2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
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
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 import jalview.api.FeatureColourI;
24 import jalview.api.ViewStyleI;
25 import jalview.api.structures.JalviewStructureDisplayI;
26 import jalview.bin.Cache;
27 import jalview.datamodel.AlignedCodonFrame;
28 import jalview.datamodel.Alignment;
29 import jalview.datamodel.AlignmentAnnotation;
30 import jalview.datamodel.AlignmentI;
31 import jalview.datamodel.PDBEntry;
32 import jalview.datamodel.RnaViewerModel;
33 import jalview.datamodel.SequenceGroup;
34 import jalview.datamodel.SequenceI;
35 import jalview.datamodel.StructureViewerModel;
36 import jalview.datamodel.StructureViewerModel.StructureData;
37 import jalview.ext.varna.RnaModel;
38 import jalview.gui.StructureViewer.ViewerType;
39 import jalview.schemabinding.version2.AlcodMap;
40 import jalview.schemabinding.version2.AlcodonFrame;
41 import jalview.schemabinding.version2.Annotation;
42 import jalview.schemabinding.version2.AnnotationColours;
43 import jalview.schemabinding.version2.AnnotationElement;
44 import jalview.schemabinding.version2.CalcIdParam;
45 import jalview.schemabinding.version2.DBRef;
46 import jalview.schemabinding.version2.Features;
47 import jalview.schemabinding.version2.Group;
48 import jalview.schemabinding.version2.HiddenColumns;
49 import jalview.schemabinding.version2.JGroup;
50 import jalview.schemabinding.version2.JSeq;
51 import jalview.schemabinding.version2.JalviewModel;
52 import jalview.schemabinding.version2.JalviewModelSequence;
53 import jalview.schemabinding.version2.MapListFrom;
54 import jalview.schemabinding.version2.MapListTo;
55 import jalview.schemabinding.version2.Mapping;
56 import jalview.schemabinding.version2.MappingChoice;
57 import jalview.schemabinding.version2.OtherData;
58 import jalview.schemabinding.version2.PdbentryItem;
59 import jalview.schemabinding.version2.Pdbids;
60 import jalview.schemabinding.version2.Property;
61 import jalview.schemabinding.version2.RnaViewer;
62 import jalview.schemabinding.version2.SecondaryStructure;
63 import jalview.schemabinding.version2.Sequence;
64 import jalview.schemabinding.version2.SequenceSet;
65 import jalview.schemabinding.version2.SequenceSetProperties;
66 import jalview.schemabinding.version2.Setting;
67 import jalview.schemabinding.version2.StructureState;
68 import jalview.schemabinding.version2.ThresholdLine;
69 import jalview.schemabinding.version2.Tree;
70 import jalview.schemabinding.version2.UserColours;
71 import jalview.schemabinding.version2.Viewport;
72 import jalview.schemes.AnnotationColourGradient;
73 import jalview.schemes.ColourSchemeI;
74 import jalview.schemes.ColourSchemeProperty;
75 import jalview.schemes.FeatureColour;
76 import jalview.schemes.ResidueColourScheme;
77 import jalview.schemes.ResidueProperties;
78 import jalview.schemes.UserColourScheme;
79 import jalview.structure.StructureSelectionManager;
80 import jalview.structures.models.AAStructureBindingModel;
81 import jalview.util.MessageManager;
82 import jalview.util.Platform;
83 import jalview.util.StringUtils;
84 import jalview.util.jarInputStreamProvider;
85 import jalview.viewmodel.AlignmentViewport;
86 import jalview.viewmodel.seqfeatures.FeatureRendererSettings;
87 import jalview.viewmodel.seqfeatures.FeaturesDisplayed;
88 import jalview.ws.jws2.Jws2Discoverer;
89 import jalview.ws.jws2.dm.AAConSettings;
90 import jalview.ws.jws2.jabaws2.Jws2Instance;
91 import jalview.ws.params.ArgumentI;
92 import jalview.ws.params.AutoCalcSetting;
93 import jalview.ws.params.WsParamSetI;
95 import java.awt.Color;
96 import java.awt.Rectangle;
97 import java.io.BufferedReader;
98 import java.io.DataInputStream;
99 import java.io.DataOutputStream;
101 import java.io.FileInputStream;
102 import java.io.FileOutputStream;
103 import java.io.IOException;
104 import java.io.InputStreamReader;
105 import java.io.OutputStreamWriter;
106 import java.io.PrintWriter;
107 import java.lang.reflect.InvocationTargetException;
108 import java.net.MalformedURLException;
110 import java.util.ArrayList;
111 import java.util.Arrays;
112 import java.util.Enumeration;
113 import java.util.HashMap;
114 import java.util.HashSet;
115 import java.util.Hashtable;
116 import java.util.IdentityHashMap;
117 import java.util.Iterator;
118 import java.util.LinkedHashMap;
119 import java.util.List;
120 import java.util.Map;
121 import java.util.Map.Entry;
122 import java.util.Set;
123 import java.util.Vector;
124 import java.util.jar.JarEntry;
125 import java.util.jar.JarInputStream;
126 import java.util.jar.JarOutputStream;
128 import javax.swing.JInternalFrame;
129 import javax.swing.JOptionPane;
130 import javax.swing.SwingUtilities;
132 import org.exolab.castor.xml.Marshaller;
133 import org.exolab.castor.xml.Unmarshaller;
136 * Write out the current jalview desktop state as a Jalview XML stream.
138 * Note: the vamsas objects referred to here are primitive versions of the
139 * VAMSAS project schema elements - they are not the same and most likely never
143 * @version $Revision: 1.134 $
145 public class Jalview2XML
147 private static final String VIEWER_PREFIX = "viewer_";
149 private static final String RNA_PREFIX = "rna_";
151 private static final String UTF_8 = "UTF-8";
153 // use this with nextCounter() to make unique names for entities
154 private int counter = 0;
157 * SequenceI reference -> XML ID string in jalview XML. Populated as XML reps
158 * of sequence objects are created.
160 IdentityHashMap<SequenceI, String> seqsToIds = null;
163 * jalview XML Sequence ID to jalview sequence object reference (both dataset
164 * and alignment sequences. Populated as XML reps of sequence objects are
167 Map<String, SequenceI> seqRefIds = null;
169 Map<String, SequenceI> incompleteSeqs = null;
171 List<SeqFref> frefedSequence = null;
173 boolean raiseGUI = true; // whether errors are raised in dialog boxes or not
176 * Map of reconstructed AlignFrame objects that appear to have come from
177 * SplitFrame objects (have a dna/protein complement view).
179 private Map<Viewport, AlignFrame> splitFrameCandidates = new HashMap<Viewport, AlignFrame>();
182 * Map from displayed rna structure models to their saved session state jar
185 private Map<RnaModel, String> rnaSessions = new HashMap<RnaModel, String>();
188 * create/return unique hash string for sq
191 * @return new or existing unique string for sq
193 String seqHash(SequenceI sq)
195 if (seqsToIds == null)
199 if (seqsToIds.containsKey(sq))
201 return seqsToIds.get(sq);
205 // create sequential key
206 String key = "sq" + (seqsToIds.size() + 1);
207 key = makeHashCode(sq, key); // check we don't have an external reference
209 seqsToIds.put(sq, key);
218 if (seqRefIds != null)
222 if (seqsToIds != null)
226 if (incompleteSeqs != null)
228 incompleteSeqs.clear();
236 warn("clearSeqRefs called when _cleartables was not set. Doing nothing.");
237 // seqRefIds = new Hashtable();
238 // seqsToIds = new IdentityHashMap();
244 if (seqsToIds == null)
246 seqsToIds = new IdentityHashMap<SequenceI, String>();
248 if (seqRefIds == null)
250 seqRefIds = new HashMap<String, SequenceI>();
252 if (incompleteSeqs == null)
254 incompleteSeqs = new HashMap<String, SequenceI>();
256 if (frefedSequence == null)
258 frefedSequence = new ArrayList<SeqFref>();
266 public Jalview2XML(boolean raiseGUI)
268 this.raiseGUI = raiseGUI;
272 * base class for resolving forward references to sequences by their ID
277 abstract class SeqFref
283 public SeqFref(String _sref, String type)
289 public String getSref()
294 public SequenceI getSrefSeq()
296 return seqRefIds.get(sref);
299 public boolean isResolvable()
301 return seqRefIds.get(sref) != null;
304 public SequenceI getSrefDatasetSeq()
306 SequenceI sq = seqRefIds.get(sref);
309 while (sq.getDatasetSequence() != null)
311 sq = sq.getDatasetSequence();
317 * @return true if the forward reference was fully resolved
319 abstract boolean resolve();
322 public String toString()
324 return type + " reference to " + sref;
329 * create forward reference for a mapping
335 public SeqFref newMappingRef(final String sref,
336 final jalview.datamodel.Mapping _jmap)
338 SeqFref fref = new SeqFref(sref, "Mapping")
340 public jalview.datamodel.Mapping jmap = _jmap;
345 SequenceI seq = getSrefDatasetSeq();
357 public SeqFref newAlcodMapRef(final String sref,
358 final AlignedCodonFrame _cf, final jalview.datamodel.Mapping _jmap)
361 SeqFref fref = new SeqFref(sref, "Codon Frame")
363 AlignedCodonFrame cf = _cf;
365 public jalview.datamodel.Mapping mp = _jmap;
370 SequenceI seq = getSrefDatasetSeq();
375 cf.addMap(seq, mp.getTo(), mp.getMap());
382 public void resolveFrefedSequences()
384 Iterator<SeqFref> nextFref=frefedSequence.iterator();
385 int toresolve=frefedSequence.size();
386 int unresolved=0,failedtoresolve=0;
387 while (nextFref.hasNext()) {
388 SeqFref ref = nextFref.next();
389 if (ref.isResolvable())
398 } catch (Exception x) {
399 System.err.println("IMPLEMENTATION ERROR: Failed to resolve forward reference for sequence "+ref.getSref());
409 System.err.println("Jalview Project Import: There were " + unresolved
410 + " forward references left unresolved on the stack.");
412 if (failedtoresolve>0)
414 System.err.println("SERIOUS! " + failedtoresolve
415 + " resolvable forward references failed to resolve.");
417 if (incompleteSeqs != null && incompleteSeqs.size() > 0)
419 System.err.println("Jalview Project Import: There are "
420 + incompleteSeqs.size()
421 + " sequences which may have incomplete metadata.");
422 if (incompleteSeqs.size() < 10)
424 for (SequenceI s : incompleteSeqs.values())
426 System.err.println(s.toString());
432 .println("Too many to report. Skipping output of incomplete sequences.");
438 * This maintains a map of viewports, the key being the seqSetId. Important to
439 * set historyItem and redoList for multiple views
441 Map<String, AlignViewport> viewportsAdded = new HashMap<String, AlignViewport>();
443 Map<String, AlignmentAnnotation> annotationIds = new HashMap<String, AlignmentAnnotation>();
445 String uniqueSetSuffix = "";
448 * List of pdbfiles added to Jar
450 List<String> pdbfiles = null;
452 // SAVES SEVERAL ALIGNMENT WINDOWS TO SAME JARFILE
453 public void saveState(File statefile)
455 FileOutputStream fos = null;
458 fos = new FileOutputStream(statefile);
459 JarOutputStream jout = new JarOutputStream(fos);
462 } catch (Exception e)
464 // TODO: inform user of the problem - they need to know if their data was
466 if (errorMessage == null)
468 errorMessage = "Couldn't write Jalview Archive to output file '"
469 + statefile + "' - See console error log for details";
473 errorMessage += "(output file was '" + statefile + "')";
483 } catch (IOException e)
493 * Writes a jalview project archive to the given Jar output stream.
497 public void saveState(JarOutputStream jout)
499 AlignFrame[] frames = Desktop.getAlignFrames();
505 saveAllFrames(Arrays.asList(frames), jout);
509 * core method for storing state for a set of AlignFrames.
512 * - frames involving all data to be exported (including containing
515 * - project output stream
517 private void saveAllFrames(List<AlignFrame> frames, JarOutputStream jout)
519 Hashtable<String, AlignFrame> dsses = new Hashtable<String, AlignFrame>();
522 * ensure cached data is clear before starting
524 // todo tidy up seqRefIds, seqsToIds initialisation / reset
526 splitFrameCandidates.clear();
531 // NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS
532 // //////////////////////////////////////////////////
534 List<String> shortNames = new ArrayList<String>();
535 List<String> viewIds = new ArrayList<String>();
538 for (int i = frames.size() - 1; i > -1; i--)
540 AlignFrame af = frames.get(i);
544 .containsKey(af.getViewport().getSequenceSetId()))
549 String shortName = makeFilename(af, shortNames);
551 int ap, apSize = af.alignPanels.size();
553 for (ap = 0; ap < apSize; ap++)
555 AlignmentPanel apanel = af.alignPanels.get(ap);
556 String fileName = apSize == 1 ? shortName : ap + shortName;
557 if (!fileName.endsWith(".xml"))
559 fileName = fileName + ".xml";
562 saveState(apanel, fileName, jout, viewIds);
564 String dssid = getDatasetIdRef(af.getViewport().getAlignment()
566 if (!dsses.containsKey(dssid))
568 dsses.put(dssid, af);
573 writeDatasetFor(dsses, "" + jout.hashCode() + " " + uniqueSetSuffix,
579 } catch (Exception foo)
584 } catch (Exception ex)
586 // TODO: inform user of the problem - they need to know if their data was
588 if (errorMessage == null)
590 errorMessage = "Couldn't write Jalview Archive - see error output for details";
592 ex.printStackTrace();
597 * Generates a distinct file name, based on the title of the AlignFrame, by
598 * appending _n for increasing n until an unused name is generated. The new
599 * name (without its extension) is added to the list.
603 * @return the generated name, with .xml extension
605 protected String makeFilename(AlignFrame af, List<String> namesUsed)
607 String shortName = af.getTitle();
609 if (shortName.indexOf(File.separatorChar) > -1)
611 shortName = shortName.substring(shortName
612 .lastIndexOf(File.separatorChar) + 1);
617 while (namesUsed.contains(shortName))
619 if (shortName.endsWith("_" + (count - 1)))
621 shortName = shortName.substring(0, shortName.lastIndexOf("_"));
624 shortName = shortName.concat("_" + count);
628 namesUsed.add(shortName);
630 if (!shortName.endsWith(".xml"))
632 shortName = shortName + ".xml";
637 // USE THIS METHOD TO SAVE A SINGLE ALIGNMENT WINDOW
638 public boolean saveAlignment(AlignFrame af, String jarFile,
643 FileOutputStream fos = new FileOutputStream(jarFile);
644 JarOutputStream jout = new JarOutputStream(fos);
645 List<AlignFrame> frames = new ArrayList<AlignFrame>();
647 // resolve splitframes
648 if (af.getViewport().getCodingComplement() != null)
650 frames = ((SplitFrame) af.getSplitViewContainer()).getAlignFrames();
656 saveAllFrames(frames, jout);
660 } catch (Exception foo)
666 } catch (Exception ex)
668 errorMessage = "Couldn't Write alignment view to Jalview Archive - see error output for details";
669 ex.printStackTrace();
674 private void writeDatasetFor(Hashtable<String, AlignFrame> dsses,
675 String fileName, JarOutputStream jout)
678 for (String dssids : dsses.keySet())
680 AlignFrame _af = dsses.get(dssids);
681 String jfileName = fileName + " Dataset for " + _af.getTitle();
682 if (!jfileName.endsWith(".xml"))
684 jfileName = jfileName + ".xml";
686 saveState(_af.alignPanel, jfileName, true, jout, null);
691 * create a JalviewModel from an alignment view and marshall it to a
695 * panel to create jalview model for
697 * name of alignment panel written to output stream
704 public JalviewModel saveState(AlignmentPanel ap, String fileName,
705 JarOutputStream jout, List<String> viewIds)
707 return saveState(ap, fileName, false, jout, viewIds);
711 * create a JalviewModel from an alignment view and marshall it to a
715 * panel to create jalview model for
717 * name of alignment panel written to output stream
719 * when true, only write the dataset for the alignment, not the data
720 * associated with the view.
726 public JalviewModel saveState(AlignmentPanel ap, String fileName,
727 boolean storeDS, JarOutputStream jout, List<String> viewIds)
731 viewIds = new ArrayList<String>();
736 List<UserColourScheme> userColours = new ArrayList<UserColourScheme>();
738 AlignViewport av = ap.av;
740 JalviewModel object = new JalviewModel();
741 object.setVamsasModel(new jalview.schemabinding.version2.VamsasModel());
743 object.setCreationDate(new java.util.Date(System.currentTimeMillis()));
744 object.setVersion(jalview.bin.Cache.getDefault("VERSION",
745 "Development Build"));
748 * rjal is full height alignment, jal is actual alignment with full metadata
749 * but excludes hidden sequences.
751 jalview.datamodel.AlignmentI rjal = av.getAlignment(), jal = rjal;
753 if (av.hasHiddenRows())
755 rjal = jal.getHiddenSequences().getFullAlignment();
758 SequenceSet vamsasSet = new SequenceSet();
760 JalviewModelSequence jms = new JalviewModelSequence();
762 vamsasSet.setGapChar(jal.getGapCharacter() + "");
764 if (jal.getDataset() != null)
766 // dataset id is the dataset's hashcode
767 vamsasSet.setDatasetId(getDatasetIdRef(jal.getDataset()));
770 // switch jal and the dataset
771 jal = jal.getDataset();
775 if (jal.getProperties() != null)
777 Enumeration en = jal.getProperties().keys();
778 while (en.hasMoreElements())
780 String key = en.nextElement().toString();
781 SequenceSetProperties ssp = new SequenceSetProperties();
783 ssp.setValue(jal.getProperties().get(key).toString());
784 vamsasSet.addSequenceSetProperties(ssp);
789 Set<String> calcIdSet = new HashSet<String>();
792 for (final SequenceI jds : rjal.getSequences())
794 final SequenceI jdatasq = jds.getDatasetSequence() == null ? jds
795 : jds.getDatasetSequence();
796 String id = seqHash(jds);
798 if (seqRefIds.get(id) != null)
800 // This happens for two reasons: 1. multiple views are being serialised.
801 // 2. the hashCode has collided with another sequence's code. This DOES
802 // HAPPEN! (PF00072.15.stk does this)
803 // JBPNote: Uncomment to debug writing out of files that do not read
804 // back in due to ArrayOutOfBoundExceptions.
805 // System.err.println("vamsasSeq backref: "+id+"");
806 // System.err.println(jds.getName()+"
807 // "+jds.getStart()+"-"+jds.getEnd()+" "+jds.getSequenceAsString());
808 // System.err.println("Hashcode: "+seqHash(jds));
809 // SequenceI rsq = (SequenceI) seqRefIds.get(id + "");
810 // System.err.println(rsq.getName()+"
811 // "+rsq.getStart()+"-"+rsq.getEnd()+" "+rsq.getSequenceAsString());
812 // System.err.println("Hashcode: "+seqHash(rsq));
816 vamsasSeq = createVamsasSequence(id, jds);
817 vamsasSet.addSequence(vamsasSeq);
818 seqRefIds.put(id, jds);
822 jseq.setStart(jds.getStart());
823 jseq.setEnd(jds.getEnd());
824 jseq.setColour(av.getSequenceColour(jds).getRGB());
826 jseq.setId(id); // jseq id should be a string not a number
829 // Store any sequences this sequence represents
830 if (av.hasHiddenRows())
832 // use rjal, contains the full height alignment
833 jseq.setHidden(av.getAlignment().getHiddenSequences()
836 if (av.isHiddenRepSequence(jds))
838 jalview.datamodel.SequenceI[] reps = av
839 .getRepresentedSequences(jds)
840 .getSequencesInOrder(rjal);
842 for (int h = 0; h < reps.length; h++)
846 jseq.addHiddenSequences(rjal.findIndex(reps[h]));
851 // mark sequence as reference - if it is the reference for this view
854 jseq.setViewreference(jds == jal.getSeqrep());
858 // TODO: omit sequence features from each alignment view's XML dump if we
859 // are storing dataset
860 if (jds.getSequenceFeatures() != null)
862 jalview.datamodel.SequenceFeature[] sf = jds.getSequenceFeatures();
864 while (index < sf.length)
866 Features features = new Features();
868 features.setBegin(sf[index].getBegin());
869 features.setEnd(sf[index].getEnd());
870 features.setDescription(sf[index].getDescription());
871 features.setType(sf[index].getType());
872 features.setFeatureGroup(sf[index].getFeatureGroup());
873 features.setScore(sf[index].getScore());
874 if (sf[index].links != null)
876 for (int l = 0; l < sf[index].links.size(); l++)
878 OtherData keyValue = new OtherData();
879 keyValue.setKey("LINK_" + l);
880 keyValue.setValue(sf[index].links.elementAt(l).toString());
881 features.addOtherData(keyValue);
884 if (sf[index].otherDetails != null)
887 Iterator<String> keys = sf[index].otherDetails.keySet()
889 while (keys.hasNext())
892 OtherData keyValue = new OtherData();
893 keyValue.setKey(key);
894 keyValue.setValue(sf[index].otherDetails.get(key).toString());
895 features.addOtherData(keyValue);
899 jseq.addFeatures(features);
904 if (jdatasq.getAllPDBEntries() != null)
906 Enumeration en = jdatasq.getAllPDBEntries().elements();
907 while (en.hasMoreElements())
909 Pdbids pdb = new Pdbids();
910 jalview.datamodel.PDBEntry entry = (jalview.datamodel.PDBEntry) en
913 String pdbId = entry.getId();
915 pdb.setType(entry.getType());
918 * Store any structure views associated with this sequence. This
919 * section copes with duplicate entries in the project, so a dataset
920 * only view *should* be coped with sensibly.
922 // This must have been loaded, is it still visible?
923 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
924 String matchedFile = null;
925 for (int f = frames.length - 1; f > -1; f--)
927 if (frames[f] instanceof StructureViewerBase)
929 StructureViewerBase viewFrame = (StructureViewerBase) frames[f];
930 matchedFile = saveStructureState(ap, jds, pdb, entry,
931 viewIds, matchedFile, viewFrame);
933 * Only store each structure viewer's state once in the project
934 * jar. First time through only (storeDS==false)
936 String viewId = viewFrame.getViewId();
937 if (!storeDS && !viewIds.contains(viewId))
942 String viewerState = viewFrame.getStateInfo();
943 writeJarEntry(jout, getViewerJarEntryName(viewId),
944 viewerState.getBytes());
945 } catch (IOException e)
947 System.err.println("Error saving viewer state: "
954 if (matchedFile != null || entry.getFile() != null)
956 if (entry.getFile() != null)
959 matchedFile = entry.getFile();
961 pdb.setFile(matchedFile); // entry.getFile());
962 if (pdbfiles == null)
964 pdbfiles = new ArrayList<String>();
967 if (!pdbfiles.contains(pdbId))
970 copyFileToJar(jout, matchedFile, pdbId);
974 if (entry.getProperty() != null && !entry.getProperty().isEmpty())
976 PdbentryItem item = new PdbentryItem();
977 Hashtable properties = entry.getProperty();
978 Enumeration en2 = properties.keys();
979 while (en2.hasMoreElements())
981 Property prop = new Property();
982 String key = en2.nextElement().toString();
984 prop.setValue(properties.get(key).toString());
985 item.addProperty(prop);
987 pdb.addPdbentryItem(item);
994 saveRnaViewers(jout, jseq, jds, viewIds, ap, storeDS);
999 if (!storeDS && av.hasHiddenRows())
1001 jal = av.getAlignment();
1005 if (storeDS && jal.getCodonFrames() != null)
1007 List<AlignedCodonFrame> jac = jal.getCodonFrames();
1008 for (AlignedCodonFrame acf : jac)
1010 AlcodonFrame alc = new AlcodonFrame();
1011 if (acf.getProtMappings() != null
1012 && acf.getProtMappings().length > 0)
1014 boolean hasMap = false;
1015 SequenceI[] dnas = acf.getdnaSeqs();
1016 jalview.datamodel.Mapping[] pmaps = acf.getProtMappings();
1017 for (int m = 0; m < pmaps.length; m++)
1019 AlcodMap alcmap = new AlcodMap();
1020 alcmap.setDnasq(seqHash(dnas[m]));
1021 alcmap.setMapping(createVamsasMapping(pmaps[m], dnas[m], null,
1023 alc.addAlcodMap(alcmap);
1028 vamsasSet.addAlcodonFrame(alc);
1031 // TODO: delete this ? dead code from 2.8.3->2.9 ?
1033 // AlcodonFrame alc = new AlcodonFrame();
1034 // vamsasSet.addAlcodonFrame(alc);
1035 // for (int p = 0; p < acf.aaWidth; p++)
1037 // Alcodon cmap = new Alcodon();
1038 // if (acf.codons[p] != null)
1040 // // Null codons indicate a gapped column in the translated peptide
1042 // cmap.setPos1(acf.codons[p][0]);
1043 // cmap.setPos2(acf.codons[p][1]);
1044 // cmap.setPos3(acf.codons[p][2]);
1046 // alc.addAlcodon(cmap);
1048 // if (acf.getProtMappings() != null
1049 // && acf.getProtMappings().length > 0)
1051 // SequenceI[] dnas = acf.getdnaSeqs();
1052 // jalview.datamodel.Mapping[] pmaps = acf.getProtMappings();
1053 // for (int m = 0; m < pmaps.length; m++)
1055 // AlcodMap alcmap = new AlcodMap();
1056 // alcmap.setDnasq(seqHash(dnas[m]));
1057 // alcmap.setMapping(createVamsasMapping(pmaps[m], dnas[m], null,
1059 // alc.addAlcodMap(alcmap);
1066 // /////////////////////////////////
1067 if (!storeDS && av.currentTree != null)
1069 // FIND ANY ASSOCIATED TREES
1070 // NOT IMPLEMENTED FOR HEADLESS STATE AT PRESENT
1071 if (Desktop.desktop != null)
1073 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1075 for (int t = 0; t < frames.length; t++)
1077 if (frames[t] instanceof TreePanel)
1079 TreePanel tp = (TreePanel) frames[t];
1081 if (tp.treeCanvas.av.getAlignment() == jal)
1083 Tree tree = new Tree();
1084 tree.setTitle(tp.getTitle());
1085 tree.setCurrentTree((av.currentTree == tp.getTree()));
1086 tree.setNewick(tp.getTree().toString());
1087 tree.setThreshold(tp.treeCanvas.threshold);
1089 tree.setFitToWindow(tp.fitToWindow.getState());
1090 tree.setFontName(tp.getTreeFont().getName());
1091 tree.setFontSize(tp.getTreeFont().getSize());
1092 tree.setFontStyle(tp.getTreeFont().getStyle());
1093 tree.setMarkUnlinked(tp.placeholdersMenu.getState());
1095 tree.setShowBootstrap(tp.bootstrapMenu.getState());
1096 tree.setShowDistances(tp.distanceMenu.getState());
1098 tree.setHeight(tp.getHeight());
1099 tree.setWidth(tp.getWidth());
1100 tree.setXpos(tp.getX());
1101 tree.setYpos(tp.getY());
1102 tree.setId(makeHashCode(tp, null));
1112 * store forward refs from an annotationRow to any groups
1114 IdentityHashMap<SequenceGroup, String> groupRefs = new IdentityHashMap<SequenceGroup, String>();
1117 for (SequenceI sq : jal.getSequences())
1119 // Store annotation on dataset sequences only
1120 AlignmentAnnotation[] aa = sq.getAnnotation();
1121 if (aa != null && aa.length > 0)
1123 storeAlignmentAnnotation(aa, groupRefs, av, calcIdSet, storeDS,
1130 if (jal.getAlignmentAnnotation() != null)
1132 // Store the annotation shown on the alignment.
1133 AlignmentAnnotation[] aa = jal.getAlignmentAnnotation();
1134 storeAlignmentAnnotation(aa, groupRefs, av, calcIdSet, storeDS,
1139 if (jal.getGroups() != null)
1141 JGroup[] groups = new JGroup[jal.getGroups().size()];
1143 for (jalview.datamodel.SequenceGroup sg : jal.getGroups())
1145 JGroup jGroup = new JGroup();
1146 groups[++i] = jGroup;
1148 jGroup.setStart(sg.getStartRes());
1149 jGroup.setEnd(sg.getEndRes());
1150 jGroup.setName(sg.getName());
1151 if (groupRefs.containsKey(sg))
1153 // group has references so set its ID field
1154 jGroup.setId(groupRefs.get(sg));
1158 if (sg.cs.conservationApplied())
1160 jGroup.setConsThreshold(sg.cs.getConservationInc());
1162 if (sg.cs instanceof jalview.schemes.UserColourScheme)
1164 jGroup.setColour(setUserColourScheme(sg.cs, userColours, jms));
1168 jGroup.setColour(ColourSchemeProperty.getColourName(sg.cs));
1171 else if (sg.cs instanceof jalview.schemes.AnnotationColourGradient)
1173 jGroup.setColour("AnnotationColourGradient");
1174 jGroup.setAnnotationColours(constructAnnotationColours(
1175 (jalview.schemes.AnnotationColourGradient) sg.cs,
1178 else if (sg.cs instanceof jalview.schemes.UserColourScheme)
1180 jGroup.setColour(setUserColourScheme(sg.cs, userColours, jms));
1184 jGroup.setColour(ColourSchemeProperty.getColourName(sg.cs));
1187 jGroup.setPidThreshold(sg.cs.getThreshold());
1190 jGroup.setOutlineColour(sg.getOutlineColour().getRGB());
1191 jGroup.setDisplayBoxes(sg.getDisplayBoxes());
1192 jGroup.setDisplayText(sg.getDisplayText());
1193 jGroup.setColourText(sg.getColourText());
1194 jGroup.setTextCol1(sg.textColour.getRGB());
1195 jGroup.setTextCol2(sg.textColour2.getRGB());
1196 jGroup.setTextColThreshold(sg.thresholdTextColour);
1197 jGroup.setShowUnconserved(sg.getShowNonconserved());
1198 jGroup.setIgnoreGapsinConsensus(sg.getIgnoreGapsConsensus());
1199 jGroup.setShowConsensusHistogram(sg.isShowConsensusHistogram());
1200 jGroup.setShowSequenceLogo(sg.isShowSequenceLogo());
1201 jGroup.setNormaliseSequenceLogo(sg.isNormaliseSequenceLogo());
1202 for (SequenceI seq : sg.getSequences())
1204 jGroup.addSeq(seqHash(seq));
1208 jms.setJGroup(groups);
1212 // /////////SAVE VIEWPORT
1213 Viewport view = new Viewport();
1214 view.setTitle(ap.alignFrame.getTitle());
1215 view.setSequenceSetId(makeHashCode(av.getSequenceSetId(),
1216 av.getSequenceSetId()));
1217 view.setId(av.getViewId());
1218 if (av.getCodingComplement() != null)
1220 view.setComplementId(av.getCodingComplement().getViewId());
1222 view.setViewName(av.viewName);
1223 view.setGatheredViews(av.isGatherViewsHere());
1225 Rectangle size = ap.av.getExplodedGeometry();
1226 Rectangle position = size;
1229 size = ap.alignFrame.getBounds();
1230 if (av.getCodingComplement() != null)
1232 position = ((SplitFrame) ap.alignFrame.getSplitViewContainer())
1240 view.setXpos(position.x);
1241 view.setYpos(position.y);
1243 view.setWidth(size.width);
1244 view.setHeight(size.height);
1246 view.setStartRes(av.startRes);
1247 view.setStartSeq(av.startSeq);
1249 if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme)
1251 view.setBgColour(setUserColourScheme(av.getGlobalColourScheme(),
1254 else if (av.getGlobalColourScheme() instanceof jalview.schemes.AnnotationColourGradient)
1256 AnnotationColours ac = constructAnnotationColours(
1257 (jalview.schemes.AnnotationColourGradient) av
1258 .getGlobalColourScheme(),
1261 view.setAnnotationColours(ac);
1262 view.setBgColour("AnnotationColourGradient");
1266 view.setBgColour(ColourSchemeProperty.getColourName(av
1267 .getGlobalColourScheme()));
1270 ColourSchemeI cs = av.getGlobalColourScheme();
1274 if (cs.conservationApplied())
1276 view.setConsThreshold(cs.getConservationInc());
1277 if (cs instanceof jalview.schemes.UserColourScheme)
1279 view.setBgColour(setUserColourScheme(cs, userColours, jms));
1283 if (cs instanceof ResidueColourScheme)
1285 view.setPidThreshold(cs.getThreshold());
1289 view.setConservationSelected(av.getConservationSelected());
1290 view.setPidSelected(av.getAbovePIDThreshold());
1291 view.setFontName(av.font.getName());
1292 view.setFontSize(av.font.getSize());
1293 view.setFontStyle(av.font.getStyle());
1294 view.setScaleProteinAsCdna(av.getViewStyle().isScaleProteinAsCdna());
1295 view.setRenderGaps(av.isRenderGaps());
1296 view.setShowAnnotation(av.isShowAnnotation());
1297 view.setShowBoxes(av.getShowBoxes());
1298 view.setShowColourText(av.getColourText());
1299 view.setShowFullId(av.getShowJVSuffix());
1300 view.setRightAlignIds(av.isRightAlignIds());
1301 view.setShowSequenceFeatures(av.isShowSequenceFeatures());
1302 view.setShowText(av.getShowText());
1303 view.setShowUnconserved(av.getShowUnconserved());
1304 view.setWrapAlignment(av.getWrapAlignment());
1305 view.setTextCol1(av.getTextColour().getRGB());
1306 view.setTextCol2(av.getTextColour2().getRGB());
1307 view.setTextColThreshold(av.getThresholdTextColour());
1308 view.setShowConsensusHistogram(av.isShowConsensusHistogram());
1309 view.setShowSequenceLogo(av.isShowSequenceLogo());
1310 view.setNormaliseSequenceLogo(av.isNormaliseSequenceLogo());
1311 view.setShowGroupConsensus(av.isShowGroupConsensus());
1312 view.setShowGroupConservation(av.isShowGroupConservation());
1313 view.setShowNPfeatureTooltip(av.isShowNPFeats());
1314 view.setShowDbRefTooltip(av.isShowDBRefs());
1315 view.setFollowHighlight(av.isFollowHighlight());
1316 view.setFollowSelection(av.followSelection);
1317 view.setIgnoreGapsinConsensus(av.isIgnoreGapsConsensus());
1318 if (av.getFeaturesDisplayed() != null)
1320 jalview.schemabinding.version2.FeatureSettings fs = new jalview.schemabinding.version2.FeatureSettings();
1322 String[] renderOrder = ap.getSeqPanel().seqCanvas
1323 .getFeatureRenderer().getRenderOrder()
1324 .toArray(new String[0]);
1326 Vector<String> settingsAdded = new Vector<String>();
1327 if (renderOrder != null)
1329 for (String featureType : renderOrder)
1331 FeatureColourI fcol = ap.getSeqPanel().seqCanvas
1332 .getFeatureRenderer()
1333 .getFeatureStyle(featureType);
1334 Setting setting = new Setting();
1335 setting.setType(featureType);
1336 if (!fcol.isSimpleColour())
1338 setting.setColour(fcol.getMaxColour().getRGB());
1339 setting.setMincolour(fcol.getMinColour().getRGB());
1340 setting.setMin(fcol.getMin());
1341 setting.setMax(fcol.getMax());
1342 setting.setColourByLabel(fcol.isColourByLabel());
1343 setting.setAutoScale(fcol.isAutoScaled());
1344 setting.setThreshold(fcol.getThreshold());
1345 // -1 = No threshold, 0 = Below, 1 = Above
1346 setting.setThreshstate(fcol.isAboveThreshold() ? 1
1347 : (fcol.isBelowThreshold() ? 0 : -1));
1351 setting.setColour(fcol.getColour().getRGB());
1354 setting.setDisplay(av.getFeaturesDisplayed().isVisible(
1356 float rorder = ap.getSeqPanel().seqCanvas.getFeatureRenderer()
1357 .getOrder(featureType);
1360 setting.setOrder(rorder);
1362 fs.addSetting(setting);
1363 settingsAdded.addElement(featureType);
1367 // is groups actually supposed to be a map here ?
1368 Iterator<String> en = ap.getSeqPanel().seqCanvas
1369 .getFeatureRenderer()
1370 .getFeatureGroups().iterator();
1371 Vector<String> groupsAdded = new Vector<String>();
1372 while (en.hasNext())
1374 String grp = en.next();
1375 if (groupsAdded.contains(grp))
1379 Group g = new Group();
1381 g.setDisplay(((Boolean) ap.getSeqPanel().seqCanvas
1382 .getFeatureRenderer().checkGroupVisibility(grp, false))
1385 groupsAdded.addElement(grp);
1387 jms.setFeatureSettings(fs);
1390 if (av.hasHiddenColumns())
1392 if (av.getColumnSelection() == null
1393 || av.getColumnSelection().getHiddenColumns() == null)
1395 warn("REPORT BUG: avoided null columnselection bug (DMAM reported). Please contact Jim about this.");
1399 for (int c = 0; c < av.getColumnSelection().getHiddenColumns()
1402 int[] region = av.getColumnSelection().getHiddenColumns()
1404 HiddenColumns hc = new HiddenColumns();
1405 hc.setStart(region[0]);
1406 hc.setEnd(region[1]);
1407 view.addHiddenColumns(hc);
1411 if (calcIdSet.size() > 0)
1413 for (String calcId : calcIdSet)
1415 if (calcId.trim().length() > 0)
1417 CalcIdParam cidp = createCalcIdParam(calcId, av);
1418 // Some calcIds have no parameters.
1421 view.addCalcIdParam(cidp);
1427 jms.addViewport(view);
1429 object.setJalviewModelSequence(jms);
1430 object.getVamsasModel().addSequenceSet(vamsasSet);
1432 if (jout != null && fileName != null)
1434 // We may not want to write the object to disk,
1435 // eg we can copy the alignViewport to a new view object
1436 // using save and then load
1439 System.out.println("Writing jar entry " + fileName);
1440 JarEntry entry = new JarEntry(fileName);
1441 jout.putNextEntry(entry);
1442 PrintWriter pout = new PrintWriter(new OutputStreamWriter(jout,
1444 Marshaller marshaller = new Marshaller(pout);
1445 marshaller.marshal(object);
1448 } catch (Exception ex)
1450 // TODO: raise error in GUI if marshalling failed.
1451 ex.printStackTrace();
1458 * Save any Varna viewers linked to this sequence. Writes an rnaViewer element
1459 * for each viewer, with
1461 * <li>viewer geometry (position, size, split pane divider location)</li>
1462 * <li>index of the selected structure in the viewer (currently shows gapped
1464 * <li>the id of the annotation holding RNA secondary structure</li>
1465 * <li>(currently only one SS is shown per viewer, may be more in future)</li>
1467 * Varna viewer state is also written out (in native Varna XML) to separate
1468 * project jar entries. A separate entry is written for each RNA structure
1469 * displayed, with the naming convention
1471 * <li>rna_viewId_sequenceId_annotationId_[gapped|trimmed]</li>
1479 * @param storeDataset
1481 protected void saveRnaViewers(JarOutputStream jout, JSeq jseq,
1482 final SequenceI jds, List<String> viewIds, AlignmentPanel ap,
1483 boolean storeDataset)
1485 if (Desktop.desktop == null)
1489 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1490 for (int f = frames.length - 1; f > -1; f--)
1492 if (frames[f] instanceof AppVarna)
1494 AppVarna varna = (AppVarna) frames[f];
1496 * link the sequence to every viewer that is showing it and is linked to
1497 * its alignment panel
1499 if (varna.isListeningFor(jds) && ap == varna.getAlignmentPanel())
1501 String viewId = varna.getViewId();
1502 RnaViewer rna = new RnaViewer();
1503 rna.setViewId(viewId);
1504 rna.setTitle(varna.getTitle());
1505 rna.setXpos(varna.getX());
1506 rna.setYpos(varna.getY());
1507 rna.setWidth(varna.getWidth());
1508 rna.setHeight(varna.getHeight());
1509 rna.setDividerLocation(varna.getDividerLocation());
1510 rna.setSelectedRna(varna.getSelectedIndex());
1511 jseq.addRnaViewer(rna);
1514 * Store each Varna panel's state once in the project per sequence.
1515 * First time through only (storeDataset==false)
1517 // boolean storeSessions = false;
1518 // String sequenceViewId = viewId + seqsToIds.get(jds);
1519 // if (!storeDataset && !viewIds.contains(sequenceViewId))
1521 // viewIds.add(sequenceViewId);
1522 // storeSessions = true;
1524 for (RnaModel model : varna.getModels())
1526 if (model.seq == jds)
1529 * VARNA saves each view (sequence or alignment secondary
1530 * structure, gapped or trimmed) as a separate XML file
1532 String jarEntryName = rnaSessions.get(model);
1533 if (jarEntryName == null)
1536 String varnaStateFile = varna.getStateInfo(model.rna);
1537 jarEntryName = RNA_PREFIX + viewId + "_" + nextCounter();
1538 copyFileToJar(jout, varnaStateFile, jarEntryName);
1539 rnaSessions.put(model, jarEntryName);
1541 SecondaryStructure ss = new SecondaryStructure();
1542 String annotationId = varna.getAnnotation(jds).annotationId;
1543 ss.setAnnotationId(annotationId);
1544 ss.setViewerState(jarEntryName);
1545 ss.setGapped(model.gapped);
1546 ss.setTitle(model.title);
1547 rna.addSecondaryStructure(ss);
1556 * Copy the contents of a file to a new entry added to the output jar
1560 * @param jarEntryName
1562 protected void copyFileToJar(JarOutputStream jout, String infilePath,
1563 String jarEntryName)
1565 DataInputStream dis = null;
1568 File file = new File(infilePath);
1569 if (file.exists() && jout != null)
1571 dis = new DataInputStream(new FileInputStream(file));
1572 byte[] data = new byte[(int) file.length()];
1573 dis.readFully(data);
1574 writeJarEntry(jout, jarEntryName, data);
1576 } catch (Exception ex)
1578 ex.printStackTrace();
1586 } catch (IOException e)
1595 * Write the data to a new entry of given name in the output jar file
1598 * @param jarEntryName
1600 * @throws IOException
1602 protected void writeJarEntry(JarOutputStream jout, String jarEntryName,
1603 byte[] data) throws IOException
1607 System.out.println("Writing jar entry " + jarEntryName);
1608 jout.putNextEntry(new JarEntry(jarEntryName));
1609 DataOutputStream dout = new DataOutputStream(jout);
1610 dout.write(data, 0, data.length);
1617 * Save the state of a structure viewer
1622 * the archive XML element under which to save the state
1625 * @param matchedFile
1629 protected String saveStructureState(AlignmentPanel ap, SequenceI jds,
1630 Pdbids pdb, PDBEntry entry, List<String> viewIds,
1631 String matchedFile, StructureViewerBase viewFrame)
1633 final AAStructureBindingModel bindingModel = viewFrame.getBinding();
1636 * Look for any bindings for this viewer to the PDB file of interest
1637 * (including part matches excluding chain id)
1639 for (int peid = 0; peid < bindingModel.getPdbCount(); peid++)
1641 final PDBEntry pdbentry = bindingModel.getPdbEntry(peid);
1642 final String pdbId = pdbentry.getId();
1643 if (!pdbId.equals(entry.getId())
1644 && !(entry.getId().length() > 4 && entry.getId()
1645 .toLowerCase().startsWith(pdbId.toLowerCase())))
1648 * not interested in a binding to a different PDB entry here
1652 if (matchedFile == null)
1654 matchedFile = pdbentry.getFile();
1656 else if (!matchedFile.equals(pdbentry.getFile()))
1659 .warn("Probably lost some PDB-Sequence mappings for this structure file (which apparently has same PDB Entry code): "
1660 + pdbentry.getFile());
1664 // can get at it if the ID
1665 // match is ambiguous (e.g.
1668 for (int smap = 0; smap < viewFrame.getBinding().getSequence()[peid].length; smap++)
1670 // if (jal.findIndex(jmol.jmb.sequence[peid][smap]) > -1)
1671 if (jds == viewFrame.getBinding().getSequence()[peid][smap])
1673 StructureState state = new StructureState();
1674 state.setVisible(true);
1675 state.setXpos(viewFrame.getX());
1676 state.setYpos(viewFrame.getY());
1677 state.setWidth(viewFrame.getWidth());
1678 state.setHeight(viewFrame.getHeight());
1679 final String viewId = viewFrame.getViewId();
1680 state.setViewId(viewId);
1681 state.setAlignwithAlignPanel(viewFrame.isUsedforaligment(ap));
1682 state.setColourwithAlignPanel(viewFrame.isUsedforcolourby(ap));
1683 state.setColourByJmol(viewFrame.isColouredByViewer());
1684 state.setType(viewFrame.getViewerType().toString());
1685 pdb.addStructureState(state);
1692 private AnnotationColours constructAnnotationColours(
1693 AnnotationColourGradient acg, List<UserColourScheme> userColours,
1694 JalviewModelSequence jms)
1696 AnnotationColours ac = new AnnotationColours();
1697 ac.setAboveThreshold(acg.getAboveThreshold());
1698 ac.setThreshold(acg.getAnnotationThreshold());
1699 ac.setAnnotation(acg.getAnnotation());
1700 if (acg.getBaseColour() instanceof jalview.schemes.UserColourScheme)
1702 ac.setColourScheme(setUserColourScheme(acg.getBaseColour(),
1707 ac.setColourScheme(ColourSchemeProperty.getColourName(acg
1711 ac.setMaxColour(acg.getMaxColour().getRGB());
1712 ac.setMinColour(acg.getMinColour().getRGB());
1713 ac.setPerSequence(acg.isSeqAssociated());
1714 ac.setPredefinedColours(acg.isPredefinedColours());
1718 private void storeAlignmentAnnotation(AlignmentAnnotation[] aa,
1719 IdentityHashMap<SequenceGroup, String> groupRefs,
1720 AlignmentViewport av, Set<String> calcIdSet, boolean storeDS,
1721 SequenceSet vamsasSet)
1724 for (int i = 0; i < aa.length; i++)
1726 Annotation an = new Annotation();
1728 AlignmentAnnotation annotation = aa[i];
1729 if (annotation.annotationId != null)
1731 annotationIds.put(annotation.annotationId, annotation);
1734 an.setId(annotation.annotationId);
1736 an.setVisible(annotation.visible);
1738 an.setDescription(annotation.description);
1740 if (annotation.sequenceRef != null)
1742 // 2.9 JAL-1781 xref on sequence id rather than name
1743 an.setSequenceRef(seqsToIds.get(annotation.sequenceRef));
1745 if (annotation.groupRef != null)
1747 String groupIdr = groupRefs.get(annotation.groupRef);
1748 if (groupIdr == null)
1750 // make a locally unique String
1752 annotation.groupRef,
1753 groupIdr = ("" + System.currentTimeMillis()
1754 + annotation.groupRef.getName() + groupRefs
1757 an.setGroupRef(groupIdr.toString());
1760 // store all visualization attributes for annotation
1761 an.setGraphHeight(annotation.graphHeight);
1762 an.setCentreColLabels(annotation.centreColLabels);
1763 an.setScaleColLabels(annotation.scaleColLabel);
1764 an.setShowAllColLabels(annotation.showAllColLabels);
1765 an.setBelowAlignment(annotation.belowAlignment);
1767 if (annotation.graph > 0)
1770 an.setGraphType(annotation.graph);
1771 an.setGraphGroup(annotation.graphGroup);
1772 if (annotation.getThreshold() != null)
1774 ThresholdLine line = new ThresholdLine();
1775 line.setLabel(annotation.getThreshold().label);
1776 line.setValue(annotation.getThreshold().value);
1777 line.setColour(annotation.getThreshold().colour.getRGB());
1778 an.setThresholdLine(line);
1786 an.setLabel(annotation.label);
1788 if (annotation == av.getAlignmentQualityAnnot()
1789 || annotation == av.getAlignmentConservationAnnotation()
1790 || annotation == av.getAlignmentConsensusAnnotation()
1791 || annotation.autoCalculated)
1793 // new way of indicating autocalculated annotation -
1794 an.setAutoCalculated(annotation.autoCalculated);
1796 if (annotation.hasScore())
1798 an.setScore(annotation.getScore());
1801 if (annotation.getCalcId() != null)
1803 calcIdSet.add(annotation.getCalcId());
1804 an.setCalcId(annotation.getCalcId());
1806 if (annotation.hasProperties())
1808 for (String pr : annotation.getProperties())
1810 Property prop = new Property();
1812 prop.setValue(annotation.getProperty(pr));
1813 an.addProperty(prop);
1817 AnnotationElement ae;
1818 if (annotation.annotations != null)
1820 an.setScoreOnly(false);
1821 for (int a = 0; a < annotation.annotations.length; a++)
1823 if ((annotation == null) || (annotation.annotations[a] == null))
1828 ae = new AnnotationElement();
1829 if (annotation.annotations[a].description != null)
1831 ae.setDescription(annotation.annotations[a].description);
1833 if (annotation.annotations[a].displayCharacter != null)
1835 ae.setDisplayCharacter(annotation.annotations[a].displayCharacter);
1838 if (!Float.isNaN(annotation.annotations[a].value))
1840 ae.setValue(annotation.annotations[a].value);
1844 if (annotation.annotations[a].secondaryStructure > ' ')
1846 ae.setSecondaryStructure(annotation.annotations[a].secondaryStructure
1850 if (annotation.annotations[a].colour != null
1851 && annotation.annotations[a].colour != java.awt.Color.black)
1853 ae.setColour(annotation.annotations[a].colour.getRGB());
1856 an.addAnnotationElement(ae);
1857 if (annotation.autoCalculated)
1859 // only write one non-null entry into the annotation row -
1860 // sufficient to get the visualization attributes necessary to
1868 an.setScoreOnly(true);
1870 if (!storeDS || (storeDS && !annotation.autoCalculated))
1872 // skip autocalculated annotation - these are only provided for
1874 vamsasSet.addAnnotation(an);
1880 private CalcIdParam createCalcIdParam(String calcId, AlignViewport av)
1882 AutoCalcSetting settings = av.getCalcIdSettingsFor(calcId);
1883 if (settings != null)
1885 CalcIdParam vCalcIdParam = new CalcIdParam();
1886 vCalcIdParam.setCalcId(calcId);
1887 vCalcIdParam.addServiceURL(settings.getServiceURI());
1888 // generic URI allowing a third party to resolve another instance of the
1889 // service used for this calculation
1890 for (String urls : settings.getServiceURLs())
1892 vCalcIdParam.addServiceURL(urls);
1894 vCalcIdParam.setVersion("1.0");
1895 if (settings.getPreset() != null)
1897 WsParamSetI setting = settings.getPreset();
1898 vCalcIdParam.setName(setting.getName());
1899 vCalcIdParam.setDescription(setting.getDescription());
1903 vCalcIdParam.setName("");
1904 vCalcIdParam.setDescription("Last used parameters");
1906 // need to be able to recover 1) settings 2) user-defined presets or
1907 // recreate settings from preset 3) predefined settings provided by
1908 // service - or settings that can be transferred (or discarded)
1909 vCalcIdParam.setParameters(settings.getWsParamFile().replace("\n",
1911 vCalcIdParam.setAutoUpdate(settings.isAutoUpdate());
1912 // todo - decide if updateImmediately is needed for any projects.
1914 return vCalcIdParam;
1919 private boolean recoverCalcIdParam(CalcIdParam calcIdParam,
1922 if (calcIdParam.getVersion().equals("1.0"))
1924 Jws2Instance service = Jws2Discoverer.getDiscoverer()
1925 .getPreferredServiceFor(calcIdParam.getServiceURL());
1926 if (service != null)
1928 WsParamSetI parmSet = null;
1931 parmSet = service.getParamStore().parseServiceParameterFile(
1932 calcIdParam.getName(), calcIdParam.getDescription(),
1933 calcIdParam.getServiceURL(),
1934 calcIdParam.getParameters().replace("|\\n|", "\n"));
1935 } catch (IOException x)
1937 warn("Couldn't parse parameter data for "
1938 + calcIdParam.getCalcId(), x);
1941 List<ArgumentI> argList = null;
1942 if (calcIdParam.getName().length() > 0)
1944 parmSet = service.getParamStore()
1945 .getPreset(calcIdParam.getName());
1946 if (parmSet != null)
1948 // TODO : check we have a good match with settings in AACon -
1949 // otherwise we'll need to create a new preset
1954 argList = parmSet.getArguments();
1957 AAConSettings settings = new AAConSettings(
1958 calcIdParam.isAutoUpdate(), service, parmSet, argList);
1959 av.setCalcIdSettingsFor(calcIdParam.getCalcId(), settings,
1960 calcIdParam.isNeedsUpdate());
1965 warn("Cannot resolve a service for the parameters used in this project. Try configuring a JABAWS server.");
1969 throw new Error(MessageManager.formatMessage(
1970 "error.unsupported_version_calcIdparam",
1971 new Object[] { calcIdParam.toString() }));
1975 * External mapping between jalview objects and objects yielding a valid and
1976 * unique object ID string. This is null for normal Jalview project IO, but
1977 * non-null when a jalview project is being read or written as part of a
1980 IdentityHashMap jv2vobj = null;
1983 * Construct a unique ID for jvobj using either existing bindings or if none
1984 * exist, the result of the hashcode call for the object.
1987 * jalview data object
1988 * @return unique ID for referring to jvobj
1990 private String makeHashCode(Object jvobj, String altCode)
1992 if (jv2vobj != null)
1994 Object id = jv2vobj.get(jvobj);
1997 return id.toString();
1999 // check string ID mappings
2000 if (jvids2vobj != null && jvobj instanceof String)
2002 id = jvids2vobj.get(jvobj);
2006 return id.toString();
2008 // give up and warn that something has gone wrong
2009 warn("Cannot find ID for object in external mapping : " + jvobj);
2015 * return local jalview object mapped to ID, if it exists
2019 * @return null or object bound to idcode
2021 private Object retrieveExistingObj(String idcode)
2023 if (idcode != null && vobj2jv != null)
2025 return vobj2jv.get(idcode);
2031 * binding from ID strings from external mapping table to jalview data model
2034 private Hashtable vobj2jv;
2036 private Sequence createVamsasSequence(String id, SequenceI jds)
2038 return createVamsasSequence(true, id, jds, null);
2041 private Sequence createVamsasSequence(boolean recurse, String id,
2042 SequenceI jds, SequenceI parentseq)
2044 Sequence vamsasSeq = new Sequence();
2045 vamsasSeq.setId(id);
2046 vamsasSeq.setName(jds.getName());
2047 vamsasSeq.setSequence(jds.getSequenceAsString());
2048 vamsasSeq.setDescription(jds.getDescription());
2049 jalview.datamodel.DBRefEntry[] dbrefs = null;
2050 if (jds.getDatasetSequence() != null)
2052 vamsasSeq.setDsseqid(seqHash(jds.getDatasetSequence()));
2056 // seqId==dsseqid so we can tell which sequences really are
2057 // dataset sequences only
2058 vamsasSeq.setDsseqid(id);
2059 dbrefs = jds.getDBRefs();
2060 if (parentseq == null)
2067 for (int d = 0; d < dbrefs.length; d++)
2069 DBRef dbref = new DBRef();
2070 dbref.setSource(dbrefs[d].getSource());
2071 dbref.setVersion(dbrefs[d].getVersion());
2072 dbref.setAccessionId(dbrefs[d].getAccessionId());
2073 if (dbrefs[d].hasMap())
2075 Mapping mp = createVamsasMapping(dbrefs[d].getMap(), parentseq,
2077 dbref.setMapping(mp);
2079 vamsasSeq.addDBRef(dbref);
2085 private Mapping createVamsasMapping(jalview.datamodel.Mapping jmp,
2086 SequenceI parentseq, SequenceI jds, boolean recurse)
2089 if (jmp.getMap() != null)
2093 jalview.util.MapList mlst = jmp.getMap();
2094 List<int[]> r = mlst.getFromRanges();
2095 for (int[] range : r)
2097 MapListFrom mfrom = new MapListFrom();
2098 mfrom.setStart(range[0]);
2099 mfrom.setEnd(range[1]);
2100 mp.addMapListFrom(mfrom);
2102 r = mlst.getToRanges();
2103 for (int[] range : r)
2105 MapListTo mto = new MapListTo();
2106 mto.setStart(range[0]);
2107 mto.setEnd(range[1]);
2108 mp.addMapListTo(mto);
2110 mp.setMapFromUnit(mlst.getFromRatio());
2111 mp.setMapToUnit(mlst.getToRatio());
2112 if (jmp.getTo() != null)
2114 MappingChoice mpc = new MappingChoice();
2116 // check/create ID for the sequence referenced by getTo()
2119 SequenceI ps = null;
2120 if (parentseq != jmp.getTo()
2121 && parentseq.getDatasetSequence() != jmp.getTo())
2123 // chaining dbref rather than a handshaking one
2124 jmpid = seqHash(ps = jmp.getTo());
2128 jmpid = seqHash(ps = parentseq);
2130 mpc.setDseqFor(jmpid);
2131 if (!seqRefIds.containsKey(mpc.getDseqFor()))
2133 jalview.bin.Cache.log.debug("creatign new DseqFor ID");
2134 seqRefIds.put(mpc.getDseqFor(), ps);
2138 jalview.bin.Cache.log.debug("reusing DseqFor ID");
2141 mp.setMappingChoice(mpc);
2147 String setUserColourScheme(jalview.schemes.ColourSchemeI cs,
2148 List<UserColourScheme> userColours, JalviewModelSequence jms)
2151 jalview.schemes.UserColourScheme ucs = (jalview.schemes.UserColourScheme) cs;
2152 boolean newucs = false;
2153 if (!userColours.contains(ucs))
2155 userColours.add(ucs);
2158 id = "ucs" + userColours.indexOf(ucs);
2161 // actually create the scheme's entry in the XML model
2162 java.awt.Color[] colours = ucs.getColours();
2163 jalview.schemabinding.version2.UserColours uc = new jalview.schemabinding.version2.UserColours();
2164 jalview.schemabinding.version2.UserColourScheme jbucs = new jalview.schemabinding.version2.UserColourScheme();
2166 for (int i = 0; i < colours.length; i++)
2168 jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();
2169 col.setName(ResidueProperties.aa[i]);
2170 col.setRGB(jalview.util.Format.getHexString(colours[i]));
2171 jbucs.addColour(col);
2173 if (ucs.getLowerCaseColours() != null)
2175 colours = ucs.getLowerCaseColours();
2176 for (int i = 0; i < colours.length; i++)
2178 jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();
2179 col.setName(ResidueProperties.aa[i].toLowerCase());
2180 col.setRGB(jalview.util.Format.getHexString(colours[i]));
2181 jbucs.addColour(col);
2186 uc.setUserColourScheme(jbucs);
2187 jms.addUserColours(uc);
2193 jalview.schemes.UserColourScheme getUserColourScheme(
2194 JalviewModelSequence jms, String id)
2196 UserColours[] uc = jms.getUserColours();
2197 UserColours colours = null;
2199 for (int i = 0; i < uc.length; i++)
2201 if (uc[i].getId().equals(id))
2209 java.awt.Color[] newColours = new java.awt.Color[24];
2211 for (int i = 0; i < 24; i++)
2213 newColours[i] = new java.awt.Color(Integer.parseInt(colours
2214 .getUserColourScheme().getColour(i).getRGB(), 16));
2217 jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(
2220 if (colours.getUserColourScheme().getColourCount() > 24)
2222 newColours = new java.awt.Color[23];
2223 for (int i = 0; i < 23; i++)
2225 newColours[i] = new java.awt.Color(Integer.parseInt(colours
2226 .getUserColourScheme().getColour(i + 24).getRGB(), 16));
2228 ucs.setLowerCaseColours(newColours);
2235 * contains last error message (if any) encountered by XML loader.
2237 String errorMessage = null;
2240 * flag to control whether the Jalview2XML_V1 parser should be deferred to if
2241 * exceptions are raised during project XML parsing
2243 public boolean attemptversion1parse = true;
2246 * Load a jalview project archive from a jar file
2249 * - HTTP URL or filename
2251 public AlignFrame loadJalviewAlign(final String file)
2254 jalview.gui.AlignFrame af = null;
2258 // create list to store references for any new Jmol viewers created
2259 newStructureViewers = new Vector<JalviewStructureDisplayI>();
2260 // UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
2261 // Workaround is to make sure caller implements the JarInputStreamProvider
2263 // so we can re-open the jar input stream for each entry.
2265 jarInputStreamProvider jprovider = createjarInputStreamProvider(file);
2266 af = loadJalviewAlign(jprovider);
2268 } catch (MalformedURLException e)
2270 errorMessage = "Invalid URL format for '" + file + "'";
2276 SwingUtilities.invokeAndWait(new Runnable()
2281 setLoadingFinishedForNewStructureViewers();
2284 } catch (Exception x)
2286 System.err.println("Error loading alignment: " + x.getMessage());
2292 private jarInputStreamProvider createjarInputStreamProvider(
2293 final String file) throws MalformedURLException
2296 errorMessage = null;
2297 uniqueSetSuffix = null;
2299 viewportsAdded.clear();
2300 frefedSequence = null;
2302 if (file.startsWith("http://"))
2304 url = new URL(file);
2306 final URL _url = url;
2307 return new jarInputStreamProvider()
2311 public JarInputStream getJarInputStream() throws IOException
2315 return new JarInputStream(_url.openStream());
2319 return new JarInputStream(new FileInputStream(file));
2324 public String getFilename()
2332 * Recover jalview session from a jalview project archive. Caller may
2333 * initialise uniqueSetSuffix, seqRefIds, viewportsAdded and frefedSequence
2334 * themselves. Any null fields will be initialised with default values,
2335 * non-null fields are left alone.
2340 public AlignFrame loadJalviewAlign(final jarInputStreamProvider jprovider)
2342 errorMessage = null;
2343 if (uniqueSetSuffix == null)
2345 uniqueSetSuffix = System.currentTimeMillis() % 100000 + "";
2347 if (seqRefIds == null)
2351 AlignFrame af = null, _af = null;
2352 IdentityHashMap<AlignmentI, AlignmentI> importedDatasets = new IdentityHashMap<AlignmentI, AlignmentI>();
2353 Map<String, AlignFrame> gatherToThisFrame = new HashMap<String, AlignFrame>();
2354 final String file = jprovider.getFilename();
2357 JarInputStream jin = null;
2358 JarEntry jarentry = null;
2363 jin = jprovider.getJarInputStream();
2364 for (int i = 0; i < entryCount; i++)
2366 jarentry = jin.getNextJarEntry();
2369 if (jarentry != null && jarentry.getName().endsWith(".xml"))
2371 InputStreamReader in = new InputStreamReader(jin, UTF_8);
2372 JalviewModel object = new JalviewModel();
2374 Unmarshaller unmar = new Unmarshaller(object);
2375 unmar.setValidation(false);
2376 object = (JalviewModel) unmar.unmarshal(in);
2377 if (true) // !skipViewport(object))
2379 _af = loadFromObject(object, file, true, jprovider);
2380 if (object.getJalviewModelSequence().getViewportCount() > 0)
2383 if (af.viewport.isGatherViewsHere())
2385 gatherToThisFrame.put(af.viewport.getSequenceSetId(), af);
2387 // Save dataset to register mappings once all resolved
2388 importedDatasets.put(af.viewport.getAlignment().getDataset(),
2389 af.viewport.getAlignment().getDataset());
2394 else if (jarentry != null)
2396 // Some other file here.
2399 } while (jarentry != null);
2400 resolveFrefedSequences();
2401 } catch (IOException ex)
2403 ex.printStackTrace();
2404 errorMessage = "Couldn't locate Jalview XML file : " + file;
2405 System.err.println("Exception whilst loading jalview XML file : "
2407 } catch (Exception ex)
2409 System.err.println("Parsing as Jalview Version 2 file failed.");
2410 ex.printStackTrace(System.err);
2411 if (attemptversion1parse)
2413 // Is Version 1 Jar file?
2416 af = new Jalview2XML_V1(raiseGUI).LoadJalviewAlign(jprovider);
2417 } catch (Exception ex2)
2419 System.err.println("Exception whilst loading as jalviewXMLV1:");
2420 ex2.printStackTrace();
2424 if (Desktop.instance != null)
2426 Desktop.instance.stopLoading();
2430 System.out.println("Successfully loaded archive file");
2433 ex.printStackTrace();
2435 System.err.println("Exception whilst loading jalview XML file : "
2437 } catch (OutOfMemoryError e)
2439 // Don't use the OOM Window here
2440 errorMessage = "Out of memory loading jalview XML file";
2441 System.err.println("Out of memory whilst loading jalview XML file");
2442 e.printStackTrace();
2445 if (Desktop.instance != null)
2447 Desktop.instance.stopLoading();
2451 * Regather multiple views (with the same sequence set id) to the frame (if
2452 * any) that is flagged as the one to gather to, i.e. convert them to tabbed
2453 * views instead of separate frames. Note this doesn't restore a state where
2454 * some expanded views in turn have tabbed views - the last "first tab" read
2455 * in will play the role of gatherer for all.
2457 for (AlignFrame fr : gatherToThisFrame.values())
2459 Desktop.instance.gatherViews(fr);
2462 restoreSplitFrames();
2463 for (AlignmentI ds : importedDatasets.keySet())
2465 if (ds.getCodonFrames() != null)
2467 StructureSelectionManager.getStructureSelectionManager(
2468 Desktop.instance).registerMappings(ds.getCodonFrames());
2471 if (errorMessage != null)
2479 * Try to reconstruct and display SplitFrame windows, where each contains
2480 * complementary dna and protein alignments. Done by pairing up AlignFrame
2481 * objects (created earlier) which have complementary viewport ids associated.
2483 protected void restoreSplitFrames()
2485 List<SplitFrame> gatherTo = new ArrayList<SplitFrame>();
2486 List<AlignFrame> addedToSplitFrames = new ArrayList<AlignFrame>();
2487 Map<String, AlignFrame> dna = new HashMap<String, AlignFrame>();
2490 * Identify the DNA alignments
2492 for (Entry<Viewport, AlignFrame> candidate : splitFrameCandidates
2495 AlignFrame af = candidate.getValue();
2496 if (af.getViewport().getAlignment().isNucleotide())
2498 dna.put(candidate.getKey().getId(), af);
2503 * Try to match up the protein complements
2505 for (Entry<Viewport, AlignFrame> candidate : splitFrameCandidates
2508 AlignFrame af = candidate.getValue();
2509 if (!af.getViewport().getAlignment().isNucleotide())
2511 String complementId = candidate.getKey().getComplementId();
2512 // only non-null complements should be in the Map
2513 if (complementId != null && dna.containsKey(complementId))
2515 final AlignFrame dnaFrame = dna.get(complementId);
2516 SplitFrame sf = createSplitFrame(dnaFrame, af);
2517 addedToSplitFrames.add(dnaFrame);
2518 addedToSplitFrames.add(af);
2519 if (af.viewport.isGatherViewsHere())
2528 * Open any that we failed to pair up (which shouldn't happen!) as
2529 * standalone AlignFrame's.
2531 for (Entry<Viewport, AlignFrame> candidate : splitFrameCandidates
2534 AlignFrame af = candidate.getValue();
2535 if (!addedToSplitFrames.contains(af))
2537 Viewport view = candidate.getKey();
2538 Desktop.addInternalFrame(af, view.getTitle(), view.getWidth(),
2540 System.err.println("Failed to restore view " + view.getTitle()
2541 + " to split frame");
2546 * Gather back into tabbed views as flagged.
2548 for (SplitFrame sf : gatherTo)
2550 Desktop.instance.gatherViews(sf);
2553 splitFrameCandidates.clear();
2557 * Construct and display one SplitFrame holding DNA and protein alignments.
2560 * @param proteinFrame
2563 protected SplitFrame createSplitFrame(AlignFrame dnaFrame,
2564 AlignFrame proteinFrame)
2566 SplitFrame splitFrame = new SplitFrame(dnaFrame, proteinFrame);
2567 String title = MessageManager.getString("label.linked_view_title");
2568 int width = (int) dnaFrame.getBounds().getWidth();
2569 int height = (int) (dnaFrame.getBounds().getHeight()
2570 + proteinFrame.getBounds().getHeight() + 50);
2573 * SplitFrame location is saved to both enclosed frames
2575 splitFrame.setLocation(dnaFrame.getX(), dnaFrame.getY());
2576 Desktop.addInternalFrame(splitFrame, title, width, height);
2579 * And compute cDNA consensus (couldn't do earlier with consensus as
2580 * mappings were not yet present)
2582 proteinFrame.viewport.alignmentChanged(proteinFrame.alignPanel);
2588 * check errorMessage for a valid error message and raise an error box in the
2589 * GUI or write the current errorMessage to stderr and then clear the error
2592 protected void reportErrors()
2594 reportErrors(false);
2597 protected void reportErrors(final boolean saving)
2599 if (errorMessage != null)
2601 final String finalErrorMessage = errorMessage;
2604 javax.swing.SwingUtilities.invokeLater(new Runnable()
2609 JOptionPane.showInternalMessageDialog(Desktop.desktop,
2610 finalErrorMessage, "Error "
2611 + (saving ? "saving" : "loading")
2612 + " Jalview file", JOptionPane.WARNING_MESSAGE);
2618 System.err.println("Problem loading Jalview file: " + errorMessage);
2621 errorMessage = null;
2624 Map<String, String> alreadyLoadedPDB = new HashMap<String, String>();
2627 * when set, local views will be updated from view stored in JalviewXML
2628 * Currently (28th Sep 2008) things will go horribly wrong in vamsas document
2629 * sync if this is set to true.
2631 private final boolean updateLocalViews = false;
2634 * Returns the path to a temporary file holding the PDB file for the given PDB
2635 * id. The first time of asking, searches for a file of that name in the
2636 * Jalview project jar, and copies it to a new temporary file. Any repeat
2637 * requests just return the path to the file previously created.
2643 String loadPDBFile(jarInputStreamProvider jprovider, String pdbId)
2645 if (alreadyLoadedPDB.containsKey(pdbId))
2647 return alreadyLoadedPDB.get(pdbId).toString();
2650 String tempFile = copyJarEntry(jprovider, pdbId, "jalview_pdb");
2651 if (tempFile != null)
2653 alreadyLoadedPDB.put(pdbId, tempFile);
2659 * Copies the jar entry of given name to a new temporary file and returns the
2660 * path to the file, or null if the entry is not found.
2663 * @param jarEntryName
2665 * a prefix for the temporary file name, must be at least three
2669 protected String copyJarEntry(jarInputStreamProvider jprovider,
2670 String jarEntryName, String prefix)
2672 BufferedReader in = null;
2673 PrintWriter out = null;
2677 JarInputStream jin = jprovider.getJarInputStream();
2679 * if (jprovider.startsWith("http://")) { jin = new JarInputStream(new
2680 * URL(jprovider).openStream()); } else { jin = new JarInputStream(new
2681 * FileInputStream(jprovider)); }
2684 JarEntry entry = null;
2687 entry = jin.getNextJarEntry();
2688 } while (entry != null && !entry.getName().equals(jarEntryName));
2691 in = new BufferedReader(new InputStreamReader(jin, UTF_8));
2692 File outFile = File.createTempFile(prefix, ".tmp");
2693 outFile.deleteOnExit();
2694 out = new PrintWriter(new FileOutputStream(outFile));
2697 while ((data = in.readLine()) != null)
2702 String t = outFile.getAbsolutePath();
2707 warn("Couldn't find entry in Jalview Jar for " + jarEntryName);
2709 } catch (Exception ex)
2711 ex.printStackTrace();
2719 } catch (IOException e)
2733 private class JvAnnotRow
2735 public JvAnnotRow(int i, AlignmentAnnotation jaa)
2742 * persisted version of annotation row from which to take vis properties
2744 public jalview.datamodel.AlignmentAnnotation template;
2747 * original position of the annotation row in the alignment
2753 * Load alignment frame from jalview XML DOM object
2758 * filename source string
2759 * @param loadTreesAndStructures
2760 * when false only create Viewport
2762 * data source provider
2763 * @return alignment frame created from view stored in DOM
2765 AlignFrame loadFromObject(JalviewModel object, String file,
2766 boolean loadTreesAndStructures, jarInputStreamProvider jprovider)
2768 SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);
2769 Sequence[] vamsasSeq = vamsasSet.getSequence();
2771 JalviewModelSequence jms = object.getJalviewModelSequence();
2773 Viewport view = (jms.getViewportCount() > 0) ? jms.getViewport(0)
2776 // ////////////////////////////////
2779 List<SequenceI> hiddenSeqs = null;
2782 List<SequenceI> tmpseqs = new ArrayList<SequenceI>();
2784 boolean multipleView = false;
2785 SequenceI referenceseqForView = null;
2786 JSeq[] jseqs = object.getJalviewModelSequence().getJSeq();
2787 int vi = 0; // counter in vamsasSeq array
2788 for (int i = 0; i < jseqs.length; i++)
2790 String seqId = jseqs[i].getId();
2792 SequenceI tmpSeq = seqRefIds.get(seqId);
2795 if (!incompleteSeqs.containsKey(seqId))
2797 // may not need this check, but keep it for at least 2.9,1 release
2798 if (tmpSeq.getStart()!=jseqs[i].getStart() || tmpSeq.getEnd()!=jseqs[i].getEnd())
2801 .println("Warning JAL-2154 regression: updating start/end for sequence "
2802 + tmpSeq.toString());
2805 incompleteSeqs.remove(seqId);
2807 tmpSeq.setStart(jseqs[i].getStart());
2808 tmpSeq.setEnd(jseqs[i].getEnd());
2809 tmpseqs.add(tmpSeq);
2810 multipleView = true;
2814 tmpSeq = new jalview.datamodel.Sequence(vamsasSeq[vi].getName(),
2815 vamsasSeq[vi].getSequence());
2816 tmpSeq.setDescription(vamsasSeq[vi].getDescription());
2817 tmpSeq.setStart(jseqs[i].getStart());
2818 tmpSeq.setEnd(jseqs[i].getEnd());
2819 tmpSeq.setVamsasId(uniqueSetSuffix + seqId);
2820 seqRefIds.put(vamsasSeq[vi].getId(), tmpSeq);
2821 tmpseqs.add(tmpSeq);
2825 if (jseqs[i].hasViewreference() && jseqs[i].getViewreference())
2827 referenceseqForView = tmpseqs.get(tmpseqs.size() - 1);
2830 if (jseqs[i].getHidden())
2832 if (hiddenSeqs == null)
2834 hiddenSeqs = new ArrayList<SequenceI>();
2837 hiddenSeqs.add(tmpSeq);
2842 // Create the alignment object from the sequence set
2843 // ///////////////////////////////
2844 SequenceI[] orderedSeqs = tmpseqs
2845 .toArray(new SequenceI[tmpseqs.size()]);
2847 AlignmentI al = null;
2848 // so we must create or recover the dataset alignment before going further
2849 // ///////////////////////////////
2850 if (vamsasSet.getDatasetId() == null || vamsasSet.getDatasetId() == "")
2852 // older jalview projects do not have a dataset - so creat alignment and
2854 al = new Alignment(orderedSeqs);
2855 al.setDataset(null);
2859 boolean isdsal = object.getJalviewModelSequence().getViewportCount() == 0;
2862 // we are importing a dataset record, so
2863 // recover reference to an alignment already materialsed as dataset
2864 al = getDatasetFor(vamsasSet.getDatasetId());
2868 // materialse the alignment
2869 al = new Alignment(orderedSeqs);
2873 addDatasetRef(vamsasSet.getDatasetId(), al);
2876 // finally, verify all data in vamsasSet is actually present in al
2877 // passing on flag indicating if it is actually a stored dataset
2878 recoverDatasetFor(vamsasSet, al, isdsal);
2881 if (referenceseqForView != null)
2883 al.setSeqrep(referenceseqForView);
2885 // / Add the alignment properties
2886 for (int i = 0; i < vamsasSet.getSequenceSetPropertiesCount(); i++)
2888 SequenceSetProperties ssp = vamsasSet.getSequenceSetProperties(i);
2889 al.setProperty(ssp.getKey(), ssp.getValue());
2892 // ///////////////////////////////
2894 Hashtable pdbloaded = new Hashtable(); // TODO nothing writes to this??
2897 // load sequence features, database references and any associated PDB
2898 // structures for the alignment
2899 for (int i = 0; i < vamsasSeq.length; i++)
2901 if (jseqs[i].getFeaturesCount() > 0)
2903 Features[] features = jseqs[i].getFeatures();
2904 for (int f = 0; f < features.length; f++)
2906 jalview.datamodel.SequenceFeature sf = new jalview.datamodel.SequenceFeature(
2907 features[f].getType(), features[f].getDescription(),
2908 features[f].getStatus(), features[f].getBegin(),
2909 features[f].getEnd(), features[f].getFeatureGroup());
2911 sf.setScore(features[f].getScore());
2912 for (int od = 0; od < features[f].getOtherDataCount(); od++)
2914 OtherData keyValue = features[f].getOtherData(od);
2915 if (keyValue.getKey().startsWith("LINK"))
2917 sf.addLink(keyValue.getValue());
2921 sf.setValue(keyValue.getKey(), keyValue.getValue());
2926 al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf);
2929 if (vamsasSeq[i].getDBRefCount() > 0)
2931 addDBRefs(al.getSequenceAt(i).getDatasetSequence(), vamsasSeq[i]);
2933 if (jseqs[i].getPdbidsCount() > 0)
2935 Pdbids[] ids = jseqs[i].getPdbids();
2936 for (int p = 0; p < ids.length; p++)
2938 jalview.datamodel.PDBEntry entry = new jalview.datamodel.PDBEntry();
2939 entry.setId(ids[p].getId());
2940 if (ids[p].getType() != null)
2942 if (ids[p].getType().equalsIgnoreCase("PDB"))
2944 entry.setType(PDBEntry.Type.PDB);
2948 entry.setType(PDBEntry.Type.FILE);
2951 if (ids[p].getFile() != null)
2953 if (!pdbloaded.containsKey(ids[p].getFile()))
2955 entry.setFile(loadPDBFile(jprovider, ids[p].getId()));
2959 entry.setFile(pdbloaded.get(ids[p].getId()).toString());
2962 StructureSelectionManager.getStructureSelectionManager(
2963 Desktop.instance).registerPDBEntry(entry);
2964 al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
2968 } // end !multipleview
2970 // ///////////////////////////////
2971 // LOAD SEQUENCE MAPPINGS
2973 if (vamsasSet.getAlcodonFrameCount() > 0)
2975 // TODO Potentially this should only be done once for all views of an
2977 AlcodonFrame[] alc = vamsasSet.getAlcodonFrame();
2978 for (int i = 0; i < alc.length; i++)
2980 AlignedCodonFrame cf = new AlignedCodonFrame();
2981 if (alc[i].getAlcodMapCount() > 0)
2983 AlcodMap[] maps = alc[i].getAlcodMap();
2984 for (int m = 0; m < maps.length; m++)
2986 SequenceI dnaseq = seqRefIds.get(maps[m].getDnasq());
2988 jalview.datamodel.Mapping mapping = null;
2989 // attach to dna sequence reference.
2990 if (maps[m].getMapping() != null)
2992 mapping = addMapping(maps[m].getMapping());
2994 if (dnaseq != null && mapping.getTo() != null)
2996 cf.addMap(dnaseq, mapping.getTo(), mapping.getMap());
3001 frefedSequence.add(newAlcodMapRef(maps[m].getDnasq(), cf,
3005 al.addCodonFrame(cf);
3010 // ////////////////////////////////
3012 List<JvAnnotRow> autoAlan = new ArrayList<JvAnnotRow>();
3015 * store any annotations which forward reference a group's ID
3017 Map<String, List<AlignmentAnnotation>> groupAnnotRefs = new Hashtable<String, List<AlignmentAnnotation>>();
3019 if (vamsasSet.getAnnotationCount() > 0)
3021 Annotation[] an = vamsasSet.getAnnotation();
3023 for (int i = 0; i < an.length; i++)
3025 Annotation annotation = an[i];
3028 * test if annotation is automatically calculated for this view only
3030 boolean autoForView = false;
3031 if (annotation.getLabel().equals("Quality")
3032 || annotation.getLabel().equals("Conservation")
3033 || annotation.getLabel().equals("Consensus"))
3035 // Kludge for pre 2.5 projects which lacked the autocalculated flag
3037 if (!annotation.hasAutoCalculated())
3039 annotation.setAutoCalculated(true);
3043 || (annotation.hasAutoCalculated() && annotation
3044 .isAutoCalculated()))
3046 // remove ID - we don't recover annotation from other views for
3047 // view-specific annotation
3048 annotation.setId(null);
3051 // set visiblity for other annotation in this view
3052 String annotationId = annotation.getId();
3053 if (annotationId != null && annotationIds.containsKey(annotationId))
3055 AlignmentAnnotation jda = annotationIds.get(annotationId);
3056 // in principle Visible should always be true for annotation displayed
3057 // in multiple views
3058 if (annotation.hasVisible())
3060 jda.visible = annotation.getVisible();
3063 al.addAnnotation(jda);
3067 // Construct new annotation from model.
3068 AnnotationElement[] ae = annotation.getAnnotationElement();
3069 jalview.datamodel.Annotation[] anot = null;
3070 java.awt.Color firstColour = null;
3072 if (!annotation.getScoreOnly())
3074 anot = new jalview.datamodel.Annotation[al.getWidth()];
3075 for (int aa = 0; aa < ae.length && aa < anot.length; aa++)
3077 anpos = ae[aa].getPosition();
3079 if (anpos >= anot.length)
3084 anot[anpos] = new jalview.datamodel.Annotation(
3086 ae[aa].getDisplayCharacter(), ae[aa].getDescription(),
3087 (ae[aa].getSecondaryStructure() == null || ae[aa]
3088 .getSecondaryStructure().length() == 0) ? ' '
3089 : ae[aa].getSecondaryStructure().charAt(0),
3093 // JBPNote: Consider verifying dataflow for IO of secondary
3094 // structure annotation read from Stockholm files
3095 // this was added to try to ensure that
3096 // if (anot[ae[aa].getPosition()].secondaryStructure>' ')
3098 // anot[ae[aa].getPosition()].displayCharacter = "";
3100 anot[anpos].colour = new java.awt.Color(ae[aa].getColour());
3101 if (firstColour == null)
3103 firstColour = anot[anpos].colour;
3107 jalview.datamodel.AlignmentAnnotation jaa = null;
3109 if (annotation.getGraph())
3111 float llim = 0, hlim = 0;
3112 // if (autoForView || an[i].isAutoCalculated()) {
3115 jaa = new jalview.datamodel.AlignmentAnnotation(
3116 annotation.getLabel(), annotation.getDescription(), anot,
3117 llim, hlim, annotation.getGraphType());
3119 jaa.graphGroup = annotation.getGraphGroup();
3120 jaa._linecolour = firstColour;
3121 if (annotation.getThresholdLine() != null)
3123 jaa.setThreshold(new jalview.datamodel.GraphLine(annotation
3124 .getThresholdLine().getValue(), annotation
3125 .getThresholdLine().getLabel(), new java.awt.Color(
3126 annotation.getThresholdLine().getColour())));
3129 if (autoForView || annotation.isAutoCalculated())
3131 // Hardwire the symbol display line to ensure that labels for
3132 // histograms are displayed
3138 jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
3139 an[i].getDescription(), anot);
3140 jaa._linecolour = firstColour;
3142 // register new annotation
3143 if (an[i].getId() != null)
3145 annotationIds.put(an[i].getId(), jaa);
3146 jaa.annotationId = an[i].getId();
3148 // recover sequence association
3149 String sequenceRef = an[i].getSequenceRef();
3150 if (sequenceRef != null)
3152 // from 2.9 sequenceRef is to sequence id (JAL-1781)
3153 SequenceI sequence = seqRefIds.get(sequenceRef);
3154 if (sequence == null)
3156 // in pre-2.9 projects sequence ref is to sequence name
3157 sequence = al.findName(sequenceRef);
3159 if (sequence != null)
3161 jaa.createSequenceMapping(sequence, 1, true);
3162 sequence.addAlignmentAnnotation(jaa);
3165 // and make a note of any group association
3166 if (an[i].getGroupRef() != null && an[i].getGroupRef().length() > 0)
3168 List<jalview.datamodel.AlignmentAnnotation> aal = groupAnnotRefs
3169 .get(an[i].getGroupRef());
3172 aal = new ArrayList<jalview.datamodel.AlignmentAnnotation>();
3173 groupAnnotRefs.put(an[i].getGroupRef(), aal);
3178 if (an[i].hasScore())
3180 jaa.setScore(an[i].getScore());
3182 if (an[i].hasVisible())
3184 jaa.visible = an[i].getVisible();
3187 if (an[i].hasCentreColLabels())
3189 jaa.centreColLabels = an[i].getCentreColLabels();
3192 if (an[i].hasScaleColLabels())
3194 jaa.scaleColLabel = an[i].getScaleColLabels();
3196 if (an[i].hasAutoCalculated() && an[i].isAutoCalculated())
3198 // newer files have an 'autoCalculated' flag and store calculation
3199 // state in viewport properties
3200 jaa.autoCalculated = true; // means annotation will be marked for
3201 // update at end of load.
3203 if (an[i].hasGraphHeight())
3205 jaa.graphHeight = an[i].getGraphHeight();
3207 if (an[i].hasBelowAlignment())
3209 jaa.belowAlignment = an[i].isBelowAlignment();
3211 jaa.setCalcId(an[i].getCalcId());
3212 if (an[i].getPropertyCount() > 0)
3214 for (jalview.schemabinding.version2.Property prop : an[i]
3217 jaa.setProperty(prop.getName(), prop.getValue());
3220 if (jaa.autoCalculated)
3222 autoAlan.add(new JvAnnotRow(i, jaa));
3225 // if (!autoForView)
3227 // add autocalculated group annotation and any user created annotation
3229 al.addAnnotation(jaa);
3233 // ///////////////////////
3235 // Create alignment markup and styles for this view
3236 if (jms.getJGroupCount() > 0)
3238 JGroup[] groups = jms.getJGroup();
3239 boolean addAnnotSchemeGroup = false;
3240 for (int i = 0; i < groups.length; i++)
3242 JGroup jGroup = groups[i];
3243 ColourSchemeI cs = null;
3244 if (jGroup.getColour() != null)
3246 if (jGroup.getColour().startsWith("ucs"))
3248 cs = getUserColourScheme(jms, jGroup.getColour());
3250 else if (jGroup.getColour().equals("AnnotationColourGradient")
3251 && jGroup.getAnnotationColours() != null)
3253 addAnnotSchemeGroup = true;
3258 cs = ColourSchemeProperty.getColour(al, jGroup.getColour());
3263 cs.setThreshold(jGroup.getPidThreshold(), true);
3267 Vector<SequenceI> seqs = new Vector<SequenceI>();
3269 for (int s = 0; s < jGroup.getSeqCount(); s++)
3271 String seqId = jGroup.getSeq(s) + "";
3272 SequenceI ts = seqRefIds.get(seqId);
3276 seqs.addElement(ts);
3280 if (seqs.size() < 1)
3285 SequenceGroup sg = new SequenceGroup(seqs, jGroup.getName(), cs,
3286 jGroup.getDisplayBoxes(), jGroup.getDisplayText(),
3287 jGroup.getColourText(), jGroup.getStart(), jGroup.getEnd());
3289 sg.setOutlineColour(new java.awt.Color(jGroup.getOutlineColour()));
3291 sg.textColour = new java.awt.Color(jGroup.getTextCol1());
3292 sg.textColour2 = new java.awt.Color(jGroup.getTextCol2());
3293 sg.setShowNonconserved(jGroup.hasShowUnconserved() ? jGroup
3294 .isShowUnconserved() : false);
3295 sg.thresholdTextColour = jGroup.getTextColThreshold();
3296 if (jGroup.hasShowConsensusHistogram())
3298 sg.setShowConsensusHistogram(jGroup.isShowConsensusHistogram());
3301 if (jGroup.hasShowSequenceLogo())
3303 sg.setshowSequenceLogo(jGroup.isShowSequenceLogo());
3305 if (jGroup.hasNormaliseSequenceLogo())
3307 sg.setNormaliseSequenceLogo(jGroup.isNormaliseSequenceLogo());
3309 if (jGroup.hasIgnoreGapsinConsensus())
3311 sg.setIgnoreGapsConsensus(jGroup.getIgnoreGapsinConsensus());
3313 if (jGroup.getConsThreshold() != 0)
3315 jalview.analysis.Conservation c = new jalview.analysis.Conservation(
3316 "All", ResidueProperties.propHash, 3,
3317 sg.getSequences(null), 0, sg.getWidth() - 1);
3319 c.verdict(false, 25);
3320 sg.cs.setConservation(c);
3323 if (jGroup.getId() != null && groupAnnotRefs.size() > 0)
3325 // re-instate unique group/annotation row reference
3326 List<AlignmentAnnotation> jaal = groupAnnotRefs.get(jGroup
3330 for (AlignmentAnnotation jaa : jaal)
3333 if (jaa.autoCalculated)
3335 // match up and try to set group autocalc alignment row for this
3337 if (jaa.label.startsWith("Consensus for "))
3339 sg.setConsensus(jaa);
3341 // match up and try to set group autocalc alignment row for this
3343 if (jaa.label.startsWith("Conservation for "))
3345 sg.setConservationRow(jaa);
3352 if (addAnnotSchemeGroup)
3354 // reconstruct the annotation colourscheme
3355 sg.cs = constructAnnotationColour(jGroup.getAnnotationColours(),
3356 null, al, jms, false);
3362 // only dataset in this model, so just return.
3365 // ///////////////////////////////
3368 // If we just load in the same jar file again, the sequenceSetId
3369 // will be the same, and we end up with multiple references
3370 // to the same sequenceSet. We must modify this id on load
3371 // so that each load of the file gives a unique id
3372 String uniqueSeqSetId = view.getSequenceSetId() + uniqueSetSuffix;
3373 String viewId = (view.getId() == null ? null : view.getId()
3375 AlignFrame af = null;
3376 AlignViewport av = null;
3377 // now check to see if we really need to create a new viewport.
3378 if (multipleView && viewportsAdded.size() == 0)
3380 // We recovered an alignment for which a viewport already exists.
3381 // TODO: fix up any settings necessary for overlaying stored state onto
3382 // state recovered from another document. (may not be necessary).
3383 // we may need a binding from a viewport in memory to one recovered from
3385 // and then recover its containing af to allow the settings to be applied.
3386 // TODO: fix for vamsas demo
3388 .println("About to recover a viewport for existing alignment: Sequence set ID is "
3390 Object seqsetobj = retrieveExistingObj(uniqueSeqSetId);
3391 if (seqsetobj != null)
3393 if (seqsetobj instanceof String)
3395 uniqueSeqSetId = (String) seqsetobj;
3397 .println("Recovered extant sequence set ID mapping for ID : New Sequence set ID is "
3403 .println("Warning : Collision between sequence set ID string and existing jalview object mapping.");
3409 * indicate that annotation colours are applied across all groups (pre
3410 * Jalview 2.8.1 behaviour)
3412 boolean doGroupAnnColour = Jalview2XML.isVersionStringLaterThan(
3413 "2.8.1", object.getVersion());
3415 AlignmentPanel ap = null;
3416 boolean isnewview = true;
3419 // Check to see if this alignment already has a view id == viewId
3420 jalview.gui.AlignmentPanel views[] = Desktop
3421 .getAlignmentPanels(uniqueSeqSetId);
3422 if (views != null && views.length > 0)
3424 for (int v = 0; v < views.length; v++)
3426 if (views[v].av.getViewId().equalsIgnoreCase(viewId))
3428 // recover the existing alignpanel, alignframe, viewport
3429 af = views[v].alignFrame;
3432 // TODO: could even skip resetting view settings if we don't want to
3433 // change the local settings from other jalview processes
3442 af = loadViewport(file, jseqs, hiddenSeqs, al, jms, view,
3443 uniqueSeqSetId, viewId, autoAlan);
3449 * Load any trees, PDB structures and viewers
3451 * Not done if flag is false (when this method is used for New View)
3453 if (loadTreesAndStructures)
3455 loadTrees(jms, view, af, av, ap);
3456 loadPDBStructures(jprovider, jseqs, af, ap);
3457 loadRnaViewers(jprovider, jseqs, ap);
3459 // and finally return.
3464 * Instantiate and link any saved RNA (Varna) viewers. The state of the Varna
3465 * panel is restored from separate jar entries, two (gapped and trimmed) per
3466 * sequence and secondary structure.
3468 * Currently each viewer shows just one sequence and structure (gapped and
3469 * trimmed), however this method is designed to support multiple sequences or
3470 * structures in viewers if wanted in future.
3476 private void loadRnaViewers(jarInputStreamProvider jprovider,
3477 JSeq[] jseqs, AlignmentPanel ap)
3480 * scan the sequences for references to viewers; create each one the first
3481 * time it is referenced, add Rna models to existing viewers
3483 for (JSeq jseq : jseqs)
3485 for (int i = 0; i < jseq.getRnaViewerCount(); i++)
3487 RnaViewer viewer = jseq.getRnaViewer(i);
3488 AppVarna appVarna = findOrCreateVarnaViewer(viewer,
3489 uniqueSetSuffix, ap);
3491 for (int j = 0; j < viewer.getSecondaryStructureCount(); j++)
3493 SecondaryStructure ss = viewer.getSecondaryStructure(j);
3494 SequenceI seq = seqRefIds.get(jseq.getId());
3495 AlignmentAnnotation ann = this.annotationIds.get(ss
3496 .getAnnotationId());
3499 * add the structure to the Varna display (with session state copied
3500 * from the jar to a temporary file)
3502 boolean gapped = ss.isGapped();
3503 String rnaTitle = ss.getTitle();
3504 String sessionState = ss.getViewerState();
3505 String tempStateFile = copyJarEntry(jprovider, sessionState,
3507 RnaModel rna = new RnaModel(rnaTitle, ann, seq, null, gapped);
3508 appVarna.addModelSession(rna, rnaTitle, tempStateFile);
3510 appVarna.setInitialSelection(viewer.getSelectedRna());
3516 * Locate and return an already instantiated matching AppVarna, or create one
3520 * @param viewIdSuffix
3524 protected AppVarna findOrCreateVarnaViewer(RnaViewer viewer,
3525 String viewIdSuffix, AlignmentPanel ap)
3528 * on each load a suffix is appended to the saved viewId, to avoid conflicts
3529 * if load is repeated
3531 String postLoadId = viewer.getViewId() + viewIdSuffix;
3532 for (JInternalFrame frame : getAllFrames())
3534 if (frame instanceof AppVarna)
3536 AppVarna varna = (AppVarna) frame;
3537 if (postLoadId.equals(varna.getViewId()))
3539 // this viewer is already instantiated
3540 // could in future here add ap as another 'parent' of the
3541 // AppVarna window; currently just 1-to-many
3548 * viewer not found - make it
3550 RnaViewerModel model = new RnaViewerModel(postLoadId,
3551 viewer.getTitle(), viewer.getXpos(), viewer.getYpos(),
3552 viewer.getWidth(), viewer.getHeight(),
3553 viewer.getDividerLocation());
3554 AppVarna varna = new AppVarna(model, ap);
3560 * Load any saved trees
3568 protected void loadTrees(JalviewModelSequence jms, Viewport view,
3569 AlignFrame af, AlignViewport av, AlignmentPanel ap)
3571 // TODO result of automated refactoring - are all these parameters needed?
3574 for (int t = 0; t < jms.getTreeCount(); t++)
3577 Tree tree = jms.getTree(t);
3579 TreePanel tp = (TreePanel) retrieveExistingObj(tree.getId());
3582 tp = af.ShowNewickTree(
3583 new jalview.io.NewickFile(tree.getNewick()),
3584 tree.getTitle(), tree.getWidth(), tree.getHeight(),
3585 tree.getXpos(), tree.getYpos());
3586 if (tree.getId() != null)
3588 // perhaps bind the tree id to something ?
3593 // update local tree attributes ?
3594 // TODO: should check if tp has been manipulated by user - if so its
3595 // settings shouldn't be modified
3596 tp.setTitle(tree.getTitle());
3597 tp.setBounds(new Rectangle(tree.getXpos(), tree.getYpos(), tree
3598 .getWidth(), tree.getHeight()));
3599 tp.av = av; // af.viewport; // TODO: verify 'associate with all
3602 tp.treeCanvas.av = av; // af.viewport;
3603 tp.treeCanvas.ap = ap; // af.alignPanel;
3608 warn("There was a problem recovering stored Newick tree: \n"
3609 + tree.getNewick());
3613 tp.fitToWindow.setState(tree.getFitToWindow());
3614 tp.fitToWindow_actionPerformed(null);
3616 if (tree.getFontName() != null)
3618 tp.setTreeFont(new java.awt.Font(tree.getFontName(), tree
3619 .getFontStyle(), tree.getFontSize()));
3623 tp.setTreeFont(new java.awt.Font(view.getFontName(), view
3624 .getFontStyle(), tree.getFontSize()));
3627 tp.showPlaceholders(tree.getMarkUnlinked());
3628 tp.showBootstrap(tree.getShowBootstrap());
3629 tp.showDistances(tree.getShowDistances());
3631 tp.treeCanvas.threshold = tree.getThreshold();
3633 if (tree.getCurrentTree())
3635 af.viewport.setCurrentTree(tp.getTree());
3639 } catch (Exception ex)
3641 ex.printStackTrace();
3646 * Load and link any saved structure viewers.
3653 protected void loadPDBStructures(jarInputStreamProvider jprovider,
3654 JSeq[] jseqs, AlignFrame af, AlignmentPanel ap)
3657 * Run through all PDB ids on the alignment, and collect mappings between
3658 * distinct view ids and all sequences referring to that view.
3660 Map<String, StructureViewerModel> structureViewers = new LinkedHashMap<String, StructureViewerModel>();
3662 for (int i = 0; i < jseqs.length; i++)
3664 if (jseqs[i].getPdbidsCount() > 0)
3666 Pdbids[] ids = jseqs[i].getPdbids();
3667 for (int p = 0; p < ids.length; p++)
3669 final int structureStateCount = ids[p].getStructureStateCount();
3670 for (int s = 0; s < structureStateCount; s++)
3672 // check to see if we haven't already created this structure view
3673 final StructureState structureState = ids[p]
3674 .getStructureState(s);
3675 String sviewid = (structureState.getViewId() == null) ? null
3676 : structureState.getViewId() + uniqueSetSuffix;
3677 jalview.datamodel.PDBEntry jpdb = new jalview.datamodel.PDBEntry();
3678 // Originally : ids[p].getFile()
3679 // : TODO: verify external PDB file recovery still works in normal
3680 // jalview project load
3681 jpdb.setFile(loadPDBFile(jprovider, ids[p].getId()));
3682 jpdb.setId(ids[p].getId());
3684 int x = structureState.getXpos();
3685 int y = structureState.getYpos();
3686 int width = structureState.getWidth();
3687 int height = structureState.getHeight();
3689 // Probably don't need to do this anymore...
3690 // Desktop.desktop.getComponentAt(x, y);
3691 // TODO: NOW: check that this recovers the PDB file correctly.
3692 String pdbFile = loadPDBFile(jprovider, ids[p].getId());
3693 jalview.datamodel.SequenceI seq = seqRefIds.get(jseqs[i]
3695 if (sviewid == null)
3697 sviewid = "_jalview_pre2_4_" + x + "," + y + "," + width
3700 if (!structureViewers.containsKey(sviewid))
3702 structureViewers.put(sviewid,
3703 new StructureViewerModel(x, y, width, height, false,
3704 false, true, structureState.getViewId(),
3705 structureState.getType()));
3706 // Legacy pre-2.7 conversion JAL-823 :
3707 // do not assume any view has to be linked for colour by
3711 // assemble String[] { pdb files }, String[] { id for each
3712 // file }, orig_fileloc, SequenceI[][] {{ seqs_file 1 }, {
3713 // seqs_file 2}, boolean[] {
3714 // linkAlignPanel,superposeWithAlignpanel}} from hash
3715 StructureViewerModel jmoldat = structureViewers.get(sviewid);
3716 jmoldat.setAlignWithPanel(jmoldat.isAlignWithPanel()
3717 | (structureState.hasAlignwithAlignPanel() ? structureState
3718 .getAlignwithAlignPanel() : false));
3721 * Default colour by linked panel to false if not specified (e.g.
3722 * for pre-2.7 projects)
3724 boolean colourWithAlignPanel = jmoldat.isColourWithAlignPanel();
3725 colourWithAlignPanel |= (structureState
3726 .hasColourwithAlignPanel() ? structureState
3727 .getColourwithAlignPanel() : false);
3728 jmoldat.setColourWithAlignPanel(colourWithAlignPanel);
3731 * Default colour by viewer to true if not specified (e.g. for
3734 boolean colourByViewer = jmoldat.isColourByViewer();
3735 colourByViewer &= structureState.hasColourByJmol() ? structureState
3736 .getColourByJmol() : true;
3737 jmoldat.setColourByViewer(colourByViewer);
3739 if (jmoldat.getStateData().length() < structureState
3740 .getContent().length())
3743 jmoldat.setStateData(structureState.getContent());
3746 if (ids[p].getFile() != null)
3748 File mapkey = new File(ids[p].getFile());
3749 StructureData seqstrmaps = jmoldat.getFileData().get(mapkey);
3750 if (seqstrmaps == null)
3752 jmoldat.getFileData().put(
3754 seqstrmaps = jmoldat.new StructureData(pdbFile,
3757 if (!seqstrmaps.getSeqList().contains(seq))
3759 seqstrmaps.getSeqList().add(seq);
3765 errorMessage = ("The Jmol views in this project were imported\nfrom an older version of Jalview.\nPlease review the sequence colour associations\nin the Colour by section of the Jmol View menu.\n\nIn the case of problems, see note at\nhttp://issues.jalview.org/browse/JAL-747");
3772 // Instantiate the associated structure views
3773 for (Entry<String, StructureViewerModel> entry : structureViewers
3778 createOrLinkStructureViewer(entry, af, ap, jprovider);
3779 } catch (Exception e)
3781 System.err.println("Error loading structure viewer: "
3783 // failed - try the next one
3795 protected void createOrLinkStructureViewer(
3796 Entry<String, StructureViewerModel> viewerData, AlignFrame af,
3797 AlignmentPanel ap, jarInputStreamProvider jprovider)
3799 final StructureViewerModel stateData = viewerData.getValue();
3802 * Search for any viewer windows already open from other alignment views
3803 * that exactly match the stored structure state
3805 StructureViewerBase comp = findMatchingViewer(viewerData);
3809 linkStructureViewer(ap, comp, stateData);
3814 * From 2.9: stateData.type contains JMOL or CHIMERA, data is in jar entry
3815 * "viewer_"+stateData.viewId
3817 if (ViewerType.CHIMERA.toString().equals(stateData.getType()))
3819 createChimeraViewer(viewerData, af, jprovider);
3824 * else Jmol (if pre-2.9, stateData contains JMOL state string)
3826 createJmolViewer(viewerData, af, jprovider);
3831 * Create a new Chimera viewer.
3837 protected void createChimeraViewer(
3838 Entry<String, StructureViewerModel> viewerData, AlignFrame af,
3839 jarInputStreamProvider jprovider)
3841 StructureViewerModel data = viewerData.getValue();
3842 String chimeraSessionFile = data.getStateData();
3845 * Copy Chimera session from jar entry "viewer_"+viewId to a temporary file
3847 * NB this is the 'saved' viewId as in the project file XML, _not_ the
3848 * 'uniquified' sviewid used to reconstruct the viewer here
3850 String viewerJarEntryName = getViewerJarEntryName(data.getViewId());
3851 chimeraSessionFile = copyJarEntry(jprovider, viewerJarEntryName,
3854 Set<Entry<File, StructureData>> fileData = data.getFileData()
3856 List<PDBEntry> pdbs = new ArrayList<PDBEntry>();
3857 List<SequenceI[]> allseqs = new ArrayList<SequenceI[]>();
3858 for (Entry<File, StructureData> pdb : fileData)
3860 String filePath = pdb.getValue().getFilePath();
3861 String pdbId = pdb.getValue().getPdbId();
3862 // pdbs.add(new PDBEntry(filePath, pdbId));
3863 pdbs.add(new PDBEntry(pdbId, null, PDBEntry.Type.PDB, filePath));
3864 final List<SequenceI> seqList = pdb.getValue().getSeqList();
3865 SequenceI[] seqs = seqList.toArray(new SequenceI[seqList.size()]);
3869 boolean colourByChimera = data.isColourByViewer();
3870 boolean colourBySequence = data.isColourWithAlignPanel();
3872 // TODO use StructureViewer as a factory here, see JAL-1761
3873 final PDBEntry[] pdbArray = pdbs.toArray(new PDBEntry[pdbs.size()]);
3874 final SequenceI[][] seqsArray = allseqs.toArray(new SequenceI[allseqs
3876 String newViewId = viewerData.getKey();
3878 ChimeraViewFrame cvf = new ChimeraViewFrame(chimeraSessionFile,
3879 af.alignPanel, pdbArray, seqsArray, colourByChimera,
3880 colourBySequence, newViewId);
3881 cvf.setSize(data.getWidth(), data.getHeight());
3882 cvf.setLocation(data.getX(), data.getY());
3886 * Create a new Jmol window. First parse the Jmol state to translate filenames
3887 * loaded into the view, and record the order in which files are shown in the
3888 * Jmol view, so we can add the sequence mappings in same order.
3894 protected void createJmolViewer(
3895 final Entry<String, StructureViewerModel> viewerData,
3896 AlignFrame af, jarInputStreamProvider jprovider)
3898 final StructureViewerModel svattrib = viewerData.getValue();
3899 String state = svattrib.getStateData();
3902 * Pre-2.9: state element value is the Jmol state string
3904 * 2.9+: @type is "JMOL", state data is in a Jar file member named "viewer_"
3907 if (ViewerType.JMOL.toString().equals(svattrib.getType()))
3909 state = readJarEntry(jprovider,
3910 getViewerJarEntryName(svattrib.getViewId()));
3913 List<String> pdbfilenames = new ArrayList<String>();
3914 List<SequenceI[]> seqmaps = new ArrayList<SequenceI[]>();
3915 List<String> pdbids = new ArrayList<String>();
3916 StringBuilder newFileLoc = new StringBuilder(64);
3917 int cp = 0, ncp, ecp;
3918 Map<File, StructureData> oldFiles = svattrib.getFileData();
3919 while ((ncp = state.indexOf("load ", cp)) > -1)
3923 // look for next filename in load statement
3924 newFileLoc.append(state.substring(cp,
3925 ncp = (state.indexOf("\"", ncp + 1) + 1)));
3926 String oldfilenam = state.substring(ncp,
3927 ecp = state.indexOf("\"", ncp));
3928 // recover the new mapping data for this old filename
3929 // have to normalize filename - since Jmol and jalview do
3931 // translation differently.
3932 StructureData filedat = oldFiles.get(new File(oldfilenam));
3933 newFileLoc.append(Platform.escapeString(filedat.getFilePath()));
3934 pdbfilenames.add(filedat.getFilePath());
3935 pdbids.add(filedat.getPdbId());
3936 seqmaps.add(filedat.getSeqList().toArray(new SequenceI[0]));
3937 newFileLoc.append("\"");
3938 cp = ecp + 1; // advance beyond last \" and set cursor so we can
3939 // look for next file statement.
3940 } while ((ncp = state.indexOf("/*file*/", cp)) > -1);
3944 // just append rest of state
3945 newFileLoc.append(state.substring(cp));
3949 System.err.print("Ignoring incomplete Jmol state for PDB ids: ");
3950 newFileLoc = new StringBuilder(state);
3951 newFileLoc.append("; load append ");
3952 for (File id : oldFiles.keySet())
3954 // add this and any other pdb files that should be present in
3956 StructureData filedat = oldFiles.get(id);
3957 newFileLoc.append(filedat.getFilePath());
3958 pdbfilenames.add(filedat.getFilePath());
3959 pdbids.add(filedat.getPdbId());
3960 seqmaps.add(filedat.getSeqList().toArray(new SequenceI[0]));
3961 newFileLoc.append(" \"");
3962 newFileLoc.append(filedat.getFilePath());
3963 newFileLoc.append("\"");
3966 newFileLoc.append(";");
3969 if (newFileLoc.length() == 0)
3973 int histbug = newFileLoc.indexOf("history = ");
3977 * change "history = [true|false];" to "history = [1|0];"
3980 int diff = histbug == -1 ? -1 : newFileLoc.indexOf(";", histbug);
3981 String val = (diff == -1) ? null : newFileLoc
3982 .substring(histbug, diff);
3983 if (val != null && val.length() >= 4)
3985 if (val.contains("e")) // eh? what can it be?
3987 if (val.trim().equals("true"))
3995 newFileLoc.replace(histbug, diff, val);
4000 final String[] pdbf = pdbfilenames.toArray(new String[pdbfilenames
4002 final String[] id = pdbids.toArray(new String[pdbids.size()]);
4003 final SequenceI[][] sq = seqmaps
4004 .toArray(new SequenceI[seqmaps.size()][]);
4005 final String fileloc = newFileLoc.toString();
4006 final String sviewid = viewerData.getKey();
4007 final AlignFrame alf = af;
4008 final Rectangle rect = new Rectangle(svattrib.getX(), svattrib.getY(),
4009 svattrib.getWidth(), svattrib.getHeight());
4012 javax.swing.SwingUtilities.invokeAndWait(new Runnable()
4017 JalviewStructureDisplayI sview = null;
4020 sview = new StructureViewer(alf.alignPanel
4021 .getStructureSelectionManager()).createView(
4022 StructureViewer.ViewerType.JMOL, pdbf, id, sq,
4023 alf.alignPanel, svattrib, fileloc, rect, sviewid);
4024 addNewStructureViewer(sview);
4025 } catch (OutOfMemoryError ex)
4027 new OOMWarning("restoring structure view for PDB id " + id,
4028 (OutOfMemoryError) ex.getCause());
4029 if (sview != null && sview.isVisible())
4031 sview.closeViewer(false);
4032 sview.setVisible(false);
4038 } catch (InvocationTargetException ex)
4040 warn("Unexpected error when opening Jmol view.", ex);
4042 } catch (InterruptedException e)
4044 // e.printStackTrace();
4050 * Generates a name for the entry in the project jar file to hold state
4051 * information for a structure viewer
4056 protected String getViewerJarEntryName(String viewId)
4058 return VIEWER_PREFIX + viewId;
4062 * Returns any open frame that matches given structure viewer data. The match
4063 * is based on the unique viewId, or (for older project versions) the frame's
4069 protected StructureViewerBase findMatchingViewer(
4070 Entry<String, StructureViewerModel> viewerData)
4072 final String sviewid = viewerData.getKey();
4073 final StructureViewerModel svattrib = viewerData.getValue();
4074 StructureViewerBase comp = null;
4075 JInternalFrame[] frames = getAllFrames();
4076 for (JInternalFrame frame : frames)
4078 if (frame instanceof StructureViewerBase)
4081 * Post jalview 2.4 schema includes structure view id
4084 && ((StructureViewerBase) frame).getViewId()
4087 comp = (StructureViewerBase) frame;
4088 break; // break added in 2.9
4091 * Otherwise test for matching position and size of viewer frame
4093 else if (frame.getX() == svattrib.getX()
4094 && frame.getY() == svattrib.getY()
4095 && frame.getHeight() == svattrib.getHeight()
4096 && frame.getWidth() == svattrib.getWidth())
4098 comp = (StructureViewerBase) frame;
4099 // no break in faint hope of an exact match on viewId
4107 * Link an AlignmentPanel to an existing structure viewer.
4112 * @param useinViewerSuperpos
4113 * @param usetoColourbyseq
4114 * @param viewerColouring
4116 protected void linkStructureViewer(AlignmentPanel ap,
4117 StructureViewerBase viewer, StructureViewerModel stateData)
4119 // NOTE: if the jalview project is part of a shared session then
4120 // view synchronization should/could be done here.
4122 final boolean useinViewerSuperpos = stateData.isAlignWithPanel();
4123 final boolean usetoColourbyseq = stateData.isColourWithAlignPanel();
4124 final boolean viewerColouring = stateData.isColourByViewer();
4125 Map<File, StructureData> oldFiles = stateData.getFileData();
4128 * Add mapping for sequences in this view to an already open viewer
4130 final AAStructureBindingModel binding = viewer.getBinding();
4131 for (File id : oldFiles.keySet())
4133 // add this and any other pdb files that should be present in the
4135 StructureData filedat = oldFiles.get(id);
4136 String pdbFile = filedat.getFilePath();
4137 SequenceI[] seq = filedat.getSeqList().toArray(new SequenceI[0]);
4138 binding.getSsm().setMapping(seq, null, pdbFile,
4139 jalview.io.AppletFormatAdapter.FILE);
4140 binding.addSequenceForStructFile(pdbFile, seq);
4142 // and add the AlignmentPanel's reference to the view panel
4143 viewer.addAlignmentPanel(ap);
4144 if (useinViewerSuperpos)
4146 viewer.useAlignmentPanelForSuperposition(ap);
4150 viewer.excludeAlignmentPanelForSuperposition(ap);
4152 if (usetoColourbyseq)
4154 viewer.useAlignmentPanelForColourbyseq(ap, !viewerColouring);
4158 viewer.excludeAlignmentPanelForColourbyseq(ap);
4163 * Get all frames within the Desktop.
4167 protected JInternalFrame[] getAllFrames()
4169 JInternalFrame[] frames = null;
4170 // TODO is this necessary - is it safe - risk of hanging?
4175 frames = Desktop.desktop.getAllFrames();
4176 } catch (ArrayIndexOutOfBoundsException e)
4178 // occasional No such child exceptions are thrown here...
4182 } catch (InterruptedException f)
4186 } while (frames == null);
4191 * Answers true if 'version' is equal to or later than 'supported', where each
4192 * is formatted as major/minor versions like "2.8.3" or "2.3.4b1" for bugfix
4193 * changes. Development and test values for 'version' are leniently treated
4197 * - minimum version we are comparing against
4199 * - version of data being processsed
4202 public static boolean isVersionStringLaterThan(String supported,
4205 if (supported == null || version == null
4206 || version.equalsIgnoreCase("DEVELOPMENT BUILD")
4207 || version.equalsIgnoreCase("Test")
4208 || version.equalsIgnoreCase("AUTOMATED BUILD"))
4210 System.err.println("Assuming project file with "
4211 + (version == null ? "null" : version)
4212 + " is compatible with Jalview version " + supported);
4217 return StringUtils.compareVersions(version, supported, "b") >= 0;
4221 Vector<JalviewStructureDisplayI> newStructureViewers = null;
4223 protected void addNewStructureViewer(JalviewStructureDisplayI sview)
4225 if (newStructureViewers != null)
4227 sview.getBinding().setFinishedLoadingFromArchive(false);
4228 newStructureViewers.add(sview);
4232 protected void setLoadingFinishedForNewStructureViewers()
4234 if (newStructureViewers != null)
4236 for (JalviewStructureDisplayI sview : newStructureViewers)
4238 sview.getBinding().setFinishedLoadingFromArchive(true);
4240 newStructureViewers.clear();
4241 newStructureViewers = null;
4245 AlignFrame loadViewport(String file, JSeq[] JSEQ,
4246 List<SequenceI> hiddenSeqs, AlignmentI al,
4247 JalviewModelSequence jms, Viewport view, String uniqueSeqSetId,
4248 String viewId, List<JvAnnotRow> autoAlan)
4250 AlignFrame af = null;
4251 af = new AlignFrame(al, view.getWidth(), view.getHeight(),
4252 uniqueSeqSetId, viewId);
4254 af.setFileName(file, "Jalview");
4256 for (int i = 0; i < JSEQ.length; i++)
4258 af.viewport.setSequenceColour(af.viewport.getAlignment()
4259 .getSequenceAt(i), new java.awt.Color(JSEQ[i].getColour()));
4264 af.getViewport().setColourByReferenceSeq(true);
4265 af.getViewport().setDisplayReferenceSeq(true);
4268 af.viewport.setGatherViewsHere(view.getGatheredViews());
4270 if (view.getSequenceSetId() != null)
4272 AlignmentViewport av = viewportsAdded.get(uniqueSeqSetId);
4274 af.viewport.setSequenceSetId(uniqueSeqSetId);
4277 // propagate shared settings to this new view
4278 af.viewport.setHistoryList(av.getHistoryList());
4279 af.viewport.setRedoList(av.getRedoList());
4283 viewportsAdded.put(uniqueSeqSetId, af.viewport);
4285 // TODO: check if this method can be called repeatedly without
4286 // side-effects if alignpanel already registered.
4287 PaintRefresher.Register(af.alignPanel, uniqueSeqSetId);
4289 // apply Hidden regions to view.
4290 if (hiddenSeqs != null)
4292 for (int s = 0; s < JSEQ.length; s++)
4294 SequenceGroup hidden = new SequenceGroup();
4295 boolean isRepresentative = false;
4296 for (int r = 0; r < JSEQ[s].getHiddenSequencesCount(); r++)
4298 isRepresentative = true;
4299 SequenceI sequenceToHide = al.getSequenceAt(JSEQ[s]
4300 .getHiddenSequences(r));
4301 hidden.addSequence(sequenceToHide, false);
4302 // remove from hiddenSeqs list so we don't try to hide it twice
4303 hiddenSeqs.remove(sequenceToHide);
4305 if (isRepresentative)
4307 SequenceI representativeSequence = al.getSequenceAt(s);
4308 hidden.addSequence(representativeSequence, false);
4309 af.viewport.hideRepSequences(representativeSequence, hidden);
4313 SequenceI[] hseqs = hiddenSeqs.toArray(new SequenceI[hiddenSeqs
4315 af.viewport.hideSequence(hseqs);
4318 // recover view properties and display parameters
4319 if (view.getViewName() != null)
4321 af.viewport.viewName = view.getViewName();
4322 af.setInitialTabVisible();
4324 af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),
4327 af.viewport.setShowAnnotation(view.getShowAnnotation());
4328 af.viewport.setAbovePIDThreshold(view.getPidSelected());
4330 af.viewport.setColourText(view.getShowColourText());
4332 af.viewport.setConservationSelected(view.getConservationSelected());
4333 af.viewport.setShowJVSuffix(view.getShowFullId());
4334 af.viewport.setRightAlignIds(view.getRightAlignIds());
4335 af.viewport.setFont(
4336 new java.awt.Font(view.getFontName(), view.getFontStyle(), view
4337 .getFontSize()), true);
4338 ViewStyleI vs = af.viewport.getViewStyle();
4339 vs.setScaleProteinAsCdna(view.isScaleProteinAsCdna());
4340 af.viewport.setViewStyle(vs);
4341 // TODO: allow custom charWidth/Heights to be restored by updating them
4342 // after setting font - which means set above to false
4343 af.viewport.setRenderGaps(view.getRenderGaps());
4344 af.viewport.setWrapAlignment(view.getWrapAlignment());
4345 af.viewport.setShowAnnotation(view.getShowAnnotation());
4347 af.viewport.setShowBoxes(view.getShowBoxes());
4349 af.viewport.setShowText(view.getShowText());
4351 af.viewport.setTextColour(new java.awt.Color(view.getTextCol1()));
4352 af.viewport.setTextColour2(new java.awt.Color(view.getTextCol2()));
4353 af.viewport.setThresholdTextColour(view.getTextColThreshold());
4354 af.viewport.setShowUnconserved(view.hasShowUnconserved() ? view
4355 .isShowUnconserved() : false);
4356 af.viewport.setStartRes(view.getStartRes());
4357 af.viewport.setStartSeq(view.getStartSeq());
4358 af.alignPanel.updateLayout();
4359 ColourSchemeI cs = null;
4360 // apply colourschemes
4361 if (view.getBgColour() != null)
4363 if (view.getBgColour().startsWith("ucs"))
4365 cs = getUserColourScheme(jms, view.getBgColour());
4367 else if (view.getBgColour().startsWith("Annotation"))
4369 AnnotationColours viewAnnColour = view.getAnnotationColours();
4370 cs = constructAnnotationColour(viewAnnColour, af, al, jms, true);
4377 cs = ColourSchemeProperty.getColour(al, view.getBgColour());
4382 cs.setThreshold(view.getPidThreshold(), true);
4383 cs.setConsensus(af.viewport.getSequenceConsensusHash());
4387 af.viewport.setGlobalColourScheme(cs);
4388 af.viewport.setColourAppliesToAllGroups(false);
4390 if (view.getConservationSelected() && cs != null)
4392 cs.setConservationInc(view.getConsThreshold());
4395 af.changeColour(cs);
4397 af.viewport.setColourAppliesToAllGroups(true);
4399 af.viewport.setShowSequenceFeatures(view.getShowSequenceFeatures());
4401 if (view.hasCentreColumnLabels())
4403 af.viewport.setCentreColumnLabels(view.getCentreColumnLabels());
4405 if (view.hasIgnoreGapsinConsensus())
4407 af.viewport.setIgnoreGapsConsensus(view.getIgnoreGapsinConsensus(),
4410 if (view.hasFollowHighlight())
4412 af.viewport.setFollowHighlight(view.getFollowHighlight());
4414 if (view.hasFollowSelection())
4416 af.viewport.followSelection = view.getFollowSelection();
4418 if (view.hasShowConsensusHistogram())
4420 af.viewport.setShowConsensusHistogram(view
4421 .getShowConsensusHistogram());
4425 af.viewport.setShowConsensusHistogram(true);
4427 if (view.hasShowSequenceLogo())
4429 af.viewport.setShowSequenceLogo(view.getShowSequenceLogo());
4433 af.viewport.setShowSequenceLogo(false);
4435 if (view.hasNormaliseSequenceLogo())
4437 af.viewport.setNormaliseSequenceLogo(view.getNormaliseSequenceLogo());
4439 if (view.hasShowDbRefTooltip())
4441 af.viewport.setShowDBRefs(view.getShowDbRefTooltip());
4443 if (view.hasShowNPfeatureTooltip())
4445 af.viewport.setShowNPFeats(view.hasShowNPfeatureTooltip());
4447 if (view.hasShowGroupConsensus())
4449 af.viewport.setShowGroupConsensus(view.getShowGroupConsensus());
4453 af.viewport.setShowGroupConsensus(false);
4455 if (view.hasShowGroupConservation())
4457 af.viewport.setShowGroupConservation(view.getShowGroupConservation());
4461 af.viewport.setShowGroupConservation(false);
4464 // recover featre settings
4465 if (jms.getFeatureSettings() != null)
4467 FeaturesDisplayed fdi;
4468 af.viewport.setFeaturesDisplayed(fdi = new FeaturesDisplayed());
4469 String[] renderOrder = new String[jms.getFeatureSettings()
4470 .getSettingCount()];
4471 Map<String, FeatureColourI> featureColours = new Hashtable<String, FeatureColourI>();
4472 Map<String, Float> featureOrder = new Hashtable<String, Float>();
4474 for (int fs = 0; fs < jms.getFeatureSettings().getSettingCount(); fs++)
4476 Setting setting = jms.getFeatureSettings().getSetting(fs);
4477 if (setting.hasMincolour())
4479 FeatureColourI gc = setting.hasMin() ? new FeatureColour(
4480 new Color(setting.getMincolour()), new Color(
4481 setting.getColour()), setting.getMin(),
4482 setting.getMax()) : new FeatureColour(new Color(
4483 setting.getMincolour()), new Color(setting.getColour()),
4485 if (setting.hasThreshold())
4487 gc.setThreshold(setting.getThreshold());
4488 int threshstate = setting.getThreshstate();
4489 // -1 = None, 0 = Below, 1 = Above threshold
4490 if (threshstate == 0)
4492 gc.setBelowThreshold(true);
4494 else if (threshstate == 1)
4496 gc.setAboveThreshold(true);
4499 gc.setAutoScaled(true); // default
4500 if (setting.hasAutoScale())
4502 gc.setAutoScaled(setting.getAutoScale());
4504 if (setting.hasColourByLabel())
4506 gc.setColourByLabel(setting.getColourByLabel());
4508 // and put in the feature colour table.
4509 featureColours.put(setting.getType(), gc);
4513 featureColours.put(setting.getType(), new FeatureColour(
4514 new Color(setting.getColour())));
4516 renderOrder[fs] = setting.getType();
4517 if (setting.hasOrder())
4519 featureOrder.put(setting.getType(), setting.getOrder());
4523 featureOrder.put(setting.getType(), new Float(fs
4524 / jms.getFeatureSettings().getSettingCount()));
4526 if (setting.getDisplay())
4528 fdi.setVisible(setting.getType());
4531 Map<String, Boolean> fgtable = new Hashtable<String, Boolean>();
4532 for (int gs = 0; gs < jms.getFeatureSettings().getGroupCount(); gs++)
4534 Group grp = jms.getFeatureSettings().getGroup(gs);
4535 fgtable.put(grp.getName(), new Boolean(grp.getDisplay()));
4537 // FeatureRendererSettings frs = new FeatureRendererSettings(renderOrder,
4538 // fgtable, featureColours, jms.getFeatureSettings().hasTransparency() ?
4539 // jms.getFeatureSettings().getTransparency() : 0.0, featureOrder);
4540 FeatureRendererSettings frs = new FeatureRendererSettings(
4541 renderOrder, fgtable, featureColours, 1.0f, featureOrder);
4542 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
4543 .transferSettings(frs);
4547 if (view.getHiddenColumnsCount() > 0)
4549 for (int c = 0; c < view.getHiddenColumnsCount(); c++)
4551 af.viewport.hideColumns(view.getHiddenColumns(c).getStart(), view
4552 .getHiddenColumns(c).getEnd() // +1
4556 if (view.getCalcIdParam() != null)
4558 for (CalcIdParam calcIdParam : view.getCalcIdParam())
4560 if (calcIdParam != null)
4562 if (recoverCalcIdParam(calcIdParam, af.viewport))
4567 warn("Couldn't recover parameters for "
4568 + calcIdParam.getCalcId());
4573 af.setMenusFromViewport(af.viewport);
4574 af.setTitle(view.getTitle());
4575 // TODO: we don't need to do this if the viewport is aready visible.
4577 * Add the AlignFrame to the desktop (it may be 'gathered' later), unless it
4578 * has a 'cdna/protein complement' view, in which case save it in order to
4579 * populate a SplitFrame once all views have been read in.
4581 String complementaryViewId = view.getComplementId();
4582 if (complementaryViewId == null)
4584 Desktop.addInternalFrame(af, view.getTitle(), view.getWidth(),
4586 // recompute any autoannotation
4587 af.alignPanel.updateAnnotation(false, true);
4588 reorderAutoannotation(af, al, autoAlan);
4589 af.alignPanel.alignmentChanged();
4593 splitFrameCandidates.put(view, af);
4598 private ColourSchemeI constructAnnotationColour(
4599 AnnotationColours viewAnnColour, AlignFrame af, AlignmentI al,
4600 JalviewModelSequence jms, boolean checkGroupAnnColour)
4602 boolean propagateAnnColour = false;
4603 ColourSchemeI cs = null;
4604 AlignmentI annAlignment = af != null ? af.viewport.getAlignment() : al;
4605 if (checkGroupAnnColour && al.getGroups() != null
4606 && al.getGroups().size() > 0)
4608 // pre 2.8.1 behaviour
4609 // check to see if we should transfer annotation colours
4610 propagateAnnColour = true;
4611 for (jalview.datamodel.SequenceGroup sg : al.getGroups())
4613 if (sg.cs instanceof AnnotationColourGradient)
4615 propagateAnnColour = false;
4619 // int find annotation
4620 if (annAlignment.getAlignmentAnnotation() != null)
4622 for (int i = 0; i < annAlignment.getAlignmentAnnotation().length; i++)
4624 if (annAlignment.getAlignmentAnnotation()[i].label
4625 .equals(viewAnnColour.getAnnotation()))
4627 if (annAlignment.getAlignmentAnnotation()[i].getThreshold() == null)
4629 annAlignment.getAlignmentAnnotation()[i]
4630 .setThreshold(new jalview.datamodel.GraphLine(
4631 viewAnnColour.getThreshold(), "Threshold",
4632 java.awt.Color.black)
4637 if (viewAnnColour.getColourScheme().equals("None"))
4639 cs = new AnnotationColourGradient(
4640 annAlignment.getAlignmentAnnotation()[i],
4641 new java.awt.Color(viewAnnColour.getMinColour()),
4642 new java.awt.Color(viewAnnColour.getMaxColour()),
4643 viewAnnColour.getAboveThreshold());
4645 else if (viewAnnColour.getColourScheme().startsWith("ucs"))
4647 cs = new AnnotationColourGradient(
4648 annAlignment.getAlignmentAnnotation()[i],
4649 getUserColourScheme(jms,
4650 viewAnnColour.getColourScheme()),
4651 viewAnnColour.getAboveThreshold());
4655 cs = new AnnotationColourGradient(
4656 annAlignment.getAlignmentAnnotation()[i],
4657 ColourSchemeProperty.getColour(al,
4658 viewAnnColour.getColourScheme()),
4659 viewAnnColour.getAboveThreshold());
4661 if (viewAnnColour.hasPerSequence())
4663 ((AnnotationColourGradient) cs).setSeqAssociated(viewAnnColour
4666 if (viewAnnColour.hasPredefinedColours())
4668 ((AnnotationColourGradient) cs)
4669 .setPredefinedColours(viewAnnColour
4670 .isPredefinedColours());
4672 if (propagateAnnColour && al.getGroups() != null)
4674 // Also use these settings for all the groups
4675 for (int g = 0; g < al.getGroups().size(); g++)
4677 jalview.datamodel.SequenceGroup sg = al.getGroups().get(g);
4685 * if (viewAnnColour.getColourScheme().equals("None" )) { sg.cs =
4686 * new AnnotationColourGradient(
4687 * annAlignment.getAlignmentAnnotation()[i], new
4688 * java.awt.Color(viewAnnColour. getMinColour()), new
4689 * java.awt.Color(viewAnnColour. getMaxColour()),
4690 * viewAnnColour.getAboveThreshold()); } else
4693 sg.cs = new AnnotationColourGradient(
4694 annAlignment.getAlignmentAnnotation()[i], sg.cs,
4695 viewAnnColour.getAboveThreshold());
4696 if (cs instanceof AnnotationColourGradient)
4698 if (viewAnnColour.hasPerSequence())
4700 ((AnnotationColourGradient) cs)
4701 .setSeqAssociated(viewAnnColour.isPerSequence());
4703 if (viewAnnColour.hasPredefinedColours())
4705 ((AnnotationColourGradient) cs)
4706 .setPredefinedColours(viewAnnColour
4707 .isPredefinedColours());
4723 private void reorderAutoannotation(AlignFrame af, AlignmentI al,
4724 List<JvAnnotRow> autoAlan)
4726 // copy over visualization settings for autocalculated annotation in the
4728 if (al.getAlignmentAnnotation() != null)
4731 * Kludge for magic autoannotation names (see JAL-811)
4733 String[] magicNames = new String[] { "Consensus", "Quality",
4735 JvAnnotRow nullAnnot = new JvAnnotRow(-1, null);
4736 Hashtable<String, JvAnnotRow> visan = new Hashtable<String, JvAnnotRow>();
4737 for (String nm : magicNames)
4739 visan.put(nm, nullAnnot);
4741 for (JvAnnotRow auan : autoAlan)
4743 visan.put(auan.template.label
4744 + (auan.template.getCalcId() == null ? "" : "\t"
4745 + auan.template.getCalcId()), auan);
4747 int hSize = al.getAlignmentAnnotation().length;
4748 List<JvAnnotRow> reorder = new ArrayList<JvAnnotRow>();
4749 // work through any autoCalculated annotation already on the view
4750 // removing it if it should be placed in a different location on the
4751 // annotation panel.
4752 List<String> remains = new ArrayList<String>(visan.keySet());
4753 for (int h = 0; h < hSize; h++)
4755 jalview.datamodel.AlignmentAnnotation jalan = al
4756 .getAlignmentAnnotation()[h];
4757 if (jalan.autoCalculated)
4760 JvAnnotRow valan = visan.get(k = jalan.label);
4761 if (jalan.getCalcId() != null)
4763 valan = visan.get(k = jalan.label + "\t" + jalan.getCalcId());
4768 // delete the auto calculated row from the alignment
4769 al.deleteAnnotation(jalan, false);
4773 if (valan != nullAnnot)
4775 if (jalan != valan.template)
4777 // newly created autoannotation row instance
4778 // so keep a reference to the visible annotation row
4779 // and copy over all relevant attributes
4780 if (valan.template.graphHeight >= 0)
4783 jalan.graphHeight = valan.template.graphHeight;
4785 jalan.visible = valan.template.visible;
4787 reorder.add(new JvAnnotRow(valan.order, jalan));
4792 // Add any (possibly stale) autocalculated rows that were not appended to
4793 // the view during construction
4794 for (String other : remains)
4796 JvAnnotRow othera = visan.get(other);
4797 if (othera != nullAnnot && othera.template.getCalcId() != null
4798 && othera.template.getCalcId().length() > 0)
4800 reorder.add(othera);
4803 // now put the automatic annotation in its correct place
4804 int s = 0, srt[] = new int[reorder.size()];
4805 JvAnnotRow[] rws = new JvAnnotRow[reorder.size()];
4806 for (JvAnnotRow jvar : reorder)
4809 srt[s++] = jvar.order;
4812 jalview.util.QuickSort.sort(srt, rws);
4813 // and re-insert the annotation at its correct position
4814 for (JvAnnotRow jvar : rws)
4816 al.addAnnotation(jvar.template, jvar.order);
4818 af.alignPanel.adjustAnnotationHeight();
4822 Hashtable skipList = null;
4825 * TODO remove this method
4828 * @return AlignFrame bound to sequenceSetId from view, if one exists. private
4829 * AlignFrame getSkippedFrame(Viewport view) { if (skipList==null) {
4830 * throw new Error("Implementation Error. No skipList defined for this
4831 * Jalview2XML instance."); } return (AlignFrame)
4832 * skipList.get(view.getSequenceSetId()); }
4836 * Check if the Jalview view contained in object should be skipped or not.
4839 * @return true if view's sequenceSetId is a key in skipList
4841 private boolean skipViewport(JalviewModel object)
4843 if (skipList == null)
4848 if (skipList.containsKey(id = object.getJalviewModelSequence()
4849 .getViewport()[0].getSequenceSetId()))
4851 if (Cache.log != null && Cache.log.isDebugEnabled())
4853 Cache.log.debug("Skipping seuqence set id " + id);
4860 public void addToSkipList(AlignFrame af)
4862 if (skipList == null)
4864 skipList = new Hashtable();
4866 skipList.put(af.getViewport().getSequenceSetId(), af);
4869 public void clearSkipList()
4871 if (skipList != null)
4878 private void recoverDatasetFor(SequenceSet vamsasSet, AlignmentI al,
4879 boolean ignoreUnrefed)
4881 jalview.datamodel.AlignmentI ds = getDatasetFor(vamsasSet
4883 Vector dseqs = null;
4886 // create a list of new dataset sequences
4887 dseqs = new Vector();
4889 for (int i = 0, iSize = vamsasSet.getSequenceCount(); i < iSize; i++)
4891 Sequence vamsasSeq = vamsasSet.getSequence(i);
4892 ensureJalviewDatasetSequence(vamsasSeq, ds, dseqs, ignoreUnrefed);
4894 // create a new dataset
4897 SequenceI[] dsseqs = new SequenceI[dseqs.size()];
4898 dseqs.copyInto(dsseqs);
4899 ds = new jalview.datamodel.Alignment(dsseqs);
4900 debug("Created new dataset " + vamsasSet.getDatasetId()
4901 + " for alignment " + System.identityHashCode(al));
4902 addDatasetRef(vamsasSet.getDatasetId(), ds);
4904 // set the dataset for the newly imported alignment.
4905 if (al.getDataset() == null && !ignoreUnrefed)
4914 * sequence definition to create/merge dataset sequence for
4918 * vector to add new dataset sequence to
4920 private void ensureJalviewDatasetSequence(Sequence vamsasSeq,
4921 AlignmentI ds, Vector dseqs, boolean ignoreUnrefed)
4923 // JBP TODO: Check this is called for AlCodonFrames to support recovery of
4925 SequenceI sq = seqRefIds.get(vamsasSeq.getId());
4926 SequenceI dsq = null;
4927 if (sq != null && sq.getDatasetSequence() != null)
4929 dsq = sq.getDatasetSequence();
4931 if (sq == null && ignoreUnrefed)
4935 String sqid = vamsasSeq.getDsseqid();
4938 // need to create or add a new dataset sequence reference to this sequence
4941 dsq = seqRefIds.get(sqid);
4946 // make a new dataset sequence
4947 dsq = sq.createDatasetSequence();
4950 // make up a new dataset reference for this sequence
4951 sqid = seqHash(dsq);
4953 dsq.setVamsasId(uniqueSetSuffix + sqid);
4954 seqRefIds.put(sqid, dsq);
4959 dseqs.addElement(dsq);
4964 ds.addSequence(dsq);
4970 { // make this dataset sequence sq's dataset sequence
4971 sq.setDatasetSequence(dsq);
4972 // and update the current dataset alignment
4977 if (!dseqs.contains(dsq))
4984 if (ds.findIndex(dsq) < 0)
4986 ds.addSequence(dsq);
4993 // TODO: refactor this as a merge dataset sequence function
4994 // now check that sq (the dataset sequence) sequence really is the union of
4995 // all references to it
4996 // boolean pre = sq.getStart() < dsq.getStart();
4997 // boolean post = sq.getEnd() > dsq.getEnd();
5001 // StringBuffer sb = new StringBuffer();
5002 String newres = jalview.analysis.AlignSeq.extractGaps(
5003 jalview.util.Comparison.GapChars, sq.getSequenceAsString());
5004 if (!newres.equalsIgnoreCase(dsq.getSequenceAsString())
5005 && newres.length() > dsq.getLength())
5007 // Update with the longer sequence.
5011 * if (pre) { sb.insert(0, newres .substring(0, dsq.getStart() -
5012 * sq.getStart())); dsq.setStart(sq.getStart()); } if (post) {
5013 * sb.append(newres.substring(newres.length() - sq.getEnd() -
5014 * dsq.getEnd())); dsq.setEnd(sq.getEnd()); }
5016 dsq.setSequence(newres);
5018 // TODO: merges will never happen if we 'know' we have the real dataset
5019 // sequence - this should be detected when id==dssid
5021 .println("DEBUG Notice: Merged dataset sequence (if you see this often, post at http://issues.jalview.org/browse/JAL-1474)"); // ("
5022 // + (pre ? "prepended" : "") + " "
5023 // + (post ? "appended" : ""));
5029 * TODO use AlignmentI here and in related methods - needs
5030 * AlignmentI.getDataset() changed to return AlignmentI instead of Alignment
5032 Hashtable<String, AlignmentI> datasetIds = null;
5034 IdentityHashMap<AlignmentI, String> dataset2Ids = null;
5036 private AlignmentI getDatasetFor(String datasetId)
5038 if (datasetIds == null)
5040 datasetIds = new Hashtable<String, AlignmentI>();
5043 if (datasetIds.containsKey(datasetId))
5045 return datasetIds.get(datasetId);
5050 private void addDatasetRef(String datasetId, AlignmentI dataset)
5052 if (datasetIds == null)
5054 datasetIds = new Hashtable<String, AlignmentI>();
5056 datasetIds.put(datasetId, dataset);
5060 * make a new dataset ID for this jalview dataset alignment
5065 private String getDatasetIdRef(AlignmentI dataset)
5067 if (dataset.getDataset() != null)
5069 warn("Serious issue! Dataset Object passed to getDatasetIdRef is not a Jalview DATASET alignment...");
5071 String datasetId = makeHashCode(dataset, null);
5072 if (datasetId == null)
5074 // make a new datasetId and record it
5075 if (dataset2Ids == null)
5077 dataset2Ids = new IdentityHashMap<AlignmentI, String>();
5081 datasetId = dataset2Ids.get(dataset);
5083 if (datasetId == null)
5085 datasetId = "ds" + dataset2Ids.size() + 1;
5086 dataset2Ids.put(dataset, datasetId);
5092 private void addDBRefs(SequenceI datasetSequence, Sequence sequence)
5094 for (int d = 0; d < sequence.getDBRefCount(); d++)
5096 DBRef dr = sequence.getDBRef(d);
5097 jalview.datamodel.DBRefEntry entry = new jalview.datamodel.DBRefEntry(
5098 sequence.getDBRef(d).getSource(), sequence.getDBRef(d)
5099 .getVersion(), sequence.getDBRef(d).getAccessionId());
5100 if (dr.getMapping() != null)
5102 entry.setMap(addMapping(dr.getMapping()));
5104 datasetSequence.addDBRef(entry);
5108 private jalview.datamodel.Mapping addMapping(Mapping m)
5110 SequenceI dsto = null;
5111 // Mapping m = dr.getMapping();
5112 int fr[] = new int[m.getMapListFromCount() * 2];
5113 Enumeration f = m.enumerateMapListFrom();
5114 for (int _i = 0; f.hasMoreElements(); _i += 2)
5116 MapListFrom mf = (MapListFrom) f.nextElement();
5117 fr[_i] = mf.getStart();
5118 fr[_i + 1] = mf.getEnd();
5120 int fto[] = new int[m.getMapListToCount() * 2];
5121 f = m.enumerateMapListTo();
5122 for (int _i = 0; f.hasMoreElements(); _i += 2)
5124 MapListTo mf = (MapListTo) f.nextElement();
5125 fto[_i] = mf.getStart();
5126 fto[_i + 1] = mf.getEnd();
5128 jalview.datamodel.Mapping jmap = new jalview.datamodel.Mapping(dsto,
5129 fr, fto, (int) m.getMapFromUnit(), (int) m.getMapToUnit());
5130 if (m.getMappingChoice() != null)
5132 MappingChoice mc = m.getMappingChoice();
5133 if (mc.getDseqFor() != null)
5135 String dsfor = "" + mc.getDseqFor();
5136 if (seqRefIds.containsKey(dsfor))
5141 jmap.setTo(seqRefIds.get(dsfor));
5145 frefedSequence.add(newMappingRef(dsfor, jmap));
5151 * local sequence definition
5153 Sequence ms = mc.getSequence();
5154 SequenceI djs = null;
5155 String sqid = ms.getDsseqid();
5156 if (sqid != null && sqid.length() > 0)
5159 * recover dataset sequence
5161 djs = seqRefIds.get(sqid);
5166 .println("Warning - making up dataset sequence id for DbRef sequence map reference");
5167 sqid = ((Object) ms).toString(); // make up a new hascode for
5168 // undefined dataset sequence hash
5169 // (unlikely to happen)
5175 * make a new dataset sequence and add it to refIds hash
5177 djs = new jalview.datamodel.Sequence(ms.getName(),
5179 djs.setStart(jmap.getMap().getToLowest());
5180 djs.setEnd(jmap.getMap().getToHighest());
5181 djs.setVamsasId(uniqueSetSuffix + sqid);
5183 incompleteSeqs.put(sqid, djs);
5184 seqRefIds.put(sqid, djs);
5187 jalview.bin.Cache.log.debug("about to recurse on addDBRefs.");
5196 public jalview.gui.AlignmentPanel copyAlignPanel(AlignmentPanel ap,
5197 boolean keepSeqRefs)
5200 JalviewModel jm = saveState(ap, null, null, null);
5205 jm.getJalviewModelSequence().getViewport(0).setSequenceSetId(null);
5209 uniqueSetSuffix = "";
5210 jm.getJalviewModelSequence().getViewport(0).setId(null); // we don't
5215 if (this.frefedSequence == null)
5217 frefedSequence = new Vector();
5220 viewportsAdded.clear();
5222 AlignFrame af = loadFromObject(jm, null, false, null);
5223 af.alignPanels.clear();
5224 af.closeMenuItem_actionPerformed(true);
5227 * if(ap.av.getAlignment().getAlignmentAnnotation()!=null) { for(int i=0;
5228 * i<ap.av.getAlignment().getAlignmentAnnotation().length; i++) {
5229 * if(!ap.av.getAlignment().getAlignmentAnnotation()[i].autoCalculated) {
5230 * af.alignPanel.av.getAlignment().getAlignmentAnnotation()[i] =
5231 * ap.av.getAlignment().getAlignmentAnnotation()[i]; } } }
5234 return af.alignPanel;
5238 * flag indicating if hashtables should be cleared on finalization TODO this
5239 * flag may not be necessary
5241 private final boolean _cleartables = true;
5243 private Hashtable jvids2vobj;
5248 * @see java.lang.Object#finalize()
5251 protected void finalize() throws Throwable
5253 // really make sure we have no buried refs left.
5258 this.seqRefIds = null;
5259 this.seqsToIds = null;
5263 private void warn(String msg)
5268 private void warn(String msg, Exception e)
5270 if (Cache.log != null)
5274 Cache.log.warn(msg, e);
5278 Cache.log.warn(msg);
5283 System.err.println("Warning: " + msg);
5286 e.printStackTrace();
5291 private void debug(String string)
5293 debug(string, null);
5296 private void debug(String msg, Exception e)
5298 if (Cache.log != null)
5302 Cache.log.debug(msg, e);
5306 Cache.log.debug(msg);
5311 System.err.println("Warning: " + msg);
5314 e.printStackTrace();
5320 * set the object to ID mapping tables used to write/recover objects and XML
5321 * ID strings for the jalview project. If external tables are provided then
5322 * finalize and clearSeqRefs will not clear the tables when the Jalview2XML
5323 * object goes out of scope. - also populates the datasetIds hashtable with
5324 * alignment objects containing dataset sequences
5327 * Map from ID strings to jalview datamodel
5329 * Map from jalview datamodel to ID strings
5333 public void setObjectMappingTables(Hashtable vobj2jv,
5334 IdentityHashMap jv2vobj)
5336 this.jv2vobj = jv2vobj;
5337 this.vobj2jv = vobj2jv;
5338 Iterator ds = jv2vobj.keySet().iterator();
5340 while (ds.hasNext())
5342 Object jvobj = ds.next();
5343 id = jv2vobj.get(jvobj).toString();
5344 if (jvobj instanceof jalview.datamodel.Alignment)
5346 if (((jalview.datamodel.Alignment) jvobj).getDataset() == null)
5348 addDatasetRef(id, (jalview.datamodel.Alignment) jvobj);
5351 else if (jvobj instanceof jalview.datamodel.Sequence)
5353 // register sequence object so the XML parser can recover it.
5354 if (seqRefIds == null)
5356 seqRefIds = new HashMap<String, SequenceI>();
5358 if (seqsToIds == null)
5360 seqsToIds = new IdentityHashMap<SequenceI, String>();
5362 seqRefIds.put(jv2vobj.get(jvobj).toString(), (SequenceI) jvobj);
5363 seqsToIds.put((SequenceI) jvobj, id);
5365 else if (jvobj instanceof jalview.datamodel.AlignmentAnnotation)
5368 AlignmentAnnotation jvann = (AlignmentAnnotation) jvobj;
5369 annotationIds.put(anid = jv2vobj.get(jvobj).toString(), jvann);
5370 if (jvann.annotationId == null)
5372 jvann.annotationId = anid;
5374 if (!jvann.annotationId.equals(anid))
5376 // TODO verify that this is the correct behaviour
5377 this.warn("Overriding Annotation ID for " + anid
5378 + " from different id : " + jvann.annotationId);
5379 jvann.annotationId = anid;
5382 else if (jvobj instanceof String)
5384 if (jvids2vobj == null)
5386 jvids2vobj = new Hashtable();
5387 jvids2vobj.put(jvobj, jv2vobj.get(jvobj).toString());
5392 Cache.log.debug("Ignoring " + jvobj.getClass() + " (ID = " + id);
5398 * set the uniqueSetSuffix used to prefix/suffix object IDs for jalview
5399 * objects created from the project archive. If string is null (default for
5400 * construction) then suffix will be set automatically.
5404 public void setUniqueSetSuffix(String string)
5406 uniqueSetSuffix = string;
5411 * uses skipList2 as the skipList for skipping views on sequence sets
5412 * associated with keys in the skipList
5416 public void setSkipList(Hashtable skipList2)
5418 skipList = skipList2;
5422 * Reads the jar entry of given name and returns its contents, or null if the
5423 * entry is not found.
5426 * @param jarEntryName
5429 protected String readJarEntry(jarInputStreamProvider jprovider,
5430 String jarEntryName)
5432 String result = null;
5433 BufferedReader in = null;
5438 * Reopen the jar input stream and traverse its entries to find a matching
5441 JarInputStream jin = jprovider.getJarInputStream();
5442 JarEntry entry = null;
5445 entry = jin.getNextJarEntry();
5446 } while (entry != null && !entry.getName().equals(jarEntryName));
5450 StringBuilder out = new StringBuilder(256);
5451 in = new BufferedReader(new InputStreamReader(jin, UTF_8));
5454 while ((data = in.readLine()) != null)
5458 result = out.toString();
5462 warn("Couldn't find entry in Jalview Jar for " + jarEntryName);
5464 } catch (Exception ex)
5466 ex.printStackTrace();
5474 } catch (IOException e)
5485 * Returns an incrementing counter (0, 1, 2...)
5489 private synchronized int nextCounter()