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;
368 public boolean isResolvable()
370 return super.isResolvable() && mp.getTo() != null;
376 SequenceI seq = getSrefDatasetSeq();
381 cf.addMap(seq, mp.getTo(), mp.getMap());
388 public void resolveFrefedSequences()
390 Iterator<SeqFref> nextFref=frefedSequence.iterator();
391 int toresolve=frefedSequence.size();
392 int unresolved=0,failedtoresolve=0;
393 while (nextFref.hasNext()) {
394 SeqFref ref = nextFref.next();
395 if (ref.isResolvable())
404 } catch (Exception x) {
405 System.err.println("IMPLEMENTATION ERROR: Failed to resolve forward reference for sequence "+ref.getSref());
415 System.err.println("Jalview Project Import: There were " + unresolved
416 + " forward references left unresolved on the stack.");
418 if (failedtoresolve>0)
420 System.err.println("SERIOUS! " + failedtoresolve
421 + " resolvable forward references failed to resolve.");
423 if (incompleteSeqs != null && incompleteSeqs.size() > 0)
425 System.err.println("Jalview Project Import: There are "
426 + incompleteSeqs.size()
427 + " sequences which may have incomplete metadata.");
428 if (incompleteSeqs.size() < 10)
430 for (SequenceI s : incompleteSeqs.values())
432 System.err.println(s.toString());
438 .println("Too many to report. Skipping output of incomplete sequences.");
444 * This maintains a map of viewports, the key being the seqSetId. Important to
445 * set historyItem and redoList for multiple views
447 Map<String, AlignViewport> viewportsAdded = new HashMap<String, AlignViewport>();
449 Map<String, AlignmentAnnotation> annotationIds = new HashMap<String, AlignmentAnnotation>();
451 String uniqueSetSuffix = "";
454 * List of pdbfiles added to Jar
456 List<String> pdbfiles = null;
458 // SAVES SEVERAL ALIGNMENT WINDOWS TO SAME JARFILE
459 public void saveState(File statefile)
461 FileOutputStream fos = null;
464 fos = new FileOutputStream(statefile);
465 JarOutputStream jout = new JarOutputStream(fos);
468 } catch (Exception e)
470 // TODO: inform user of the problem - they need to know if their data was
472 if (errorMessage == null)
474 errorMessage = "Couldn't write Jalview Archive to output file '"
475 + statefile + "' - See console error log for details";
479 errorMessage += "(output file was '" + statefile + "')";
489 } catch (IOException e)
499 * Writes a jalview project archive to the given Jar output stream.
503 public void saveState(JarOutputStream jout)
505 AlignFrame[] frames = Desktop.getAlignFrames();
511 saveAllFrames(Arrays.asList(frames), jout);
515 * core method for storing state for a set of AlignFrames.
518 * - frames involving all data to be exported (including containing
521 * - project output stream
523 private void saveAllFrames(List<AlignFrame> frames, JarOutputStream jout)
525 Hashtable<String, AlignFrame> dsses = new Hashtable<String, AlignFrame>();
528 * ensure cached data is clear before starting
530 // todo tidy up seqRefIds, seqsToIds initialisation / reset
532 splitFrameCandidates.clear();
537 // NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS
538 // //////////////////////////////////////////////////
540 List<String> shortNames = new ArrayList<String>();
541 List<String> viewIds = new ArrayList<String>();
544 for (int i = frames.size() - 1; i > -1; i--)
546 AlignFrame af = frames.get(i);
550 .containsKey(af.getViewport().getSequenceSetId()))
555 String shortName = makeFilename(af, shortNames);
557 int ap, apSize = af.alignPanels.size();
559 for (ap = 0; ap < apSize; ap++)
561 AlignmentPanel apanel = af.alignPanels.get(ap);
562 String fileName = apSize == 1 ? shortName : ap + shortName;
563 if (!fileName.endsWith(".xml"))
565 fileName = fileName + ".xml";
568 saveState(apanel, fileName, jout, viewIds);
570 String dssid = getDatasetIdRef(af.getViewport().getAlignment()
572 if (!dsses.containsKey(dssid))
574 dsses.put(dssid, af);
579 writeDatasetFor(dsses, "" + jout.hashCode() + " " + uniqueSetSuffix,
585 } catch (Exception foo)
590 } catch (Exception ex)
592 // TODO: inform user of the problem - they need to know if their data was
594 if (errorMessage == null)
596 errorMessage = "Couldn't write Jalview Archive - see error output for details";
598 ex.printStackTrace();
603 * Generates a distinct file name, based on the title of the AlignFrame, by
604 * appending _n for increasing n until an unused name is generated. The new
605 * name (without its extension) is added to the list.
609 * @return the generated name, with .xml extension
611 protected String makeFilename(AlignFrame af, List<String> namesUsed)
613 String shortName = af.getTitle();
615 if (shortName.indexOf(File.separatorChar) > -1)
617 shortName = shortName.substring(shortName
618 .lastIndexOf(File.separatorChar) + 1);
623 while (namesUsed.contains(shortName))
625 if (shortName.endsWith("_" + (count - 1)))
627 shortName = shortName.substring(0, shortName.lastIndexOf("_"));
630 shortName = shortName.concat("_" + count);
634 namesUsed.add(shortName);
636 if (!shortName.endsWith(".xml"))
638 shortName = shortName + ".xml";
643 // USE THIS METHOD TO SAVE A SINGLE ALIGNMENT WINDOW
644 public boolean saveAlignment(AlignFrame af, String jarFile,
649 FileOutputStream fos = new FileOutputStream(jarFile);
650 JarOutputStream jout = new JarOutputStream(fos);
651 List<AlignFrame> frames = new ArrayList<AlignFrame>();
653 // resolve splitframes
654 if (af.getViewport().getCodingComplement() != null)
656 frames = ((SplitFrame) af.getSplitViewContainer()).getAlignFrames();
662 saveAllFrames(frames, jout);
666 } catch (Exception foo)
672 } catch (Exception ex)
674 errorMessage = "Couldn't Write alignment view to Jalview Archive - see error output for details";
675 ex.printStackTrace();
680 private void writeDatasetFor(Hashtable<String, AlignFrame> dsses,
681 String fileName, JarOutputStream jout)
684 for (String dssids : dsses.keySet())
686 AlignFrame _af = dsses.get(dssids);
687 String jfileName = fileName + " Dataset for " + _af.getTitle();
688 if (!jfileName.endsWith(".xml"))
690 jfileName = jfileName + ".xml";
692 saveState(_af.alignPanel, jfileName, true, jout, null);
697 * create a JalviewModel from an alignment view and marshall it to a
701 * panel to create jalview model for
703 * name of alignment panel written to output stream
710 public JalviewModel saveState(AlignmentPanel ap, String fileName,
711 JarOutputStream jout, List<String> viewIds)
713 return saveState(ap, fileName, false, jout, viewIds);
717 * create a JalviewModel from an alignment view and marshall it to a
721 * panel to create jalview model for
723 * name of alignment panel written to output stream
725 * when true, only write the dataset for the alignment, not the data
726 * associated with the view.
732 public JalviewModel saveState(AlignmentPanel ap, String fileName,
733 boolean storeDS, JarOutputStream jout, List<String> viewIds)
737 viewIds = new ArrayList<String>();
742 List<UserColourScheme> userColours = new ArrayList<UserColourScheme>();
744 AlignViewport av = ap.av;
746 JalviewModel object = new JalviewModel();
747 object.setVamsasModel(new jalview.schemabinding.version2.VamsasModel());
749 object.setCreationDate(new java.util.Date(System.currentTimeMillis()));
750 object.setVersion(jalview.bin.Cache.getDefault("VERSION",
751 "Development Build"));
754 * rjal is full height alignment, jal is actual alignment with full metadata
755 * but excludes hidden sequences.
757 jalview.datamodel.AlignmentI rjal = av.getAlignment(), jal = rjal;
759 if (av.hasHiddenRows())
761 rjal = jal.getHiddenSequences().getFullAlignment();
764 SequenceSet vamsasSet = new SequenceSet();
766 JalviewModelSequence jms = new JalviewModelSequence();
768 vamsasSet.setGapChar(jal.getGapCharacter() + "");
770 if (jal.getDataset() != null)
772 // dataset id is the dataset's hashcode
773 vamsasSet.setDatasetId(getDatasetIdRef(jal.getDataset()));
776 // switch jal and the dataset
777 jal = jal.getDataset();
781 if (jal.getProperties() != null)
783 Enumeration en = jal.getProperties().keys();
784 while (en.hasMoreElements())
786 String key = en.nextElement().toString();
787 SequenceSetProperties ssp = new SequenceSetProperties();
789 ssp.setValue(jal.getProperties().get(key).toString());
790 vamsasSet.addSequenceSetProperties(ssp);
795 Set<String> calcIdSet = new HashSet<String>();
796 // record the set of vamsas sequence XML POJO we create.
797 HashMap<String,Sequence> vamsasSetIds = new HashMap<String,Sequence>();
799 for (final SequenceI jds : rjal.getSequences())
801 final SequenceI jdatasq = jds.getDatasetSequence() == null ? jds
802 : jds.getDatasetSequence();
803 String id = seqHash(jds);
804 if (vamsasSetIds.get(id) == null)
806 if (seqRefIds.get(id) != null && !storeDS)
808 // This happens for two reasons: 1. multiple views are being
810 // 2. the hashCode has collided with another sequence's code. This
812 // HAPPEN! (PF00072.15.stk does this)
813 // JBPNote: Uncomment to debug writing out of files that do not read
814 // back in due to ArrayOutOfBoundExceptions.
815 // System.err.println("vamsasSeq backref: "+id+"");
816 // System.err.println(jds.getName()+"
817 // "+jds.getStart()+"-"+jds.getEnd()+" "+jds.getSequenceAsString());
818 // System.err.println("Hashcode: "+seqHash(jds));
819 // SequenceI rsq = (SequenceI) seqRefIds.get(id + "");
820 // System.err.println(rsq.getName()+"
821 // "+rsq.getStart()+"-"+rsq.getEnd()+" "+rsq.getSequenceAsString());
822 // System.err.println("Hashcode: "+seqHash(rsq));
826 vamsasSeq = createVamsasSequence(id, jds);
827 vamsasSet.addSequence(vamsasSeq);
828 vamsasSetIds.put(id, vamsasSeq);
829 seqRefIds.put(id, jds);
833 jseq.setStart(jds.getStart());
834 jseq.setEnd(jds.getEnd());
835 jseq.setColour(av.getSequenceColour(jds).getRGB());
837 jseq.setId(id); // jseq id should be a string not a number
840 // Store any sequences this sequence represents
841 if (av.hasHiddenRows())
843 // use rjal, contains the full height alignment
844 jseq.setHidden(av.getAlignment().getHiddenSequences()
847 if (av.isHiddenRepSequence(jds))
849 jalview.datamodel.SequenceI[] reps = av
850 .getRepresentedSequences(jds)
851 .getSequencesInOrder(rjal);
853 for (int h = 0; h < reps.length; h++)
857 jseq.addHiddenSequences(rjal.findIndex(reps[h]));
862 // mark sequence as reference - if it is the reference for this view
865 jseq.setViewreference(jds == jal.getSeqrep());
869 // TODO: omit sequence features from each alignment view's XML dump if we
870 // are storing dataset
871 if (jds.getSequenceFeatures() != null)
873 jalview.datamodel.SequenceFeature[] sf = jds.getSequenceFeatures();
875 while (index < sf.length)
877 Features features = new Features();
879 features.setBegin(sf[index].getBegin());
880 features.setEnd(sf[index].getEnd());
881 features.setDescription(sf[index].getDescription());
882 features.setType(sf[index].getType());
883 features.setFeatureGroup(sf[index].getFeatureGroup());
884 features.setScore(sf[index].getScore());
885 if (sf[index].links != null)
887 for (int l = 0; l < sf[index].links.size(); l++)
889 OtherData keyValue = new OtherData();
890 keyValue.setKey("LINK_" + l);
891 keyValue.setValue(sf[index].links.elementAt(l).toString());
892 features.addOtherData(keyValue);
895 if (sf[index].otherDetails != null)
898 Iterator<String> keys = sf[index].otherDetails.keySet()
900 while (keys.hasNext())
903 OtherData keyValue = new OtherData();
904 keyValue.setKey(key);
905 keyValue.setValue(sf[index].otherDetails.get(key).toString());
906 features.addOtherData(keyValue);
910 jseq.addFeatures(features);
915 if (jdatasq.getAllPDBEntries() != null)
917 Enumeration en = jdatasq.getAllPDBEntries().elements();
918 while (en.hasMoreElements())
920 Pdbids pdb = new Pdbids();
921 jalview.datamodel.PDBEntry entry = (jalview.datamodel.PDBEntry) en
924 String pdbId = entry.getId();
926 pdb.setType(entry.getType());
929 * Store any structure views associated with this sequence. This
930 * section copes with duplicate entries in the project, so a dataset
931 * only view *should* be coped with sensibly.
933 // This must have been loaded, is it still visible?
934 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
935 String matchedFile = null;
936 for (int f = frames.length - 1; f > -1; f--)
938 if (frames[f] instanceof StructureViewerBase)
940 StructureViewerBase viewFrame = (StructureViewerBase) frames[f];
941 matchedFile = saveStructureState(ap, jds, pdb, entry,
942 viewIds, matchedFile, viewFrame);
944 * Only store each structure viewer's state once in the project
945 * jar. First time through only (storeDS==false)
947 String viewId = viewFrame.getViewId();
948 if (!storeDS && !viewIds.contains(viewId))
953 String viewerState = viewFrame.getStateInfo();
954 writeJarEntry(jout, getViewerJarEntryName(viewId),
955 viewerState.getBytes());
956 } catch (IOException e)
958 System.err.println("Error saving viewer state: "
965 if (matchedFile != null || entry.getFile() != null)
967 if (entry.getFile() != null)
970 matchedFile = entry.getFile();
972 pdb.setFile(matchedFile); // entry.getFile());
973 if (pdbfiles == null)
975 pdbfiles = new ArrayList<String>();
978 if (!pdbfiles.contains(pdbId))
981 copyFileToJar(jout, matchedFile, pdbId);
985 if (entry.getProperty() != null && !entry.getProperty().isEmpty())
987 PdbentryItem item = new PdbentryItem();
988 Hashtable properties = entry.getProperty();
989 Enumeration en2 = properties.keys();
990 while (en2.hasMoreElements())
992 Property prop = new Property();
993 String key = en2.nextElement().toString();
995 prop.setValue(properties.get(key).toString());
996 item.addProperty(prop);
998 pdb.addPdbentryItem(item);
1001 jseq.addPdbids(pdb);
1005 saveRnaViewers(jout, jseq, jds, viewIds, ap, storeDS);
1010 if (!storeDS && av.hasHiddenRows())
1012 jal = av.getAlignment();
1016 if (storeDS && jal.getCodonFrames() != null)
1018 List<AlignedCodonFrame> jac = jal.getCodonFrames();
1019 for (AlignedCodonFrame acf : jac)
1021 AlcodonFrame alc = new AlcodonFrame();
1022 if (acf.getProtMappings() != null
1023 && acf.getProtMappings().length > 0)
1025 boolean hasMap = false;
1026 SequenceI[] dnas = acf.getdnaSeqs();
1027 jalview.datamodel.Mapping[] pmaps = acf.getProtMappings();
1028 for (int m = 0; m < pmaps.length; m++)
1030 AlcodMap alcmap = new AlcodMap();
1031 alcmap.setDnasq(seqHash(dnas[m]));
1032 alcmap.setMapping(createVamsasMapping(pmaps[m], dnas[m], null,
1034 alc.addAlcodMap(alcmap);
1039 vamsasSet.addAlcodonFrame(alc);
1042 // TODO: delete this ? dead code from 2.8.3->2.9 ?
1044 // AlcodonFrame alc = new AlcodonFrame();
1045 // vamsasSet.addAlcodonFrame(alc);
1046 // for (int p = 0; p < acf.aaWidth; p++)
1048 // Alcodon cmap = new Alcodon();
1049 // if (acf.codons[p] != null)
1051 // // Null codons indicate a gapped column in the translated peptide
1053 // cmap.setPos1(acf.codons[p][0]);
1054 // cmap.setPos2(acf.codons[p][1]);
1055 // cmap.setPos3(acf.codons[p][2]);
1057 // alc.addAlcodon(cmap);
1059 // if (acf.getProtMappings() != null
1060 // && acf.getProtMappings().length > 0)
1062 // SequenceI[] dnas = acf.getdnaSeqs();
1063 // jalview.datamodel.Mapping[] pmaps = acf.getProtMappings();
1064 // for (int m = 0; m < pmaps.length; m++)
1066 // AlcodMap alcmap = new AlcodMap();
1067 // alcmap.setDnasq(seqHash(dnas[m]));
1068 // alcmap.setMapping(createVamsasMapping(pmaps[m], dnas[m], null,
1070 // alc.addAlcodMap(alcmap);
1077 // /////////////////////////////////
1078 if (!storeDS && av.currentTree != null)
1080 // FIND ANY ASSOCIATED TREES
1081 // NOT IMPLEMENTED FOR HEADLESS STATE AT PRESENT
1082 if (Desktop.desktop != null)
1084 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1086 for (int t = 0; t < frames.length; t++)
1088 if (frames[t] instanceof TreePanel)
1090 TreePanel tp = (TreePanel) frames[t];
1092 if (tp.treeCanvas.av.getAlignment() == jal)
1094 Tree tree = new Tree();
1095 tree.setTitle(tp.getTitle());
1096 tree.setCurrentTree((av.currentTree == tp.getTree()));
1097 tree.setNewick(tp.getTree().toString());
1098 tree.setThreshold(tp.treeCanvas.threshold);
1100 tree.setFitToWindow(tp.fitToWindow.getState());
1101 tree.setFontName(tp.getTreeFont().getName());
1102 tree.setFontSize(tp.getTreeFont().getSize());
1103 tree.setFontStyle(tp.getTreeFont().getStyle());
1104 tree.setMarkUnlinked(tp.placeholdersMenu.getState());
1106 tree.setShowBootstrap(tp.bootstrapMenu.getState());
1107 tree.setShowDistances(tp.distanceMenu.getState());
1109 tree.setHeight(tp.getHeight());
1110 tree.setWidth(tp.getWidth());
1111 tree.setXpos(tp.getX());
1112 tree.setYpos(tp.getY());
1113 tree.setId(makeHashCode(tp, null));
1123 * store forward refs from an annotationRow to any groups
1125 IdentityHashMap<SequenceGroup, String> groupRefs = new IdentityHashMap<SequenceGroup, String>();
1128 for (SequenceI sq : jal.getSequences())
1130 // Store annotation on dataset sequences only
1131 AlignmentAnnotation[] aa = sq.getAnnotation();
1132 if (aa != null && aa.length > 0)
1134 storeAlignmentAnnotation(aa, groupRefs, av, calcIdSet, storeDS,
1141 if (jal.getAlignmentAnnotation() != null)
1143 // Store the annotation shown on the alignment.
1144 AlignmentAnnotation[] aa = jal.getAlignmentAnnotation();
1145 storeAlignmentAnnotation(aa, groupRefs, av, calcIdSet, storeDS,
1150 if (jal.getGroups() != null)
1152 JGroup[] groups = new JGroup[jal.getGroups().size()];
1154 for (jalview.datamodel.SequenceGroup sg : jal.getGroups())
1156 JGroup jGroup = new JGroup();
1157 groups[++i] = jGroup;
1159 jGroup.setStart(sg.getStartRes());
1160 jGroup.setEnd(sg.getEndRes());
1161 jGroup.setName(sg.getName());
1162 if (groupRefs.containsKey(sg))
1164 // group has references so set its ID field
1165 jGroup.setId(groupRefs.get(sg));
1169 if (sg.cs.conservationApplied())
1171 jGroup.setConsThreshold(sg.cs.getConservationInc());
1173 if (sg.cs instanceof jalview.schemes.UserColourScheme)
1175 jGroup.setColour(setUserColourScheme(sg.cs, userColours, jms));
1179 jGroup.setColour(ColourSchemeProperty.getColourName(sg.cs));
1182 else if (sg.cs instanceof jalview.schemes.AnnotationColourGradient)
1184 jGroup.setColour("AnnotationColourGradient");
1185 jGroup.setAnnotationColours(constructAnnotationColours(
1186 (jalview.schemes.AnnotationColourGradient) sg.cs,
1189 else if (sg.cs instanceof jalview.schemes.UserColourScheme)
1191 jGroup.setColour(setUserColourScheme(sg.cs, userColours, jms));
1195 jGroup.setColour(ColourSchemeProperty.getColourName(sg.cs));
1198 jGroup.setPidThreshold(sg.cs.getThreshold());
1201 jGroup.setOutlineColour(sg.getOutlineColour().getRGB());
1202 jGroup.setDisplayBoxes(sg.getDisplayBoxes());
1203 jGroup.setDisplayText(sg.getDisplayText());
1204 jGroup.setColourText(sg.getColourText());
1205 jGroup.setTextCol1(sg.textColour.getRGB());
1206 jGroup.setTextCol2(sg.textColour2.getRGB());
1207 jGroup.setTextColThreshold(sg.thresholdTextColour);
1208 jGroup.setShowUnconserved(sg.getShowNonconserved());
1209 jGroup.setIgnoreGapsinConsensus(sg.getIgnoreGapsConsensus());
1210 jGroup.setShowConsensusHistogram(sg.isShowConsensusHistogram());
1211 jGroup.setShowSequenceLogo(sg.isShowSequenceLogo());
1212 jGroup.setNormaliseSequenceLogo(sg.isNormaliseSequenceLogo());
1213 for (SequenceI seq : sg.getSequences())
1215 jGroup.addSeq(seqHash(seq));
1219 jms.setJGroup(groups);
1223 // /////////SAVE VIEWPORT
1224 Viewport view = new Viewport();
1225 view.setTitle(ap.alignFrame.getTitle());
1226 view.setSequenceSetId(makeHashCode(av.getSequenceSetId(),
1227 av.getSequenceSetId()));
1228 view.setId(av.getViewId());
1229 if (av.getCodingComplement() != null)
1231 view.setComplementId(av.getCodingComplement().getViewId());
1233 view.setViewName(av.viewName);
1234 view.setGatheredViews(av.isGatherViewsHere());
1236 Rectangle size = ap.av.getExplodedGeometry();
1237 Rectangle position = size;
1240 size = ap.alignFrame.getBounds();
1241 if (av.getCodingComplement() != null)
1243 position = ((SplitFrame) ap.alignFrame.getSplitViewContainer())
1251 view.setXpos(position.x);
1252 view.setYpos(position.y);
1254 view.setWidth(size.width);
1255 view.setHeight(size.height);
1257 view.setStartRes(av.startRes);
1258 view.setStartSeq(av.startSeq);
1260 if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme)
1262 view.setBgColour(setUserColourScheme(av.getGlobalColourScheme(),
1265 else if (av.getGlobalColourScheme() instanceof jalview.schemes.AnnotationColourGradient)
1267 AnnotationColours ac = constructAnnotationColours(
1268 (jalview.schemes.AnnotationColourGradient) av
1269 .getGlobalColourScheme(),
1272 view.setAnnotationColours(ac);
1273 view.setBgColour("AnnotationColourGradient");
1277 view.setBgColour(ColourSchemeProperty.getColourName(av
1278 .getGlobalColourScheme()));
1281 ColourSchemeI cs = av.getGlobalColourScheme();
1285 if (cs.conservationApplied())
1287 view.setConsThreshold(cs.getConservationInc());
1288 if (cs instanceof jalview.schemes.UserColourScheme)
1290 view.setBgColour(setUserColourScheme(cs, userColours, jms));
1294 if (cs instanceof ResidueColourScheme)
1296 view.setPidThreshold(cs.getThreshold());
1300 view.setConservationSelected(av.getConservationSelected());
1301 view.setPidSelected(av.getAbovePIDThreshold());
1302 view.setFontName(av.font.getName());
1303 view.setFontSize(av.font.getSize());
1304 view.setFontStyle(av.font.getStyle());
1305 view.setScaleProteinAsCdna(av.getViewStyle().isScaleProteinAsCdna());
1306 view.setRenderGaps(av.isRenderGaps());
1307 view.setShowAnnotation(av.isShowAnnotation());
1308 view.setShowBoxes(av.getShowBoxes());
1309 view.setShowColourText(av.getColourText());
1310 view.setShowFullId(av.getShowJVSuffix());
1311 view.setRightAlignIds(av.isRightAlignIds());
1312 view.setShowSequenceFeatures(av.isShowSequenceFeatures());
1313 view.setShowText(av.getShowText());
1314 view.setShowUnconserved(av.getShowUnconserved());
1315 view.setWrapAlignment(av.getWrapAlignment());
1316 view.setTextCol1(av.getTextColour().getRGB());
1317 view.setTextCol2(av.getTextColour2().getRGB());
1318 view.setTextColThreshold(av.getThresholdTextColour());
1319 view.setShowConsensusHistogram(av.isShowConsensusHistogram());
1320 view.setShowSequenceLogo(av.isShowSequenceLogo());
1321 view.setNormaliseSequenceLogo(av.isNormaliseSequenceLogo());
1322 view.setShowGroupConsensus(av.isShowGroupConsensus());
1323 view.setShowGroupConservation(av.isShowGroupConservation());
1324 view.setShowNPfeatureTooltip(av.isShowNPFeats());
1325 view.setShowDbRefTooltip(av.isShowDBRefs());
1326 view.setFollowHighlight(av.isFollowHighlight());
1327 view.setFollowSelection(av.followSelection);
1328 view.setIgnoreGapsinConsensus(av.isIgnoreGapsConsensus());
1329 if (av.getFeaturesDisplayed() != null)
1331 jalview.schemabinding.version2.FeatureSettings fs = new jalview.schemabinding.version2.FeatureSettings();
1333 String[] renderOrder = ap.getSeqPanel().seqCanvas
1334 .getFeatureRenderer().getRenderOrder()
1335 .toArray(new String[0]);
1337 Vector<String> settingsAdded = new Vector<String>();
1338 if (renderOrder != null)
1340 for (String featureType : renderOrder)
1342 FeatureColourI fcol = ap.getSeqPanel().seqCanvas
1343 .getFeatureRenderer()
1344 .getFeatureStyle(featureType);
1345 Setting setting = new Setting();
1346 setting.setType(featureType);
1347 if (!fcol.isSimpleColour())
1349 setting.setColour(fcol.getMaxColour().getRGB());
1350 setting.setMincolour(fcol.getMinColour().getRGB());
1351 setting.setMin(fcol.getMin());
1352 setting.setMax(fcol.getMax());
1353 setting.setColourByLabel(fcol.isColourByLabel());
1354 setting.setAutoScale(fcol.isAutoScaled());
1355 setting.setThreshold(fcol.getThreshold());
1356 // -1 = No threshold, 0 = Below, 1 = Above
1357 setting.setThreshstate(fcol.isAboveThreshold() ? 1
1358 : (fcol.isBelowThreshold() ? 0 : -1));
1362 setting.setColour(fcol.getColour().getRGB());
1365 setting.setDisplay(av.getFeaturesDisplayed().isVisible(
1367 float rorder = ap.getSeqPanel().seqCanvas.getFeatureRenderer()
1368 .getOrder(featureType);
1371 setting.setOrder(rorder);
1373 fs.addSetting(setting);
1374 settingsAdded.addElement(featureType);
1378 // is groups actually supposed to be a map here ?
1379 Iterator<String> en = ap.getSeqPanel().seqCanvas
1380 .getFeatureRenderer()
1381 .getFeatureGroups().iterator();
1382 Vector<String> groupsAdded = new Vector<String>();
1383 while (en.hasNext())
1385 String grp = en.next();
1386 if (groupsAdded.contains(grp))
1390 Group g = new Group();
1392 g.setDisplay(((Boolean) ap.getSeqPanel().seqCanvas
1393 .getFeatureRenderer().checkGroupVisibility(grp, false))
1396 groupsAdded.addElement(grp);
1398 jms.setFeatureSettings(fs);
1401 if (av.hasHiddenColumns())
1403 if (av.getColumnSelection() == null
1404 || av.getColumnSelection().getHiddenColumns() == null)
1406 warn("REPORT BUG: avoided null columnselection bug (DMAM reported). Please contact Jim about this.");
1410 for (int c = 0; c < av.getColumnSelection().getHiddenColumns()
1413 int[] region = av.getColumnSelection().getHiddenColumns()
1415 HiddenColumns hc = new HiddenColumns();
1416 hc.setStart(region[0]);
1417 hc.setEnd(region[1]);
1418 view.addHiddenColumns(hc);
1422 if (calcIdSet.size() > 0)
1424 for (String calcId : calcIdSet)
1426 if (calcId.trim().length() > 0)
1428 CalcIdParam cidp = createCalcIdParam(calcId, av);
1429 // Some calcIds have no parameters.
1432 view.addCalcIdParam(cidp);
1438 jms.addViewport(view);
1440 object.setJalviewModelSequence(jms);
1441 object.getVamsasModel().addSequenceSet(vamsasSet);
1443 if (jout != null && fileName != null)
1445 // We may not want to write the object to disk,
1446 // eg we can copy the alignViewport to a new view object
1447 // using save and then load
1450 System.out.println("Writing jar entry " + fileName);
1451 JarEntry entry = new JarEntry(fileName);
1452 jout.putNextEntry(entry);
1453 PrintWriter pout = new PrintWriter(new OutputStreamWriter(jout,
1455 Marshaller marshaller = new Marshaller(pout);
1456 marshaller.marshal(object);
1459 } catch (Exception ex)
1461 // TODO: raise error in GUI if marshalling failed.
1462 ex.printStackTrace();
1469 * Save any Varna viewers linked to this sequence. Writes an rnaViewer element
1470 * for each viewer, with
1472 * <li>viewer geometry (position, size, split pane divider location)</li>
1473 * <li>index of the selected structure in the viewer (currently shows gapped
1475 * <li>the id of the annotation holding RNA secondary structure</li>
1476 * <li>(currently only one SS is shown per viewer, may be more in future)</li>
1478 * Varna viewer state is also written out (in native Varna XML) to separate
1479 * project jar entries. A separate entry is written for each RNA structure
1480 * displayed, with the naming convention
1482 * <li>rna_viewId_sequenceId_annotationId_[gapped|trimmed]</li>
1490 * @param storeDataset
1492 protected void saveRnaViewers(JarOutputStream jout, JSeq jseq,
1493 final SequenceI jds, List<String> viewIds, AlignmentPanel ap,
1494 boolean storeDataset)
1496 if (Desktop.desktop == null)
1500 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1501 for (int f = frames.length - 1; f > -1; f--)
1503 if (frames[f] instanceof AppVarna)
1505 AppVarna varna = (AppVarna) frames[f];
1507 * link the sequence to every viewer that is showing it and is linked to
1508 * its alignment panel
1510 if (varna.isListeningFor(jds) && ap == varna.getAlignmentPanel())
1512 String viewId = varna.getViewId();
1513 RnaViewer rna = new RnaViewer();
1514 rna.setViewId(viewId);
1515 rna.setTitle(varna.getTitle());
1516 rna.setXpos(varna.getX());
1517 rna.setYpos(varna.getY());
1518 rna.setWidth(varna.getWidth());
1519 rna.setHeight(varna.getHeight());
1520 rna.setDividerLocation(varna.getDividerLocation());
1521 rna.setSelectedRna(varna.getSelectedIndex());
1522 jseq.addRnaViewer(rna);
1525 * Store each Varna panel's state once in the project per sequence.
1526 * First time through only (storeDataset==false)
1528 // boolean storeSessions = false;
1529 // String sequenceViewId = viewId + seqsToIds.get(jds);
1530 // if (!storeDataset && !viewIds.contains(sequenceViewId))
1532 // viewIds.add(sequenceViewId);
1533 // storeSessions = true;
1535 for (RnaModel model : varna.getModels())
1537 if (model.seq == jds)
1540 * VARNA saves each view (sequence or alignment secondary
1541 * structure, gapped or trimmed) as a separate XML file
1543 String jarEntryName = rnaSessions.get(model);
1544 if (jarEntryName == null)
1547 String varnaStateFile = varna.getStateInfo(model.rna);
1548 jarEntryName = RNA_PREFIX + viewId + "_" + nextCounter();
1549 copyFileToJar(jout, varnaStateFile, jarEntryName);
1550 rnaSessions.put(model, jarEntryName);
1552 SecondaryStructure ss = new SecondaryStructure();
1553 String annotationId = varna.getAnnotation(jds).annotationId;
1554 ss.setAnnotationId(annotationId);
1555 ss.setViewerState(jarEntryName);
1556 ss.setGapped(model.gapped);
1557 ss.setTitle(model.title);
1558 rna.addSecondaryStructure(ss);
1567 * Copy the contents of a file to a new entry added to the output jar
1571 * @param jarEntryName
1573 protected void copyFileToJar(JarOutputStream jout, String infilePath,
1574 String jarEntryName)
1576 DataInputStream dis = null;
1579 File file = new File(infilePath);
1580 if (file.exists() && jout != null)
1582 dis = new DataInputStream(new FileInputStream(file));
1583 byte[] data = new byte[(int) file.length()];
1584 dis.readFully(data);
1585 writeJarEntry(jout, jarEntryName, data);
1587 } catch (Exception ex)
1589 ex.printStackTrace();
1597 } catch (IOException e)
1606 * Write the data to a new entry of given name in the output jar file
1609 * @param jarEntryName
1611 * @throws IOException
1613 protected void writeJarEntry(JarOutputStream jout, String jarEntryName,
1614 byte[] data) throws IOException
1618 System.out.println("Writing jar entry " + jarEntryName);
1619 jout.putNextEntry(new JarEntry(jarEntryName));
1620 DataOutputStream dout = new DataOutputStream(jout);
1621 dout.write(data, 0, data.length);
1628 * Save the state of a structure viewer
1633 * the archive XML element under which to save the state
1636 * @param matchedFile
1640 protected String saveStructureState(AlignmentPanel ap, SequenceI jds,
1641 Pdbids pdb, PDBEntry entry, List<String> viewIds,
1642 String matchedFile, StructureViewerBase viewFrame)
1644 final AAStructureBindingModel bindingModel = viewFrame.getBinding();
1647 * Look for any bindings for this viewer to the PDB file of interest
1648 * (including part matches excluding chain id)
1650 for (int peid = 0; peid < bindingModel.getPdbCount(); peid++)
1652 final PDBEntry pdbentry = bindingModel.getPdbEntry(peid);
1653 final String pdbId = pdbentry.getId();
1654 if (!pdbId.equals(entry.getId())
1655 && !(entry.getId().length() > 4 && entry.getId()
1656 .toLowerCase().startsWith(pdbId.toLowerCase())))
1659 * not interested in a binding to a different PDB entry here
1663 if (matchedFile == null)
1665 matchedFile = pdbentry.getFile();
1667 else if (!matchedFile.equals(pdbentry.getFile()))
1670 .warn("Probably lost some PDB-Sequence mappings for this structure file (which apparently has same PDB Entry code): "
1671 + pdbentry.getFile());
1675 // can get at it if the ID
1676 // match is ambiguous (e.g.
1679 for (int smap = 0; smap < viewFrame.getBinding().getSequence()[peid].length; smap++)
1681 // if (jal.findIndex(jmol.jmb.sequence[peid][smap]) > -1)
1682 if (jds == viewFrame.getBinding().getSequence()[peid][smap])
1684 StructureState state = new StructureState();
1685 state.setVisible(true);
1686 state.setXpos(viewFrame.getX());
1687 state.setYpos(viewFrame.getY());
1688 state.setWidth(viewFrame.getWidth());
1689 state.setHeight(viewFrame.getHeight());
1690 final String viewId = viewFrame.getViewId();
1691 state.setViewId(viewId);
1692 state.setAlignwithAlignPanel(viewFrame.isUsedforaligment(ap));
1693 state.setColourwithAlignPanel(viewFrame.isUsedforcolourby(ap));
1694 state.setColourByJmol(viewFrame.isColouredByViewer());
1695 state.setType(viewFrame.getViewerType().toString());
1696 pdb.addStructureState(state);
1703 private AnnotationColours constructAnnotationColours(
1704 AnnotationColourGradient acg, List<UserColourScheme> userColours,
1705 JalviewModelSequence jms)
1707 AnnotationColours ac = new AnnotationColours();
1708 ac.setAboveThreshold(acg.getAboveThreshold());
1709 ac.setThreshold(acg.getAnnotationThreshold());
1710 ac.setAnnotation(acg.getAnnotation());
1711 if (acg.getBaseColour() instanceof jalview.schemes.UserColourScheme)
1713 ac.setColourScheme(setUserColourScheme(acg.getBaseColour(),
1718 ac.setColourScheme(ColourSchemeProperty.getColourName(acg
1722 ac.setMaxColour(acg.getMaxColour().getRGB());
1723 ac.setMinColour(acg.getMinColour().getRGB());
1724 ac.setPerSequence(acg.isSeqAssociated());
1725 ac.setPredefinedColours(acg.isPredefinedColours());
1729 private void storeAlignmentAnnotation(AlignmentAnnotation[] aa,
1730 IdentityHashMap<SequenceGroup, String> groupRefs,
1731 AlignmentViewport av, Set<String> calcIdSet, boolean storeDS,
1732 SequenceSet vamsasSet)
1735 for (int i = 0; i < aa.length; i++)
1737 Annotation an = new Annotation();
1739 AlignmentAnnotation annotation = aa[i];
1740 if (annotation.annotationId != null)
1742 annotationIds.put(annotation.annotationId, annotation);
1745 an.setId(annotation.annotationId);
1747 an.setVisible(annotation.visible);
1749 an.setDescription(annotation.description);
1751 if (annotation.sequenceRef != null)
1753 // 2.9 JAL-1781 xref on sequence id rather than name
1754 an.setSequenceRef(seqsToIds.get(annotation.sequenceRef));
1756 if (annotation.groupRef != null)
1758 String groupIdr = groupRefs.get(annotation.groupRef);
1759 if (groupIdr == null)
1761 // make a locally unique String
1763 annotation.groupRef,
1764 groupIdr = ("" + System.currentTimeMillis()
1765 + annotation.groupRef.getName() + groupRefs
1768 an.setGroupRef(groupIdr.toString());
1771 // store all visualization attributes for annotation
1772 an.setGraphHeight(annotation.graphHeight);
1773 an.setCentreColLabels(annotation.centreColLabels);
1774 an.setScaleColLabels(annotation.scaleColLabel);
1775 an.setShowAllColLabels(annotation.showAllColLabels);
1776 an.setBelowAlignment(annotation.belowAlignment);
1778 if (annotation.graph > 0)
1781 an.setGraphType(annotation.graph);
1782 an.setGraphGroup(annotation.graphGroup);
1783 if (annotation.getThreshold() != null)
1785 ThresholdLine line = new ThresholdLine();
1786 line.setLabel(annotation.getThreshold().label);
1787 line.setValue(annotation.getThreshold().value);
1788 line.setColour(annotation.getThreshold().colour.getRGB());
1789 an.setThresholdLine(line);
1797 an.setLabel(annotation.label);
1799 if (annotation == av.getAlignmentQualityAnnot()
1800 || annotation == av.getAlignmentConservationAnnotation()
1801 || annotation == av.getAlignmentConsensusAnnotation()
1802 || annotation.autoCalculated)
1804 // new way of indicating autocalculated annotation -
1805 an.setAutoCalculated(annotation.autoCalculated);
1807 if (annotation.hasScore())
1809 an.setScore(annotation.getScore());
1812 if (annotation.getCalcId() != null)
1814 calcIdSet.add(annotation.getCalcId());
1815 an.setCalcId(annotation.getCalcId());
1817 if (annotation.hasProperties())
1819 for (String pr : annotation.getProperties())
1821 Property prop = new Property();
1823 prop.setValue(annotation.getProperty(pr));
1824 an.addProperty(prop);
1828 AnnotationElement ae;
1829 if (annotation.annotations != null)
1831 an.setScoreOnly(false);
1832 for (int a = 0; a < annotation.annotations.length; a++)
1834 if ((annotation == null) || (annotation.annotations[a] == null))
1839 ae = new AnnotationElement();
1840 if (annotation.annotations[a].description != null)
1842 ae.setDescription(annotation.annotations[a].description);
1844 if (annotation.annotations[a].displayCharacter != null)
1846 ae.setDisplayCharacter(annotation.annotations[a].displayCharacter);
1849 if (!Float.isNaN(annotation.annotations[a].value))
1851 ae.setValue(annotation.annotations[a].value);
1855 if (annotation.annotations[a].secondaryStructure > ' ')
1857 ae.setSecondaryStructure(annotation.annotations[a].secondaryStructure
1861 if (annotation.annotations[a].colour != null
1862 && annotation.annotations[a].colour != java.awt.Color.black)
1864 ae.setColour(annotation.annotations[a].colour.getRGB());
1867 an.addAnnotationElement(ae);
1868 if (annotation.autoCalculated)
1870 // only write one non-null entry into the annotation row -
1871 // sufficient to get the visualization attributes necessary to
1879 an.setScoreOnly(true);
1881 if (!storeDS || (storeDS && !annotation.autoCalculated))
1883 // skip autocalculated annotation - these are only provided for
1885 vamsasSet.addAnnotation(an);
1891 private CalcIdParam createCalcIdParam(String calcId, AlignViewport av)
1893 AutoCalcSetting settings = av.getCalcIdSettingsFor(calcId);
1894 if (settings != null)
1896 CalcIdParam vCalcIdParam = new CalcIdParam();
1897 vCalcIdParam.setCalcId(calcId);
1898 vCalcIdParam.addServiceURL(settings.getServiceURI());
1899 // generic URI allowing a third party to resolve another instance of the
1900 // service used for this calculation
1901 for (String urls : settings.getServiceURLs())
1903 vCalcIdParam.addServiceURL(urls);
1905 vCalcIdParam.setVersion("1.0");
1906 if (settings.getPreset() != null)
1908 WsParamSetI setting = settings.getPreset();
1909 vCalcIdParam.setName(setting.getName());
1910 vCalcIdParam.setDescription(setting.getDescription());
1914 vCalcIdParam.setName("");
1915 vCalcIdParam.setDescription("Last used parameters");
1917 // need to be able to recover 1) settings 2) user-defined presets or
1918 // recreate settings from preset 3) predefined settings provided by
1919 // service - or settings that can be transferred (or discarded)
1920 vCalcIdParam.setParameters(settings.getWsParamFile().replace("\n",
1922 vCalcIdParam.setAutoUpdate(settings.isAutoUpdate());
1923 // todo - decide if updateImmediately is needed for any projects.
1925 return vCalcIdParam;
1930 private boolean recoverCalcIdParam(CalcIdParam calcIdParam,
1933 if (calcIdParam.getVersion().equals("1.0"))
1935 Jws2Instance service = Jws2Discoverer.getDiscoverer()
1936 .getPreferredServiceFor(calcIdParam.getServiceURL());
1937 if (service != null)
1939 WsParamSetI parmSet = null;
1942 parmSet = service.getParamStore().parseServiceParameterFile(
1943 calcIdParam.getName(), calcIdParam.getDescription(),
1944 calcIdParam.getServiceURL(),
1945 calcIdParam.getParameters().replace("|\\n|", "\n"));
1946 } catch (IOException x)
1948 warn("Couldn't parse parameter data for "
1949 + calcIdParam.getCalcId(), x);
1952 List<ArgumentI> argList = null;
1953 if (calcIdParam.getName().length() > 0)
1955 parmSet = service.getParamStore()
1956 .getPreset(calcIdParam.getName());
1957 if (parmSet != null)
1959 // TODO : check we have a good match with settings in AACon -
1960 // otherwise we'll need to create a new preset
1965 argList = parmSet.getArguments();
1968 AAConSettings settings = new AAConSettings(
1969 calcIdParam.isAutoUpdate(), service, parmSet, argList);
1970 av.setCalcIdSettingsFor(calcIdParam.getCalcId(), settings,
1971 calcIdParam.isNeedsUpdate());
1976 warn("Cannot resolve a service for the parameters used in this project. Try configuring a JABAWS server.");
1980 throw new Error(MessageManager.formatMessage(
1981 "error.unsupported_version_calcIdparam",
1982 new Object[] { calcIdParam.toString() }));
1986 * External mapping between jalview objects and objects yielding a valid and
1987 * unique object ID string. This is null for normal Jalview project IO, but
1988 * non-null when a jalview project is being read or written as part of a
1991 IdentityHashMap jv2vobj = null;
1994 * Construct a unique ID for jvobj using either existing bindings or if none
1995 * exist, the result of the hashcode call for the object.
1998 * jalview data object
1999 * @return unique ID for referring to jvobj
2001 private String makeHashCode(Object jvobj, String altCode)
2003 if (jv2vobj != null)
2005 Object id = jv2vobj.get(jvobj);
2008 return id.toString();
2010 // check string ID mappings
2011 if (jvids2vobj != null && jvobj instanceof String)
2013 id = jvids2vobj.get(jvobj);
2017 return id.toString();
2019 // give up and warn that something has gone wrong
2020 warn("Cannot find ID for object in external mapping : " + jvobj);
2026 * return local jalview object mapped to ID, if it exists
2030 * @return null or object bound to idcode
2032 private Object retrieveExistingObj(String idcode)
2034 if (idcode != null && vobj2jv != null)
2036 return vobj2jv.get(idcode);
2042 * binding from ID strings from external mapping table to jalview data model
2045 private Hashtable vobj2jv;
2047 private Sequence createVamsasSequence(String id, SequenceI jds)
2049 return createVamsasSequence(true, id, jds, null);
2052 private Sequence createVamsasSequence(boolean recurse, String id,
2053 SequenceI jds, SequenceI parentseq)
2055 Sequence vamsasSeq = new Sequence();
2056 vamsasSeq.setId(id);
2057 vamsasSeq.setName(jds.getName());
2058 vamsasSeq.setSequence(jds.getSequenceAsString());
2059 vamsasSeq.setDescription(jds.getDescription());
2060 jalview.datamodel.DBRefEntry[] dbrefs = null;
2061 if (jds.getDatasetSequence() != null)
2063 vamsasSeq.setDsseqid(seqHash(jds.getDatasetSequence()));
2067 // seqId==dsseqid so we can tell which sequences really are
2068 // dataset sequences only
2069 vamsasSeq.setDsseqid(id);
2070 dbrefs = jds.getDBRefs();
2071 if (parentseq == null)
2078 for (int d = 0; d < dbrefs.length; d++)
2080 DBRef dbref = new DBRef();
2081 dbref.setSource(dbrefs[d].getSource());
2082 dbref.setVersion(dbrefs[d].getVersion());
2083 dbref.setAccessionId(dbrefs[d].getAccessionId());
2084 if (dbrefs[d].hasMap())
2086 Mapping mp = createVamsasMapping(dbrefs[d].getMap(), parentseq,
2088 dbref.setMapping(mp);
2090 vamsasSeq.addDBRef(dbref);
2096 private Mapping createVamsasMapping(jalview.datamodel.Mapping jmp,
2097 SequenceI parentseq, SequenceI jds, boolean recurse)
2100 if (jmp.getMap() != null)
2104 jalview.util.MapList mlst = jmp.getMap();
2105 List<int[]> r = mlst.getFromRanges();
2106 for (int[] range : r)
2108 MapListFrom mfrom = new MapListFrom();
2109 mfrom.setStart(range[0]);
2110 mfrom.setEnd(range[1]);
2111 mp.addMapListFrom(mfrom);
2113 r = mlst.getToRanges();
2114 for (int[] range : r)
2116 MapListTo mto = new MapListTo();
2117 mto.setStart(range[0]);
2118 mto.setEnd(range[1]);
2119 mp.addMapListTo(mto);
2121 mp.setMapFromUnit(mlst.getFromRatio());
2122 mp.setMapToUnit(mlst.getToRatio());
2123 if (jmp.getTo() != null)
2125 MappingChoice mpc = new MappingChoice();
2127 // check/create ID for the sequence referenced by getTo()
2130 SequenceI ps = null;
2131 if (parentseq != jmp.getTo()
2132 && parentseq.getDatasetSequence() != jmp.getTo())
2134 // chaining dbref rather than a handshaking one
2135 jmpid = seqHash(ps = jmp.getTo());
2139 jmpid = seqHash(ps = parentseq);
2141 mpc.setDseqFor(jmpid);
2142 if (!seqRefIds.containsKey(mpc.getDseqFor()))
2144 jalview.bin.Cache.log.debug("creatign new DseqFor ID");
2145 seqRefIds.put(mpc.getDseqFor(), ps);
2149 jalview.bin.Cache.log.debug("reusing DseqFor ID");
2152 mp.setMappingChoice(mpc);
2158 String setUserColourScheme(jalview.schemes.ColourSchemeI cs,
2159 List<UserColourScheme> userColours, JalviewModelSequence jms)
2162 jalview.schemes.UserColourScheme ucs = (jalview.schemes.UserColourScheme) cs;
2163 boolean newucs = false;
2164 if (!userColours.contains(ucs))
2166 userColours.add(ucs);
2169 id = "ucs" + userColours.indexOf(ucs);
2172 // actually create the scheme's entry in the XML model
2173 java.awt.Color[] colours = ucs.getColours();
2174 jalview.schemabinding.version2.UserColours uc = new jalview.schemabinding.version2.UserColours();
2175 jalview.schemabinding.version2.UserColourScheme jbucs = new jalview.schemabinding.version2.UserColourScheme();
2177 for (int i = 0; i < colours.length; i++)
2179 jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();
2180 col.setName(ResidueProperties.aa[i]);
2181 col.setRGB(jalview.util.Format.getHexString(colours[i]));
2182 jbucs.addColour(col);
2184 if (ucs.getLowerCaseColours() != null)
2186 colours = ucs.getLowerCaseColours();
2187 for (int i = 0; i < colours.length; i++)
2189 jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();
2190 col.setName(ResidueProperties.aa[i].toLowerCase());
2191 col.setRGB(jalview.util.Format.getHexString(colours[i]));
2192 jbucs.addColour(col);
2197 uc.setUserColourScheme(jbucs);
2198 jms.addUserColours(uc);
2204 jalview.schemes.UserColourScheme getUserColourScheme(
2205 JalviewModelSequence jms, String id)
2207 UserColours[] uc = jms.getUserColours();
2208 UserColours colours = null;
2210 for (int i = 0; i < uc.length; i++)
2212 if (uc[i].getId().equals(id))
2220 java.awt.Color[] newColours = new java.awt.Color[24];
2222 for (int i = 0; i < 24; i++)
2224 newColours[i] = new java.awt.Color(Integer.parseInt(colours
2225 .getUserColourScheme().getColour(i).getRGB(), 16));
2228 jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(
2231 if (colours.getUserColourScheme().getColourCount() > 24)
2233 newColours = new java.awt.Color[23];
2234 for (int i = 0; i < 23; i++)
2236 newColours[i] = new java.awt.Color(Integer.parseInt(colours
2237 .getUserColourScheme().getColour(i + 24).getRGB(), 16));
2239 ucs.setLowerCaseColours(newColours);
2246 * contains last error message (if any) encountered by XML loader.
2248 String errorMessage = null;
2251 * flag to control whether the Jalview2XML_V1 parser should be deferred to if
2252 * exceptions are raised during project XML parsing
2254 public boolean attemptversion1parse = true;
2257 * Load a jalview project archive from a jar file
2260 * - HTTP URL or filename
2262 public AlignFrame loadJalviewAlign(final String file)
2265 jalview.gui.AlignFrame af = null;
2269 // create list to store references for any new Jmol viewers created
2270 newStructureViewers = new Vector<JalviewStructureDisplayI>();
2271 // UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
2272 // Workaround is to make sure caller implements the JarInputStreamProvider
2274 // so we can re-open the jar input stream for each entry.
2276 jarInputStreamProvider jprovider = createjarInputStreamProvider(file);
2277 af = loadJalviewAlign(jprovider);
2279 } catch (MalformedURLException e)
2281 errorMessage = "Invalid URL format for '" + file + "'";
2287 SwingUtilities.invokeAndWait(new Runnable()
2292 setLoadingFinishedForNewStructureViewers();
2295 } catch (Exception x)
2297 System.err.println("Error loading alignment: " + x.getMessage());
2303 private jarInputStreamProvider createjarInputStreamProvider(
2304 final String file) throws MalformedURLException
2307 errorMessage = null;
2308 uniqueSetSuffix = null;
2310 viewportsAdded.clear();
2311 frefedSequence = null;
2313 if (file.startsWith("http://"))
2315 url = new URL(file);
2317 final URL _url = url;
2318 return new jarInputStreamProvider()
2322 public JarInputStream getJarInputStream() throws IOException
2326 return new JarInputStream(_url.openStream());
2330 return new JarInputStream(new FileInputStream(file));
2335 public String getFilename()
2343 * Recover jalview session from a jalview project archive. Caller may
2344 * initialise uniqueSetSuffix, seqRefIds, viewportsAdded and frefedSequence
2345 * themselves. Any null fields will be initialised with default values,
2346 * non-null fields are left alone.
2351 public AlignFrame loadJalviewAlign(final jarInputStreamProvider jprovider)
2353 errorMessage = null;
2354 if (uniqueSetSuffix == null)
2356 uniqueSetSuffix = System.currentTimeMillis() % 100000 + "";
2358 if (seqRefIds == null)
2362 AlignFrame af = null, _af = null;
2363 IdentityHashMap<AlignmentI, AlignmentI> importedDatasets = new IdentityHashMap<AlignmentI, AlignmentI>();
2364 Map<String, AlignFrame> gatherToThisFrame = new HashMap<String, AlignFrame>();
2365 final String file = jprovider.getFilename();
2368 JarInputStream jin = null;
2369 JarEntry jarentry = null;
2374 jin = jprovider.getJarInputStream();
2375 for (int i = 0; i < entryCount; i++)
2377 jarentry = jin.getNextJarEntry();
2380 if (jarentry != null && jarentry.getName().endsWith(".xml"))
2382 InputStreamReader in = new InputStreamReader(jin, UTF_8);
2383 JalviewModel object = new JalviewModel();
2385 Unmarshaller unmar = new Unmarshaller(object);
2386 unmar.setValidation(false);
2387 object = (JalviewModel) unmar.unmarshal(in);
2388 if (true) // !skipViewport(object))
2390 _af = loadFromObject(object, file, true, jprovider);
2392 && object.getJalviewModelSequence().getViewportCount() > 0)
2396 // store a reference to the first view
2399 if (_af.viewport.isGatherViewsHere())
2401 // if this is a gathered view, keep its reference since
2402 // after gathering views, only this frame will remain
2404 gatherToThisFrame.put(_af.viewport.getSequenceSetId(), _af);
2406 // Save dataset to register mappings once all resolved
2407 importedDatasets.put(af.viewport.getAlignment().getDataset(),
2408 af.viewport.getAlignment().getDataset());
2413 else if (jarentry != null)
2415 // Some other file here.
2418 } while (jarentry != null);
2419 resolveFrefedSequences();
2420 } catch (IOException ex)
2422 ex.printStackTrace();
2423 errorMessage = "Couldn't locate Jalview XML file : " + file;
2424 System.err.println("Exception whilst loading jalview XML file : "
2426 } catch (Exception ex)
2428 System.err.println("Parsing as Jalview Version 2 file failed.");
2429 ex.printStackTrace(System.err);
2430 if (attemptversion1parse)
2432 // Is Version 1 Jar file?
2435 af = new Jalview2XML_V1(raiseGUI).LoadJalviewAlign(jprovider);
2436 } catch (Exception ex2)
2438 System.err.println("Exception whilst loading as jalviewXMLV1:");
2439 ex2.printStackTrace();
2443 if (Desktop.instance != null)
2445 Desktop.instance.stopLoading();
2449 System.out.println("Successfully loaded archive file");
2452 ex.printStackTrace();
2454 System.err.println("Exception whilst loading jalview XML file : "
2456 } catch (OutOfMemoryError e)
2458 // Don't use the OOM Window here
2459 errorMessage = "Out of memory loading jalview XML file";
2460 System.err.println("Out of memory whilst loading jalview XML file");
2461 e.printStackTrace();
2465 * Regather multiple views (with the same sequence set id) to the frame (if
2466 * any) that is flagged as the one to gather to, i.e. convert them to tabbed
2467 * views instead of separate frames. Note this doesn't restore a state where
2468 * some expanded views in turn have tabbed views - the last "first tab" read
2469 * in will play the role of gatherer for all.
2471 for (AlignFrame fr : gatherToThisFrame.values())
2473 Desktop.instance.gatherViews(fr);
2476 restoreSplitFrames();
2477 for (AlignmentI ds : importedDatasets.keySet())
2479 if (ds.getCodonFrames() != null)
2481 StructureSelectionManager.getStructureSelectionManager(
2482 Desktop.instance).registerMappings(ds.getCodonFrames());
2485 if (errorMessage != null)
2490 if (Desktop.instance != null)
2492 Desktop.instance.stopLoading();
2499 * Try to reconstruct and display SplitFrame windows, where each contains
2500 * complementary dna and protein alignments. Done by pairing up AlignFrame
2501 * objects (created earlier) which have complementary viewport ids associated.
2503 protected void restoreSplitFrames()
2505 List<SplitFrame> gatherTo = new ArrayList<SplitFrame>();
2506 List<AlignFrame> addedToSplitFrames = new ArrayList<AlignFrame>();
2507 Map<String, AlignFrame> dna = new HashMap<String, AlignFrame>();
2510 * Identify the DNA alignments
2512 for (Entry<Viewport, AlignFrame> candidate : splitFrameCandidates
2515 AlignFrame af = candidate.getValue();
2516 if (af.getViewport().getAlignment().isNucleotide())
2518 dna.put(candidate.getKey().getId(), af);
2523 * Try to match up the protein complements
2525 for (Entry<Viewport, AlignFrame> candidate : splitFrameCandidates
2528 AlignFrame af = candidate.getValue();
2529 if (!af.getViewport().getAlignment().isNucleotide())
2531 String complementId = candidate.getKey().getComplementId();
2532 // only non-null complements should be in the Map
2533 if (complementId != null && dna.containsKey(complementId))
2535 final AlignFrame dnaFrame = dna.get(complementId);
2536 SplitFrame sf = createSplitFrame(dnaFrame, af);
2537 addedToSplitFrames.add(dnaFrame);
2538 addedToSplitFrames.add(af);
2539 if (af.viewport.isGatherViewsHere())
2548 * Open any that we failed to pair up (which shouldn't happen!) as
2549 * standalone AlignFrame's.
2551 for (Entry<Viewport, AlignFrame> candidate : splitFrameCandidates
2554 AlignFrame af = candidate.getValue();
2555 if (!addedToSplitFrames.contains(af))
2557 Viewport view = candidate.getKey();
2558 Desktop.addInternalFrame(af, view.getTitle(), view.getWidth(),
2560 System.err.println("Failed to restore view " + view.getTitle()
2561 + " to split frame");
2566 * Gather back into tabbed views as flagged.
2568 for (SplitFrame sf : gatherTo)
2570 Desktop.instance.gatherViews(sf);
2573 splitFrameCandidates.clear();
2577 * Construct and display one SplitFrame holding DNA and protein alignments.
2580 * @param proteinFrame
2583 protected SplitFrame createSplitFrame(AlignFrame dnaFrame,
2584 AlignFrame proteinFrame)
2586 SplitFrame splitFrame = new SplitFrame(dnaFrame, proteinFrame);
2587 String title = MessageManager.getString("label.linked_view_title");
2588 int width = (int) dnaFrame.getBounds().getWidth();
2589 int height = (int) (dnaFrame.getBounds().getHeight()
2590 + proteinFrame.getBounds().getHeight() + 50);
2593 * SplitFrame location is saved to both enclosed frames
2595 splitFrame.setLocation(dnaFrame.getX(), dnaFrame.getY());
2596 Desktop.addInternalFrame(splitFrame, title, width, height);
2599 * And compute cDNA consensus (couldn't do earlier with consensus as
2600 * mappings were not yet present)
2602 proteinFrame.viewport.alignmentChanged(proteinFrame.alignPanel);
2608 * check errorMessage for a valid error message and raise an error box in the
2609 * GUI or write the current errorMessage to stderr and then clear the error
2612 protected void reportErrors()
2614 reportErrors(false);
2617 protected void reportErrors(final boolean saving)
2619 if (errorMessage != null)
2621 final String finalErrorMessage = errorMessage;
2624 javax.swing.SwingUtilities.invokeLater(new Runnable()
2629 JOptionPane.showInternalMessageDialog(Desktop.desktop,
2630 finalErrorMessage, "Error "
2631 + (saving ? "saving" : "loading")
2632 + " Jalview file", JOptionPane.WARNING_MESSAGE);
2638 System.err.println("Problem loading Jalview file: " + errorMessage);
2641 errorMessage = null;
2644 Map<String, String> alreadyLoadedPDB = new HashMap<String, String>();
2647 * when set, local views will be updated from view stored in JalviewXML
2648 * Currently (28th Sep 2008) things will go horribly wrong in vamsas document
2649 * sync if this is set to true.
2651 private final boolean updateLocalViews = false;
2654 * Returns the path to a temporary file holding the PDB file for the given PDB
2655 * id. The first time of asking, searches for a file of that name in the
2656 * Jalview project jar, and copies it to a new temporary file. Any repeat
2657 * requests just return the path to the file previously created.
2663 String loadPDBFile(jarInputStreamProvider jprovider, String pdbId)
2665 if (alreadyLoadedPDB.containsKey(pdbId))
2667 return alreadyLoadedPDB.get(pdbId).toString();
2670 String tempFile = copyJarEntry(jprovider, pdbId, "jalview_pdb");
2671 if (tempFile != null)
2673 alreadyLoadedPDB.put(pdbId, tempFile);
2679 * Copies the jar entry of given name to a new temporary file and returns the
2680 * path to the file, or null if the entry is not found.
2683 * @param jarEntryName
2685 * a prefix for the temporary file name, must be at least three
2689 protected String copyJarEntry(jarInputStreamProvider jprovider,
2690 String jarEntryName, String prefix)
2692 BufferedReader in = null;
2693 PrintWriter out = null;
2697 JarInputStream jin = jprovider.getJarInputStream();
2699 * if (jprovider.startsWith("http://")) { jin = new JarInputStream(new
2700 * URL(jprovider).openStream()); } else { jin = new JarInputStream(new
2701 * FileInputStream(jprovider)); }
2704 JarEntry entry = null;
2707 entry = jin.getNextJarEntry();
2708 } while (entry != null && !entry.getName().equals(jarEntryName));
2711 in = new BufferedReader(new InputStreamReader(jin, UTF_8));
2712 File outFile = File.createTempFile(prefix, ".tmp");
2713 outFile.deleteOnExit();
2714 out = new PrintWriter(new FileOutputStream(outFile));
2717 while ((data = in.readLine()) != null)
2722 String t = outFile.getAbsolutePath();
2727 warn("Couldn't find entry in Jalview Jar for " + jarEntryName);
2729 } catch (Exception ex)
2731 ex.printStackTrace();
2739 } catch (IOException e)
2753 private class JvAnnotRow
2755 public JvAnnotRow(int i, AlignmentAnnotation jaa)
2762 * persisted version of annotation row from which to take vis properties
2764 public jalview.datamodel.AlignmentAnnotation template;
2767 * original position of the annotation row in the alignment
2773 * Load alignment frame from jalview XML DOM object
2778 * filename source string
2779 * @param loadTreesAndStructures
2780 * when false only create Viewport
2782 * data source provider
2783 * @return alignment frame created from view stored in DOM
2785 AlignFrame loadFromObject(JalviewModel object, String file,
2786 boolean loadTreesAndStructures, jarInputStreamProvider jprovider)
2788 SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);
2789 Sequence[] vamsasSeq = vamsasSet.getSequence();
2791 JalviewModelSequence jms = object.getJalviewModelSequence();
2793 Viewport view = (jms.getViewportCount() > 0) ? jms.getViewport(0)
2796 // ////////////////////////////////
2799 List<SequenceI> hiddenSeqs = null;
2802 List<SequenceI> tmpseqs = new ArrayList<SequenceI>();
2804 boolean multipleView = false;
2805 SequenceI referenceseqForView = null;
2806 JSeq[] jseqs = object.getJalviewModelSequence().getJSeq();
2807 int vi = 0; // counter in vamsasSeq array
2808 for (int i = 0; i < jseqs.length; i++)
2810 String seqId = jseqs[i].getId();
2812 SequenceI tmpSeq = seqRefIds.get(seqId);
2815 if (!incompleteSeqs.containsKey(seqId))
2817 // may not need this check, but keep it for at least 2.9,1 release
2818 if (tmpSeq.getStart()!=jseqs[i].getStart() || tmpSeq.getEnd()!=jseqs[i].getEnd())
2821 .println("Warning JAL-2154 regression: updating start/end for sequence "
2822 + tmpSeq.toString() + " to " + jseqs[i]);
2825 incompleteSeqs.remove(seqId);
2827 if (vamsasSeq.length > vi && vamsasSeq[vi].getId().equals(seqId))
2829 // most likely we are reading a dataset XML document so
2830 // update from vamsasSeq section of XML for this sequence
2831 tmpSeq.setName(vamsasSeq[vi].getName());
2832 tmpSeq.setDescription(vamsasSeq[vi].getDescription());
2833 tmpSeq.setSequence(vamsasSeq[vi].getSequence());
2838 // reading multiple views, so vamsasSeq set is a subset of JSeq
2839 multipleView = true;
2841 tmpSeq.setStart(jseqs[i].getStart());
2842 tmpSeq.setEnd(jseqs[i].getEnd());
2843 tmpseqs.add(tmpSeq);
2847 tmpSeq = new jalview.datamodel.Sequence(vamsasSeq[vi].getName(),
2848 vamsasSeq[vi].getSequence());
2849 tmpSeq.setDescription(vamsasSeq[vi].getDescription());
2850 tmpSeq.setStart(jseqs[i].getStart());
2851 tmpSeq.setEnd(jseqs[i].getEnd());
2852 tmpSeq.setVamsasId(uniqueSetSuffix + seqId);
2853 seqRefIds.put(vamsasSeq[vi].getId(), tmpSeq);
2854 tmpseqs.add(tmpSeq);
2858 if (jseqs[i].hasViewreference() && jseqs[i].getViewreference())
2860 referenceseqForView = tmpseqs.get(tmpseqs.size() - 1);
2863 if (jseqs[i].getHidden())
2865 if (hiddenSeqs == null)
2867 hiddenSeqs = new ArrayList<SequenceI>();
2870 hiddenSeqs.add(tmpSeq);
2875 // Create the alignment object from the sequence set
2876 // ///////////////////////////////
2877 SequenceI[] orderedSeqs = tmpseqs
2878 .toArray(new SequenceI[tmpseqs.size()]);
2880 AlignmentI al = null;
2881 // so we must create or recover the dataset alignment before going further
2882 // ///////////////////////////////
2883 if (vamsasSet.getDatasetId() == null || vamsasSet.getDatasetId() == "")
2885 // older jalview projects do not have a dataset - so creat alignment and
2887 al = new Alignment(orderedSeqs);
2888 al.setDataset(null);
2892 boolean isdsal = object.getJalviewModelSequence().getViewportCount() == 0;
2895 // we are importing a dataset record, so
2896 // recover reference to an alignment already materialsed as dataset
2897 al = getDatasetFor(vamsasSet.getDatasetId());
2901 // materialse the alignment
2902 al = new Alignment(orderedSeqs);
2906 addDatasetRef(vamsasSet.getDatasetId(), al);
2909 // finally, verify all data in vamsasSet is actually present in al
2910 // passing on flag indicating if it is actually a stored dataset
2911 recoverDatasetFor(vamsasSet, al, isdsal);
2914 if (referenceseqForView != null)
2916 al.setSeqrep(referenceseqForView);
2918 // / Add the alignment properties
2919 for (int i = 0; i < vamsasSet.getSequenceSetPropertiesCount(); i++)
2921 SequenceSetProperties ssp = vamsasSet.getSequenceSetProperties(i);
2922 al.setProperty(ssp.getKey(), ssp.getValue());
2925 // ///////////////////////////////
2927 Hashtable pdbloaded = new Hashtable(); // TODO nothing writes to this??
2930 // load sequence features, database references and any associated PDB
2931 // structures for the alignment
2933 // prior to 2.10, this part would only be executed the first time a
2934 // sequence was encountered, but not afterwards.
2935 // now, for 2.10 projects, this is also done if the xml doc includes
2936 // dataset sequences not actually present in any particular view.
2938 for (int i = 0; i < vamsasSeq.length; i++)
2940 if (jseqs[i].getFeaturesCount() > 0)
2942 Features[] features = jseqs[i].getFeatures();
2943 for (int f = 0; f < features.length; f++)
2945 jalview.datamodel.SequenceFeature sf = new jalview.datamodel.SequenceFeature(
2946 features[f].getType(), features[f].getDescription(),
2947 features[f].getStatus(), features[f].getBegin(),
2948 features[f].getEnd(), features[f].getFeatureGroup());
2950 sf.setScore(features[f].getScore());
2951 for (int od = 0; od < features[f].getOtherDataCount(); od++)
2953 OtherData keyValue = features[f].getOtherData(od);
2954 if (keyValue.getKey().startsWith("LINK"))
2956 sf.addLink(keyValue.getValue());
2960 sf.setValue(keyValue.getKey(), keyValue.getValue());
2964 // adds feature to datasequence's feature set (since Jalview 2.10)
2965 al.getSequenceAt(i).addSequenceFeature(sf);
2968 if (vamsasSeq[i].getDBRefCount() > 0)
2970 // adds dbrefs to datasequence's set (since Jalview 2.10)
2972 al.getSequenceAt(i).getDatasetSequence() == null ? al.getSequenceAt(i)
2973 : al.getSequenceAt(i).getDatasetSequence(),
2976 if (jseqs[i].getPdbidsCount() > 0)
2978 Pdbids[] ids = jseqs[i].getPdbids();
2979 for (int p = 0; p < ids.length; p++)
2981 jalview.datamodel.PDBEntry entry = new jalview.datamodel.PDBEntry();
2982 entry.setId(ids[p].getId());
2983 if (ids[p].getType() != null)
2985 if (ids[p].getType().equalsIgnoreCase("PDB"))
2987 entry.setType(PDBEntry.Type.PDB);
2991 entry.setType(PDBEntry.Type.FILE);
2994 if (ids[p].getFile() != null)
2996 if (!pdbloaded.containsKey(ids[p].getFile()))
2998 entry.setFile(loadPDBFile(jprovider, ids[p].getId()));
3002 entry.setFile(pdbloaded.get(ids[p].getId()).toString());
3005 StructureSelectionManager.getStructureSelectionManager(
3006 Desktop.instance).registerPDBEntry(entry);
3007 // adds PDBEntry to datasequence's set (since Jalview 2.10)
3008 if (al.getSequenceAt(i).getDatasetSequence() != null)
3010 al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
3014 al.getSequenceAt(i).addPDBId(entry);
3019 } // end !multipleview
3021 // ///////////////////////////////
3022 // LOAD SEQUENCE MAPPINGS
3024 if (vamsasSet.getAlcodonFrameCount() > 0)
3026 // TODO Potentially this should only be done once for all views of an
3028 AlcodonFrame[] alc = vamsasSet.getAlcodonFrame();
3029 for (int i = 0; i < alc.length; i++)
3031 AlignedCodonFrame cf = new AlignedCodonFrame();
3032 if (alc[i].getAlcodMapCount() > 0)
3034 AlcodMap[] maps = alc[i].getAlcodMap();
3035 for (int m = 0; m < maps.length; m++)
3037 SequenceI dnaseq = seqRefIds.get(maps[m].getDnasq());
3039 jalview.datamodel.Mapping mapping = null;
3040 // attach to dna sequence reference.
3041 if (maps[m].getMapping() != null)
3043 mapping = addMapping(maps[m].getMapping());
3044 if (dnaseq != null && mapping.getTo() != null)
3046 cf.addMap(dnaseq, mapping.getTo(), mapping.getMap());
3051 frefedSequence.add(newAlcodMapRef(maps[m].getDnasq(), cf,
3056 al.addCodonFrame(cf);
3061 // ////////////////////////////////
3063 List<JvAnnotRow> autoAlan = new ArrayList<JvAnnotRow>();
3066 * store any annotations which forward reference a group's ID
3068 Map<String, List<AlignmentAnnotation>> groupAnnotRefs = new Hashtable<String, List<AlignmentAnnotation>>();
3070 if (vamsasSet.getAnnotationCount() > 0)
3072 Annotation[] an = vamsasSet.getAnnotation();
3074 for (int i = 0; i < an.length; i++)
3076 Annotation annotation = an[i];
3079 * test if annotation is automatically calculated for this view only
3081 boolean autoForView = false;
3082 if (annotation.getLabel().equals("Quality")
3083 || annotation.getLabel().equals("Conservation")
3084 || annotation.getLabel().equals("Consensus"))
3086 // Kludge for pre 2.5 projects which lacked the autocalculated flag
3088 if (!annotation.hasAutoCalculated())
3090 annotation.setAutoCalculated(true);
3094 || (annotation.hasAutoCalculated() && annotation
3095 .isAutoCalculated()))
3097 // remove ID - we don't recover annotation from other views for
3098 // view-specific annotation
3099 annotation.setId(null);
3102 // set visiblity for other annotation in this view
3103 String annotationId = annotation.getId();
3104 if (annotationId != null && annotationIds.containsKey(annotationId))
3106 AlignmentAnnotation jda = annotationIds.get(annotationId);
3107 // in principle Visible should always be true for annotation displayed
3108 // in multiple views
3109 if (annotation.hasVisible())
3111 jda.visible = annotation.getVisible();
3114 al.addAnnotation(jda);
3118 // Construct new annotation from model.
3119 AnnotationElement[] ae = annotation.getAnnotationElement();
3120 jalview.datamodel.Annotation[] anot = null;
3121 java.awt.Color firstColour = null;
3123 if (!annotation.getScoreOnly())
3125 anot = new jalview.datamodel.Annotation[al.getWidth()];
3126 for (int aa = 0; aa < ae.length && aa < anot.length; aa++)
3128 anpos = ae[aa].getPosition();
3130 if (anpos >= anot.length)
3135 anot[anpos] = new jalview.datamodel.Annotation(
3137 ae[aa].getDisplayCharacter(), ae[aa].getDescription(),
3138 (ae[aa].getSecondaryStructure() == null || ae[aa]
3139 .getSecondaryStructure().length() == 0) ? ' '
3140 : ae[aa].getSecondaryStructure().charAt(0),
3144 // JBPNote: Consider verifying dataflow for IO of secondary
3145 // structure annotation read from Stockholm files
3146 // this was added to try to ensure that
3147 // if (anot[ae[aa].getPosition()].secondaryStructure>' ')
3149 // anot[ae[aa].getPosition()].displayCharacter = "";
3151 anot[anpos].colour = new java.awt.Color(ae[aa].getColour());
3152 if (firstColour == null)
3154 firstColour = anot[anpos].colour;
3158 jalview.datamodel.AlignmentAnnotation jaa = null;
3160 if (annotation.getGraph())
3162 float llim = 0, hlim = 0;
3163 // if (autoForView || an[i].isAutoCalculated()) {
3166 jaa = new jalview.datamodel.AlignmentAnnotation(
3167 annotation.getLabel(), annotation.getDescription(), anot,
3168 llim, hlim, annotation.getGraphType());
3170 jaa.graphGroup = annotation.getGraphGroup();
3171 jaa._linecolour = firstColour;
3172 if (annotation.getThresholdLine() != null)
3174 jaa.setThreshold(new jalview.datamodel.GraphLine(annotation
3175 .getThresholdLine().getValue(), annotation
3176 .getThresholdLine().getLabel(), new java.awt.Color(
3177 annotation.getThresholdLine().getColour())));
3180 if (autoForView || annotation.isAutoCalculated())
3182 // Hardwire the symbol display line to ensure that labels for
3183 // histograms are displayed
3189 jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
3190 an[i].getDescription(), anot);
3191 jaa._linecolour = firstColour;
3193 // register new annotation
3194 if (an[i].getId() != null)
3196 annotationIds.put(an[i].getId(), jaa);
3197 jaa.annotationId = an[i].getId();
3199 // recover sequence association
3200 String sequenceRef = an[i].getSequenceRef();
3201 if (sequenceRef != null)
3203 // from 2.9 sequenceRef is to sequence id (JAL-1781)
3204 SequenceI sequence = seqRefIds.get(sequenceRef);
3205 if (sequence == null)
3207 // in pre-2.9 projects sequence ref is to sequence name
3208 sequence = al.findName(sequenceRef);
3210 if (sequence != null)
3212 jaa.createSequenceMapping(sequence, 1, true);
3213 sequence.addAlignmentAnnotation(jaa);
3216 // and make a note of any group association
3217 if (an[i].getGroupRef() != null && an[i].getGroupRef().length() > 0)
3219 List<jalview.datamodel.AlignmentAnnotation> aal = groupAnnotRefs
3220 .get(an[i].getGroupRef());
3223 aal = new ArrayList<jalview.datamodel.AlignmentAnnotation>();
3224 groupAnnotRefs.put(an[i].getGroupRef(), aal);
3229 if (an[i].hasScore())
3231 jaa.setScore(an[i].getScore());
3233 if (an[i].hasVisible())
3235 jaa.visible = an[i].getVisible();
3238 if (an[i].hasCentreColLabels())
3240 jaa.centreColLabels = an[i].getCentreColLabels();
3243 if (an[i].hasScaleColLabels())
3245 jaa.scaleColLabel = an[i].getScaleColLabels();
3247 if (an[i].hasAutoCalculated() && an[i].isAutoCalculated())
3249 // newer files have an 'autoCalculated' flag and store calculation
3250 // state in viewport properties
3251 jaa.autoCalculated = true; // means annotation will be marked for
3252 // update at end of load.
3254 if (an[i].hasGraphHeight())
3256 jaa.graphHeight = an[i].getGraphHeight();
3258 if (an[i].hasBelowAlignment())
3260 jaa.belowAlignment = an[i].isBelowAlignment();
3262 jaa.setCalcId(an[i].getCalcId());
3263 if (an[i].getPropertyCount() > 0)
3265 for (jalview.schemabinding.version2.Property prop : an[i]
3268 jaa.setProperty(prop.getName(), prop.getValue());
3271 if (jaa.autoCalculated)
3273 autoAlan.add(new JvAnnotRow(i, jaa));
3276 // if (!autoForView)
3278 // add autocalculated group annotation and any user created annotation
3280 al.addAnnotation(jaa);
3284 // ///////////////////////
3286 // Create alignment markup and styles for this view
3287 if (jms.getJGroupCount() > 0)
3289 JGroup[] groups = jms.getJGroup();
3290 boolean addAnnotSchemeGroup = false;
3291 for (int i = 0; i < groups.length; i++)
3293 JGroup jGroup = groups[i];
3294 ColourSchemeI cs = null;
3295 if (jGroup.getColour() != null)
3297 if (jGroup.getColour().startsWith("ucs"))
3299 cs = getUserColourScheme(jms, jGroup.getColour());
3301 else if (jGroup.getColour().equals("AnnotationColourGradient")
3302 && jGroup.getAnnotationColours() != null)
3304 addAnnotSchemeGroup = true;
3309 cs = ColourSchemeProperty.getColour(al, jGroup.getColour());
3314 cs.setThreshold(jGroup.getPidThreshold(), true);
3318 Vector<SequenceI> seqs = new Vector<SequenceI>();
3320 for (int s = 0; s < jGroup.getSeqCount(); s++)
3322 String seqId = jGroup.getSeq(s) + "";
3323 SequenceI ts = seqRefIds.get(seqId);
3327 seqs.addElement(ts);
3331 if (seqs.size() < 1)
3336 SequenceGroup sg = new SequenceGroup(seqs, jGroup.getName(), cs,
3337 jGroup.getDisplayBoxes(), jGroup.getDisplayText(),
3338 jGroup.getColourText(), jGroup.getStart(), jGroup.getEnd());
3340 sg.setOutlineColour(new java.awt.Color(jGroup.getOutlineColour()));
3342 sg.textColour = new java.awt.Color(jGroup.getTextCol1());
3343 sg.textColour2 = new java.awt.Color(jGroup.getTextCol2());
3344 sg.setShowNonconserved(jGroup.hasShowUnconserved() ? jGroup
3345 .isShowUnconserved() : false);
3346 sg.thresholdTextColour = jGroup.getTextColThreshold();
3347 if (jGroup.hasShowConsensusHistogram())
3349 sg.setShowConsensusHistogram(jGroup.isShowConsensusHistogram());
3352 if (jGroup.hasShowSequenceLogo())
3354 sg.setshowSequenceLogo(jGroup.isShowSequenceLogo());
3356 if (jGroup.hasNormaliseSequenceLogo())
3358 sg.setNormaliseSequenceLogo(jGroup.isNormaliseSequenceLogo());
3360 if (jGroup.hasIgnoreGapsinConsensus())
3362 sg.setIgnoreGapsConsensus(jGroup.getIgnoreGapsinConsensus());
3364 if (jGroup.getConsThreshold() != 0)
3366 jalview.analysis.Conservation c = new jalview.analysis.Conservation(
3367 "All", ResidueProperties.propHash, 3,
3368 sg.getSequences(null), 0, sg.getWidth() - 1);
3370 c.verdict(false, 25);
3371 sg.cs.setConservation(c);
3374 if (jGroup.getId() != null && groupAnnotRefs.size() > 0)
3376 // re-instate unique group/annotation row reference
3377 List<AlignmentAnnotation> jaal = groupAnnotRefs.get(jGroup
3381 for (AlignmentAnnotation jaa : jaal)
3384 if (jaa.autoCalculated)
3386 // match up and try to set group autocalc alignment row for this
3388 if (jaa.label.startsWith("Consensus for "))
3390 sg.setConsensus(jaa);
3392 // match up and try to set group autocalc alignment row for this
3394 if (jaa.label.startsWith("Conservation for "))
3396 sg.setConservationRow(jaa);
3403 if (addAnnotSchemeGroup)
3405 // reconstruct the annotation colourscheme
3406 sg.cs = constructAnnotationColour(jGroup.getAnnotationColours(),
3407 null, al, jms, false);
3413 // only dataset in this model, so just return.
3416 // ///////////////////////////////
3419 // If we just load in the same jar file again, the sequenceSetId
3420 // will be the same, and we end up with multiple references
3421 // to the same sequenceSet. We must modify this id on load
3422 // so that each load of the file gives a unique id
3423 String uniqueSeqSetId = view.getSequenceSetId() + uniqueSetSuffix;
3424 String viewId = (view.getId() == null ? null : view.getId()
3426 AlignFrame af = null;
3427 AlignViewport av = null;
3428 // now check to see if we really need to create a new viewport.
3429 if (multipleView && viewportsAdded.size() == 0)
3431 // We recovered an alignment for which a viewport already exists.
3432 // TODO: fix up any settings necessary for overlaying stored state onto
3433 // state recovered from another document. (may not be necessary).
3434 // we may need a binding from a viewport in memory to one recovered from
3436 // and then recover its containing af to allow the settings to be applied.
3437 // TODO: fix for vamsas demo
3439 .println("About to recover a viewport for existing alignment: Sequence set ID is "
3441 Object seqsetobj = retrieveExistingObj(uniqueSeqSetId);
3442 if (seqsetobj != null)
3444 if (seqsetobj instanceof String)
3446 uniqueSeqSetId = (String) seqsetobj;
3448 .println("Recovered extant sequence set ID mapping for ID : New Sequence set ID is "
3454 .println("Warning : Collision between sequence set ID string and existing jalview object mapping.");
3460 * indicate that annotation colours are applied across all groups (pre
3461 * Jalview 2.8.1 behaviour)
3463 boolean doGroupAnnColour = Jalview2XML.isVersionStringLaterThan(
3464 "2.8.1", object.getVersion());
3466 AlignmentPanel ap = null;
3467 boolean isnewview = true;
3470 // Check to see if this alignment already has a view id == viewId
3471 jalview.gui.AlignmentPanel views[] = Desktop
3472 .getAlignmentPanels(uniqueSeqSetId);
3473 if (views != null && views.length > 0)
3475 for (int v = 0; v < views.length; v++)
3477 if (views[v].av.getViewId().equalsIgnoreCase(viewId))
3479 // recover the existing alignpanel, alignframe, viewport
3480 af = views[v].alignFrame;
3483 // TODO: could even skip resetting view settings if we don't want to
3484 // change the local settings from other jalview processes
3493 af = loadViewport(file, jseqs, hiddenSeqs, al, jms, view,
3494 uniqueSeqSetId, viewId, autoAlan);
3500 * Load any trees, PDB structures and viewers
3502 * Not done if flag is false (when this method is used for New View)
3504 if (loadTreesAndStructures)
3506 loadTrees(jms, view, af, av, ap);
3507 loadPDBStructures(jprovider, jseqs, af, ap);
3508 loadRnaViewers(jprovider, jseqs, ap);
3510 // and finally return.
3515 * Instantiate and link any saved RNA (Varna) viewers. The state of the Varna
3516 * panel is restored from separate jar entries, two (gapped and trimmed) per
3517 * sequence and secondary structure.
3519 * Currently each viewer shows just one sequence and structure (gapped and
3520 * trimmed), however this method is designed to support multiple sequences or
3521 * structures in viewers if wanted in future.
3527 private void loadRnaViewers(jarInputStreamProvider jprovider,
3528 JSeq[] jseqs, AlignmentPanel ap)
3531 * scan the sequences for references to viewers; create each one the first
3532 * time it is referenced, add Rna models to existing viewers
3534 for (JSeq jseq : jseqs)
3536 for (int i = 0; i < jseq.getRnaViewerCount(); i++)
3538 RnaViewer viewer = jseq.getRnaViewer(i);
3539 AppVarna appVarna = findOrCreateVarnaViewer(viewer,
3540 uniqueSetSuffix, ap);
3542 for (int j = 0; j < viewer.getSecondaryStructureCount(); j++)
3544 SecondaryStructure ss = viewer.getSecondaryStructure(j);
3545 SequenceI seq = seqRefIds.get(jseq.getId());
3546 AlignmentAnnotation ann = this.annotationIds.get(ss
3547 .getAnnotationId());
3550 * add the structure to the Varna display (with session state copied
3551 * from the jar to a temporary file)
3553 boolean gapped = ss.isGapped();
3554 String rnaTitle = ss.getTitle();
3555 String sessionState = ss.getViewerState();
3556 String tempStateFile = copyJarEntry(jprovider, sessionState,
3558 RnaModel rna = new RnaModel(rnaTitle, ann, seq, null, gapped);
3559 appVarna.addModelSession(rna, rnaTitle, tempStateFile);
3561 appVarna.setInitialSelection(viewer.getSelectedRna());
3567 * Locate and return an already instantiated matching AppVarna, or create one
3571 * @param viewIdSuffix
3575 protected AppVarna findOrCreateVarnaViewer(RnaViewer viewer,
3576 String viewIdSuffix, AlignmentPanel ap)
3579 * on each load a suffix is appended to the saved viewId, to avoid conflicts
3580 * if load is repeated
3582 String postLoadId = viewer.getViewId() + viewIdSuffix;
3583 for (JInternalFrame frame : getAllFrames())
3585 if (frame instanceof AppVarna)
3587 AppVarna varna = (AppVarna) frame;
3588 if (postLoadId.equals(varna.getViewId()))
3590 // this viewer is already instantiated
3591 // could in future here add ap as another 'parent' of the
3592 // AppVarna window; currently just 1-to-many
3599 * viewer not found - make it
3601 RnaViewerModel model = new RnaViewerModel(postLoadId,
3602 viewer.getTitle(), viewer.getXpos(), viewer.getYpos(),
3603 viewer.getWidth(), viewer.getHeight(),
3604 viewer.getDividerLocation());
3605 AppVarna varna = new AppVarna(model, ap);
3611 * Load any saved trees
3619 protected void loadTrees(JalviewModelSequence jms, Viewport view,
3620 AlignFrame af, AlignViewport av, AlignmentPanel ap)
3622 // TODO result of automated refactoring - are all these parameters needed?
3625 for (int t = 0; t < jms.getTreeCount(); t++)
3628 Tree tree = jms.getTree(t);
3630 TreePanel tp = (TreePanel) retrieveExistingObj(tree.getId());
3633 tp = af.ShowNewickTree(
3634 new jalview.io.NewickFile(tree.getNewick()),
3635 tree.getTitle(), tree.getWidth(), tree.getHeight(),
3636 tree.getXpos(), tree.getYpos());
3637 if (tree.getId() != null)
3639 // perhaps bind the tree id to something ?
3644 // update local tree attributes ?
3645 // TODO: should check if tp has been manipulated by user - if so its
3646 // settings shouldn't be modified
3647 tp.setTitle(tree.getTitle());
3648 tp.setBounds(new Rectangle(tree.getXpos(), tree.getYpos(), tree
3649 .getWidth(), tree.getHeight()));
3650 tp.av = av; // af.viewport; // TODO: verify 'associate with all
3653 tp.treeCanvas.av = av; // af.viewport;
3654 tp.treeCanvas.ap = ap; // af.alignPanel;
3659 warn("There was a problem recovering stored Newick tree: \n"
3660 + tree.getNewick());
3664 tp.fitToWindow.setState(tree.getFitToWindow());
3665 tp.fitToWindow_actionPerformed(null);
3667 if (tree.getFontName() != null)
3669 tp.setTreeFont(new java.awt.Font(tree.getFontName(), tree
3670 .getFontStyle(), tree.getFontSize()));
3674 tp.setTreeFont(new java.awt.Font(view.getFontName(), view
3675 .getFontStyle(), tree.getFontSize()));
3678 tp.showPlaceholders(tree.getMarkUnlinked());
3679 tp.showBootstrap(tree.getShowBootstrap());
3680 tp.showDistances(tree.getShowDistances());
3682 tp.treeCanvas.threshold = tree.getThreshold();
3684 if (tree.getCurrentTree())
3686 af.viewport.setCurrentTree(tp.getTree());
3690 } catch (Exception ex)
3692 ex.printStackTrace();
3697 * Load and link any saved structure viewers.
3704 protected void loadPDBStructures(jarInputStreamProvider jprovider,
3705 JSeq[] jseqs, AlignFrame af, AlignmentPanel ap)
3708 * Run through all PDB ids on the alignment, and collect mappings between
3709 * distinct view ids and all sequences referring to that view.
3711 Map<String, StructureViewerModel> structureViewers = new LinkedHashMap<String, StructureViewerModel>();
3713 for (int i = 0; i < jseqs.length; i++)
3715 if (jseqs[i].getPdbidsCount() > 0)
3717 Pdbids[] ids = jseqs[i].getPdbids();
3718 for (int p = 0; p < ids.length; p++)
3720 final int structureStateCount = ids[p].getStructureStateCount();
3721 for (int s = 0; s < structureStateCount; s++)
3723 // check to see if we haven't already created this structure view
3724 final StructureState structureState = ids[p]
3725 .getStructureState(s);
3726 String sviewid = (structureState.getViewId() == null) ? null
3727 : structureState.getViewId() + uniqueSetSuffix;
3728 jalview.datamodel.PDBEntry jpdb = new jalview.datamodel.PDBEntry();
3729 // Originally : ids[p].getFile()
3730 // : TODO: verify external PDB file recovery still works in normal
3731 // jalview project load
3732 jpdb.setFile(loadPDBFile(jprovider, ids[p].getId()));
3733 jpdb.setId(ids[p].getId());
3735 int x = structureState.getXpos();
3736 int y = structureState.getYpos();
3737 int width = structureState.getWidth();
3738 int height = structureState.getHeight();
3740 // Probably don't need to do this anymore...
3741 // Desktop.desktop.getComponentAt(x, y);
3742 // TODO: NOW: check that this recovers the PDB file correctly.
3743 String pdbFile = loadPDBFile(jprovider, ids[p].getId());
3744 jalview.datamodel.SequenceI seq = seqRefIds.get(jseqs[i]
3746 if (sviewid == null)
3748 sviewid = "_jalview_pre2_4_" + x + "," + y + "," + width
3751 if (!structureViewers.containsKey(sviewid))
3753 structureViewers.put(sviewid,
3754 new StructureViewerModel(x, y, width, height, false,
3755 false, true, structureState.getViewId(),
3756 structureState.getType()));
3757 // Legacy pre-2.7 conversion JAL-823 :
3758 // do not assume any view has to be linked for colour by
3762 // assemble String[] { pdb files }, String[] { id for each
3763 // file }, orig_fileloc, SequenceI[][] {{ seqs_file 1 }, {
3764 // seqs_file 2}, boolean[] {
3765 // linkAlignPanel,superposeWithAlignpanel}} from hash
3766 StructureViewerModel jmoldat = structureViewers.get(sviewid);
3767 jmoldat.setAlignWithPanel(jmoldat.isAlignWithPanel()
3768 | (structureState.hasAlignwithAlignPanel() ? structureState
3769 .getAlignwithAlignPanel() : false));
3772 * Default colour by linked panel to false if not specified (e.g.
3773 * for pre-2.7 projects)
3775 boolean colourWithAlignPanel = jmoldat.isColourWithAlignPanel();
3776 colourWithAlignPanel |= (structureState
3777 .hasColourwithAlignPanel() ? structureState
3778 .getColourwithAlignPanel() : false);
3779 jmoldat.setColourWithAlignPanel(colourWithAlignPanel);
3782 * Default colour by viewer to true if not specified (e.g. for
3785 boolean colourByViewer = jmoldat.isColourByViewer();
3786 colourByViewer &= structureState.hasColourByJmol() ? structureState
3787 .getColourByJmol() : true;
3788 jmoldat.setColourByViewer(colourByViewer);
3790 if (jmoldat.getStateData().length() < structureState
3791 .getContent().length())
3794 jmoldat.setStateData(structureState.getContent());
3797 if (ids[p].getFile() != null)
3799 File mapkey = new File(ids[p].getFile());
3800 StructureData seqstrmaps = jmoldat.getFileData().get(mapkey);
3801 if (seqstrmaps == null)
3803 jmoldat.getFileData().put(
3805 seqstrmaps = jmoldat.new StructureData(pdbFile,
3808 if (!seqstrmaps.getSeqList().contains(seq))
3810 seqstrmaps.getSeqList().add(seq);
3816 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");
3823 // Instantiate the associated structure views
3824 for (Entry<String, StructureViewerModel> entry : structureViewers
3829 createOrLinkStructureViewer(entry, af, ap, jprovider);
3830 } catch (Exception e)
3832 System.err.println("Error loading structure viewer: "
3834 // failed - try the next one
3846 protected void createOrLinkStructureViewer(
3847 Entry<String, StructureViewerModel> viewerData, AlignFrame af,
3848 AlignmentPanel ap, jarInputStreamProvider jprovider)
3850 final StructureViewerModel stateData = viewerData.getValue();
3853 * Search for any viewer windows already open from other alignment views
3854 * that exactly match the stored structure state
3856 StructureViewerBase comp = findMatchingViewer(viewerData);
3860 linkStructureViewer(ap, comp, stateData);
3865 * From 2.9: stateData.type contains JMOL or CHIMERA, data is in jar entry
3866 * "viewer_"+stateData.viewId
3868 if (ViewerType.CHIMERA.toString().equals(stateData.getType()))
3870 createChimeraViewer(viewerData, af, jprovider);
3875 * else Jmol (if pre-2.9, stateData contains JMOL state string)
3877 createJmolViewer(viewerData, af, jprovider);
3882 * Create a new Chimera viewer.
3888 protected void createChimeraViewer(
3889 Entry<String, StructureViewerModel> viewerData, AlignFrame af,
3890 jarInputStreamProvider jprovider)
3892 StructureViewerModel data = viewerData.getValue();
3893 String chimeraSessionFile = data.getStateData();
3896 * Copy Chimera session from jar entry "viewer_"+viewId to a temporary file
3898 * NB this is the 'saved' viewId as in the project file XML, _not_ the
3899 * 'uniquified' sviewid used to reconstruct the viewer here
3901 String viewerJarEntryName = getViewerJarEntryName(data.getViewId());
3902 chimeraSessionFile = copyJarEntry(jprovider, viewerJarEntryName,
3905 Set<Entry<File, StructureData>> fileData = data.getFileData()
3907 List<PDBEntry> pdbs = new ArrayList<PDBEntry>();
3908 List<SequenceI[]> allseqs = new ArrayList<SequenceI[]>();
3909 for (Entry<File, StructureData> pdb : fileData)
3911 String filePath = pdb.getValue().getFilePath();
3912 String pdbId = pdb.getValue().getPdbId();
3913 // pdbs.add(new PDBEntry(filePath, pdbId));
3914 pdbs.add(new PDBEntry(pdbId, null, PDBEntry.Type.PDB, filePath));
3915 final List<SequenceI> seqList = pdb.getValue().getSeqList();
3916 SequenceI[] seqs = seqList.toArray(new SequenceI[seqList.size()]);
3920 boolean colourByChimera = data.isColourByViewer();
3921 boolean colourBySequence = data.isColourWithAlignPanel();
3923 // TODO use StructureViewer as a factory here, see JAL-1761
3924 final PDBEntry[] pdbArray = pdbs.toArray(new PDBEntry[pdbs.size()]);
3925 final SequenceI[][] seqsArray = allseqs.toArray(new SequenceI[allseqs
3927 String newViewId = viewerData.getKey();
3929 ChimeraViewFrame cvf = new ChimeraViewFrame(chimeraSessionFile,
3930 af.alignPanel, pdbArray, seqsArray, colourByChimera,
3931 colourBySequence, newViewId);
3932 cvf.setSize(data.getWidth(), data.getHeight());
3933 cvf.setLocation(data.getX(), data.getY());
3937 * Create a new Jmol window. First parse the Jmol state to translate filenames
3938 * loaded into the view, and record the order in which files are shown in the
3939 * Jmol view, so we can add the sequence mappings in same order.
3945 protected void createJmolViewer(
3946 final Entry<String, StructureViewerModel> viewerData,
3947 AlignFrame af, jarInputStreamProvider jprovider)
3949 final StructureViewerModel svattrib = viewerData.getValue();
3950 String state = svattrib.getStateData();
3953 * Pre-2.9: state element value is the Jmol state string
3955 * 2.9+: @type is "JMOL", state data is in a Jar file member named "viewer_"
3958 if (ViewerType.JMOL.toString().equals(svattrib.getType()))
3960 state = readJarEntry(jprovider,
3961 getViewerJarEntryName(svattrib.getViewId()));
3964 List<String> pdbfilenames = new ArrayList<String>();
3965 List<SequenceI[]> seqmaps = new ArrayList<SequenceI[]>();
3966 List<String> pdbids = new ArrayList<String>();
3967 StringBuilder newFileLoc = new StringBuilder(64);
3968 int cp = 0, ncp, ecp;
3969 Map<File, StructureData> oldFiles = svattrib.getFileData();
3970 while ((ncp = state.indexOf("load ", cp)) > -1)
3974 // look for next filename in load statement
3975 newFileLoc.append(state.substring(cp,
3976 ncp = (state.indexOf("\"", ncp + 1) + 1)));
3977 String oldfilenam = state.substring(ncp,
3978 ecp = state.indexOf("\"", ncp));
3979 // recover the new mapping data for this old filename
3980 // have to normalize filename - since Jmol and jalview do
3982 // translation differently.
3983 StructureData filedat = oldFiles.get(new File(oldfilenam));
3984 newFileLoc.append(Platform.escapeString(filedat.getFilePath()));
3985 pdbfilenames.add(filedat.getFilePath());
3986 pdbids.add(filedat.getPdbId());
3987 seqmaps.add(filedat.getSeqList().toArray(new SequenceI[0]));
3988 newFileLoc.append("\"");
3989 cp = ecp + 1; // advance beyond last \" and set cursor so we can
3990 // look for next file statement.
3991 } while ((ncp = state.indexOf("/*file*/", cp)) > -1);
3995 // just append rest of state
3996 newFileLoc.append(state.substring(cp));
4000 System.err.print("Ignoring incomplete Jmol state for PDB ids: ");
4001 newFileLoc = new StringBuilder(state);
4002 newFileLoc.append("; load append ");
4003 for (File id : oldFiles.keySet())
4005 // add this and any other pdb files that should be present in
4007 StructureData filedat = oldFiles.get(id);
4008 newFileLoc.append(filedat.getFilePath());
4009 pdbfilenames.add(filedat.getFilePath());
4010 pdbids.add(filedat.getPdbId());
4011 seqmaps.add(filedat.getSeqList().toArray(new SequenceI[0]));
4012 newFileLoc.append(" \"");
4013 newFileLoc.append(filedat.getFilePath());
4014 newFileLoc.append("\"");
4017 newFileLoc.append(";");
4020 if (newFileLoc.length() == 0)
4024 int histbug = newFileLoc.indexOf("history = ");
4028 * change "history = [true|false];" to "history = [1|0];"
4031 int diff = histbug == -1 ? -1 : newFileLoc.indexOf(";", histbug);
4032 String val = (diff == -1) ? null : newFileLoc
4033 .substring(histbug, diff);
4034 if (val != null && val.length() >= 4)
4036 if (val.contains("e")) // eh? what can it be?
4038 if (val.trim().equals("true"))
4046 newFileLoc.replace(histbug, diff, val);
4051 final String[] pdbf = pdbfilenames.toArray(new String[pdbfilenames
4053 final String[] id = pdbids.toArray(new String[pdbids.size()]);
4054 final SequenceI[][] sq = seqmaps
4055 .toArray(new SequenceI[seqmaps.size()][]);
4056 final String fileloc = newFileLoc.toString();
4057 final String sviewid = viewerData.getKey();
4058 final AlignFrame alf = af;
4059 final Rectangle rect = new Rectangle(svattrib.getX(), svattrib.getY(),
4060 svattrib.getWidth(), svattrib.getHeight());
4063 javax.swing.SwingUtilities.invokeAndWait(new Runnable()
4068 JalviewStructureDisplayI sview = null;
4071 sview = new StructureViewer(alf.alignPanel
4072 .getStructureSelectionManager()).createView(
4073 StructureViewer.ViewerType.JMOL, pdbf, id, sq,
4074 alf.alignPanel, svattrib, fileloc, rect, sviewid);
4075 addNewStructureViewer(sview);
4076 } catch (OutOfMemoryError ex)
4078 new OOMWarning("restoring structure view for PDB id " + id,
4079 (OutOfMemoryError) ex.getCause());
4080 if (sview != null && sview.isVisible())
4082 sview.closeViewer(false);
4083 sview.setVisible(false);
4089 } catch (InvocationTargetException ex)
4091 warn("Unexpected error when opening Jmol view.", ex);
4093 } catch (InterruptedException e)
4095 // e.printStackTrace();
4101 * Generates a name for the entry in the project jar file to hold state
4102 * information for a structure viewer
4107 protected String getViewerJarEntryName(String viewId)
4109 return VIEWER_PREFIX + viewId;
4113 * Returns any open frame that matches given structure viewer data. The match
4114 * is based on the unique viewId, or (for older project versions) the frame's
4120 protected StructureViewerBase findMatchingViewer(
4121 Entry<String, StructureViewerModel> viewerData)
4123 final String sviewid = viewerData.getKey();
4124 final StructureViewerModel svattrib = viewerData.getValue();
4125 StructureViewerBase comp = null;
4126 JInternalFrame[] frames = getAllFrames();
4127 for (JInternalFrame frame : frames)
4129 if (frame instanceof StructureViewerBase)
4132 * Post jalview 2.4 schema includes structure view id
4135 && ((StructureViewerBase) frame).getViewId()
4138 comp = (StructureViewerBase) frame;
4139 break; // break added in 2.9
4142 * Otherwise test for matching position and size of viewer frame
4144 else if (frame.getX() == svattrib.getX()
4145 && frame.getY() == svattrib.getY()
4146 && frame.getHeight() == svattrib.getHeight()
4147 && frame.getWidth() == svattrib.getWidth())
4149 comp = (StructureViewerBase) frame;
4150 // no break in faint hope of an exact match on viewId
4158 * Link an AlignmentPanel to an existing structure viewer.
4163 * @param useinViewerSuperpos
4164 * @param usetoColourbyseq
4165 * @param viewerColouring
4167 protected void linkStructureViewer(AlignmentPanel ap,
4168 StructureViewerBase viewer, StructureViewerModel stateData)
4170 // NOTE: if the jalview project is part of a shared session then
4171 // view synchronization should/could be done here.
4173 final boolean useinViewerSuperpos = stateData.isAlignWithPanel();
4174 final boolean usetoColourbyseq = stateData.isColourWithAlignPanel();
4175 final boolean viewerColouring = stateData.isColourByViewer();
4176 Map<File, StructureData> oldFiles = stateData.getFileData();
4179 * Add mapping for sequences in this view to an already open viewer
4181 final AAStructureBindingModel binding = viewer.getBinding();
4182 for (File id : oldFiles.keySet())
4184 // add this and any other pdb files that should be present in the
4186 StructureData filedat = oldFiles.get(id);
4187 String pdbFile = filedat.getFilePath();
4188 SequenceI[] seq = filedat.getSeqList().toArray(new SequenceI[0]);
4189 binding.getSsm().setMapping(seq, null, pdbFile,
4190 jalview.io.AppletFormatAdapter.FILE);
4191 binding.addSequenceForStructFile(pdbFile, seq);
4193 // and add the AlignmentPanel's reference to the view panel
4194 viewer.addAlignmentPanel(ap);
4195 if (useinViewerSuperpos)
4197 viewer.useAlignmentPanelForSuperposition(ap);
4201 viewer.excludeAlignmentPanelForSuperposition(ap);
4203 if (usetoColourbyseq)
4205 viewer.useAlignmentPanelForColourbyseq(ap, !viewerColouring);
4209 viewer.excludeAlignmentPanelForColourbyseq(ap);
4214 * Get all frames within the Desktop.
4218 protected JInternalFrame[] getAllFrames()
4220 JInternalFrame[] frames = null;
4221 // TODO is this necessary - is it safe - risk of hanging?
4226 frames = Desktop.desktop.getAllFrames();
4227 } catch (ArrayIndexOutOfBoundsException e)
4229 // occasional No such child exceptions are thrown here...
4233 } catch (InterruptedException f)
4237 } while (frames == null);
4242 * Answers true if 'version' is equal to or later than 'supported', where each
4243 * is formatted as major/minor versions like "2.8.3" or "2.3.4b1" for bugfix
4244 * changes. Development and test values for 'version' are leniently treated
4248 * - minimum version we are comparing against
4250 * - version of data being processsed
4253 public static boolean isVersionStringLaterThan(String supported,
4256 if (supported == null || version == null
4257 || version.equalsIgnoreCase("DEVELOPMENT BUILD")
4258 || version.equalsIgnoreCase("Test")
4259 || version.equalsIgnoreCase("AUTOMATED BUILD"))
4261 System.err.println("Assuming project file with "
4262 + (version == null ? "null" : version)
4263 + " is compatible with Jalview version " + supported);
4268 return StringUtils.compareVersions(version, supported, "b") >= 0;
4272 Vector<JalviewStructureDisplayI> newStructureViewers = null;
4274 protected void addNewStructureViewer(JalviewStructureDisplayI sview)
4276 if (newStructureViewers != null)
4278 sview.getBinding().setFinishedLoadingFromArchive(false);
4279 newStructureViewers.add(sview);
4283 protected void setLoadingFinishedForNewStructureViewers()
4285 if (newStructureViewers != null)
4287 for (JalviewStructureDisplayI sview : newStructureViewers)
4289 sview.getBinding().setFinishedLoadingFromArchive(true);
4291 newStructureViewers.clear();
4292 newStructureViewers = null;
4296 AlignFrame loadViewport(String file, JSeq[] JSEQ,
4297 List<SequenceI> hiddenSeqs, AlignmentI al,
4298 JalviewModelSequence jms, Viewport view, String uniqueSeqSetId,
4299 String viewId, List<JvAnnotRow> autoAlan)
4301 AlignFrame af = null;
4302 af = new AlignFrame(al, view.getWidth(), view.getHeight(),
4303 uniqueSeqSetId, viewId);
4305 af.setFileName(file, "Jalview");
4307 for (int i = 0; i < JSEQ.length; i++)
4309 af.viewport.setSequenceColour(af.viewport.getAlignment()
4310 .getSequenceAt(i), new java.awt.Color(JSEQ[i].getColour()));
4315 af.getViewport().setColourByReferenceSeq(true);
4316 af.getViewport().setDisplayReferenceSeq(true);
4319 af.viewport.setGatherViewsHere(view.getGatheredViews());
4321 if (view.getSequenceSetId() != null)
4323 AlignmentViewport av = viewportsAdded.get(uniqueSeqSetId);
4325 af.viewport.setSequenceSetId(uniqueSeqSetId);
4328 // propagate shared settings to this new view
4329 af.viewport.setHistoryList(av.getHistoryList());
4330 af.viewport.setRedoList(av.getRedoList());
4334 viewportsAdded.put(uniqueSeqSetId, af.viewport);
4336 // TODO: check if this method can be called repeatedly without
4337 // side-effects if alignpanel already registered.
4338 PaintRefresher.Register(af.alignPanel, uniqueSeqSetId);
4340 // apply Hidden regions to view.
4341 if (hiddenSeqs != null)
4343 for (int s = 0; s < JSEQ.length; s++)
4345 SequenceGroup hidden = new SequenceGroup();
4346 boolean isRepresentative = false;
4347 for (int r = 0; r < JSEQ[s].getHiddenSequencesCount(); r++)
4349 isRepresentative = true;
4350 SequenceI sequenceToHide = al.getSequenceAt(JSEQ[s]
4351 .getHiddenSequences(r));
4352 hidden.addSequence(sequenceToHide, false);
4353 // remove from hiddenSeqs list so we don't try to hide it twice
4354 hiddenSeqs.remove(sequenceToHide);
4356 if (isRepresentative)
4358 SequenceI representativeSequence = al.getSequenceAt(s);
4359 hidden.addSequence(representativeSequence, false);
4360 af.viewport.hideRepSequences(representativeSequence, hidden);
4364 SequenceI[] hseqs = hiddenSeqs.toArray(new SequenceI[hiddenSeqs
4366 af.viewport.hideSequence(hseqs);
4369 // recover view properties and display parameters
4370 if (view.getViewName() != null)
4372 af.viewport.viewName = view.getViewName();
4373 af.setInitialTabVisible();
4375 af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),
4378 af.viewport.setShowAnnotation(view.getShowAnnotation());
4379 af.viewport.setAbovePIDThreshold(view.getPidSelected());
4381 af.viewport.setColourText(view.getShowColourText());
4383 af.viewport.setConservationSelected(view.getConservationSelected());
4384 af.viewport.setShowJVSuffix(view.getShowFullId());
4385 af.viewport.setRightAlignIds(view.getRightAlignIds());
4386 af.viewport.setFont(
4387 new java.awt.Font(view.getFontName(), view.getFontStyle(), view
4388 .getFontSize()), true);
4389 ViewStyleI vs = af.viewport.getViewStyle();
4390 vs.setScaleProteinAsCdna(view.isScaleProteinAsCdna());
4391 af.viewport.setViewStyle(vs);
4392 // TODO: allow custom charWidth/Heights to be restored by updating them
4393 // after setting font - which means set above to false
4394 af.viewport.setRenderGaps(view.getRenderGaps());
4395 af.viewport.setWrapAlignment(view.getWrapAlignment());
4396 af.viewport.setShowAnnotation(view.getShowAnnotation());
4398 af.viewport.setShowBoxes(view.getShowBoxes());
4400 af.viewport.setShowText(view.getShowText());
4402 af.viewport.setTextColour(new java.awt.Color(view.getTextCol1()));
4403 af.viewport.setTextColour2(new java.awt.Color(view.getTextCol2()));
4404 af.viewport.setThresholdTextColour(view.getTextColThreshold());
4405 af.viewport.setShowUnconserved(view.hasShowUnconserved() ? view
4406 .isShowUnconserved() : false);
4407 af.viewport.setStartRes(view.getStartRes());
4408 af.viewport.setStartSeq(view.getStartSeq());
4409 af.alignPanel.updateLayout();
4410 ColourSchemeI cs = null;
4411 // apply colourschemes
4412 if (view.getBgColour() != null)
4414 if (view.getBgColour().startsWith("ucs"))
4416 cs = getUserColourScheme(jms, view.getBgColour());
4418 else if (view.getBgColour().startsWith("Annotation"))
4420 AnnotationColours viewAnnColour = view.getAnnotationColours();
4421 cs = constructAnnotationColour(viewAnnColour, af, al, jms, true);
4428 cs = ColourSchemeProperty.getColour(al, view.getBgColour());
4433 cs.setThreshold(view.getPidThreshold(), true);
4434 cs.setConsensus(af.viewport.getSequenceConsensusHash());
4438 af.viewport.setGlobalColourScheme(cs);
4439 af.viewport.setColourAppliesToAllGroups(false);
4441 if (view.getConservationSelected() && cs != null)
4443 cs.setConservationInc(view.getConsThreshold());
4446 af.changeColour(cs);
4448 af.viewport.setColourAppliesToAllGroups(true);
4450 af.viewport.setShowSequenceFeatures(view.getShowSequenceFeatures());
4452 if (view.hasCentreColumnLabels())
4454 af.viewport.setCentreColumnLabels(view.getCentreColumnLabels());
4456 if (view.hasIgnoreGapsinConsensus())
4458 af.viewport.setIgnoreGapsConsensus(view.getIgnoreGapsinConsensus(),
4461 if (view.hasFollowHighlight())
4463 af.viewport.setFollowHighlight(view.getFollowHighlight());
4465 if (view.hasFollowSelection())
4467 af.viewport.followSelection = view.getFollowSelection();
4469 if (view.hasShowConsensusHistogram())
4471 af.viewport.setShowConsensusHistogram(view
4472 .getShowConsensusHistogram());
4476 af.viewport.setShowConsensusHistogram(true);
4478 if (view.hasShowSequenceLogo())
4480 af.viewport.setShowSequenceLogo(view.getShowSequenceLogo());
4484 af.viewport.setShowSequenceLogo(false);
4486 if (view.hasNormaliseSequenceLogo())
4488 af.viewport.setNormaliseSequenceLogo(view.getNormaliseSequenceLogo());
4490 if (view.hasShowDbRefTooltip())
4492 af.viewport.setShowDBRefs(view.getShowDbRefTooltip());
4494 if (view.hasShowNPfeatureTooltip())
4496 af.viewport.setShowNPFeats(view.hasShowNPfeatureTooltip());
4498 if (view.hasShowGroupConsensus())
4500 af.viewport.setShowGroupConsensus(view.getShowGroupConsensus());
4504 af.viewport.setShowGroupConsensus(false);
4506 if (view.hasShowGroupConservation())
4508 af.viewport.setShowGroupConservation(view.getShowGroupConservation());
4512 af.viewport.setShowGroupConservation(false);
4515 // recover featre settings
4516 if (jms.getFeatureSettings() != null)
4518 FeaturesDisplayed fdi;
4519 af.viewport.setFeaturesDisplayed(fdi = new FeaturesDisplayed());
4520 String[] renderOrder = new String[jms.getFeatureSettings()
4521 .getSettingCount()];
4522 Map<String, FeatureColourI> featureColours = new Hashtable<String, FeatureColourI>();
4523 Map<String, Float> featureOrder = new Hashtable<String, Float>();
4525 for (int fs = 0; fs < jms.getFeatureSettings().getSettingCount(); fs++)
4527 Setting setting = jms.getFeatureSettings().getSetting(fs);
4528 if (setting.hasMincolour())
4530 FeatureColourI gc = setting.hasMin() ? new FeatureColour(
4531 new Color(setting.getMincolour()), new Color(
4532 setting.getColour()), setting.getMin(),
4533 setting.getMax()) : new FeatureColour(new Color(
4534 setting.getMincolour()), new Color(setting.getColour()),
4536 if (setting.hasThreshold())
4538 gc.setThreshold(setting.getThreshold());
4539 int threshstate = setting.getThreshstate();
4540 // -1 = None, 0 = Below, 1 = Above threshold
4541 if (threshstate == 0)
4543 gc.setBelowThreshold(true);
4545 else if (threshstate == 1)
4547 gc.setAboveThreshold(true);
4550 gc.setAutoScaled(true); // default
4551 if (setting.hasAutoScale())
4553 gc.setAutoScaled(setting.getAutoScale());
4555 if (setting.hasColourByLabel())
4557 gc.setColourByLabel(setting.getColourByLabel());
4559 // and put in the feature colour table.
4560 featureColours.put(setting.getType(), gc);
4564 featureColours.put(setting.getType(), new FeatureColour(
4565 new Color(setting.getColour())));
4567 renderOrder[fs] = setting.getType();
4568 if (setting.hasOrder())
4570 featureOrder.put(setting.getType(), setting.getOrder());
4574 featureOrder.put(setting.getType(), new Float(fs
4575 / jms.getFeatureSettings().getSettingCount()));
4577 if (setting.getDisplay())
4579 fdi.setVisible(setting.getType());
4582 Map<String, Boolean> fgtable = new Hashtable<String, Boolean>();
4583 for (int gs = 0; gs < jms.getFeatureSettings().getGroupCount(); gs++)
4585 Group grp = jms.getFeatureSettings().getGroup(gs);
4586 fgtable.put(grp.getName(), new Boolean(grp.getDisplay()));
4588 // FeatureRendererSettings frs = new FeatureRendererSettings(renderOrder,
4589 // fgtable, featureColours, jms.getFeatureSettings().hasTransparency() ?
4590 // jms.getFeatureSettings().getTransparency() : 0.0, featureOrder);
4591 FeatureRendererSettings frs = new FeatureRendererSettings(
4592 renderOrder, fgtable, featureColours, 1.0f, featureOrder);
4593 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
4594 .transferSettings(frs);
4598 if (view.getHiddenColumnsCount() > 0)
4600 for (int c = 0; c < view.getHiddenColumnsCount(); c++)
4602 af.viewport.hideColumns(view.getHiddenColumns(c).getStart(), view
4603 .getHiddenColumns(c).getEnd() // +1
4607 if (view.getCalcIdParam() != null)
4609 for (CalcIdParam calcIdParam : view.getCalcIdParam())
4611 if (calcIdParam != null)
4613 if (recoverCalcIdParam(calcIdParam, af.viewport))
4618 warn("Couldn't recover parameters for "
4619 + calcIdParam.getCalcId());
4624 af.setMenusFromViewport(af.viewport);
4625 af.setTitle(view.getTitle());
4626 // TODO: we don't need to do this if the viewport is aready visible.
4628 * Add the AlignFrame to the desktop (it may be 'gathered' later), unless it
4629 * has a 'cdna/protein complement' view, in which case save it in order to
4630 * populate a SplitFrame once all views have been read in.
4632 String complementaryViewId = view.getComplementId();
4633 if (complementaryViewId == null)
4635 Desktop.addInternalFrame(af, view.getTitle(), view.getWidth(),
4637 // recompute any autoannotation
4638 af.alignPanel.updateAnnotation(false, true);
4639 reorderAutoannotation(af, al, autoAlan);
4640 af.alignPanel.alignmentChanged();
4644 splitFrameCandidates.put(view, af);
4649 private ColourSchemeI constructAnnotationColour(
4650 AnnotationColours viewAnnColour, AlignFrame af, AlignmentI al,
4651 JalviewModelSequence jms, boolean checkGroupAnnColour)
4653 boolean propagateAnnColour = false;
4654 ColourSchemeI cs = null;
4655 AlignmentI annAlignment = af != null ? af.viewport.getAlignment() : al;
4656 if (checkGroupAnnColour && al.getGroups() != null
4657 && al.getGroups().size() > 0)
4659 // pre 2.8.1 behaviour
4660 // check to see if we should transfer annotation colours
4661 propagateAnnColour = true;
4662 for (jalview.datamodel.SequenceGroup sg : al.getGroups())
4664 if (sg.cs instanceof AnnotationColourGradient)
4666 propagateAnnColour = false;
4670 // int find annotation
4671 if (annAlignment.getAlignmentAnnotation() != null)
4673 for (int i = 0; i < annAlignment.getAlignmentAnnotation().length; i++)
4675 if (annAlignment.getAlignmentAnnotation()[i].label
4676 .equals(viewAnnColour.getAnnotation()))
4678 if (annAlignment.getAlignmentAnnotation()[i].getThreshold() == null)
4680 annAlignment.getAlignmentAnnotation()[i]
4681 .setThreshold(new jalview.datamodel.GraphLine(
4682 viewAnnColour.getThreshold(), "Threshold",
4683 java.awt.Color.black)
4688 if (viewAnnColour.getColourScheme().equals("None"))
4690 cs = new AnnotationColourGradient(
4691 annAlignment.getAlignmentAnnotation()[i],
4692 new java.awt.Color(viewAnnColour.getMinColour()),
4693 new java.awt.Color(viewAnnColour.getMaxColour()),
4694 viewAnnColour.getAboveThreshold());
4696 else if (viewAnnColour.getColourScheme().startsWith("ucs"))
4698 cs = new AnnotationColourGradient(
4699 annAlignment.getAlignmentAnnotation()[i],
4700 getUserColourScheme(jms,
4701 viewAnnColour.getColourScheme()),
4702 viewAnnColour.getAboveThreshold());
4706 cs = new AnnotationColourGradient(
4707 annAlignment.getAlignmentAnnotation()[i],
4708 ColourSchemeProperty.getColour(al,
4709 viewAnnColour.getColourScheme()),
4710 viewAnnColour.getAboveThreshold());
4712 if (viewAnnColour.hasPerSequence())
4714 ((AnnotationColourGradient) cs).setSeqAssociated(viewAnnColour
4717 if (viewAnnColour.hasPredefinedColours())
4719 ((AnnotationColourGradient) cs)
4720 .setPredefinedColours(viewAnnColour
4721 .isPredefinedColours());
4723 if (propagateAnnColour && al.getGroups() != null)
4725 // Also use these settings for all the groups
4726 for (int g = 0; g < al.getGroups().size(); g++)
4728 jalview.datamodel.SequenceGroup sg = al.getGroups().get(g);
4736 * if (viewAnnColour.getColourScheme().equals("None" )) { sg.cs =
4737 * new AnnotationColourGradient(
4738 * annAlignment.getAlignmentAnnotation()[i], new
4739 * java.awt.Color(viewAnnColour. getMinColour()), new
4740 * java.awt.Color(viewAnnColour. getMaxColour()),
4741 * viewAnnColour.getAboveThreshold()); } else
4744 sg.cs = new AnnotationColourGradient(
4745 annAlignment.getAlignmentAnnotation()[i], sg.cs,
4746 viewAnnColour.getAboveThreshold());
4747 if (cs instanceof AnnotationColourGradient)
4749 if (viewAnnColour.hasPerSequence())
4751 ((AnnotationColourGradient) cs)
4752 .setSeqAssociated(viewAnnColour.isPerSequence());
4754 if (viewAnnColour.hasPredefinedColours())
4756 ((AnnotationColourGradient) cs)
4757 .setPredefinedColours(viewAnnColour
4758 .isPredefinedColours());
4774 private void reorderAutoannotation(AlignFrame af, AlignmentI al,
4775 List<JvAnnotRow> autoAlan)
4777 // copy over visualization settings for autocalculated annotation in the
4779 if (al.getAlignmentAnnotation() != null)
4782 * Kludge for magic autoannotation names (see JAL-811)
4784 String[] magicNames = new String[] { "Consensus", "Quality",
4786 JvAnnotRow nullAnnot = new JvAnnotRow(-1, null);
4787 Hashtable<String, JvAnnotRow> visan = new Hashtable<String, JvAnnotRow>();
4788 for (String nm : magicNames)
4790 visan.put(nm, nullAnnot);
4792 for (JvAnnotRow auan : autoAlan)
4794 visan.put(auan.template.label
4795 + (auan.template.getCalcId() == null ? "" : "\t"
4796 + auan.template.getCalcId()), auan);
4798 int hSize = al.getAlignmentAnnotation().length;
4799 List<JvAnnotRow> reorder = new ArrayList<JvAnnotRow>();
4800 // work through any autoCalculated annotation already on the view
4801 // removing it if it should be placed in a different location on the
4802 // annotation panel.
4803 List<String> remains = new ArrayList<String>(visan.keySet());
4804 for (int h = 0; h < hSize; h++)
4806 jalview.datamodel.AlignmentAnnotation jalan = al
4807 .getAlignmentAnnotation()[h];
4808 if (jalan.autoCalculated)
4811 JvAnnotRow valan = visan.get(k = jalan.label);
4812 if (jalan.getCalcId() != null)
4814 valan = visan.get(k = jalan.label + "\t" + jalan.getCalcId());
4819 // delete the auto calculated row from the alignment
4820 al.deleteAnnotation(jalan, false);
4824 if (valan != nullAnnot)
4826 if (jalan != valan.template)
4828 // newly created autoannotation row instance
4829 // so keep a reference to the visible annotation row
4830 // and copy over all relevant attributes
4831 if (valan.template.graphHeight >= 0)
4834 jalan.graphHeight = valan.template.graphHeight;
4836 jalan.visible = valan.template.visible;
4838 reorder.add(new JvAnnotRow(valan.order, jalan));
4843 // Add any (possibly stale) autocalculated rows that were not appended to
4844 // the view during construction
4845 for (String other : remains)
4847 JvAnnotRow othera = visan.get(other);
4848 if (othera != nullAnnot && othera.template.getCalcId() != null
4849 && othera.template.getCalcId().length() > 0)
4851 reorder.add(othera);
4854 // now put the automatic annotation in its correct place
4855 int s = 0, srt[] = new int[reorder.size()];
4856 JvAnnotRow[] rws = new JvAnnotRow[reorder.size()];
4857 for (JvAnnotRow jvar : reorder)
4860 srt[s++] = jvar.order;
4863 jalview.util.QuickSort.sort(srt, rws);
4864 // and re-insert the annotation at its correct position
4865 for (JvAnnotRow jvar : rws)
4867 al.addAnnotation(jvar.template, jvar.order);
4869 af.alignPanel.adjustAnnotationHeight();
4873 Hashtable skipList = null;
4876 * TODO remove this method
4879 * @return AlignFrame bound to sequenceSetId from view, if one exists. private
4880 * AlignFrame getSkippedFrame(Viewport view) { if (skipList==null) {
4881 * throw new Error("Implementation Error. No skipList defined for this
4882 * Jalview2XML instance."); } return (AlignFrame)
4883 * skipList.get(view.getSequenceSetId()); }
4887 * Check if the Jalview view contained in object should be skipped or not.
4890 * @return true if view's sequenceSetId is a key in skipList
4892 private boolean skipViewport(JalviewModel object)
4894 if (skipList == null)
4899 if (skipList.containsKey(id = object.getJalviewModelSequence()
4900 .getViewport()[0].getSequenceSetId()))
4902 if (Cache.log != null && Cache.log.isDebugEnabled())
4904 Cache.log.debug("Skipping seuqence set id " + id);
4911 public void addToSkipList(AlignFrame af)
4913 if (skipList == null)
4915 skipList = new Hashtable();
4917 skipList.put(af.getViewport().getSequenceSetId(), af);
4920 public void clearSkipList()
4922 if (skipList != null)
4929 private void recoverDatasetFor(SequenceSet vamsasSet, AlignmentI al,
4930 boolean ignoreUnrefed)
4932 jalview.datamodel.AlignmentI ds = getDatasetFor(vamsasSet
4934 Vector dseqs = null;
4937 // create a list of new dataset sequences
4938 dseqs = new Vector();
4940 for (int i = 0, iSize = vamsasSet.getSequenceCount(); i < iSize; i++)
4942 Sequence vamsasSeq = vamsasSet.getSequence(i);
4943 ensureJalviewDatasetSequence(vamsasSeq, ds, dseqs, ignoreUnrefed, i);
4945 // create a new dataset
4948 SequenceI[] dsseqs = new SequenceI[dseqs.size()];
4949 dseqs.copyInto(dsseqs);
4950 ds = new jalview.datamodel.Alignment(dsseqs);
4951 debug("Created new dataset " + vamsasSet.getDatasetId()
4952 + " for alignment " + System.identityHashCode(al));
4953 addDatasetRef(vamsasSet.getDatasetId(), ds);
4955 // set the dataset for the newly imported alignment.
4956 if (al.getDataset() == null && !ignoreUnrefed)
4965 * sequence definition to create/merge dataset sequence for
4969 * vector to add new dataset sequence to
4970 * @param ignoreUnrefed
4971 * - when true, don't create new sequences from vamsasSeq if it's id
4972 * doesn't already have an asssociated Jalview sequence.
4974 * - used to reorder the sequence in the alignment according to the
4975 * vamsasSeq array ordering, to preserve ordering of dataset
4977 private void ensureJalviewDatasetSequence(Sequence vamsasSeq,
4978 AlignmentI ds, Vector dseqs, boolean ignoreUnrefed, int vseqpos)
4980 // JBP TODO: Check this is called for AlCodonFrames to support recovery of
4982 SequenceI sq = seqRefIds.get(vamsasSeq.getId());
4983 boolean reorder = false;
4984 SequenceI dsq = null;
4985 if (sq != null && sq.getDatasetSequence() != null)
4987 dsq = sq.getDatasetSequence();
4993 if (sq == null && ignoreUnrefed)
4997 String sqid = vamsasSeq.getDsseqid();
5000 // need to create or add a new dataset sequence reference to this sequence
5003 dsq = seqRefIds.get(sqid);
5008 // make a new dataset sequence
5009 dsq = sq.createDatasetSequence();
5012 // make up a new dataset reference for this sequence
5013 sqid = seqHash(dsq);
5015 dsq.setVamsasId(uniqueSetSuffix + sqid);
5016 seqRefIds.put(sqid, dsq);
5021 dseqs.addElement(dsq);
5026 ds.addSequence(dsq);
5032 { // make this dataset sequence sq's dataset sequence
5033 sq.setDatasetSequence(dsq);
5034 // and update the current dataset alignment
5039 if (!dseqs.contains(dsq))
5046 if (ds.findIndex(dsq) < 0)
5048 ds.addSequence(dsq);
5055 // TODO: refactor this as a merge dataset sequence function
5056 // now check that sq (the dataset sequence) sequence really is the union of
5057 // all references to it
5058 // boolean pre = sq.getStart() < dsq.getStart();
5059 // boolean post = sq.getEnd() > dsq.getEnd();
5063 // StringBuffer sb = new StringBuffer();
5064 String newres = jalview.analysis.AlignSeq.extractGaps(
5065 jalview.util.Comparison.GapChars, sq.getSequenceAsString());
5066 if (!newres.equalsIgnoreCase(dsq.getSequenceAsString())
5067 && newres.length() > dsq.getLength())
5069 // Update with the longer sequence.
5073 * if (pre) { sb.insert(0, newres .substring(0, dsq.getStart() -
5074 * sq.getStart())); dsq.setStart(sq.getStart()); } if (post) {
5075 * sb.append(newres.substring(newres.length() - sq.getEnd() -
5076 * dsq.getEnd())); dsq.setEnd(sq.getEnd()); }
5078 dsq.setSequence(newres);
5080 // TODO: merges will never happen if we 'know' we have the real dataset
5081 // sequence - this should be detected when id==dssid
5083 .println("DEBUG Notice: Merged dataset sequence (if you see this often, post at http://issues.jalview.org/browse/JAL-1474)"); // ("
5084 // + (pre ? "prepended" : "") + " "
5085 // + (post ? "appended" : ""));
5090 // sequence refs are identical. We may need to update the existing dataset
5091 // alignment with this one, though.
5092 if (ds != null && dseqs == null)
5094 int opos = ds.findIndex(dsq);
5095 SequenceI tseq = null;
5096 if (opos != -1 && vseqpos != opos)
5098 // remove from old position
5099 ds.deleteSequence(dsq);
5101 if (vseqpos < ds.getHeight())
5103 if (vseqpos != opos)
5105 // save sequence at destination position
5106 tseq = ds.getSequenceAt(vseqpos);
5107 ds.replaceSequenceAt(vseqpos, dsq);
5108 ds.addSequence(tseq);
5113 ds.addSequence(dsq);
5120 * TODO use AlignmentI here and in related methods - needs
5121 * AlignmentI.getDataset() changed to return AlignmentI instead of Alignment
5123 Hashtable<String, AlignmentI> datasetIds = null;
5125 IdentityHashMap<AlignmentI, String> dataset2Ids = null;
5127 private AlignmentI getDatasetFor(String datasetId)
5129 if (datasetIds == null)
5131 datasetIds = new Hashtable<String, AlignmentI>();
5134 if (datasetIds.containsKey(datasetId))
5136 return datasetIds.get(datasetId);
5141 private void addDatasetRef(String datasetId, AlignmentI dataset)
5143 if (datasetIds == null)
5145 datasetIds = new Hashtable<String, AlignmentI>();
5147 datasetIds.put(datasetId, dataset);
5151 * make a new dataset ID for this jalview dataset alignment
5156 private String getDatasetIdRef(AlignmentI dataset)
5158 if (dataset.getDataset() != null)
5160 warn("Serious issue! Dataset Object passed to getDatasetIdRef is not a Jalview DATASET alignment...");
5162 String datasetId = makeHashCode(dataset, null);
5163 if (datasetId == null)
5165 // make a new datasetId and record it
5166 if (dataset2Ids == null)
5168 dataset2Ids = new IdentityHashMap<AlignmentI, String>();
5172 datasetId = dataset2Ids.get(dataset);
5174 if (datasetId == null)
5176 datasetId = "ds" + dataset2Ids.size() + 1;
5177 dataset2Ids.put(dataset, datasetId);
5183 private void addDBRefs(SequenceI datasetSequence, Sequence sequence)
5185 for (int d = 0; d < sequence.getDBRefCount(); d++)
5187 DBRef dr = sequence.getDBRef(d);
5188 jalview.datamodel.DBRefEntry entry = new jalview.datamodel.DBRefEntry(
5189 sequence.getDBRef(d).getSource(), sequence.getDBRef(d)
5190 .getVersion(), sequence.getDBRef(d).getAccessionId());
5191 if (dr.getMapping() != null)
5193 entry.setMap(addMapping(dr.getMapping()));
5195 datasetSequence.addDBRef(entry);
5199 private jalview.datamodel.Mapping addMapping(Mapping m)
5201 SequenceI dsto = null;
5202 // Mapping m = dr.getMapping();
5203 int fr[] = new int[m.getMapListFromCount() * 2];
5204 Enumeration f = m.enumerateMapListFrom();
5205 for (int _i = 0; f.hasMoreElements(); _i += 2)
5207 MapListFrom mf = (MapListFrom) f.nextElement();
5208 fr[_i] = mf.getStart();
5209 fr[_i + 1] = mf.getEnd();
5211 int fto[] = new int[m.getMapListToCount() * 2];
5212 f = m.enumerateMapListTo();
5213 for (int _i = 0; f.hasMoreElements(); _i += 2)
5215 MapListTo mf = (MapListTo) f.nextElement();
5216 fto[_i] = mf.getStart();
5217 fto[_i + 1] = mf.getEnd();
5219 jalview.datamodel.Mapping jmap = new jalview.datamodel.Mapping(dsto,
5220 fr, fto, (int) m.getMapFromUnit(), (int) m.getMapToUnit());
5221 if (m.getMappingChoice() != null)
5223 MappingChoice mc = m.getMappingChoice();
5224 if (mc.getDseqFor() != null)
5226 String dsfor = "" + mc.getDseqFor();
5227 if (seqRefIds.containsKey(dsfor))
5232 jmap.setTo(seqRefIds.get(dsfor));
5236 frefedSequence.add(newMappingRef(dsfor, jmap));
5242 * local sequence definition
5244 Sequence ms = mc.getSequence();
5245 SequenceI djs = null;
5246 String sqid = ms.getDsseqid();
5247 if (sqid != null && sqid.length() > 0)
5250 * recover dataset sequence
5252 djs = seqRefIds.get(sqid);
5257 .println("Warning - making up dataset sequence id for DbRef sequence map reference");
5258 sqid = ((Object) ms).toString(); // make up a new hascode for
5259 // undefined dataset sequence hash
5260 // (unlikely to happen)
5266 * make a new dataset sequence and add it to refIds hash
5268 djs = new jalview.datamodel.Sequence(ms.getName(),
5270 djs.setStart(jmap.getMap().getToLowest());
5271 djs.setEnd(jmap.getMap().getToHighest());
5272 djs.setVamsasId(uniqueSetSuffix + sqid);
5274 incompleteSeqs.put(sqid, djs);
5275 seqRefIds.put(sqid, djs);
5278 jalview.bin.Cache.log.debug("about to recurse on addDBRefs.");
5287 public jalview.gui.AlignmentPanel copyAlignPanel(AlignmentPanel ap,
5288 boolean keepSeqRefs)
5291 JalviewModel jm = saveState(ap, null, null, null);
5296 jm.getJalviewModelSequence().getViewport(0).setSequenceSetId(null);
5300 uniqueSetSuffix = "";
5301 jm.getJalviewModelSequence().getViewport(0).setId(null); // we don't
5306 if (this.frefedSequence == null)
5308 frefedSequence = new Vector();
5311 viewportsAdded.clear();
5313 AlignFrame af = loadFromObject(jm, null, false, null);
5314 af.alignPanels.clear();
5315 af.closeMenuItem_actionPerformed(true);
5318 * if(ap.av.getAlignment().getAlignmentAnnotation()!=null) { for(int i=0;
5319 * i<ap.av.getAlignment().getAlignmentAnnotation().length; i++) {
5320 * if(!ap.av.getAlignment().getAlignmentAnnotation()[i].autoCalculated) {
5321 * af.alignPanel.av.getAlignment().getAlignmentAnnotation()[i] =
5322 * ap.av.getAlignment().getAlignmentAnnotation()[i]; } } }
5325 return af.alignPanel;
5329 * flag indicating if hashtables should be cleared on finalization TODO this
5330 * flag may not be necessary
5332 private final boolean _cleartables = true;
5334 private Hashtable jvids2vobj;
5339 * @see java.lang.Object#finalize()
5342 protected void finalize() throws Throwable
5344 // really make sure we have no buried refs left.
5349 this.seqRefIds = null;
5350 this.seqsToIds = null;
5354 private void warn(String msg)
5359 private void warn(String msg, Exception e)
5361 if (Cache.log != null)
5365 Cache.log.warn(msg, e);
5369 Cache.log.warn(msg);
5374 System.err.println("Warning: " + msg);
5377 e.printStackTrace();
5382 private void debug(String string)
5384 debug(string, null);
5387 private void debug(String msg, Exception e)
5389 if (Cache.log != null)
5393 Cache.log.debug(msg, e);
5397 Cache.log.debug(msg);
5402 System.err.println("Warning: " + msg);
5405 e.printStackTrace();
5411 * set the object to ID mapping tables used to write/recover objects and XML
5412 * ID strings for the jalview project. If external tables are provided then
5413 * finalize and clearSeqRefs will not clear the tables when the Jalview2XML
5414 * object goes out of scope. - also populates the datasetIds hashtable with
5415 * alignment objects containing dataset sequences
5418 * Map from ID strings to jalview datamodel
5420 * Map from jalview datamodel to ID strings
5424 public void setObjectMappingTables(Hashtable vobj2jv,
5425 IdentityHashMap jv2vobj)
5427 this.jv2vobj = jv2vobj;
5428 this.vobj2jv = vobj2jv;
5429 Iterator ds = jv2vobj.keySet().iterator();
5431 while (ds.hasNext())
5433 Object jvobj = ds.next();
5434 id = jv2vobj.get(jvobj).toString();
5435 if (jvobj instanceof jalview.datamodel.Alignment)
5437 if (((jalview.datamodel.Alignment) jvobj).getDataset() == null)
5439 addDatasetRef(id, (jalview.datamodel.Alignment) jvobj);
5442 else if (jvobj instanceof jalview.datamodel.Sequence)
5444 // register sequence object so the XML parser can recover it.
5445 if (seqRefIds == null)
5447 seqRefIds = new HashMap<String, SequenceI>();
5449 if (seqsToIds == null)
5451 seqsToIds = new IdentityHashMap<SequenceI, String>();
5453 seqRefIds.put(jv2vobj.get(jvobj).toString(), (SequenceI) jvobj);
5454 seqsToIds.put((SequenceI) jvobj, id);
5456 else if (jvobj instanceof jalview.datamodel.AlignmentAnnotation)
5459 AlignmentAnnotation jvann = (AlignmentAnnotation) jvobj;
5460 annotationIds.put(anid = jv2vobj.get(jvobj).toString(), jvann);
5461 if (jvann.annotationId == null)
5463 jvann.annotationId = anid;
5465 if (!jvann.annotationId.equals(anid))
5467 // TODO verify that this is the correct behaviour
5468 this.warn("Overriding Annotation ID for " + anid
5469 + " from different id : " + jvann.annotationId);
5470 jvann.annotationId = anid;
5473 else if (jvobj instanceof String)
5475 if (jvids2vobj == null)
5477 jvids2vobj = new Hashtable();
5478 jvids2vobj.put(jvobj, jv2vobj.get(jvobj).toString());
5483 Cache.log.debug("Ignoring " + jvobj.getClass() + " (ID = " + id);
5489 * set the uniqueSetSuffix used to prefix/suffix object IDs for jalview
5490 * objects created from the project archive. If string is null (default for
5491 * construction) then suffix will be set automatically.
5495 public void setUniqueSetSuffix(String string)
5497 uniqueSetSuffix = string;
5502 * uses skipList2 as the skipList for skipping views on sequence sets
5503 * associated with keys in the skipList
5507 public void setSkipList(Hashtable skipList2)
5509 skipList = skipList2;
5513 * Reads the jar entry of given name and returns its contents, or null if the
5514 * entry is not found.
5517 * @param jarEntryName
5520 protected String readJarEntry(jarInputStreamProvider jprovider,
5521 String jarEntryName)
5523 String result = null;
5524 BufferedReader in = null;
5529 * Reopen the jar input stream and traverse its entries to find a matching
5532 JarInputStream jin = jprovider.getJarInputStream();
5533 JarEntry entry = null;
5536 entry = jin.getNextJarEntry();
5537 } while (entry != null && !entry.getName().equals(jarEntryName));
5541 StringBuilder out = new StringBuilder(256);
5542 in = new BufferedReader(new InputStreamReader(jin, UTF_8));
5545 while ((data = in.readLine()) != null)
5549 result = out.toString();
5553 warn("Couldn't find entry in Jalview Jar for " + jarEntryName);
5555 } catch (Exception ex)
5557 ex.printStackTrace();
5565 } catch (IOException e)
5576 * Returns an incrementing counter (0, 1, 2...)
5580 private synchronized int nextCounter()