2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
3 * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
5 * This program is free software; you can redistribute it and/or
6 * modify it under the terms of the GNU General Public License
7 * as published by the Free Software Foundation; either version 2
8 * of the License, or (at your option) any later version.
10 * This program is distributed in the hope that it will be useful,
11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
13 * GNU General Public License for more details.
15 * You should have received a copy of the GNU General Public License
16 * along with this program; if not, write to the Free Software
17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
21 import java.awt.Rectangle;
25 import java.util.jar.*;
29 import org.exolab.castor.xml.*;
31 import uk.ac.vamsas.objects.utils.MapList;
32 import jalview.bin.Cache;
33 import jalview.datamodel.Alignment;
34 import jalview.datamodel.AlignmentI;
35 import jalview.datamodel.SequenceI;
36 import jalview.schemabinding.version2.*;
37 import jalview.schemes.*;
38 import jalview.structure.StructureSelectionManager;
39 import jalview.util.jarInputStreamProvider;
42 * Write out the current jalview desktop state as a Jalview XML stream.
44 * Note: the vamsas objects referred to here are primitive versions of the
45 * VAMSAS project schema elements - they are not the same and most likely never
51 public class Jalview2XML
54 * create/return unique hash string for sq
57 * @return new or existing unique string for sq
59 String seqHash(SequenceI sq)
61 if (seqsToIds == null)
65 if (seqsToIds.containsKey(sq))
67 return (String) seqsToIds.get(sq);
71 // create sequential key
72 String key = "sq" + (seqsToIds.size() + 1);
73 key = makeHashCode(sq, key); // check we don't have an external reference
75 seqsToIds.put(sq, key);
84 if (seqRefIds != null)
88 if (seqsToIds != null)
98 warn("clearSeqRefs called when _cleartables was not set. Doing nothing.");
99 // seqRefIds = new Hashtable();
100 // seqsToIds = new IdentityHashMap();
106 if (seqsToIds == null)
108 seqsToIds = new IdentityHashMap();
110 if (seqRefIds == null)
112 seqRefIds = new Hashtable();
117 * SequenceI reference -> XML ID string in jalview XML. Populated as XML reps
118 * of sequence objects are created.
120 java.util.IdentityHashMap seqsToIds = null;
123 * jalview XML Sequence ID to jalview sequence object reference (both dataset
124 * and alignment sequences. Populated as XML reps of sequence objects are
127 java.util.Hashtable seqRefIds = null; // key->SequenceI resolution
129 Vector frefedSequence = null;
131 boolean raiseGUI = true; // whether errors are raised in dialog boxes or not
137 public Jalview2XML(boolean raiseGUI)
139 this.raiseGUI = raiseGUI;
142 public void resolveFrefedSequences()
144 if (frefedSequence.size() > 0)
146 int r = 0, rSize = frefedSequence.size();
149 Object[] ref = (Object[]) frefedSequence.elementAt(r);
152 String sref = (String) ref[0];
153 if (seqRefIds.containsKey(sref))
155 if (ref[1] instanceof jalview.datamodel.Mapping)
157 SequenceI seq = (SequenceI) seqRefIds.get(sref);
158 while (seq.getDatasetSequence() != null)
160 seq = seq.getDatasetSequence();
162 ((jalview.datamodel.Mapping) ref[1]).setTo(seq);
166 if (ref[1] instanceof jalview.datamodel.AlignedCodonFrame)
168 SequenceI seq = (SequenceI) seqRefIds.get(sref);
169 while (seq.getDatasetSequence() != null)
171 seq = seq.getDatasetSequence();
174 && ref[2] instanceof jalview.datamodel.Mapping)
176 jalview.datamodel.Mapping mp = (jalview.datamodel.Mapping) ref[2];
177 ((jalview.datamodel.AlignedCodonFrame) ref[1]).addMap(
178 seq, mp.getTo(), mp.getMap());
183 .println("IMPLEMENTATION ERROR: Unimplemented forward sequence references for AlcodonFrames involving "
184 + ref[2].getClass() + " type objects.");
190 .println("IMPLEMENTATION ERROR: Unimplemented forward sequence references for "
191 + ref[1].getClass() + " type objects.");
194 frefedSequence.remove(r);
200 .println("IMPLEMENTATION WARNING: Unresolved forward reference for hash string "
202 + " with objecttype "
203 + ref[1].getClass());
210 frefedSequence.remove(r);
218 * This maintains a list of viewports, the key being the seqSetId. Important
219 * to set historyItem and redoList for multiple views
221 Hashtable viewportsAdded;
223 Hashtable annotationIds = new Hashtable();
225 String uniqueSetSuffix = "";
228 * List of pdbfiles added to Jar
230 Vector pdbfiles = null;
232 // SAVES SEVERAL ALIGNMENT WINDOWS TO SAME JARFILE
233 public void SaveState(File statefile)
237 FileOutputStream fos = new FileOutputStream(statefile);
238 JarOutputStream jout = new JarOutputStream(fos);
241 } catch (Exception e)
243 // TODO: inform user of the problem - they need to know if their data was
245 if (errorMessage == null)
247 errorMessage = "Couldn't write Jalview Archive to output file '"
248 + statefile + "' - See console error log for details";
252 errorMessage += "(output file was '" + statefile + "')";
260 * Writes a jalview project archive to the given Jar output stream.
264 public void SaveState(JarOutputStream jout)
266 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
276 // NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS
277 // //////////////////////////////////////////////////
278 // NOTE ALSO new PrintWriter must be used for each new JarEntry
279 PrintWriter out = null;
281 Vector shortNames = new Vector();
284 for (int i = frames.length - 1; i > -1; i--)
286 if (frames[i] instanceof AlignFrame)
288 AlignFrame af = (AlignFrame) frames[i];
291 && skipList.containsKey(af.getViewport()
292 .getSequenceSetId()))
297 String shortName = af.getTitle();
299 if (shortName.indexOf(File.separatorChar) > -1)
301 shortName = shortName.substring(shortName
302 .lastIndexOf(File.separatorChar) + 1);
307 while (shortNames.contains(shortName))
309 if (shortName.endsWith("_" + (count - 1)))
311 shortName = shortName
312 .substring(0, shortName.lastIndexOf("_"));
315 shortName = shortName.concat("_" + count);
319 shortNames.addElement(shortName);
321 if (!shortName.endsWith(".xml"))
323 shortName = shortName + ".xml";
326 int ap, apSize = af.alignPanels.size();
327 for (ap = 0; ap < apSize; ap++)
329 AlignmentPanel apanel = (AlignmentPanel) af.alignPanels
331 String fileName = apSize == 1 ? shortName : ap + shortName;
332 if (!fileName.endsWith(".xml"))
334 fileName = fileName + ".xml";
337 SaveState(apanel, fileName, jout);
344 } catch (Exception foo)
349 } catch (Exception ex)
351 // TODO: inform user of the problem - they need to know if their data was
353 if (errorMessage == null)
355 errorMessage = "Couldn't write Jalview Archive - see error output for details";
357 ex.printStackTrace();
361 // USE THIS METHOD TO SAVE A SINGLE ALIGNMENT WINDOW
362 public boolean SaveAlignment(AlignFrame af, String jarFile,
367 int ap, apSize = af.alignPanels.size();
368 FileOutputStream fos = new FileOutputStream(jarFile);
369 JarOutputStream jout = new JarOutputStream(fos);
370 for (ap = 0; ap < apSize; ap++)
372 AlignmentPanel apanel = (AlignmentPanel) af.alignPanels
374 String jfileName = apSize == 1 ? fileName : fileName + ap;
375 if (!jfileName.endsWith(".xml"))
377 jfileName = jfileName + ".xml";
379 SaveState(apanel, jfileName, jout);
385 } catch (Exception foo)
391 } catch (Exception ex)
393 errorMessage = "Couldn't Write alignment view to Jalview Archive - see error output for details";
394 ex.printStackTrace();
400 * create a JalviewModel from an algnment view and marshall it to a
404 * panel to create jalview model for
406 * name of alignment panel written to output stream
412 public JalviewModel SaveState(AlignmentPanel ap, String fileName,
413 JarOutputStream jout)
417 Vector userColours = new Vector();
419 AlignViewport av = ap.av;
421 JalviewModel object = new JalviewModel();
422 object.setVamsasModel(new jalview.schemabinding.version2.VamsasModel());
424 object.setCreationDate(new java.util.Date(System.currentTimeMillis()));
425 object.setVersion(jalview.bin.Cache.getProperty("VERSION"));
427 jalview.datamodel.AlignmentI jal = av.alignment;
429 if (av.hasHiddenRows)
431 jal = jal.getHiddenSequences().getFullAlignment();
434 SequenceSet vamsasSet = new SequenceSet();
436 JalviewModelSequence jms = new JalviewModelSequence();
438 vamsasSet.setGapChar(jal.getGapCharacter() + "");
440 if (jal.getDataset() != null)
442 // dataset id is the dataset's hashcode
443 vamsasSet.setDatasetId(getDatasetIdRef(jal.getDataset()));
445 if (jal.getProperties() != null)
447 Enumeration en = jal.getProperties().keys();
448 while (en.hasMoreElements())
450 String key = en.nextElement().toString();
451 SequenceSetProperties ssp = new SequenceSetProperties();
453 ssp.setValue(jal.getProperties().get(key).toString());
454 vamsasSet.addSequenceSetProperties(ssp);
462 jalview.datamodel.SequenceI jds;
463 for (int i = 0; i < jal.getHeight(); i++)
465 jds = jal.getSequenceAt(i);
468 if (seqRefIds.get(id) != null)
470 // This happens for two reasons: 1. multiple views are being serialised.
471 // 2. the hashCode has collided with another sequence's code. This DOES
472 // HAPPEN! (PF00072.15.stk does this)
473 // JBPNote: Uncomment to debug writing out of files that do not read
474 // back in due to ArrayOutOfBoundExceptions.
475 // System.err.println("vamsasSeq backref: "+id+"");
476 // System.err.println(jds.getName()+"
477 // "+jds.getStart()+"-"+jds.getEnd()+" "+jds.getSequenceAsString());
478 // System.err.println("Hashcode: "+seqHash(jds));
479 // SequenceI rsq = (SequenceI) seqRefIds.get(id + "");
480 // System.err.println(rsq.getName()+"
481 // "+rsq.getStart()+"-"+rsq.getEnd()+" "+rsq.getSequenceAsString());
482 // System.err.println("Hashcode: "+seqHash(rsq));
486 vamsasSeq = createVamsasSequence(id, jds);
487 vamsasSet.addSequence(vamsasSeq);
488 seqRefIds.put(id, jds);
492 jseq.setStart(jds.getStart());
493 jseq.setEnd(jds.getEnd());
494 jseq.setColour(av.getSequenceColour(jds).getRGB());
496 jseq.setId(id); // jseq id should be a string not a number
498 if (av.hasHiddenRows)
500 jseq.setHidden(av.alignment.getHiddenSequences().isHidden(jds));
502 if (av.hiddenRepSequences != null
503 && av.hiddenRepSequences.containsKey(jal.getSequenceAt(i)))
505 jalview.datamodel.SequenceI[] reps = ((jalview.datamodel.SequenceGroup) av.hiddenRepSequences
506 .get(jal.getSequenceAt(i))).getSequencesInOrder(jal);
508 for (int h = 0; h < reps.length; h++)
510 if (reps[h] != jal.getSequenceAt(i))
512 jseq.addHiddenSequences(jal.findIndex(reps[h]));
518 if (jds.getDatasetSequence().getSequenceFeatures() != null)
520 jalview.datamodel.SequenceFeature[] sf = jds.getDatasetSequence()
521 .getSequenceFeatures();
523 while (index < sf.length)
525 Features features = new Features();
527 features.setBegin(sf[index].getBegin());
528 features.setEnd(sf[index].getEnd());
529 features.setDescription(sf[index].getDescription());
530 features.setType(sf[index].getType());
531 features.setFeatureGroup(sf[index].getFeatureGroup());
532 features.setScore(sf[index].getScore());
533 if (sf[index].links != null)
535 for (int l = 0; l < sf[index].links.size(); l++)
537 OtherData keyValue = new OtherData();
538 keyValue.setKey("LINK_" + l);
539 keyValue.setValue(sf[index].links.elementAt(l).toString());
540 features.addOtherData(keyValue);
543 if (sf[index].otherDetails != null)
546 Enumeration keys = sf[index].otherDetails.keys();
547 while (keys.hasMoreElements())
549 key = keys.nextElement().toString();
550 OtherData keyValue = new OtherData();
551 keyValue.setKey(key);
552 keyValue.setValue(sf[index].otherDetails.get(key).toString());
553 features.addOtherData(keyValue);
557 jseq.addFeatures(features);
562 if (jds.getDatasetSequence().getPDBId() != null)
564 Enumeration en = jds.getDatasetSequence().getPDBId().elements();
565 while (en.hasMoreElements())
567 Pdbids pdb = new Pdbids();
568 jalview.datamodel.PDBEntry entry = (jalview.datamodel.PDBEntry) en
571 pdb.setId(entry.getId());
572 pdb.setType(entry.getType());
575 // This must have been loaded, is it still visible?
576 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
577 for (int f = frames.length - 1; f > -1; f--)
579 if (frames[f] instanceof AppJmol)
581 jmol = (AppJmol) frames[f];
582 if (!jmol.pdbentry.getId().equals(entry.getId())
583 && !(entry.getId().length()>4
584 && entry.getId().startsWith(jmol.pdbentry.getId())))
587 StructureState state = new StructureState();
588 state.setVisible(true);
589 state.setXpos(jmol.getX());
590 state.setYpos(jmol.getY());
591 state.setWidth(jmol.getWidth());
592 state.setHeight(jmol.getHeight());
593 state.setViewId(jmol.getViewId());
594 String statestring = jmol.viewer.getStateInfo();
597 state.setContent(statestring.replaceAll("\n", ""));
599 for (int s = 0; s < jmol.sequence.length; s++)
601 if (jal.findIndex(jmol.sequence[s]) > -1)
603 pdb.addStructureState(state);
609 if (entry.getFile() != null)
611 pdb.setFile(entry.getFile());
612 if (pdbfiles == null)
614 pdbfiles = new Vector();
617 if (!pdbfiles.contains(entry.getId()))
619 pdbfiles.addElement(entry.getId());
622 File file = new File(entry.getFile());
623 if (file.exists() && jout != null)
625 byte[] data = new byte[(int) file.length()];
626 jout.putNextEntry(new JarEntry(entry.getId()));
627 DataInputStream dis = new DataInputStream(
628 new FileInputStream(file));
631 DataOutputStream dout = new DataOutputStream(jout);
632 dout.write(data, 0, data.length);
636 } catch (Exception ex)
638 ex.printStackTrace();
644 if (entry.getProperty() != null)
646 PdbentryItem item = new PdbentryItem();
647 Hashtable properties = entry.getProperty();
648 Enumeration en2 = properties.keys();
649 while (en2.hasMoreElements())
651 Property prop = new Property();
652 String key = en2.nextElement().toString();
654 prop.setValue(properties.get(key).toString());
655 item.addProperty(prop);
657 pdb.addPdbentryItem(item);
667 if (av.hasHiddenRows)
672 if (jal.getCodonFrames() != null && jal.getCodonFrames().length > 0)
674 jalview.datamodel.AlignedCodonFrame[] jac = jal.getCodonFrames();
675 for (int i = 0; i < jac.length; i++)
677 AlcodonFrame alc = new AlcodonFrame();
678 vamsasSet.addAlcodonFrame(alc);
679 for (int p = 0; p < jac[i].aaWidth; p++)
681 Alcodon cmap = new Alcodon();
682 if (jac[i].codons[p]!=null)
684 // Null codons indicate a gapped column in the translated peptide alignment.
685 cmap.setPos1(jac[i].codons[p][0]);
686 cmap.setPos2(jac[i].codons[p][1]);
687 cmap.setPos3(jac[i].codons[p][2]);
689 alc.addAlcodon(cmap);
691 if (jac[i].getProtMappings() != null
692 && jac[i].getProtMappings().length > 0)
694 SequenceI[] dnas = jac[i].getdnaSeqs();
695 jalview.datamodel.Mapping[] pmaps = jac[i].getProtMappings();
696 for (int m = 0; m < pmaps.length; m++)
698 AlcodMap alcmap = new AlcodMap();
699 alcmap.setDnasq(seqHash(dnas[m]));
700 alcmap.setMapping(createVamsasMapping(pmaps[m], dnas[m], null,
702 alc.addAlcodMap(alcmap);
709 // /////////////////////////////////
710 if (av.currentTree != null)
712 // FIND ANY ASSOCIATED TREES
713 // NOT IMPLEMENTED FOR HEADLESS STATE AT PRESENT
714 if (Desktop.desktop != null)
716 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
718 for (int t = 0; t < frames.length; t++)
720 if (frames[t] instanceof TreePanel)
722 TreePanel tp = (TreePanel) frames[t];
724 if (tp.treeCanvas.av.alignment == jal)
726 Tree tree = new Tree();
727 tree.setTitle(tp.getTitle());
728 tree.setCurrentTree((av.currentTree == tp.getTree()));
729 tree.setNewick(tp.getTree().toString());
730 tree.setThreshold(tp.treeCanvas.threshold);
732 tree.setFitToWindow(tp.fitToWindow.getState());
733 tree.setFontName(tp.getTreeFont().getName());
734 tree.setFontSize(tp.getTreeFont().getSize());
735 tree.setFontStyle(tp.getTreeFont().getStyle());
736 tree.setMarkUnlinked(tp.placeholdersMenu.getState());
738 tree.setShowBootstrap(tp.bootstrapMenu.getState());
739 tree.setShowDistances(tp.distanceMenu.getState());
741 tree.setHeight(tp.getHeight());
742 tree.setWidth(tp.getWidth());
743 tree.setXpos(tp.getX());
744 tree.setYpos(tp.getY());
745 tree.setId(makeHashCode(tp, null));
754 if (jal.getAlignmentAnnotation() != null)
756 jalview.datamodel.AlignmentAnnotation[] aa = jal
757 .getAlignmentAnnotation();
759 for (int i = 0; i < aa.length; i++)
761 Annotation an = new Annotation();
763 if (aa[i].annotationId != null)
765 annotationIds.put(aa[i].annotationId, aa[i]);
768 an.setId(aa[i].annotationId);
770 if (aa[i] == av.quality || aa[i] == av.conservation
771 || aa[i] == av.consensus)
773 an.setLabel(aa[i].label);
775 vamsasSet.addAnnotation(an);
779 an.setVisible(aa[i].visible);
781 an.setDescription(aa[i].description);
783 if (aa[i].sequenceRef != null)
785 // TODO later annotation sequenceRef should be the XML ID of the
786 // sequence rather than its display name
787 an.setSequenceRef(aa[i].sequenceRef.getName());
793 an.setGraphType(aa[i].graph);
794 an.setGraphGroup(aa[i].graphGroup);
795 if (aa[i].getThreshold() != null)
797 ThresholdLine line = new ThresholdLine();
798 line.setLabel(aa[i].getThreshold().label);
799 line.setValue(aa[i].getThreshold().value);
800 line.setColour(aa[i].getThreshold().colour.getRGB());
801 an.setThresholdLine(line);
809 an.setLabel(aa[i].label);
810 if (aa[i].hasScore())
812 an.setScore(aa[i].getScore());
814 AnnotationElement ae;
815 if (aa[i].annotations != null)
817 an.setScoreOnly(false);
818 for (int a = 0; a < aa[i].annotations.length; a++)
820 if ((aa[i] == null) || (aa[i].annotations[a] == null))
825 ae = new AnnotationElement();
826 if (aa[i].annotations[a].description != null)
827 ae.setDescription(aa[i].annotations[a].description);
828 if (aa[i].annotations[a].displayCharacter != null)
829 ae.setDisplayCharacter(aa[i].annotations[a].displayCharacter);
831 if (!Float.isNaN(aa[i].annotations[a].value))
832 ae.setValue(aa[i].annotations[a].value);
835 if (aa[i].annotations[a].secondaryStructure != ' '
836 && aa[i].annotations[a].secondaryStructure != '\0')
838 .setSecondaryStructure(aa[i].annotations[a].secondaryStructure
841 if (aa[i].annotations[a].colour != null
842 && aa[i].annotations[a].colour != java.awt.Color.black)
844 ae.setColour(aa[i].annotations[a].colour.getRGB());
847 an.addAnnotationElement(ae);
852 an.setScoreOnly(true);
854 vamsasSet.addAnnotation(an);
859 if (jal.getGroups() != null)
861 JGroup[] groups = new JGroup[jal.getGroups().size()];
863 for (int i = 0; i < groups.length; i++)
865 groups[i] = new JGroup();
867 jalview.datamodel.SequenceGroup sg = (jalview.datamodel.SequenceGroup) jal
868 .getGroups().elementAt(i);
869 groups[i].setStart(sg.getStartRes());
870 groups[i].setEnd(sg.getEndRes());
871 groups[i].setName(sg.getName()); // TODO later sequence group should
872 // specify IDs of sequences, not just
876 if (sg.cs.conservationApplied())
878 groups[i].setConsThreshold(sg.cs.getConservationInc());
880 if (sg.cs instanceof jalview.schemes.UserColourScheme)
882 groups[i].setColour(SetUserColourScheme(sg.cs, userColours,
888 .setColour(ColourSchemeProperty.getColourName(sg.cs));
891 else if (sg.cs instanceof jalview.schemes.AnnotationColourGradient)
894 .setColour(ColourSchemeProperty
895 .getColourName(((jalview.schemes.AnnotationColourGradient) sg.cs)
898 else if (sg.cs instanceof jalview.schemes.UserColourScheme)
901 .setColour(SetUserColourScheme(sg.cs, userColours, jms));
905 groups[i].setColour(ColourSchemeProperty.getColourName(sg.cs));
908 groups[i].setPidThreshold(sg.cs.getThreshold());
911 groups[i].setOutlineColour(sg.getOutlineColour().getRGB());
912 groups[i].setDisplayBoxes(sg.getDisplayBoxes());
913 groups[i].setDisplayText(sg.getDisplayText());
914 groups[i].setColourText(sg.getColourText());
915 groups[i].setTextCol1(sg.textColour.getRGB());
916 groups[i].setTextCol2(sg.textColour2.getRGB());
917 groups[i].setTextColThreshold(sg.thresholdTextColour);
918 groups[i].setShowUnconserved(sg.getShowunconserved());
919 for (int s = 0; s < sg.getSize(); s++)
921 jalview.datamodel.Sequence seq = (jalview.datamodel.Sequence) sg
923 groups[i].addSeq(seqHash(seq));
927 jms.setJGroup(groups);
930 // /////////SAVE VIEWPORT
931 Viewport view = new Viewport();
932 view.setTitle(ap.alignFrame.getTitle());
933 view.setSequenceSetId(makeHashCode(av.getSequenceSetId(), av
934 .getSequenceSetId()));
935 view.setId(av.getViewId());
936 view.setViewName(av.viewName);
937 view.setGatheredViews(av.gatherViewsHere);
939 if (ap.av.explodedPosition != null)
941 view.setXpos(av.explodedPosition.x);
942 view.setYpos(av.explodedPosition.y);
943 view.setWidth(av.explodedPosition.width);
944 view.setHeight(av.explodedPosition.height);
948 view.setXpos(ap.alignFrame.getBounds().x);
949 view.setYpos(ap.alignFrame.getBounds().y);
950 view.setWidth(ap.alignFrame.getBounds().width);
951 view.setHeight(ap.alignFrame.getBounds().height);
954 view.setStartRes(av.startRes);
955 view.setStartSeq(av.startSeq);
957 if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme)
959 view.setBgColour(SetUserColourScheme(av.getGlobalColourScheme(),
962 else if (av.getGlobalColourScheme() instanceof jalview.schemes.AnnotationColourGradient)
964 jalview.schemes.AnnotationColourGradient acg = (jalview.schemes.AnnotationColourGradient) av
965 .getGlobalColourScheme();
967 AnnotationColours ac = new AnnotationColours();
968 ac.setAboveThreshold(acg.getAboveThreshold());
969 ac.setThreshold(acg.getAnnotationThreshold());
970 ac.setAnnotation(acg.getAnnotation());
971 if (acg.getBaseColour() instanceof jalview.schemes.UserColourScheme)
973 ac.setColourScheme(SetUserColourScheme(acg.getBaseColour(),
978 ac.setColourScheme(ColourSchemeProperty.getColourName(acg
982 ac.setMaxColour(acg.getMaxColour().getRGB());
983 ac.setMinColour(acg.getMinColour().getRGB());
984 view.setAnnotationColours(ac);
985 view.setBgColour("AnnotationColourGradient");
989 view.setBgColour(ColourSchemeProperty.getColourName(av
990 .getGlobalColourScheme()));
993 ColourSchemeI cs = av.getGlobalColourScheme();
997 if (cs.conservationApplied())
999 view.setConsThreshold(cs.getConservationInc());
1000 if (cs instanceof jalview.schemes.UserColourScheme)
1002 view.setBgColour(SetUserColourScheme(cs, userColours, jms));
1006 if (cs instanceof ResidueColourScheme)
1008 view.setPidThreshold(cs.getThreshold());
1012 view.setConservationSelected(av.getConservationSelected());
1013 view.setPidSelected(av.getAbovePIDThreshold());
1014 view.setFontName(av.font.getName());
1015 view.setFontSize(av.font.getSize());
1016 view.setFontStyle(av.font.getStyle());
1017 view.setRenderGaps(av.renderGaps);
1018 view.setShowAnnotation(av.getShowAnnotation());
1019 view.setShowBoxes(av.getShowBoxes());
1020 view.setShowColourText(av.getColourText());
1021 view.setShowFullId(av.getShowJVSuffix());
1022 view.setRightAlignIds(av.rightAlignIds);
1023 view.setShowSequenceFeatures(av.showSequenceFeatures);
1024 view.setShowText(av.getShowText());
1025 view.setShowUnconserved(av.getShowUnconserved());
1026 view.setWrapAlignment(av.getWrapAlignment());
1027 view.setTextCol1(av.textColour.getRGB());
1028 view.setTextCol2(av.textColour2.getRGB());
1029 view.setTextColThreshold(av.thresholdTextColour);
1031 if (av.featuresDisplayed != null)
1033 jalview.schemabinding.version2.FeatureSettings fs = new jalview.schemabinding.version2.FeatureSettings();
1035 String[] renderOrder = ap.seqPanel.seqCanvas.getFeatureRenderer().renderOrder;
1037 Vector settingsAdded = new Vector();
1038 for (int ro = 0; ro < renderOrder.length; ro++)
1040 Setting setting = new Setting();
1041 setting.setType(renderOrder[ro]);
1042 setting.setColour(ap.seqPanel.seqCanvas.getFeatureRenderer()
1043 .getColour(renderOrder[ro]).getRGB());
1045 setting.setDisplay(av.featuresDisplayed
1046 .containsKey(renderOrder[ro]));
1047 float rorder = ap.seqPanel.seqCanvas.getFeatureRenderer().getOrder(
1051 setting.setOrder(rorder);
1053 fs.addSetting(setting);
1054 settingsAdded.addElement(renderOrder[ro]);
1057 // Make sure we save none displayed feature settings
1058 Enumeration en = ap.seqPanel.seqCanvas.getFeatureRenderer().featureColours
1060 while (en.hasMoreElements())
1062 String key = en.nextElement().toString();
1063 if (settingsAdded.contains(key))
1068 Setting setting = new Setting();
1069 setting.setType(key);
1070 setting.setColour(ap.seqPanel.seqCanvas.getFeatureRenderer()
1071 .getColour(key).getRGB());
1073 setting.setDisplay(false);
1074 float rorder = ap.seqPanel.seqCanvas.getFeatureRenderer().getOrder(
1078 setting.setOrder(rorder);
1080 fs.addSetting(setting);
1081 settingsAdded.addElement(key);
1083 en = ap.seqPanel.seqCanvas.getFeatureRenderer().featureGroups.keys();
1084 Vector groupsAdded = new Vector();
1085 while (en.hasMoreElements())
1087 String grp = en.nextElement().toString();
1088 if (groupsAdded.contains(grp))
1092 Group g = new Group();
1095 .setDisplay(((Boolean) ap.seqPanel.seqCanvas
1096 .getFeatureRenderer().featureGroups.get(grp))
1099 groupsAdded.addElement(grp);
1101 jms.setFeatureSettings(fs);
1105 if (av.hasHiddenColumns)
1107 for (int c = 0; c < av.getColumnSelection().getHiddenColumns().size(); c++)
1109 int[] region = (int[]) av.getColumnSelection().getHiddenColumns()
1111 HiddenColumns hc = new HiddenColumns();
1112 hc.setStart(region[0]);
1113 hc.setEnd(region[1]);
1114 view.addHiddenColumns(hc);
1118 jms.addViewport(view);
1120 object.setJalviewModelSequence(jms);
1121 object.getVamsasModel().addSequenceSet(vamsasSet);
1123 if (jout != null && fileName != null)
1125 // We may not want to write the object to disk,
1126 // eg we can copy the alignViewport to a new view object
1127 // using save and then load
1130 JarEntry entry = new JarEntry(fileName);
1131 jout.putNextEntry(entry);
1132 PrintWriter pout = new PrintWriter(new OutputStreamWriter(jout,
1134 org.exolab.castor.xml.Marshaller marshaller = new org.exolab.castor.xml.Marshaller(
1136 marshaller.marshal(object);
1139 } catch (Exception ex)
1141 // TODO: raise error in GUI if marshalling failed.
1142 ex.printStackTrace();
1149 * External mapping between jalview objects and objects yielding a valid and
1150 * unique object ID string. This is null for normal Jalview project IO, but
1151 * non-null when a jalview project is being read or written as part of a
1154 IdentityHashMap jv2vobj = null;
1157 * Construct a unique ID for jvobj using either existing bindings or if none
1158 * exist, the result of the hashcode call for the object.
1161 * jalview data object
1162 * @return unique ID for referring to jvobj
1164 private String makeHashCode(Object jvobj, String altCode)
1166 if (jv2vobj != null)
1168 Object id = jv2vobj.get(jvobj);
1171 return id.toString();
1173 // check string ID mappings
1174 if (jvids2vobj != null && jvobj instanceof String)
1176 id = jvids2vobj.get(jvobj);
1180 return id.toString();
1182 // give up and warn that something has gone wrong
1183 warn("Cannot find ID for object in external mapping : " + jvobj);
1189 * return local jalview object mapped to ID, if it exists
1193 * @return null or object bound to idcode
1195 private Object retrieveExistingObj(String idcode)
1197 if (idcode != null && vobj2jv != null)
1199 return vobj2jv.get(idcode);
1205 * binding from ID strings from external mapping table to jalview data model
1208 private Hashtable vobj2jv;
1210 private Sequence createVamsasSequence(String id, SequenceI jds)
1212 return createVamsasSequence(true, id, jds, null);
1215 private Sequence createVamsasSequence(boolean recurse, String id,
1216 SequenceI jds, SequenceI parentseq)
1218 Sequence vamsasSeq = new Sequence();
1219 vamsasSeq.setId(id);
1220 vamsasSeq.setName(jds.getName());
1221 vamsasSeq.setSequence(jds.getSequenceAsString());
1222 vamsasSeq.setDescription(jds.getDescription());
1223 jalview.datamodel.DBRefEntry[] dbrefs = null;
1224 if (jds.getDatasetSequence() != null)
1226 vamsasSeq.setDsseqid(seqHash(jds.getDatasetSequence()));
1227 if (jds.getDatasetSequence().getDBRef() != null)
1229 dbrefs = jds.getDatasetSequence().getDBRef();
1234 vamsasSeq.setDsseqid(id); // so we can tell which sequences really are
1235 // dataset sequences only
1236 dbrefs = jds.getDBRef();
1240 for (int d = 0; d < dbrefs.length; d++)
1242 DBRef dbref = new DBRef();
1243 dbref.setSource(dbrefs[d].getSource());
1244 dbref.setVersion(dbrefs[d].getVersion());
1245 dbref.setAccessionId(dbrefs[d].getAccessionId());
1246 if (dbrefs[d].hasMap())
1248 Mapping mp = createVamsasMapping(dbrefs[d].getMap(), parentseq,
1250 dbref.setMapping(mp);
1252 vamsasSeq.addDBRef(dbref);
1258 private Mapping createVamsasMapping(jalview.datamodel.Mapping jmp,
1259 SequenceI parentseq, SequenceI jds, boolean recurse)
1262 if (jmp.getMap() != null)
1266 jalview.util.MapList mlst = jmp.getMap();
1267 int r[] = mlst.getFromRanges();
1268 for (int s = 0; s < r.length; s += 2)
1270 MapListFrom mfrom = new MapListFrom();
1271 mfrom.setStart(r[s]);
1272 mfrom.setEnd(r[s + 1]);
1273 mp.addMapListFrom(mfrom);
1275 r = mlst.getToRanges();
1276 for (int s = 0; s < r.length; s += 2)
1278 MapListTo mto = new MapListTo();
1280 mto.setEnd(r[s + 1]);
1281 mp.addMapListTo(mto);
1283 mp.setMapFromUnit(mlst.getFromRatio());
1284 mp.setMapToUnit(mlst.getToRatio());
1285 if (jmp.getTo() != null)
1287 MappingChoice mpc = new MappingChoice();
1289 && (parentseq != jmp.getTo() || parentseq
1290 .getDatasetSequence() != jmp.getTo()))
1292 mpc.setSequence(createVamsasSequence(false, seqHash(jmp.getTo()),
1298 SequenceI ps = null;
1299 if (parentseq != jmp.getTo()
1300 && parentseq.getDatasetSequence() != jmp.getTo())
1302 // chaining dbref rather than a handshaking one
1303 jmpid = seqHash(ps = jmp.getTo());
1307 jmpid = seqHash(ps = parentseq);
1309 mpc.setDseqFor(jmpid);
1310 if (!seqRefIds.containsKey(mpc.getDseqFor()))
1312 jalview.bin.Cache.log.debug("creatign new DseqFor ID");
1313 seqRefIds.put(mpc.getDseqFor(), ps);
1317 jalview.bin.Cache.log.debug("reusing DseqFor ID");
1320 mp.setMappingChoice(mpc);
1326 String SetUserColourScheme(jalview.schemes.ColourSchemeI cs,
1327 Vector userColours, JalviewModelSequence jms)
1330 jalview.schemes.UserColourScheme ucs = (jalview.schemes.UserColourScheme) cs;
1332 if (!userColours.contains(ucs))
1334 userColours.add(ucs);
1336 java.awt.Color[] colours = ucs.getColours();
1337 jalview.schemabinding.version2.UserColours uc = new jalview.schemabinding.version2.UserColours();
1338 jalview.schemabinding.version2.UserColourScheme jbucs = new jalview.schemabinding.version2.UserColourScheme();
1340 for (int i = 0; i < colours.length; i++)
1342 jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();
1343 col.setName(ResidueProperties.aa[i]);
1344 col.setRGB(jalview.util.Format.getHexString(colours[i]));
1345 jbucs.addColour(col);
1347 if (ucs.getLowerCaseColours() != null)
1349 colours = ucs.getLowerCaseColours();
1350 for (int i = 0; i < colours.length; i++)
1352 jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();
1353 col.setName(ResidueProperties.aa[i].toLowerCase());
1354 col.setRGB(jalview.util.Format.getHexString(colours[i]));
1355 jbucs.addColour(col);
1359 id = "ucs" + userColours.indexOf(ucs);
1361 uc.setUserColourScheme(jbucs);
1362 jms.addUserColours(uc);
1368 jalview.schemes.UserColourScheme GetUserColourScheme(
1369 JalviewModelSequence jms, String id)
1371 UserColours[] uc = jms.getUserColours();
1372 UserColours colours = null;
1374 for (int i = 0; i < uc.length; i++)
1376 if (uc[i].getId().equals(id))
1384 java.awt.Color[] newColours = new java.awt.Color[24];
1386 for (int i = 0; i < 24; i++)
1388 newColours[i] = new java.awt.Color(Integer.parseInt(colours
1389 .getUserColourScheme().getColour(i).getRGB(), 16));
1392 jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(
1395 if (colours.getUserColourScheme().getColourCount() > 24)
1397 newColours = new java.awt.Color[23];
1398 for (int i = 0; i < 23; i++)
1400 newColours[i] = new java.awt.Color(Integer.parseInt(colours
1401 .getUserColourScheme().getColour(i + 24).getRGB(), 16));
1403 ucs.setLowerCaseColours(newColours);
1410 * contains last error message (if any) encountered by XML loader.
1412 String errorMessage = null;
1415 * flag to control whether the Jalview2XML_V1 parser should be deferred to if
1416 * exceptions are raised during project XML parsing
1418 public boolean attemptversion1parse = true;
1421 * Load a jalview project archive from a jar file
1424 * HTTP URL or filename
1426 public AlignFrame LoadJalviewAlign(final String file)
1429 jalview.gui.AlignFrame af = null;
1433 // UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
1434 // Workaround is to make sure caller implements the JarInputStreamProvider
1436 // so we can re-open the jar input stream for each entry.
1438 jarInputStreamProvider jprovider = createjarInputStreamProvider(file);
1439 af = LoadJalviewAlign(jprovider);
1440 } catch (MalformedURLException e)
1442 errorMessage = "Invalid URL format for '" + file + "'";
1448 private jarInputStreamProvider createjarInputStreamProvider(
1449 final String file) throws MalformedURLException
1452 errorMessage = null;
1453 uniqueSetSuffix = null;
1455 viewportsAdded = null;
1456 frefedSequence = null;
1458 if (file.startsWith("http://"))
1460 url = new URL(file);
1462 final URL _url = url;
1463 return new jarInputStreamProvider()
1466 public JarInputStream getJarInputStream() throws IOException
1470 return new JarInputStream(_url.openStream());
1474 return new JarInputStream(new FileInputStream(file));
1478 public String getFilename()
1486 * Recover jalview session from a jalview project archive. Caller may
1487 * initialise uniqueSetSuffix, seqRefIds, viewportsAdded and frefedSequence
1488 * themselves. Any null fields will be initialised with default values,
1489 * non-null fields are left alone.
1494 public AlignFrame LoadJalviewAlign(final jarInputStreamProvider jprovider)
1496 errorMessage = null;
1497 if (uniqueSetSuffix == null)
1499 uniqueSetSuffix = System.currentTimeMillis() % 100000 + "";
1501 if (seqRefIds == null)
1503 seqRefIds = new Hashtable();
1505 if (viewportsAdded == null)
1507 viewportsAdded = new Hashtable();
1509 if (frefedSequence == null)
1511 frefedSequence = new Vector();
1514 jalview.gui.AlignFrame af = null;
1515 Hashtable gatherToThisFrame = new Hashtable();
1516 final String file = jprovider.getFilename();
1519 JarInputStream jin = null;
1520 JarEntry jarentry = null;
1525 jin = jprovider.getJarInputStream();
1526 for (int i = 0; i < entryCount; i++)
1528 jarentry = jin.getNextJarEntry();
1531 if (jarentry != null && jarentry.getName().endsWith(".xml"))
1533 InputStreamReader in = new InputStreamReader(jin, "UTF-8");
1534 JalviewModel object = new JalviewModel();
1536 Unmarshaller unmar = new Unmarshaller(object);
1537 unmar.setValidation(false);
1538 object = (JalviewModel) unmar.unmarshal(in);
1539 if (true) // !skipViewport(object))
1541 af = LoadFromObject(object, file, true, jprovider);
1542 if (af.viewport.gatherViewsHere)
1544 gatherToThisFrame.put(af.viewport.getSequenceSetId(), af);
1549 else if (jarentry != null)
1551 // Some other file here.
1554 } while (jarentry != null);
1555 resolveFrefedSequences();
1556 } catch (java.io.FileNotFoundException ex)
1558 ex.printStackTrace();
1559 errorMessage = "Couldn't locate Jalview XML file : " + file;
1560 System.err.println("Exception whilst loading jalview XML file : "
1562 } catch (java.net.UnknownHostException ex)
1564 ex.printStackTrace();
1565 errorMessage = "Couldn't locate Jalview XML file : " + file;
1566 System.err.println("Exception whilst loading jalview XML file : "
1568 } catch (Exception ex)
1570 System.err.println("Parsing as Jalview Version 2 file failed.");
1571 ex.printStackTrace(System.err);
1572 if (attemptversion1parse)
1574 // Is Version 1 Jar file?
1577 af = new Jalview2XML_V1(raiseGUI).LoadJalviewAlign(jprovider);
1578 } catch (Exception ex2)
1580 System.err.println("Exception whilst loading as jalviewXMLV1:");
1581 ex2.printStackTrace();
1585 if (Desktop.instance != null)
1587 Desktop.instance.stopLoading();
1591 System.out.println("Successfully loaded archive file");
1594 ex.printStackTrace();
1596 System.err.println("Exception whilst loading jalview XML file : "
1598 } catch (OutOfMemoryError e)
1600 new jalview.gui.OOMWarning("loading jalview XML file", e,
1604 if (Desktop.instance != null)
1606 Desktop.instance.stopLoading();
1609 Enumeration en = gatherToThisFrame.elements();
1610 while (en.hasMoreElements())
1612 Desktop.instance.gatherViews((AlignFrame) en.nextElement());
1614 if (errorMessage != null)
1622 * check errorMessage for a valid error message and raise an error box in the
1623 * GUI or write the current errorMessage to stderr and then clear the error
1626 protected void reportErrors()
1628 reportErrors(false);
1631 protected void reportErrors(final boolean saving)
1633 if (errorMessage != null)
1635 final String finalErrorMessage = errorMessage;
1638 javax.swing.SwingUtilities.invokeLater(new Runnable()
1642 JOptionPane.showInternalMessageDialog(Desktop.desktop,
1643 finalErrorMessage, "Error "
1644 + (saving ? "saving" : "loading")
1645 + " Jalview file", JOptionPane.WARNING_MESSAGE);
1651 System.err.println("Problem loading Jalview file: " + errorMessage);
1654 errorMessage = null;
1657 Hashtable alreadyLoadedPDB;
1660 * when set, local views will be updated from view stored in JalviewXML
1661 * Currently (28th Sep 2008) things will go horribly wrong in vamsas document
1662 * sync if this is set to true.
1664 private boolean updateLocalViews = false;
1666 String loadPDBFile(jarInputStreamProvider jprovider, String pdbId)
1668 if (alreadyLoadedPDB == null)
1669 alreadyLoadedPDB = new Hashtable();
1671 if (alreadyLoadedPDB.containsKey(pdbId))
1672 return alreadyLoadedPDB.get(pdbId).toString();
1676 JarInputStream jin = jprovider.getJarInputStream();
1678 * if (jprovider.startsWith("http://")) { jin = new JarInputStream(new
1679 * URL(jprovider).openStream()); } else { jin = new JarInputStream(new
1680 * FileInputStream(jprovider)); }
1683 JarEntry entry = null;
1686 entry = jin.getNextJarEntry();
1687 } while (entry != null && !entry.getName().equals(pdbId));
1690 BufferedReader in = new BufferedReader(new InputStreamReader(jin));
1691 File outFile = File.createTempFile("jalview_pdb", ".txt");
1692 outFile.deleteOnExit();
1693 PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
1696 while ((data = in.readLine()) != null)
1703 } catch (Exception foo)
1709 alreadyLoadedPDB.put(pdbId, outFile.getAbsolutePath());
1710 return outFile.getAbsolutePath();
1714 warn("Couldn't find PDB file entry in Jalview Jar for " + pdbId);
1716 } catch (Exception ex)
1718 ex.printStackTrace();
1725 * Load alignment frame from jalview XML DOM object
1730 * filename source string
1731 * @param loadTreesAndStructures
1732 * when false only create Viewport
1734 * data source provider
1735 * @return alignment frame created from view stored in DOM
1737 AlignFrame LoadFromObject(JalviewModel object, String file,
1738 boolean loadTreesAndStructures, jarInputStreamProvider jprovider)
1740 SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);
1741 Sequence[] vamsasSeq = vamsasSet.getSequence();
1743 JalviewModelSequence jms = object.getJalviewModelSequence();
1745 Viewport view = jms.getViewport(0);
1746 // ////////////////////////////////
1749 Vector hiddenSeqs = null;
1750 jalview.datamodel.Sequence jseq;
1752 ArrayList tmpseqs = new ArrayList();
1754 boolean multipleView = false;
1756 JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq();
1757 int vi = 0; // counter in vamsasSeq array
1758 for (int i = 0; i < JSEQ.length; i++)
1760 String seqId = JSEQ[i].getId();
1762 if (seqRefIds.get(seqId) != null)
1764 tmpseqs.add((jalview.datamodel.Sequence) seqRefIds.get(seqId));
1765 multipleView = true;
1769 jseq = new jalview.datamodel.Sequence(vamsasSeq[vi].getName(),
1770 vamsasSeq[vi].getSequence());
1771 jseq.setDescription(vamsasSeq[vi].getDescription());
1772 jseq.setStart(JSEQ[i].getStart());
1773 jseq.setEnd(JSEQ[i].getEnd());
1774 jseq.setVamsasId(uniqueSetSuffix + seqId);
1775 seqRefIds.put(vamsasSeq[vi].getId(), jseq);
1780 if (JSEQ[i].getHidden())
1782 if (hiddenSeqs == null)
1784 hiddenSeqs = new Vector();
1787 hiddenSeqs.addElement((jalview.datamodel.Sequence) seqRefIds
1794 // Create the alignment object from the sequence set
1795 // ///////////////////////////////
1796 jalview.datamodel.Sequence[] orderedSeqs = new jalview.datamodel.Sequence[tmpseqs
1799 tmpseqs.toArray(orderedSeqs);
1801 jalview.datamodel.Alignment al = new jalview.datamodel.Alignment(
1804 // / Add the alignment properties
1805 for (int i = 0; i < vamsasSet.getSequenceSetPropertiesCount(); i++)
1807 SequenceSetProperties ssp = vamsasSet.getSequenceSetProperties(i);
1808 al.setProperty(ssp.getKey(), ssp.getValue());
1812 // SequenceFeatures are added to the DatasetSequence,
1813 // so we must create or recover the dataset before loading features
1814 // ///////////////////////////////
1815 if (vamsasSet.getDatasetId() == null || vamsasSet.getDatasetId() == "")
1817 // older jalview projects do not have a dataset id.
1818 al.setDataset(null);
1822 recoverDatasetFor(vamsasSet, al);
1824 // ///////////////////////////////
1826 Hashtable pdbloaded = new Hashtable();
1829 // load sequence features, database references and any associated PDB
1830 // structures for the alignment
1831 for (int i = 0; i < vamsasSeq.length; i++)
1833 if (JSEQ[i].getFeaturesCount() > 0)
1835 Features[] features = JSEQ[i].getFeatures();
1836 for (int f = 0; f < features.length; f++)
1838 jalview.datamodel.SequenceFeature sf = new jalview.datamodel.SequenceFeature(
1839 features[f].getType(), features[f].getDescription(),
1840 features[f].getStatus(), features[f].getBegin(),
1841 features[f].getEnd(), features[f].getFeatureGroup());
1843 sf.setScore(features[f].getScore());
1844 for (int od = 0; od < features[f].getOtherDataCount(); od++)
1846 OtherData keyValue = features[f].getOtherData(od);
1847 if (keyValue.getKey().startsWith("LINK"))
1849 sf.addLink(keyValue.getValue());
1853 sf.setValue(keyValue.getKey(), keyValue.getValue());
1858 al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf);
1861 if (vamsasSeq[i].getDBRefCount() > 0)
1863 addDBRefs(al.getSequenceAt(i).getDatasetSequence(), vamsasSeq[i]);
1865 if (JSEQ[i].getPdbidsCount() > 0)
1867 Pdbids[] ids = JSEQ[i].getPdbids();
1868 for (int p = 0; p < ids.length; p++)
1870 jalview.datamodel.PDBEntry entry = new jalview.datamodel.PDBEntry();
1871 entry.setId(ids[p].getId());
1872 entry.setType(ids[p].getType());
1873 if (ids[p].getFile() != null)
1875 if (!pdbloaded.containsKey(ids[p].getFile()))
1877 entry.setFile(loadPDBFile(jprovider, ids[p].getId()));
1881 entry.setFile(pdbloaded.get(ids[p].getId()).toString());
1885 al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
1889 } // end !multipleview
1891 // ///////////////////////////////
1892 // LOAD SEQUENCE MAPPINGS
1894 if (vamsasSet.getAlcodonFrameCount() > 0)
1896 // TODO Potentially this should only be done once for all views of an
1898 AlcodonFrame[] alc = vamsasSet.getAlcodonFrame();
1899 for (int i = 0; i < alc.length; i++)
1901 jalview.datamodel.AlignedCodonFrame cf = new jalview.datamodel.AlignedCodonFrame(
1902 alc[i].getAlcodonCount());
1903 if (alc[i].getAlcodonCount() > 0)
1905 Alcodon[] alcods = alc[i].getAlcodon();
1906 for (int p = 0; p < cf.codons.length; p++)
1908 if (alcods[p].hasPos1() && alcods[p].hasPos2() && alcods[p].hasPos3())
1910 // translated codons require three valid positions
1911 cf.codons[p] = new int[3];
1912 cf.codons[p][0] = (int) alcods[p].getPos1();
1913 cf.codons[p][1] = (int) alcods[p].getPos2();
1914 cf.codons[p][2] = (int) alcods[p].getPos3();
1916 cf.codons[p] = null;
1920 if (alc[i].getAlcodMapCount() > 0)
1922 AlcodMap[] maps = alc[i].getAlcodMap();
1923 for (int m = 0; m < maps.length; m++)
1925 SequenceI dnaseq = (SequenceI) seqRefIds
1926 .get(maps[m].getDnasq());
1928 jalview.datamodel.Mapping mapping = null;
1929 // attach to dna sequence reference.
1930 if (maps[m].getMapping() != null)
1932 mapping = addMapping(maps[m].getMapping());
1936 cf.addMap(dnaseq, mapping.getTo(), mapping.getMap());
1941 frefedSequence.add(new Object[]
1942 { maps[m].getDnasq(), cf, mapping });
1946 al.addCodonFrame(cf);
1951 // ////////////////////////////////
1953 boolean hideQuality = true, hideConservation = true, hideConsensus = true;
1955 if (vamsasSet.getAnnotationCount() > 0)
1957 Annotation[] an = vamsasSet.getAnnotation();
1959 for (int i = 0; i < an.length; i++)
1961 // set visibility for automatic annotation for this view
1962 if (an[i].getLabel().equals("Quality"))
1964 hideQuality = false;
1967 else if (an[i].getLabel().equals("Conservation"))
1969 hideConservation = false;
1972 else if (an[i].getLabel().equals("Consensus"))
1974 hideConsensus = false;
1977 // set visiblity for other annotation in this view
1978 if (an[i].getId() != null
1979 && annotationIds.containsKey(an[i].getId()))
1981 jalview.datamodel.AlignmentAnnotation jda = (jalview.datamodel.AlignmentAnnotation) annotationIds
1982 .get(an[i].getId());
1983 // in principle Visible should always be true for annotation displayed
1984 // in multiple views
1985 if (an[i].hasVisible())
1986 jda.visible = an[i].getVisible();
1988 al.addAnnotation(jda);
1992 // Construct new annotation from model.
1993 AnnotationElement[] ae = an[i].getAnnotationElement();
1994 jalview.datamodel.Annotation[] anot = null;
1996 if (!an[i].getScoreOnly())
1998 anot = new jalview.datamodel.Annotation[al.getWidth()];
2000 for (int aa = 0; aa < ae.length && aa < anot.length; aa++)
2002 if (ae[aa].getPosition() >= anot.length)
2005 anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(
2007 ae[aa].getDisplayCharacter(), ae[aa].getDescription(), (ae[aa]
2008 .getSecondaryStructure() == null || ae[aa]
2009 .getSecondaryStructure().length() == 0) ? ' ' : ae[aa]
2010 .getSecondaryStructure().charAt(0), ae[aa].getValue()
2013 // JBPNote: Consider verifying dataflow for IO of secondary
2014 // structure annotation read from Stockholm files
2015 // this was added to try to ensure that
2016 // if (anot[ae[aa].getPosition()].secondaryStructure>' ')
2018 // anot[ae[aa].getPosition()].displayCharacter = "";
2020 anot[ae[aa].getPosition()].colour = new java.awt.Color(ae[aa]
2024 jalview.datamodel.AlignmentAnnotation jaa = null;
2026 if (an[i].getGraph())
2028 jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
2029 an[i].getDescription(), anot, 0, 0, an[i].getGraphType());
2031 jaa.graphGroup = an[i].getGraphGroup();
2033 if (an[i].getThresholdLine() != null)
2035 jaa.setThreshold(new jalview.datamodel.GraphLine(an[i]
2036 .getThresholdLine().getValue(), an[i]
2037 .getThresholdLine().getLabel(), new java.awt.Color(
2038 an[i].getThresholdLine().getColour())));
2045 jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
2046 an[i].getDescription(), anot);
2048 // register new annotation
2049 if (an[i].getId() != null)
2051 annotationIds.put(an[i].getId(), jaa);
2052 jaa.annotationId = an[i].getId();
2054 // recover sequence association
2055 if (an[i].getSequenceRef() != null)
2057 if (al.findName(an[i].getSequenceRef()) != null)
2059 jaa.createSequenceMapping(al.findName(an[i].getSequenceRef()),
2061 al.findName(an[i].getSequenceRef()).addAlignmentAnnotation(jaa);
2064 if (an[i].hasScore())
2066 jaa.setScore(an[i].getScore());
2069 if (an[i].hasVisible())
2070 jaa.visible = an[i].getVisible();
2072 al.addAnnotation(jaa);
2076 // ///////////////////////
2078 // Create alignment markup and styles for this view
2079 if (jms.getJGroupCount() > 0)
2081 JGroup[] groups = jms.getJGroup();
2083 for (int i = 0; i < groups.length; i++)
2085 ColourSchemeI cs = null;
2087 if (groups[i].getColour() != null)
2089 if (groups[i].getColour().startsWith("ucs"))
2091 cs = GetUserColourScheme(jms, groups[i].getColour());
2095 cs = ColourSchemeProperty.getColour(al, groups[i].getColour());
2100 cs.setThreshold(groups[i].getPidThreshold(), true);
2104 Vector seqs = new Vector();
2106 for (int s = 0; s < groups[i].getSeqCount(); s++)
2108 String seqId = groups[i].getSeq(s) + "";
2109 jalview.datamodel.SequenceI ts = (jalview.datamodel.SequenceI) seqRefIds
2114 seqs.addElement(ts);
2118 if (seqs.size() < 1)
2123 jalview.datamodel.SequenceGroup sg = new jalview.datamodel.SequenceGroup(
2124 seqs, groups[i].getName(), cs, groups[i].getDisplayBoxes(),
2125 groups[i].getDisplayText(), groups[i].getColourText(),
2126 groups[i].getStart(), groups[i].getEnd());
2129 .setOutlineColour(new java.awt.Color(groups[i]
2130 .getOutlineColour()));
2132 sg.textColour = new java.awt.Color(groups[i].getTextCol1());
2133 sg.textColour2 = new java.awt.Color(groups[i].getTextCol2());
2134 sg.setShowunconserved(groups[i].hasShowUnconserved() ? groups[i].isShowUnconserved() : false);
2135 sg.thresholdTextColour = groups[i].getTextColThreshold();
2137 if (groups[i].getConsThreshold() != 0)
2139 jalview.analysis.Conservation c = new jalview.analysis.Conservation(
2140 "All", ResidueProperties.propHash, 3, sg
2141 .getSequences(null), 0, sg.getWidth() - 1);
2143 c.verdict(false, 25);
2144 sg.cs.setConservation(c);
2151 // ///////////////////////////////
2154 // If we just load in the same jar file again, the sequenceSetId
2155 // will be the same, and we end up with multiple references
2156 // to the same sequenceSet. We must modify this id on load
2157 // so that each load of the file gives a unique id
2158 String uniqueSeqSetId = view.getSequenceSetId() + uniqueSetSuffix;
2159 String viewId = (view.getId() == null ? null : view.getId()
2161 AlignFrame af = null;
2162 AlignViewport av = null;
2163 // now check to see if we really need to create a new viewport.
2164 if (multipleView && viewportsAdded.size() == 0)
2166 // We recovered an alignment for which a viewport already exists.
2167 // TODO: fix up any settings necessary for overlaying stored state onto
2168 // state recovered from another document. (may not be necessary).
2169 // we may need a binding from a viewport in memory to one recovered from
2171 // and then recover its containing af to allow the settings to be applied.
2172 // TODO: fix for vamsas demo
2174 .println("About to recover a viewport for existing alignment: Sequence set ID is "
2176 Object seqsetobj = retrieveExistingObj(uniqueSeqSetId);
2177 if (seqsetobj != null)
2179 if (seqsetobj instanceof String)
2181 uniqueSeqSetId = (String) seqsetobj;
2183 .println("Recovered extant sequence set ID mapping for ID : New Sequence set ID is "
2189 .println("Warning : Collision between sequence set ID string and existing jalview object mapping.");
2194 AlignmentPanel ap = null;
2195 boolean isnewview = true;
2198 // Check to see if this alignment already has a view id == viewId
2199 jalview.gui.AlignmentPanel views[] = Desktop
2200 .getAlignmentPanels(uniqueSeqSetId);
2201 if (views != null && views.length > 0)
2203 for (int v = 0; v < views.length; v++)
2205 if (views[v].av.getViewId().equalsIgnoreCase(viewId))
2207 // recover the existing alignpanel, alignframe, viewport
2208 af = views[v].alignFrame;
2211 // TODO: could even skip resetting view settings if we don't want to
2212 // change the local settings from other jalview processes
2221 af = loadViewport(file, JSEQ, hiddenSeqs, al, hideConsensus,
2222 hideQuality, hideConservation, jms, view, uniqueSeqSetId,
2228 // /////////////////////////////////////
2229 if (loadTreesAndStructures && jms.getTreeCount() > 0)
2233 for (int t = 0; t < jms.getTreeCount(); t++)
2236 Tree tree = jms.getTree(t);
2238 TreePanel tp = (TreePanel) retrieveExistingObj(tree.getId());
2241 tp = af.ShowNewickTree(new jalview.io.NewickFile(tree
2242 .getNewick()), tree.getTitle(), tree.getWidth(), tree
2243 .getHeight(), tree.getXpos(), tree.getYpos());
2244 if (tree.getId() != null)
2251 // update local tree attributes ?
2252 tp.setTitle(tree.getTitle());
2253 tp.setBounds(new Rectangle(tree.getXpos(), tree.getYpos(), tree
2254 .getWidth(), tree.getHeight()));
2255 tp.av = av; // af.viewport; // TODO: verify 'associate with all
2258 tp.treeCanvas.av = av; // af.viewport;
2259 tp.treeCanvas.ap = ap; // af.alignPanel;
2264 warn("There was a problem recovering stored Newick tree: \n"+tree.getNewick());
2268 tp.fitToWindow.setState(tree.getFitToWindow());
2269 tp.fitToWindow_actionPerformed(null);
2271 if (tree.getFontName() != null)
2273 tp.setTreeFont(new java.awt.Font(tree.getFontName(), tree
2274 .getFontStyle(), tree.getFontSize()));
2278 tp.setTreeFont(new java.awt.Font(view.getFontName(), view
2279 .getFontStyle(), tree.getFontSize()));
2282 tp.showPlaceholders(tree.getMarkUnlinked());
2283 tp.showBootstrap(tree.getShowBootstrap());
2284 tp.showDistances(tree.getShowDistances());
2286 tp.treeCanvas.threshold = tree.getThreshold();
2288 if (tree.getCurrentTree())
2290 af.viewport.setCurrentTree(tp.getTree());
2294 } catch (Exception ex)
2296 ex.printStackTrace();
2300 // //LOAD STRUCTURES
2301 if (loadTreesAndStructures)
2303 for (int i = 0; i < JSEQ.length; i++)
2305 if (JSEQ[i].getPdbidsCount() > 0)
2307 Pdbids[] ids = JSEQ[i].getPdbids();
2308 for (int p = 0; p < ids.length; p++)
2310 for (int s = 0; s < ids[p].getStructureStateCount(); s++)
2312 // check to see if we haven't already created this structure view
2313 String sviewid = (ids[p].getStructureState(s).getViewId() == null) ? null
2314 : ids[p].getStructureState(s).getViewId()
2316 jalview.datamodel.PDBEntry jpdb = new jalview.datamodel.PDBEntry();
2317 // Originally : ids[p].getFile()
2318 // : TODO: verify external PDB file recovery still works in normal
2319 // jalview project load
2320 jpdb.setFile(loadPDBFile(jprovider, ids[p].getId()));
2321 jpdb.setId(ids[p].getId());
2323 int x = ids[p].getStructureState(s).getXpos();
2324 int y = ids[p].getStructureState(s).getYpos();
2325 int width = ids[p].getStructureState(s).getWidth();
2326 int height = ids[p].getStructureState(s).getHeight();
2327 AppJmol comp = null;
2328 JInternalFrame[] frames = null;
2333 frames = Desktop.desktop.getAllFrames();
2334 } catch (ArrayIndexOutOfBoundsException e)
2336 // occasional No such child exceptions are thrown here...
2341 } catch (Exception f)
2346 } while (frames == null);
2347 // search for any Jmol windows already open from other
2348 // alignment views that exactly match the stored structure state
2349 for (int f = 0; comp == null && f < frames.length; f++)
2351 if (frames[f] instanceof AppJmol)
2354 && ((AppJmol) frames[f]).getViewId().equals(
2357 // post jalview 2.4 schema includes structure view id
2358 comp = (AppJmol) frames[f];
2360 else if (frames[f].getX() == x && frames[f].getY() == y
2361 && frames[f].getHeight() == height
2362 && frames[f].getWidth() == width)
2364 comp = (AppJmol) frames[f];
2368 Desktop.desktop.getComponentAt(x, y);
2370 String pdbFile = loadPDBFile(jprovider, ids[p].getId());
2372 jalview.datamodel.SequenceI[] seq = new jalview.datamodel.SequenceI[]
2373 { (jalview.datamodel.SequenceI) seqRefIds.get(JSEQ[i].getId()
2378 // create a new Jmol window
2379 String state = ids[p].getStructureState(s).getContent();
2381 StringBuffer newFileLoc = new StringBuffer(state.substring(
2382 0, state.indexOf("\"", state.indexOf("load")) + 1));
2384 newFileLoc.append(jpdb.getFile());
2385 newFileLoc.append(state.substring(state.indexOf("\"", state
2386 .indexOf("load \"") + 6)));
2388 new AppJmol(pdbFile, ids[p].getId(), seq, af.alignPanel,
2389 newFileLoc.toString(), new java.awt.Rectangle(x, y,
2390 width, height), sviewid);
2394 // if (comp != null)
2396 // NOTE: if the jalview project is part of a shared session then
2397 // view synchronization should/could be done here.
2399 // add mapping for this sequence to the already open Jmol
2400 // instance (if it doesn't already exist)
2402 StructureSelectionManager.getStructureSelectionManager()
2403 .setMapping(seq, null, pdbFile,
2404 jalview.io.AppletFormatAdapter.FILE);
2406 ((AppJmol) comp).addSequence(seq);
2417 AlignFrame loadViewport(String file, JSeq[] JSEQ, Vector hiddenSeqs,
2418 Alignment al, boolean hideConsensus, boolean hideQuality,
2419 boolean hideConservation, JalviewModelSequence jms,
2420 Viewport view, String uniqueSeqSetId, String viewId)
2422 AlignFrame af = null;
2423 af = new AlignFrame(al, view.getWidth(), view.getHeight(),
2424 uniqueSeqSetId, viewId);
2426 af.setFileName(file, "Jalview");
2428 for (int i = 0; i < JSEQ.length; i++)
2430 af.viewport.setSequenceColour(af.viewport.alignment.getSequenceAt(i),
2431 new java.awt.Color(JSEQ[i].getColour()));
2434 af.viewport.gatherViewsHere = view.getGatheredViews();
2436 if (view.getSequenceSetId() != null)
2438 jalview.gui.AlignViewport av = (jalview.gui.AlignViewport) viewportsAdded
2439 .get(uniqueSeqSetId);
2441 af.viewport.sequenceSetID = uniqueSeqSetId;
2444 // propagate shared settings to this new view
2445 af.viewport.historyList = av.historyList;
2446 af.viewport.redoList = av.redoList;
2450 viewportsAdded.put(uniqueSeqSetId, af.viewport);
2452 // TODO: check if this method can be called repeatedly without
2453 // side-effects if alignpanel already registered.
2454 PaintRefresher.Register(af.alignPanel, uniqueSeqSetId);
2456 // apply Hidden regions to view.
2457 if (hiddenSeqs != null)
2459 for (int s = 0; s < JSEQ.length; s++)
2461 jalview.datamodel.SequenceGroup hidden = new jalview.datamodel.SequenceGroup();
2463 for (int r = 0; r < JSEQ[s].getHiddenSequencesCount(); r++)
2465 hidden.addSequence(al
2466 .getSequenceAt(JSEQ[s].getHiddenSequences(r)), false);
2468 af.viewport.hideRepSequences(al.getSequenceAt(s), hidden);
2471 jalview.datamodel.SequenceI[] hseqs = new jalview.datamodel.SequenceI[hiddenSeqs
2474 for (int s = 0; s < hiddenSeqs.size(); s++)
2476 hseqs[s] = (jalview.datamodel.SequenceI) hiddenSeqs.elementAt(s);
2479 af.viewport.hideSequence(hseqs);
2482 // set visibility of annotation in view
2483 if ((hideConsensus || hideQuality || hideConservation)
2484 && al.getAlignmentAnnotation() != null)
2486 int hSize = al.getAlignmentAnnotation().length;
2487 for (int h = 0; h < hSize; h++)
2489 if ((hideConsensus && al.getAlignmentAnnotation()[h].label
2490 .equals("Consensus"))
2491 || (hideQuality && al.getAlignmentAnnotation()[h].label
2493 || (hideConservation && al.getAlignmentAnnotation()[h].label
2494 .equals("Conservation")))
2496 al.deleteAnnotation(al.getAlignmentAnnotation()[h]);
2501 af.alignPanel.adjustAnnotationHeight();
2503 // recover view properties and display parameters
2504 if (view.getViewName() != null)
2506 af.viewport.viewName = view.getViewName();
2507 af.setInitialTabVisible();
2509 af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(), view
2512 af.viewport.setShowAnnotation(view.getShowAnnotation());
2513 af.viewport.setAbovePIDThreshold(view.getPidSelected());
2515 af.viewport.setColourText(view.getShowColourText());
2517 af.viewport.setConservationSelected(view.getConservationSelected());
2518 af.viewport.setShowJVSuffix(view.getShowFullId());
2519 af.viewport.rightAlignIds = view.getRightAlignIds();
2520 af.viewport.setFont(new java.awt.Font(view.getFontName(), view
2521 .getFontStyle(), view.getFontSize()));
2522 af.alignPanel.fontChanged();
2523 af.viewport.setRenderGaps(view.getRenderGaps());
2524 af.viewport.setWrapAlignment(view.getWrapAlignment());
2525 af.alignPanel.setWrapAlignment(view.getWrapAlignment());
2526 af.viewport.setShowAnnotation(view.getShowAnnotation());
2527 af.alignPanel.setAnnotationVisible(view.getShowAnnotation());
2529 af.viewport.setShowBoxes(view.getShowBoxes());
2531 af.viewport.setShowText(view.getShowText());
2533 af.viewport.textColour = new java.awt.Color(view.getTextCol1());
2534 af.viewport.textColour2 = new java.awt.Color(view.getTextCol2());
2535 af.viewport.thresholdTextColour = view.getTextColThreshold();
2536 af.viewport.setShowUnconserved(view.hasShowUnconserved() ? view.isShowUnconserved() : false);
2537 af.viewport.setStartRes(view.getStartRes());
2538 af.viewport.setStartSeq(view.getStartSeq());
2540 ColourSchemeI cs = null;
2541 // apply colourschemes
2542 if (view.getBgColour() != null)
2544 if (view.getBgColour().startsWith("ucs"))
2546 cs = GetUserColourScheme(jms, view.getBgColour());
2548 else if (view.getBgColour().startsWith("Annotation"))
2550 // int find annotation
2551 for (int i = 0; i < af.viewport.alignment.getAlignmentAnnotation().length; i++)
2553 if (af.viewport.alignment.getAlignmentAnnotation()[i].label
2554 .equals(view.getAnnotationColours().getAnnotation()))
2556 if (af.viewport.alignment.getAlignmentAnnotation()[i]
2557 .getThreshold() == null)
2559 af.viewport.alignment.getAlignmentAnnotation()[i]
2560 .setThreshold(new jalview.datamodel.GraphLine(view
2561 .getAnnotationColours().getThreshold(),
2562 "Threshold", java.awt.Color.black)
2567 if (view.getAnnotationColours().getColourScheme()
2570 cs = new AnnotationColourGradient(af.viewport.alignment
2571 .getAlignmentAnnotation()[i], new java.awt.Color(view
2572 .getAnnotationColours().getMinColour()),
2573 new java.awt.Color(view.getAnnotationColours()
2574 .getMaxColour()), view.getAnnotationColours()
2575 .getAboveThreshold());
2577 else if (view.getAnnotationColours().getColourScheme()
2580 cs = new AnnotationColourGradient(af.viewport.alignment
2581 .getAlignmentAnnotation()[i], GetUserColourScheme(
2582 jms, view.getAnnotationColours().getColourScheme()),
2583 view.getAnnotationColours().getAboveThreshold());
2587 cs = new AnnotationColourGradient(af.viewport.alignment
2588 .getAlignmentAnnotation()[i], ColourSchemeProperty
2589 .getColour(al, view.getAnnotationColours()
2590 .getColourScheme()), view
2591 .getAnnotationColours().getAboveThreshold());
2594 // Also use these settings for all the groups
2595 if (al.getGroups() != null)
2597 for (int g = 0; g < al.getGroups().size(); g++)
2599 jalview.datamodel.SequenceGroup sg = (jalview.datamodel.SequenceGroup) al
2600 .getGroups().elementAt(g);
2609 * (view.getAnnotationColours().getColourScheme().equals("None")) {
2610 * sg.cs = new AnnotationColourGradient(
2611 * af.viewport.alignment.getAlignmentAnnotation()[i], new
2612 * java.awt.Color(view.getAnnotationColours(). getMinColour()),
2613 * new java.awt.Color(view.getAnnotationColours().
2615 * view.getAnnotationColours().getAboveThreshold()); } else
2618 sg.cs = new AnnotationColourGradient(
2619 af.viewport.alignment.getAlignmentAnnotation()[i],
2620 sg.cs, view.getAnnotationColours()
2621 .getAboveThreshold());
2634 cs = ColourSchemeProperty.getColour(al, view.getBgColour());
2639 cs.setThreshold(view.getPidThreshold(), true);
2640 cs.setConsensus(af.viewport.hconsensus);
2644 af.viewport.setGlobalColourScheme(cs);
2645 af.viewport.setColourAppliesToAllGroups(false);
2647 if (view.getConservationSelected() && cs != null)
2649 cs.setConservationInc(view.getConsThreshold());
2652 af.changeColour(cs);
2654 af.viewport.setColourAppliesToAllGroups(true);
2656 if (view.getShowSequenceFeatures())
2658 af.viewport.showSequenceFeatures = true;
2660 // recover featre settings
2661 if (jms.getFeatureSettings() != null)
2663 af.viewport.featuresDisplayed = new Hashtable();
2664 String[] renderOrder = new String[jms.getFeatureSettings()
2665 .getSettingCount()];
2666 for (int fs = 0; fs < jms.getFeatureSettings().getSettingCount(); fs++)
2668 Setting setting = jms.getFeatureSettings().getSetting(fs);
2669 if (setting.hasMincolour())
2671 // TODO: determine how to set data independent bounds for a graduated colour scheme's range.
2672 GraduatedColor gc = new GraduatedColor(new java.awt.Color(setting.getMincolour()), new java.awt.Color(setting.getColour()),
2674 if (setting.hasThreshold()) {
2675 gc.setThresh(setting.getThreshold());
2676 gc.setThreshType(setting.getThreshstate());
2679 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(
2680 setting.getType(), new java.awt.Color(setting.getColour()));
2682 renderOrder[fs] = setting.getType();
2683 if (setting.hasOrder())
2684 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setOrder(
2685 setting.getType(), setting.getOrder());
2687 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setOrder(
2689 fs / jms.getFeatureSettings().getSettingCount());
2690 if (setting.getDisplay())
2692 af.viewport.featuresDisplayed.put(setting.getType(), new Integer(
2693 setting.getColour()));
2696 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder = renderOrder;
2698 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureGroups = fgtable = new Hashtable();
2699 for (int gs = 0; gs < jms.getFeatureSettings().getGroupCount(); gs++)
2701 Group grp = jms.getFeatureSettings().getGroup(gs);
2702 fgtable.put(grp.getName(), new Boolean(grp.getDisplay()));
2706 if (view.getHiddenColumnsCount() > 0)
2708 for (int c = 0; c < view.getHiddenColumnsCount(); c++)
2710 af.viewport.hideColumns(view.getHiddenColumns(c).getStart(), view
2711 .getHiddenColumns(c).getEnd() // +1
2716 af.setMenusFromViewport(af.viewport);
2717 // TODO: we don't need to do this if the viewport is aready visible.
2718 Desktop.addInternalFrame(af, view.getTitle(), view.getWidth(), view
2723 Hashtable skipList = null;
2726 * TODO remove this method
2729 * @return AlignFrame bound to sequenceSetId from view, if one exists. private
2730 * AlignFrame getSkippedFrame(Viewport view) { if (skipList==null) {
2731 * throw new Error("Implementation Error. No skipList defined for this
2732 * Jalview2XML instance."); } return (AlignFrame)
2733 * skipList.get(view.getSequenceSetId()); }
2737 * Check if the Jalview view contained in object should be skipped or not.
2740 * @return true if view's sequenceSetId is a key in skipList
2742 private boolean skipViewport(JalviewModel object)
2744 if (skipList == null)
2749 if (skipList.containsKey(id = object.getJalviewModelSequence()
2750 .getViewport()[0].getSequenceSetId()))
2752 if (Cache.log != null && Cache.log.isDebugEnabled())
2754 Cache.log.debug("Skipping seuqence set id " + id);
2761 public void AddToSkipList(AlignFrame af)
2763 if (skipList == null)
2765 skipList = new Hashtable();
2767 skipList.put(af.getViewport().getSequenceSetId(), af);
2770 public void clearSkipList()
2772 if (skipList != null)
2779 private void recoverDatasetFor(SequenceSet vamsasSet, Alignment al)
2781 jalview.datamodel.Alignment ds = getDatasetFor(vamsasSet.getDatasetId());
2782 Vector dseqs = null;
2785 // create a list of new dataset sequences
2786 dseqs = new Vector();
2788 for (int i = 0, iSize = vamsasSet.getSequenceCount(); i < iSize; i++)
2790 Sequence vamsasSeq = vamsasSet.getSequence(i);
2791 ensureJalviewDatasetSequence(vamsasSeq, ds, dseqs);
2793 // create a new dataset
2796 SequenceI[] dsseqs = new SequenceI[dseqs.size()];
2797 dseqs.copyInto(dsseqs);
2798 ds = new jalview.datamodel.Alignment(dsseqs);
2799 addDatasetRef(vamsasSet.getDatasetId(), ds);
2801 // set the dataset for the newly imported alignment.
2802 if (al.getDataset() == null)
2811 * sequence definition to create/merge dataset sequence for
2815 * vector to add new dataset sequence to
2817 private void ensureJalviewDatasetSequence(Sequence vamsasSeq,
2818 AlignmentI ds, Vector dseqs)
2820 // JBP TODO: Check this is called for AlCodonFrames to support recovery of
2822 jalview.datamodel.Sequence sq = (jalview.datamodel.Sequence) seqRefIds
2823 .get(vamsasSeq.getId());
2824 jalview.datamodel.SequenceI dsq = null;
2825 if (sq != null && sq.getDatasetSequence() != null)
2827 dsq = (jalview.datamodel.SequenceI) sq.getDatasetSequence();
2830 String sqid = vamsasSeq.getDsseqid();
2833 // need to create or add a new dataset sequence reference to this sequence
2836 dsq = (jalview.datamodel.SequenceI) seqRefIds.get(sqid);
2841 // make a new dataset sequence
2842 dsq = sq.createDatasetSequence();
2845 // make up a new dataset reference for this sequence
2846 sqid = seqHash(dsq);
2848 dsq.setVamsasId(uniqueSetSuffix + sqid);
2849 seqRefIds.put(sqid, dsq);
2854 dseqs.addElement(dsq);
2859 ds.addSequence(dsq);
2865 { // make this dataset sequence sq's dataset sequence
2866 sq.setDatasetSequence(dsq);
2870 // TODO: refactor this as a merge dataset sequence function
2871 // now check that sq (the dataset sequence) sequence really is the union of
2872 // all references to it
2873 // boolean pre = sq.getStart() < dsq.getStart();
2874 // boolean post = sq.getEnd() > dsq.getEnd();
2878 StringBuffer sb = new StringBuffer();
2879 String newres = jalview.analysis.AlignSeq.extractGaps(
2880 jalview.util.Comparison.GapChars, sq.getSequenceAsString());
2881 if (!newres.equalsIgnoreCase(dsq.getSequenceAsString())
2882 && newres.length() > dsq.getLength())
2884 // Update with the longer sequence.
2888 * if (pre) { sb.insert(0, newres .substring(0, dsq.getStart() -
2889 * sq.getStart())); dsq.setStart(sq.getStart()); } if (post) {
2890 * sb.append(newres.substring(newres.length() - sq.getEnd() -
2891 * dsq.getEnd())); dsq.setEnd(sq.getEnd()); }
2893 dsq.setSequence(sb.toString());
2895 // TODO: merges will never happen if we 'know' we have the real dataset
2896 // sequence - this should be detected when id==dssid
2897 System.err.println("DEBUG Notice: Merged dataset sequence"); // ("
2898 // + (pre ? "prepended" : "") + " "
2899 // + (post ? "appended" : ""));
2904 java.util.Hashtable datasetIds = null;
2905 java.util.IdentityHashMap dataset2Ids = null;
2906 private Alignment getDatasetFor(String datasetId)
2908 if (datasetIds == null)
2910 datasetIds = new Hashtable();
2913 if (datasetIds.containsKey(datasetId))
2915 return (Alignment) datasetIds.get(datasetId);
2920 private void addDatasetRef(String datasetId, Alignment dataset)
2922 if (datasetIds == null)
2924 datasetIds = new Hashtable();
2926 datasetIds.put(datasetId, dataset);
2929 * make a new dataset ID for this jalview dataset alignment
2933 private String getDatasetIdRef(jalview.datamodel.Alignment dataset)
2935 if (dataset.getDataset()!=null)
2937 warn("Serious issue! Dataset Object passed to getDatasetIdRef is not a Jalview DATASET alignment...");
2939 String datasetId=makeHashCode(dataset, null);
2940 if (datasetId==null)
2942 // make a new datasetId and record it
2943 if (dataset2Ids == null)
2945 dataset2Ids = new IdentityHashMap();
2947 datasetId = (String) dataset2Ids.get(dataset);
2949 if (datasetId==null)
2951 datasetId = "ds"+dataset2Ids.size()+1;
2952 dataset2Ids.put(dataset,datasetId);
2957 private void addDBRefs(SequenceI datasetSequence, Sequence sequence)
2959 for (int d = 0; d < sequence.getDBRefCount(); d++)
2961 DBRef dr = sequence.getDBRef(d);
2962 jalview.datamodel.DBRefEntry entry = new jalview.datamodel.DBRefEntry(
2963 sequence.getDBRef(d).getSource(), sequence.getDBRef(d)
2964 .getVersion(), sequence.getDBRef(d).getAccessionId());
2965 if (dr.getMapping() != null)
2967 entry.setMap(addMapping(dr.getMapping()));
2969 datasetSequence.addDBRef(entry);
2973 private jalview.datamodel.Mapping addMapping(Mapping m)
2975 SequenceI dsto = null;
2976 // Mapping m = dr.getMapping();
2977 int fr[] = new int[m.getMapListFromCount() * 2];
2978 Enumeration f = m.enumerateMapListFrom();
2979 for (int _i = 0; f.hasMoreElements(); _i += 2)
2981 MapListFrom mf = (MapListFrom) f.nextElement();
2982 fr[_i] = mf.getStart();
2983 fr[_i + 1] = mf.getEnd();
2985 int fto[] = new int[m.getMapListToCount() * 2];
2986 f = m.enumerateMapListTo();
2987 for (int _i = 0; f.hasMoreElements(); _i += 2)
2989 MapListTo mf = (MapListTo) f.nextElement();
2990 fto[_i] = mf.getStart();
2991 fto[_i + 1] = mf.getEnd();
2993 jalview.datamodel.Mapping jmap = new jalview.datamodel.Mapping(dsto,
2994 fr, fto, (int) m.getMapFromUnit(), (int) m.getMapToUnit());
2995 if (m.getMappingChoice() != null)
2997 MappingChoice mc = m.getMappingChoice();
2998 if (mc.getDseqFor() != null)
3000 String dsfor = ""+mc.getDseqFor();
3001 if (seqRefIds.containsKey(dsfor))
3006 jmap.setTo((SequenceI) seqRefIds.get(dsfor));
3010 frefedSequence.add(new Object[]
3017 * local sequence definition
3019 Sequence ms = mc.getSequence();
3020 jalview.datamodel.Sequence djs = null;
3021 String sqid = ms.getDsseqid();
3022 if (sqid != null && sqid.length() > 0)
3025 * recover dataset sequence
3027 djs = (jalview.datamodel.Sequence) seqRefIds.get(sqid);
3032 .println("Warning - making up dataset sequence id for DbRef sequence map reference");
3033 sqid = ((Object) ms).toString(); // make up a new hascode for
3034 // undefined dataset sequence hash
3035 // (unlikely to happen)
3041 * make a new dataset sequence and add it to refIds hash
3043 djs = new jalview.datamodel.Sequence(ms.getName(), ms
3045 djs.setStart(jmap.getMap().getToLowest());
3046 djs.setEnd(jmap.getMap().getToHighest());
3047 djs.setVamsasId(uniqueSetSuffix + sqid);
3049 seqRefIds.put(sqid, djs);
3052 jalview.bin.Cache.log.debug("about to recurse on addDBRefs.");
3061 public jalview.gui.AlignmentPanel copyAlignPanel(AlignmentPanel ap,
3062 boolean keepSeqRefs)
3065 jalview.schemabinding.version2.JalviewModel jm = SaveState(ap, null,
3071 jm.getJalviewModelSequence().getViewport(0).setSequenceSetId(null);
3075 uniqueSetSuffix = "";
3076 jm.getJalviewModelSequence().getViewport(0).setId(null); // we don't overwrite the view we just copied
3078 if (this.frefedSequence==null)
3080 frefedSequence = new Vector();
3083 viewportsAdded = new Hashtable();
3085 AlignFrame af = LoadFromObject(jm, null, false, null);
3086 af.alignPanels.clear();
3087 af.closeMenuItem_actionPerformed(true);
3090 * if(ap.av.alignment.getAlignmentAnnotation()!=null) { for(int i=0; i<ap.av.alignment.getAlignmentAnnotation().length;
3091 * i++) { if(!ap.av.alignment.getAlignmentAnnotation()[i].autoCalculated) {
3092 * af.alignPanel.av.alignment.getAlignmentAnnotation()[i] =
3093 * ap.av.alignment.getAlignmentAnnotation()[i]; } } }
3096 return af.alignPanel;
3100 * flag indicating if hashtables should be cleared on finalization TODO this
3101 * flag may not be necessary
3103 private boolean _cleartables = true;
3105 private Hashtable jvids2vobj;
3110 * @see java.lang.Object#finalize()
3112 protected void finalize() throws Throwable
3114 // really make sure we have no buried refs left.
3119 this.seqRefIds = null;
3120 this.seqsToIds = null;
3124 private void warn(String msg)
3129 private void warn(String msg, Exception e)
3131 if (Cache.log != null)
3135 Cache.log.warn(msg, e);
3139 Cache.log.warn(msg);
3144 System.err.println("Warning: " + msg);
3147 e.printStackTrace();
3153 * set the object to ID mapping tables used to write/recover objects and XML
3154 * ID strings for the jalview project. If external tables are provided then
3155 * finalize and clearSeqRefs will not clear the tables when the Jalview2XML
3156 * object goes out of scope. - also populates the datasetIds hashtable with
3157 * alignment objects containing dataset sequences
3160 * Map from ID strings to jalview datamodel
3162 * Map from jalview datamodel to ID strings
3166 public void setObjectMappingTables(Hashtable vobj2jv,
3167 IdentityHashMap jv2vobj)
3169 this.jv2vobj = jv2vobj;
3170 this.vobj2jv = vobj2jv;
3171 Iterator ds = jv2vobj.keySet().iterator();
3173 while (ds.hasNext())
3175 Object jvobj = ds.next();
3176 id = jv2vobj.get(jvobj).toString();
3177 if (jvobj instanceof jalview.datamodel.Alignment)
3179 if (((jalview.datamodel.Alignment) jvobj).getDataset() == null)
3181 addDatasetRef(id, (jalview.datamodel.Alignment) jvobj);
3184 else if (jvobj instanceof jalview.datamodel.Sequence)
3186 // register sequence object so the XML parser can recover it.
3187 if (seqRefIds == null)
3189 seqRefIds = new Hashtable();
3191 if (seqsToIds == null)
3193 seqsToIds = new IdentityHashMap();
3195 seqRefIds.put(jv2vobj.get(jvobj).toString(), jvobj);
3196 seqsToIds.put(jvobj, id);
3198 else if (jvobj instanceof jalview.datamodel.AlignmentAnnotation)
3200 if (annotationIds == null)
3202 annotationIds = new Hashtable();
3205 annotationIds.put(anid = jv2vobj.get(jvobj).toString(), jvobj);
3206 jalview.datamodel.AlignmentAnnotation jvann = (jalview.datamodel.AlignmentAnnotation) jvobj;
3207 if (jvann.annotationId == null)
3209 jvann.annotationId = anid;
3211 if (!jvann.annotationId.equals(anid))
3213 // TODO verify that this is the correct behaviour
3214 this.warn("Overriding Annotation ID for " + anid
3215 + " from different id : " + jvann.annotationId);
3216 jvann.annotationId = anid;
3219 else if (jvobj instanceof String)
3221 if (jvids2vobj == null)
3223 jvids2vobj = new Hashtable();
3224 jvids2vobj.put(jvobj, jv2vobj.get(jvobj).toString());
3228 Cache.log.debug("Ignoring " + jvobj.getClass() + " (ID = " + id);
3233 * set the uniqueSetSuffix used to prefix/suffix object IDs for jalview
3234 * objects created from the project archive. If string is null (default for
3235 * construction) then suffix will be set automatically.
3239 public void setUniqueSetSuffix(String string)
3241 uniqueSetSuffix = string;
3246 * uses skipList2 as the skipList for skipping views on sequence sets
3247 * associated with keys in the skipList
3251 public void setSkipList(Hashtable skipList2)
3253 skipList = skipList2;