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,
2666 if (alreadyLoadedPDB.containsKey(pdbId))
2668 return alreadyLoadedPDB.get(pdbId).toString();
2671 String tempFile = copyJarEntry(jprovider, pdbId, "jalview_pdb",
2673 if (tempFile != null)
2675 alreadyLoadedPDB.put(pdbId, tempFile);
2681 * Copies the jar entry of given name to a new temporary file and returns the
2682 * path to the file, or null if the entry is not found.
2685 * @param jarEntryName
2687 * a prefix for the temporary file name, must be at least three
2690 * null or original file - so new file can be given the same suffix
2694 protected String copyJarEntry(jarInputStreamProvider jprovider,
2695 String jarEntryName, String prefix, String origFile)
2697 BufferedReader in = null;
2698 PrintWriter out = null;
2699 String suffix = ".tmp";
2700 if (origFile == null)
2702 origFile = jarEntryName;
2704 int sfpos = origFile.lastIndexOf(".");
2705 if (sfpos > -1 && sfpos < (origFile.length() - 3))
2707 suffix = "." + origFile.substring(sfpos + 1);
2711 JarInputStream jin = jprovider.getJarInputStream();
2713 * if (jprovider.startsWith("http://")) { jin = new JarInputStream(new
2714 * URL(jprovider).openStream()); } else { jin = new JarInputStream(new
2715 * FileInputStream(jprovider)); }
2718 JarEntry entry = null;
2721 entry = jin.getNextJarEntry();
2722 } while (entry != null && !entry.getName().equals(jarEntryName));
2725 in = new BufferedReader(new InputStreamReader(jin, UTF_8));
2726 File outFile = File.createTempFile(prefix, suffix);
2727 outFile.deleteOnExit();
2728 out = new PrintWriter(new FileOutputStream(outFile));
2731 while ((data = in.readLine()) != null)
2736 String t = outFile.getAbsolutePath();
2741 warn("Couldn't find entry in Jalview Jar for " + jarEntryName);
2743 } catch (Exception ex)
2745 ex.printStackTrace();
2753 } catch (IOException e)
2767 private class JvAnnotRow
2769 public JvAnnotRow(int i, AlignmentAnnotation jaa)
2776 * persisted version of annotation row from which to take vis properties
2778 public jalview.datamodel.AlignmentAnnotation template;
2781 * original position of the annotation row in the alignment
2787 * Load alignment frame from jalview XML DOM object
2792 * filename source string
2793 * @param loadTreesAndStructures
2794 * when false only create Viewport
2796 * data source provider
2797 * @return alignment frame created from view stored in DOM
2799 AlignFrame loadFromObject(JalviewModel object, String file,
2800 boolean loadTreesAndStructures, jarInputStreamProvider jprovider)
2802 SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);
2803 Sequence[] vamsasSeq = vamsasSet.getSequence();
2805 JalviewModelSequence jms = object.getJalviewModelSequence();
2807 Viewport view = (jms.getViewportCount() > 0) ? jms.getViewport(0)
2810 // ////////////////////////////////
2813 List<SequenceI> hiddenSeqs = null;
2816 List<SequenceI> tmpseqs = new ArrayList<SequenceI>();
2818 boolean multipleView = false;
2819 SequenceI referenceseqForView = null;
2820 JSeq[] jseqs = object.getJalviewModelSequence().getJSeq();
2821 int vi = 0; // counter in vamsasSeq array
2822 for (int i = 0; i < jseqs.length; i++)
2824 String seqId = jseqs[i].getId();
2826 SequenceI tmpSeq = seqRefIds.get(seqId);
2829 if (!incompleteSeqs.containsKey(seqId))
2831 // may not need this check, but keep it for at least 2.9,1 release
2832 if (tmpSeq.getStart()!=jseqs[i].getStart() || tmpSeq.getEnd()!=jseqs[i].getEnd())
2835 .println("Warning JAL-2154 regression: updating start/end for sequence "
2836 + tmpSeq.toString() + " to " + jseqs[i]);
2839 incompleteSeqs.remove(seqId);
2841 if (vamsasSeq.length > vi && vamsasSeq[vi].getId().equals(seqId))
2843 // most likely we are reading a dataset XML document so
2844 // update from vamsasSeq section of XML for this sequence
2845 tmpSeq.setName(vamsasSeq[vi].getName());
2846 tmpSeq.setDescription(vamsasSeq[vi].getDescription());
2847 tmpSeq.setSequence(vamsasSeq[vi].getSequence());
2852 // reading multiple views, so vamsasSeq set is a subset of JSeq
2853 multipleView = true;
2855 tmpSeq.setStart(jseqs[i].getStart());
2856 tmpSeq.setEnd(jseqs[i].getEnd());
2857 tmpseqs.add(tmpSeq);
2861 tmpSeq = new jalview.datamodel.Sequence(vamsasSeq[vi].getName(),
2862 vamsasSeq[vi].getSequence());
2863 tmpSeq.setDescription(vamsasSeq[vi].getDescription());
2864 tmpSeq.setStart(jseqs[i].getStart());
2865 tmpSeq.setEnd(jseqs[i].getEnd());
2866 tmpSeq.setVamsasId(uniqueSetSuffix + seqId);
2867 seqRefIds.put(vamsasSeq[vi].getId(), tmpSeq);
2868 tmpseqs.add(tmpSeq);
2872 if (jseqs[i].hasViewreference() && jseqs[i].getViewreference())
2874 referenceseqForView = tmpseqs.get(tmpseqs.size() - 1);
2877 if (jseqs[i].getHidden())
2879 if (hiddenSeqs == null)
2881 hiddenSeqs = new ArrayList<SequenceI>();
2884 hiddenSeqs.add(tmpSeq);
2889 // Create the alignment object from the sequence set
2890 // ///////////////////////////////
2891 SequenceI[] orderedSeqs = tmpseqs
2892 .toArray(new SequenceI[tmpseqs.size()]);
2894 AlignmentI al = null;
2895 // so we must create or recover the dataset alignment before going further
2896 // ///////////////////////////////
2897 if (vamsasSet.getDatasetId() == null || vamsasSet.getDatasetId() == "")
2899 // older jalview projects do not have a dataset - so creat alignment and
2901 al = new Alignment(orderedSeqs);
2902 al.setDataset(null);
2906 boolean isdsal = object.getJalviewModelSequence().getViewportCount() == 0;
2909 // we are importing a dataset record, so
2910 // recover reference to an alignment already materialsed as dataset
2911 al = getDatasetFor(vamsasSet.getDatasetId());
2915 // materialse the alignment
2916 al = new Alignment(orderedSeqs);
2920 addDatasetRef(vamsasSet.getDatasetId(), al);
2923 // finally, verify all data in vamsasSet is actually present in al
2924 // passing on flag indicating if it is actually a stored dataset
2925 recoverDatasetFor(vamsasSet, al, isdsal);
2928 if (referenceseqForView != null)
2930 al.setSeqrep(referenceseqForView);
2932 // / Add the alignment properties
2933 for (int i = 0; i < vamsasSet.getSequenceSetPropertiesCount(); i++)
2935 SequenceSetProperties ssp = vamsasSet.getSequenceSetProperties(i);
2936 al.setProperty(ssp.getKey(), ssp.getValue());
2939 // ///////////////////////////////
2941 Hashtable pdbloaded = new Hashtable(); // TODO nothing writes to this??
2944 // load sequence features, database references and any associated PDB
2945 // structures for the alignment
2947 // prior to 2.10, this part would only be executed the first time a
2948 // sequence was encountered, but not afterwards.
2949 // now, for 2.10 projects, this is also done if the xml doc includes
2950 // dataset sequences not actually present in any particular view.
2952 for (int i = 0; i < vamsasSeq.length; i++)
2954 if (jseqs[i].getFeaturesCount() > 0)
2956 Features[] features = jseqs[i].getFeatures();
2957 for (int f = 0; f < features.length; f++)
2959 jalview.datamodel.SequenceFeature sf = new jalview.datamodel.SequenceFeature(
2960 features[f].getType(), features[f].getDescription(),
2961 features[f].getStatus(), features[f].getBegin(),
2962 features[f].getEnd(), features[f].getFeatureGroup());
2964 sf.setScore(features[f].getScore());
2965 for (int od = 0; od < features[f].getOtherDataCount(); od++)
2967 OtherData keyValue = features[f].getOtherData(od);
2968 if (keyValue.getKey().startsWith("LINK"))
2970 sf.addLink(keyValue.getValue());
2974 sf.setValue(keyValue.getKey(), keyValue.getValue());
2978 // adds feature to datasequence's feature set (since Jalview 2.10)
2979 al.getSequenceAt(i).addSequenceFeature(sf);
2982 if (vamsasSeq[i].getDBRefCount() > 0)
2984 // adds dbrefs to datasequence's set (since Jalview 2.10)
2986 al.getSequenceAt(i).getDatasetSequence() == null ? al.getSequenceAt(i)
2987 : al.getSequenceAt(i).getDatasetSequence(),
2990 if (jseqs[i].getPdbidsCount() > 0)
2992 Pdbids[] ids = jseqs[i].getPdbids();
2993 for (int p = 0; p < ids.length; p++)
2995 jalview.datamodel.PDBEntry entry = new jalview.datamodel.PDBEntry();
2996 entry.setId(ids[p].getId());
2997 if (ids[p].getType() != null)
2999 if (PDBEntry.Type.getType(ids[p].getType()) != null)
3001 entry.setType(PDBEntry.Type.getType(ids[p].getType()));
3005 entry.setType(PDBEntry.Type.FILE);
3008 if (ids[p].getFile() != null)
3010 if (!pdbloaded.containsKey(ids[p].getFile()))
3012 entry.setFile(loadPDBFile(jprovider, ids[p].getId(),
3017 entry.setFile(pdbloaded.get(ids[p].getId()).toString());
3020 if (ids[p].getPdbentryItem() != null)
3022 entry.setProperty(new Hashtable());
3023 for (PdbentryItem item : ids[p].getPdbentryItem())
3025 for (Property pr : item.getProperty())
3027 entry.getProperty().put(pr.getName(), pr.getValue());
3031 StructureSelectionManager.getStructureSelectionManager(
3032 Desktop.instance).registerPDBEntry(entry);
3033 // adds PDBEntry to datasequence's set (since Jalview 2.10)
3034 if (al.getSequenceAt(i).getDatasetSequence() != null)
3036 al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
3040 al.getSequenceAt(i).addPDBId(entry);
3045 } // end !multipleview
3047 // ///////////////////////////////
3048 // LOAD SEQUENCE MAPPINGS
3050 if (vamsasSet.getAlcodonFrameCount() > 0)
3052 // TODO Potentially this should only be done once for all views of an
3054 AlcodonFrame[] alc = vamsasSet.getAlcodonFrame();
3055 for (int i = 0; i < alc.length; i++)
3057 AlignedCodonFrame cf = new AlignedCodonFrame();
3058 if (alc[i].getAlcodMapCount() > 0)
3060 AlcodMap[] maps = alc[i].getAlcodMap();
3061 for (int m = 0; m < maps.length; m++)
3063 SequenceI dnaseq = seqRefIds.get(maps[m].getDnasq());
3065 jalview.datamodel.Mapping mapping = null;
3066 // attach to dna sequence reference.
3067 if (maps[m].getMapping() != null)
3069 mapping = addMapping(maps[m].getMapping());
3070 if (dnaseq != null && mapping.getTo() != null)
3072 cf.addMap(dnaseq, mapping.getTo(), mapping.getMap());
3077 frefedSequence.add(newAlcodMapRef(maps[m].getDnasq(), cf,
3082 al.addCodonFrame(cf);
3087 // ////////////////////////////////
3089 List<JvAnnotRow> autoAlan = new ArrayList<JvAnnotRow>();
3092 * store any annotations which forward reference a group's ID
3094 Map<String, List<AlignmentAnnotation>> groupAnnotRefs = new Hashtable<String, List<AlignmentAnnotation>>();
3096 if (vamsasSet.getAnnotationCount() > 0)
3098 Annotation[] an = vamsasSet.getAnnotation();
3100 for (int i = 0; i < an.length; i++)
3102 Annotation annotation = an[i];
3105 * test if annotation is automatically calculated for this view only
3107 boolean autoForView = false;
3108 if (annotation.getLabel().equals("Quality")
3109 || annotation.getLabel().equals("Conservation")
3110 || annotation.getLabel().equals("Consensus"))
3112 // Kludge for pre 2.5 projects which lacked the autocalculated flag
3114 if (!annotation.hasAutoCalculated())
3116 annotation.setAutoCalculated(true);
3120 || (annotation.hasAutoCalculated() && annotation
3121 .isAutoCalculated()))
3123 // remove ID - we don't recover annotation from other views for
3124 // view-specific annotation
3125 annotation.setId(null);
3128 // set visiblity for other annotation in this view
3129 String annotationId = annotation.getId();
3130 if (annotationId != null && annotationIds.containsKey(annotationId))
3132 AlignmentAnnotation jda = annotationIds.get(annotationId);
3133 // in principle Visible should always be true for annotation displayed
3134 // in multiple views
3135 if (annotation.hasVisible())
3137 jda.visible = annotation.getVisible();
3140 al.addAnnotation(jda);
3144 // Construct new annotation from model.
3145 AnnotationElement[] ae = annotation.getAnnotationElement();
3146 jalview.datamodel.Annotation[] anot = null;
3147 java.awt.Color firstColour = null;
3149 if (!annotation.getScoreOnly())
3151 anot = new jalview.datamodel.Annotation[al.getWidth()];
3152 for (int aa = 0; aa < ae.length && aa < anot.length; aa++)
3154 anpos = ae[aa].getPosition();
3156 if (anpos >= anot.length)
3161 anot[anpos] = new jalview.datamodel.Annotation(
3163 ae[aa].getDisplayCharacter(), ae[aa].getDescription(),
3164 (ae[aa].getSecondaryStructure() == null || ae[aa]
3165 .getSecondaryStructure().length() == 0) ? ' '
3166 : ae[aa].getSecondaryStructure().charAt(0),
3170 // JBPNote: Consider verifying dataflow for IO of secondary
3171 // structure annotation read from Stockholm files
3172 // this was added to try to ensure that
3173 // if (anot[ae[aa].getPosition()].secondaryStructure>' ')
3175 // anot[ae[aa].getPosition()].displayCharacter = "";
3177 anot[anpos].colour = new java.awt.Color(ae[aa].getColour());
3178 if (firstColour == null)
3180 firstColour = anot[anpos].colour;
3184 jalview.datamodel.AlignmentAnnotation jaa = null;
3186 if (annotation.getGraph())
3188 float llim = 0, hlim = 0;
3189 // if (autoForView || an[i].isAutoCalculated()) {
3192 jaa = new jalview.datamodel.AlignmentAnnotation(
3193 annotation.getLabel(), annotation.getDescription(), anot,
3194 llim, hlim, annotation.getGraphType());
3196 jaa.graphGroup = annotation.getGraphGroup();
3197 jaa._linecolour = firstColour;
3198 if (annotation.getThresholdLine() != null)
3200 jaa.setThreshold(new jalview.datamodel.GraphLine(annotation
3201 .getThresholdLine().getValue(), annotation
3202 .getThresholdLine().getLabel(), new java.awt.Color(
3203 annotation.getThresholdLine().getColour())));
3206 if (autoForView || annotation.isAutoCalculated())
3208 // Hardwire the symbol display line to ensure that labels for
3209 // histograms are displayed
3215 jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
3216 an[i].getDescription(), anot);
3217 jaa._linecolour = firstColour;
3219 // register new annotation
3220 if (an[i].getId() != null)
3222 annotationIds.put(an[i].getId(), jaa);
3223 jaa.annotationId = an[i].getId();
3225 // recover sequence association
3226 String sequenceRef = an[i].getSequenceRef();
3227 if (sequenceRef != null)
3229 // from 2.9 sequenceRef is to sequence id (JAL-1781)
3230 SequenceI sequence = seqRefIds.get(sequenceRef);
3231 if (sequence == null)
3233 // in pre-2.9 projects sequence ref is to sequence name
3234 sequence = al.findName(sequenceRef);
3236 if (sequence != null)
3238 jaa.createSequenceMapping(sequence, 1, true);
3239 sequence.addAlignmentAnnotation(jaa);
3242 // and make a note of any group association
3243 if (an[i].getGroupRef() != null && an[i].getGroupRef().length() > 0)
3245 List<jalview.datamodel.AlignmentAnnotation> aal = groupAnnotRefs
3246 .get(an[i].getGroupRef());
3249 aal = new ArrayList<jalview.datamodel.AlignmentAnnotation>();
3250 groupAnnotRefs.put(an[i].getGroupRef(), aal);
3255 if (an[i].hasScore())
3257 jaa.setScore(an[i].getScore());
3259 if (an[i].hasVisible())
3261 jaa.visible = an[i].getVisible();
3264 if (an[i].hasCentreColLabels())
3266 jaa.centreColLabels = an[i].getCentreColLabels();
3269 if (an[i].hasScaleColLabels())
3271 jaa.scaleColLabel = an[i].getScaleColLabels();
3273 if (an[i].hasAutoCalculated() && an[i].isAutoCalculated())
3275 // newer files have an 'autoCalculated' flag and store calculation
3276 // state in viewport properties
3277 jaa.autoCalculated = true; // means annotation will be marked for
3278 // update at end of load.
3280 if (an[i].hasGraphHeight())
3282 jaa.graphHeight = an[i].getGraphHeight();
3284 if (an[i].hasBelowAlignment())
3286 jaa.belowAlignment = an[i].isBelowAlignment();
3288 jaa.setCalcId(an[i].getCalcId());
3289 if (an[i].getPropertyCount() > 0)
3291 for (jalview.schemabinding.version2.Property prop : an[i]
3294 jaa.setProperty(prop.getName(), prop.getValue());
3297 if (jaa.autoCalculated)
3299 autoAlan.add(new JvAnnotRow(i, jaa));
3302 // if (!autoForView)
3304 // add autocalculated group annotation and any user created annotation
3306 al.addAnnotation(jaa);
3310 // ///////////////////////
3312 // Create alignment markup and styles for this view
3313 if (jms.getJGroupCount() > 0)
3315 JGroup[] groups = jms.getJGroup();
3316 boolean addAnnotSchemeGroup = false;
3317 for (int i = 0; i < groups.length; i++)
3319 JGroup jGroup = groups[i];
3320 ColourSchemeI cs = null;
3321 if (jGroup.getColour() != null)
3323 if (jGroup.getColour().startsWith("ucs"))
3325 cs = getUserColourScheme(jms, jGroup.getColour());
3327 else if (jGroup.getColour().equals("AnnotationColourGradient")
3328 && jGroup.getAnnotationColours() != null)
3330 addAnnotSchemeGroup = true;
3335 cs = ColourSchemeProperty.getColour(al, jGroup.getColour());
3340 cs.setThreshold(jGroup.getPidThreshold(), true);
3344 Vector<SequenceI> seqs = new Vector<SequenceI>();
3346 for (int s = 0; s < jGroup.getSeqCount(); s++)
3348 String seqId = jGroup.getSeq(s) + "";
3349 SequenceI ts = seqRefIds.get(seqId);
3353 seqs.addElement(ts);
3357 if (seqs.size() < 1)
3362 SequenceGroup sg = new SequenceGroup(seqs, jGroup.getName(), cs,
3363 jGroup.getDisplayBoxes(), jGroup.getDisplayText(),
3364 jGroup.getColourText(), jGroup.getStart(), jGroup.getEnd());
3366 sg.setOutlineColour(new java.awt.Color(jGroup.getOutlineColour()));
3368 sg.textColour = new java.awt.Color(jGroup.getTextCol1());
3369 sg.textColour2 = new java.awt.Color(jGroup.getTextCol2());
3370 sg.setShowNonconserved(jGroup.hasShowUnconserved() ? jGroup
3371 .isShowUnconserved() : false);
3372 sg.thresholdTextColour = jGroup.getTextColThreshold();
3373 if (jGroup.hasShowConsensusHistogram())
3375 sg.setShowConsensusHistogram(jGroup.isShowConsensusHistogram());
3378 if (jGroup.hasShowSequenceLogo())
3380 sg.setshowSequenceLogo(jGroup.isShowSequenceLogo());
3382 if (jGroup.hasNormaliseSequenceLogo())
3384 sg.setNormaliseSequenceLogo(jGroup.isNormaliseSequenceLogo());
3386 if (jGroup.hasIgnoreGapsinConsensus())
3388 sg.setIgnoreGapsConsensus(jGroup.getIgnoreGapsinConsensus());
3390 if (jGroup.getConsThreshold() != 0)
3392 jalview.analysis.Conservation c = new jalview.analysis.Conservation(
3393 "All", ResidueProperties.propHash, 3,
3394 sg.getSequences(null), 0, sg.getWidth() - 1);
3396 c.verdict(false, 25);
3397 sg.cs.setConservation(c);
3400 if (jGroup.getId() != null && groupAnnotRefs.size() > 0)
3402 // re-instate unique group/annotation row reference
3403 List<AlignmentAnnotation> jaal = groupAnnotRefs.get(jGroup
3407 for (AlignmentAnnotation jaa : jaal)
3410 if (jaa.autoCalculated)
3412 // match up and try to set group autocalc alignment row for this
3414 if (jaa.label.startsWith("Consensus for "))
3416 sg.setConsensus(jaa);
3418 // match up and try to set group autocalc alignment row for this
3420 if (jaa.label.startsWith("Conservation for "))
3422 sg.setConservationRow(jaa);
3429 if (addAnnotSchemeGroup)
3431 // reconstruct the annotation colourscheme
3432 sg.cs = constructAnnotationColour(jGroup.getAnnotationColours(),
3433 null, al, jms, false);
3439 // only dataset in this model, so just return.
3442 // ///////////////////////////////
3445 // If we just load in the same jar file again, the sequenceSetId
3446 // will be the same, and we end up with multiple references
3447 // to the same sequenceSet. We must modify this id on load
3448 // so that each load of the file gives a unique id
3449 String uniqueSeqSetId = view.getSequenceSetId() + uniqueSetSuffix;
3450 String viewId = (view.getId() == null ? null : view.getId()
3452 AlignFrame af = null;
3453 AlignViewport av = null;
3454 // now check to see if we really need to create a new viewport.
3455 if (multipleView && viewportsAdded.size() == 0)
3457 // We recovered an alignment for which a viewport already exists.
3458 // TODO: fix up any settings necessary for overlaying stored state onto
3459 // state recovered from another document. (may not be necessary).
3460 // we may need a binding from a viewport in memory to one recovered from
3462 // and then recover its containing af to allow the settings to be applied.
3463 // TODO: fix for vamsas demo
3465 .println("About to recover a viewport for existing alignment: Sequence set ID is "
3467 Object seqsetobj = retrieveExistingObj(uniqueSeqSetId);
3468 if (seqsetobj != null)
3470 if (seqsetobj instanceof String)
3472 uniqueSeqSetId = (String) seqsetobj;
3474 .println("Recovered extant sequence set ID mapping for ID : New Sequence set ID is "
3480 .println("Warning : Collision between sequence set ID string and existing jalview object mapping.");
3486 * indicate that annotation colours are applied across all groups (pre
3487 * Jalview 2.8.1 behaviour)
3489 boolean doGroupAnnColour = Jalview2XML.isVersionStringLaterThan(
3490 "2.8.1", object.getVersion());
3492 AlignmentPanel ap = null;
3493 boolean isnewview = true;
3496 // Check to see if this alignment already has a view id == viewId
3497 jalview.gui.AlignmentPanel views[] = Desktop
3498 .getAlignmentPanels(uniqueSeqSetId);
3499 if (views != null && views.length > 0)
3501 for (int v = 0; v < views.length; v++)
3503 if (views[v].av.getViewId().equalsIgnoreCase(viewId))
3505 // recover the existing alignpanel, alignframe, viewport
3506 af = views[v].alignFrame;
3509 // TODO: could even skip resetting view settings if we don't want to
3510 // change the local settings from other jalview processes
3519 af = loadViewport(file, jseqs, hiddenSeqs, al, jms, view,
3520 uniqueSeqSetId, viewId, autoAlan);
3526 * Load any trees, PDB structures and viewers
3528 * Not done if flag is false (when this method is used for New View)
3530 if (loadTreesAndStructures)
3532 loadTrees(jms, view, af, av, ap);
3533 loadPDBStructures(jprovider, jseqs, af, ap);
3534 loadRnaViewers(jprovider, jseqs, ap);
3536 // and finally return.
3541 * Instantiate and link any saved RNA (Varna) viewers. The state of the Varna
3542 * panel is restored from separate jar entries, two (gapped and trimmed) per
3543 * sequence and secondary structure.
3545 * Currently each viewer shows just one sequence and structure (gapped and
3546 * trimmed), however this method is designed to support multiple sequences or
3547 * structures in viewers if wanted in future.
3553 private void loadRnaViewers(jarInputStreamProvider jprovider,
3554 JSeq[] jseqs, AlignmentPanel ap)
3557 * scan the sequences for references to viewers; create each one the first
3558 * time it is referenced, add Rna models to existing viewers
3560 for (JSeq jseq : jseqs)
3562 for (int i = 0; i < jseq.getRnaViewerCount(); i++)
3564 RnaViewer viewer = jseq.getRnaViewer(i);
3565 AppVarna appVarna = findOrCreateVarnaViewer(viewer,
3566 uniqueSetSuffix, ap);
3568 for (int j = 0; j < viewer.getSecondaryStructureCount(); j++)
3570 SecondaryStructure ss = viewer.getSecondaryStructure(j);
3571 SequenceI seq = seqRefIds.get(jseq.getId());
3572 AlignmentAnnotation ann = this.annotationIds.get(ss
3573 .getAnnotationId());
3576 * add the structure to the Varna display (with session state copied
3577 * from the jar to a temporary file)
3579 boolean gapped = ss.isGapped();
3580 String rnaTitle = ss.getTitle();
3581 String sessionState = ss.getViewerState();
3582 String tempStateFile = copyJarEntry(jprovider, sessionState,
3584 RnaModel rna = new RnaModel(rnaTitle, ann, seq, null, gapped);
3585 appVarna.addModelSession(rna, rnaTitle, tempStateFile);
3587 appVarna.setInitialSelection(viewer.getSelectedRna());
3593 * Locate and return an already instantiated matching AppVarna, or create one
3597 * @param viewIdSuffix
3601 protected AppVarna findOrCreateVarnaViewer(RnaViewer viewer,
3602 String viewIdSuffix, AlignmentPanel ap)
3605 * on each load a suffix is appended to the saved viewId, to avoid conflicts
3606 * if load is repeated
3608 String postLoadId = viewer.getViewId() + viewIdSuffix;
3609 for (JInternalFrame frame : getAllFrames())
3611 if (frame instanceof AppVarna)
3613 AppVarna varna = (AppVarna) frame;
3614 if (postLoadId.equals(varna.getViewId()))
3616 // this viewer is already instantiated
3617 // could in future here add ap as another 'parent' of the
3618 // AppVarna window; currently just 1-to-many
3625 * viewer not found - make it
3627 RnaViewerModel model = new RnaViewerModel(postLoadId,
3628 viewer.getTitle(), viewer.getXpos(), viewer.getYpos(),
3629 viewer.getWidth(), viewer.getHeight(),
3630 viewer.getDividerLocation());
3631 AppVarna varna = new AppVarna(model, ap);
3637 * Load any saved trees
3645 protected void loadTrees(JalviewModelSequence jms, Viewport view,
3646 AlignFrame af, AlignViewport av, AlignmentPanel ap)
3648 // TODO result of automated refactoring - are all these parameters needed?
3651 for (int t = 0; t < jms.getTreeCount(); t++)
3654 Tree tree = jms.getTree(t);
3656 TreePanel tp = (TreePanel) retrieveExistingObj(tree.getId());
3659 tp = af.ShowNewickTree(
3660 new jalview.io.NewickFile(tree.getNewick()),
3661 tree.getTitle(), tree.getWidth(), tree.getHeight(),
3662 tree.getXpos(), tree.getYpos());
3663 if (tree.getId() != null)
3665 // perhaps bind the tree id to something ?
3670 // update local tree attributes ?
3671 // TODO: should check if tp has been manipulated by user - if so its
3672 // settings shouldn't be modified
3673 tp.setTitle(tree.getTitle());
3674 tp.setBounds(new Rectangle(tree.getXpos(), tree.getYpos(), tree
3675 .getWidth(), tree.getHeight()));
3676 tp.av = av; // af.viewport; // TODO: verify 'associate with all
3679 tp.treeCanvas.av = av; // af.viewport;
3680 tp.treeCanvas.ap = ap; // af.alignPanel;
3685 warn("There was a problem recovering stored Newick tree: \n"
3686 + tree.getNewick());
3690 tp.fitToWindow.setState(tree.getFitToWindow());
3691 tp.fitToWindow_actionPerformed(null);
3693 if (tree.getFontName() != null)
3695 tp.setTreeFont(new java.awt.Font(tree.getFontName(), tree
3696 .getFontStyle(), tree.getFontSize()));
3700 tp.setTreeFont(new java.awt.Font(view.getFontName(), view
3701 .getFontStyle(), tree.getFontSize()));
3704 tp.showPlaceholders(tree.getMarkUnlinked());
3705 tp.showBootstrap(tree.getShowBootstrap());
3706 tp.showDistances(tree.getShowDistances());
3708 tp.treeCanvas.threshold = tree.getThreshold();
3710 if (tree.getCurrentTree())
3712 af.viewport.setCurrentTree(tp.getTree());
3716 } catch (Exception ex)
3718 ex.printStackTrace();
3723 * Load and link any saved structure viewers.
3730 protected void loadPDBStructures(jarInputStreamProvider jprovider,
3731 JSeq[] jseqs, AlignFrame af, AlignmentPanel ap)
3734 * Run through all PDB ids on the alignment, and collect mappings between
3735 * distinct view ids and all sequences referring to that view.
3737 Map<String, StructureViewerModel> structureViewers = new LinkedHashMap<String, StructureViewerModel>();
3739 for (int i = 0; i < jseqs.length; i++)
3741 if (jseqs[i].getPdbidsCount() > 0)
3743 Pdbids[] ids = jseqs[i].getPdbids();
3744 for (int p = 0; p < ids.length; p++)
3746 final int structureStateCount = ids[p].getStructureStateCount();
3747 for (int s = 0; s < structureStateCount; s++)
3749 // check to see if we haven't already created this structure view
3750 final StructureState structureState = ids[p]
3751 .getStructureState(s);
3752 String sviewid = (structureState.getViewId() == null) ? null
3753 : structureState.getViewId() + uniqueSetSuffix;
3754 jalview.datamodel.PDBEntry jpdb = new jalview.datamodel.PDBEntry();
3755 // Originally : ids[p].getFile()
3756 // : TODO: verify external PDB file recovery still works in normal
3757 // jalview project load
3758 jpdb.setFile(loadPDBFile(jprovider, ids[p].getId(),
3760 jpdb.setId(ids[p].getId());
3762 int x = structureState.getXpos();
3763 int y = structureState.getYpos();
3764 int width = structureState.getWidth();
3765 int height = structureState.getHeight();
3767 // Probably don't need to do this anymore...
3768 // Desktop.desktop.getComponentAt(x, y);
3769 // TODO: NOW: check that this recovers the PDB file correctly.
3770 String pdbFile = loadPDBFile(jprovider, ids[p].getId(),
3772 jalview.datamodel.SequenceI seq = seqRefIds.get(jseqs[i]
3774 if (sviewid == null)
3776 sviewid = "_jalview_pre2_4_" + x + "," + y + "," + width
3779 if (!structureViewers.containsKey(sviewid))
3781 structureViewers.put(sviewid,
3782 new StructureViewerModel(x, y, width, height, false,
3783 false, true, structureState.getViewId(),
3784 structureState.getType()));
3785 // Legacy pre-2.7 conversion JAL-823 :
3786 // do not assume any view has to be linked for colour by
3790 // assemble String[] { pdb files }, String[] { id for each
3791 // file }, orig_fileloc, SequenceI[][] {{ seqs_file 1 }, {
3792 // seqs_file 2}, boolean[] {
3793 // linkAlignPanel,superposeWithAlignpanel}} from hash
3794 StructureViewerModel jmoldat = structureViewers.get(sviewid);
3795 jmoldat.setAlignWithPanel(jmoldat.isAlignWithPanel()
3796 | (structureState.hasAlignwithAlignPanel() ? structureState
3797 .getAlignwithAlignPanel() : false));
3800 * Default colour by linked panel to false if not specified (e.g.
3801 * for pre-2.7 projects)
3803 boolean colourWithAlignPanel = jmoldat.isColourWithAlignPanel();
3804 colourWithAlignPanel |= (structureState
3805 .hasColourwithAlignPanel() ? structureState
3806 .getColourwithAlignPanel() : false);
3807 jmoldat.setColourWithAlignPanel(colourWithAlignPanel);
3810 * Default colour by viewer to true if not specified (e.g. for
3813 boolean colourByViewer = jmoldat.isColourByViewer();
3814 colourByViewer &= structureState.hasColourByJmol() ? structureState
3815 .getColourByJmol() : true;
3816 jmoldat.setColourByViewer(colourByViewer);
3818 if (jmoldat.getStateData().length() < structureState
3819 .getContent().length())
3822 jmoldat.setStateData(structureState.getContent());
3825 if (ids[p].getFile() != null)
3827 File mapkey = new File(ids[p].getFile());
3828 StructureData seqstrmaps = jmoldat.getFileData().get(mapkey);
3829 if (seqstrmaps == null)
3831 jmoldat.getFileData().put(
3833 seqstrmaps = jmoldat.new StructureData(pdbFile,
3836 if (!seqstrmaps.getSeqList().contains(seq))
3838 seqstrmaps.getSeqList().add(seq);
3844 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");
3851 // Instantiate the associated structure views
3852 for (Entry<String, StructureViewerModel> entry : structureViewers
3857 createOrLinkStructureViewer(entry, af, ap, jprovider);
3858 } catch (Exception e)
3860 System.err.println("Error loading structure viewer: "
3862 // failed - try the next one
3874 protected void createOrLinkStructureViewer(
3875 Entry<String, StructureViewerModel> viewerData, AlignFrame af,
3876 AlignmentPanel ap, jarInputStreamProvider jprovider)
3878 final StructureViewerModel stateData = viewerData.getValue();
3881 * Search for any viewer windows already open from other alignment views
3882 * that exactly match the stored structure state
3884 StructureViewerBase comp = findMatchingViewer(viewerData);
3888 linkStructureViewer(ap, comp, stateData);
3893 * From 2.9: stateData.type contains JMOL or CHIMERA, data is in jar entry
3894 * "viewer_"+stateData.viewId
3896 if (ViewerType.CHIMERA.toString().equals(stateData.getType()))
3898 createChimeraViewer(viewerData, af, jprovider);
3903 * else Jmol (if pre-2.9, stateData contains JMOL state string)
3905 createJmolViewer(viewerData, af, jprovider);
3910 * Create a new Chimera viewer.
3916 protected void createChimeraViewer(
3917 Entry<String, StructureViewerModel> viewerData, AlignFrame af,
3918 jarInputStreamProvider jprovider)
3920 StructureViewerModel data = viewerData.getValue();
3921 String chimeraSessionFile = data.getStateData();
3924 * Copy Chimera session from jar entry "viewer_"+viewId to a temporary file
3926 * NB this is the 'saved' viewId as in the project file XML, _not_ the
3927 * 'uniquified' sviewid used to reconstruct the viewer here
3929 String viewerJarEntryName = getViewerJarEntryName(data.getViewId());
3930 chimeraSessionFile = copyJarEntry(jprovider, viewerJarEntryName,
3933 Set<Entry<File, StructureData>> fileData = data.getFileData()
3935 List<PDBEntry> pdbs = new ArrayList<PDBEntry>();
3936 List<SequenceI[]> allseqs = new ArrayList<SequenceI[]>();
3937 for (Entry<File, StructureData> pdb : fileData)
3939 String filePath = pdb.getValue().getFilePath();
3940 String pdbId = pdb.getValue().getPdbId();
3941 // pdbs.add(new PDBEntry(filePath, pdbId));
3942 pdbs.add(new PDBEntry(pdbId, null, PDBEntry.Type.PDB, filePath));
3943 final List<SequenceI> seqList = pdb.getValue().getSeqList();
3944 SequenceI[] seqs = seqList.toArray(new SequenceI[seqList.size()]);
3948 boolean colourByChimera = data.isColourByViewer();
3949 boolean colourBySequence = data.isColourWithAlignPanel();
3951 // TODO use StructureViewer as a factory here, see JAL-1761
3952 final PDBEntry[] pdbArray = pdbs.toArray(new PDBEntry[pdbs.size()]);
3953 final SequenceI[][] seqsArray = allseqs.toArray(new SequenceI[allseqs
3955 String newViewId = viewerData.getKey();
3957 ChimeraViewFrame cvf = new ChimeraViewFrame(chimeraSessionFile,
3958 af.alignPanel, pdbArray, seqsArray, colourByChimera,
3959 colourBySequence, newViewId);
3960 cvf.setSize(data.getWidth(), data.getHeight());
3961 cvf.setLocation(data.getX(), data.getY());
3965 * Create a new Jmol window. First parse the Jmol state to translate filenames
3966 * loaded into the view, and record the order in which files are shown in the
3967 * Jmol view, so we can add the sequence mappings in same order.
3973 protected void createJmolViewer(
3974 final Entry<String, StructureViewerModel> viewerData,
3975 AlignFrame af, jarInputStreamProvider jprovider)
3977 final StructureViewerModel svattrib = viewerData.getValue();
3978 String state = svattrib.getStateData();
3981 * Pre-2.9: state element value is the Jmol state string
3983 * 2.9+: @type is "JMOL", state data is in a Jar file member named "viewer_"
3986 if (ViewerType.JMOL.toString().equals(svattrib.getType()))
3988 state = readJarEntry(jprovider,
3989 getViewerJarEntryName(svattrib.getViewId()));
3992 List<String> pdbfilenames = new ArrayList<String>();
3993 List<SequenceI[]> seqmaps = new ArrayList<SequenceI[]>();
3994 List<String> pdbids = new ArrayList<String>();
3995 StringBuilder newFileLoc = new StringBuilder(64);
3996 int cp = 0, ncp, ecp;
3997 Map<File, StructureData> oldFiles = svattrib.getFileData();
3998 while ((ncp = state.indexOf("load ", cp)) > -1)
4002 // look for next filename in load statement
4003 newFileLoc.append(state.substring(cp,
4004 ncp = (state.indexOf("\"", ncp + 1) + 1)));
4005 String oldfilenam = state.substring(ncp,
4006 ecp = state.indexOf("\"", ncp));
4007 // recover the new mapping data for this old filename
4008 // have to normalize filename - since Jmol and jalview do
4010 // translation differently.
4011 StructureData filedat = oldFiles.get(new File(oldfilenam));
4012 newFileLoc.append(Platform.escapeString(filedat.getFilePath()));
4013 pdbfilenames.add(filedat.getFilePath());
4014 pdbids.add(filedat.getPdbId());
4015 seqmaps.add(filedat.getSeqList().toArray(new SequenceI[0]));
4016 newFileLoc.append("\"");
4017 cp = ecp + 1; // advance beyond last \" and set cursor so we can
4018 // look for next file statement.
4019 } while ((ncp = state.indexOf("/*file*/", cp)) > -1);
4023 // just append rest of state
4024 newFileLoc.append(state.substring(cp));
4028 System.err.print("Ignoring incomplete Jmol state for PDB ids: ");
4029 newFileLoc = new StringBuilder(state);
4030 newFileLoc.append("; load append ");
4031 for (File id : oldFiles.keySet())
4033 // add this and any other pdb files that should be present in
4035 StructureData filedat = oldFiles.get(id);
4036 newFileLoc.append(filedat.getFilePath());
4037 pdbfilenames.add(filedat.getFilePath());
4038 pdbids.add(filedat.getPdbId());
4039 seqmaps.add(filedat.getSeqList().toArray(new SequenceI[0]));
4040 newFileLoc.append(" \"");
4041 newFileLoc.append(filedat.getFilePath());
4042 newFileLoc.append("\"");
4045 newFileLoc.append(";");
4048 if (newFileLoc.length() == 0)
4052 int histbug = newFileLoc.indexOf("history = ");
4056 * change "history = [true|false];" to "history = [1|0];"
4059 int diff = histbug == -1 ? -1 : newFileLoc.indexOf(";", histbug);
4060 String val = (diff == -1) ? null : newFileLoc
4061 .substring(histbug, diff);
4062 if (val != null && val.length() >= 4)
4064 if (val.contains("e")) // eh? what can it be?
4066 if (val.trim().equals("true"))
4074 newFileLoc.replace(histbug, diff, val);
4079 final String[] pdbf = pdbfilenames.toArray(new String[pdbfilenames
4081 final String[] id = pdbids.toArray(new String[pdbids.size()]);
4082 final SequenceI[][] sq = seqmaps
4083 .toArray(new SequenceI[seqmaps.size()][]);
4084 final String fileloc = newFileLoc.toString();
4085 final String sviewid = viewerData.getKey();
4086 final AlignFrame alf = af;
4087 final Rectangle rect = new Rectangle(svattrib.getX(), svattrib.getY(),
4088 svattrib.getWidth(), svattrib.getHeight());
4091 javax.swing.SwingUtilities.invokeAndWait(new Runnable()
4096 JalviewStructureDisplayI sview = null;
4099 sview = new StructureViewer(alf.alignPanel
4100 .getStructureSelectionManager()).createView(
4101 StructureViewer.ViewerType.JMOL, pdbf, id, sq,
4102 alf.alignPanel, svattrib, fileloc, rect, sviewid);
4103 addNewStructureViewer(sview);
4104 } catch (OutOfMemoryError ex)
4106 new OOMWarning("restoring structure view for PDB id " + id,
4107 (OutOfMemoryError) ex.getCause());
4108 if (sview != null && sview.isVisible())
4110 sview.closeViewer(false);
4111 sview.setVisible(false);
4117 } catch (InvocationTargetException ex)
4119 warn("Unexpected error when opening Jmol view.", ex);
4121 } catch (InterruptedException e)
4123 // e.printStackTrace();
4129 * Generates a name for the entry in the project jar file to hold state
4130 * information for a structure viewer
4135 protected String getViewerJarEntryName(String viewId)
4137 return VIEWER_PREFIX + viewId;
4141 * Returns any open frame that matches given structure viewer data. The match
4142 * is based on the unique viewId, or (for older project versions) the frame's
4148 protected StructureViewerBase findMatchingViewer(
4149 Entry<String, StructureViewerModel> viewerData)
4151 final String sviewid = viewerData.getKey();
4152 final StructureViewerModel svattrib = viewerData.getValue();
4153 StructureViewerBase comp = null;
4154 JInternalFrame[] frames = getAllFrames();
4155 for (JInternalFrame frame : frames)
4157 if (frame instanceof StructureViewerBase)
4160 * Post jalview 2.4 schema includes structure view id
4163 && ((StructureViewerBase) frame).getViewId()
4166 comp = (StructureViewerBase) frame;
4167 break; // break added in 2.9
4170 * Otherwise test for matching position and size of viewer frame
4172 else if (frame.getX() == svattrib.getX()
4173 && frame.getY() == svattrib.getY()
4174 && frame.getHeight() == svattrib.getHeight()
4175 && frame.getWidth() == svattrib.getWidth())
4177 comp = (StructureViewerBase) frame;
4178 // no break in faint hope of an exact match on viewId
4186 * Link an AlignmentPanel to an existing structure viewer.
4191 * @param useinViewerSuperpos
4192 * @param usetoColourbyseq
4193 * @param viewerColouring
4195 protected void linkStructureViewer(AlignmentPanel ap,
4196 StructureViewerBase viewer, StructureViewerModel stateData)
4198 // NOTE: if the jalview project is part of a shared session then
4199 // view synchronization should/could be done here.
4201 final boolean useinViewerSuperpos = stateData.isAlignWithPanel();
4202 final boolean usetoColourbyseq = stateData.isColourWithAlignPanel();
4203 final boolean viewerColouring = stateData.isColourByViewer();
4204 Map<File, StructureData> oldFiles = stateData.getFileData();
4207 * Add mapping for sequences in this view to an already open viewer
4209 final AAStructureBindingModel binding = viewer.getBinding();
4210 for (File id : oldFiles.keySet())
4212 // add this and any other pdb files that should be present in the
4214 StructureData filedat = oldFiles.get(id);
4215 String pdbFile = filedat.getFilePath();
4216 SequenceI[] seq = filedat.getSeqList().toArray(new SequenceI[0]);
4217 binding.getSsm().setMapping(seq, null, pdbFile,
4218 jalview.io.AppletFormatAdapter.FILE);
4219 binding.addSequenceForStructFile(pdbFile, seq);
4221 // and add the AlignmentPanel's reference to the view panel
4222 viewer.addAlignmentPanel(ap);
4223 if (useinViewerSuperpos)
4225 viewer.useAlignmentPanelForSuperposition(ap);
4229 viewer.excludeAlignmentPanelForSuperposition(ap);
4231 if (usetoColourbyseq)
4233 viewer.useAlignmentPanelForColourbyseq(ap, !viewerColouring);
4237 viewer.excludeAlignmentPanelForColourbyseq(ap);
4242 * Get all frames within the Desktop.
4246 protected JInternalFrame[] getAllFrames()
4248 JInternalFrame[] frames = null;
4249 // TODO is this necessary - is it safe - risk of hanging?
4254 frames = Desktop.desktop.getAllFrames();
4255 } catch (ArrayIndexOutOfBoundsException e)
4257 // occasional No such child exceptions are thrown here...
4261 } catch (InterruptedException f)
4265 } while (frames == null);
4270 * Answers true if 'version' is equal to or later than 'supported', where each
4271 * is formatted as major/minor versions like "2.8.3" or "2.3.4b1" for bugfix
4272 * changes. Development and test values for 'version' are leniently treated
4276 * - minimum version we are comparing against
4278 * - version of data being processsed
4281 public static boolean isVersionStringLaterThan(String supported,
4284 if (supported == null || version == null
4285 || version.equalsIgnoreCase("DEVELOPMENT BUILD")
4286 || version.equalsIgnoreCase("Test")
4287 || version.equalsIgnoreCase("AUTOMATED BUILD"))
4289 System.err.println("Assuming project file with "
4290 + (version == null ? "null" : version)
4291 + " is compatible with Jalview version " + supported);
4296 return StringUtils.compareVersions(version, supported, "b") >= 0;
4300 Vector<JalviewStructureDisplayI> newStructureViewers = null;
4302 protected void addNewStructureViewer(JalviewStructureDisplayI sview)
4304 if (newStructureViewers != null)
4306 sview.getBinding().setFinishedLoadingFromArchive(false);
4307 newStructureViewers.add(sview);
4311 protected void setLoadingFinishedForNewStructureViewers()
4313 if (newStructureViewers != null)
4315 for (JalviewStructureDisplayI sview : newStructureViewers)
4317 sview.getBinding().setFinishedLoadingFromArchive(true);
4319 newStructureViewers.clear();
4320 newStructureViewers = null;
4324 AlignFrame loadViewport(String file, JSeq[] JSEQ,
4325 List<SequenceI> hiddenSeqs, AlignmentI al,
4326 JalviewModelSequence jms, Viewport view, String uniqueSeqSetId,
4327 String viewId, List<JvAnnotRow> autoAlan)
4329 AlignFrame af = null;
4330 af = new AlignFrame(al, view.getWidth(), view.getHeight(),
4331 uniqueSeqSetId, viewId);
4333 af.setFileName(file, "Jalview");
4335 for (int i = 0; i < JSEQ.length; i++)
4337 af.viewport.setSequenceColour(af.viewport.getAlignment()
4338 .getSequenceAt(i), new java.awt.Color(JSEQ[i].getColour()));
4343 af.getViewport().setColourByReferenceSeq(true);
4344 af.getViewport().setDisplayReferenceSeq(true);
4347 af.viewport.setGatherViewsHere(view.getGatheredViews());
4349 if (view.getSequenceSetId() != null)
4351 AlignmentViewport av = viewportsAdded.get(uniqueSeqSetId);
4353 af.viewport.setSequenceSetId(uniqueSeqSetId);
4356 // propagate shared settings to this new view
4357 af.viewport.setHistoryList(av.getHistoryList());
4358 af.viewport.setRedoList(av.getRedoList());
4362 viewportsAdded.put(uniqueSeqSetId, af.viewport);
4364 // TODO: check if this method can be called repeatedly without
4365 // side-effects if alignpanel already registered.
4366 PaintRefresher.Register(af.alignPanel, uniqueSeqSetId);
4368 // apply Hidden regions to view.
4369 if (hiddenSeqs != null)
4371 for (int s = 0; s < JSEQ.length; s++)
4373 SequenceGroup hidden = new SequenceGroup();
4374 boolean isRepresentative = false;
4375 for (int r = 0; r < JSEQ[s].getHiddenSequencesCount(); r++)
4377 isRepresentative = true;
4378 SequenceI sequenceToHide = al.getSequenceAt(JSEQ[s]
4379 .getHiddenSequences(r));
4380 hidden.addSequence(sequenceToHide, false);
4381 // remove from hiddenSeqs list so we don't try to hide it twice
4382 hiddenSeqs.remove(sequenceToHide);
4384 if (isRepresentative)
4386 SequenceI representativeSequence = al.getSequenceAt(s);
4387 hidden.addSequence(representativeSequence, false);
4388 af.viewport.hideRepSequences(representativeSequence, hidden);
4392 SequenceI[] hseqs = hiddenSeqs.toArray(new SequenceI[hiddenSeqs
4394 af.viewport.hideSequence(hseqs);
4397 // recover view properties and display parameters
4398 if (view.getViewName() != null)
4400 af.viewport.viewName = view.getViewName();
4401 af.setInitialTabVisible();
4403 af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),
4406 af.viewport.setShowAnnotation(view.getShowAnnotation());
4407 af.viewport.setAbovePIDThreshold(view.getPidSelected());
4409 af.viewport.setColourText(view.getShowColourText());
4411 af.viewport.setConservationSelected(view.getConservationSelected());
4412 af.viewport.setShowJVSuffix(view.getShowFullId());
4413 af.viewport.setRightAlignIds(view.getRightAlignIds());
4414 af.viewport.setFont(
4415 new java.awt.Font(view.getFontName(), view.getFontStyle(), view
4416 .getFontSize()), true);
4417 ViewStyleI vs = af.viewport.getViewStyle();
4418 vs.setScaleProteinAsCdna(view.isScaleProteinAsCdna());
4419 af.viewport.setViewStyle(vs);
4420 // TODO: allow custom charWidth/Heights to be restored by updating them
4421 // after setting font - which means set above to false
4422 af.viewport.setRenderGaps(view.getRenderGaps());
4423 af.viewport.setWrapAlignment(view.getWrapAlignment());
4424 af.viewport.setShowAnnotation(view.getShowAnnotation());
4426 af.viewport.setShowBoxes(view.getShowBoxes());
4428 af.viewport.setShowText(view.getShowText());
4430 af.viewport.setTextColour(new java.awt.Color(view.getTextCol1()));
4431 af.viewport.setTextColour2(new java.awt.Color(view.getTextCol2()));
4432 af.viewport.setThresholdTextColour(view.getTextColThreshold());
4433 af.viewport.setShowUnconserved(view.hasShowUnconserved() ? view
4434 .isShowUnconserved() : false);
4435 af.viewport.setStartRes(view.getStartRes());
4436 af.viewport.setStartSeq(view.getStartSeq());
4437 af.alignPanel.updateLayout();
4438 ColourSchemeI cs = null;
4439 // apply colourschemes
4440 if (view.getBgColour() != null)
4442 if (view.getBgColour().startsWith("ucs"))
4444 cs = getUserColourScheme(jms, view.getBgColour());
4446 else if (view.getBgColour().startsWith("Annotation"))
4448 AnnotationColours viewAnnColour = view.getAnnotationColours();
4449 cs = constructAnnotationColour(viewAnnColour, af, al, jms, true);
4456 cs = ColourSchemeProperty.getColour(al, view.getBgColour());
4461 cs.setThreshold(view.getPidThreshold(), true);
4462 cs.setConsensus(af.viewport.getSequenceConsensusHash());
4466 af.viewport.setGlobalColourScheme(cs);
4467 af.viewport.setColourAppliesToAllGroups(false);
4469 if (view.getConservationSelected() && cs != null)
4471 cs.setConservationInc(view.getConsThreshold());
4474 af.changeColour(cs);
4476 af.viewport.setColourAppliesToAllGroups(true);
4478 af.viewport.setShowSequenceFeatures(view.getShowSequenceFeatures());
4480 if (view.hasCentreColumnLabels())
4482 af.viewport.setCentreColumnLabels(view.getCentreColumnLabels());
4484 if (view.hasIgnoreGapsinConsensus())
4486 af.viewport.setIgnoreGapsConsensus(view.getIgnoreGapsinConsensus(),
4489 if (view.hasFollowHighlight())
4491 af.viewport.setFollowHighlight(view.getFollowHighlight());
4493 if (view.hasFollowSelection())
4495 af.viewport.followSelection = view.getFollowSelection();
4497 if (view.hasShowConsensusHistogram())
4499 af.viewport.setShowConsensusHistogram(view
4500 .getShowConsensusHistogram());
4504 af.viewport.setShowConsensusHistogram(true);
4506 if (view.hasShowSequenceLogo())
4508 af.viewport.setShowSequenceLogo(view.getShowSequenceLogo());
4512 af.viewport.setShowSequenceLogo(false);
4514 if (view.hasNormaliseSequenceLogo())
4516 af.viewport.setNormaliseSequenceLogo(view.getNormaliseSequenceLogo());
4518 if (view.hasShowDbRefTooltip())
4520 af.viewport.setShowDBRefs(view.getShowDbRefTooltip());
4522 if (view.hasShowNPfeatureTooltip())
4524 af.viewport.setShowNPFeats(view.hasShowNPfeatureTooltip());
4526 if (view.hasShowGroupConsensus())
4528 af.viewport.setShowGroupConsensus(view.getShowGroupConsensus());
4532 af.viewport.setShowGroupConsensus(false);
4534 if (view.hasShowGroupConservation())
4536 af.viewport.setShowGroupConservation(view.getShowGroupConservation());
4540 af.viewport.setShowGroupConservation(false);
4543 // recover featre settings
4544 if (jms.getFeatureSettings() != null)
4546 FeaturesDisplayed fdi;
4547 af.viewport.setFeaturesDisplayed(fdi = new FeaturesDisplayed());
4548 String[] renderOrder = new String[jms.getFeatureSettings()
4549 .getSettingCount()];
4550 Map<String, FeatureColourI> featureColours = new Hashtable<String, FeatureColourI>();
4551 Map<String, Float> featureOrder = new Hashtable<String, Float>();
4553 for (int fs = 0; fs < jms.getFeatureSettings().getSettingCount(); fs++)
4555 Setting setting = jms.getFeatureSettings().getSetting(fs);
4556 if (setting.hasMincolour())
4558 FeatureColourI gc = setting.hasMin() ? new FeatureColour(
4559 new Color(setting.getMincolour()), new Color(
4560 setting.getColour()), setting.getMin(),
4561 setting.getMax()) : new FeatureColour(new Color(
4562 setting.getMincolour()), new Color(setting.getColour()),
4564 if (setting.hasThreshold())
4566 gc.setThreshold(setting.getThreshold());
4567 int threshstate = setting.getThreshstate();
4568 // -1 = None, 0 = Below, 1 = Above threshold
4569 if (threshstate == 0)
4571 gc.setBelowThreshold(true);
4573 else if (threshstate == 1)
4575 gc.setAboveThreshold(true);
4578 gc.setAutoScaled(true); // default
4579 if (setting.hasAutoScale())
4581 gc.setAutoScaled(setting.getAutoScale());
4583 if (setting.hasColourByLabel())
4585 gc.setColourByLabel(setting.getColourByLabel());
4587 // and put in the feature colour table.
4588 featureColours.put(setting.getType(), gc);
4592 featureColours.put(setting.getType(), new FeatureColour(
4593 new Color(setting.getColour())));
4595 renderOrder[fs] = setting.getType();
4596 if (setting.hasOrder())
4598 featureOrder.put(setting.getType(), setting.getOrder());
4602 featureOrder.put(setting.getType(), new Float(fs
4603 / jms.getFeatureSettings().getSettingCount()));
4605 if (setting.getDisplay())
4607 fdi.setVisible(setting.getType());
4610 Map<String, Boolean> fgtable = new Hashtable<String, Boolean>();
4611 for (int gs = 0; gs < jms.getFeatureSettings().getGroupCount(); gs++)
4613 Group grp = jms.getFeatureSettings().getGroup(gs);
4614 fgtable.put(grp.getName(), new Boolean(grp.getDisplay()));
4616 // FeatureRendererSettings frs = new FeatureRendererSettings(renderOrder,
4617 // fgtable, featureColours, jms.getFeatureSettings().hasTransparency() ?
4618 // jms.getFeatureSettings().getTransparency() : 0.0, featureOrder);
4619 FeatureRendererSettings frs = new FeatureRendererSettings(
4620 renderOrder, fgtable, featureColours, 1.0f, featureOrder);
4621 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
4622 .transferSettings(frs);
4626 if (view.getHiddenColumnsCount() > 0)
4628 for (int c = 0; c < view.getHiddenColumnsCount(); c++)
4630 af.viewport.hideColumns(view.getHiddenColumns(c).getStart(), view
4631 .getHiddenColumns(c).getEnd() // +1
4635 if (view.getCalcIdParam() != null)
4637 for (CalcIdParam calcIdParam : view.getCalcIdParam())
4639 if (calcIdParam != null)
4641 if (recoverCalcIdParam(calcIdParam, af.viewport))
4646 warn("Couldn't recover parameters for "
4647 + calcIdParam.getCalcId());
4652 af.setMenusFromViewport(af.viewport);
4653 af.setTitle(view.getTitle());
4654 // TODO: we don't need to do this if the viewport is aready visible.
4656 * Add the AlignFrame to the desktop (it may be 'gathered' later), unless it
4657 * has a 'cdna/protein complement' view, in which case save it in order to
4658 * populate a SplitFrame once all views have been read in.
4660 String complementaryViewId = view.getComplementId();
4661 if (complementaryViewId == null)
4663 Desktop.addInternalFrame(af, view.getTitle(), view.getWidth(),
4665 // recompute any autoannotation
4666 af.alignPanel.updateAnnotation(false, true);
4667 reorderAutoannotation(af, al, autoAlan);
4668 af.alignPanel.alignmentChanged();
4672 splitFrameCandidates.put(view, af);
4677 private ColourSchemeI constructAnnotationColour(
4678 AnnotationColours viewAnnColour, AlignFrame af, AlignmentI al,
4679 JalviewModelSequence jms, boolean checkGroupAnnColour)
4681 boolean propagateAnnColour = false;
4682 ColourSchemeI cs = null;
4683 AlignmentI annAlignment = af != null ? af.viewport.getAlignment() : al;
4684 if (checkGroupAnnColour && al.getGroups() != null
4685 && al.getGroups().size() > 0)
4687 // pre 2.8.1 behaviour
4688 // check to see if we should transfer annotation colours
4689 propagateAnnColour = true;
4690 for (jalview.datamodel.SequenceGroup sg : al.getGroups())
4692 if (sg.cs instanceof AnnotationColourGradient)
4694 propagateAnnColour = false;
4698 // int find annotation
4699 if (annAlignment.getAlignmentAnnotation() != null)
4701 for (int i = 0; i < annAlignment.getAlignmentAnnotation().length; i++)
4703 if (annAlignment.getAlignmentAnnotation()[i].label
4704 .equals(viewAnnColour.getAnnotation()))
4706 if (annAlignment.getAlignmentAnnotation()[i].getThreshold() == null)
4708 annAlignment.getAlignmentAnnotation()[i]
4709 .setThreshold(new jalview.datamodel.GraphLine(
4710 viewAnnColour.getThreshold(), "Threshold",
4711 java.awt.Color.black)
4716 if (viewAnnColour.getColourScheme().equals("None"))
4718 cs = new AnnotationColourGradient(
4719 annAlignment.getAlignmentAnnotation()[i],
4720 new java.awt.Color(viewAnnColour.getMinColour()),
4721 new java.awt.Color(viewAnnColour.getMaxColour()),
4722 viewAnnColour.getAboveThreshold());
4724 else if (viewAnnColour.getColourScheme().startsWith("ucs"))
4726 cs = new AnnotationColourGradient(
4727 annAlignment.getAlignmentAnnotation()[i],
4728 getUserColourScheme(jms,
4729 viewAnnColour.getColourScheme()),
4730 viewAnnColour.getAboveThreshold());
4734 cs = new AnnotationColourGradient(
4735 annAlignment.getAlignmentAnnotation()[i],
4736 ColourSchemeProperty.getColour(al,
4737 viewAnnColour.getColourScheme()),
4738 viewAnnColour.getAboveThreshold());
4740 if (viewAnnColour.hasPerSequence())
4742 ((AnnotationColourGradient) cs).setSeqAssociated(viewAnnColour
4745 if (viewAnnColour.hasPredefinedColours())
4747 ((AnnotationColourGradient) cs)
4748 .setPredefinedColours(viewAnnColour
4749 .isPredefinedColours());
4751 if (propagateAnnColour && al.getGroups() != null)
4753 // Also use these settings for all the groups
4754 for (int g = 0; g < al.getGroups().size(); g++)
4756 jalview.datamodel.SequenceGroup sg = al.getGroups().get(g);
4764 * if (viewAnnColour.getColourScheme().equals("None" )) { sg.cs =
4765 * new AnnotationColourGradient(
4766 * annAlignment.getAlignmentAnnotation()[i], new
4767 * java.awt.Color(viewAnnColour. getMinColour()), new
4768 * java.awt.Color(viewAnnColour. getMaxColour()),
4769 * viewAnnColour.getAboveThreshold()); } else
4772 sg.cs = new AnnotationColourGradient(
4773 annAlignment.getAlignmentAnnotation()[i], sg.cs,
4774 viewAnnColour.getAboveThreshold());
4775 if (cs instanceof AnnotationColourGradient)
4777 if (viewAnnColour.hasPerSequence())
4779 ((AnnotationColourGradient) cs)
4780 .setSeqAssociated(viewAnnColour.isPerSequence());
4782 if (viewAnnColour.hasPredefinedColours())
4784 ((AnnotationColourGradient) cs)
4785 .setPredefinedColours(viewAnnColour
4786 .isPredefinedColours());
4802 private void reorderAutoannotation(AlignFrame af, AlignmentI al,
4803 List<JvAnnotRow> autoAlan)
4805 // copy over visualization settings for autocalculated annotation in the
4807 if (al.getAlignmentAnnotation() != null)
4810 * Kludge for magic autoannotation names (see JAL-811)
4812 String[] magicNames = new String[] { "Consensus", "Quality",
4814 JvAnnotRow nullAnnot = new JvAnnotRow(-1, null);
4815 Hashtable<String, JvAnnotRow> visan = new Hashtable<String, JvAnnotRow>();
4816 for (String nm : magicNames)
4818 visan.put(nm, nullAnnot);
4820 for (JvAnnotRow auan : autoAlan)
4822 visan.put(auan.template.label
4823 + (auan.template.getCalcId() == null ? "" : "\t"
4824 + auan.template.getCalcId()), auan);
4826 int hSize = al.getAlignmentAnnotation().length;
4827 List<JvAnnotRow> reorder = new ArrayList<JvAnnotRow>();
4828 // work through any autoCalculated annotation already on the view
4829 // removing it if it should be placed in a different location on the
4830 // annotation panel.
4831 List<String> remains = new ArrayList<String>(visan.keySet());
4832 for (int h = 0; h < hSize; h++)
4834 jalview.datamodel.AlignmentAnnotation jalan = al
4835 .getAlignmentAnnotation()[h];
4836 if (jalan.autoCalculated)
4839 JvAnnotRow valan = visan.get(k = jalan.label);
4840 if (jalan.getCalcId() != null)
4842 valan = visan.get(k = jalan.label + "\t" + jalan.getCalcId());
4847 // delete the auto calculated row from the alignment
4848 al.deleteAnnotation(jalan, false);
4852 if (valan != nullAnnot)
4854 if (jalan != valan.template)
4856 // newly created autoannotation row instance
4857 // so keep a reference to the visible annotation row
4858 // and copy over all relevant attributes
4859 if (valan.template.graphHeight >= 0)
4862 jalan.graphHeight = valan.template.graphHeight;
4864 jalan.visible = valan.template.visible;
4866 reorder.add(new JvAnnotRow(valan.order, jalan));
4871 // Add any (possibly stale) autocalculated rows that were not appended to
4872 // the view during construction
4873 for (String other : remains)
4875 JvAnnotRow othera = visan.get(other);
4876 if (othera != nullAnnot && othera.template.getCalcId() != null
4877 && othera.template.getCalcId().length() > 0)
4879 reorder.add(othera);
4882 // now put the automatic annotation in its correct place
4883 int s = 0, srt[] = new int[reorder.size()];
4884 JvAnnotRow[] rws = new JvAnnotRow[reorder.size()];
4885 for (JvAnnotRow jvar : reorder)
4888 srt[s++] = jvar.order;
4891 jalview.util.QuickSort.sort(srt, rws);
4892 // and re-insert the annotation at its correct position
4893 for (JvAnnotRow jvar : rws)
4895 al.addAnnotation(jvar.template, jvar.order);
4897 af.alignPanel.adjustAnnotationHeight();
4901 Hashtable skipList = null;
4904 * TODO remove this method
4907 * @return AlignFrame bound to sequenceSetId from view, if one exists. private
4908 * AlignFrame getSkippedFrame(Viewport view) { if (skipList==null) {
4909 * throw new Error("Implementation Error. No skipList defined for this
4910 * Jalview2XML instance."); } return (AlignFrame)
4911 * skipList.get(view.getSequenceSetId()); }
4915 * Check if the Jalview view contained in object should be skipped or not.
4918 * @return true if view's sequenceSetId is a key in skipList
4920 private boolean skipViewport(JalviewModel object)
4922 if (skipList == null)
4927 if (skipList.containsKey(id = object.getJalviewModelSequence()
4928 .getViewport()[0].getSequenceSetId()))
4930 if (Cache.log != null && Cache.log.isDebugEnabled())
4932 Cache.log.debug("Skipping seuqence set id " + id);
4939 public void addToSkipList(AlignFrame af)
4941 if (skipList == null)
4943 skipList = new Hashtable();
4945 skipList.put(af.getViewport().getSequenceSetId(), af);
4948 public void clearSkipList()
4950 if (skipList != null)
4957 private void recoverDatasetFor(SequenceSet vamsasSet, AlignmentI al,
4958 boolean ignoreUnrefed)
4960 jalview.datamodel.AlignmentI ds = getDatasetFor(vamsasSet
4962 Vector dseqs = null;
4965 // create a list of new dataset sequences
4966 dseqs = new Vector();
4968 for (int i = 0, iSize = vamsasSet.getSequenceCount(); i < iSize; i++)
4970 Sequence vamsasSeq = vamsasSet.getSequence(i);
4971 ensureJalviewDatasetSequence(vamsasSeq, ds, dseqs, ignoreUnrefed, i);
4973 // create a new dataset
4976 SequenceI[] dsseqs = new SequenceI[dseqs.size()];
4977 dseqs.copyInto(dsseqs);
4978 ds = new jalview.datamodel.Alignment(dsseqs);
4979 debug("Created new dataset " + vamsasSet.getDatasetId()
4980 + " for alignment " + System.identityHashCode(al));
4981 addDatasetRef(vamsasSet.getDatasetId(), ds);
4983 // set the dataset for the newly imported alignment.
4984 if (al.getDataset() == null && !ignoreUnrefed)
4993 * sequence definition to create/merge dataset sequence for
4997 * vector to add new dataset sequence to
4998 * @param ignoreUnrefed
4999 * - when true, don't create new sequences from vamsasSeq if it's id
5000 * doesn't already have an asssociated Jalview sequence.
5002 * - used to reorder the sequence in the alignment according to the
5003 * vamsasSeq array ordering, to preserve ordering of dataset
5005 private void ensureJalviewDatasetSequence(Sequence vamsasSeq,
5006 AlignmentI ds, Vector dseqs, boolean ignoreUnrefed, int vseqpos)
5008 // JBP TODO: Check this is called for AlCodonFrames to support recovery of
5010 SequenceI sq = seqRefIds.get(vamsasSeq.getId());
5011 boolean reorder = false;
5012 SequenceI dsq = null;
5013 if (sq != null && sq.getDatasetSequence() != null)
5015 dsq = sq.getDatasetSequence();
5021 if (sq == null && ignoreUnrefed)
5025 String sqid = vamsasSeq.getDsseqid();
5028 // need to create or add a new dataset sequence reference to this sequence
5031 dsq = seqRefIds.get(sqid);
5036 // make a new dataset sequence
5037 dsq = sq.createDatasetSequence();
5040 // make up a new dataset reference for this sequence
5041 sqid = seqHash(dsq);
5043 dsq.setVamsasId(uniqueSetSuffix + sqid);
5044 seqRefIds.put(sqid, dsq);
5049 dseqs.addElement(dsq);
5054 ds.addSequence(dsq);
5060 { // make this dataset sequence sq's dataset sequence
5061 sq.setDatasetSequence(dsq);
5062 // and update the current dataset alignment
5067 if (!dseqs.contains(dsq))
5074 if (ds.findIndex(dsq) < 0)
5076 ds.addSequence(dsq);
5083 // TODO: refactor this as a merge dataset sequence function
5084 // now check that sq (the dataset sequence) sequence really is the union of
5085 // all references to it
5086 // boolean pre = sq.getStart() < dsq.getStart();
5087 // boolean post = sq.getEnd() > dsq.getEnd();
5091 // StringBuffer sb = new StringBuffer();
5092 String newres = jalview.analysis.AlignSeq.extractGaps(
5093 jalview.util.Comparison.GapChars, sq.getSequenceAsString());
5094 if (!newres.equalsIgnoreCase(dsq.getSequenceAsString())
5095 && newres.length() > dsq.getLength())
5097 // Update with the longer sequence.
5101 * if (pre) { sb.insert(0, newres .substring(0, dsq.getStart() -
5102 * sq.getStart())); dsq.setStart(sq.getStart()); } if (post) {
5103 * sb.append(newres.substring(newres.length() - sq.getEnd() -
5104 * dsq.getEnd())); dsq.setEnd(sq.getEnd()); }
5106 dsq.setSequence(newres);
5108 // TODO: merges will never happen if we 'know' we have the real dataset
5109 // sequence - this should be detected when id==dssid
5111 .println("DEBUG Notice: Merged dataset sequence (if you see this often, post at http://issues.jalview.org/browse/JAL-1474)"); // ("
5112 // + (pre ? "prepended" : "") + " "
5113 // + (post ? "appended" : ""));
5118 // sequence refs are identical. We may need to update the existing dataset
5119 // alignment with this one, though.
5120 if (ds != null && dseqs == null)
5122 int opos = ds.findIndex(dsq);
5123 SequenceI tseq = null;
5124 if (opos != -1 && vseqpos != opos)
5126 // remove from old position
5127 ds.deleteSequence(dsq);
5129 if (vseqpos < ds.getHeight())
5131 if (vseqpos != opos)
5133 // save sequence at destination position
5134 tseq = ds.getSequenceAt(vseqpos);
5135 ds.replaceSequenceAt(vseqpos, dsq);
5136 ds.addSequence(tseq);
5141 ds.addSequence(dsq);
5148 * TODO use AlignmentI here and in related methods - needs
5149 * AlignmentI.getDataset() changed to return AlignmentI instead of Alignment
5151 Hashtable<String, AlignmentI> datasetIds = null;
5153 IdentityHashMap<AlignmentI, String> dataset2Ids = null;
5155 private AlignmentI getDatasetFor(String datasetId)
5157 if (datasetIds == null)
5159 datasetIds = new Hashtable<String, AlignmentI>();
5162 if (datasetIds.containsKey(datasetId))
5164 return datasetIds.get(datasetId);
5169 private void addDatasetRef(String datasetId, AlignmentI dataset)
5171 if (datasetIds == null)
5173 datasetIds = new Hashtable<String, AlignmentI>();
5175 datasetIds.put(datasetId, dataset);
5179 * make a new dataset ID for this jalview dataset alignment
5184 private String getDatasetIdRef(AlignmentI dataset)
5186 if (dataset.getDataset() != null)
5188 warn("Serious issue! Dataset Object passed to getDatasetIdRef is not a Jalview DATASET alignment...");
5190 String datasetId = makeHashCode(dataset, null);
5191 if (datasetId == null)
5193 // make a new datasetId and record it
5194 if (dataset2Ids == null)
5196 dataset2Ids = new IdentityHashMap<AlignmentI, String>();
5200 datasetId = dataset2Ids.get(dataset);
5202 if (datasetId == null)
5204 datasetId = "ds" + dataset2Ids.size() + 1;
5205 dataset2Ids.put(dataset, datasetId);
5211 private void addDBRefs(SequenceI datasetSequence, Sequence sequence)
5213 for (int d = 0; d < sequence.getDBRefCount(); d++)
5215 DBRef dr = sequence.getDBRef(d);
5216 jalview.datamodel.DBRefEntry entry = new jalview.datamodel.DBRefEntry(
5217 sequence.getDBRef(d).getSource(), sequence.getDBRef(d)
5218 .getVersion(), sequence.getDBRef(d).getAccessionId());
5219 if (dr.getMapping() != null)
5221 entry.setMap(addMapping(dr.getMapping()));
5223 datasetSequence.addDBRef(entry);
5227 private jalview.datamodel.Mapping addMapping(Mapping m)
5229 SequenceI dsto = null;
5230 // Mapping m = dr.getMapping();
5231 int fr[] = new int[m.getMapListFromCount() * 2];
5232 Enumeration f = m.enumerateMapListFrom();
5233 for (int _i = 0; f.hasMoreElements(); _i += 2)
5235 MapListFrom mf = (MapListFrom) f.nextElement();
5236 fr[_i] = mf.getStart();
5237 fr[_i + 1] = mf.getEnd();
5239 int fto[] = new int[m.getMapListToCount() * 2];
5240 f = m.enumerateMapListTo();
5241 for (int _i = 0; f.hasMoreElements(); _i += 2)
5243 MapListTo mf = (MapListTo) f.nextElement();
5244 fto[_i] = mf.getStart();
5245 fto[_i + 1] = mf.getEnd();
5247 jalview.datamodel.Mapping jmap = new jalview.datamodel.Mapping(dsto,
5248 fr, fto, (int) m.getMapFromUnit(), (int) m.getMapToUnit());
5249 if (m.getMappingChoice() != null)
5251 MappingChoice mc = m.getMappingChoice();
5252 if (mc.getDseqFor() != null)
5254 String dsfor = "" + mc.getDseqFor();
5255 if (seqRefIds.containsKey(dsfor))
5260 jmap.setTo(seqRefIds.get(dsfor));
5264 frefedSequence.add(newMappingRef(dsfor, jmap));
5270 * local sequence definition
5272 Sequence ms = mc.getSequence();
5273 SequenceI djs = null;
5274 String sqid = ms.getDsseqid();
5275 if (sqid != null && sqid.length() > 0)
5278 * recover dataset sequence
5280 djs = seqRefIds.get(sqid);
5285 .println("Warning - making up dataset sequence id for DbRef sequence map reference");
5286 sqid = ((Object) ms).toString(); // make up a new hascode for
5287 // undefined dataset sequence hash
5288 // (unlikely to happen)
5294 * make a new dataset sequence and add it to refIds hash
5296 djs = new jalview.datamodel.Sequence(ms.getName(),
5298 djs.setStart(jmap.getMap().getToLowest());
5299 djs.setEnd(jmap.getMap().getToHighest());
5300 djs.setVamsasId(uniqueSetSuffix + sqid);
5302 incompleteSeqs.put(sqid, djs);
5303 seqRefIds.put(sqid, djs);
5306 jalview.bin.Cache.log.debug("about to recurse on addDBRefs.");
5315 public jalview.gui.AlignmentPanel copyAlignPanel(AlignmentPanel ap,
5316 boolean keepSeqRefs)
5319 JalviewModel jm = saveState(ap, null, null, null);
5324 jm.getJalviewModelSequence().getViewport(0).setSequenceSetId(null);
5328 uniqueSetSuffix = "";
5329 jm.getJalviewModelSequence().getViewport(0).setId(null); // we don't
5334 if (this.frefedSequence == null)
5336 frefedSequence = new Vector();
5339 viewportsAdded.clear();
5341 AlignFrame af = loadFromObject(jm, null, false, null);
5342 af.alignPanels.clear();
5343 af.closeMenuItem_actionPerformed(true);
5346 * if(ap.av.getAlignment().getAlignmentAnnotation()!=null) { for(int i=0;
5347 * i<ap.av.getAlignment().getAlignmentAnnotation().length; i++) {
5348 * if(!ap.av.getAlignment().getAlignmentAnnotation()[i].autoCalculated) {
5349 * af.alignPanel.av.getAlignment().getAlignmentAnnotation()[i] =
5350 * ap.av.getAlignment().getAlignmentAnnotation()[i]; } } }
5353 return af.alignPanel;
5357 * flag indicating if hashtables should be cleared on finalization TODO this
5358 * flag may not be necessary
5360 private final boolean _cleartables = true;
5362 private Hashtable jvids2vobj;
5367 * @see java.lang.Object#finalize()
5370 protected void finalize() throws Throwable
5372 // really make sure we have no buried refs left.
5377 this.seqRefIds = null;
5378 this.seqsToIds = null;
5382 private void warn(String msg)
5387 private void warn(String msg, Exception e)
5389 if (Cache.log != null)
5393 Cache.log.warn(msg, e);
5397 Cache.log.warn(msg);
5402 System.err.println("Warning: " + msg);
5405 e.printStackTrace();
5410 private void debug(String string)
5412 debug(string, null);
5415 private void debug(String msg, Exception e)
5417 if (Cache.log != null)
5421 Cache.log.debug(msg, e);
5425 Cache.log.debug(msg);
5430 System.err.println("Warning: " + msg);
5433 e.printStackTrace();
5439 * set the object to ID mapping tables used to write/recover objects and XML
5440 * ID strings for the jalview project. If external tables are provided then
5441 * finalize and clearSeqRefs will not clear the tables when the Jalview2XML
5442 * object goes out of scope. - also populates the datasetIds hashtable with
5443 * alignment objects containing dataset sequences
5446 * Map from ID strings to jalview datamodel
5448 * Map from jalview datamodel to ID strings
5452 public void setObjectMappingTables(Hashtable vobj2jv,
5453 IdentityHashMap jv2vobj)
5455 this.jv2vobj = jv2vobj;
5456 this.vobj2jv = vobj2jv;
5457 Iterator ds = jv2vobj.keySet().iterator();
5459 while (ds.hasNext())
5461 Object jvobj = ds.next();
5462 id = jv2vobj.get(jvobj).toString();
5463 if (jvobj instanceof jalview.datamodel.Alignment)
5465 if (((jalview.datamodel.Alignment) jvobj).getDataset() == null)
5467 addDatasetRef(id, (jalview.datamodel.Alignment) jvobj);
5470 else if (jvobj instanceof jalview.datamodel.Sequence)
5472 // register sequence object so the XML parser can recover it.
5473 if (seqRefIds == null)
5475 seqRefIds = new HashMap<String, SequenceI>();
5477 if (seqsToIds == null)
5479 seqsToIds = new IdentityHashMap<SequenceI, String>();
5481 seqRefIds.put(jv2vobj.get(jvobj).toString(), (SequenceI) jvobj);
5482 seqsToIds.put((SequenceI) jvobj, id);
5484 else if (jvobj instanceof jalview.datamodel.AlignmentAnnotation)
5487 AlignmentAnnotation jvann = (AlignmentAnnotation) jvobj;
5488 annotationIds.put(anid = jv2vobj.get(jvobj).toString(), jvann);
5489 if (jvann.annotationId == null)
5491 jvann.annotationId = anid;
5493 if (!jvann.annotationId.equals(anid))
5495 // TODO verify that this is the correct behaviour
5496 this.warn("Overriding Annotation ID for " + anid
5497 + " from different id : " + jvann.annotationId);
5498 jvann.annotationId = anid;
5501 else if (jvobj instanceof String)
5503 if (jvids2vobj == null)
5505 jvids2vobj = new Hashtable();
5506 jvids2vobj.put(jvobj, jv2vobj.get(jvobj).toString());
5511 Cache.log.debug("Ignoring " + jvobj.getClass() + " (ID = " + id);
5517 * set the uniqueSetSuffix used to prefix/suffix object IDs for jalview
5518 * objects created from the project archive. If string is null (default for
5519 * construction) then suffix will be set automatically.
5523 public void setUniqueSetSuffix(String string)
5525 uniqueSetSuffix = string;
5530 * uses skipList2 as the skipList for skipping views on sequence sets
5531 * associated with keys in the skipList
5535 public void setSkipList(Hashtable skipList2)
5537 skipList = skipList2;
5541 * Reads the jar entry of given name and returns its contents, or null if the
5542 * entry is not found.
5545 * @param jarEntryName
5548 protected String readJarEntry(jarInputStreamProvider jprovider,
5549 String jarEntryName)
5551 String result = null;
5552 BufferedReader in = null;
5557 * Reopen the jar input stream and traverse its entries to find a matching
5560 JarInputStream jin = jprovider.getJarInputStream();
5561 JarEntry entry = null;
5564 entry = jin.getNextJarEntry();
5565 } while (entry != null && !entry.getName().equals(jarEntryName));
5569 StringBuilder out = new StringBuilder(256);
5570 in = new BufferedReader(new InputStreamReader(jin, UTF_8));
5573 while ((data = in.readLine()) != null)
5577 result = out.toString();
5581 warn("Couldn't find entry in Jalview Jar for " + jarEntryName);
5583 } catch (Exception ex)
5585 ex.printStackTrace();
5593 } catch (IOException e)
5604 * Returns an incrementing counter (0, 1, 2...)
5608 private synchronized int nextCounter()