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 Map<String, AlignFrame> gatherToThisFrame = new HashMap<String, AlignFrame>();
2353 final String file = jprovider.getFilename();
2356 JarInputStream jin = null;
2357 JarEntry jarentry = null;
2362 jin = jprovider.getJarInputStream();
2363 for (int i = 0; i < entryCount; i++)
2365 jarentry = jin.getNextJarEntry();
2368 if (jarentry != null && jarentry.getName().endsWith(".xml"))
2370 InputStreamReader in = new InputStreamReader(jin, UTF_8);
2371 JalviewModel object = new JalviewModel();
2373 Unmarshaller unmar = new Unmarshaller(object);
2374 unmar.setValidation(false);
2375 object = (JalviewModel) unmar.unmarshal(in);
2376 if (true) // !skipViewport(object))
2378 _af = loadFromObject(object, file, true, jprovider);
2379 if (object.getJalviewModelSequence().getViewportCount() > 0)
2382 if (af.viewport.isGatherViewsHere())
2384 gatherToThisFrame.put(af.viewport.getSequenceSetId(), af);
2390 else if (jarentry != null)
2392 // Some other file here.
2395 } while (jarentry != null);
2396 resolveFrefedSequences();
2397 } catch (IOException ex)
2399 ex.printStackTrace();
2400 errorMessage = "Couldn't locate Jalview XML file : " + file;
2401 System.err.println("Exception whilst loading jalview XML file : "
2403 } catch (Exception ex)
2405 System.err.println("Parsing as Jalview Version 2 file failed.");
2406 ex.printStackTrace(System.err);
2407 if (attemptversion1parse)
2409 // Is Version 1 Jar file?
2412 af = new Jalview2XML_V1(raiseGUI).LoadJalviewAlign(jprovider);
2413 } catch (Exception ex2)
2415 System.err.println("Exception whilst loading as jalviewXMLV1:");
2416 ex2.printStackTrace();
2420 if (Desktop.instance != null)
2422 Desktop.instance.stopLoading();
2426 System.out.println("Successfully loaded archive file");
2429 ex.printStackTrace();
2431 System.err.println("Exception whilst loading jalview XML file : "
2433 } catch (OutOfMemoryError e)
2435 // Don't use the OOM Window here
2436 errorMessage = "Out of memory loading jalview XML file";
2437 System.err.println("Out of memory whilst loading jalview XML file");
2438 e.printStackTrace();
2441 if (Desktop.instance != null)
2443 Desktop.instance.stopLoading();
2447 * Regather multiple views (with the same sequence set id) to the frame (if
2448 * any) that is flagged as the one to gather to, i.e. convert them to tabbed
2449 * views instead of separate frames. Note this doesn't restore a state where
2450 * some expanded views in turn have tabbed views - the last "first tab" read
2451 * in will play the role of gatherer for all.
2453 for (AlignFrame fr : gatherToThisFrame.values())
2455 Desktop.instance.gatherViews(fr);
2458 restoreSplitFrames();
2460 if (errorMessage != null)
2468 * Try to reconstruct and display SplitFrame windows, where each contains
2469 * complementary dna and protein alignments. Done by pairing up AlignFrame
2470 * objects (created earlier) which have complementary viewport ids associated.
2472 protected void restoreSplitFrames()
2474 List<SplitFrame> gatherTo = new ArrayList<SplitFrame>();
2475 List<AlignFrame> addedToSplitFrames = new ArrayList<AlignFrame>();
2476 Map<String, AlignFrame> dna = new HashMap<String, AlignFrame>();
2479 * Identify the DNA alignments
2481 for (Entry<Viewport, AlignFrame> candidate : splitFrameCandidates
2484 AlignFrame af = candidate.getValue();
2485 if (af.getViewport().getAlignment().isNucleotide())
2487 dna.put(candidate.getKey().getId(), af);
2492 * Try to match up the protein complements
2494 for (Entry<Viewport, AlignFrame> candidate : splitFrameCandidates
2497 AlignFrame af = candidate.getValue();
2498 if (!af.getViewport().getAlignment().isNucleotide())
2500 String complementId = candidate.getKey().getComplementId();
2501 // only non-null complements should be in the Map
2502 if (complementId != null && dna.containsKey(complementId))
2504 final AlignFrame dnaFrame = dna.get(complementId);
2505 SplitFrame sf = createSplitFrame(dnaFrame, af);
2506 addedToSplitFrames.add(dnaFrame);
2507 addedToSplitFrames.add(af);
2508 if (af.viewport.isGatherViewsHere())
2517 * Open any that we failed to pair up (which shouldn't happen!) as
2518 * standalone AlignFrame's.
2520 for (Entry<Viewport, AlignFrame> candidate : splitFrameCandidates
2523 AlignFrame af = candidate.getValue();
2524 if (!addedToSplitFrames.contains(af))
2526 Viewport view = candidate.getKey();
2527 Desktop.addInternalFrame(af, view.getTitle(), view.getWidth(),
2529 System.err.println("Failed to restore view " + view.getTitle()
2530 + " to split frame");
2535 * Gather back into tabbed views as flagged.
2537 for (SplitFrame sf : gatherTo)
2539 Desktop.instance.gatherViews(sf);
2542 splitFrameCandidates.clear();
2546 * Construct and display one SplitFrame holding DNA and protein alignments.
2549 * @param proteinFrame
2552 protected SplitFrame createSplitFrame(AlignFrame dnaFrame,
2553 AlignFrame proteinFrame)
2555 SplitFrame splitFrame = new SplitFrame(dnaFrame, proteinFrame);
2556 String title = MessageManager.getString("label.linked_view_title");
2557 int width = (int) dnaFrame.getBounds().getWidth();
2558 int height = (int) (dnaFrame.getBounds().getHeight()
2559 + proteinFrame.getBounds().getHeight() + 50);
2562 * SplitFrame location is saved to both enclosed frames
2564 splitFrame.setLocation(dnaFrame.getX(), dnaFrame.getY());
2565 Desktop.addInternalFrame(splitFrame, title, width, height);
2568 * And compute cDNA consensus (couldn't do earlier with consensus as
2569 * mappings were not yet present)
2571 proteinFrame.viewport.alignmentChanged(proteinFrame.alignPanel);
2577 * check errorMessage for a valid error message and raise an error box in the
2578 * GUI or write the current errorMessage to stderr and then clear the error
2581 protected void reportErrors()
2583 reportErrors(false);
2586 protected void reportErrors(final boolean saving)
2588 if (errorMessage != null)
2590 final String finalErrorMessage = errorMessage;
2593 javax.swing.SwingUtilities.invokeLater(new Runnable()
2598 JOptionPane.showInternalMessageDialog(Desktop.desktop,
2599 finalErrorMessage, "Error "
2600 + (saving ? "saving" : "loading")
2601 + " Jalview file", JOptionPane.WARNING_MESSAGE);
2607 System.err.println("Problem loading Jalview file: " + errorMessage);
2610 errorMessage = null;
2613 Map<String, String> alreadyLoadedPDB = new HashMap<String, String>();
2616 * when set, local views will be updated from view stored in JalviewXML
2617 * Currently (28th Sep 2008) things will go horribly wrong in vamsas document
2618 * sync if this is set to true.
2620 private final boolean updateLocalViews = false;
2623 * Returns the path to a temporary file holding the PDB file for the given PDB
2624 * id. The first time of asking, searches for a file of that name in the
2625 * Jalview project jar, and copies it to a new temporary file. Any repeat
2626 * requests just return the path to the file previously created.
2632 String loadPDBFile(jarInputStreamProvider jprovider, String pdbId)
2634 if (alreadyLoadedPDB.containsKey(pdbId))
2636 return alreadyLoadedPDB.get(pdbId).toString();
2639 String tempFile = copyJarEntry(jprovider, pdbId, "jalview_pdb");
2640 if (tempFile != null)
2642 alreadyLoadedPDB.put(pdbId, tempFile);
2648 * Copies the jar entry of given name to a new temporary file and returns the
2649 * path to the file, or null if the entry is not found.
2652 * @param jarEntryName
2654 * a prefix for the temporary file name, must be at least three
2658 protected String copyJarEntry(jarInputStreamProvider jprovider,
2659 String jarEntryName, String prefix)
2661 BufferedReader in = null;
2662 PrintWriter out = null;
2666 JarInputStream jin = jprovider.getJarInputStream();
2668 * if (jprovider.startsWith("http://")) { jin = new JarInputStream(new
2669 * URL(jprovider).openStream()); } else { jin = new JarInputStream(new
2670 * FileInputStream(jprovider)); }
2673 JarEntry entry = null;
2676 entry = jin.getNextJarEntry();
2677 } while (entry != null && !entry.getName().equals(jarEntryName));
2680 in = new BufferedReader(new InputStreamReader(jin, UTF_8));
2681 File outFile = File.createTempFile(prefix, ".tmp");
2682 outFile.deleteOnExit();
2683 out = new PrintWriter(new FileOutputStream(outFile));
2686 while ((data = in.readLine()) != null)
2691 String t = outFile.getAbsolutePath();
2696 warn("Couldn't find entry in Jalview Jar for " + jarEntryName);
2698 } catch (Exception ex)
2700 ex.printStackTrace();
2708 } catch (IOException e)
2722 private class JvAnnotRow
2724 public JvAnnotRow(int i, AlignmentAnnotation jaa)
2731 * persisted version of annotation row from which to take vis properties
2733 public jalview.datamodel.AlignmentAnnotation template;
2736 * original position of the annotation row in the alignment
2742 * Load alignment frame from jalview XML DOM object
2747 * filename source string
2748 * @param loadTreesAndStructures
2749 * when false only create Viewport
2751 * data source provider
2752 * @return alignment frame created from view stored in DOM
2754 AlignFrame loadFromObject(JalviewModel object, String file,
2755 boolean loadTreesAndStructures, jarInputStreamProvider jprovider)
2757 SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);
2758 Sequence[] vamsasSeq = vamsasSet.getSequence();
2760 JalviewModelSequence jms = object.getJalviewModelSequence();
2762 Viewport view = (jms.getViewportCount() > 0) ? jms.getViewport(0)
2765 // ////////////////////////////////
2768 List<SequenceI> hiddenSeqs = null;
2771 List<SequenceI> tmpseqs = new ArrayList<SequenceI>();
2773 boolean multipleView = false;
2774 SequenceI referenceseqForView = null;
2775 JSeq[] jseqs = object.getJalviewModelSequence().getJSeq();
2776 int vi = 0; // counter in vamsasSeq array
2777 for (int i = 0; i < jseqs.length; i++)
2779 String seqId = jseqs[i].getId();
2781 SequenceI tmpSeq = seqRefIds.get(seqId);
2784 if (!incompleteSeqs.containsKey(seqId))
2786 // may not need this check, but keep it for at least 2.9,1 release
2787 if (tmpSeq.getStart()!=jseqs[i].getStart() || tmpSeq.getEnd()!=jseqs[i].getEnd())
2790 .println("Warning JAL-2154 regression: updating start/end for sequence "
2791 + tmpSeq.toString());
2794 incompleteSeqs.remove(seqId);
2796 tmpSeq.setStart(jseqs[i].getStart());
2797 tmpSeq.setEnd(jseqs[i].getEnd());
2798 tmpseqs.add(tmpSeq);
2799 multipleView = true;
2803 tmpSeq = new jalview.datamodel.Sequence(vamsasSeq[vi].getName(),
2804 vamsasSeq[vi].getSequence());
2805 tmpSeq.setDescription(vamsasSeq[vi].getDescription());
2806 tmpSeq.setStart(jseqs[i].getStart());
2807 tmpSeq.setEnd(jseqs[i].getEnd());
2808 tmpSeq.setVamsasId(uniqueSetSuffix + seqId);
2809 seqRefIds.put(vamsasSeq[vi].getId(), tmpSeq);
2810 tmpseqs.add(tmpSeq);
2814 if (jseqs[i].hasViewreference() && jseqs[i].getViewreference())
2816 referenceseqForView = tmpseqs.get(tmpseqs.size() - 1);
2819 if (jseqs[i].getHidden())
2821 if (hiddenSeqs == null)
2823 hiddenSeqs = new ArrayList<SequenceI>();
2826 hiddenSeqs.add(tmpSeq);
2831 // Create the alignment object from the sequence set
2832 // ///////////////////////////////
2833 SequenceI[] orderedSeqs = tmpseqs
2834 .toArray(new SequenceI[tmpseqs.size()]);
2836 AlignmentI al = null;
2837 // so we must create or recover the dataset alignment before going further
2838 // ///////////////////////////////
2839 if (vamsasSet.getDatasetId() == null || vamsasSet.getDatasetId() == "")
2841 // older jalview projects do not have a dataset - so creat alignment and
2843 al = new Alignment(orderedSeqs);
2844 al.setDataset(null);
2848 boolean isdsal = object.getJalviewModelSequence().getViewportCount() == 0;
2851 // we are importing a dataset record, so
2852 // recover reference to an alignment already materialsed as dataset
2853 al = getDatasetFor(vamsasSet.getDatasetId());
2857 // materialse the alignment
2858 al = new Alignment(orderedSeqs);
2862 addDatasetRef(vamsasSet.getDatasetId(), al);
2865 // finally, verify all data in vamsasSet is actually present in al
2866 // passing on flag indicating if it is actually a stored dataset
2867 recoverDatasetFor(vamsasSet, al, isdsal);
2870 if (referenceseqForView != null)
2872 al.setSeqrep(referenceseqForView);
2874 // / Add the alignment properties
2875 for (int i = 0; i < vamsasSet.getSequenceSetPropertiesCount(); i++)
2877 SequenceSetProperties ssp = vamsasSet.getSequenceSetProperties(i);
2878 al.setProperty(ssp.getKey(), ssp.getValue());
2881 // ///////////////////////////////
2883 Hashtable pdbloaded = new Hashtable(); // TODO nothing writes to this??
2886 // load sequence features, database references and any associated PDB
2887 // structures for the alignment
2888 for (int i = 0; i < vamsasSeq.length; i++)
2890 if (jseqs[i].getFeaturesCount() > 0)
2892 Features[] features = jseqs[i].getFeatures();
2893 for (int f = 0; f < features.length; f++)
2895 jalview.datamodel.SequenceFeature sf = new jalview.datamodel.SequenceFeature(
2896 features[f].getType(), features[f].getDescription(),
2897 features[f].getStatus(), features[f].getBegin(),
2898 features[f].getEnd(), features[f].getFeatureGroup());
2900 sf.setScore(features[f].getScore());
2901 for (int od = 0; od < features[f].getOtherDataCount(); od++)
2903 OtherData keyValue = features[f].getOtherData(od);
2904 if (keyValue.getKey().startsWith("LINK"))
2906 sf.addLink(keyValue.getValue());
2910 sf.setValue(keyValue.getKey(), keyValue.getValue());
2915 al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf);
2918 if (vamsasSeq[i].getDBRefCount() > 0)
2920 addDBRefs(al.getSequenceAt(i).getDatasetSequence(), vamsasSeq[i]);
2922 if (jseqs[i].getPdbidsCount() > 0)
2924 Pdbids[] ids = jseqs[i].getPdbids();
2925 for (int p = 0; p < ids.length; p++)
2927 jalview.datamodel.PDBEntry entry = new jalview.datamodel.PDBEntry();
2928 entry.setId(ids[p].getId());
2929 if (ids[p].getType() != null)
2931 if (ids[p].getType().equalsIgnoreCase("PDB"))
2933 entry.setType(PDBEntry.Type.PDB);
2937 entry.setType(PDBEntry.Type.FILE);
2940 if (ids[p].getFile() != null)
2942 if (!pdbloaded.containsKey(ids[p].getFile()))
2944 entry.setFile(loadPDBFile(jprovider, ids[p].getId()));
2948 entry.setFile(pdbloaded.get(ids[p].getId()).toString());
2951 StructureSelectionManager.getStructureSelectionManager(
2952 Desktop.instance).registerPDBEntry(entry);
2953 al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
2957 } // end !multipleview
2959 // ///////////////////////////////
2960 // LOAD SEQUENCE MAPPINGS
2962 if (vamsasSet.getAlcodonFrameCount() > 0)
2964 // TODO Potentially this should only be done once for all views of an
2966 AlcodonFrame[] alc = vamsasSet.getAlcodonFrame();
2967 for (int i = 0; i < alc.length; i++)
2969 AlignedCodonFrame cf = new AlignedCodonFrame();
2970 if (alc[i].getAlcodMapCount() > 0)
2972 AlcodMap[] maps = alc[i].getAlcodMap();
2973 for (int m = 0; m < maps.length; m++)
2975 SequenceI dnaseq = seqRefIds.get(maps[m].getDnasq());
2977 jalview.datamodel.Mapping mapping = null;
2978 // attach to dna sequence reference.
2979 if (maps[m].getMapping() != null)
2981 mapping = addMapping(maps[m].getMapping());
2983 if (dnaseq != null && mapping.getTo() != null)
2985 cf.addMap(dnaseq, mapping.getTo(), mapping.getMap());
2990 frefedSequence.add(newAlcodMapRef(maps[m].getDnasq(), cf,
2994 al.addCodonFrame(cf);
2999 // ////////////////////////////////
3001 List<JvAnnotRow> autoAlan = new ArrayList<JvAnnotRow>();
3004 * store any annotations which forward reference a group's ID
3006 Map<String, List<AlignmentAnnotation>> groupAnnotRefs = new Hashtable<String, List<AlignmentAnnotation>>();
3008 if (vamsasSet.getAnnotationCount() > 0)
3010 Annotation[] an = vamsasSet.getAnnotation();
3012 for (int i = 0; i < an.length; i++)
3014 Annotation annotation = an[i];
3017 * test if annotation is automatically calculated for this view only
3019 boolean autoForView = false;
3020 if (annotation.getLabel().equals("Quality")
3021 || annotation.getLabel().equals("Conservation")
3022 || annotation.getLabel().equals("Consensus"))
3024 // Kludge for pre 2.5 projects which lacked the autocalculated flag
3026 if (!annotation.hasAutoCalculated())
3028 annotation.setAutoCalculated(true);
3032 || (annotation.hasAutoCalculated() && annotation
3033 .isAutoCalculated()))
3035 // remove ID - we don't recover annotation from other views for
3036 // view-specific annotation
3037 annotation.setId(null);
3040 // set visiblity for other annotation in this view
3041 String annotationId = annotation.getId();
3042 if (annotationId != null && annotationIds.containsKey(annotationId))
3044 AlignmentAnnotation jda = annotationIds.get(annotationId);
3045 // in principle Visible should always be true for annotation displayed
3046 // in multiple views
3047 if (annotation.hasVisible())
3049 jda.visible = annotation.getVisible();
3052 al.addAnnotation(jda);
3056 // Construct new annotation from model.
3057 AnnotationElement[] ae = annotation.getAnnotationElement();
3058 jalview.datamodel.Annotation[] anot = null;
3059 java.awt.Color firstColour = null;
3061 if (!annotation.getScoreOnly())
3063 anot = new jalview.datamodel.Annotation[al.getWidth()];
3064 for (int aa = 0; aa < ae.length && aa < anot.length; aa++)
3066 anpos = ae[aa].getPosition();
3068 if (anpos >= anot.length)
3073 anot[anpos] = new jalview.datamodel.Annotation(
3075 ae[aa].getDisplayCharacter(), ae[aa].getDescription(),
3076 (ae[aa].getSecondaryStructure() == null || ae[aa]
3077 .getSecondaryStructure().length() == 0) ? ' '
3078 : ae[aa].getSecondaryStructure().charAt(0),
3082 // JBPNote: Consider verifying dataflow for IO of secondary
3083 // structure annotation read from Stockholm files
3084 // this was added to try to ensure that
3085 // if (anot[ae[aa].getPosition()].secondaryStructure>' ')
3087 // anot[ae[aa].getPosition()].displayCharacter = "";
3089 anot[anpos].colour = new java.awt.Color(ae[aa].getColour());
3090 if (firstColour == null)
3092 firstColour = anot[anpos].colour;
3096 jalview.datamodel.AlignmentAnnotation jaa = null;
3098 if (annotation.getGraph())
3100 float llim = 0, hlim = 0;
3101 // if (autoForView || an[i].isAutoCalculated()) {
3104 jaa = new jalview.datamodel.AlignmentAnnotation(
3105 annotation.getLabel(), annotation.getDescription(), anot,
3106 llim, hlim, annotation.getGraphType());
3108 jaa.graphGroup = annotation.getGraphGroup();
3109 jaa._linecolour = firstColour;
3110 if (annotation.getThresholdLine() != null)
3112 jaa.setThreshold(new jalview.datamodel.GraphLine(annotation
3113 .getThresholdLine().getValue(), annotation
3114 .getThresholdLine().getLabel(), new java.awt.Color(
3115 annotation.getThresholdLine().getColour())));
3118 if (autoForView || annotation.isAutoCalculated())
3120 // Hardwire the symbol display line to ensure that labels for
3121 // histograms are displayed
3127 jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
3128 an[i].getDescription(), anot);
3129 jaa._linecolour = firstColour;
3131 // register new annotation
3132 if (an[i].getId() != null)
3134 annotationIds.put(an[i].getId(), jaa);
3135 jaa.annotationId = an[i].getId();
3137 // recover sequence association
3138 String sequenceRef = an[i].getSequenceRef();
3139 if (sequenceRef != null)
3141 // from 2.9 sequenceRef is to sequence id (JAL-1781)
3142 SequenceI sequence = seqRefIds.get(sequenceRef);
3143 if (sequence == null)
3145 // in pre-2.9 projects sequence ref is to sequence name
3146 sequence = al.findName(sequenceRef);
3148 if (sequence != null)
3150 jaa.createSequenceMapping(sequence, 1, true);
3151 sequence.addAlignmentAnnotation(jaa);
3154 // and make a note of any group association
3155 if (an[i].getGroupRef() != null && an[i].getGroupRef().length() > 0)
3157 List<jalview.datamodel.AlignmentAnnotation> aal = groupAnnotRefs
3158 .get(an[i].getGroupRef());
3161 aal = new ArrayList<jalview.datamodel.AlignmentAnnotation>();
3162 groupAnnotRefs.put(an[i].getGroupRef(), aal);
3167 if (an[i].hasScore())
3169 jaa.setScore(an[i].getScore());
3171 if (an[i].hasVisible())
3173 jaa.visible = an[i].getVisible();
3176 if (an[i].hasCentreColLabels())
3178 jaa.centreColLabels = an[i].getCentreColLabels();
3181 if (an[i].hasScaleColLabels())
3183 jaa.scaleColLabel = an[i].getScaleColLabels();
3185 if (an[i].hasAutoCalculated() && an[i].isAutoCalculated())
3187 // newer files have an 'autoCalculated' flag and store calculation
3188 // state in viewport properties
3189 jaa.autoCalculated = true; // means annotation will be marked for
3190 // update at end of load.
3192 if (an[i].hasGraphHeight())
3194 jaa.graphHeight = an[i].getGraphHeight();
3196 if (an[i].hasBelowAlignment())
3198 jaa.belowAlignment = an[i].isBelowAlignment();
3200 jaa.setCalcId(an[i].getCalcId());
3201 if (an[i].getPropertyCount() > 0)
3203 for (jalview.schemabinding.version2.Property prop : an[i]
3206 jaa.setProperty(prop.getName(), prop.getValue());
3209 if (jaa.autoCalculated)
3211 autoAlan.add(new JvAnnotRow(i, jaa));
3214 // if (!autoForView)
3216 // add autocalculated group annotation and any user created annotation
3218 al.addAnnotation(jaa);
3222 // ///////////////////////
3224 // Create alignment markup and styles for this view
3225 if (jms.getJGroupCount() > 0)
3227 JGroup[] groups = jms.getJGroup();
3228 boolean addAnnotSchemeGroup = false;
3229 for (int i = 0; i < groups.length; i++)
3231 JGroup jGroup = groups[i];
3232 ColourSchemeI cs = null;
3233 if (jGroup.getColour() != null)
3235 if (jGroup.getColour().startsWith("ucs"))
3237 cs = getUserColourScheme(jms, jGroup.getColour());
3239 else if (jGroup.getColour().equals("AnnotationColourGradient")
3240 && jGroup.getAnnotationColours() != null)
3242 addAnnotSchemeGroup = true;
3247 cs = ColourSchemeProperty.getColour(al, jGroup.getColour());
3252 cs.setThreshold(jGroup.getPidThreshold(), true);
3256 Vector<SequenceI> seqs = new Vector<SequenceI>();
3258 for (int s = 0; s < jGroup.getSeqCount(); s++)
3260 String seqId = jGroup.getSeq(s) + "";
3261 SequenceI ts = seqRefIds.get(seqId);
3265 seqs.addElement(ts);
3269 if (seqs.size() < 1)
3274 SequenceGroup sg = new SequenceGroup(seqs, jGroup.getName(), cs,
3275 jGroup.getDisplayBoxes(), jGroup.getDisplayText(),
3276 jGroup.getColourText(), jGroup.getStart(), jGroup.getEnd());
3278 sg.setOutlineColour(new java.awt.Color(jGroup.getOutlineColour()));
3280 sg.textColour = new java.awt.Color(jGroup.getTextCol1());
3281 sg.textColour2 = new java.awt.Color(jGroup.getTextCol2());
3282 sg.setShowNonconserved(jGroup.hasShowUnconserved() ? jGroup
3283 .isShowUnconserved() : false);
3284 sg.thresholdTextColour = jGroup.getTextColThreshold();
3285 if (jGroup.hasShowConsensusHistogram())
3287 sg.setShowConsensusHistogram(jGroup.isShowConsensusHistogram());
3290 if (jGroup.hasShowSequenceLogo())
3292 sg.setshowSequenceLogo(jGroup.isShowSequenceLogo());
3294 if (jGroup.hasNormaliseSequenceLogo())
3296 sg.setNormaliseSequenceLogo(jGroup.isNormaliseSequenceLogo());
3298 if (jGroup.hasIgnoreGapsinConsensus())
3300 sg.setIgnoreGapsConsensus(jGroup.getIgnoreGapsinConsensus());
3302 if (jGroup.getConsThreshold() != 0)
3304 jalview.analysis.Conservation c = new jalview.analysis.Conservation(
3305 "All", ResidueProperties.propHash, 3,
3306 sg.getSequences(null), 0, sg.getWidth() - 1);
3308 c.verdict(false, 25);
3309 sg.cs.setConservation(c);
3312 if (jGroup.getId() != null && groupAnnotRefs.size() > 0)
3314 // re-instate unique group/annotation row reference
3315 List<AlignmentAnnotation> jaal = groupAnnotRefs.get(jGroup
3319 for (AlignmentAnnotation jaa : jaal)
3322 if (jaa.autoCalculated)
3324 // match up and try to set group autocalc alignment row for this
3326 if (jaa.label.startsWith("Consensus for "))
3328 sg.setConsensus(jaa);
3330 // match up and try to set group autocalc alignment row for this
3332 if (jaa.label.startsWith("Conservation for "))
3334 sg.setConservationRow(jaa);
3341 if (addAnnotSchemeGroup)
3343 // reconstruct the annotation colourscheme
3344 sg.cs = constructAnnotationColour(jGroup.getAnnotationColours(),
3345 null, al, jms, false);
3351 // only dataset in this model, so just return.
3354 // ///////////////////////////////
3357 // If we just load in the same jar file again, the sequenceSetId
3358 // will be the same, and we end up with multiple references
3359 // to the same sequenceSet. We must modify this id on load
3360 // so that each load of the file gives a unique id
3361 String uniqueSeqSetId = view.getSequenceSetId() + uniqueSetSuffix;
3362 String viewId = (view.getId() == null ? null : view.getId()
3364 AlignFrame af = null;
3365 AlignViewport av = null;
3366 // now check to see if we really need to create a new viewport.
3367 if (multipleView && viewportsAdded.size() == 0)
3369 // We recovered an alignment for which a viewport already exists.
3370 // TODO: fix up any settings necessary for overlaying stored state onto
3371 // state recovered from another document. (may not be necessary).
3372 // we may need a binding from a viewport in memory to one recovered from
3374 // and then recover its containing af to allow the settings to be applied.
3375 // TODO: fix for vamsas demo
3377 .println("About to recover a viewport for existing alignment: Sequence set ID is "
3379 Object seqsetobj = retrieveExistingObj(uniqueSeqSetId);
3380 if (seqsetobj != null)
3382 if (seqsetobj instanceof String)
3384 uniqueSeqSetId = (String) seqsetobj;
3386 .println("Recovered extant sequence set ID mapping for ID : New Sequence set ID is "
3392 .println("Warning : Collision between sequence set ID string and existing jalview object mapping.");
3398 * indicate that annotation colours are applied across all groups (pre
3399 * Jalview 2.8.1 behaviour)
3401 boolean doGroupAnnColour = Jalview2XML.isVersionStringLaterThan(
3402 "2.8.1", object.getVersion());
3404 AlignmentPanel ap = null;
3405 boolean isnewview = true;
3408 // Check to see if this alignment already has a view id == viewId
3409 jalview.gui.AlignmentPanel views[] = Desktop
3410 .getAlignmentPanels(uniqueSeqSetId);
3411 if (views != null && views.length > 0)
3413 for (int v = 0; v < views.length; v++)
3415 if (views[v].av.getViewId().equalsIgnoreCase(viewId))
3417 // recover the existing alignpanel, alignframe, viewport
3418 af = views[v].alignFrame;
3421 // TODO: could even skip resetting view settings if we don't want to
3422 // change the local settings from other jalview processes
3431 af = loadViewport(file, jseqs, hiddenSeqs, al, jms, view,
3432 uniqueSeqSetId, viewId, autoAlan);
3438 * Load any trees, PDB structures and viewers
3440 * Not done if flag is false (when this method is used for New View)
3442 if (loadTreesAndStructures)
3444 loadTrees(jms, view, af, av, ap);
3445 loadPDBStructures(jprovider, jseqs, af, ap);
3446 loadRnaViewers(jprovider, jseqs, ap);
3448 // and finally return.
3453 * Instantiate and link any saved RNA (Varna) viewers. The state of the Varna
3454 * panel is restored from separate jar entries, two (gapped and trimmed) per
3455 * sequence and secondary structure.
3457 * Currently each viewer shows just one sequence and structure (gapped and
3458 * trimmed), however this method is designed to support multiple sequences or
3459 * structures in viewers if wanted in future.
3465 private void loadRnaViewers(jarInputStreamProvider jprovider,
3466 JSeq[] jseqs, AlignmentPanel ap)
3469 * scan the sequences for references to viewers; create each one the first
3470 * time it is referenced, add Rna models to existing viewers
3472 for (JSeq jseq : jseqs)
3474 for (int i = 0; i < jseq.getRnaViewerCount(); i++)
3476 RnaViewer viewer = jseq.getRnaViewer(i);
3477 AppVarna appVarna = findOrCreateVarnaViewer(viewer,
3478 uniqueSetSuffix, ap);
3480 for (int j = 0; j < viewer.getSecondaryStructureCount(); j++)
3482 SecondaryStructure ss = viewer.getSecondaryStructure(j);
3483 SequenceI seq = seqRefIds.get(jseq.getId());
3484 AlignmentAnnotation ann = this.annotationIds.get(ss
3485 .getAnnotationId());
3488 * add the structure to the Varna display (with session state copied
3489 * from the jar to a temporary file)
3491 boolean gapped = ss.isGapped();
3492 String rnaTitle = ss.getTitle();
3493 String sessionState = ss.getViewerState();
3494 String tempStateFile = copyJarEntry(jprovider, sessionState,
3496 RnaModel rna = new RnaModel(rnaTitle, ann, seq, null, gapped);
3497 appVarna.addModelSession(rna, rnaTitle, tempStateFile);
3499 appVarna.setInitialSelection(viewer.getSelectedRna());
3505 * Locate and return an already instantiated matching AppVarna, or create one
3509 * @param viewIdSuffix
3513 protected AppVarna findOrCreateVarnaViewer(RnaViewer viewer,
3514 String viewIdSuffix, AlignmentPanel ap)
3517 * on each load a suffix is appended to the saved viewId, to avoid conflicts
3518 * if load is repeated
3520 String postLoadId = viewer.getViewId() + viewIdSuffix;
3521 for (JInternalFrame frame : getAllFrames())
3523 if (frame instanceof AppVarna)
3525 AppVarna varna = (AppVarna) frame;
3526 if (postLoadId.equals(varna.getViewId()))
3528 // this viewer is already instantiated
3529 // could in future here add ap as another 'parent' of the
3530 // AppVarna window; currently just 1-to-many
3537 * viewer not found - make it
3539 RnaViewerModel model = new RnaViewerModel(postLoadId,
3540 viewer.getTitle(), viewer.getXpos(), viewer.getYpos(),
3541 viewer.getWidth(), viewer.getHeight(),
3542 viewer.getDividerLocation());
3543 AppVarna varna = new AppVarna(model, ap);
3549 * Load any saved trees
3557 protected void loadTrees(JalviewModelSequence jms, Viewport view,
3558 AlignFrame af, AlignViewport av, AlignmentPanel ap)
3560 // TODO result of automated refactoring - are all these parameters needed?
3563 for (int t = 0; t < jms.getTreeCount(); t++)
3566 Tree tree = jms.getTree(t);
3568 TreePanel tp = (TreePanel) retrieveExistingObj(tree.getId());
3571 tp = af.ShowNewickTree(
3572 new jalview.io.NewickFile(tree.getNewick()),
3573 tree.getTitle(), tree.getWidth(), tree.getHeight(),
3574 tree.getXpos(), tree.getYpos());
3575 if (tree.getId() != null)
3577 // perhaps bind the tree id to something ?
3582 // update local tree attributes ?
3583 // TODO: should check if tp has been manipulated by user - if so its
3584 // settings shouldn't be modified
3585 tp.setTitle(tree.getTitle());
3586 tp.setBounds(new Rectangle(tree.getXpos(), tree.getYpos(), tree
3587 .getWidth(), tree.getHeight()));
3588 tp.av = av; // af.viewport; // TODO: verify 'associate with all
3591 tp.treeCanvas.av = av; // af.viewport;
3592 tp.treeCanvas.ap = ap; // af.alignPanel;
3597 warn("There was a problem recovering stored Newick tree: \n"
3598 + tree.getNewick());
3602 tp.fitToWindow.setState(tree.getFitToWindow());
3603 tp.fitToWindow_actionPerformed(null);
3605 if (tree.getFontName() != null)
3607 tp.setTreeFont(new java.awt.Font(tree.getFontName(), tree
3608 .getFontStyle(), tree.getFontSize()));
3612 tp.setTreeFont(new java.awt.Font(view.getFontName(), view
3613 .getFontStyle(), tree.getFontSize()));
3616 tp.showPlaceholders(tree.getMarkUnlinked());
3617 tp.showBootstrap(tree.getShowBootstrap());
3618 tp.showDistances(tree.getShowDistances());
3620 tp.treeCanvas.threshold = tree.getThreshold();
3622 if (tree.getCurrentTree())
3624 af.viewport.setCurrentTree(tp.getTree());
3628 } catch (Exception ex)
3630 ex.printStackTrace();
3635 * Load and link any saved structure viewers.
3642 protected void loadPDBStructures(jarInputStreamProvider jprovider,
3643 JSeq[] jseqs, AlignFrame af, AlignmentPanel ap)
3646 * Run through all PDB ids on the alignment, and collect mappings between
3647 * distinct view ids and all sequences referring to that view.
3649 Map<String, StructureViewerModel> structureViewers = new LinkedHashMap<String, StructureViewerModel>();
3651 for (int i = 0; i < jseqs.length; i++)
3653 if (jseqs[i].getPdbidsCount() > 0)
3655 Pdbids[] ids = jseqs[i].getPdbids();
3656 for (int p = 0; p < ids.length; p++)
3658 final int structureStateCount = ids[p].getStructureStateCount();
3659 for (int s = 0; s < structureStateCount; s++)
3661 // check to see if we haven't already created this structure view
3662 final StructureState structureState = ids[p]
3663 .getStructureState(s);
3664 String sviewid = (structureState.getViewId() == null) ? null
3665 : structureState.getViewId() + uniqueSetSuffix;
3666 jalview.datamodel.PDBEntry jpdb = new jalview.datamodel.PDBEntry();
3667 // Originally : ids[p].getFile()
3668 // : TODO: verify external PDB file recovery still works in normal
3669 // jalview project load
3670 jpdb.setFile(loadPDBFile(jprovider, ids[p].getId()));
3671 jpdb.setId(ids[p].getId());
3673 int x = structureState.getXpos();
3674 int y = structureState.getYpos();
3675 int width = structureState.getWidth();
3676 int height = structureState.getHeight();
3678 // Probably don't need to do this anymore...
3679 // Desktop.desktop.getComponentAt(x, y);
3680 // TODO: NOW: check that this recovers the PDB file correctly.
3681 String pdbFile = loadPDBFile(jprovider, ids[p].getId());
3682 jalview.datamodel.SequenceI seq = seqRefIds.get(jseqs[i]
3684 if (sviewid == null)
3686 sviewid = "_jalview_pre2_4_" + x + "," + y + "," + width
3689 if (!structureViewers.containsKey(sviewid))
3691 structureViewers.put(sviewid,
3692 new StructureViewerModel(x, y, width, height, false,
3693 false, true, structureState.getViewId(),
3694 structureState.getType()));
3695 // Legacy pre-2.7 conversion JAL-823 :
3696 // do not assume any view has to be linked for colour by
3700 // assemble String[] { pdb files }, String[] { id for each
3701 // file }, orig_fileloc, SequenceI[][] {{ seqs_file 1 }, {
3702 // seqs_file 2}, boolean[] {
3703 // linkAlignPanel,superposeWithAlignpanel}} from hash
3704 StructureViewerModel jmoldat = structureViewers.get(sviewid);
3705 jmoldat.setAlignWithPanel(jmoldat.isAlignWithPanel()
3706 | (structureState.hasAlignwithAlignPanel() ? structureState
3707 .getAlignwithAlignPanel() : false));
3710 * Default colour by linked panel to false if not specified (e.g.
3711 * for pre-2.7 projects)
3713 boolean colourWithAlignPanel = jmoldat.isColourWithAlignPanel();
3714 colourWithAlignPanel |= (structureState
3715 .hasColourwithAlignPanel() ? structureState
3716 .getColourwithAlignPanel() : false);
3717 jmoldat.setColourWithAlignPanel(colourWithAlignPanel);
3720 * Default colour by viewer to true if not specified (e.g. for
3723 boolean colourByViewer = jmoldat.isColourByViewer();
3724 colourByViewer &= structureState.hasColourByJmol() ? structureState
3725 .getColourByJmol() : true;
3726 jmoldat.setColourByViewer(colourByViewer);
3728 if (jmoldat.getStateData().length() < structureState
3729 .getContent().length())
3732 jmoldat.setStateData(structureState.getContent());
3735 if (ids[p].getFile() != null)
3737 File mapkey = new File(ids[p].getFile());
3738 StructureData seqstrmaps = jmoldat.getFileData().get(mapkey);
3739 if (seqstrmaps == null)
3741 jmoldat.getFileData().put(
3743 seqstrmaps = jmoldat.new StructureData(pdbFile,
3746 if (!seqstrmaps.getSeqList().contains(seq))
3748 seqstrmaps.getSeqList().add(seq);
3754 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");
3761 // Instantiate the associated structure views
3762 for (Entry<String, StructureViewerModel> entry : structureViewers
3767 createOrLinkStructureViewer(entry, af, ap, jprovider);
3768 } catch (Exception e)
3770 System.err.println("Error loading structure viewer: "
3772 // failed - try the next one
3784 protected void createOrLinkStructureViewer(
3785 Entry<String, StructureViewerModel> viewerData, AlignFrame af,
3786 AlignmentPanel ap, jarInputStreamProvider jprovider)
3788 final StructureViewerModel stateData = viewerData.getValue();
3791 * Search for any viewer windows already open from other alignment views
3792 * that exactly match the stored structure state
3794 StructureViewerBase comp = findMatchingViewer(viewerData);
3798 linkStructureViewer(ap, comp, stateData);
3803 * From 2.9: stateData.type contains JMOL or CHIMERA, data is in jar entry
3804 * "viewer_"+stateData.viewId
3806 if (ViewerType.CHIMERA.toString().equals(stateData.getType()))
3808 createChimeraViewer(viewerData, af, jprovider);
3813 * else Jmol (if pre-2.9, stateData contains JMOL state string)
3815 createJmolViewer(viewerData, af, jprovider);
3820 * Create a new Chimera viewer.
3826 protected void createChimeraViewer(
3827 Entry<String, StructureViewerModel> viewerData, AlignFrame af,
3828 jarInputStreamProvider jprovider)
3830 StructureViewerModel data = viewerData.getValue();
3831 String chimeraSessionFile = data.getStateData();
3834 * Copy Chimera session from jar entry "viewer_"+viewId to a temporary file
3836 * NB this is the 'saved' viewId as in the project file XML, _not_ the
3837 * 'uniquified' sviewid used to reconstruct the viewer here
3839 String viewerJarEntryName = getViewerJarEntryName(data.getViewId());
3840 chimeraSessionFile = copyJarEntry(jprovider, viewerJarEntryName,
3843 Set<Entry<File, StructureData>> fileData = data.getFileData()
3845 List<PDBEntry> pdbs = new ArrayList<PDBEntry>();
3846 List<SequenceI[]> allseqs = new ArrayList<SequenceI[]>();
3847 for (Entry<File, StructureData> pdb : fileData)
3849 String filePath = pdb.getValue().getFilePath();
3850 String pdbId = pdb.getValue().getPdbId();
3851 // pdbs.add(new PDBEntry(filePath, pdbId));
3852 pdbs.add(new PDBEntry(pdbId, null, PDBEntry.Type.PDB, filePath));
3853 final List<SequenceI> seqList = pdb.getValue().getSeqList();
3854 SequenceI[] seqs = seqList.toArray(new SequenceI[seqList.size()]);
3858 boolean colourByChimera = data.isColourByViewer();
3859 boolean colourBySequence = data.isColourWithAlignPanel();
3861 // TODO use StructureViewer as a factory here, see JAL-1761
3862 final PDBEntry[] pdbArray = pdbs.toArray(new PDBEntry[pdbs.size()]);
3863 final SequenceI[][] seqsArray = allseqs.toArray(new SequenceI[allseqs
3865 String newViewId = viewerData.getKey();
3867 ChimeraViewFrame cvf = new ChimeraViewFrame(chimeraSessionFile,
3868 af.alignPanel, pdbArray, seqsArray, colourByChimera,
3869 colourBySequence, newViewId);
3870 cvf.setSize(data.getWidth(), data.getHeight());
3871 cvf.setLocation(data.getX(), data.getY());
3875 * Create a new Jmol window. First parse the Jmol state to translate filenames
3876 * loaded into the view, and record the order in which files are shown in the
3877 * Jmol view, so we can add the sequence mappings in same order.
3883 protected void createJmolViewer(
3884 final Entry<String, StructureViewerModel> viewerData,
3885 AlignFrame af, jarInputStreamProvider jprovider)
3887 final StructureViewerModel svattrib = viewerData.getValue();
3888 String state = svattrib.getStateData();
3891 * Pre-2.9: state element value is the Jmol state string
3893 * 2.9+: @type is "JMOL", state data is in a Jar file member named "viewer_"
3896 if (ViewerType.JMOL.toString().equals(svattrib.getType()))
3898 state = readJarEntry(jprovider,
3899 getViewerJarEntryName(svattrib.getViewId()));
3902 List<String> pdbfilenames = new ArrayList<String>();
3903 List<SequenceI[]> seqmaps = new ArrayList<SequenceI[]>();
3904 List<String> pdbids = new ArrayList<String>();
3905 StringBuilder newFileLoc = new StringBuilder(64);
3906 int cp = 0, ncp, ecp;
3907 Map<File, StructureData> oldFiles = svattrib.getFileData();
3908 while ((ncp = state.indexOf("load ", cp)) > -1)
3912 // look for next filename in load statement
3913 newFileLoc.append(state.substring(cp,
3914 ncp = (state.indexOf("\"", ncp + 1) + 1)));
3915 String oldfilenam = state.substring(ncp,
3916 ecp = state.indexOf("\"", ncp));
3917 // recover the new mapping data for this old filename
3918 // have to normalize filename - since Jmol and jalview do
3920 // translation differently.
3921 StructureData filedat = oldFiles.get(new File(oldfilenam));
3922 newFileLoc.append(Platform.escapeString(filedat.getFilePath()));
3923 pdbfilenames.add(filedat.getFilePath());
3924 pdbids.add(filedat.getPdbId());
3925 seqmaps.add(filedat.getSeqList().toArray(new SequenceI[0]));
3926 newFileLoc.append("\"");
3927 cp = ecp + 1; // advance beyond last \" and set cursor so we can
3928 // look for next file statement.
3929 } while ((ncp = state.indexOf("/*file*/", cp)) > -1);
3933 // just append rest of state
3934 newFileLoc.append(state.substring(cp));
3938 System.err.print("Ignoring incomplete Jmol state for PDB ids: ");
3939 newFileLoc = new StringBuilder(state);
3940 newFileLoc.append("; load append ");
3941 for (File id : oldFiles.keySet())
3943 // add this and any other pdb files that should be present in
3945 StructureData filedat = oldFiles.get(id);
3946 newFileLoc.append(filedat.getFilePath());
3947 pdbfilenames.add(filedat.getFilePath());
3948 pdbids.add(filedat.getPdbId());
3949 seqmaps.add(filedat.getSeqList().toArray(new SequenceI[0]));
3950 newFileLoc.append(" \"");
3951 newFileLoc.append(filedat.getFilePath());
3952 newFileLoc.append("\"");
3955 newFileLoc.append(";");
3958 if (newFileLoc.length() == 0)
3962 int histbug = newFileLoc.indexOf("history = ");
3966 * change "history = [true|false];" to "history = [1|0];"
3969 int diff = histbug == -1 ? -1 : newFileLoc.indexOf(";", histbug);
3970 String val = (diff == -1) ? null : newFileLoc
3971 .substring(histbug, diff);
3972 if (val != null && val.length() >= 4)
3974 if (val.contains("e")) // eh? what can it be?
3976 if (val.trim().equals("true"))
3984 newFileLoc.replace(histbug, diff, val);
3989 final String[] pdbf = pdbfilenames.toArray(new String[pdbfilenames
3991 final String[] id = pdbids.toArray(new String[pdbids.size()]);
3992 final SequenceI[][] sq = seqmaps
3993 .toArray(new SequenceI[seqmaps.size()][]);
3994 final String fileloc = newFileLoc.toString();
3995 final String sviewid = viewerData.getKey();
3996 final AlignFrame alf = af;
3997 final Rectangle rect = new Rectangle(svattrib.getX(), svattrib.getY(),
3998 svattrib.getWidth(), svattrib.getHeight());
4001 javax.swing.SwingUtilities.invokeAndWait(new Runnable()
4006 JalviewStructureDisplayI sview = null;
4009 sview = new StructureViewer(alf.alignPanel
4010 .getStructureSelectionManager()).createView(
4011 StructureViewer.ViewerType.JMOL, pdbf, id, sq,
4012 alf.alignPanel, svattrib, fileloc, rect, sviewid);
4013 addNewStructureViewer(sview);
4014 } catch (OutOfMemoryError ex)
4016 new OOMWarning("restoring structure view for PDB id " + id,
4017 (OutOfMemoryError) ex.getCause());
4018 if (sview != null && sview.isVisible())
4020 sview.closeViewer(false);
4021 sview.setVisible(false);
4027 } catch (InvocationTargetException ex)
4029 warn("Unexpected error when opening Jmol view.", ex);
4031 } catch (InterruptedException e)
4033 // e.printStackTrace();
4039 * Generates a name for the entry in the project jar file to hold state
4040 * information for a structure viewer
4045 protected String getViewerJarEntryName(String viewId)
4047 return VIEWER_PREFIX + viewId;
4051 * Returns any open frame that matches given structure viewer data. The match
4052 * is based on the unique viewId, or (for older project versions) the frame's
4058 protected StructureViewerBase findMatchingViewer(
4059 Entry<String, StructureViewerModel> viewerData)
4061 final String sviewid = viewerData.getKey();
4062 final StructureViewerModel svattrib = viewerData.getValue();
4063 StructureViewerBase comp = null;
4064 JInternalFrame[] frames = getAllFrames();
4065 for (JInternalFrame frame : frames)
4067 if (frame instanceof StructureViewerBase)
4070 * Post jalview 2.4 schema includes structure view id
4073 && ((StructureViewerBase) frame).getViewId()
4076 comp = (StructureViewerBase) frame;
4077 break; // break added in 2.9
4080 * Otherwise test for matching position and size of viewer frame
4082 else if (frame.getX() == svattrib.getX()
4083 && frame.getY() == svattrib.getY()
4084 && frame.getHeight() == svattrib.getHeight()
4085 && frame.getWidth() == svattrib.getWidth())
4087 comp = (StructureViewerBase) frame;
4088 // no break in faint hope of an exact match on viewId
4096 * Link an AlignmentPanel to an existing structure viewer.
4101 * @param useinViewerSuperpos
4102 * @param usetoColourbyseq
4103 * @param viewerColouring
4105 protected void linkStructureViewer(AlignmentPanel ap,
4106 StructureViewerBase viewer, StructureViewerModel stateData)
4108 // NOTE: if the jalview project is part of a shared session then
4109 // view synchronization should/could be done here.
4111 final boolean useinViewerSuperpos = stateData.isAlignWithPanel();
4112 final boolean usetoColourbyseq = stateData.isColourWithAlignPanel();
4113 final boolean viewerColouring = stateData.isColourByViewer();
4114 Map<File, StructureData> oldFiles = stateData.getFileData();
4117 * Add mapping for sequences in this view to an already open viewer
4119 final AAStructureBindingModel binding = viewer.getBinding();
4120 for (File id : oldFiles.keySet())
4122 // add this and any other pdb files that should be present in the
4124 StructureData filedat = oldFiles.get(id);
4125 String pdbFile = filedat.getFilePath();
4126 SequenceI[] seq = filedat.getSeqList().toArray(new SequenceI[0]);
4127 binding.getSsm().setMapping(seq, null, pdbFile,
4128 jalview.io.AppletFormatAdapter.FILE);
4129 binding.addSequenceForStructFile(pdbFile, seq);
4131 // and add the AlignmentPanel's reference to the view panel
4132 viewer.addAlignmentPanel(ap);
4133 if (useinViewerSuperpos)
4135 viewer.useAlignmentPanelForSuperposition(ap);
4139 viewer.excludeAlignmentPanelForSuperposition(ap);
4141 if (usetoColourbyseq)
4143 viewer.useAlignmentPanelForColourbyseq(ap, !viewerColouring);
4147 viewer.excludeAlignmentPanelForColourbyseq(ap);
4152 * Get all frames within the Desktop.
4156 protected JInternalFrame[] getAllFrames()
4158 JInternalFrame[] frames = null;
4159 // TODO is this necessary - is it safe - risk of hanging?
4164 frames = Desktop.desktop.getAllFrames();
4165 } catch (ArrayIndexOutOfBoundsException e)
4167 // occasional No such child exceptions are thrown here...
4171 } catch (InterruptedException f)
4175 } while (frames == null);
4180 * Answers true if 'version' is equal to or later than 'supported', where each
4181 * is formatted as major/minor versions like "2.8.3" or "2.3.4b1" for bugfix
4182 * changes. Development and test values for 'version' are leniently treated
4186 * - minimum version we are comparing against
4188 * - version of data being processsed
4191 public static boolean isVersionStringLaterThan(String supported,
4194 if (supported == null || version == null
4195 || version.equalsIgnoreCase("DEVELOPMENT BUILD")
4196 || version.equalsIgnoreCase("Test")
4197 || version.equalsIgnoreCase("AUTOMATED BUILD"))
4199 System.err.println("Assuming project file with "
4200 + (version == null ? "null" : version)
4201 + " is compatible with Jalview version " + supported);
4206 return StringUtils.compareVersions(version, supported, "b") >= 0;
4210 Vector<JalviewStructureDisplayI> newStructureViewers = null;
4212 protected void addNewStructureViewer(JalviewStructureDisplayI sview)
4214 if (newStructureViewers != null)
4216 sview.getBinding().setFinishedLoadingFromArchive(false);
4217 newStructureViewers.add(sview);
4221 protected void setLoadingFinishedForNewStructureViewers()
4223 if (newStructureViewers != null)
4225 for (JalviewStructureDisplayI sview : newStructureViewers)
4227 sview.getBinding().setFinishedLoadingFromArchive(true);
4229 newStructureViewers.clear();
4230 newStructureViewers = null;
4234 AlignFrame loadViewport(String file, JSeq[] JSEQ,
4235 List<SequenceI> hiddenSeqs, AlignmentI al,
4236 JalviewModelSequence jms, Viewport view, String uniqueSeqSetId,
4237 String viewId, List<JvAnnotRow> autoAlan)
4239 AlignFrame af = null;
4240 af = new AlignFrame(al, view.getWidth(), view.getHeight(),
4241 uniqueSeqSetId, viewId);
4243 af.setFileName(file, "Jalview");
4245 for (int i = 0; i < JSEQ.length; i++)
4247 af.viewport.setSequenceColour(af.viewport.getAlignment()
4248 .getSequenceAt(i), new java.awt.Color(JSEQ[i].getColour()));
4253 af.getViewport().setColourByReferenceSeq(true);
4254 af.getViewport().setDisplayReferenceSeq(true);
4257 af.viewport.setGatherViewsHere(view.getGatheredViews());
4259 if (view.getSequenceSetId() != null)
4261 AlignmentViewport av = viewportsAdded.get(uniqueSeqSetId);
4263 af.viewport.setSequenceSetId(uniqueSeqSetId);
4266 // propagate shared settings to this new view
4267 af.viewport.setHistoryList(av.getHistoryList());
4268 af.viewport.setRedoList(av.getRedoList());
4272 viewportsAdded.put(uniqueSeqSetId, af.viewport);
4274 // TODO: check if this method can be called repeatedly without
4275 // side-effects if alignpanel already registered.
4276 PaintRefresher.Register(af.alignPanel, uniqueSeqSetId);
4278 // apply Hidden regions to view.
4279 if (hiddenSeqs != null)
4281 for (int s = 0; s < JSEQ.length; s++)
4283 SequenceGroup hidden = new SequenceGroup();
4284 boolean isRepresentative = false;
4285 for (int r = 0; r < JSEQ[s].getHiddenSequencesCount(); r++)
4287 isRepresentative = true;
4288 SequenceI sequenceToHide = al.getSequenceAt(JSEQ[s]
4289 .getHiddenSequences(r));
4290 hidden.addSequence(sequenceToHide, false);
4291 // remove from hiddenSeqs list so we don't try to hide it twice
4292 hiddenSeqs.remove(sequenceToHide);
4294 if (isRepresentative)
4296 SequenceI representativeSequence = al.getSequenceAt(s);
4297 hidden.addSequence(representativeSequence, false);
4298 af.viewport.hideRepSequences(representativeSequence, hidden);
4302 SequenceI[] hseqs = hiddenSeqs.toArray(new SequenceI[hiddenSeqs
4304 af.viewport.hideSequence(hseqs);
4307 // recover view properties and display parameters
4308 if (view.getViewName() != null)
4310 af.viewport.viewName = view.getViewName();
4311 af.setInitialTabVisible();
4313 af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),
4316 af.viewport.setShowAnnotation(view.getShowAnnotation());
4317 af.viewport.setAbovePIDThreshold(view.getPidSelected());
4319 af.viewport.setColourText(view.getShowColourText());
4321 af.viewport.setConservationSelected(view.getConservationSelected());
4322 af.viewport.setShowJVSuffix(view.getShowFullId());
4323 af.viewport.setRightAlignIds(view.getRightAlignIds());
4324 af.viewport.setFont(
4325 new java.awt.Font(view.getFontName(), view.getFontStyle(), view
4326 .getFontSize()), true);
4327 ViewStyleI vs = af.viewport.getViewStyle();
4328 vs.setScaleProteinAsCdna(view.isScaleProteinAsCdna());
4329 af.viewport.setViewStyle(vs);
4330 // TODO: allow custom charWidth/Heights to be restored by updating them
4331 // after setting font - which means set above to false
4332 af.viewport.setRenderGaps(view.getRenderGaps());
4333 af.viewport.setWrapAlignment(view.getWrapAlignment());
4334 af.viewport.setShowAnnotation(view.getShowAnnotation());
4336 af.viewport.setShowBoxes(view.getShowBoxes());
4338 af.viewport.setShowText(view.getShowText());
4340 af.viewport.setTextColour(new java.awt.Color(view.getTextCol1()));
4341 af.viewport.setTextColour2(new java.awt.Color(view.getTextCol2()));
4342 af.viewport.setThresholdTextColour(view.getTextColThreshold());
4343 af.viewport.setShowUnconserved(view.hasShowUnconserved() ? view
4344 .isShowUnconserved() : false);
4345 af.viewport.setStartRes(view.getStartRes());
4346 af.viewport.setStartSeq(view.getStartSeq());
4347 af.alignPanel.updateLayout();
4348 ColourSchemeI cs = null;
4349 // apply colourschemes
4350 if (view.getBgColour() != null)
4352 if (view.getBgColour().startsWith("ucs"))
4354 cs = getUserColourScheme(jms, view.getBgColour());
4356 else if (view.getBgColour().startsWith("Annotation"))
4358 AnnotationColours viewAnnColour = view.getAnnotationColours();
4359 cs = constructAnnotationColour(viewAnnColour, af, al, jms, true);
4366 cs = ColourSchemeProperty.getColour(al, view.getBgColour());
4371 cs.setThreshold(view.getPidThreshold(), true);
4372 cs.setConsensus(af.viewport.getSequenceConsensusHash());
4376 af.viewport.setGlobalColourScheme(cs);
4377 af.viewport.setColourAppliesToAllGroups(false);
4379 if (view.getConservationSelected() && cs != null)
4381 cs.setConservationInc(view.getConsThreshold());
4384 af.changeColour(cs);
4386 af.viewport.setColourAppliesToAllGroups(true);
4388 af.viewport.setShowSequenceFeatures(view.getShowSequenceFeatures());
4390 if (view.hasCentreColumnLabels())
4392 af.viewport.setCentreColumnLabels(view.getCentreColumnLabels());
4394 if (view.hasIgnoreGapsinConsensus())
4396 af.viewport.setIgnoreGapsConsensus(view.getIgnoreGapsinConsensus(),
4399 if (view.hasFollowHighlight())
4401 af.viewport.setFollowHighlight(view.getFollowHighlight());
4403 if (view.hasFollowSelection())
4405 af.viewport.followSelection = view.getFollowSelection();
4407 if (view.hasShowConsensusHistogram())
4409 af.viewport.setShowConsensusHistogram(view
4410 .getShowConsensusHistogram());
4414 af.viewport.setShowConsensusHistogram(true);
4416 if (view.hasShowSequenceLogo())
4418 af.viewport.setShowSequenceLogo(view.getShowSequenceLogo());
4422 af.viewport.setShowSequenceLogo(false);
4424 if (view.hasNormaliseSequenceLogo())
4426 af.viewport.setNormaliseSequenceLogo(view.getNormaliseSequenceLogo());
4428 if (view.hasShowDbRefTooltip())
4430 af.viewport.setShowDBRefs(view.getShowDbRefTooltip());
4432 if (view.hasShowNPfeatureTooltip())
4434 af.viewport.setShowNPFeats(view.hasShowNPfeatureTooltip());
4436 if (view.hasShowGroupConsensus())
4438 af.viewport.setShowGroupConsensus(view.getShowGroupConsensus());
4442 af.viewport.setShowGroupConsensus(false);
4444 if (view.hasShowGroupConservation())
4446 af.viewport.setShowGroupConservation(view.getShowGroupConservation());
4450 af.viewport.setShowGroupConservation(false);
4453 // recover featre settings
4454 if (jms.getFeatureSettings() != null)
4456 FeaturesDisplayed fdi;
4457 af.viewport.setFeaturesDisplayed(fdi = new FeaturesDisplayed());
4458 String[] renderOrder = new String[jms.getFeatureSettings()
4459 .getSettingCount()];
4460 Map<String, FeatureColourI> featureColours = new Hashtable<String, FeatureColourI>();
4461 Map<String, Float> featureOrder = new Hashtable<String, Float>();
4463 for (int fs = 0; fs < jms.getFeatureSettings().getSettingCount(); fs++)
4465 Setting setting = jms.getFeatureSettings().getSetting(fs);
4466 if (setting.hasMincolour())
4468 FeatureColourI gc = setting.hasMin() ? new FeatureColour(
4469 new Color(setting.getMincolour()), new Color(
4470 setting.getColour()), setting.getMin(),
4471 setting.getMax()) : new FeatureColour(new Color(
4472 setting.getMincolour()), new Color(setting.getColour()),
4474 if (setting.hasThreshold())
4476 gc.setThreshold(setting.getThreshold());
4477 int threshstate = setting.getThreshstate();
4478 // -1 = None, 0 = Below, 1 = Above threshold
4479 if (threshstate == 0)
4481 gc.setBelowThreshold(true);
4483 else if (threshstate == 1)
4485 gc.setAboveThreshold(true);
4488 gc.setAutoScaled(true); // default
4489 if (setting.hasAutoScale())
4491 gc.setAutoScaled(setting.getAutoScale());
4493 if (setting.hasColourByLabel())
4495 gc.setColourByLabel(setting.getColourByLabel());
4497 // and put in the feature colour table.
4498 featureColours.put(setting.getType(), gc);
4502 featureColours.put(setting.getType(), new FeatureColour(
4503 new Color(setting.getColour())));
4505 renderOrder[fs] = setting.getType();
4506 if (setting.hasOrder())
4508 featureOrder.put(setting.getType(), setting.getOrder());
4512 featureOrder.put(setting.getType(), new Float(fs
4513 / jms.getFeatureSettings().getSettingCount()));
4515 if (setting.getDisplay())
4517 fdi.setVisible(setting.getType());
4520 Map<String, Boolean> fgtable = new Hashtable<String, Boolean>();
4521 for (int gs = 0; gs < jms.getFeatureSettings().getGroupCount(); gs++)
4523 Group grp = jms.getFeatureSettings().getGroup(gs);
4524 fgtable.put(grp.getName(), new Boolean(grp.getDisplay()));
4526 // FeatureRendererSettings frs = new FeatureRendererSettings(renderOrder,
4527 // fgtable, featureColours, jms.getFeatureSettings().hasTransparency() ?
4528 // jms.getFeatureSettings().getTransparency() : 0.0, featureOrder);
4529 FeatureRendererSettings frs = new FeatureRendererSettings(
4530 renderOrder, fgtable, featureColours, 1.0f, featureOrder);
4531 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
4532 .transferSettings(frs);
4536 if (view.getHiddenColumnsCount() > 0)
4538 for (int c = 0; c < view.getHiddenColumnsCount(); c++)
4540 af.viewport.hideColumns(view.getHiddenColumns(c).getStart(), view
4541 .getHiddenColumns(c).getEnd() // +1
4545 if (view.getCalcIdParam() != null)
4547 for (CalcIdParam calcIdParam : view.getCalcIdParam())
4549 if (calcIdParam != null)
4551 if (recoverCalcIdParam(calcIdParam, af.viewport))
4556 warn("Couldn't recover parameters for "
4557 + calcIdParam.getCalcId());
4562 af.setMenusFromViewport(af.viewport);
4563 af.setTitle(view.getTitle());
4564 // TODO: we don't need to do this if the viewport is aready visible.
4566 * Add the AlignFrame to the desktop (it may be 'gathered' later), unless it
4567 * has a 'cdna/protein complement' view, in which case save it in order to
4568 * populate a SplitFrame once all views have been read in.
4570 String complementaryViewId = view.getComplementId();
4571 if (complementaryViewId == null)
4573 Desktop.addInternalFrame(af, view.getTitle(), view.getWidth(),
4575 // recompute any autoannotation
4576 af.alignPanel.updateAnnotation(false, true);
4577 reorderAutoannotation(af, al, autoAlan);
4578 af.alignPanel.alignmentChanged();
4582 splitFrameCandidates.put(view, af);
4587 private ColourSchemeI constructAnnotationColour(
4588 AnnotationColours viewAnnColour, AlignFrame af, AlignmentI al,
4589 JalviewModelSequence jms, boolean checkGroupAnnColour)
4591 boolean propagateAnnColour = false;
4592 ColourSchemeI cs = null;
4593 AlignmentI annAlignment = af != null ? af.viewport.getAlignment() : al;
4594 if (checkGroupAnnColour && al.getGroups() != null
4595 && al.getGroups().size() > 0)
4597 // pre 2.8.1 behaviour
4598 // check to see if we should transfer annotation colours
4599 propagateAnnColour = true;
4600 for (jalview.datamodel.SequenceGroup sg : al.getGroups())
4602 if (sg.cs instanceof AnnotationColourGradient)
4604 propagateAnnColour = false;
4608 // int find annotation
4609 if (annAlignment.getAlignmentAnnotation() != null)
4611 for (int i = 0; i < annAlignment.getAlignmentAnnotation().length; i++)
4613 if (annAlignment.getAlignmentAnnotation()[i].label
4614 .equals(viewAnnColour.getAnnotation()))
4616 if (annAlignment.getAlignmentAnnotation()[i].getThreshold() == null)
4618 annAlignment.getAlignmentAnnotation()[i]
4619 .setThreshold(new jalview.datamodel.GraphLine(
4620 viewAnnColour.getThreshold(), "Threshold",
4621 java.awt.Color.black)
4626 if (viewAnnColour.getColourScheme().equals("None"))
4628 cs = new AnnotationColourGradient(
4629 annAlignment.getAlignmentAnnotation()[i],
4630 new java.awt.Color(viewAnnColour.getMinColour()),
4631 new java.awt.Color(viewAnnColour.getMaxColour()),
4632 viewAnnColour.getAboveThreshold());
4634 else if (viewAnnColour.getColourScheme().startsWith("ucs"))
4636 cs = new AnnotationColourGradient(
4637 annAlignment.getAlignmentAnnotation()[i],
4638 getUserColourScheme(jms,
4639 viewAnnColour.getColourScheme()),
4640 viewAnnColour.getAboveThreshold());
4644 cs = new AnnotationColourGradient(
4645 annAlignment.getAlignmentAnnotation()[i],
4646 ColourSchemeProperty.getColour(al,
4647 viewAnnColour.getColourScheme()),
4648 viewAnnColour.getAboveThreshold());
4650 if (viewAnnColour.hasPerSequence())
4652 ((AnnotationColourGradient) cs).setSeqAssociated(viewAnnColour
4655 if (viewAnnColour.hasPredefinedColours())
4657 ((AnnotationColourGradient) cs)
4658 .setPredefinedColours(viewAnnColour
4659 .isPredefinedColours());
4661 if (propagateAnnColour && al.getGroups() != null)
4663 // Also use these settings for all the groups
4664 for (int g = 0; g < al.getGroups().size(); g++)
4666 jalview.datamodel.SequenceGroup sg = al.getGroups().get(g);
4674 * if (viewAnnColour.getColourScheme().equals("None" )) { sg.cs =
4675 * new AnnotationColourGradient(
4676 * annAlignment.getAlignmentAnnotation()[i], new
4677 * java.awt.Color(viewAnnColour. getMinColour()), new
4678 * java.awt.Color(viewAnnColour. getMaxColour()),
4679 * viewAnnColour.getAboveThreshold()); } else
4682 sg.cs = new AnnotationColourGradient(
4683 annAlignment.getAlignmentAnnotation()[i], sg.cs,
4684 viewAnnColour.getAboveThreshold());
4685 if (cs instanceof AnnotationColourGradient)
4687 if (viewAnnColour.hasPerSequence())
4689 ((AnnotationColourGradient) cs)
4690 .setSeqAssociated(viewAnnColour.isPerSequence());
4692 if (viewAnnColour.hasPredefinedColours())
4694 ((AnnotationColourGradient) cs)
4695 .setPredefinedColours(viewAnnColour
4696 .isPredefinedColours());
4712 private void reorderAutoannotation(AlignFrame af, AlignmentI al,
4713 List<JvAnnotRow> autoAlan)
4715 // copy over visualization settings for autocalculated annotation in the
4717 if (al.getAlignmentAnnotation() != null)
4720 * Kludge for magic autoannotation names (see JAL-811)
4722 String[] magicNames = new String[] { "Consensus", "Quality",
4724 JvAnnotRow nullAnnot = new JvAnnotRow(-1, null);
4725 Hashtable<String, JvAnnotRow> visan = new Hashtable<String, JvAnnotRow>();
4726 for (String nm : magicNames)
4728 visan.put(nm, nullAnnot);
4730 for (JvAnnotRow auan : autoAlan)
4732 visan.put(auan.template.label
4733 + (auan.template.getCalcId() == null ? "" : "\t"
4734 + auan.template.getCalcId()), auan);
4736 int hSize = al.getAlignmentAnnotation().length;
4737 List<JvAnnotRow> reorder = new ArrayList<JvAnnotRow>();
4738 // work through any autoCalculated annotation already on the view
4739 // removing it if it should be placed in a different location on the
4740 // annotation panel.
4741 List<String> remains = new ArrayList<String>(visan.keySet());
4742 for (int h = 0; h < hSize; h++)
4744 jalview.datamodel.AlignmentAnnotation jalan = al
4745 .getAlignmentAnnotation()[h];
4746 if (jalan.autoCalculated)
4749 JvAnnotRow valan = visan.get(k = jalan.label);
4750 if (jalan.getCalcId() != null)
4752 valan = visan.get(k = jalan.label + "\t" + jalan.getCalcId());
4757 // delete the auto calculated row from the alignment
4758 al.deleteAnnotation(jalan, false);
4762 if (valan != nullAnnot)
4764 if (jalan != valan.template)
4766 // newly created autoannotation row instance
4767 // so keep a reference to the visible annotation row
4768 // and copy over all relevant attributes
4769 if (valan.template.graphHeight >= 0)
4772 jalan.graphHeight = valan.template.graphHeight;
4774 jalan.visible = valan.template.visible;
4776 reorder.add(new JvAnnotRow(valan.order, jalan));
4781 // Add any (possibly stale) autocalculated rows that were not appended to
4782 // the view during construction
4783 for (String other : remains)
4785 JvAnnotRow othera = visan.get(other);
4786 if (othera != nullAnnot && othera.template.getCalcId() != null
4787 && othera.template.getCalcId().length() > 0)
4789 reorder.add(othera);
4792 // now put the automatic annotation in its correct place
4793 int s = 0, srt[] = new int[reorder.size()];
4794 JvAnnotRow[] rws = new JvAnnotRow[reorder.size()];
4795 for (JvAnnotRow jvar : reorder)
4798 srt[s++] = jvar.order;
4801 jalview.util.QuickSort.sort(srt, rws);
4802 // and re-insert the annotation at its correct position
4803 for (JvAnnotRow jvar : rws)
4805 al.addAnnotation(jvar.template, jvar.order);
4807 af.alignPanel.adjustAnnotationHeight();
4811 Hashtable skipList = null;
4814 * TODO remove this method
4817 * @return AlignFrame bound to sequenceSetId from view, if one exists. private
4818 * AlignFrame getSkippedFrame(Viewport view) { if (skipList==null) {
4819 * throw new Error("Implementation Error. No skipList defined for this
4820 * Jalview2XML instance."); } return (AlignFrame)
4821 * skipList.get(view.getSequenceSetId()); }
4825 * Check if the Jalview view contained in object should be skipped or not.
4828 * @return true if view's sequenceSetId is a key in skipList
4830 private boolean skipViewport(JalviewModel object)
4832 if (skipList == null)
4837 if (skipList.containsKey(id = object.getJalviewModelSequence()
4838 .getViewport()[0].getSequenceSetId()))
4840 if (Cache.log != null && Cache.log.isDebugEnabled())
4842 Cache.log.debug("Skipping seuqence set id " + id);
4849 public void addToSkipList(AlignFrame af)
4851 if (skipList == null)
4853 skipList = new Hashtable();
4855 skipList.put(af.getViewport().getSequenceSetId(), af);
4858 public void clearSkipList()
4860 if (skipList != null)
4867 private void recoverDatasetFor(SequenceSet vamsasSet, AlignmentI al,
4868 boolean ignoreUnrefed)
4870 jalview.datamodel.AlignmentI ds = getDatasetFor(vamsasSet
4872 Vector dseqs = null;
4875 // create a list of new dataset sequences
4876 dseqs = new Vector();
4878 for (int i = 0, iSize = vamsasSet.getSequenceCount(); i < iSize; i++)
4880 Sequence vamsasSeq = vamsasSet.getSequence(i);
4881 ensureJalviewDatasetSequence(vamsasSeq, ds, dseqs, ignoreUnrefed);
4883 // create a new dataset
4886 SequenceI[] dsseqs = new SequenceI[dseqs.size()];
4887 dseqs.copyInto(dsseqs);
4888 ds = new jalview.datamodel.Alignment(dsseqs);
4889 debug("Created new dataset " + vamsasSet.getDatasetId()
4890 + " for alignment " + System.identityHashCode(al));
4891 addDatasetRef(vamsasSet.getDatasetId(), ds);
4893 // set the dataset for the newly imported alignment.
4894 if (al.getDataset() == null && !ignoreUnrefed)
4903 * sequence definition to create/merge dataset sequence for
4907 * vector to add new dataset sequence to
4909 private void ensureJalviewDatasetSequence(Sequence vamsasSeq,
4910 AlignmentI ds, Vector dseqs, boolean ignoreUnrefed)
4912 // JBP TODO: Check this is called for AlCodonFrames to support recovery of
4914 SequenceI sq = seqRefIds.get(vamsasSeq.getId());
4915 SequenceI dsq = null;
4916 if (sq != null && sq.getDatasetSequence() != null)
4918 dsq = sq.getDatasetSequence();
4920 if (sq == null && ignoreUnrefed)
4924 String sqid = vamsasSeq.getDsseqid();
4927 // need to create or add a new dataset sequence reference to this sequence
4930 dsq = seqRefIds.get(sqid);
4935 // make a new dataset sequence
4936 dsq = sq.createDatasetSequence();
4939 // make up a new dataset reference for this sequence
4940 sqid = seqHash(dsq);
4942 dsq.setVamsasId(uniqueSetSuffix + sqid);
4943 seqRefIds.put(sqid, dsq);
4948 dseqs.addElement(dsq);
4953 ds.addSequence(dsq);
4959 { // make this dataset sequence sq's dataset sequence
4960 sq.setDatasetSequence(dsq);
4961 // and update the current dataset alignment
4966 if (!dseqs.contains(dsq))
4973 if (ds.findIndex(dsq) < 0)
4975 ds.addSequence(dsq);
4982 // TODO: refactor this as a merge dataset sequence function
4983 // now check that sq (the dataset sequence) sequence really is the union of
4984 // all references to it
4985 // boolean pre = sq.getStart() < dsq.getStart();
4986 // boolean post = sq.getEnd() > dsq.getEnd();
4990 // StringBuffer sb = new StringBuffer();
4991 String newres = jalview.analysis.AlignSeq.extractGaps(
4992 jalview.util.Comparison.GapChars, sq.getSequenceAsString());
4993 if (!newres.equalsIgnoreCase(dsq.getSequenceAsString())
4994 && newres.length() > dsq.getLength())
4996 // Update with the longer sequence.
5000 * if (pre) { sb.insert(0, newres .substring(0, dsq.getStart() -
5001 * sq.getStart())); dsq.setStart(sq.getStart()); } if (post) {
5002 * sb.append(newres.substring(newres.length() - sq.getEnd() -
5003 * dsq.getEnd())); dsq.setEnd(sq.getEnd()); }
5005 dsq.setSequence(newres);
5007 // TODO: merges will never happen if we 'know' we have the real dataset
5008 // sequence - this should be detected when id==dssid
5010 .println("DEBUG Notice: Merged dataset sequence (if you see this often, post at http://issues.jalview.org/browse/JAL-1474)"); // ("
5011 // + (pre ? "prepended" : "") + " "
5012 // + (post ? "appended" : ""));
5018 * TODO use AlignmentI here and in related methods - needs
5019 * AlignmentI.getDataset() changed to return AlignmentI instead of Alignment
5021 Hashtable<String, AlignmentI> datasetIds = null;
5023 IdentityHashMap<AlignmentI, String> dataset2Ids = null;
5025 private AlignmentI getDatasetFor(String datasetId)
5027 if (datasetIds == null)
5029 datasetIds = new Hashtable<String, AlignmentI>();
5032 if (datasetIds.containsKey(datasetId))
5034 return datasetIds.get(datasetId);
5039 private void addDatasetRef(String datasetId, AlignmentI dataset)
5041 if (datasetIds == null)
5043 datasetIds = new Hashtable<String, AlignmentI>();
5045 datasetIds.put(datasetId, dataset);
5049 * make a new dataset ID for this jalview dataset alignment
5054 private String getDatasetIdRef(AlignmentI dataset)
5056 if (dataset.getDataset() != null)
5058 warn("Serious issue! Dataset Object passed to getDatasetIdRef is not a Jalview DATASET alignment...");
5060 String datasetId = makeHashCode(dataset, null);
5061 if (datasetId == null)
5063 // make a new datasetId and record it
5064 if (dataset2Ids == null)
5066 dataset2Ids = new IdentityHashMap<AlignmentI, String>();
5070 datasetId = dataset2Ids.get(dataset);
5072 if (datasetId == null)
5074 datasetId = "ds" + dataset2Ids.size() + 1;
5075 dataset2Ids.put(dataset, datasetId);
5081 private void addDBRefs(SequenceI datasetSequence, Sequence sequence)
5083 for (int d = 0; d < sequence.getDBRefCount(); d++)
5085 DBRef dr = sequence.getDBRef(d);
5086 jalview.datamodel.DBRefEntry entry = new jalview.datamodel.DBRefEntry(
5087 sequence.getDBRef(d).getSource(), sequence.getDBRef(d)
5088 .getVersion(), sequence.getDBRef(d).getAccessionId());
5089 if (dr.getMapping() != null)
5091 entry.setMap(addMapping(dr.getMapping()));
5093 datasetSequence.addDBRef(entry);
5097 private jalview.datamodel.Mapping addMapping(Mapping m)
5099 SequenceI dsto = null;
5100 // Mapping m = dr.getMapping();
5101 int fr[] = new int[m.getMapListFromCount() * 2];
5102 Enumeration f = m.enumerateMapListFrom();
5103 for (int _i = 0; f.hasMoreElements(); _i += 2)
5105 MapListFrom mf = (MapListFrom) f.nextElement();
5106 fr[_i] = mf.getStart();
5107 fr[_i + 1] = mf.getEnd();
5109 int fto[] = new int[m.getMapListToCount() * 2];
5110 f = m.enumerateMapListTo();
5111 for (int _i = 0; f.hasMoreElements(); _i += 2)
5113 MapListTo mf = (MapListTo) f.nextElement();
5114 fto[_i] = mf.getStart();
5115 fto[_i + 1] = mf.getEnd();
5117 jalview.datamodel.Mapping jmap = new jalview.datamodel.Mapping(dsto,
5118 fr, fto, (int) m.getMapFromUnit(), (int) m.getMapToUnit());
5119 if (m.getMappingChoice() != null)
5121 MappingChoice mc = m.getMappingChoice();
5122 if (mc.getDseqFor() != null)
5124 String dsfor = "" + mc.getDseqFor();
5125 if (seqRefIds.containsKey(dsfor))
5130 jmap.setTo(seqRefIds.get(dsfor));
5134 frefedSequence.add(newMappingRef(dsfor, jmap));
5140 * local sequence definition
5142 Sequence ms = mc.getSequence();
5143 SequenceI djs = null;
5144 String sqid = ms.getDsseqid();
5145 if (sqid != null && sqid.length() > 0)
5148 * recover dataset sequence
5150 djs = seqRefIds.get(sqid);
5155 .println("Warning - making up dataset sequence id for DbRef sequence map reference");
5156 sqid = ((Object) ms).toString(); // make up a new hascode for
5157 // undefined dataset sequence hash
5158 // (unlikely to happen)
5164 * make a new dataset sequence and add it to refIds hash
5166 djs = new jalview.datamodel.Sequence(ms.getName(),
5168 djs.setStart(jmap.getMap().getToLowest());
5169 djs.setEnd(jmap.getMap().getToHighest());
5170 djs.setVamsasId(uniqueSetSuffix + sqid);
5172 incompleteSeqs.put(sqid, djs);
5173 seqRefIds.put(sqid, djs);
5176 jalview.bin.Cache.log.debug("about to recurse on addDBRefs.");
5185 public jalview.gui.AlignmentPanel copyAlignPanel(AlignmentPanel ap,
5186 boolean keepSeqRefs)
5189 JalviewModel jm = saveState(ap, null, null, null);
5194 jm.getJalviewModelSequence().getViewport(0).setSequenceSetId(null);
5198 uniqueSetSuffix = "";
5199 jm.getJalviewModelSequence().getViewport(0).setId(null); // we don't
5204 if (this.frefedSequence == null)
5206 frefedSequence = new Vector();
5209 viewportsAdded.clear();
5211 AlignFrame af = loadFromObject(jm, null, false, null);
5212 af.alignPanels.clear();
5213 af.closeMenuItem_actionPerformed(true);
5216 * if(ap.av.getAlignment().getAlignmentAnnotation()!=null) { for(int i=0;
5217 * i<ap.av.getAlignment().getAlignmentAnnotation().length; i++) {
5218 * if(!ap.av.getAlignment().getAlignmentAnnotation()[i].autoCalculated) {
5219 * af.alignPanel.av.getAlignment().getAlignmentAnnotation()[i] =
5220 * ap.av.getAlignment().getAlignmentAnnotation()[i]; } } }
5223 return af.alignPanel;
5227 * flag indicating if hashtables should be cleared on finalization TODO this
5228 * flag may not be necessary
5230 private final boolean _cleartables = true;
5232 private Hashtable jvids2vobj;
5237 * @see java.lang.Object#finalize()
5240 protected void finalize() throws Throwable
5242 // really make sure we have no buried refs left.
5247 this.seqRefIds = null;
5248 this.seqsToIds = null;
5252 private void warn(String msg)
5257 private void warn(String msg, Exception e)
5259 if (Cache.log != null)
5263 Cache.log.warn(msg, e);
5267 Cache.log.warn(msg);
5272 System.err.println("Warning: " + msg);
5275 e.printStackTrace();
5280 private void debug(String string)
5282 debug(string, null);
5285 private void debug(String msg, Exception e)
5287 if (Cache.log != null)
5291 Cache.log.debug(msg, e);
5295 Cache.log.debug(msg);
5300 System.err.println("Warning: " + msg);
5303 e.printStackTrace();
5309 * set the object to ID mapping tables used to write/recover objects and XML
5310 * ID strings for the jalview project. If external tables are provided then
5311 * finalize and clearSeqRefs will not clear the tables when the Jalview2XML
5312 * object goes out of scope. - also populates the datasetIds hashtable with
5313 * alignment objects containing dataset sequences
5316 * Map from ID strings to jalview datamodel
5318 * Map from jalview datamodel to ID strings
5322 public void setObjectMappingTables(Hashtable vobj2jv,
5323 IdentityHashMap jv2vobj)
5325 this.jv2vobj = jv2vobj;
5326 this.vobj2jv = vobj2jv;
5327 Iterator ds = jv2vobj.keySet().iterator();
5329 while (ds.hasNext())
5331 Object jvobj = ds.next();
5332 id = jv2vobj.get(jvobj).toString();
5333 if (jvobj instanceof jalview.datamodel.Alignment)
5335 if (((jalview.datamodel.Alignment) jvobj).getDataset() == null)
5337 addDatasetRef(id, (jalview.datamodel.Alignment) jvobj);
5340 else if (jvobj instanceof jalview.datamodel.Sequence)
5342 // register sequence object so the XML parser can recover it.
5343 if (seqRefIds == null)
5345 seqRefIds = new HashMap<String, SequenceI>();
5347 if (seqsToIds == null)
5349 seqsToIds = new IdentityHashMap<SequenceI, String>();
5351 seqRefIds.put(jv2vobj.get(jvobj).toString(), (SequenceI) jvobj);
5352 seqsToIds.put((SequenceI) jvobj, id);
5354 else if (jvobj instanceof jalview.datamodel.AlignmentAnnotation)
5357 AlignmentAnnotation jvann = (AlignmentAnnotation) jvobj;
5358 annotationIds.put(anid = jv2vobj.get(jvobj).toString(), jvann);
5359 if (jvann.annotationId == null)
5361 jvann.annotationId = anid;
5363 if (!jvann.annotationId.equals(anid))
5365 // TODO verify that this is the correct behaviour
5366 this.warn("Overriding Annotation ID for " + anid
5367 + " from different id : " + jvann.annotationId);
5368 jvann.annotationId = anid;
5371 else if (jvobj instanceof String)
5373 if (jvids2vobj == null)
5375 jvids2vobj = new Hashtable();
5376 jvids2vobj.put(jvobj, jv2vobj.get(jvobj).toString());
5381 Cache.log.debug("Ignoring " + jvobj.getClass() + " (ID = " + id);
5387 * set the uniqueSetSuffix used to prefix/suffix object IDs for jalview
5388 * objects created from the project archive. If string is null (default for
5389 * construction) then suffix will be set automatically.
5393 public void setUniqueSetSuffix(String string)
5395 uniqueSetSuffix = string;
5400 * uses skipList2 as the skipList for skipping views on sequence sets
5401 * associated with keys in the skipList
5405 public void setSkipList(Hashtable skipList2)
5407 skipList = skipList2;
5411 * Reads the jar entry of given name and returns its contents, or null if the
5412 * entry is not found.
5415 * @param jarEntryName
5418 protected String readJarEntry(jarInputStreamProvider jprovider,
5419 String jarEntryName)
5421 String result = null;
5422 BufferedReader in = null;
5427 * Reopen the jar input stream and traverse its entries to find a matching
5430 JarInputStream jin = jprovider.getJarInputStream();
5431 JarEntry entry = null;
5434 entry = jin.getNextJarEntry();
5435 } while (entry != null && !entry.getName().equals(jarEntryName));
5439 StringBuilder out = new StringBuilder(256);
5440 in = new BufferedReader(new InputStreamReader(jin, UTF_8));
5443 while ((data = in.readLine()) != null)
5447 result = out.toString();
5451 warn("Couldn't find entry in Jalview Jar for " + jarEntryName);
5453 } catch (Exception ex)
5455 ex.printStackTrace();
5463 } catch (IOException e)
5474 * Returns an incrementing counter (0, 1, 2...)
5478 private synchronized int nextCounter()