean newucs = false;
1430 if (!userColours.contains(ucs))
1432 userColours.add(ucs);
1435 id = "ucs" + userColours.indexOf(ucs);
1438 // actually create the scheme's entry in the XML model
1439 java.awt.Color[] colours = ucs.getColours();
1440 jalview.schemabinding.version2.UserColours uc = new jalview.schemabinding.version2.UserColours();
1441 jalview.schemabinding.version2.UserColourScheme jbucs = new jalview.schemabinding.version2.UserColourScheme();
1443 for (int i = 0; i < colours.length; i++)
1445 jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();
1446 col.setName(ResidueProperties.aa[i]);
1447 col.setRGB(jalview.util.Format.getHexString(colours[i]));
1448 jbucs.addColour(col);
1450 if (ucs.getLowerCaseColours() != null)
1452 colours = ucs.getLowerCaseColours();
1453 for (int i = 0; i < colours.length; i++)
1455 jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();
1456 col.setName(ResidueProperties.aa[i].toLowerCase());
1457 col.setRGB(jalview.util.Format.getHexString(colours[i]));
1458 jbucs.addColour(col);
1463 uc.setUserColourScheme(jbucs);
1464 jms.addUserColours(uc);
1470 jalview.schemes.UserColourScheme GetUserColourScheme(
1471 JalviewModelSequence jms, String id)
1473 UserColours[] uc = jms.getUserColours();
1474 UserColours colours = null;
1476 for (int i = 0; i < uc.length; i++)
1478 if (uc[i].getId().equals(id))
1486 java.awt.Color[] newColours = new java.awt.Color[24];
1488 for (int i = 0; i < 24; i++)
1490 newColours[i] = new java.awt.Color(Integer.parseInt(colours
1491 .getUserColourScheme().getColour(i).getRGB(), 16));
1494 jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(
1497 if (colours.getUserColourScheme().getColourCount() > 24)
1499 newColours = new java.awt.Color[23];
1500 for (int i = 0; i < 23; i++)
1502 newColours[i] = new java.awt.Color(Integer.parseInt(colours
1503 .getUserColourScheme().getColour(i + 24).getRGB(), 16));
1505 ucs.setLowerCaseColours(newColours);
1512 * contains last error message (if any) encountered by XML loader.
1514 String errorMessage = null;
1517 * flag to control whether the Jalview2XML_V1 parser should be deferred to if
1518 * exceptions are raised during project XML parsing
1520 public boolean attemptversion1parse = true;
1523 * Load a jalview project archive from a jar file
1526 * - HTTP URL or filename
1528 public AlignFrame LoadJalviewAlign(final String file)
1531 jalview.gui.AlignFrame af = null;
1535 // UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
1536 // Workaround is to make sure caller implements the JarInputStreamProvider
1538 // so we can re-open the jar input stream for each entry.
1540 jarInputStreamProvider jprovider = createjarInputStreamProvider(file);
1541 af = LoadJalviewAlign(jprovider);
1542 } catch (MalformedURLException e)
1544 errorMessage = "Invalid URL format for '" + file + "'";
1550 private jarInputStreamProvider createjarInputStreamProvider(
1551 final String file) throws MalformedURLException
1554 errorMessage = null;
1555 uniqueSetSuffix = null;
1557 viewportsAdded = null;
1558 frefedSequence = null;
1560 if (file.startsWith("http://"))
1562 url = new URL(file);
1564 final URL _url = url;
1565 return new jarInputStreamProvider()
1568 public JarInputStream getJarInputStream() throws IOException
1572 return new JarInputStream(_url.openStream());
1576 return new JarInputStream(new FileInputStream(file));
1580 public String getFilename()
1588 * Recover jalview session from a jalview project archive. Caller may
1589 * initialise uniqueSetSuffix, seqRefIds, viewportsAdded and frefedSequence
1590 * themselves. Any null fields will be initialised with default values,
1591 * non-null fields are left alone.
1596 public AlignFrame LoadJalviewAlign(final jarInputStreamProvider jprovider)
1598 errorMessage = null;
1599 if (uniqueSetSuffix == null)
1601 uniqueSetSuffix = System.currentTimeMillis() % 100000 + "";
1603 if (seqRefIds == null)
1605 seqRefIds = new Hashtable();
1607 if (viewportsAdded == null)
1609 viewportsAdded = new Hashtable();
1611 if (frefedSequence == null)
1613 frefedSequence = new Vector();
1616 jalview.gui.AlignFrame af = null;
1617 Hashtable gatherToThisFrame = new Hashtable();
1618 final String file = jprovider.getFilename();
1621 JarInputStream jin = null;
1622 JarEntry jarentry = null;
1627 jin = jprovider.getJarInputStream();
1628 for (int i = 0; i < entryCount; i++)
1630 jarentry = jin.getNextJarEntry();
1633 if (jarentry != null && jarentry.getName().endsWith(".xml"))
1635 InputStreamReader in = new InputStreamReader(jin, "UTF-8");
1636 JalviewModel object = new JalviewModel();
1638 Unmarshaller unmar = new Unmarshaller(object);
1639 unmar.setValidation(false);
1640 object = (JalviewModel) unmar.unmarshal(in);
1641 if (true) // !skipViewport(object))
1643 af = LoadFromObject(object, file, true, jprovider);
1644 if (af.viewport.gatherViewsHere)
1646 gatherToThisFrame.put(af.viewport.getSequenceSetId(), af);
1651 else if (jarentry != null)
1653 // Some other file here.
1656 } while (jarentry != null);
1657 resolveFrefedSequences();
1658 } catch (java.io.FileNotFoundException ex)
1660 ex.printStackTrace();
1661 errorMessage = "Couldn't locate Jalview XML file : " + file;
1662 System.err.println("Exception whilst loading jalview XML file : "
1664 } catch (java.net.UnknownHostException ex)
1666 ex.printStackTrace();
1667 errorMessage = "Couldn't locate Jalview XML file : " + file;
1668 System.err.println("Exception whilst loading jalview XML file : "
1670 } catch (Exception ex)
1672 System.err.println("Parsing as Jalview Version 2 file failed.");
1673 ex.printStackTrace(System.err);
1674 if (attemptversion1parse)
1676 // Is Version 1 Jar file?
1679 af = new Jalview2XML_V1(raiseGUI).LoadJalviewAlign(jprovider);
1680 } catch (Exception ex2)
1682 System.err.println("Exception whilst loading as jalviewXMLV1:");
1683 ex2.printStackTrace();
1687 if (Desktop.instance != null)
1689 Desktop.instance.stopLoading();
1693 System.out.println("Successfully loaded archive file");
1696 ex.printStackTrace();
1698 System.err.println("Exception whilst loading jalview XML file : "
1700 } catch (OutOfMemoryError e)
1702 // Don't use the OOM Window here
1703 errorMessage = "Out of memory loading jalview XML file";
1704 System.err.println("Out of memory whilst loading jalview XML file");
1705 e.printStackTrace();
1708 if (Desktop.instance != null)
1710 Desktop.instance.stopLoading();
1713 Enumeration en = gatherToThisFrame.elements();
1714 while (en.hasMoreElements())
1716 Desktop.instance.gatherViews((AlignFrame) en.nextElement());
1718 if (errorMessage != null)
1726 * check errorMessage for a valid error message and raise an error box in the
1727 * GUI or write the current errorMessage to stderr and then clear the error
1730 protected void reportErrors()
1732 reportErrors(false);
1735 protected void reportErrors(final boolean saving)
1737 if (errorMessage != null)
1739 final String finalErrorMessage = errorMessage;
1742 javax.swing.SwingUtilities.invokeLater(new Runnable()
1746 JOptionPane.showInternalMessageDialog(Desktop.desktop,
1747 finalErrorMessage, "Error "
1748 + (saving ? "saving" : "loading")
1749 + " Jalview file", JOptionPane.WARNING_MESSAGE);
1755 System.err.println("Problem loading Jalview file: " + errorMessage);
1758 errorMessage = null;
1761 Hashtable alreadyLoadedPDB;
1764 * when set, local views will be updated from view stored in JalviewXML
1765 * Currently (28th Sep 2008) things will go horribly wrong in vamsas document
1766 * sync if this is set to true.
1768 private boolean updateLocalViews = false;
1770 String loadPDBFile(jarInputStreamProvider jprovider, String pdbId)
1772 if (alreadyLoadedPDB == null)
1773 alreadyLoadedPDB = new Hashtable();
1775 if (alreadyLoadedPDB.containsKey(pdbId))
1776 return alreadyLoadedPDB.get(pdbId).toString();
1780 JarInputStream jin = jprovider.getJarInputStream();
1782 * if (jprovider.startsWith("http://")) { jin = new JarInputStream(new
1783 * URL(jprovider).openStream()); } else { jin = new JarInputStream(new
1784 * FileInputStream(jprovider)); }
1787 JarEntry entry = null;
1790 entry = jin.getNextJarEntry();
1791 } while (entry != null && !entry.getName().equals(pdbId));
1794 BufferedReader in = new BufferedReader(new InputStreamReader(jin));
1795 File outFile = File.createTempFile("jalview_pdb", ".txt");
1796 outFile.deleteOnExit();
1797 PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
1800 while ((data = in.readLine()) != null)
1807 } catch (Exception foo)
1813 alreadyLoadedPDB.put(pdbId, outFile.getAbsolutePath());
1814 return outFile.getAbsolutePath();
1818 warn("Couldn't find PDB file entry in Jalview Jar for " + pdbId);
1820 } catch (Exception ex)
1822 ex.printStackTrace();
1829 * Load alignment frame from jalview XML DOM object
1834 * filename source string
1835 * @param loadTreesAndStructures
1836 * when false only create Viewport
1838 * data source provider
1839 * @return alignment frame created from view stored in DOM
1841 AlignFrame LoadFromObject(JalviewModel object, String file,
1842 boolean loadTreesAndStructures, jarInputStreamProvider jprovider)
1844 SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);
1845 Sequence[] vamsasSeq = vamsasSet.getSequence();
1847 JalviewModelSequence jms = object.getJalviewModelSequence();
1849 Viewport view = jms.getViewport(0);
1850 // ////////////////////////////////
1853 Vector hiddenSeqs = null;
1854 jalview.datamodel.Sequence jseq;
1856 ArrayList tmpseqs = new ArrayList();
1858 boolean multipleView = false;
1860 JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq();
1861 int vi = 0; // counter in vamsasSeq array
1862 for (int i = 0; i < JSEQ.length; i++)
1864 String seqId = JSEQ[i].getId();
1866 if (seqRefIds.get(seqId) != null)
1868 tmpseqs.add((jalview.datamodel.Sequence) seqRefIds.get(seqId));
1869 multipleView = true;
1873 jseq = new jalview.datamodel.Sequence(vamsasSeq[vi].getName(),
1874 vamsasSeq[vi].getSequence());
1875 jseq.setDescription(vamsasSeq[vi].getDescription());
1876 jseq.setStart(JSEQ[i].getStart());
1877 jseq.setEnd(JSEQ[i].getEnd());
1878 jseq.setVamsasId(uniqueSetSuffix + seqId);
1879 seqRefIds.put(vamsasSeq[vi].getId(), jseq);
1884 if (JSEQ[i].getHidden())
1886 if (hiddenSeqs == null)
1888 hiddenSeqs = new Vector();
1891 hiddenSeqs.addElement((jalview.datamodel.Sequence) seqRefIds
1898 // Create the alignment object from the sequence set
1899 // ///////////////////////////////
1900 jalview.datamodel.Sequence[] orderedSeqs = new jalview.datamodel.Sequence[tmpseqs
1903 tmpseqs.toArray(orderedSeqs);
1905 jalview.datamodel.Alignment al = new jalview.datamodel.Alignment(
1908 // / Add the alignment properties
1909 for (int i = 0; i < vamsasSet.getSequenceSetPropertiesCount(); i++)
1911 SequenceSetProperties ssp = vamsasSet.getSequenceSetProperties(i);
1912 al.setProperty(ssp.getKey(), ssp.getValue());
1916 // SequenceFeatures are added to the DatasetSequence,
1917 // so we must create or recover the dataset before loading features
1918 // ///////////////////////////////
1919 if (vamsasSet.getDatasetId() == null || vamsasSet.getDatasetId() == "")
1921 // older jalview projects do not have a dataset id.
1922 al.setDataset(null);
1926 recoverDatasetFor(vamsasSet, al);
1928 // ///////////////////////////////
1930 Hashtable pdbloaded = new Hashtable();
1933 // load sequence features, database references and any associated PDB
1934 // structures for the alignment
1935 for (int i = 0; i < vamsasSeq.length; i++)
1937 if (JSEQ[i].getFeaturesCount() > 0)
1939 Features[] features = JSEQ[i].getFeatures();
1940 for (int f = 0; f < features.length; f++)
1942 jalview.datamodel.SequenceFeature sf = new jalview.datamodel.SequenceFeature(
1943 features[f].getType(), features[f].getDescription(),
1944 features[f].getStatus(), features[f].getBegin(),
1945 features[f].getEnd(), features[f].getFeatureGroup());
1947 sf.setScore(features[f].getScore());
1948 for (int od = 0; od < features[f].getOtherDataCount(); od++)
1950 OtherData keyValue = features[f].getOtherData(od);
1951 if (keyValue.getKey().startsWith("LINK"))
1953 sf.addLink(keyValue.getValue());
1957 sf.setValue(keyValue.getKey(), keyValue.getValue());
1962 al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf);
1965 if (vamsasSeq[i].getDBRefCount() > 0)
1967 addDBRefs(al.getSequenceAt(i).getDatasetSequence(), vamsasSeq[i]);
1969 if (JSEQ[i].getPdbidsCount() > 0)
1971 Pdbids[] ids = JSEQ[i].getPdbids();
1972 for (int p = 0; p < ids.length; p++)
1974 jalview.datamodel.PDBEntry entry = new jalview.datamodel.PDBEntry();
1975 entry.setId(ids[p].getId());
1976 entry.setType(ids[p].getType());
1977 if (ids[p].getFile() != null)
1979 if (!pdbloaded.containsKey(ids[p].getFile()))
1981 entry.setFile(loadPDBFile(jprovider, ids[p].getId()));
1985 entry.setFile(pdbloaded.get(ids[p].getId()).toString());
1989 al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
1993 } // end !multipleview
1995 // ///////////////////////////////
1996 // LOAD SEQUENCE MAPPINGS
1998 if (vamsasSet.getAlcodonFrameCount() > 0)
2000 // TODO Potentially this should only be done once for all views of an
2002 AlcodonFrame[] alc = vamsasSet.getAlcodonFrame();
2003 for (int i = 0; i < alc.length; i++)
2005 jalview.datamodel.AlignedCodonFrame cf = new jalview.datamodel.AlignedCodonFrame(
2006 alc[i].getAlcodonCount());
2007 if (alc[i].getAlcodonCount() > 0)
2009 Alcodon[] alcods = alc[i].getAlcodon();
2010 for (int p = 0; p < cf.codons.length; p++)
2012 if (alcods[p].hasPos1() && alcods[p].hasPos2()
2013 && alcods[p].hasPos3())
2015 // translated codons require three valid positions
2016 cf.codons[p] = new int[3];
2017 cf.codons[p][0] = (int) alcods[p].getPos1();
2018 cf.codons[p][1] = (int) alcods[p].getPos2();
2019 cf.codons[p][2] = (int) alcods[p].getPos3();
2023 cf.codons[p] = null;
2027 if (alc[i].getAlcodMapCount() > 0)
2029 AlcodMap[] maps = alc[i].getAlcodMap();
2030 for (int m = 0; m < maps.length; m++)
2032 SequenceI dnaseq = (SequenceI) seqRefIds
2033 .get(maps[m].getDnasq());
2035 jalview.datamodel.Mapping mapping = null;
2036 // attach to dna sequence reference.
2037 if (maps[m].getMapping() != null)
2039 mapping = addMapping(maps[m].getMapping());
2043 cf.addMap(dnaseq, mapping.getTo(), mapping.getMap());
2048 frefedSequence.add(new Object[]
2049 { maps[m].getDnasq(), cf, mapping });
2053 al.addCodonFrame(cf);
2058 // ////////////////////////////////
2060 boolean hideQuality = true, hideConservation = true, hideConsensus = true;
2062 * store any annotations which forward reference a group's ID
2064 Hashtable groupAnnotRefs = new Hashtable();
2066 if (vamsasSet.getAnnotationCount() > 0)
2068 Annotation[] an = vamsasSet.getAnnotation();
2070 for (int i = 0; i < an.length; i++)
2072 // set visibility for automatic annotation for this view
2073 if (an[i].getLabel().equals("Quality"))
2075 hideQuality = false;
2078 else if (an[i].getLabel().equals("Conservation"))
2080 hideConservation = false;
2083 else if (an[i].getLabel().equals("Consensus"))
2085 hideConsensus = false;
2088 // set visiblity for other annotation in this view
2089 if (an[i].getId() != null
2090 && annotationIds.containsKey(an[i].getId()))
2092 jalview.datamodel.AlignmentAnnotation jda = (jalview.datamodel.AlignmentAnnotation) annotationIds
2093 .get(an[i].getId());
2094 // in principle Visible should always be true for annotation displayed
2095 // in multiple views
2096 if (an[i].hasVisible())
2097 jda.visible = an[i].getVisible();
2099 al.addAnnotation(jda);
2103 // Construct new annotation from model.
2104 AnnotationElement[] ae = an[i].getAnnotationElement();
2105 jalview.datamodel.Annotation[] anot = null;
2107 if (!an[i].getScoreOnly())
2109 anot = new jalview.datamodel.Annotation[al.getWidth()];
2111 for (int aa = 0; aa < ae.length && aa < anot.length; aa++)
2113 if (ae[aa].getPosition() >= anot.length)
2116 anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(
2118 ae[aa].getDisplayCharacter(), ae[aa].getDescription(),
2119 (ae[aa].getSecondaryStructure() == null || ae[aa]
2120 .getSecondaryStructure().length() == 0) ? ' '
2121 : ae[aa].getSecondaryStructure().charAt(0),
2125 // JBPNote: Consider verifying dataflow for IO of secondary
2126 // structure annotation read from Stockholm files
2127 // this was added to try to ensure that
2128 // if (anot[ae[aa].getPosition()].secondaryStructure>' ')
2130 // anot[ae[aa].getPosition()].displayCharacter = "";
2132 anot[ae[aa].getPosition()].colour = new java.awt.Color(
2133 ae[aa].getColour());
2136 jalview.datamodel.AlignmentAnnotation jaa = null;
2138 if (an[i].getGraph())
2140 jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
2141 an[i].getDescription(), anot, 0, 0, an[i].getGraphType());
2143 jaa.graphGroup = an[i].getGraphGroup();
2145 if (an[i].getThresholdLine() != null)
2147 jaa.setThreshold(new jalview.datamodel.GraphLine(an[i]
2148 .getThresholdLine().getValue(), an[i]
2149 .getThresholdLine().getLabel(), new java.awt.Color(
2150 an[i].getThresholdLine().getColour())));
2157 jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
2158 an[i].getDescription(), anot);
2160 // register new annotation
2161 if (an[i].getId() != null)
2163 annotationIds.put(an[i].getId(), jaa);
2164 jaa.annotationId = an[i].getId();
2166 // recover sequence association
2167 if (an[i].getSequenceRef() != null)
2169 if (al.findName(an[i].getSequenceRef()) != null)
2171 jaa.createSequenceMapping(al.findName(an[i].getSequenceRef()),
2173 al.findName(an[i].getSequenceRef()).addAlignmentAnnotation(jaa);
2176 // and make a note of any group association
2177 if (an[i].getGroupRef() != null && an[i].getGroupRef().length() > 0)
2179 groupAnnotRefs.put(an[i].getGroupRef(), jaa);
2182 if (an[i].hasScore())
2184 jaa.setScore(an[i].getScore());
2186 if (an[i].hasVisible())
2187 jaa.visible = an[i].getVisible();
2189 if (an[i].hasCentreColLabels())
2190 jaa.centreColLabels = an[i].getCentreColLabels();
2192 if (an[i].hasScaleColLabels())
2194 jaa.scaleColLabel = an[i].getScaleColLabels();
2196 if (an[i].hasAutoCalculated() && an[i].isAutoCalculated())
2198 // newer files have an 'autoCalculated' flag and store calculation
2199 // state in viewport properties
2200 jaa.autoCalculated = true; // means annotation will be marked for
2201 // update at end of load.
2203 al.addAnnotation(jaa);
2207 // ///////////////////////
2209 // Create alignment markup and styles for this view
2210 if (jms.getJGroupCount() > 0)
2212 JGroup[] groups = jms.getJGroup();
2214 for (int i = 0; i < groups.length; i++)
2216 ColourSchemeI cs = null;
2218 if (groups[i].getColour() != null)
2220 if (groups[i].getColour().startsWith("ucs"))
2222 cs = GetUserColourScheme(jms, groups[i].getColour());
2226 cs = ColourSchemeProperty.getColour(al, groups[i].getColour());
2231 cs.setThreshold(groups[i].getPidThreshold(), true);
2235 Vector seqs = new Vector();
2237 for (int s = 0; s < groups[i].getSeqCount(); s++)
2239 String seqId = groups[i].getSeq(s) + "";
2240 jalview.datamodel.SequenceI ts = (jalview.datamodel.SequenceI) seqRefIds
2245 seqs.addElement(ts);
2249 if (seqs.size() < 1)
2254 jalview.datamodel.SequenceGroup sg = new jalview.datamodel.SequenceGroup(
2255 seqs, groups[i].getName(), cs, groups[i].getDisplayBoxes(),
2256 groups[i].getDisplayText(), groups[i].getColourText(),
2257 groups[i].getStart(), groups[i].getEnd());
2259 sg.setOutlineColour(new java.awt.Color(groups[i].getOutlineColour()));
2261 sg.textColour = new java.awt.Color(groups[i].getTextCol1());
2262 sg.textColour2 = new java.awt.Color(groups[i].getTextCol2());
2263 sg.setShowNonconserved(groups[i].hasShowUnconserved() ? groups[i]
2264 .isShowUnconserved() : false);
2265 sg.thresholdTextColour = groups[i].getTextColThreshold();
2266 if (groups[i].hasShowConsensusHistogram())
2268 sg.setShowConsensusHistogram(groups[i].isShowConsensusHistogram());
2271 if (groups[i].hasShowSequenceLogo())
2273 sg.setshowSequenceLogo(groups[i].isShowSequenceLogo());
2275 if (groups[i].hasIgnoreGapsinConsensus())
2277 sg.setIgnoreGapsConsensus(groups[i].getIgnoreGapsinConsensus());
2279 if (groups[i].getConsThreshold() != 0)
2281 jalview.analysis.Conservation c = new jalview.analysis.Conservation(
2282 "All", ResidueProperties.propHash, 3,
2283 sg.getSequences(null), 0, sg.getWidth() - 1);
2285 c.verdict(false, 25);
2286 sg.cs.setConservation(c);
2289 if (groups[i].getId() != null && groupAnnotRefs.size() > 0)
2291 // re-instate unique group/annotation row reference
2292 jalview.datamodel.AlignmentAnnotation jaa = (jalview.datamodel.AlignmentAnnotation) groupAnnotRefs
2293 .get(groups[i].getId());
2304 // ///////////////////////////////
2307 // If we just load in the same jar file again, the sequenceSetId
2308 // will be the same, and we end up with multiple references
2309 // to the same sequenceSet. We must modify this id on load
2310 // so that each load of the file gives a unique id
2311 String uniqueSeqSetId = view.getSequenceSetId() + uniqueSetSuffix;
2312 String viewId = (view.getId() == null ? null : view.getId()
2314 AlignFrame af = null;
2315 AlignViewport av = null;
2316 // now check to see if we really need to create a new viewport.
2317 if (multipleView && viewportsAdded.size() == 0)
2319 // We recovered an alignment for which a viewport already exists.
2320 // TODO: fix up any settings necessary for overlaying stored state onto
2321 // state recovered from another document. (may not be necessary).
2322 // we may need a binding from a viewport in memory to one recovered from
2324 // and then recover its containing af to allow the settings to be applied.
2325 // TODO: fix for vamsas demo
2327 .println("About to recover a viewport for existing alignment: Sequence set ID is "
2329 Object seqsetobj = retrieveExistingObj(uniqueSeqSetId);
2330 if (seqsetobj != null)
2332 if (seqsetobj instanceof String)
2334 uniqueSeqSetId = (String) seqsetobj;
2336 .println("Recovered extant sequence set ID mapping for ID : New Sequence set ID is "
2342 .println("Warning : Collision between sequence set ID string and existing jalview object mapping.");
2347 AlignmentPanel ap = null;
2348 boolean isnewview = true;
2351 // Check to see if this alignment already has a view id == viewId
2352 jalview.gui.AlignmentPanel views[] = Desktop
2353 .getAlignmentPanels(uniqueSeqSetId);
2354 if (views != null && views.length > 0)
2356 for (int v = 0; v < views.length; v++)
2358 if (views[v].av.getViewId().equalsIgnoreCase(viewId))
2360 // recover the existing alignpanel, alignframe, viewport
2361 af = views[v].alignFrame;
2364 // TODO: could even skip resetting view settings if we don't want to
2365 // change the local settings from other jalview processes
2374 af = loadViewport(file, JSEQ, hiddenSeqs, al, hideConsensus,
2375 hideQuality, hideConservation, jms, view, uniqueSeqSetId,
2381 // /////////////////////////////////////
2382 if (loadTreesAndStructures && jms.getTreeCount() > 0)
2386 for (int t = 0; t < jms.getTreeCount(); t++)
2389 Tree tree = jms.getTree(t);
2391 TreePanel tp = (TreePanel) retrieveExistingObj(tree.getId());
2394 tp = af.ShowNewickTree(
2395 new jalview.io.NewickFile(tree.getNewick()),
2396 tree.getTitle(), tree.getWidth(), tree.getHeight(),
2397 tree.getXpos(), tree.getYpos());
2398 if (tree.getId() != null)
2400 // perhaps bind the tree id to something ?
2405 // update local tree attributes ?
2406 // TODO: should check if tp has been manipulated by user - if so its
2407 // settings shouldn't be modified
2408 tp.setTitle(tree.getTitle());
2409 tp.setBounds(new Rectangle(tree.getXpos(), tree.getYpos(), tree
2410 .getWidth(), tree.getHeight()));
2411 tp.av = av; // af.viewport; // TODO: verify 'associate with all
2414 tp.treeCanvas.av = av; // af.viewport;
2415 tp.treeCanvas.ap = ap; // af.alignPanel;
2420 warn("There was a problem recovering stored Newick tree: \n"
2421 + tree.getNewick());
2425 tp.fitToWindow.setState(tree.getFitToWindow());
2426 tp.fitToWindow_actionPerformed(null);
2428 if (tree.getFontName() != null)
2430 tp.setTreeFont(new java.awt.Font(tree.getFontName(), tree
2431 .getFontStyle(), tree.getFontSize()));
2435 tp.setTreeFont(new java.awt.Font(view.getFontName(), view
2436 .getFontStyle(), tree.getFontSize()));
2439 tp.showPlaceholders(tree.getMarkUnlinked());
2440 tp.showBootstrap(tree.getShowBootstrap());
2441 tp.showDistances(tree.getShowDistances());
2443 tp.treeCanvas.threshold = tree.getThreshold();
2445 if (tree.getCurrentTree())
2447 af.viewport.setCurrentTree(tp.getTree());
2451 } catch (Exception ex)
2453 ex.printStackTrace();
2457 // //LOAD STRUCTURES
2458 if (loadTreesAndStructures)
2460 // run through all PDB ids on the alignment, and collect mappings between
2461 // jmol view ids and all sequences referring to it
2462 Hashtable<String, Object[]> jmolViewIds = new Hashtable();
2464 for (int i = 0; i < JSEQ.length; i++)
2466 if (JSEQ[i].getPdbidsCount() > 0)
2468 Pdbids[] ids = JSEQ[i].getPdbids();
2469 for (int p = 0; p < ids.length; p++)
2471 for (int s = 0; s < ids[p].getStructureStateCount(); s++)
2473 // check to see if we haven't already created this structure view
2474 String sviewid = (ids[p].getStructureState(s).getViewId() == null) ? null
2475 : ids[p].getStructureState(s).getViewId()
2477 jalview.datamodel.PDBEntry jpdb = new jalview.datamodel.PDBEntry();
2478 // Originally : ids[p].getFile()
2479 // : TODO: verify external PDB file recovery still works in normal
2480 // jalview project load
2481 jpdb.setFile(loadPDBFile(jprovider, ids[p].getId()));
2482 jpdb.setId(ids[p].getId());
2484 int x = ids[p].getStructureState(s).getXpos();
2485 int y = ids[p].getStructureState(s).getYpos();
2486 int width = ids[p].getStructureState(s).getWidth();
2487 int height = ids[p].getStructureState(s).getHeight();
2489 // Probably don't need to do this anymore...
2490 // Desktop.desktop.getComponentAt(x, y);
2491 // TODO: NOW: check that this recovers the PDB file correctly.
2492 String pdbFile = loadPDBFile(jprovider, ids[p].getId());
2493 jalview.datamodel.SequenceI seq = (jalview.datamodel.SequenceI) seqRefIds
2494 .get(JSEQ[i].getId() + "");
2495 if (sviewid == null)
2497 sviewid = "_jalview_pre2_4_" + x + "," + y + "," + width
2500 if (!jmolViewIds.containsKey(sviewid))
2502 jmolViewIds.put(sviewid, new Object[]
2505 { x, y, width, height },
2507 new Hashtable<String, Object[]>(),
2511 // Legacy->2.7 conversion: if there is no attribute for
2512 // colouring with the alignPanel then by default we set the
2513 // first encountered view to be the default source of colour
2516 // TODO: assemble String[] { pdb files }, String[] { id for each
2517 // file }, orig_fileloc, SequenceI[][] {{ seqs_file 1 }, {
2518 // seqs_file 2}, boolean[] {
2519 // linkAlignPanel,superposeWithAlignpanel}} from hash
2520 Object[] jmoldat = (Object[]) jmolViewIds.get(sviewid);
2521 ((boolean[]) jmoldat[3])[0] |= ids[p].getStructureState(s)
2522 .hasAlignwithAlignPanel() ? ids[p].getStructureState(
2523 s).getAlignwithAlignPanel() : false;
2524 // always colour by linked panel if not specified
2525 ((boolean[]) jmoldat[3])[1] |= ids[p].getStructureState(s)
2526 .hasColourwithAlignPanel() ? ids[p]
2527 .getStructureState(s).getColourwithAlignPanel()
2530 if (((String) jmoldat[1]).length() < ids[p]
2531 .getStructureState(s).getContent().length())
2534 jmoldat[1] = ids[p].getStructureState(s).getContent();
2537 Object[] seqstrmaps = (Object[]) ((Hashtable) jmoldat[2])
2538 .get(ids[p].getFile());
2539 if (seqstrmaps == null)
2541 ((Hashtable) jmoldat[2]).put(
2542 new File(ids[p].getFile()).toString(),
2543 seqstrmaps = new Object[]
2544 { pdbFile, ids[p].getId(), new Vector(),
2547 if (!((Vector) seqstrmaps[2]).contains(seq))
2549 ((Vector) seqstrmaps[2]).addElement(seq);
2550 // ((Vector)seqstrmaps[3]).addElement(n) : in principle, chains
2551 // should be stored here : do we need to
2552 // TODO: store and recover seq/pdb_id : chain mappings
2560 // Instantiate the associated Jmol views
2561 for (Entry<String, Object[]> entry : jmolViewIds.entrySet())
2563 String sviewid = entry.getKey();
2564 Object[] svattrib = entry.getValue();
2565 int[] geom = (int[]) svattrib[0];
2566 String state = (String) svattrib[1];
2567 Hashtable<String, Object[]> oldFiles = (Hashtable<String, Object[]>) svattrib[2];
2568 final boolean useinJmolsuperpos = ((boolean[]) svattrib[3])[0], usetoColourbyseq = ((boolean[]) svattrib[3])[1];
2569 int x = geom[0], y = geom[1], width = geom[2], height = geom[3];
2570 // collate the pdbfile -> sequence mappings from this view
2571 Vector<String> pdbfilenames = new Vector<String>();
2572 Vector<SequenceI[]> seqmaps = new Vector<SequenceI[]>();
2573 Vector<String> pdbids = new Vector<String>();
2575 // Search to see if we've already created this Jmol view
2576 AppJmol comp = null;
2577 JInternalFrame[] frames = null;
2582 frames = Desktop.desktop.getAllFrames();
2583 } catch (ArrayIndexOutOfBoundsException e)
2585 // occasional No such child exceptions are thrown here...
2590 } catch (Exception f)
2595 } while (frames == null);
2596 // search for any Jmol windows already open from other
2597 // alignment views that exactly match the stored structure state
2598 for (int f = 0; comp == null && f < frames.length; f++)
2600 if (frames[f] instanceof AppJmol)
2603 && ((AppJmol) frames[f]).getViewId().equals(sviewid))
2605 // post jalview 2.4 schema includes structure view id
2606 comp = (AppJmol) frames[f];
2608 else if (frames[f].getX() == x && frames[f].getY() == y
2609 && frames[f].getHeight() == height
2610 && frames[f].getWidth() == width)
2612 comp = (AppJmol) frames[f];
2619 // create a new Jmol window.
2620 // First parse the Jmol state to translate filenames loaded into the
2621 // view, and record the order in which files are shown in the Jmol
2622 // view, so we can add the sequence mappings in same order.
2623 StringBuffer newFileLoc = null;
2624 int cp = 0, ncp, ecp;
2625 while ((ncp = state.indexOf("load ", cp)) > -1)
2627 if (newFileLoc == null)
2629 newFileLoc = new StringBuffer();
2631 newFileLoc.append(state.substring(cp,
2632 ncp = (state.indexOf("\"", ncp + 1) + 1)));
2633 String oldfilenam = state.substring(ncp,
2634 ecp = state.indexOf("\"", ncp));
2635 // recover the new mapping data for this old filename
2636 // have to normalize filename - since Jmol and jalview do filename
2637 // translation differently.
2638 Object[] filedat = oldFiles.get(new File(oldfilenam)
2640 newFileLoc.append(((String) filedat[0]));
2641 pdbfilenames.addElement((String) filedat[0]);
2642 pdbids.addElement((String) filedat[1]);
2643 seqmaps.addElement((SequenceI[]) ((Vector<SequenceI>) filedat[2])
2644 .toArray(new SequenceI[0]));
2645 newFileLoc.append("\"");
2646 cp = ecp + 1; // advance beyond last \" and set cursor so we can
2647 // look for next file statement.
2651 // just append rest of state
2652 newFileLoc.append(state.substring(cp));
2657 .print("Ignoring incomplete Jmol state for PDB ids: ");
2658 newFileLoc = new StringBuffer(state);
2659 newFileLoc.append("; load append ");
2660 for (String id : oldFiles.keySet())
2662 // add this and any other pdb files that should be present in
2664 Object[] filedat = oldFiles.get(id);
2666 newFileLoc.append(((String) filedat[0]));
2667 pdbfilenames.addElement((String) filedat[0]);
2668 pdbids.addElement((String) filedat[1]);
2669 seqmaps.addElement((SequenceI[]) ((Vector<SequenceI>) filedat[2])
2670 .toArray(new SequenceI[0]));
2671 newFileLoc.append(" \"");
2672 newFileLoc.append((String) filedat[0]);
2673 newFileLoc.append("\"");
2676 newFileLoc.append(";");
2679 if (newFileLoc != null)
2681 int histbug = newFileLoc.indexOf("history = ");
2683 int diff = histbug == -1 ? -1 : newFileLoc.indexOf(";",
2685 String val = (diff == -1) ? null : newFileLoc.substring(
2687 if (val != null && val.length() >= 4)
2689 if (val.contains("e"))
2691 if (val.trim().equals("true"))
2699 newFileLoc.replace(histbug, diff, val);
2702 // TODO: assemble String[] { pdb files }, String[] { id for each
2703 // file }, orig_fileloc, SequenceI[][] {{ seqs_file 1 }, {
2704 // seqs_file 2}} from hash
2705 final String[] pdbf = (String[]) pdbfilenames
2706 .toArray(new String[pdbfilenames.size()]), id = (String[]) pdbids
2707 .toArray(new String[pdbids.size()]);
2708 final SequenceI[][] sq = (SequenceI[][]) seqmaps
2709 .toArray(new SequenceI[seqmaps.size()][]);
2710 final String fileloc = newFileLoc.toString(), vid = sviewid;
2711 final AlignFrame alf = af;
2712 final java.awt.Rectangle rect = new java.awt.Rectangle(x, y,
2716 javax.swing.SwingUtilities.invokeAndWait(new Runnable()
2720 AppJmol sview = null;
2723 sview = new AppJmol(pdbf, id, sq, alf.alignPanel,
2724 useinJmolsuperpos, usetoColourbyseq,
2727 } catch (OutOfMemoryError ex)
2729 new OOMWarning("restoring structure view for PDB id "
2730 + id, (OutOfMemoryError) ex.getCause());
2731 if (sview != null && sview.isVisible())
2733 sview.closeViewer();
2734 sview.setVisible(false);
2740 } catch (InvocationTargetException ex)
2742 warn("Unexpected error when opening Jmol view.", ex);
2744 } catch (InterruptedException e)
2746 // e.printStackTrace();
2752 // if (comp != null)
2754 // NOTE: if the jalview project is part of a shared session then
2755 // view synchronization should/could be done here.
2757 // add mapping for sequences in this view to an already open Jmol
2759 for (String id : oldFiles.keySet())
2761 // add this and any other pdb files that should be present in the
2763 Object[] filedat = oldFiles.get(id);
2764 String pdbFile = (String) filedat[0];
2765 SequenceI[] seq = (SequenceI[]) ((Vector<SequenceI>) filedat[2])
2766 .toArray(new SequenceI[0]);
2767 StructureSelectionManager.getStructureSelectionManager()
2768 .setMapping(seq, null, pdbFile,
2769 jalview.io.AppletFormatAdapter.FILE);
2770 ((AppJmol) comp).jmb.addSequenceForStructFile(pdbFile, seq);
2772 // and add the AlignmentPanel's reference to the Jmol view
2773 ((AppJmol) comp).addAlignmentPanel(ap);
2774 if (useinJmolsuperpos)
2776 ((AppJmol) comp).useAlignmentPanelForSuperposition(ap);
2780 ((AppJmol) comp).excludeAlignmentPanelForSuperposition(ap);
2782 if (usetoColourbyseq)
2784 ((AppJmol) comp).useAlignmentPanelForColourbyseq(ap);
2788 ((AppJmol) comp).excludeAlignmentPanelForColourbyseq(ap);
2794 // and finally return.
2798 AlignFrame loadViewport(String file, JSeq[] JSEQ, Vector hiddenSeqs,
2799 Alignment al, boolean hideConsensus, boolean hideQuality,
2800 boolean hideConservation, JalviewModelSequence jms,
2801 Viewport view, String uniqueSeqSetId, String viewId)
2803 AlignFrame af = null;
2804 af = new AlignFrame(al, view.getWidth(), view.getHeight(),
2805 uniqueSeqSetId, viewId);
2807 af.setFileName(file, "Jalview");
2809 for (int i = 0; i < JSEQ.length; i++)
2811 af.viewport.setSequenceColour(af.viewport.alignment.getSequenceAt(i),
2812 new java.awt.Color(JSEQ[i].getColour()));
2815 af.viewport.gatherViewsHere = view.getGatheredViews();
2817 if (view.getSequenceSetId() != null)
2819 jalview.gui.AlignViewport av = (jalview.gui.AlignViewport) viewportsAdded
2820 .get(uniqueSeqSetId);
2822 af.viewport.sequenceSetID = uniqueSeqSetId;
2825 // propagate shared settings to this new view
2826 af.viewport.historyList = av.historyList;
2827 af.viewport.redoList = av.redoList;
2831 viewportsAdded.put(uniqueSeqSetId, af.viewport);
2833 // TODO: check if this method can be called repeatedly without
2834 // side-effects if alignpanel already registered.
2835 PaintRefresher.Register(af.alignPanel, uniqueSeqSetId);
2837 // apply Hidden regions to view.
2838 if (hiddenSeqs != null)
2840 for (int s = 0; s < JSEQ.length; s++)
2842 jalview.datamodel.SequenceGroup hidden = new jalview.datamodel.SequenceGroup();
2844 for (int r = 0; r < JSEQ[s].getHiddenSequencesCount(); r++)
2847 al.getSequenceAt(JSEQ[s].getHiddenSequences(r)), false);
2849 af.viewport.hideRepSequences(al.getSequenceAt(s), hidden);
2852 jalview.datamodel.SequenceI[] hseqs = new jalview.datamodel.SequenceI[hiddenSeqs
2855 for (int s = 0; s < hiddenSeqs.size(); s++)
2857 hseqs[s] = (jalview.datamodel.SequenceI) hiddenSeqs.elementAt(s);
2860 af.viewport.hideSequence(hseqs);
2863 // set visibility of annotation in view
2864 if ((hideConsensus || hideQuality || hideConservation)
2865 && al.getAlignmentAnnotation() != null)
2867 int hSize = al.getAlignmentAnnotation().length;
2868 for (int h = 0; h < hSize; h++)
2870 if ((hideConsensus && al.getAlignmentAnnotation()[h].label
2871 .equals("Consensus"))
2872 || (hideQuality && al.getAlignmentAnnotation()[h].label
2874 || (hideConservation && al.getAlignmentAnnotation()[h].label
2875 .equals("Conservation")))
2877 al.deleteAnnotation(al.getAlignmentAnnotation()[h]);
2882 af.alignPanel.adjustAnnotationHeight();
2884 // recover view properties and display parameters
2885 if (view.getViewName() != null)
2887 af.viewport.viewName = view.getViewName();
2888 af.setInitialTabVisible();
2890 af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),
2893 af.viewport.setShowAnnotation(view.getShowAnnotation());
2894 af.viewport.setAbovePIDThreshold(view.getPidSelected());
2896 af.viewport.setColourText(view.getShowColourText());
2898 af.viewport.setConservationSelected(view.getConservationSelected());
2899 af.viewport.setShowJVSuffix(view.getShowFullId());
2900 af.viewport.rightAlignIds = view.getRightAlignIds();
2901 af.viewport.setFont(new java.awt.Font(view.getFontName(), view
2902 .getFontStyle(), view.getFontSize()));
2903 af.alignPanel.fontChanged();
2904 af.viewport.setRenderGaps(view.getRenderGaps());
2905 af.viewport.setWrapAlignment(view.getWrapAlignment());
2906 af.alignPanel.setWrapAlignment(view.getWrapAlignment());
2907 af.viewport.setShowAnnotation(view.getShowAnnotation());
2908 af.alignPanel.setAnnotationVisible(view.getShowAnnotation());
2910 af.viewport.setShowBoxes(view.getShowBoxes());
2912 af.viewport.setShowText(view.getShowText());
2914 af.viewport.textColour = new java.awt.Color(view.getTextCol1());
2915 af.viewport.textColour2 = new java.awt.Color(view.getTextCol2());
2916 af.viewport.thresholdTextColour = view.getTextColThreshold();
2917 af.viewport.setShowUnconserved(view.hasShowUnconserved() ? view
2918 .isShowUnconserved() : false);
2919 af.viewport.setStartRes(view.getStartRes());
2920 af.viewport.setStartSeq(view.getStartSeq());
2922 ColourSchemeI cs = null;
2923 // apply colourschemes
2924 if (view.getBgColour() != null)
2926 if (view.getBgColour().startsWith("ucs"))
2928 cs = GetUserColourScheme(jms, view.getBgColour());
2930 else if (view.getBgColour().startsWith("Annotation"))
2932 // int find annotation
2933 if (af.viewport.alignment.getAlignmentAnnotation() != null)
2935 for (int i = 0; i < af.viewport.alignment
2936 .getAlignmentAnnotation().length; i++)
2938 if (af.viewport.alignment.getAlignmentAnnotation()[i].label
2939 .equals(view.getAnnotationColours().getAnnotation()))
2941 if (af.viewport.alignment.getAlignmentAnnotation()[i]
2942 .getThreshold() == null)
2944 af.viewport.alignment.getAlignmentAnnotation()[i]
2945 .setThreshold(new jalview.datamodel.GraphLine(view
2946 .getAnnotationColours().getThreshold(),
2947 "Threshold", java.awt.Color.black)
2952 if (view.getAnnotationColours().getColourScheme()
2955 cs = new AnnotationColourGradient(
2956 af.viewport.alignment.getAlignmentAnnotation()[i],
2957 new java.awt.Color(view.getAnnotationColours()
2958 .getMinColour()), new java.awt.Color(view
2959 .getAnnotationColours().getMaxColour()),
2960 view.getAnnotationColours().getAboveThreshold());
2962 else if (view.getAnnotationColours().getColourScheme()
2965 cs = new AnnotationColourGradient(
2966 af.viewport.alignment.getAlignmentAnnotation()[i],
2967 GetUserColourScheme(jms, view
2968 .getAnnotationColours().getColourScheme()),
2969 view.getAnnotationColours().getAboveThreshold());
2973 cs = new AnnotationColourGradient(
2974 af.viewport.alignment.getAlignmentAnnotation()[i],
2975 ColourSchemeProperty.getColour(al, view
2976 .getAnnotationColours().getColourScheme()),
2977 view.getAnnotationColours().getAboveThreshold());
2980 // Also use these settings for all the groups
2981 if (al.getGroups() != null)
2983 for (int g = 0; g < al.getGroups().size(); g++)
2985 jalview.datamodel.SequenceGroup sg = (jalview.datamodel.SequenceGroup) al
2986 .getGroups().elementAt(g);
2995 * (view.getAnnotationColours().getColourScheme().equals("None"
2996 * )) { sg.cs = new AnnotationColourGradient(
2997 * af.viewport.alignment.getAlignmentAnnotation()[i], new
2998 * java.awt.Color(view.getAnnotationColours().
2999 * getMinColour()), new
3000 * java.awt.Color(view.getAnnotationColours().
3002 * view.getAnnotationColours().getAboveThreshold()); } else
3005 sg.cs = new AnnotationColourGradient(
3006 af.viewport.alignment.getAlignmentAnnotation()[i],
3007 sg.cs, view.getAnnotationColours()
3008 .getAboveThreshold());
3022 cs = ColourSchemeProperty.getColour(al, view.getBgColour());
3027 cs.setThreshold(view.getPidThreshold(), true);
3028 cs.setConsensus(af.viewport.hconsensus);
3032 af.viewport.setGlobalColourScheme(cs);
3033 af.viewport.setColourAppliesToAllGroups(false);
3035 if (view.getConservationSelected() && cs != null)
3037 cs.setConservationInc(view.getConsThreshold());
3040 af.changeColour(cs);
3042 af.viewport.setColourAppliesToAllGroups(true);
3044 if (view.getShowSequenceFeatures())
3046 af.viewport.showSequenceFeatures = true;
3048 if (view.hasCentreColumnLabels())
3050 af.viewport.setCentreColumnLabels(view.getCentreColumnLabels());
3052 if (view.hasIgnoreGapsinConsensus())
3054 af.viewport.ignoreGapsInConsensusCalculation = view
3055 .getIgnoreGapsinConsensus();
3057 if (view.hasFollowHighlight())
3059 af.viewport.followHighlight = view.getFollowHighlight();
3061 if (view.hasFollowSelection())
3063 af.viewport.followSelection = view.getFollowSelection();
3065 if (view.hasShowConsensusHistogram())
3067 af.viewport.setShowConsensusHistogram(view
3068 .getShowConsensusHistogram());
3072 af.viewport.setShowConsensusHistogram(true);
3074 if (view.hasShowSequenceLogo())
3076 af.viewport.showSequenceLogo = view.getShowSequenceLogo();
3080 af.viewport.showSequenceLogo = false;
3082 if (view.hasShowDbRefTooltip())
3084 af.viewport.setShowDbRefs(view.getShowDbRefTooltip());
3086 if (view.hasShowNPfeatureTooltip())
3088 af.viewport.setShowNpFeats(view.hasShowNPfeatureTooltip());
3090 if (view.hasShowGroupConsensus())
3092 af.viewport.setShowGroupConsensus(view.getShowGroupConsensus());
3096 af.viewport.setShowGroupConsensus(false);
3098 if (view.hasShowGroupConservation())
3100 af.viewport.setShowGroupConservation(view.getShowGroupConservation());
3104 af.viewport.setShowGroupConservation(false);
3107 // recover featre settings
3108 if (jms.getFeatureSettings() != null)
3110 af.viewport.featuresDisplayed = new Hashtable();
3111 String[] renderOrder = new String[jms.getFeatureSettings()
3112 .getSettingCount()];
3113 for (int fs = 0; fs < jms.getFeatureSettings().getSettingCount(); fs++)
3115 Setting setting = jms.getFeatureSettings().getSetting(fs);
3116 if (setting.hasMincolour())
3118 GraduatedColor gc = setting.hasMin() ? new GraduatedColor(
3119 new java.awt.Color(setting.getMincolour()),
3120 new java.awt.Color(setting.getColour()),
3121 setting.getMin(), setting.getMax()) : new GraduatedColor(
3122 new java.awt.Color(setting.getMincolour()),
3123 new java.awt.Color(setting.getColour()), 0, 1);
3124 if (setting.hasThreshold())
3126 gc.setThresh(setting.getThreshold());
3127 gc.setThreshType(setting.getThreshstate());
3129 gc.setAutoScaled(true); // default
3130 if (setting.hasAutoScale())
3132 gc.setAutoScaled(setting.getAutoScale());
3134 if (setting.hasColourByLabel())
3136 gc.setColourByLabel(setting.getColourByLabel());
3138 // and put in the feature colour table.
3139 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(
3140 setting.getType(), gc);
3144 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(
3146 new java.awt.Color(setting.getColour()));
3148 renderOrder[fs] = setting.getType();
3149 if (setting.hasOrder())
3150 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setOrder(
3151 setting.getType(), setting.getOrder());
3153 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setOrder(
3155 fs / jms.getFeatureSettings().getSettingCount());
3156 if (setting.getDisplay())
3158 af.viewport.featuresDisplayed.put(setting.getType(), new Integer(
3159 setting.getColour()));
3162 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder = renderOrder;
3164 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureGroups = fgtable = new Hashtable();
3165 for (int gs = 0; gs < jms.getFeatureSettings().getGroupCount(); gs++)
3167 Group grp = jms.getFeatureSettings().getGroup(gs);
3168 fgtable.put(grp.getName(), new Boolean(grp.getDisplay()));
3172 if (view.getHiddenColumnsCount() > 0)
3174 for (int c = 0; c < view.getHiddenColumnsCount(); c++)
3176 af.viewport.hideColumns(view.getHiddenColumns(c).getStart(), view
3177 .getHiddenColumns(c).getEnd() // +1
3182 af.setMenusFromViewport(af.viewport);
3183 // TODO: we don't need to do this if the viewport is aready visible.
3184 Desktop.addInternalFrame(af, view.getTitle(), view.getWidth(),
3186 af.alignPanel.updateAnnotation(false); // recompute any autoannotation
3190 Hashtable skipList = null;
3193 * TODO remove this method
3196 * @return AlignFrame bound to sequenceSetId from view, if one exists. private
3197 * AlignFrame getSkippedFrame(Viewport view) { if (skipList==null) {
3198 * throw new Error("Implementation Error. No skipList defined for this
3199 * Jalview2XML instance."); } return (AlignFrame)
3200 * skipList.get(view.getSequenceSetId()); }
3204 * Check if the Jalview view contained in object should be skipped or not.
3207 * @return true if view's sequenceSetId is a key in skipList
3209 private boolean skipViewport(JalviewModel object)
3211 if (skipList == null)
3216 if (skipList.containsKey(id = object.getJalviewModelSequence()
3217 .getViewport()[0].getSequenceSetId()))
3219 if (Cache.log != null && Cache.log.isDebugEnabled())
3221 Cache.log.debug("Skipping seuqence set id " + id);
3228 public void AddToSkipList(AlignFrame af)
3230 if (skipList == null)
3232 skipList = new Hashtable();
3234 skipList.put(af.getViewport().getSequenceSetId(), af);
3237 public void clearSkipList()
3239 if (skipList != null)
3246 private void recoverDatasetFor(SequenceSet vamsasSet, Alignment al)
3248 jalview.datamodel.Alignment ds = getDatasetFor(vamsasSet.getDatasetId());
3249 Vector dseqs = null;
3252 // create a list of new dataset sequences
3253 dseqs = new Vector();
3255 for (int i = 0, iSize = vamsasSet.getSequenceCount(); i < iSize; i++)
3257 Sequence vamsasSeq = vamsasSet.getSequence(i);
3258 ensureJalviewDatasetSequence(vamsasSeq, ds, dseqs);
3260 // create a new dataset
3263 SequenceI[] dsseqs = new SequenceI[dseqs.size()];
3264 dseqs.copyInto(dsseqs);
3265 ds = new jalview.datamodel.Alignment(dsseqs);
3266 debug("Created new dataset " + vamsasSet.getDatasetId()
3267 + " for alignment " + System.identityHashCode(al));
3268 addDatasetRef(vamsasSet.getDatasetId(), ds);
3270 // set the dataset for the newly imported alignment.
3271 if (al.getDataset() == null)
3280 * sequence definition to create/merge dataset sequence for
3284 * vector to add new dataset sequence to
3286 private void ensureJalviewDatasetSequence(Sequence vamsasSeq,
3287 AlignmentI ds, Vector dseqs)
3289 // JBP TODO: Check this is called for AlCodonFrames to support recovery of
3291 jalview.datamodel.Sequence sq = (jalview.datamodel.Sequence) seqRefIds
3292 .get(vamsasSeq.getId());
3293 jalview.datamodel.SequenceI dsq = null;
3294 if (sq != null && sq.getDatasetSequence() != null)
3296 dsq = (jalview.datamodel.SequenceI) sq.getDatasetSequence();
3299 String sqid = vamsasSeq.getDsseqid();
3302 // need to create or add a new dataset sequence reference to this sequence
3305 dsq = (jalview.datamodel.SequenceI) seqRefIds.get(sqid);
3310 // make a new dataset sequence
3311 dsq = sq.createDatasetSequence();
3314 // make up a new dataset reference for this sequence
3315 sqid = seqHash(dsq);
3317 dsq.setVamsasId(uniqueSetSuffix + sqid);
3318 seqRefIds.put(sqid, dsq);
3323 dseqs.addElement(dsq);
3328 ds.addSequence(dsq);
3334 { // make this dataset sequence sq's dataset sequence
3335 sq.setDatasetSequence(dsq);
3339 // TODO: refactor this as a merge dataset sequence function
3340 // now check that sq (the dataset sequence) sequence really is the union of
3341 // all references to it
3342 // boolean pre = sq.getStart() < dsq.getStart();
3343 // boolean post = sq.getEnd() > dsq.getEnd();
3347 StringBuffer sb = new StringBuffer();
3348 String newres = jalview.analysis.AlignSeq.extractGaps(
3349 jalview.util.Comparison.GapChars, sq.getSequenceAsString());
3350 if (!newres.equalsIgnoreCase(dsq.getSequenceAsString())
3351 && newres.length() > dsq.getLength())
3353 // Update with the longer sequence.
3357 * if (pre) { sb.insert(0, newres .substring(0, dsq.getStart() -
3358 * sq.getStart())); dsq.setStart(sq.getStart()); } if (post) {
3359 * sb.append(newres.substring(newres.length() - sq.getEnd() -
3360 * dsq.getEnd())); dsq.setEnd(sq.getEnd()); }
3362 dsq.setSequence(sb.toString());
3364 // TODO: merges will never happen if we 'know' we have the real dataset
3365 // sequence - this should be detected when id==dssid
3366 System.err.println("DEBUG Notice: Merged dataset sequence"); // ("
3367 // + (pre ? "prepended" : "") + " "
3368 // + (post ? "appended" : ""));
3373 java.util.Hashtable datasetIds = null;
3375 java.util.IdentityHashMap dataset2Ids = null;
3377 private Alignment getDatasetFor(String datasetId)
3379 if (datasetIds == null)
3381 datasetIds = new Hashtable();
3384 if (datasetIds.containsKey(datasetId))
3386 return (Alignment) datasetIds.get(datasetId);
3391 private void addDatasetRef(String datasetId, Alignment dataset)
3393 if (datasetIds == null)
3395 datasetIds = new Hashtable();
3397 datasetIds.put(datasetId, dataset);
3401 * make a new dataset ID for this jalview dataset alignment
3406 private String getDatasetIdRef(jalview.datamodel.Alignment dataset)
3408 if (dataset.getDataset() != null)
3410 warn("Serious issue! Dataset Object passed to getDatasetIdRef is not a Jalview DATASET alignment...");
3412 String datasetId = makeHashCode(dataset, null);
3413 if (datasetId == null)
3415 // make a new datasetId and record it
3416 if (dataset2Ids == null)
3418 dataset2Ids = new IdentityHashMap();
3422 datasetId = (String) dataset2Ids.get(dataset);
3424 if (datasetId == null)
3426 datasetId = "ds" + dataset2Ids.size() + 1;
3427 dataset2Ids.put(dataset, datasetId);
3433 private void addDBRefs(SequenceI datasetSequence, Sequence sequence)
3435 for (int d = 0; d < sequence.getDBRefCount(); d++)
3437 DBRef dr = sequence.getDBRef(d);
3438 jalview.datamodel.DBRefEntry entry = new jalview.datamodel.DBRefEntry(
3439 sequence.getDBRef(d).getSource(), sequence.getDBRef(d)
3440 .getVersion(), sequence.getDBRef(d).getAccessionId());
3441 if (dr.getMapping() != null)
3443 entry.setMap(addMapping(dr.getMapping()));
3445 datasetSequence.addDBRef(entry);
3449 private jalview.datamodel.Mapping addMapping(Mapping m)
3451 SequenceI dsto = null;
3452 // Mapping m = dr.getMapping();
3453 int fr[] = new int[m.getMapListFromCount() * 2];
3454 Enumeration f = m.enumerateMapListFrom();
3455 for (int _i = 0; f.hasMoreElements(); _i += 2)
3457 MapListFrom mf = (MapListFrom) f.nextElement();
3458 fr[_i] = mf.getStart();
3459 fr[_i + 1] = mf.getEnd();
3461 int fto[] = new int[m.getMapListToCount() * 2];
3462 f = m.enumerateMapListTo();
3463 for (int _i = 0; f.hasMoreElements(); _i += 2)
3465 MapListTo mf = (MapListTo) f.nextElement();
3466 fto[_i] = mf.getStart();
3467 fto[_i + 1] = mf.getEnd();
3469 jalview.datamodel.Mapping jmap = new jalview.datamodel.Mapping(dsto,
3470 fr, fto, (int) m.getMapFromUnit(), (int) m.getMapToUnit());
3471 if (m.getMappingChoice() != null)
3473 MappingChoice mc = m.getMappingChoice();
3474 if (mc.getDseqFor() != null)
3476 String dsfor = "" + mc.getDseqFor();
3477 if (seqRefIds.containsKey(dsfor))
3482 jmap.setTo((SequenceI) seqRefIds.get(dsfor));
3486 frefedSequence.add(new Object[]
3493 * local sequence definition
3495 Sequence ms = mc.getSequence();
3496 jalview.datamodel.Sequence djs = null;
3497 String sqid = ms.getDsseqid();
3498 if (sqid != null && sqid.length() > 0)
3501 * recover dataset sequence
3503 djs = (jalview.datamodel.Sequence) seqRefIds.get(sqid);
3508 .println("Warning - making up dataset sequence id for DbRef sequence map reference");
3509 sqid = ((Object) ms).toString(); // make up a new hascode for
3510 // undefined dataset sequence hash
3511 // (unlikely to happen)
3517 * make a new dataset sequence and add it to refIds hash
3519 djs = new jalview.datamodel.Sequence(ms.getName(),
3521 djs.setStart(jmap.getMap().getToLowest());
3522 djs.setEnd(jmap.getMap().getToHighest());
3523 djs.setVamsasId(uniqueSetSuffix + sqid);
3525 seqRefIds.put(sqid, djs);
3528 jalview.bin.Cache.log.debug("about to recurse on addDBRefs.");
3537 public jalview.gui.AlignmentPanel copyAlignPanel(AlignmentPanel ap,
3538 boolean keepSeqRefs)
3541 jalview.schemabinding.version2.JalviewModel jm = SaveState(ap, null,
3547 jm.getJalviewModelSequence().getViewport(0).setSequenceSetId(null);
3551 uniqueSetSuffix = "";
3552 jm.getJalviewModelSequence().getViewport(0).setId(null); // we don't
3557 if (this.frefedSequence == null)
3559 frefedSequence = new Vector();
3562 viewportsAdded = new Hashtable();
3564 AlignFrame af = LoadFromObject(jm, null, false, null);
3565 af.alignPanels.clear();
3566 af.closeMenuItem_actionPerformed(true);
3569 * if(ap.av.alignment.getAlignmentAnnotation()!=null) { for(int i=0;
3570 * i<ap.av.alignment.getAlignmentAnnotation().length; i++) {
3571 * if(!ap.av.alignment.getAlignmentAnnotation()[i].autoCalculated) {
3572 * af.alignPanel.av.alignment.getAlignmentAnnotation()[i] =
3573 * ap.av.alignment.getAlignmentAnnotation()[i]; } } }
3576 return af.alignPanel;
3580 * flag indicating if hashtables should be cleared on finalization TODO this
3581 * flag may not be necessary
3583 private boolean _cleartables = true;
3585 private Hashtable jvids2vobj;
3590 * @see java.lang.Object#finalize()
3592 protected void finalize() throws Throwable
3594 // really make sure we have no buried refs left.
3599 this.seqRefIds = null;
3600 this.seqsToIds = null;
3604 private void warn(String msg)
3609 private void warn(String msg, Exception e)
3611 if (Cache.log != null)
3615 Cache.log.warn(msg, e);
3619 Cache.log.warn(msg);
3624 System.err.println("Warning: " + msg);
3627 e.printStackTrace();
3632 private void debug(String string)
3634 debug(string, null);
3637 private void debug(String msg, Exception e)
3639 if (Cache.log != null)
3643 Cache.log.debug(msg, e);
3647 Cache.log.debug(msg);
3652 System.err.println("Warning: " + msg);
3655 e.printStackTrace();
3661 * set the object to ID mapping tables used to write/recover objects and XML
3662 * ID strings for the jalview project. If external tables are provided then
3663 * finalize and clearSeqRefs will not clear the tables when the Jalview2XML
3664 * object goes out of scope. - also populates the datasetIds hashtable with
3665 * alignment objects containing dataset sequences
3668 * Map from ID strings to jalview datamodel
3670 * Map from jalview datamodel to ID strings
3674 public void setObjectMappingTables(Hashtable vobj2jv,
3675 IdentityHashMap jv2vobj)
3677 this.jv2vobj = jv2vobj;
3678 this.vobj2jv = vobj2jv;
3679 Iterator ds = jv2vobj.keySet().iterator();
3681 while (ds.hasNext())
3683 Object jvobj = ds.next();
3684 id = jv2vobj.get(jvobj).toString();
3685 if (jvobj instanceof jalview.datamodel.Alignment)
3687 if (((jalview.datamodel.Alignment) jvobj).getDataset() == null)
3689 addDatasetRef(id, (jalview.datamodel.Alignment) jvobj);
3692 else if (jvobj instanceof jalview.datamodel.Sequence)
3694 // register sequence object so the XML parser can recover it.
3695 if (seqRefIds == null)
3697 seqRefIds = new Hashtable();
3699 if (seqsToIds == null)
3701 seqsToIds = new IdentityHashMap();
3703 seqRefIds.put(jv2vobj.get(jvobj).toString(), jvobj);
3704 seqsToIds.put(jvobj, id);
3706 else if (jvobj instanceof jalview.datamodel.AlignmentAnnotation)
3708 if (annotationIds == null)
3710 annotationIds = new Hashtable();
3713 annotationIds.put(anid = jv2vobj.get(jvobj).toString(), jvobj);
3714 jalview.datamodel.AlignmentAnnotation jvann = (jalview.datamodel.AlignmentAnnotation) jvobj;
3715 if (jvann.annotationId == null)
3717 jvann.annotationId = anid;
3719 if (!jvann.annotationId.equals(anid))
3721 // TODO verify that this is the correct behaviour
3722 this.warn("Overriding Annotation ID for " + anid
3723 + " from different id : " + jvann.annotationId);
3724 jvann.annotationId = anid;
3727 else if (jvobj instanceof String)
3729 if (jvids2vobj == null)
3731 jvids2vobj = new Hashtable();
3732 jvids2vobj.put(jvobj, jv2vobj.get(jvobj).toString());
3736 Cache.log.debug("Ignoring " + jvobj.getClass() + " (ID = " + id);
3741 * set the uniqueSetSuffix used to prefix/suffix object IDs for jalview
3742 * objects created from the project archive. If string is null (default for
3743 * construction) then suffix will be set automatically.
3747 public void setUniqueSetSuffix(String string)
3749 uniqueSetSuffix = string;
3754 * uses skipList2 as the skipList for skipping views on sequence sets
3755 * associated with keys in the skipList
3759 public void setSkipList(Hashtable skipList2)
3761 skipList = skipList2;