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.AlignmentAnnotation;
36 import jalview.datamodel.AlignmentI;
37 import jalview.datamodel.SequenceI;
38 import jalview.schemabinding.version2.*;
39 import jalview.schemes.*;
40 import jalview.structure.StructureSelectionManager;
41 import jalview.util.jarInputStreamProvider;
44 * Write out the current jalview desktop state as a Jalview XML stream.
46 * Note: the vamsas objects referred to here are primitive versions of the
47 * VAMSAS project schema elements - they are not the same and most likely never
51 * @version $Revision: 1.134 $
53 public class Jalview2XML
56 * create/return unique hash string for sq
59 * @return new or existing unique string for sq
61 String seqHash(SequenceI sq)
63 if (seqsToIds == null)
67 if (seqsToIds.containsKey(sq))
69 return (String) seqsToIds.get(sq);
73 // create sequential key
74 String key = "sq" + (seqsToIds.size() + 1);
75 key = makeHashCode(sq, key); // check we don't have an external reference
77 seqsToIds.put(sq, key);
86 if (seqRefIds != null)
90 if (seqsToIds != null)
100 warn("clearSeqRefs called when _cleartables was not set. Doing nothing.");
101 // seqRefIds = new Hashtable();
102 // seqsToIds = new IdentityHashMap();
108 if (seqsToIds == null)
110 seqsToIds = new IdentityHashMap();
112 if (seqRefIds == null)
114 seqRefIds = new Hashtable();
119 * SequenceI reference -> XML ID string in jalview XML. Populated as XML reps
120 * of sequence objects are created.
122 java.util.IdentityHashMap seqsToIds = null;
125 * jalview XML Sequence ID to jalview sequence object reference (both dataset
126 * and alignment sequences. Populated as XML reps of sequence objects are
129 java.util.Hashtable seqRefIds = null; // key->SequenceI resolution
131 Vector frefedSequence = null;
133 boolean raiseGUI = true; // whether errors are raised in dialog boxes or not
139 public Jalview2XML(boolean raiseGUI)
141 this.raiseGUI = raiseGUI;
144 public void resolveFrefedSequences()
146 if (frefedSequence.size() > 0)
148 int r = 0, rSize = frefedSequence.size();
151 Object[] ref = (Object[]) frefedSequence.elementAt(r);
154 String sref = (String) ref[0];
155 if (seqRefIds.containsKey(sref))
157 if (ref[1] instanceof jalview.datamodel.Mapping)
159 SequenceI seq = (SequenceI) seqRefIds.get(sref);
160 while (seq.getDatasetSequence() != null)
162 seq = seq.getDatasetSequence();
164 ((jalview.datamodel.Mapping) ref[1]).setTo(seq);
168 if (ref[1] instanceof jalview.datamodel.AlignedCodonFrame)
170 SequenceI seq = (SequenceI) seqRefIds.get(sref);
171 while (seq.getDatasetSequence() != null)
173 seq = seq.getDatasetSequence();
176 && ref[2] instanceof jalview.datamodel.Mapping)
178 jalview.datamodel.Mapping mp = (jalview.datamodel.Mapping) ref[2];
179 ((jalview.datamodel.AlignedCodonFrame) ref[1]).addMap(
180 seq, mp.getTo(), mp.getMap());
185 .println("IMPLEMENTATION ERROR: Unimplemented forward sequence references for AlcodonFrames involving "
186 + ref[2].getClass() + " type objects.");
192 .println("IMPLEMENTATION ERROR: Unimplemented forward sequence references for "
193 + ref[1].getClass() + " type objects.");
196 frefedSequence.remove(r);
202 .println("IMPLEMENTATION WARNING: Unresolved forward reference for hash string "
204 + " with objecttype "
205 + ref[1].getClass());
212 frefedSequence.remove(r);
220 * This maintains a list of viewports, the key being the seqSetId. Important
221 * to set historyItem and redoList for multiple views
223 Hashtable viewportsAdded;
225 Hashtable annotationIds = new Hashtable();
227 String uniqueSetSuffix = "";
230 * List of pdbfiles added to Jar
232 Vector pdbfiles = null;
234 // SAVES SEVERAL ALIGNMENT WINDOWS TO SAME JARFILE
235 public void SaveState(File statefile)
239 FileOutputStream fos = new FileOutputStream(statefile);
240 JarOutputStream jout = new JarOutputStream(fos);
243 } catch (Exception e)
245 // TODO: inform user of the problem - they need to know if their data was
247 if (errorMessage == null)
249 errorMessage = "Couldn't write Jalview Archive to output file '"
250 + statefile + "' - See console error log for details";
254 errorMessage += "(output file was '" + statefile + "')";
262 * Writes a jalview project archive to the given Jar output stream.
266 public void SaveState(JarOutputStream jout)
268 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
278 // NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS
279 // //////////////////////////////////////////////////
280 // NOTE ALSO new PrintWriter must be used for each new JarEntry
281 PrintWriter out = null;
283 Vector shortNames = new Vector();
286 for (int i = frames.length - 1; i > -1; i--)
288 if (frames[i] instanceof AlignFrame)
290 AlignFrame af = (AlignFrame) frames[i];
293 && skipList.containsKey(af.getViewport()
294 .getSequenceSetId()))
299 String shortName = af.getTitle();
301 if (shortName.indexOf(File.separatorChar) > -1)
303 shortName = shortName.substring(shortName
304 .lastIndexOf(File.separatorChar) + 1);
309 while (shortNames.contains(shortName))
311 if (shortName.endsWith("_" + (count - 1)))
313 shortName = shortName
314 .substring(0, shortName.lastIndexOf("_"));
317 shortName = shortName.concat("_" + count);
321 shortNames.addElement(shortName);
323 if (!shortName.endsWith(".xml"))
325 shortName = shortName + ".xml";
328 int ap, apSize = af.alignPanels.size();
329 for (ap = 0; ap < apSize; ap++)
331 AlignmentPanel apanel = (AlignmentPanel) af.alignPanels
333 String fileName = apSize == 1 ? shortName : ap + shortName;
334 if (!fileName.endsWith(".xml"))
336 fileName = fileName + ".xml";
339 SaveState(apanel, fileName, jout);
346 } catch (Exception foo)
351 } catch (Exception ex)
353 // TODO: inform user of the problem - they need to know if their data was
355 if (errorMessage == null)
357 errorMessage = "Couldn't write Jalview Archive - see error output for details";
359 ex.printStackTrace();
363 // USE THIS METHOD TO SAVE A SINGLE ALIGNMENT WINDOW
364 public boolean SaveAlignment(AlignFrame af, String jarFile,
369 int ap, apSize = af.alignPanels.size();
370 FileOutputStream fos = new FileOutputStream(jarFile);
371 JarOutputStream jout = new JarOutputStream(fos);
372 for (ap = 0; ap < apSize; ap++)
374 AlignmentPanel apanel = (AlignmentPanel) af.alignPanels
376 String jfileName = apSize == 1 ? fileName : fileName + ap;
377 if (!jfileName.endsWith(".xml"))
379 jfileName = jfileName + ".xml";
381 SaveState(apanel, jfileName, jout);
387 } catch (Exception foo)
393 } catch (Exception ex)
395 errorMessage = "Couldn't Write alignment view to Jalview Archive - see error output for details";
396 ex.printStackTrace();
402 * create a JalviewModel from an algnment view and marshall it to a
406 * panel to create jalview model for
408 * name of alignment panel written to output stream
414 public JalviewModel SaveState(AlignmentPanel ap, String fileName,
415 JarOutputStream jout)
418 Vector jmolViewIds = new Vector(); //
419 Vector userColours = new Vector();
421 AlignViewport av = ap.av;
423 JalviewModel object = new JalviewModel();
424 object.setVamsasModel(new jalview.schemabinding.version2.VamsasModel());
426 object.setCreationDate(new java.util.Date(System.currentTimeMillis()));
427 object.setVersion(jalview.bin.Cache.getProperty("VERSION"));
429 jalview.datamodel.AlignmentI jal = av.alignment;
431 if (av.hasHiddenRows)
433 jal = jal.getHiddenSequences().getFullAlignment();
436 SequenceSet vamsasSet = new SequenceSet();
438 JalviewModelSequence jms = new JalviewModelSequence();
440 vamsasSet.setGapChar(jal.getGapCharacter() + "");
442 if (jal.getDataset() != null)
444 // dataset id is the dataset's hashcode
445 vamsasSet.setDatasetId(getDatasetIdRef(jal.getDataset()));
447 if (jal.getProperties() != null)
449 Enumeration en = jal.getProperties().keys();
450 while (en.hasMoreElements())
452 String key = en.nextElement().toString();
453 SequenceSetProperties ssp = new SequenceSetProperties();
455 ssp.setValue(jal.getProperties().get(key).toString());
456 vamsasSet.addSequenceSetProperties(ssp);
464 jalview.datamodel.SequenceI jds;
465 for (int i = 0; i < jal.getHeight(); i++)
467 jds = jal.getSequenceAt(i);
470 if (seqRefIds.get(id) != null)
472 // This happens for two reasons: 1. multiple views are being serialised.
473 // 2. the hashCode has collided with another sequence's code. This DOES
474 // HAPPEN! (PF00072.15.stk does this)
475 // JBPNote: Uncomment to debug writing out of files that do not read
476 // back in due to ArrayOutOfBoundExceptions.
477 // System.err.println("vamsasSeq backref: "+id+"");
478 // System.err.println(jds.getName()+"
479 // "+jds.getStart()+"-"+jds.getEnd()+" "+jds.getSequenceAsString());
480 // System.err.println("Hashcode: "+seqHash(jds));
481 // SequenceI rsq = (SequenceI) seqRefIds.get(id + "");
482 // System.err.println(rsq.getName()+"
483 // "+rsq.getStart()+"-"+rsq.getEnd()+" "+rsq.getSequenceAsString());
484 // System.err.println("Hashcode: "+seqHash(rsq));
488 vamsasSeq = createVamsasSequence(id, jds);
489 vamsasSet.addSequence(vamsasSeq);
490 seqRefIds.put(id, jds);
494 jseq.setStart(jds.getStart());
495 jseq.setEnd(jds.getEnd());
496 jseq.setColour(av.getSequenceColour(jds).getRGB());
498 jseq.setId(id); // jseq id should be a string not a number
500 if (av.hasHiddenRows)
502 jseq.setHidden(av.alignment.getHiddenSequences().isHidden(jds));
504 if (av.hiddenRepSequences != null
505 && av.hiddenRepSequences.containsKey(jal.getSequenceAt(i)))
507 jalview.datamodel.SequenceI[] reps = ((jalview.datamodel.SequenceGroup) av.hiddenRepSequences
508 .get(jal.getSequenceAt(i))).getSequencesInOrder(jal);
510 for (int h = 0; h < reps.length; h++)
512 if (reps[h] != jal.getSequenceAt(i))
514 jseq.addHiddenSequences(jal.findIndex(reps[h]));
520 if (jds.getDatasetSequence().getSequenceFeatures() != null)
522 jalview.datamodel.SequenceFeature[] sf = jds.getDatasetSequence()
523 .getSequenceFeatures();
525 while (index < sf.length)
527 Features features = new Features();
529 features.setBegin(sf[index].getBegin());
530 features.setEnd(sf[index].getEnd());
531 features.setDescription(sf[index].getDescription());
532 features.setType(sf[index].getType());
533 features.setFeatureGroup(sf[index].getFeatureGroup());
534 features.setScore(sf[index].getScore());
535 if (sf[index].links != null)
537 for (int l = 0; l < sf[index].links.size(); l++)
539 OtherData keyValue = new OtherData();
540 keyValue.setKey("LINK_" + l);
541 keyValue.setValue(sf[index].links.elementAt(l).toString());
542 features.addOtherData(keyValue);
545 if (sf[index].otherDetails != null)
548 Enumeration keys = sf[index].otherDetails.keys();
549 while (keys.hasMoreElements())
551 key = keys.nextElement().toString();
552 OtherData keyValue = new OtherData();
553 keyValue.setKey(key);
554 keyValue.setValue(sf[index].otherDetails.get(key).toString());
555 features.addOtherData(keyValue);
559 jseq.addFeatures(features);
564 if (jds.getDatasetSequence().getPDBId() != null)
566 Enumeration en = jds.getDatasetSequence().getPDBId().elements();
567 while (en.hasMoreElements())
569 Pdbids pdb = new Pdbids();
570 jalview.datamodel.PDBEntry entry = (jalview.datamodel.PDBEntry) en
573 pdb.setId(entry.getId());
574 pdb.setType(entry.getType());
577 // This must have been loaded, is it still visible?
578 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
579 String matchedFile = null;
580 for (int f = frames.length - 1; f > -1; f--)
582 if (frames[f] instanceof AppJmol)
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 state.setAlignwithAlignPanel(jmol.isUsedforaligment(ap));
625 state.setColourwithAlignPanel(jmol
626 .isUsedforcolourby(ap));
627 state.setColourByJmol(jmol.isColouredByJmol());
628 if (!jmolViewIds.contains(state.getViewId()))
630 // Make sure we only store a Jmol state once in each XML
632 jmolViewIds.addElement(state.getViewId());
633 state.setContent(statestring.replaceAll("\n", ""));
637 state.setContent("# duplicate state");
639 pdb.addStructureState(state);
646 if (matchedFile != null || entry.getFile() != null)
648 if (entry.getFile() != null)
651 matchedFile = entry.getFile();
653 pdb.setFile(matchedFile); // entry.getFile());
654 if (pdbfiles == null)
656 pdbfiles = new Vector();
659 if (!pdbfiles.contains(entry.getId()))
661 pdbfiles.addElement(entry.getId());
664 File file = new File(matchedFile);
665 if (file.exists() && jout != null)
667 byte[] data = new byte[(int) file.length()];
668 jout.putNextEntry(new JarEntry(entry.getId()));
669 DataInputStream dis = new DataInputStream(
670 new FileInputStream(file));
673 DataOutputStream dout = new DataOutputStream(jout);
674 dout.write(data, 0, data.length);
678 } catch (Exception ex)
680 ex.printStackTrace();
686 if (entry.getProperty() != null)
688 PdbentryItem item = new PdbentryItem();
689 Hashtable properties = entry.getProperty();
690 Enumeration en2 = properties.keys();
691 while (en2.hasMoreElements())
693 Property prop = new Property();
694 String key = en2.nextElement().toString();
696 prop.setValue(properties.get(key).toString());
697 item.addProperty(prop);
699 pdb.addPdbentryItem(item);
709 if (av.hasHiddenRows)
714 if (jal.getCodonFrames() != null && jal.getCodonFrames().length > 0)
716 jalview.datamodel.AlignedCodonFrame[] jac = jal.getCodonFrames();
717 for (int i = 0; i < jac.length; i++)
719 AlcodonFrame alc = new AlcodonFrame();
720 vamsasSet.addAlcodonFrame(alc);
721 for (int p = 0; p < jac[i].aaWidth; p++)
723 Alcodon cmap = new Alcodon();
724 if (jac[i].codons[p] != null)
726 // Null codons indicate a gapped column in the translated peptide
728 cmap.setPos1(jac[i].codons[p][0]);
729 cmap.setPos2(jac[i].codons[p][1]);
730 cmap.setPos3(jac[i].codons[p][2]);
732 alc.addAlcodon(cmap);
734 if (jac[i].getProtMappings() != null
735 && jac[i].getProtMappings().length > 0)
737 SequenceI[] dnas = jac[i].getdnaSeqs();
738 jalview.datamodel.Mapping[] pmaps = jac[i].getProtMappings();
739 for (int m = 0; m < pmaps.length; m++)
741 AlcodMap alcmap = new AlcodMap();
742 alcmap.setDnasq(seqHash(dnas[m]));
743 alcmap.setMapping(createVamsasMapping(pmaps[m], dnas[m], null,
745 alc.addAlcodMap(alcmap);
752 // /////////////////////////////////
753 if (av.currentTree != null)
755 // FIND ANY ASSOCIATED TREES
756 // NOT IMPLEMENTED FOR HEADLESS STATE AT PRESENT
757 if (Desktop.desktop != null)
759 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
761 for (int t = 0; t < frames.length; t++)
763 if (frames[t] instanceof TreePanel)
765 TreePanel tp = (TreePanel) frames[t];
767 if (tp.treeCanvas.av.alignment == jal)
769 Tree tree = new Tree();
770 tree.setTitle(tp.getTitle());
771 tree.setCurrentTree((av.currentTree == tp.getTree()));
772 tree.setNewick(tp.getTree().toString());
773 tree.setThreshold(tp.treeCanvas.threshold);
775 tree.setFitToWindow(tp.fitToWindow.getState());
776 tree.setFontName(tp.getTreeFont().getName());
777 tree.setFontSize(tp.getTreeFont().getSize());
778 tree.setFontStyle(tp.getTreeFont().getStyle());
779 tree.setMarkUnlinked(tp.placeholdersMenu.getState());
781 tree.setShowBootstrap(tp.bootstrapMenu.getState());
782 tree.setShowDistances(tp.distanceMenu.getState());
784 tree.setHeight(tp.getHeight());
785 tree.setWidth(tp.getWidth());
786 tree.setXpos(tp.getX());
787 tree.setYpos(tp.getY());
788 tree.setId(makeHashCode(tp, null));
798 * store forward refs from an annotationRow to any groups
800 IdentityHashMap groupRefs = new IdentityHashMap();
801 if (jal.getAlignmentAnnotation() != null)
803 jalview.datamodel.AlignmentAnnotation[] aa = jal
804 .getAlignmentAnnotation();
806 for (int i = 0; i < aa.length; i++)
808 Annotation an = new Annotation();
810 if (aa[i].annotationId != null)
812 annotationIds.put(aa[i].annotationId, aa[i]);
815 an.setId(aa[i].annotationId);
817 an.setVisible(aa[i].visible);
819 an.setDescription(aa[i].description);
821 if (aa[i].sequenceRef != null)
823 // TODO later annotation sequenceRef should be the XML ID of the
824 // sequence rather than its display name
825 an.setSequenceRef(aa[i].sequenceRef.getName());
827 if (aa[i].groupRef != null)
829 Object groupIdr = groupRefs.get(aa[i].groupRef);
830 if (groupIdr == null)
832 // make a locally unique String
833 groupRefs.put(aa[i].groupRef,
834 groupIdr = ("" + System.currentTimeMillis()
835 + aa[i].groupRef.getName() + groupRefs.size()));
837 an.setGroupRef(groupIdr.toString());
840 // store all visualization attributes for annotation
841 an.setGraphHeight(aa[i].graphHeight);
842 an.setCentreColLabels(aa[i].centreColLabels);
843 an.setScaleColLabels(aa[i].scaleColLabel);
844 an.setShowAllColLabels(aa[i].showAllColLabels);
849 an.setGraphType(aa[i].graph);
850 an.setGraphGroup(aa[i].graphGroup);
851 if (aa[i].getThreshold() != null)
853 ThresholdLine line = new ThresholdLine();
854 line.setLabel(aa[i].getThreshold().label);
855 line.setValue(aa[i].getThreshold().value);
856 line.setColour(aa[i].getThreshold().colour.getRGB());
857 an.setThresholdLine(line);
865 an.setLabel(aa[i].label);
867 if (aa[i] == av.quality || aa[i] == av.conservation
868 || aa[i] == av.consensus || aa[i].autoCalculated)
870 // new way of indicating autocalculated annotation -
871 an.setAutoCalculated(aa[i].autoCalculated);
873 if (aa[i].hasScore())
875 an.setScore(aa[i].getScore());
877 AnnotationElement ae;
878 if (aa[i].annotations != null)
880 an.setScoreOnly(false);
881 for (int a = 0; a < aa[i].annotations.length; a++)
883 if ((aa[i] == null) || (aa[i].annotations[a] == null))
888 ae = new AnnotationElement();
889 if (aa[i].annotations[a].description != null)
890 ae.setDescription(aa[i].annotations[a].description);
891 if (aa[i].annotations[a].displayCharacter != null)
892 ae.setDisplayCharacter(aa[i].annotations[a].displayCharacter);
894 if (!Float.isNaN(aa[i].annotations[a].value))
895 ae.setValue(aa[i].annotations[a].value);
898 if (aa[i].annotations[a].secondaryStructure != ' '
899 && aa[i].annotations[a].secondaryStructure != '\0')
900 ae.setSecondaryStructure(aa[i].annotations[a].secondaryStructure
903 if (aa[i].annotations[a].colour != null
904 && aa[i].annotations[a].colour != java.awt.Color.black)
906 ae.setColour(aa[i].annotations[a].colour.getRGB());
909 an.addAnnotationElement(ae);
910 if (aa[i].autoCalculated)
912 // only write one non-null entry into the annotation row -
913 // sufficient to get the visualization attributes necessary to
921 an.setScoreOnly(true);
923 vamsasSet.addAnnotation(an);
927 if (jal.getGroups() != null)
929 JGroup[] groups = new JGroup[jal.getGroups().size()];
931 for (int i = 0; i < groups.length; i++)
933 groups[i] = new JGroup();
935 jalview.datamodel.SequenceGroup sg = (jalview.datamodel.SequenceGroup) jal
936 .getGroups().elementAt(i);
937 groups[i].setStart(sg.getStartRes());
938 groups[i].setEnd(sg.getEndRes());
939 groups[i].setName(sg.getName());
940 if (groupRefs.containsKey(sg))
942 // group has references so set it's ID field
943 groups[i].setId(groupRefs.get(sg).toString());
947 if (sg.cs.conservationApplied())
949 groups[i].setConsThreshold(sg.cs.getConservationInc());
951 if (sg.cs instanceof jalview.schemes.UserColourScheme)
953 groups[i].setColour(SetUserColourScheme(sg.cs, userColours,
959 .setColour(ColourSchemeProperty.getColourName(sg.cs));
962 else if (sg.cs instanceof jalview.schemes.AnnotationColourGradient)
965 .setColour(ColourSchemeProperty
966 .getColourName(((jalview.schemes.AnnotationColourGradient) sg.cs)
969 else if (sg.cs instanceof jalview.schemes.UserColourScheme)
972 .setColour(SetUserColourScheme(sg.cs, userColours, jms));
976 groups[i].setColour(ColourSchemeProperty.getColourName(sg.cs));
979 groups[i].setPidThreshold(sg.cs.getThreshold());
982 groups[i].setOutlineColour(sg.getOutlineColour().getRGB());
983 groups[i].setDisplayBoxes(sg.getDisplayBoxes());
984 groups[i].setDisplayText(sg.getDisplayText());
985 groups[i].setColourText(sg.getColourText());
986 groups[i].setTextCol1(sg.textColour.getRGB());
987 groups[i].setTextCol2(sg.textColour2.getRGB());
988 groups[i].setTextColThreshold(sg.thresholdTextColour);
989 groups[i].setShowUnconserved(sg.getShowNonconserved());
990 groups[i].setIgnoreGapsinConsensus(sg.getIgnoreGapsConsensus());
991 groups[i].setShowConsensusHistogram(sg.isShowConsensusHistogram());
992 groups[i].setShowSequenceLogo(sg.isShowSequenceLogo());
993 for (int s = 0; s < sg.getSize(); s++)
995 jalview.datamodel.Sequence seq = (jalview.datamodel.Sequence) sg
997 groups[i].addSeq(seqHash(seq));
1001 jms.setJGroup(groups);
1004 // /////////SAVE VIEWPORT
1005 Viewport view = new Viewport();
1006 view.setTitle(ap.alignFrame.getTitle());
1007 view.setSequenceSetId(makeHashCode(av.getSequenceSetId(),
1008 av.getSequenceSetId()));
1009 view.setId(av.getViewId());
1010 view.setViewName(av.viewName);
1011 view.setGatheredViews(av.gatherViewsHere);
1013 if (ap.av.explodedPosition != null)
1015 view.setXpos(av.explodedPosition.x);
1016 view.setYpos(av.explodedPosition.y);
1017 view.setWidth(av.explodedPosition.width);
1018 view.setHeight(av.explodedPosition.height);
1022 view.setXpos(ap.alignFrame.getBounds().x);
1023 view.setYpos(ap.alignFrame.getBounds().y);
1024 view.setWidth(ap.alignFrame.getBounds().width);
1025 view.setHeight(ap.alignFrame.getBounds().height);
1028 view.setStartRes(av.startRes);
1029 view.setStartSeq(av.startSeq);
1031 if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme)
1033 view.setBgColour(SetUserColourScheme(av.getGlobalColourScheme(),
1036 else if (av.getGlobalColourScheme() instanceof jalview.schemes.AnnotationColourGradient)
1038 jalview.schemes.AnnotationColourGradient acg = (jalview.schemes.AnnotationColourGradient) av
1039 .getGlobalColourScheme();
1041 AnnotationColours ac = new AnnotationColours();
1042 ac.setAboveThreshold(acg.getAboveThreshold());
1043 ac.setThreshold(acg.getAnnotationThreshold());
1044 ac.setAnnotation(acg.getAnnotation());
1045 if (acg.getBaseColour() instanceof jalview.schemes.UserColourScheme)
1047 ac.setColourScheme(SetUserColourScheme(acg.getBaseColour(),
1052 ac.setColourScheme(ColourSchemeProperty.getColourName(acg
1056 ac.setMaxColour(acg.getMaxColour().getRGB());
1057 ac.setMinColour(acg.getMinColour().getRGB());
1058 view.setAnnotationColours(ac);
1059 view.setBgColour("AnnotationColourGradient");
1063 view.setBgColour(ColourSchemeProperty.getColourName(av
1064 .getGlobalColourScheme()));
1067 ColourSchemeI cs = av.getGlobalColourScheme();
1071 if (cs.conservationApplied())
1073 view.setConsThreshold(cs.getConservationInc());
1074 if (cs instanceof jalview.schemes.UserColourScheme)
1076 view.setBgColour(SetUserColourScheme(cs, userColours, jms));
1080 if (cs instanceof ResidueColourScheme)
1082 view.setPidThreshold(cs.getThreshold());
1086 view.setConservationSelected(av.getConservationSelected());
1087 view.setPidSelected(av.getAbovePIDThreshold());
1088 view.setFontName(av.font.getName());
1089 view.setFontSize(av.font.getSize());
1090 view.setFontStyle(av.font.getStyle());
1091 view.setRenderGaps(av.renderGaps);
1092 view.setShowAnnotation(av.getShowAnnotation());
1093 view.setShowBoxes(av.getShowBoxes());
1094 view.setShowColourText(av.getColourText());
1095 view.setShowFullId(av.getShowJVSuffix());
1096 view.setRightAlignIds(av.rightAlignIds);
1097 view.setShowSequenceFeatures(av.showSequenceFeatures);
1098 view.setShowText(av.getShowText());
1099 view.setShowUnconserved(av.getShowUnconserved());
1100 view.setWrapAlignment(av.getWrapAlignment());
1101 view.setTextCol1(av.textColour.getRGB());
1102 view.setTextCol2(av.textColour2.getRGB());
1103 view.setTextColThreshold(av.thresholdTextColour);
1104 view.setShowConsensusHistogram(av.isShowConsensusHistogram());
1105 view.setShowSequenceLogo(av.isShowSequenceLogo());
1106 view.setShowGroupConsensus(av.isShowGroupConsensus());
1107 view.setShowGroupConservation(av.isShowGroupConservation());
1108 view.setShowNPfeatureTooltip(av.isShowNpFeats());
1109 view.setShowDbRefTooltip(av.isShowDbRefs());
1110 view.setFollowHighlight(av.followHighlight);
1111 view.setFollowSelection(av.followSelection);
1112 view.setIgnoreGapsinConsensus(av.getIgnoreGapsConsensus());
1113 if (av.featuresDisplayed != null)
1115 jalview.schemabinding.version2.FeatureSettings fs = new jalview.schemabinding.version2.FeatureSettings();
1117 String[] renderOrder = ap.seqPanel.seqCanvas.getFeatureRenderer().renderOrder;
1119 Vector settingsAdded = new Vector();
1120 Object gstyle = null;
1121 GraduatedColor gcol = null;
1122 if (renderOrder != null)
1124 for (int ro = 0; ro < renderOrder.length; ro++)
1126 gstyle = ap.seqPanel.seqCanvas.getFeatureRenderer()
1127 .getFeatureStyle(renderOrder[ro]);
1128 Setting setting = new Setting();
1129 setting.setType(renderOrder[ro]);
1130 if (gstyle instanceof GraduatedColor)
1132 gcol = (GraduatedColor) gstyle;
1133 setting.setColour(gcol.getMaxColor().getRGB());
1134 setting.setMincolour(gcol.getMinColor().getRGB());
1135 setting.setMin(gcol.getMin());
1136 setting.setMax(gcol.getMax());
1137 setting.setColourByLabel(gcol.isColourByLabel());
1138 setting.setAutoScale(gcol.isAutoScale());
1139 setting.setThreshold(gcol.getThresh());
1140 setting.setThreshstate(gcol.getThreshType());
1144 setting.setColour(ap.seqPanel.seqCanvas.getFeatureRenderer()
1145 .getColour(renderOrder[ro]).getRGB());
1148 setting.setDisplay(av.featuresDisplayed
1149 .containsKey(renderOrder[ro]));
1150 float rorder = ap.seqPanel.seqCanvas.getFeatureRenderer()
1151 .getOrder(renderOrder[ro]);
1154 setting.setOrder(rorder);
1156 fs.addSetting(setting);
1157 settingsAdded.addElement(renderOrder[ro]);
1161 // Make sure we save none displayed feature settings
1162 Enumeration en = ap.seqPanel.seqCanvas.getFeatureRenderer().featureColours
1164 while (en.hasMoreElements())
1166 String key = en.nextElement().toString();
1167 if (settingsAdded.contains(key))
1172 Setting setting = new Setting();
1173 setting.setType(key);
1174 setting.setColour(ap.seqPanel.seqCanvas.getFeatureRenderer()
1175 .getColour(key).getRGB());
1177 setting.setDisplay(false);
1178 float rorder = ap.seqPanel.seqCanvas.getFeatureRenderer().getOrder(
1182 setting.setOrder(rorder);
1184 fs.addSetting(setting);
1185 settingsAdded.addElement(key);
1187 en = ap.seqPanel.seqCanvas.getFeatureRenderer().featureGroups.keys();
1188 Vector groupsAdded = new Vector();
1189 while (en.hasMoreElements())
1191 String grp = en.nextElement().toString();
1192 if (groupsAdded.contains(grp))
1196 Group g = new Group();
1198 g.setDisplay(((Boolean) ap.seqPanel.seqCanvas.getFeatureRenderer().featureGroups
1199 .get(grp)).booleanValue());
1201 groupsAdded.addElement(grp);
1203 jms.setFeatureSettings(fs);
1207 if (av.hasHiddenColumns)
1209 if (av.getColumnSelection() == null
1210 || av.getColumnSelection().getHiddenColumns() == null)
1212 warn("REPORT BUG: avoided null columnselection bug (DMAM reported). Please contact Jim about this.");
1216 for (int c = 0; c < av.getColumnSelection().getHiddenColumns()
1219 int[] region = (int[]) av.getColumnSelection().getHiddenColumns()
1221 HiddenColumns hc = new HiddenColumns();
1222 hc.setStart(region[0]);
1223 hc.setEnd(region[1]);
1224 view.addHiddenColumns(hc);
1229 jms.addViewport(view);
1231 object.setJalviewModelSequence(jms);
1232 object.getVamsasModel().addSequenceSet(vamsasSet);
1234 if (jout != null && fileName != null)
1236 // We may not want to write the object to disk,
1237 // eg we can copy the alignViewport to a new view object
1238 // using save and then load
1241 JarEntry entry = new JarEntry(fileName);
1242 jout.putNextEntry(entry);
1243 PrintWriter pout = new PrintWriter(new OutputStreamWriter(jout,
1245 org.exolab.castor.xml.Marshaller marshaller = new org.exolab.castor.xml.Marshaller(
1247 marshaller.marshal(object);
1250 } catch (Exception ex)
1252 // TODO: raise error in GUI if marshalling failed.
1253 ex.printStackTrace();
1260 * External mapping between jalview objects and objects yielding a valid and
1261 * unique object ID string. This is null for normal Jalview project IO, but
1262 * non-null when a jalview project is being read or written as part of a
1265 IdentityHashMap jv2vobj = null;
1268 * Construct a unique ID for jvobj using either existing bindings or if none
1269 * exist, the result of the hashcode call for the object.
1272 * jalview data object
1273 * @return unique ID for referring to jvobj
1275 private String makeHashCode(Object jvobj, String altCode)
1277 if (jv2vobj != null)
1279 Object id = jv2vobj.get(jvobj);
1282 return id.toString();
1284 // check string ID mappings
1285 if (jvids2vobj != null && jvobj instanceof String)
1287 id = jvids2vobj.get(jvobj);
1291 return id.toString();
1293 // give up and warn that something has gone wrong
1294 warn("Cannot find ID for object in external mapping : " + jvobj);
1300 * return local jalview object mapped to ID, if it exists
1304 * @return null or object bound to idcode
1306 private Object retrieveExistingObj(String idcode)
1308 if (idcode != null && vobj2jv != null)
1310 return vobj2jv.get(idcode);
1316 * binding from ID strings from external mapping table to jalview data model
1319 private Hashtable vobj2jv;
1321 private Sequence createVamsasSequence(String id, SequenceI jds)
1323 return createVamsasSequence(true, id, jds, null);
1326 private Sequence createVamsasSequence(boolean recurse, String id,
1327 SequenceI jds, SequenceI parentseq)
1329 Sequence vamsasSeq = new Sequence();
1330 vamsasSeq.setId(id);
1331 vamsasSeq.setName(jds.getName());
1332 vamsasSeq.setSequence(jds.getSequenceAsString());
1333 vamsasSeq.setDescription(jds.getDescription());
1334 jalview.datamodel.DBRefEntry[] dbrefs = null;
1335 if (jds.getDatasetSequence() != null)
1337 vamsasSeq.setDsseqid(seqHash(jds.getDatasetSequence()));
1338 if (jds.getDatasetSequence().getDBRef() != null)
1340 dbrefs = jds.getDatasetSequence().getDBRef();
1345 vamsasSeq.setDsseqid(id); // so we can tell which sequences really are
1346 // dataset sequences only
1347 dbrefs = jds.getDBRef();
1351 for (int d = 0; d < dbrefs.length; d++)
1353 DBRef dbref = new DBRef();
1354 dbref.setSource(dbrefs[d].getSource());
1355 dbref.setVersion(dbrefs[d].getVersion());
1356 dbref.setAccessionId(dbrefs[d].getAccessionId());
1357 if (dbrefs[d].hasMap())
1359 Mapping mp = createVamsasMapping(dbrefs[d].getMap(), parentseq,
1361 dbref.setMapping(mp);
1363 vamsasSeq.addDBRef(dbref);
1369 private Mapping createVamsasMapping(jalview.datamodel.Mapping jmp,
1370 SequenceI parentseq, SequenceI jds, boolean recurse)
1373 if (jmp.getMap() != null)
1377 jalview.util.MapList mlst = jmp.getMap();
1378 int r[] = mlst.getFromRanges();
1379 for (int s = 0; s < r.length; s += 2)
1381 MapListFrom mfrom = new MapListFrom();
1382 mfrom.setStart(r[s]);
1383 mfrom.setEnd(r[s + 1]);
1384 mp.addMapListFrom(mfrom);
1386 r = mlst.getToRanges();
1387 for (int s = 0; s < r.length; s += 2)
1389 MapListTo mto = new MapListTo();
1391 mto.setEnd(r[s + 1]);
1392 mp.addMapListTo(mto);
1394 mp.setMapFromUnit(mlst.getFromRatio());
1395 mp.setMapToUnit(mlst.getToRatio());
1396 if (jmp.getTo() != null)
1398 MappingChoice mpc = new MappingChoice();
1400 && (parentseq != jmp.getTo() || parentseq
1401 .getDatasetSequence() != jmp.getTo()))
1403 mpc.setSequence(createVamsasSequence(false, seqHash(jmp.getTo()),
1409 SequenceI ps = null;
1410 if (parentseq != jmp.getTo()
1411 && parentseq.getDatasetSequence() != jmp.getTo())
1413 // chaining dbref rather than a handshaking one
1414 jmpid = seqHash(ps = jmp.getTo());
1418 jmpid = seqHash(ps = parentseq);
1420 mpc.setDseqFor(jmpid);
1421 if (!seqRefIds.containsKey(mpc.getDseqFor()))
1423 jalview.bin.Cache.log.debug("creatign new DseqFor ID");
1424 seqRefIds.put(mpc.getDseqFor(), ps);
1428 jalview.bin.Cache.log.debug("reusing DseqFor ID");
1431 mp.setMappingChoice(mpc);
1437 String SetUserColourScheme(jalview.schemes.ColourSchemeI cs,
1438 Vector userColours, JalviewModelSequence jms)
1441 jalview.schemes.UserColourScheme ucs = (jalview.schemes.UserColourScheme) cs;
1442 boolean newucs = false;
1443 if (!userColours.contains(ucs))
1445 userColours.add(ucs);
1448 id = "ucs" + userColours.indexOf(ucs);
1451 // actually create the scheme's entry in the XML model
1452 java.awt.Color[] colours = ucs.getColours();
1453 jalview.schemabinding.version2.UserColours uc = new jalview.schemabinding.version2.UserColours();
1454 jalview.schemabinding.version2.UserColourScheme jbucs = new jalview.schemabinding.version2.UserColourScheme();
1456 for (int i = 0; i < colours.length; i++)
1458 jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();
1459 col.setName(ResidueProperties.aa[i]);
1460 col.setRGB(jalview.util.Format.getHexString(colours[i]));
1461 jbucs.addColour(col);
1463 if (ucs.getLowerCaseColours() != null)
1465 colours = ucs.getLowerCaseColours();
1466 for (int i = 0; i < colours.length; i++)
1468 jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();
1469 col.setName(ResidueProperties.aa[i].toLowerCase());
1470 col.setRGB(jalview.util.Format.getHexString(colours[i]));
1471 jbucs.addColour(col);
1476 uc.setUserColourScheme(jbucs);
1477 jms.addUserColours(uc);
1483 jalview.schemes.UserColourScheme GetUserColourScheme(
1484 JalviewModelSequence jms, String id)
1486 UserColours[] uc = jms.getUserColours();
1487 UserColours colours = null;
1489 for (int i = 0; i < uc.length; i++)
1491 if (uc[i].getId().equals(id))
1499 java.awt.Color[] newColours = new java.awt.Color[24];
1501 for (int i = 0; i < 24; i++)
1503 newColours[i] = new java.awt.Color(Integer.parseInt(colours
1504 .getUserColourScheme().getColour(i).getRGB(), 16));
1507 jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(
1510 if (colours.getUserColourScheme().getColourCount() > 24)
1512 newColours = new java.awt.Color[23];
1513 for (int i = 0; i < 23; i++)
1515 newColours[i] = new java.awt.Color(Integer.parseInt(colours
1516 .getUserColourScheme().getColour(i + 24).getRGB(), 16));
1518 ucs.setLowerCaseColours(newColours);
1525 * contains last error message (if any) encountered by XML loader.
1527 String errorMessage = null;
1530 * flag to control whether the Jalview2XML_V1 parser should be deferred to if
1531 * exceptions are raised during project XML parsing
1533 public boolean attemptversion1parse = true;
1536 * Load a jalview project archive from a jar file
1539 * - HTTP URL or filename
1541 public AlignFrame LoadJalviewAlign(final String file)
1544 jalview.gui.AlignFrame af = null;
1548 // UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
1549 // Workaround is to make sure caller implements the JarInputStreamProvider
1551 // so we can re-open the jar input stream for each entry.
1553 jarInputStreamProvider jprovider = createjarInputStreamProvider(file);
1554 af = LoadJalviewAlign(jprovider);
1555 } catch (MalformedURLException e)
1557 errorMessage = "Invalid URL format for '" + file + "'";
1563 private jarInputStreamProvider createjarInputStreamProvider(
1564 final String file) throws MalformedURLException
1567 errorMessage = null;
1568 uniqueSetSuffix = null;
1570 viewportsAdded = null;
1571 frefedSequence = null;
1573 if (file.startsWith("http://"))
1575 url = new URL(file);
1577 final URL _url = url;
1578 return new jarInputStreamProvider()
1581 public JarInputStream getJarInputStream() throws IOException
1585 return new JarInputStream(_url.openStream());
1589 return new JarInputStream(new FileInputStream(file));
1593 public String getFilename()
1601 * Recover jalview session from a jalview project archive. Caller may
1602 * initialise uniqueSetSuffix, seqRefIds, viewportsAdded and frefedSequence
1603 * themselves. Any null fields will be initialised with default values,
1604 * non-null fields are left alone.
1609 public AlignFrame LoadJalviewAlign(final jarInputStreamProvider jprovider)
1611 errorMessage = null;
1612 if (uniqueSetSuffix == null)
1614 uniqueSetSuffix = System.currentTimeMillis() % 100000 + "";
1616 if (seqRefIds == null)
1618 seqRefIds = new Hashtable();
1620 if (viewportsAdded == null)
1622 viewportsAdded = new Hashtable();
1624 if (frefedSequence == null)
1626 frefedSequence = new Vector();
1629 jalview.gui.AlignFrame af = null;
1630 Hashtable gatherToThisFrame = new Hashtable();
1631 final String file = jprovider.getFilename();
1634 JarInputStream jin = null;
1635 JarEntry jarentry = null;
1640 jin = jprovider.getJarInputStream();
1641 for (int i = 0; i < entryCount; i++)
1643 jarentry = jin.getNextJarEntry();
1646 if (jarentry != null && jarentry.getName().endsWith(".xml"))
1648 InputStreamReader in = new InputStreamReader(jin, "UTF-8");
1649 JalviewModel object = new JalviewModel();
1651 Unmarshaller unmar = new Unmarshaller(object);
1652 unmar.setValidation(false);
1653 object = (JalviewModel) unmar.unmarshal(in);
1654 if (true) // !skipViewport(object))
1656 af = LoadFromObject(object, file, true, jprovider);
1657 if (af.viewport.gatherViewsHere)
1659 gatherToThisFrame.put(af.viewport.getSequenceSetId(), af);
1664 else if (jarentry != null)
1666 // Some other file here.
1669 } while (jarentry != null);
1670 resolveFrefedSequences();
1671 } catch (java.io.FileNotFoundException ex)
1673 ex.printStackTrace();
1674 errorMessage = "Couldn't locate Jalview XML file : " + file;
1675 System.err.println("Exception whilst loading jalview XML file : "
1677 } catch (java.net.UnknownHostException ex)
1679 ex.printStackTrace();
1680 errorMessage = "Couldn't locate Jalview XML file : " + file;
1681 System.err.println("Exception whilst loading jalview XML file : "
1683 } catch (Exception ex)
1685 System.err.println("Parsing as Jalview Version 2 file failed.");
1686 ex.printStackTrace(System.err);
1687 if (attemptversion1parse)
1689 // Is Version 1 Jar file?
1692 af = new Jalview2XML_V1(raiseGUI).LoadJalviewAlign(jprovider);
1693 } catch (Exception ex2)
1695 System.err.println("Exception whilst loading as jalviewXMLV1:");
1696 ex2.printStackTrace();
1700 if (Desktop.instance != null)
1702 Desktop.instance.stopLoading();
1706 System.out.println("Successfully loaded archive file");
1709 ex.printStackTrace();
1711 System.err.println("Exception whilst loading jalview XML file : "
1713 } catch (OutOfMemoryError e)
1715 // Don't use the OOM Window here
1716 errorMessage = "Out of memory loading jalview XML file";
1717 System.err.println("Out of memory whilst loading jalview XML file");
1718 e.printStackTrace();
1721 if (Desktop.instance != null)
1723 Desktop.instance.stopLoading();
1726 Enumeration en = gatherToThisFrame.elements();
1727 while (en.hasMoreElements())
1729 Desktop.instance.gatherViews((AlignFrame) en.nextElement());
1731 if (errorMessage != null)
1739 * check errorMessage for a valid error message and raise an error box in the
1740 * GUI or write the current errorMessage to stderr and then clear the error
1743 protected void reportErrors()
1745 reportErrors(false);
1748 protected void reportErrors(final boolean saving)
1750 if (errorMessage != null)
1752 final String finalErrorMessage = errorMessage;
1755 javax.swing.SwingUtilities.invokeLater(new Runnable()
1759 JOptionPane.showInternalMessageDialog(Desktop.desktop,
1760 finalErrorMessage, "Error "
1761 + (saving ? "saving" : "loading")
1762 + " Jalview file", JOptionPane.WARNING_MESSAGE);
1768 System.err.println("Problem loading Jalview file: " + errorMessage);
1771 errorMessage = null;
1774 Hashtable alreadyLoadedPDB;
1777 * when set, local views will be updated from view stored in JalviewXML
1778 * Currently (28th Sep 2008) things will go horribly wrong in vamsas document
1779 * sync if this is set to true.
1781 private boolean updateLocalViews = false;
1783 String loadPDBFile(jarInputStreamProvider jprovider, String pdbId)
1785 if (alreadyLoadedPDB == null)
1786 alreadyLoadedPDB = new Hashtable();
1788 if (alreadyLoadedPDB.containsKey(pdbId))
1789 return alreadyLoadedPDB.get(pdbId).toString();
1793 JarInputStream jin = jprovider.getJarInputStream();
1795 * if (jprovider.startsWith("http://")) { jin = new JarInputStream(new
1796 * URL(jprovider).openStream()); } else { jin = new JarInputStream(new
1797 * FileInputStream(jprovider)); }
1800 JarEntry entry = null;
1803 entry = jin.getNextJarEntry();
1804 } while (entry != null && !entry.getName().equals(pdbId));
1807 BufferedReader in = new BufferedReader(new InputStreamReader(jin));
1808 File outFile = File.createTempFile("jalview_pdb", ".txt");
1809 outFile.deleteOnExit();
1810 PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
1813 while ((data = in.readLine()) != null)
1820 } catch (Exception foo)
1826 alreadyLoadedPDB.put(pdbId, outFile.getAbsolutePath());
1827 return outFile.getAbsolutePath();
1831 warn("Couldn't find PDB file entry in Jalview Jar for " + pdbId);
1833 } catch (Exception ex)
1835 ex.printStackTrace();
1841 private class JvAnnotRow
1843 public JvAnnotRow(int i, AlignmentAnnotation jaa)
1850 * persisted version of annotation row from which to take vis properties
1852 public jalview.datamodel.AlignmentAnnotation template;
1855 * original position of the annotation row in the alignment
1861 * Load alignment frame from jalview XML DOM object
1866 * filename source string
1867 * @param loadTreesAndStructures
1868 * when false only create Viewport
1870 * data source provider
1871 * @return alignment frame created from view stored in DOM
1873 AlignFrame LoadFromObject(JalviewModel object, String file,
1874 boolean loadTreesAndStructures, jarInputStreamProvider jprovider)
1876 SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);
1877 Sequence[] vamsasSeq = vamsasSet.getSequence();
1879 JalviewModelSequence jms = object.getJalviewModelSequence();
1881 Viewport view = jms.getViewport(0);
1882 // ////////////////////////////////
1885 Vector hiddenSeqs = null;
1886 jalview.datamodel.Sequence jseq;
1888 ArrayList tmpseqs = new ArrayList();
1890 boolean multipleView = false;
1892 JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq();
1893 int vi = 0; // counter in vamsasSeq array
1894 for (int i = 0; i < JSEQ.length; i++)
1896 String seqId = JSEQ[i].getId();
1898 if (seqRefIds.get(seqId) != null)
1900 tmpseqs.add((jalview.datamodel.Sequence) seqRefIds.get(seqId));
1901 multipleView = true;
1905 jseq = new jalview.datamodel.Sequence(vamsasSeq[vi].getName(),
1906 vamsasSeq[vi].getSequence());
1907 jseq.setDescription(vamsasSeq[vi].getDescription());
1908 jseq.setStart(JSEQ[i].getStart());
1909 jseq.setEnd(JSEQ[i].getEnd());
1910 jseq.setVamsasId(uniqueSetSuffix + seqId);
1911 seqRefIds.put(vamsasSeq[vi].getId(), jseq);
1916 if (JSEQ[i].getHidden())
1918 if (hiddenSeqs == null)
1920 hiddenSeqs = new Vector();
1923 hiddenSeqs.addElement((jalview.datamodel.Sequence) seqRefIds
1930 // Create the alignment object from the sequence set
1931 // ///////////////////////////////
1932 jalview.datamodel.Sequence[] orderedSeqs = new jalview.datamodel.Sequence[tmpseqs
1935 tmpseqs.toArray(orderedSeqs);
1937 jalview.datamodel.Alignment al = new jalview.datamodel.Alignment(
1940 // / Add the alignment properties
1941 for (int i = 0; i < vamsasSet.getSequenceSetPropertiesCount(); i++)
1943 SequenceSetProperties ssp = vamsasSet.getSequenceSetProperties(i);
1944 al.setProperty(ssp.getKey(), ssp.getValue());
1948 // SequenceFeatures are added to the DatasetSequence,
1949 // so we must create or recover the dataset before loading features
1950 // ///////////////////////////////
1951 if (vamsasSet.getDatasetId() == null || vamsasSet.getDatasetId() == "")
1953 // older jalview projects do not have a dataset id.
1954 al.setDataset(null);
1958 recoverDatasetFor(vamsasSet, al);
1960 // ///////////////////////////////
1962 Hashtable pdbloaded = new Hashtable();
1965 // load sequence features, database references and any associated PDB
1966 // structures for the alignment
1967 for (int i = 0; i < vamsasSeq.length; i++)
1969 if (JSEQ[i].getFeaturesCount() > 0)
1971 Features[] features = JSEQ[i].getFeatures();
1972 for (int f = 0; f < features.length; f++)
1974 jalview.datamodel.SequenceFeature sf = new jalview.datamodel.SequenceFeature(
1975 features[f].getType(), features[f].getDescription(),
1976 features[f].getStatus(), features[f].getBegin(),
1977 features[f].getEnd(), features[f].getFeatureGroup());
1979 sf.setScore(features[f].getScore());
1980 for (int od = 0; od < features[f].getOtherDataCount(); od++)
1982 OtherData keyValue = features[f].getOtherData(od);
1983 if (keyValue.getKey().startsWith("LINK"))
1985 sf.addLink(keyValue.getValue());
1989 sf.setValue(keyValue.getKey(), keyValue.getValue());
1994 al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf);
1997 if (vamsasSeq[i].getDBRefCount() > 0)
1999 addDBRefs(al.getSequenceAt(i).getDatasetSequence(), vamsasSeq[i]);
2001 if (JSEQ[i].getPdbidsCount() > 0)
2003 Pdbids[] ids = JSEQ[i].getPdbids();
2004 for (int p = 0; p < ids.length; p++)
2006 jalview.datamodel.PDBEntry entry = new jalview.datamodel.PDBEntry();
2007 entry.setId(ids[p].getId());
2008 entry.setType(ids[p].getType());
2009 if (ids[p].getFile() != null)
2011 if (!pdbloaded.containsKey(ids[p].getFile()))
2013 entry.setFile(loadPDBFile(jprovider, ids[p].getId()));
2017 entry.setFile(pdbloaded.get(ids[p].getId()).toString());
2021 al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
2025 } // end !multipleview
2027 // ///////////////////////////////
2028 // LOAD SEQUENCE MAPPINGS
2030 if (vamsasSet.getAlcodonFrameCount() > 0)
2032 // TODO Potentially this should only be done once for all views of an
2034 AlcodonFrame[] alc = vamsasSet.getAlcodonFrame();
2035 for (int i = 0; i < alc.length; i++)
2037 jalview.datamodel.AlignedCodonFrame cf = new jalview.datamodel.AlignedCodonFrame(
2038 alc[i].getAlcodonCount());
2039 if (alc[i].getAlcodonCount() > 0)
2041 Alcodon[] alcods = alc[i].getAlcodon();
2042 for (int p = 0; p < cf.codons.length; p++)
2044 if (alcods[p].hasPos1() && alcods[p].hasPos2()
2045 && alcods[p].hasPos3())
2047 // translated codons require three valid positions
2048 cf.codons[p] = new int[3];
2049 cf.codons[p][0] = (int) alcods[p].getPos1();
2050 cf.codons[p][1] = (int) alcods[p].getPos2();
2051 cf.codons[p][2] = (int) alcods[p].getPos3();
2055 cf.codons[p] = null;
2059 if (alc[i].getAlcodMapCount() > 0)
2061 AlcodMap[] maps = alc[i].getAlcodMap();
2062 for (int m = 0; m < maps.length; m++)
2064 SequenceI dnaseq = (SequenceI) seqRefIds
2065 .get(maps[m].getDnasq());
2067 jalview.datamodel.Mapping mapping = null;
2068 // attach to dna sequence reference.
2069 if (maps[m].getMapping() != null)
2071 mapping = addMapping(maps[m].getMapping());
2075 cf.addMap(dnaseq, mapping.getTo(), mapping.getMap());
2080 frefedSequence.add(new Object[]
2081 { maps[m].getDnasq(), cf, mapping });
2085 al.addCodonFrame(cf);
2090 // ////////////////////////////////
2092 ArrayList<JvAnnotRow> autoAlan = new ArrayList<JvAnnotRow>();
2094 * store any annotations which forward reference a group's ID
2096 Hashtable<String, ArrayList<jalview.datamodel.AlignmentAnnotation>> groupAnnotRefs = new Hashtable<String, ArrayList<jalview.datamodel.AlignmentAnnotation>>();
2098 if (vamsasSet.getAnnotationCount() > 0)
2100 Annotation[] an = vamsasSet.getAnnotation();
2102 for (int i = 0; i < an.length; i++)
2105 * test if annotation is automatically calculated for this view only
2107 boolean autoForView = false;
2108 if (an[i].getLabel().equals("Quality")
2109 || an[i].getLabel().equals("Conservation")
2110 || an[i].getLabel().equals("Consensus"))
2112 // Kludge for pre 2.5 projects which lacked the autocalculated flag
2114 if (!an[i].hasAutoCalculated())
2116 an[i].setAutoCalculated(true);
2120 || (an[i].hasAutoCalculated() && an[i].isAutoCalculated()))
2122 // remove ID - we don't recover annotation from other views for
2123 // view-specific annotation
2127 // set visiblity for other annotation in this view
2128 if (an[i].getId() != null
2129 && annotationIds.containsKey(an[i].getId()))
2131 jalview.datamodel.AlignmentAnnotation jda = (jalview.datamodel.AlignmentAnnotation) annotationIds
2132 .get(an[i].getId());
2133 // in principle Visible should always be true for annotation displayed
2134 // in multiple views
2135 if (an[i].hasVisible())
2136 jda.visible = an[i].getVisible();
2138 al.addAnnotation(jda);
2142 // Construct new annotation from model.
2143 AnnotationElement[] ae = an[i].getAnnotationElement();
2144 jalview.datamodel.Annotation[] anot = null;
2146 if (!an[i].getScoreOnly())
2148 anot = new jalview.datamodel.Annotation[al.getWidth()];
2149 for (int aa = 0; aa < ae.length && aa < anot.length; aa++)
2151 if (ae[aa].getPosition() >= anot.length)
2154 anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(
2156 ae[aa].getDisplayCharacter(), ae[aa].getDescription(),
2157 (ae[aa].getSecondaryStructure() == null || ae[aa]
2158 .getSecondaryStructure().length() == 0) ? ' '
2159 : ae[aa].getSecondaryStructure().charAt(0),
2163 // JBPNote: Consider verifying dataflow for IO of secondary
2164 // structure annotation read from Stockholm files
2165 // this was added to try to ensure that
2166 // if (anot[ae[aa].getPosition()].secondaryStructure>' ')
2168 // anot[ae[aa].getPosition()].displayCharacter = "";
2170 anot[ae[aa].getPosition()].colour = new java.awt.Color(
2171 ae[aa].getColour());
2174 jalview.datamodel.AlignmentAnnotation jaa = null;
2176 if (an[i].getGraph())
2178 float llim = 0, hlim = 0;
2179 // if (autoForView || an[i].isAutoCalculated()) {
2182 jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
2183 an[i].getDescription(), anot, llim, hlim,
2184 an[i].getGraphType());
2186 jaa.graphGroup = an[i].getGraphGroup();
2188 if (an[i].getThresholdLine() != null)
2190 jaa.setThreshold(new jalview.datamodel.GraphLine(an[i]
2191 .getThresholdLine().getValue(), an[i]
2192 .getThresholdLine().getLabel(), new java.awt.Color(
2193 an[i].getThresholdLine().getColour())));
2196 if (autoForView || an[i].isAutoCalculated())
2198 // Hardwire the symbol display line to ensure that labels for
2199 // histograms are displayed
2205 jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
2206 an[i].getDescription(), anot);
2210 // register new annotation
2211 if (an[i].getId() != null)
2213 annotationIds.put(an[i].getId(), jaa);
2214 jaa.annotationId = an[i].getId();
2216 // recover sequence association
2217 if (an[i].getSequenceRef() != null)
2219 if (al.findName(an[i].getSequenceRef()) != null)
2221 jaa.createSequenceMapping(
2222 al.findName(an[i].getSequenceRef()), 1, true);
2223 al.findName(an[i].getSequenceRef()).addAlignmentAnnotation(
2228 // and make a note of any group association
2229 if (an[i].getGroupRef() != null && an[i].getGroupRef().length() > 0)
2231 ArrayList<jalview.datamodel.AlignmentAnnotation> aal = groupAnnotRefs
2232 .get(an[i].getGroupRef());
2235 aal = new ArrayList<jalview.datamodel.AlignmentAnnotation>();
2236 groupAnnotRefs.put(an[i].getGroupRef(), aal);
2241 if (an[i].hasScore())
2243 jaa.setScore(an[i].getScore());
2245 if (an[i].hasVisible())
2246 jaa.visible = an[i].getVisible();
2248 if (an[i].hasCentreColLabels())
2249 jaa.centreColLabels = an[i].getCentreColLabels();
2251 if (an[i].hasScaleColLabels())
2253 jaa.scaleColLabel = an[i].getScaleColLabels();
2255 if (an[i].hasAutoCalculated() && an[i].isAutoCalculated())
2257 // newer files have an 'autoCalculated' flag and store calculation
2258 // state in viewport properties
2259 jaa.autoCalculated = true; // means annotation will be marked for
2260 // update at end of load.
2262 if (an[i].hasGraphHeight())
2264 jaa.graphHeight = an[i].getGraphHeight();
2266 if (jaa.autoCalculated)
2268 autoAlan.add(new JvAnnotRow(i, jaa));
2271 // if (!autoForView)
2273 // add autocalculated group annotation and any user created annotation
2275 al.addAnnotation(jaa);
2280 // ///////////////////////
2282 // Create alignment markup and styles for this view
2283 if (jms.getJGroupCount() > 0)
2285 JGroup[] groups = jms.getJGroup();
2287 for (int i = 0; i < groups.length; i++)
2289 ColourSchemeI cs = null;
2291 if (groups[i].getColour() != null)
2293 if (groups[i].getColour().startsWith("ucs"))
2295 cs = GetUserColourScheme(jms, groups[i].getColour());
2299 cs = ColourSchemeProperty.getColour(al, groups[i].getColour());
2304 cs.setThreshold(groups[i].getPidThreshold(), true);
2308 Vector seqs = new Vector();
2310 for (int s = 0; s < groups[i].getSeqCount(); s++)
2312 String seqId = groups[i].getSeq(s) + "";
2313 jalview.datamodel.SequenceI ts = (jalview.datamodel.SequenceI) seqRefIds
2318 seqs.addElement(ts);
2322 if (seqs.size() < 1)
2327 jalview.datamodel.SequenceGroup sg = new jalview.datamodel.SequenceGroup(
2328 seqs, groups[i].getName(), cs, groups[i].getDisplayBoxes(),
2329 groups[i].getDisplayText(), groups[i].getColourText(),
2330 groups[i].getStart(), groups[i].getEnd());
2332 sg.setOutlineColour(new java.awt.Color(groups[i].getOutlineColour()));
2334 sg.textColour = new java.awt.Color(groups[i].getTextCol1());
2335 sg.textColour2 = new java.awt.Color(groups[i].getTextCol2());
2336 sg.setShowNonconserved(groups[i].hasShowUnconserved() ? groups[i]
2337 .isShowUnconserved() : false);
2338 sg.thresholdTextColour = groups[i].getTextColThreshold();
2339 if (groups[i].hasShowConsensusHistogram())
2341 sg.setShowConsensusHistogram(groups[i].isShowConsensusHistogram());
2344 if (groups[i].hasShowSequenceLogo())
2346 sg.setshowSequenceLogo(groups[i].isShowSequenceLogo());
2348 if (groups[i].hasIgnoreGapsinConsensus())
2350 sg.setIgnoreGapsConsensus(groups[i].getIgnoreGapsinConsensus());
2352 if (groups[i].getConsThreshold() != 0)
2354 jalview.analysis.Conservation c = new jalview.analysis.Conservation(
2355 "All", ResidueProperties.propHash, 3,
2356 sg.getSequences(null), 0, sg.getWidth() - 1);
2358 c.verdict(false, 25);
2359 sg.cs.setConservation(c);
2362 if (groups[i].getId() != null && groupAnnotRefs.size() > 0)
2364 // re-instate unique group/annotation row reference
2365 ArrayList<jalview.datamodel.AlignmentAnnotation> jaal = groupAnnotRefs
2366 .get(groups[i].getId());
2369 for (jalview.datamodel.AlignmentAnnotation jaa : jaal)
2372 if (jaa.autoCalculated)
2374 // match up and try to set group autocalc alignment row for this
2376 if (jaa.label.startsWith("Consensus for "))
2378 sg.setConsensus(jaa);
2380 // match up and try to set group autocalc alignment row for this
2382 if (jaa.label.startsWith("Conservation for "))
2384 sg.setConservationRow(jaa);
2395 // ///////////////////////////////
2398 // If we just load in the same jar file again, the sequenceSetId
2399 // will be the same, and we end up with multiple references
2400 // to the same sequenceSet. We must modify this id on load
2401 // so that each load of the file gives a unique id
2402 String uniqueSeqSetId = view.getSequenceSetId() + uniqueSetSuffix;
2403 String viewId = (view.getId() == null ? null : view.getId()
2405 AlignFrame af = null;
2406 AlignViewport av = null;
2407 // now check to see if we really need to create a new viewport.
2408 if (multipleView && viewportsAdded.size() == 0)
2410 // We recovered an alignment for which a viewport already exists.
2411 // TODO: fix up any settings necessary for overlaying stored state onto
2412 // state recovered from another document. (may not be necessary).
2413 // we may need a binding from a viewport in memory to one recovered from
2415 // and then recover its containing af to allow the settings to be applied.
2416 // TODO: fix for vamsas demo
2418 .println("About to recover a viewport for existing alignment: Sequence set ID is "
2420 Object seqsetobj = retrieveExistingObj(uniqueSeqSetId);
2421 if (seqsetobj != null)
2423 if (seqsetobj instanceof String)
2425 uniqueSeqSetId = (String) seqsetobj;
2427 .println("Recovered extant sequence set ID mapping for ID : New Sequence set ID is "
2433 .println("Warning : Collision between sequence set ID string and existing jalview object mapping.");
2438 AlignmentPanel ap = null;
2439 boolean isnewview = true;
2442 // Check to see if this alignment already has a view id == viewId
2443 jalview.gui.AlignmentPanel views[] = Desktop
2444 .getAlignmentPanels(uniqueSeqSetId);
2445 if (views != null && views.length > 0)
2447 for (int v = 0; v < views.length; v++)
2449 if (views[v].av.getViewId().equalsIgnoreCase(viewId))
2451 // recover the existing alignpanel, alignframe, viewport
2452 af = views[v].alignFrame;
2455 // TODO: could even skip resetting view settings if we don't want to
2456 // change the local settings from other jalview processes
2465 af = loadViewport(file, JSEQ, hiddenSeqs, al, jms, view,
2466 uniqueSeqSetId, viewId, autoAlan);
2471 // /////////////////////////////////////
2472 if (loadTreesAndStructures && jms.getTreeCount() > 0)
2476 for (int t = 0; t < jms.getTreeCount(); t++)
2479 Tree tree = jms.getTree(t);
2481 TreePanel tp = (TreePanel) retrieveExistingObj(tree.getId());
2484 tp = af.ShowNewickTree(
2485 new jalview.io.NewickFile(tree.getNewick()),
2486 tree.getTitle(), tree.getWidth(), tree.getHeight(),
2487 tree.getXpos(), tree.getYpos());
2488 if (tree.getId() != null)
2490 // perhaps bind the tree id to something ?
2495 // update local tree attributes ?
2496 // TODO: should check if tp has been manipulated by user - if so its
2497 // settings shouldn't be modified
2498 tp.setTitle(tree.getTitle());
2499 tp.setBounds(new Rectangle(tree.getXpos(), tree.getYpos(), tree
2500 .getWidth(), tree.getHeight()));
2501 tp.av = av; // af.viewport; // TODO: verify 'associate with all
2504 tp.treeCanvas.av = av; // af.viewport;
2505 tp.treeCanvas.ap = ap; // af.alignPanel;
2510 warn("There was a problem recovering stored Newick tree: \n"
2511 + tree.getNewick());
2515 tp.fitToWindow.setState(tree.getFitToWindow());
2516 tp.fitToWindow_actionPerformed(null);
2518 if (tree.getFontName() != null)
2520 tp.setTreeFont(new java.awt.Font(tree.getFontName(), tree
2521 .getFontStyle(), tree.getFontSize()));
2525 tp.setTreeFont(new java.awt.Font(view.getFontName(), view
2526 .getFontStyle(), tree.getFontSize()));
2529 tp.showPlaceholders(tree.getMarkUnlinked());
2530 tp.showBootstrap(tree.getShowBootstrap());
2531 tp.showDistances(tree.getShowDistances());
2533 tp.treeCanvas.threshold = tree.getThreshold();
2535 if (tree.getCurrentTree())
2537 af.viewport.setCurrentTree(tp.getTree());
2541 } catch (Exception ex)
2543 ex.printStackTrace();
2547 // //LOAD STRUCTURES
2548 if (loadTreesAndStructures)
2550 // run through all PDB ids on the alignment, and collect mappings between
2551 // jmol view ids and all sequences referring to it
2552 Hashtable<String, Object[]> jmolViewIds = new Hashtable();
2554 for (int i = 0; i < JSEQ.length; i++)
2556 if (JSEQ[i].getPdbidsCount() > 0)
2558 Pdbids[] ids = JSEQ[i].getPdbids();
2559 for (int p = 0; p < ids.length; p++)
2561 for (int s = 0; s < ids[p].getStructureStateCount(); s++)
2563 // check to see if we haven't already created this structure view
2564 String sviewid = (ids[p].getStructureState(s).getViewId() == null) ? null
2565 : ids[p].getStructureState(s).getViewId()
2567 jalview.datamodel.PDBEntry jpdb = new jalview.datamodel.PDBEntry();
2568 // Originally : ids[p].getFile()
2569 // : TODO: verify external PDB file recovery still works in normal
2570 // jalview project load
2571 jpdb.setFile(loadPDBFile(jprovider, ids[p].getId()));
2572 jpdb.setId(ids[p].getId());
2574 int x = ids[p].getStructureState(s).getXpos();
2575 int y = ids[p].getStructureState(s).getYpos();
2576 int width = ids[p].getStructureState(s).getWidth();
2577 int height = ids[p].getStructureState(s).getHeight();
2579 // Probably don't need to do this anymore...
2580 // Desktop.desktop.getComponentAt(x, y);
2581 // TODO: NOW: check that this recovers the PDB file correctly.
2582 String pdbFile = loadPDBFile(jprovider, ids[p].getId());
2583 jalview.datamodel.SequenceI seq = (jalview.datamodel.SequenceI) seqRefIds
2584 .get(JSEQ[i].getId() + "");
2585 if (sviewid == null)
2587 sviewid = "_jalview_pre2_4_" + x + "," + y + "," + width
2590 if (!jmolViewIds.containsKey(sviewid))
2592 jmolViewIds.put(sviewid, new Object[]
2594 { x, y, width, height }, "",
2595 new Hashtable<String, Object[]>(), new boolean[]
2596 { false, false, true } });
2597 // Legacy pre-2.7 conversion JAL-823 :
2598 // do not assume any view has to be linked for colour by
2602 // assemble String[] { pdb files }, String[] { id for each
2603 // file }, orig_fileloc, SequenceI[][] {{ seqs_file 1 }, {
2604 // seqs_file 2}, boolean[] {
2605 // linkAlignPanel,superposeWithAlignpanel}} from hash
2606 Object[] jmoldat = (Object[]) jmolViewIds.get(sviewid);
2607 ((boolean[]) jmoldat[3])[0] |= ids[p].getStructureState(s)
2608 .hasAlignwithAlignPanel() ? ids[p].getStructureState(
2609 s).getAlignwithAlignPanel() : false;
2610 // never colour by linked panel if not specified
2611 ((boolean[]) jmoldat[3])[1] |= ids[p].getStructureState(s)
2612 .hasColourwithAlignPanel() ? ids[p]
2613 .getStructureState(s).getColourwithAlignPanel()
2615 // default for pre-2.7 projects is that Jmol colouring is enabled
2616 ((boolean[]) jmoldat[3])[2] &= ids[p].getStructureState(s)
2617 .hasColourByJmol() ? ids[p].getStructureState(s)
2618 .getColourByJmol() : true;
2620 if (((String) jmoldat[1]).length() < ids[p]
2621 .getStructureState(s).getContent().length())
2624 jmoldat[1] = ids[p].getStructureState(s).getContent();
2627 if (ids[p].getFile() != null)
2629 Object[] seqstrmaps = (Object[]) ((Hashtable) jmoldat[2])
2630 .get(ids[p].getFile());
2631 if (seqstrmaps == null)
2633 ((Hashtable) jmoldat[2]).put(
2634 new File(ids[p].getFile()).toString(),
2635 seqstrmaps = new Object[]
2636 { pdbFile, ids[p].getId(), new Vector(),
2639 if (!((Vector) seqstrmaps[2]).contains(seq))
2641 ((Vector) seqstrmaps[2]).addElement(seq);
2642 // ((Vector)seqstrmaps[3]).addElement(n) :
2643 // in principle, chains
2644 // should be stored here : do we need to
2645 // TODO: store and recover seq/pdb_id :
2651 errorMessage = ("The Jmol views in the Jalview 2 project may\nnot be correctly bound to sequences in the alignment.\nIn the case of problems, see note at\nhttp://issues.jalview.org/browse/JAL-747");
2660 // Instantiate the associated Jmol views
2661 for (Entry<String, Object[]> entry : jmolViewIds.entrySet())
2663 String sviewid = entry.getKey();
2664 Object[] svattrib = entry.getValue();
2665 int[] geom = (int[]) svattrib[0];
2666 String state = (String) svattrib[1];
2667 Hashtable<String, Object[]> oldFiles = (Hashtable<String, Object[]>) svattrib[2];
2668 final boolean useinJmolsuperpos = ((boolean[]) svattrib[3])[0], usetoColourbyseq = ((boolean[]) svattrib[3])[1], jmolColouring = ((boolean[]) svattrib[3])[2];
2669 int x = geom[0], y = geom[1], width = geom[2], height = geom[3];
2670 // collate the pdbfile -> sequence mappings from this view
2671 Vector<String> pdbfilenames = new Vector<String>();
2672 Vector<SequenceI[]> seqmaps = new Vector<SequenceI[]>();
2673 Vector<String> pdbids = new Vector<String>();
2675 // Search to see if we've already created this Jmol view
2676 AppJmol comp = null;
2677 JInternalFrame[] frames = null;
2682 frames = Desktop.desktop.getAllFrames();
2683 } catch (ArrayIndexOutOfBoundsException e)
2685 // occasional No such child exceptions are thrown here...
2690 } catch (Exception f)
2695 } while (frames == null);
2696 // search for any Jmol windows already open from other
2697 // alignment views that exactly match the stored structure state
2698 for (int f = 0; comp == null && f < frames.length; f++)
2700 if (frames[f] instanceof AppJmol)
2703 && ((AppJmol) frames[f]).getViewId().equals(sviewid))
2705 // post jalview 2.4 schema includes structure view id
2706 comp = (AppJmol) frames[f];
2708 else if (frames[f].getX() == x && frames[f].getY() == y
2709 && frames[f].getHeight() == height
2710 && frames[f].getWidth() == width)
2712 comp = (AppJmol) frames[f];
2719 // create a new Jmol window.
2720 // First parse the Jmol state to translate filenames loaded into the
2721 // view, and record the order in which files are shown in the Jmol
2722 // view, so we can add the sequence mappings in same order.
2723 StringBuffer newFileLoc = null;
2724 int cp = 0, ncp, ecp;
2725 while ((ncp = state.indexOf("load ", cp)) > -1)
2727 if (newFileLoc == null)
2729 newFileLoc = new StringBuffer();
2731 newFileLoc.append(state.substring(cp,
2732 ncp = (state.indexOf("\"", ncp + 1) + 1)));
2733 String oldfilenam = state.substring(ncp,
2734 ecp = state.indexOf("\"", ncp));
2735 // recover the new mapping data for this old filename
2736 // have to normalize filename - since Jmol and jalview do filename
2737 // translation differently.
2738 Object[] filedat = oldFiles.get(new File(oldfilenam)
2740 newFileLoc.append(((String) filedat[0]));
2741 pdbfilenames.addElement((String) filedat[0]);
2742 pdbids.addElement((String) filedat[1]);
2743 seqmaps.addElement((SequenceI[]) ((Vector<SequenceI>) filedat[2])
2744 .toArray(new SequenceI[0]));
2745 newFileLoc.append("\"");
2746 cp = ecp + 1; // advance beyond last \" and set cursor so we can
2747 // look for next file statement.
2751 // just append rest of state
2752 newFileLoc.append(state.substring(cp));
2757 .print("Ignoring incomplete Jmol state for PDB ids: ");
2758 newFileLoc = new StringBuffer(state);
2759 newFileLoc.append("; load append ");
2760 for (String id : oldFiles.keySet())
2762 // add this and any other pdb files that should be present in
2764 Object[] filedat = oldFiles.get(id);
2766 newFileLoc.append(((String) filedat[0]));
2767 pdbfilenames.addElement((String) filedat[0]);
2768 pdbids.addElement((String) filedat[1]);
2769 seqmaps.addElement((SequenceI[]) ((Vector<SequenceI>) filedat[2])
2770 .toArray(new SequenceI[0]));
2771 newFileLoc.append(" \"");
2772 newFileLoc.append((String) filedat[0]);
2773 newFileLoc.append("\"");
2776 newFileLoc.append(";");
2779 if (newFileLoc != null)
2781 int histbug = newFileLoc.indexOf("history = ");
2783 int diff = histbug == -1 ? -1 : newFileLoc.indexOf(";",
2785 String val = (diff == -1) ? null : newFileLoc.substring(
2787 if (val != null && val.length() >= 4)
2789 if (val.contains("e"))
2791 if (val.trim().equals("true"))
2799 newFileLoc.replace(histbug, diff, val);
2802 // TODO: assemble String[] { pdb files }, String[] { id for each
2803 // file }, orig_fileloc, SequenceI[][] {{ seqs_file 1 }, {
2804 // seqs_file 2}} from hash
2805 final String[] pdbf = (String[]) pdbfilenames
2806 .toArray(new String[pdbfilenames.size()]), id = (String[]) pdbids
2807 .toArray(new String[pdbids.size()]);
2808 final SequenceI[][] sq = (SequenceI[][]) seqmaps
2809 .toArray(new SequenceI[seqmaps.size()][]);
2810 final String fileloc = newFileLoc.toString(), vid = sviewid;
2811 final AlignFrame alf = af;
2812 final java.awt.Rectangle rect = new java.awt.Rectangle(x, y,
2816 javax.swing.SwingUtilities.invokeAndWait(new Runnable()
2820 AppJmol sview = null;
2823 sview = new AppJmol(pdbf, id, sq, alf.alignPanel,
2824 useinJmolsuperpos, usetoColourbyseq,
2825 jmolColouring, fileloc, rect, vid);
2826 } catch (OutOfMemoryError ex)
2828 new OOMWarning("restoring structure view for PDB id "
2829 + id, (OutOfMemoryError) ex.getCause());
2830 if (sview != null && sview.isVisible())
2832 sview.closeViewer();
2833 sview.setVisible(false);
2839 } catch (InvocationTargetException ex)
2841 warn("Unexpected error when opening Jmol view.", ex);
2843 } catch (InterruptedException e)
2845 // e.printStackTrace();
2851 // if (comp != null)
2853 // NOTE: if the jalview project is part of a shared session then
2854 // view synchronization should/could be done here.
2856 // add mapping for sequences in this view to an already open Jmol
2858 for (String id : oldFiles.keySet())
2860 // add this and any other pdb files that should be present in the
2862 Object[] filedat = oldFiles.get(id);
2863 String pdbFile = (String) filedat[0];
2864 SequenceI[] seq = (SequenceI[]) ((Vector<SequenceI>) filedat[2])
2865 .toArray(new SequenceI[0]);
2866 ((AppJmol) comp).jmb.ssm.setMapping(seq, null, pdbFile,
2867 jalview.io.AppletFormatAdapter.FILE);
2868 ((AppJmol) comp).jmb.addSequenceForStructFile(pdbFile, seq);
2870 // and add the AlignmentPanel's reference to the Jmol view
2871 ((AppJmol) comp).addAlignmentPanel(ap);
2872 if (useinJmolsuperpos)
2874 ((AppJmol) comp).useAlignmentPanelForSuperposition(ap);
2878 ((AppJmol) comp).excludeAlignmentPanelForSuperposition(ap);
2880 if (usetoColourbyseq)
2882 ((AppJmol) comp).useAlignmentPanelForColourbyseq(ap,
2887 ((AppJmol) comp).excludeAlignmentPanelForColourbyseq(ap);
2893 // and finally return.
2897 AlignFrame loadViewport(String file, JSeq[] JSEQ, Vector hiddenSeqs,
2898 Alignment al, JalviewModelSequence jms, Viewport view,
2899 String uniqueSeqSetId, String viewId,
2900 ArrayList<JvAnnotRow> autoAlan)
2902 AlignFrame af = null;
2903 af = new AlignFrame(al, view.getWidth(), view.getHeight(),
2904 uniqueSeqSetId, viewId);
2906 af.setFileName(file, "Jalview");
2908 for (int i = 0; i < JSEQ.length; i++)
2910 af.viewport.setSequenceColour(af.viewport.alignment.getSequenceAt(i),
2911 new java.awt.Color(JSEQ[i].getColour()));
2914 af.viewport.gatherViewsHere = view.getGatheredViews();
2916 if (view.getSequenceSetId() != null)
2918 jalview.gui.AlignViewport av = (jalview.gui.AlignViewport) viewportsAdded
2919 .get(uniqueSeqSetId);
2921 af.viewport.sequenceSetID = uniqueSeqSetId;
2924 // propagate shared settings to this new view
2925 af.viewport.historyList = av.historyList;
2926 af.viewport.redoList = av.redoList;
2930 viewportsAdded.put(uniqueSeqSetId, af.viewport);
2932 // TODO: check if this method can be called repeatedly without
2933 // side-effects if alignpanel already registered.
2934 PaintRefresher.Register(af.alignPanel, uniqueSeqSetId);
2936 // apply Hidden regions to view.
2937 if (hiddenSeqs != null)
2939 for (int s = 0; s < JSEQ.length; s++)
2941 jalview.datamodel.SequenceGroup hidden = new jalview.datamodel.SequenceGroup();
2943 for (int r = 0; r < JSEQ[s].getHiddenSequencesCount(); r++)
2946 al.getSequenceAt(JSEQ[s].getHiddenSequences(r)), false);
2948 af.viewport.hideRepSequences(al.getSequenceAt(s), hidden);
2951 jalview.datamodel.SequenceI[] hseqs = new jalview.datamodel.SequenceI[hiddenSeqs
2954 for (int s = 0; s < hiddenSeqs.size(); s++)
2956 hseqs[s] = (jalview.datamodel.SequenceI) hiddenSeqs.elementAt(s);
2959 af.viewport.hideSequence(hseqs);
2962 // recover view properties and display parameters
2963 if (view.getViewName() != null)
2965 af.viewport.viewName = view.getViewName();
2966 af.setInitialTabVisible();
2968 af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),
2971 af.viewport.setShowAnnotation(view.getShowAnnotation());
2972 af.viewport.setAbovePIDThreshold(view.getPidSelected());
2974 af.viewport.setColourText(view.getShowColourText());
2976 af.viewport.setConservationSelected(view.getConservationSelected());
2977 af.viewport.setShowJVSuffix(view.getShowFullId());
2978 af.viewport.rightAlignIds = view.getRightAlignIds();
2979 af.viewport.setFont(new java.awt.Font(view.getFontName(), view
2980 .getFontStyle(), view.getFontSize()));
2981 af.alignPanel.fontChanged();
2982 af.viewport.setRenderGaps(view.getRenderGaps());
2983 af.viewport.setWrapAlignment(view.getWrapAlignment());
2984 af.alignPanel.setWrapAlignment(view.getWrapAlignment());
2985 af.viewport.setShowAnnotation(view.getShowAnnotation());
2986 af.alignPanel.setAnnotationVisible(view.getShowAnnotation());
2988 af.viewport.setShowBoxes(view.getShowBoxes());
2990 af.viewport.setShowText(view.getShowText());
2992 af.viewport.textColour = new java.awt.Color(view.getTextCol1());
2993 af.viewport.textColour2 = new java.awt.Color(view.getTextCol2());
2994 af.viewport.thresholdTextColour = view.getTextColThreshold();
2995 af.viewport.setShowUnconserved(view.hasShowUnconserved() ? view
2996 .isShowUnconserved() : false);
2997 af.viewport.setStartRes(view.getStartRes());
2998 af.viewport.setStartSeq(view.getStartSeq());
3000 ColourSchemeI cs = null;
3001 // apply colourschemes
3002 if (view.getBgColour() != null)
3004 if (view.getBgColour().startsWith("ucs"))
3006 cs = GetUserColourScheme(jms, view.getBgColour());
3008 else if (view.getBgColour().startsWith("Annotation"))
3010 // int find annotation
3011 if (af.viewport.alignment.getAlignmentAnnotation() != null)
3013 for (int i = 0; i < af.viewport.alignment
3014 .getAlignmentAnnotation().length; i++)
3016 if (af.viewport.alignment.getAlignmentAnnotation()[i].label
3017 .equals(view.getAnnotationColours().getAnnotation()))
3019 if (af.viewport.alignment.getAlignmentAnnotation()[i]
3020 .getThreshold() == null)
3022 af.viewport.alignment.getAlignmentAnnotation()[i]
3023 .setThreshold(new jalview.datamodel.GraphLine(view
3024 .getAnnotationColours().getThreshold(),
3025 "Threshold", java.awt.Color.black)
3030 if (view.getAnnotationColours().getColourScheme()
3033 cs = new AnnotationColourGradient(
3034 af.viewport.alignment.getAlignmentAnnotation()[i],
3035 new java.awt.Color(view.getAnnotationColours()
3036 .getMinColour()), new java.awt.Color(view
3037 .getAnnotationColours().getMaxColour()),
3038 view.getAnnotationColours().getAboveThreshold());
3040 else if (view.getAnnotationColours().getColourScheme()
3043 cs = new AnnotationColourGradient(
3044 af.viewport.alignment.getAlignmentAnnotation()[i],
3045 GetUserColourScheme(jms, view
3046 .getAnnotationColours().getColourScheme()),
3047 view.getAnnotationColours().getAboveThreshold());
3051 cs = new AnnotationColourGradient(
3052 af.viewport.alignment.getAlignmentAnnotation()[i],
3053 ColourSchemeProperty.getColour(al, view
3054 .getAnnotationColours().getColourScheme()),
3055 view.getAnnotationColours().getAboveThreshold());
3058 // Also use these settings for all the groups
3059 if (al.getGroups() != null)
3061 for (int g = 0; g < al.getGroups().size(); g++)
3063 jalview.datamodel.SequenceGroup sg = (jalview.datamodel.SequenceGroup) al
3064 .getGroups().elementAt(g);
3073 * (view.getAnnotationColours().getColourScheme().equals("None"
3074 * )) { sg.cs = new AnnotationColourGradient(
3075 * af.viewport.alignment.getAlignmentAnnotation()[i], new
3076 * java.awt.Color(view.getAnnotationColours().
3077 * getMinColour()), new
3078 * java.awt.Color(view.getAnnotationColours().
3080 * view.getAnnotationColours().getAboveThreshold()); } else
3083 sg.cs = new AnnotationColourGradient(
3084 af.viewport.alignment.getAlignmentAnnotation()[i],
3085 sg.cs, view.getAnnotationColours()
3086 .getAboveThreshold());
3100 cs = ColourSchemeProperty.getColour(al, view.getBgColour());
3105 cs.setThreshold(view.getPidThreshold(), true);
3106 cs.setConsensus(af.viewport.hconsensus);
3110 af.viewport.setGlobalColourScheme(cs);
3111 af.viewport.setColourAppliesToAllGroups(false);
3113 if (view.getConservationSelected() && cs != null)
3115 cs.setConservationInc(view.getConsThreshold());
3118 af.changeColour(cs);
3120 af.viewport.setColourAppliesToAllGroups(true);
3122 if (view.getShowSequenceFeatures())
3124 af.viewport.showSequenceFeatures = true;
3126 if (view.hasCentreColumnLabels())
3128 af.viewport.setCentreColumnLabels(view.getCentreColumnLabels());
3130 if (view.hasIgnoreGapsinConsensus())
3132 af.viewport.ignoreGapsInConsensusCalculation = view
3133 .getIgnoreGapsinConsensus();
3135 if (view.hasFollowHighlight())
3137 af.viewport.followHighlight = view.getFollowHighlight();
3139 if (view.hasFollowSelection())
3141 af.viewport.followSelection = view.getFollowSelection();
3143 if (view.hasShowConsensusHistogram())
3145 af.viewport.setShowConsensusHistogram(view
3146 .getShowConsensusHistogram());
3150 af.viewport.setShowConsensusHistogram(true);
3152 if (view.hasShowSequenceLogo())
3154 af.viewport.showSequenceLogo = view.getShowSequenceLogo();
3158 af.viewport.showSequenceLogo = false;
3160 if (view.hasShowDbRefTooltip())
3162 af.viewport.setShowDbRefs(view.getShowDbRefTooltip());
3164 if (view.hasShowNPfeatureTooltip())
3166 af.viewport.setShowNpFeats(view.hasShowNPfeatureTooltip());
3168 if (view.hasShowGroupConsensus())
3170 af.viewport.setShowGroupConsensus(view.getShowGroupConsensus());
3174 af.viewport.setShowGroupConsensus(false);
3176 if (view.hasShowGroupConservation())
3178 af.viewport.setShowGroupConservation(view.getShowGroupConservation());
3182 af.viewport.setShowGroupConservation(false);
3185 // recover featre settings
3186 if (jms.getFeatureSettings() != null)
3188 af.viewport.featuresDisplayed = new Hashtable();
3189 String[] renderOrder = new String[jms.getFeatureSettings()
3190 .getSettingCount()];
3191 for (int fs = 0; fs < jms.getFeatureSettings().getSettingCount(); fs++)
3193 Setting setting = jms.getFeatureSettings().getSetting(fs);
3194 if (setting.hasMincolour())
3196 GraduatedColor gc = setting.hasMin() ? new GraduatedColor(
3197 new java.awt.Color(setting.getMincolour()),
3198 new java.awt.Color(setting.getColour()),
3199 setting.getMin(), setting.getMax()) : new GraduatedColor(
3200 new java.awt.Color(setting.getMincolour()),
3201 new java.awt.Color(setting.getColour()), 0, 1);
3202 if (setting.hasThreshold())
3204 gc.setThresh(setting.getThreshold());
3205 gc.setThreshType(setting.getThreshstate());
3207 gc.setAutoScaled(true); // default
3208 if (setting.hasAutoScale())
3210 gc.setAutoScaled(setting.getAutoScale());
3212 if (setting.hasColourByLabel())
3214 gc.setColourByLabel(setting.getColourByLabel());
3216 // and put in the feature colour table.
3217 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(
3218 setting.getType(), gc);
3222 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(
3224 new java.awt.Color(setting.getColour()));
3226 renderOrder[fs] = setting.getType();
3227 if (setting.hasOrder())
3228 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setOrder(
3229 setting.getType(), setting.getOrder());
3231 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setOrder(
3233 fs / jms.getFeatureSettings().getSettingCount());
3234 if (setting.getDisplay())
3236 af.viewport.featuresDisplayed.put(setting.getType(), new Integer(
3237 setting.getColour()));
3240 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder = renderOrder;
3242 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureGroups = fgtable = new Hashtable();
3243 for (int gs = 0; gs < jms.getFeatureSettings().getGroupCount(); gs++)
3245 Group grp = jms.getFeatureSettings().getGroup(gs);
3246 fgtable.put(grp.getName(), new Boolean(grp.getDisplay()));
3250 if (view.getHiddenColumnsCount() > 0)
3252 for (int c = 0; c < view.getHiddenColumnsCount(); c++)
3254 af.viewport.hideColumns(view.getHiddenColumns(c).getStart(), view
3255 .getHiddenColumns(c).getEnd() // +1
3260 af.setMenusFromViewport(af.viewport);
3261 // TODO: we don't need to do this if the viewport is aready visible.
3262 Desktop.addInternalFrame(af, view.getTitle(), view.getWidth(),
3264 af.alignPanel.updateAnnotation(false); // recompute any autoannotation
3265 reorderAutoannotation(af, al, autoAlan);
3269 private void reorderAutoannotation(AlignFrame af, Alignment al,
3270 ArrayList<JvAnnotRow> autoAlan)
3272 // copy over visualization settings for autocalculated annotation in the
3274 if (al.getAlignmentAnnotation() != null)
3277 * Kludge for magic autoannotation names (see JAL-811)
3279 String[] magicNames = new String[]
3280 { "Consensus", "Quality", "Conservation" };
3281 JvAnnotRow nullAnnot = new JvAnnotRow(-1, null);
3282 Hashtable<String, JvAnnotRow> visan = new Hashtable<String, JvAnnotRow>();
3283 for (String nm : magicNames)
3285 visan.put(nm, nullAnnot);
3287 for (JvAnnotRow auan : autoAlan)
3289 visan.put(auan.template.label, auan);
3291 int hSize = al.getAlignmentAnnotation().length;
3292 ArrayList<JvAnnotRow> reorder = new ArrayList<JvAnnotRow>();
3293 for (int h = 0; h < hSize; h++)
3295 jalview.datamodel.AlignmentAnnotation jalan = al
3296 .getAlignmentAnnotation()[h];
3297 if (jalan.autoCalculated)
3299 JvAnnotRow valan = visan.get(jalan.label);
3302 // delete the auto calculated row from the alignment
3303 al.deleteAnnotation(al.getAlignmentAnnotation()[h], false);
3306 if (valan != nullAnnot)
3308 if (jalan != valan.template)
3310 // newly created autoannotation row instance
3311 // so keep a reference to the visible annotation row
3312 // and copy over all relevant attributes
3313 if (valan.template.graphHeight >= 0)
3316 jalan.graphHeight = valan.template.graphHeight;
3318 jalan.visible = valan.template.visible;
3320 reorder.add(new JvAnnotRow(valan.order, jalan));
3325 int s = 0, srt[] = new int[reorder.size()];
3326 JvAnnotRow[] rws = new JvAnnotRow[reorder.size()];
3327 for (JvAnnotRow jvar : reorder)
3330 srt[s++] = jvar.order;
3333 jalview.util.QuickSort.sort(srt, rws);
3334 // and re-insert the annotation at its correct position
3335 for (JvAnnotRow jvar : rws)
3337 al.addAnnotation(jvar.template, jvar.order);
3339 af.alignPanel.adjustAnnotationHeight();
3343 Hashtable skipList = null;
3346 * TODO remove this method
3349 * @return AlignFrame bound to sequenceSetId from view, if one exists. private
3350 * AlignFrame getSkippedFrame(Viewport view) { if (skipList==null) {
3351 * throw new Error("Implementation Error. No skipList defined for this
3352 * Jalview2XML instance."); } return (AlignFrame)
3353 * skipList.get(view.getSequenceSetId()); }
3357 * Check if the Jalview view contained in object should be skipped or not.
3360 * @return true if view's sequenceSetId is a key in skipList
3362 private boolean skipViewport(JalviewModel object)
3364 if (skipList == null)
3369 if (skipList.containsKey(id = object.getJalviewModelSequence()
3370 .getViewport()[0].getSequenceSetId()))
3372 if (Cache.log != null && Cache.log.isDebugEnabled())
3374 Cache.log.debug("Skipping seuqence set id " + id);
3381 public void AddToSkipList(AlignFrame af)
3383 if (skipList == null)
3385 skipList = new Hashtable();
3387 skipList.put(af.getViewport().getSequenceSetId(), af);
3390 public void clearSkipList()
3392 if (skipList != null)
3399 private void recoverDatasetFor(SequenceSet vamsasSet, Alignment al)
3401 jalview.datamodel.Alignment ds = getDatasetFor(vamsasSet.getDatasetId());
3402 Vector dseqs = null;
3405 // create a list of new dataset sequences
3406 dseqs = new Vector();
3408 for (int i = 0, iSize = vamsasSet.getSequenceCount(); i < iSize; i++)
3410 Sequence vamsasSeq = vamsasSet.getSequence(i);
3411 ensureJalviewDatasetSequence(vamsasSeq, ds, dseqs);
3413 // create a new dataset
3416 SequenceI[] dsseqs = new SequenceI[dseqs.size()];
3417 dseqs.copyInto(dsseqs);
3418 ds = new jalview.datamodel.Alignment(dsseqs);
3419 debug("Created new dataset " + vamsasSet.getDatasetId()
3420 + " for alignment " + System.identityHashCode(al));
3421 addDatasetRef(vamsasSet.getDatasetId(), ds);
3423 // set the dataset for the newly imported alignment.
3424 if (al.getDataset() == null)
3433 * sequence definition to create/merge dataset sequence for
3437 * vector to add new dataset sequence to
3439 private void ensureJalviewDatasetSequence(Sequence vamsasSeq,
3440 AlignmentI ds, Vector dseqs)
3442 // JBP TODO: Check this is called for AlCodonFrames to support recovery of
3444 jalview.datamodel.Sequence sq = (jalview.datamodel.Sequence) seqRefIds
3445 .get(vamsasSeq.getId());
3446 jalview.datamodel.SequenceI dsq = null;
3447 if (sq != null && sq.getDatasetSequence() != null)
3449 dsq = (jalview.datamodel.SequenceI) sq.getDatasetSequence();
3452 String sqid = vamsasSeq.getDsseqid();
3455 // need to create or add a new dataset sequence reference to this sequence
3458 dsq = (jalview.datamodel.SequenceI) seqRefIds.get(sqid);
3463 // make a new dataset sequence
3464 dsq = sq.createDatasetSequence();
3467 // make up a new dataset reference for this sequence
3468 sqid = seqHash(dsq);
3470 dsq.setVamsasId(uniqueSetSuffix + sqid);
3471 seqRefIds.put(sqid, dsq);
3476 dseqs.addElement(dsq);
3481 ds.addSequence(dsq);
3487 { // make this dataset sequence sq's dataset sequence
3488 sq.setDatasetSequence(dsq);
3492 // TODO: refactor this as a merge dataset sequence function
3493 // now check that sq (the dataset sequence) sequence really is the union of
3494 // all references to it
3495 // boolean pre = sq.getStart() < dsq.getStart();
3496 // boolean post = sq.getEnd() > dsq.getEnd();
3500 StringBuffer sb = new StringBuffer();
3501 String newres = jalview.analysis.AlignSeq.extractGaps(
3502 jalview.util.Comparison.GapChars, sq.getSequenceAsString());
3503 if (!newres.equalsIgnoreCase(dsq.getSequenceAsString())
3504 && newres.length() > dsq.getLength())
3506 // Update with the longer sequence.
3510 * if (pre) { sb.insert(0, newres .substring(0, dsq.getStart() -
3511 * sq.getStart())); dsq.setStart(sq.getStart()); } if (post) {
3512 * sb.append(newres.substring(newres.length() - sq.getEnd() -
3513 * dsq.getEnd())); dsq.setEnd(sq.getEnd()); }
3515 dsq.setSequence(sb.toString());
3517 // TODO: merges will never happen if we 'know' we have the real dataset
3518 // sequence - this should be detected when id==dssid
3519 System.err.println("DEBUG Notice: Merged dataset sequence"); // ("
3520 // + (pre ? "prepended" : "") + " "
3521 // + (post ? "appended" : ""));
3526 java.util.Hashtable datasetIds = null;
3528 java.util.IdentityHashMap dataset2Ids = null;
3530 private Alignment getDatasetFor(String datasetId)
3532 if (datasetIds == null)
3534 datasetIds = new Hashtable();
3537 if (datasetIds.containsKey(datasetId))
3539 return (Alignment) datasetIds.get(datasetId);
3544 private void addDatasetRef(String datasetId, Alignment dataset)
3546 if (datasetIds == null)
3548 datasetIds = new Hashtable();
3550 datasetIds.put(datasetId, dataset);
3554 * make a new dataset ID for this jalview dataset alignment
3559 private String getDatasetIdRef(jalview.datamodel.Alignment dataset)
3561 if (dataset.getDataset() != null)
3563 warn("Serious issue! Dataset Object passed to getDatasetIdRef is not a Jalview DATASET alignment...");
3565 String datasetId = makeHashCode(dataset, null);
3566 if (datasetId == null)
3568 // make a new datasetId and record it
3569 if (dataset2Ids == null)
3571 dataset2Ids = new IdentityHashMap();
3575 datasetId = (String) dataset2Ids.get(dataset);
3577 if (datasetId == null)
3579 datasetId = "ds" + dataset2Ids.size() + 1;
3580 dataset2Ids.put(dataset, datasetId);
3586 private void addDBRefs(SequenceI datasetSequence, Sequence sequence)
3588 for (int d = 0; d < sequence.getDBRefCount(); d++)
3590 DBRef dr = sequence.getDBRef(d);
3591 jalview.datamodel.DBRefEntry entry = new jalview.datamodel.DBRefEntry(
3592 sequence.getDBRef(d).getSource(), sequence.getDBRef(d)
3593 .getVersion(), sequence.getDBRef(d).getAccessionId());
3594 if (dr.getMapping() != null)
3596 entry.setMap(addMapping(dr.getMapping()));
3598 datasetSequence.addDBRef(entry);
3602 private jalview.datamodel.Mapping addMapping(Mapping m)
3604 SequenceI dsto = null;
3605 // Mapping m = dr.getMapping();
3606 int fr[] = new int[m.getMapListFromCount() * 2];
3607 Enumeration f = m.enumerateMapListFrom();
3608 for (int _i = 0; f.hasMoreElements(); _i += 2)
3610 MapListFrom mf = (MapListFrom) f.nextElement();
3611 fr[_i] = mf.getStart();
3612 fr[_i + 1] = mf.getEnd();
3614 int fto[] = new int[m.getMapListToCount() * 2];
3615 f = m.enumerateMapListTo();
3616 for (int _i = 0; f.hasMoreElements(); _i += 2)
3618 MapListTo mf = (MapListTo) f.nextElement();
3619 fto[_i] = mf.getStart();
3620 fto[_i + 1] = mf.getEnd();
3622 jalview.datamodel.Mapping jmap = new jalview.datamodel.Mapping(dsto,
3623 fr, fto, (int) m.getMapFromUnit(), (int) m.getMapToUnit());
3624 if (m.getMappingChoice() != null)
3626 MappingChoice mc = m.getMappingChoice();
3627 if (mc.getDseqFor() != null)
3629 String dsfor = "" + mc.getDseqFor();
3630 if (seqRefIds.containsKey(dsfor))
3635 jmap.setTo((SequenceI) seqRefIds.get(dsfor));
3639 frefedSequence.add(new Object[]
3646 * local sequence definition
3648 Sequence ms = mc.getSequence();
3649 jalview.datamodel.Sequence djs = null;
3650 String sqid = ms.getDsseqid();
3651 if (sqid != null && sqid.length() > 0)
3654 * recover dataset sequence
3656 djs = (jalview.datamodel.Sequence) seqRefIds.get(sqid);
3661 .println("Warning - making up dataset sequence id for DbRef sequence map reference");
3662 sqid = ((Object) ms).toString(); // make up a new hascode for
3663 // undefined dataset sequence hash
3664 // (unlikely to happen)
3670 * make a new dataset sequence and add it to refIds hash
3672 djs = new jalview.datamodel.Sequence(ms.getName(),
3674 djs.setStart(jmap.getMap().getToLowest());
3675 djs.setEnd(jmap.getMap().getToHighest());
3676 djs.setVamsasId(uniqueSetSuffix + sqid);
3678 seqRefIds.put(sqid, djs);
3681 jalview.bin.Cache.log.debug("about to recurse on addDBRefs.");
3690 public jalview.gui.AlignmentPanel copyAlignPanel(AlignmentPanel ap,
3691 boolean keepSeqRefs)
3694 jalview.schemabinding.version2.JalviewModel jm = SaveState(ap, null,
3700 jm.getJalviewModelSequence().getViewport(0).setSequenceSetId(null);
3704 uniqueSetSuffix = "";
3705 jm.getJalviewModelSequence().getViewport(0).setId(null); // we don't
3710 if (this.frefedSequence == null)
3712 frefedSequence = new Vector();
3715 viewportsAdded = new Hashtable();
3717 AlignFrame af = LoadFromObject(jm, null, false, null);
3718 af.alignPanels.clear();
3719 af.closeMenuItem_actionPerformed(true);
3722 * if(ap.av.alignment.getAlignmentAnnotation()!=null) { for(int i=0;
3723 * i<ap.av.alignment.getAlignmentAnnotation().length; i++) {
3724 * if(!ap.av.alignment.getAlignmentAnnotation()[i].autoCalculated) {
3725 * af.alignPanel.av.alignment.getAlignmentAnnotation()[i] =
3726 * ap.av.alignment.getAlignmentAnnotation()[i]; } } }
3729 return af.alignPanel;
3733 * flag indicating if hashtables should be cleared on finalization TODO this
3734 * flag may not be necessary
3736 private boolean _cleartables = true;
3738 private Hashtable jvids2vobj;
3743 * @see java.lang.Object#finalize()
3745 protected void finalize() throws Throwable
3747 // really make sure we have no buried refs left.
3752 this.seqRefIds = null;
3753 this.seqsToIds = null;
3757 private void warn(String msg)
3762 private void warn(String msg, Exception e)
3764 if (Cache.log != null)
3768 Cache.log.warn(msg, e);
3772 Cache.log.warn(msg);
3777 System.err.println("Warning: " + msg);
3780 e.printStackTrace();
3785 private void debug(String string)
3787 debug(string, null);
3790 private void debug(String msg, Exception e)
3792 if (Cache.log != null)
3796 Cache.log.debug(msg, e);
3800 Cache.log.debug(msg);
3805 System.err.println("Warning: " + msg);
3808 e.printStackTrace();
3814 * set the object to ID mapping tables used to write/recover objects and XML
3815 * ID strings for the jalview project. If external tables are provided then
3816 * finalize and clearSeqRefs will not clear the tables when the Jalview2XML
3817 * object goes out of scope. - also populates the datasetIds hashtable with
3818 * alignment objects containing dataset sequences
3821 * Map from ID strings to jalview datamodel
3823 * Map from jalview datamodel to ID strings
3827 public void setObjectMappingTables(Hashtable vobj2jv,
3828 IdentityHashMap jv2vobj)
3830 this.jv2vobj = jv2vobj;
3831 this.vobj2jv = vobj2jv;
3832 Iterator ds = jv2vobj.keySet().iterator();
3834 while (ds.hasNext())
3836 Object jvobj = ds.next();
3837 id = jv2vobj.get(jvobj).toString();
3838 if (jvobj instanceof jalview.datamodel.Alignment)
3840 if (((jalview.datamodel.Alignment) jvobj).getDataset() == null)
3842 addDatasetRef(id, (jalview.datamodel.Alignment) jvobj);
3845 else if (jvobj instanceof jalview.datamodel.Sequence)
3847 // register sequence object so the XML parser can recover it.
3848 if (seqRefIds == null)
3850 seqRefIds = new Hashtable();
3852 if (seqsToIds == null)
3854 seqsToIds = new IdentityHashMap();
3856 seqRefIds.put(jv2vobj.get(jvobj).toString(), jvobj);
3857 seqsToIds.put(jvobj, id);
3859 else if (jvobj instanceof jalview.datamodel.AlignmentAnnotation)
3861 if (annotationIds == null)
3863 annotationIds = new Hashtable();
3866 annotationIds.put(anid = jv2vobj.get(jvobj).toString(), jvobj);
3867 jalview.datamodel.AlignmentAnnotation jvann = (jalview.datamodel.AlignmentAnnotation) jvobj;
3868 if (jvann.annotationId == null)
3870 jvann.annotationId = anid;
3872 if (!jvann.annotationId.equals(anid))
3874 // TODO verify that this is the correct behaviour
3875 this.warn("Overriding Annotation ID for " + anid
3876 + " from different id : " + jvann.annotationId);
3877 jvann.annotationId = anid;
3880 else if (jvobj instanceof String)
3882 if (jvids2vobj == null)
3884 jvids2vobj = new Hashtable();
3885 jvids2vobj.put(jvobj, jv2vobj.get(jvobj).toString());
3889 Cache.log.debug("Ignoring " + jvobj.getClass() + " (ID = " + id);
3894 * set the uniqueSetSuffix used to prefix/suffix object IDs for jalview
3895 * objects created from the project archive. If string is null (default for
3896 * construction) then suffix will be set automatically.
3900 public void setUniqueSetSuffix(String string)
3902 uniqueSetSuffix = string;
3907 * uses skipList2 as the skipList for skipping views on sequence sets
3908 * associated with keys in the skipList
3912 public void setSkipList(Hashtable skipList2)
3914 skipList = skipList2;