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.Enumeration;
112 import java.util.HashMap;
113 import java.util.HashSet;
114 import java.util.Hashtable;
115 import java.util.IdentityHashMap;
116 import java.util.Iterator;
117 import java.util.LinkedHashMap;
118 import java.util.List;
119 import java.util.Map;
120 import java.util.Map.Entry;
121 import java.util.Set;
122 import java.util.Vector;
123 import java.util.jar.JarEntry;
124 import java.util.jar.JarInputStream;
125 import java.util.jar.JarOutputStream;
127 import javax.swing.JInternalFrame;
128 import javax.swing.JOptionPane;
129 import javax.swing.SwingUtilities;
131 import org.exolab.castor.xml.Marshaller;
132 import org.exolab.castor.xml.Unmarshaller;
135 * Write out the current jalview desktop state as a Jalview XML stream.
137 * Note: the vamsas objects referred to here are primitive versions of the
138 * VAMSAS project schema elements - they are not the same and most likely never
142 * @version $Revision: 1.134 $
144 public class Jalview2XML
146 private static final String VIEWER_PREFIX = "viewer_";
148 private static final String RNA_PREFIX = "rna_";
150 private static final String UTF_8 = "UTF-8";
152 // use this with nextCounter() to make unique names for entities
153 private int counter = 0;
156 * SequenceI reference -> XML ID string in jalview XML. Populated as XML reps
157 * of sequence objects are created.
159 IdentityHashMap<SequenceI, String> seqsToIds = null;
162 * jalview XML Sequence ID to jalview sequence object reference (both dataset
163 * and alignment sequences. Populated as XML reps of sequence objects are
166 Map<String, SequenceI> seqRefIds = null;
168 Vector<Object[]> frefedSequence = null;
170 boolean raiseGUI = true; // whether errors are raised in dialog boxes or not
173 * Map of reconstructed AlignFrame objects that appear to have come from
174 * SplitFrame objects (have a dna/protein complement view).
176 private Map<Viewport, AlignFrame> splitFrameCandidates = new HashMap<Viewport, AlignFrame>();
179 * Map from displayed rna structure models to their saved session state jar
182 private Map<RnaModel, String> rnaSessions = new HashMap<RnaModel, String>();
185 * create/return unique hash string for sq
188 * @return new or existing unique string for sq
190 String seqHash(SequenceI sq)
192 if (seqsToIds == null)
196 if (seqsToIds.containsKey(sq))
198 return seqsToIds.get(sq);
202 // create sequential key
203 String key = "sq" + (seqsToIds.size() + 1);
204 key = makeHashCode(sq, key); // check we don't have an external reference
206 seqsToIds.put(sq, key);
215 if (seqRefIds != null)
219 if (seqsToIds != null)
229 warn("clearSeqRefs called when _cleartables was not set. Doing nothing.");
230 // seqRefIds = new Hashtable();
231 // seqsToIds = new IdentityHashMap();
237 if (seqsToIds == null)
239 seqsToIds = new IdentityHashMap<SequenceI, String>();
241 if (seqRefIds == null)
243 seqRefIds = new HashMap<String, SequenceI>();
251 public Jalview2XML(boolean raiseGUI)
253 this.raiseGUI = raiseGUI;
256 public void resolveFrefedSequences()
258 if (frefedSequence.size() > 0)
260 int r = 0, rSize = frefedSequence.size();
263 Object[] ref = frefedSequence.elementAt(r);
266 String sref = (String) ref[0];
267 if (seqRefIds.containsKey(sref))
269 if (ref[1] instanceof jalview.datamodel.Mapping)
271 SequenceI seq = seqRefIds.get(sref);
272 while (seq.getDatasetSequence() != null)
274 seq = seq.getDatasetSequence();
276 ((jalview.datamodel.Mapping) ref[1]).setTo(seq);
280 if (ref[1] instanceof jalview.datamodel.AlignedCodonFrame)
282 SequenceI seq = seqRefIds.get(sref);
283 while (seq.getDatasetSequence() != null)
285 seq = seq.getDatasetSequence();
288 && ref[2] instanceof jalview.datamodel.Mapping)
290 jalview.datamodel.Mapping mp = (jalview.datamodel.Mapping) ref[2];
291 ((jalview.datamodel.AlignedCodonFrame) ref[1]).addMap(
292 seq, mp.getTo(), mp.getMap());
297 .println("IMPLEMENTATION ERROR: Unimplemented forward sequence references for AlcodonFrames involving "
298 + ref[2].getClass() + " type objects.");
304 .println("IMPLEMENTATION ERROR: Unimplemented forward sequence references for "
305 + ref[1].getClass() + " type objects.");
308 frefedSequence.remove(r);
314 .println("IMPLEMENTATION WARNING: Unresolved forward reference for hash string "
316 + " with objecttype "
317 + ref[1].getClass());
324 frefedSequence.remove(r);
332 * This maintains a map of viewports, the key being the seqSetId. Important to
333 * set historyItem and redoList for multiple views
335 Map<String, AlignViewport> viewportsAdded = new HashMap<String, AlignViewport>();
337 Map<String, AlignmentAnnotation> annotationIds = new HashMap<String, AlignmentAnnotation>();
339 String uniqueSetSuffix = "";
342 * List of pdbfiles added to Jar
344 List<String> pdbfiles = null;
346 // SAVES SEVERAL ALIGNMENT WINDOWS TO SAME JARFILE
347 public void saveState(File statefile)
349 FileOutputStream fos = null;
352 fos = new FileOutputStream(statefile);
353 JarOutputStream jout = new JarOutputStream(fos);
356 } catch (Exception e)
358 // TODO: inform user of the problem - they need to know if their data was
360 if (errorMessage == null)
362 errorMessage = "Couldn't write Jalview Archive to output file '"
363 + statefile + "' - See console error log for details";
367 errorMessage += "(output file was '" + statefile + "')";
377 } catch (IOException e)
387 * Writes a jalview project archive to the given Jar output stream.
391 public void saveState(JarOutputStream jout)
393 AlignFrame[] frames = Desktop.getAlignFrames();
400 Hashtable<String, AlignFrame> dsses = new Hashtable<String, AlignFrame>();
403 * ensure cached data is clear before starting
405 // todo tidy up seqRefIds, seqsToIds initialisation / reset
407 splitFrameCandidates.clear();
412 // NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS
413 // //////////////////////////////////////////////////
415 List<String> shortNames = new ArrayList<String>();
416 List<String> viewIds = new ArrayList<String>();
419 for (int i = frames.length - 1; i > -1; i--)
421 AlignFrame af = frames[i];
425 .containsKey(af.getViewport().getSequenceSetId()))
430 String shortName = makeFilename(af, shortNames);
432 int ap, apSize = af.alignPanels.size();
434 for (ap = 0; ap < apSize; ap++)
436 AlignmentPanel apanel = af.alignPanels.get(ap);
437 String fileName = apSize == 1 ? shortName : ap + shortName;
438 if (!fileName.endsWith(".xml"))
440 fileName = fileName + ".xml";
443 saveState(apanel, fileName, jout, viewIds);
445 String dssid = getDatasetIdRef(af.getViewport().getAlignment()
447 if (!dsses.containsKey(dssid))
449 dsses.put(dssid, af);
454 writeDatasetFor(dsses, "" + jout.hashCode() + " " + uniqueSetSuffix,
460 } catch (Exception foo)
465 } catch (Exception ex)
467 // TODO: inform user of the problem - they need to know if their data was
469 if (errorMessage == null)
471 errorMessage = "Couldn't write Jalview Archive - see error output for details";
473 ex.printStackTrace();
478 * Generates a distinct file name, based on the title of the AlignFrame, by
479 * appending _n for increasing n until an unused name is generated. The new
480 * name (without its extension) is added to the list.
484 * @return the generated name, with .xml extension
486 protected String makeFilename(AlignFrame af, List<String> namesUsed)
488 String shortName = af.getTitle();
490 if (shortName.indexOf(File.separatorChar) > -1)
492 shortName = shortName.substring(shortName
493 .lastIndexOf(File.separatorChar) + 1);
498 while (namesUsed.contains(shortName))
500 if (shortName.endsWith("_" + (count - 1)))
502 shortName = shortName.substring(0, shortName.lastIndexOf("_"));
505 shortName = shortName.concat("_" + count);
509 namesUsed.add(shortName);
511 if (!shortName.endsWith(".xml"))
513 shortName = shortName + ".xml";
518 // USE THIS METHOD TO SAVE A SINGLE ALIGNMENT WINDOW
519 public boolean saveAlignment(AlignFrame af, String jarFile,
525 int apSize = af.alignPanels.size();
526 FileOutputStream fos = new FileOutputStream(jarFile);
527 JarOutputStream jout = new JarOutputStream(fos);
528 Hashtable<String, AlignFrame> dsses = new Hashtable<String, AlignFrame>();
529 List<String> viewIds = new ArrayList<String>();
531 for (AlignmentPanel apanel : af.alignPanels)
533 String jfileName = apSize == 1 ? fileName : fileName + ap;
535 if (!jfileName.endsWith(".xml"))
537 jfileName = jfileName + ".xml";
539 saveState(apanel, jfileName, jout, viewIds);
540 String dssid = getDatasetIdRef(af.getViewport().getAlignment()
542 if (!dsses.containsKey(dssid))
544 dsses.put(dssid, af);
547 writeDatasetFor(dsses, fileName, jout);
551 } catch (Exception foo)
557 } catch (Exception ex)
559 errorMessage = "Couldn't Write alignment view to Jalview Archive - see error output for details";
560 ex.printStackTrace();
565 private void writeDatasetFor(Hashtable<String, AlignFrame> dsses,
566 String fileName, JarOutputStream jout)
569 for (String dssids : dsses.keySet())
571 AlignFrame _af = dsses.get(dssids);
572 String jfileName = fileName + " Dataset for " + _af.getTitle();
573 if (!jfileName.endsWith(".xml"))
575 jfileName = jfileName + ".xml";
577 saveState(_af.alignPanel, jfileName, true, jout, null);
582 * create a JalviewModel from an alignment view and marshall it to a
586 * panel to create jalview model for
588 * name of alignment panel written to output stream
595 public JalviewModel saveState(AlignmentPanel ap, String fileName,
596 JarOutputStream jout, List<String> viewIds)
598 return saveState(ap, fileName, false, jout, viewIds);
602 * create a JalviewModel from an alignment view and marshall it to a
606 * panel to create jalview model for
608 * name of alignment panel written to output stream
610 * when true, only write the dataset for the alignment, not the data
611 * associated with the view.
617 public JalviewModel saveState(AlignmentPanel ap, String fileName,
618 boolean storeDS, JarOutputStream jout, List<String> viewIds)
622 viewIds = new ArrayList<String>();
627 List<UserColourScheme> userColours = new ArrayList<UserColourScheme>();
629 AlignViewport av = ap.av;
631 JalviewModel object = new JalviewModel();
632 object.setVamsasModel(new jalview.schemabinding.version2.VamsasModel());
634 object.setCreationDate(new java.util.Date(System.currentTimeMillis()));
635 object.setVersion(jalview.bin.Cache.getDefault("VERSION",
636 "Development Build"));
639 * rjal is full height alignment, jal is actual alignment with full metadata
640 * but excludes hidden sequences.
642 jalview.datamodel.AlignmentI rjal = av.getAlignment(), jal = rjal;
644 if (av.hasHiddenRows())
646 rjal = jal.getHiddenSequences().getFullAlignment();
649 SequenceSet vamsasSet = new SequenceSet();
651 JalviewModelSequence jms = new JalviewModelSequence();
653 vamsasSet.setGapChar(jal.getGapCharacter() + "");
655 if (jal.getDataset() != null)
657 // dataset id is the dataset's hashcode
658 vamsasSet.setDatasetId(getDatasetIdRef(jal.getDataset()));
661 // switch jal and the dataset
662 jal = jal.getDataset();
666 if (jal.getProperties() != null)
668 Enumeration en = jal.getProperties().keys();
669 while (en.hasMoreElements())
671 String key = en.nextElement().toString();
672 SequenceSetProperties ssp = new SequenceSetProperties();
674 ssp.setValue(jal.getProperties().get(key).toString());
675 vamsasSet.addSequenceSetProperties(ssp);
680 Set<String> calcIdSet = new HashSet<String>();
683 for (final SequenceI jds : rjal.getSequences())
685 final SequenceI jdatasq = jds.getDatasetSequence() == null ? jds
686 : jds.getDatasetSequence();
687 String id = seqHash(jds);
689 if (seqRefIds.get(id) != null)
691 // This happens for two reasons: 1. multiple views are being serialised.
692 // 2. the hashCode has collided with another sequence's code. This DOES
693 // HAPPEN! (PF00072.15.stk does this)
694 // JBPNote: Uncomment to debug writing out of files that do not read
695 // back in due to ArrayOutOfBoundExceptions.
696 // System.err.println("vamsasSeq backref: "+id+"");
697 // System.err.println(jds.getName()+"
698 // "+jds.getStart()+"-"+jds.getEnd()+" "+jds.getSequenceAsString());
699 // System.err.println("Hashcode: "+seqHash(jds));
700 // SequenceI rsq = (SequenceI) seqRefIds.get(id + "");
701 // System.err.println(rsq.getName()+"
702 // "+rsq.getStart()+"-"+rsq.getEnd()+" "+rsq.getSequenceAsString());
703 // System.err.println("Hashcode: "+seqHash(rsq));
707 vamsasSeq = createVamsasSequence(id, jds);
708 vamsasSet.addSequence(vamsasSeq);
709 seqRefIds.put(id, jds);
713 jseq.setStart(jds.getStart());
714 jseq.setEnd(jds.getEnd());
715 jseq.setColour(av.getSequenceColour(jds).getRGB());
717 jseq.setId(id); // jseq id should be a string not a number
720 // Store any sequences this sequence represents
721 if (av.hasHiddenRows())
723 // use rjal, contains the full height alignment
724 jseq.setHidden(av.getAlignment().getHiddenSequences()
727 if (av.isHiddenRepSequence(jds))
729 jalview.datamodel.SequenceI[] reps = av
730 .getRepresentedSequences(jds)
731 .getSequencesInOrder(rjal);
733 for (int h = 0; h < reps.length; h++)
737 jseq.addHiddenSequences(rjal.findIndex(reps[h]));
742 // mark sequence as reference - if it is the reference for this view
745 jseq.setViewreference(jds == jal.getSeqrep());
749 // TODO: omit sequence features from each alignment view's XML dump if we
750 // are storing dataset
751 if (jds.getSequenceFeatures() != null)
753 jalview.datamodel.SequenceFeature[] sf = jds.getSequenceFeatures();
755 while (index < sf.length)
757 Features features = new Features();
759 features.setBegin(sf[index].getBegin());
760 features.setEnd(sf[index].getEnd());
761 features.setDescription(sf[index].getDescription());
762 features.setType(sf[index].getType());
763 features.setFeatureGroup(sf[index].getFeatureGroup());
764 features.setScore(sf[index].getScore());
765 if (sf[index].links != null)
767 for (int l = 0; l < sf[index].links.size(); l++)
769 OtherData keyValue = new OtherData();
770 keyValue.setKey("LINK_" + l);
771 keyValue.setValue(sf[index].links.elementAt(l).toString());
772 features.addOtherData(keyValue);
775 if (sf[index].otherDetails != null)
778 Iterator<String> keys = sf[index].otherDetails.keySet()
780 while (keys.hasNext())
783 OtherData keyValue = new OtherData();
784 keyValue.setKey(key);
785 keyValue.setValue(sf[index].otherDetails.get(key).toString());
786 features.addOtherData(keyValue);
790 jseq.addFeatures(features);
795 if (jdatasq.getAllPDBEntries() != null)
797 Enumeration en = jdatasq.getAllPDBEntries().elements();
798 while (en.hasMoreElements())
800 Pdbids pdb = new Pdbids();
801 jalview.datamodel.PDBEntry entry = (jalview.datamodel.PDBEntry) en
804 String pdbId = entry.getId();
806 pdb.setType(entry.getType());
809 * Store any structure views associated with this sequence. This
810 * section copes with duplicate entries in the project, so a dataset
811 * only view *should* be coped with sensibly.
813 // This must have been loaded, is it still visible?
814 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
815 String matchedFile = null;
816 for (int f = frames.length - 1; f > -1; f--)
818 if (frames[f] instanceof StructureViewerBase)
820 StructureViewerBase viewFrame = (StructureViewerBase) frames[f];
821 matchedFile = saveStructureState(ap, jds, pdb, entry,
822 viewIds, matchedFile, viewFrame);
824 * Only store each structure viewer's state once in the project
825 * jar. First time through only (storeDS==false)
827 String viewId = viewFrame.getViewId();
828 if (!storeDS && !viewIds.contains(viewId))
833 String viewerState = viewFrame.getStateInfo();
834 writeJarEntry(jout, getViewerJarEntryName(viewId),
835 viewerState.getBytes());
836 } catch (IOException e)
838 System.err.println("Error saving viewer state: "
845 if (matchedFile != null || entry.getFile() != null)
847 if (entry.getFile() != null)
850 matchedFile = entry.getFile();
852 pdb.setFile(matchedFile); // entry.getFile());
853 if (pdbfiles == null)
855 pdbfiles = new ArrayList<String>();
858 if (!pdbfiles.contains(pdbId))
861 copyFileToJar(jout, matchedFile, pdbId);
865 if (entry.getProperty() != null && !entry.getProperty().isEmpty())
867 PdbentryItem item = new PdbentryItem();
868 Hashtable properties = entry.getProperty();
869 Enumeration en2 = properties.keys();
870 while (en2.hasMoreElements())
872 Property prop = new Property();
873 String key = en2.nextElement().toString();
875 prop.setValue(properties.get(key).toString());
876 item.addProperty(prop);
878 pdb.addPdbentryItem(item);
885 saveRnaViewers(jout, jseq, jds, viewIds, ap, storeDS);
890 if (!storeDS && av.hasHiddenRows())
892 jal = av.getAlignment();
895 if (jal.getCodonFrames() != null)
897 List<AlignedCodonFrame> jac = jal.getCodonFrames();
898 for (AlignedCodonFrame acf : jac)
900 AlcodonFrame alc = new AlcodonFrame();
901 if (acf.getProtMappings() != null
902 && acf.getProtMappings().length > 0)
904 boolean hasMap = false;
905 SequenceI[] dnas = acf.getdnaSeqs();
906 jalview.datamodel.Mapping[] pmaps = acf.getProtMappings();
907 for (int m = 0; m < pmaps.length; m++)
909 AlcodMap alcmap = new AlcodMap();
910 alcmap.setDnasq(seqHash(dnas[m]));
911 alcmap.setMapping(createVamsasMapping(pmaps[m], dnas[m], null,
913 alc.addAlcodMap(alcmap);
918 vamsasSet.addAlcodonFrame(alc);
921 // TODO: delete this ? dead code from 2.8.3->2.9 ?
923 // AlcodonFrame alc = new AlcodonFrame();
924 // vamsasSet.addAlcodonFrame(alc);
925 // for (int p = 0; p < acf.aaWidth; p++)
927 // Alcodon cmap = new Alcodon();
928 // if (acf.codons[p] != null)
930 // // Null codons indicate a gapped column in the translated peptide
932 // cmap.setPos1(acf.codons[p][0]);
933 // cmap.setPos2(acf.codons[p][1]);
934 // cmap.setPos3(acf.codons[p][2]);
936 // alc.addAlcodon(cmap);
938 // if (acf.getProtMappings() != null
939 // && acf.getProtMappings().length > 0)
941 // SequenceI[] dnas = acf.getdnaSeqs();
942 // jalview.datamodel.Mapping[] pmaps = acf.getProtMappings();
943 // for (int m = 0; m < pmaps.length; m++)
945 // AlcodMap alcmap = new AlcodMap();
946 // alcmap.setDnasq(seqHash(dnas[m]));
947 // alcmap.setMapping(createVamsasMapping(pmaps[m], dnas[m], null,
949 // alc.addAlcodMap(alcmap);
956 // /////////////////////////////////
957 if (!storeDS && av.currentTree != null)
959 // FIND ANY ASSOCIATED TREES
960 // NOT IMPLEMENTED FOR HEADLESS STATE AT PRESENT
961 if (Desktop.desktop != null)
963 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
965 for (int t = 0; t < frames.length; t++)
967 if (frames[t] instanceof TreePanel)
969 TreePanel tp = (TreePanel) frames[t];
971 if (tp.treeCanvas.av.getAlignment() == jal)
973 Tree tree = new Tree();
974 tree.setTitle(tp.getTitle());
975 tree.setCurrentTree((av.currentTree == tp.getTree()));
976 tree.setNewick(tp.getTree().toString());
977 tree.setThreshold(tp.treeCanvas.threshold);
979 tree.setFitToWindow(tp.fitToWindow.getState());
980 tree.setFontName(tp.getTreeFont().getName());
981 tree.setFontSize(tp.getTreeFont().getSize());
982 tree.setFontStyle(tp.getTreeFont().getStyle());
983 tree.setMarkUnlinked(tp.placeholdersMenu.getState());
985 tree.setShowBootstrap(tp.bootstrapMenu.getState());
986 tree.setShowDistances(tp.distanceMenu.getState());
988 tree.setHeight(tp.getHeight());
989 tree.setWidth(tp.getWidth());
990 tree.setXpos(tp.getX());
991 tree.setYpos(tp.getY());
992 tree.setId(makeHashCode(tp, null));
1002 * store forward refs from an annotationRow to any groups
1004 IdentityHashMap<SequenceGroup, String> groupRefs = new IdentityHashMap<SequenceGroup, String>();
1007 for (SequenceI sq : jal.getSequences())
1009 // Store annotation on dataset sequences only
1010 AlignmentAnnotation[] aa = sq.getAnnotation();
1011 if (aa != null && aa.length > 0)
1013 storeAlignmentAnnotation(aa, groupRefs, av, calcIdSet, storeDS,
1020 if (jal.getAlignmentAnnotation() != null)
1022 // Store the annotation shown on the alignment.
1023 AlignmentAnnotation[] aa = jal.getAlignmentAnnotation();
1024 storeAlignmentAnnotation(aa, groupRefs, av, calcIdSet, storeDS,
1029 if (jal.getGroups() != null)
1031 JGroup[] groups = new JGroup[jal.getGroups().size()];
1033 for (jalview.datamodel.SequenceGroup sg : jal.getGroups())
1035 JGroup jGroup = new JGroup();
1036 groups[++i] = jGroup;
1038 jGroup.setStart(sg.getStartRes());
1039 jGroup.setEnd(sg.getEndRes());
1040 jGroup.setName(sg.getName());
1041 if (groupRefs.containsKey(sg))
1043 // group has references so set its ID field
1044 jGroup.setId(groupRefs.get(sg));
1048 if (sg.cs.conservationApplied())
1050 jGroup.setConsThreshold(sg.cs.getConservationInc());
1052 if (sg.cs instanceof jalview.schemes.UserColourScheme)
1054 jGroup.setColour(setUserColourScheme(sg.cs, userColours, jms));
1058 jGroup.setColour(ColourSchemeProperty.getColourName(sg.cs));
1061 else if (sg.cs instanceof jalview.schemes.AnnotationColourGradient)
1063 jGroup.setColour("AnnotationColourGradient");
1064 jGroup.setAnnotationColours(constructAnnotationColours(
1065 (jalview.schemes.AnnotationColourGradient) sg.cs,
1068 else if (sg.cs instanceof jalview.schemes.UserColourScheme)
1070 jGroup.setColour(setUserColourScheme(sg.cs, userColours, jms));
1074 jGroup.setColour(ColourSchemeProperty.getColourName(sg.cs));
1077 jGroup.setPidThreshold(sg.cs.getThreshold());
1080 jGroup.setOutlineColour(sg.getOutlineColour().getRGB());
1081 jGroup.setDisplayBoxes(sg.getDisplayBoxes());
1082 jGroup.setDisplayText(sg.getDisplayText());
1083 jGroup.setColourText(sg.getColourText());
1084 jGroup.setTextCol1(sg.textColour.getRGB());
1085 jGroup.setTextCol2(sg.textColour2.getRGB());
1086 jGroup.setTextColThreshold(sg.thresholdTextColour);
1087 jGroup.setShowUnconserved(sg.getShowNonconserved());
1088 jGroup.setIgnoreGapsinConsensus(sg.getIgnoreGapsConsensus());
1089 jGroup.setShowConsensusHistogram(sg.isShowConsensusHistogram());
1090 jGroup.setShowSequenceLogo(sg.isShowSequenceLogo());
1091 jGroup.setNormaliseSequenceLogo(sg.isNormaliseSequenceLogo());
1092 for (SequenceI seq : sg.getSequences())
1094 jGroup.addSeq(seqHash(seq));
1098 jms.setJGroup(groups);
1102 // /////////SAVE VIEWPORT
1103 Viewport view = new Viewport();
1104 view.setTitle(ap.alignFrame.getTitle());
1105 view.setSequenceSetId(makeHashCode(av.getSequenceSetId(),
1106 av.getSequenceSetId()));
1107 view.setId(av.getViewId());
1108 if (av.getCodingComplement() != null)
1110 view.setComplementId(av.getCodingComplement().getViewId());
1112 view.setViewName(av.viewName);
1113 view.setGatheredViews(av.isGatherViewsHere());
1115 Rectangle size = ap.av.getExplodedGeometry();
1116 Rectangle position = size;
1119 size = ap.alignFrame.getBounds();
1120 if (av.getCodingComplement() != null)
1122 position = ((SplitFrame) ap.alignFrame.getSplitViewContainer())
1130 view.setXpos(position.x);
1131 view.setYpos(position.y);
1133 view.setWidth(size.width);
1134 view.setHeight(size.height);
1136 view.setStartRes(av.startRes);
1137 view.setStartSeq(av.startSeq);
1139 if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme)
1141 view.setBgColour(setUserColourScheme(av.getGlobalColourScheme(),
1144 else if (av.getGlobalColourScheme() instanceof jalview.schemes.AnnotationColourGradient)
1146 AnnotationColours ac = constructAnnotationColours(
1147 (jalview.schemes.AnnotationColourGradient) av
1148 .getGlobalColourScheme(),
1151 view.setAnnotationColours(ac);
1152 view.setBgColour("AnnotationColourGradient");
1156 view.setBgColour(ColourSchemeProperty.getColourName(av
1157 .getGlobalColourScheme()));
1160 ColourSchemeI cs = av.getGlobalColourScheme();
1164 if (cs.conservationApplied())
1166 view.setConsThreshold(cs.getConservationInc());
1167 if (cs instanceof jalview.schemes.UserColourScheme)
1169 view.setBgColour(setUserColourScheme(cs, userColours, jms));
1173 if (cs instanceof ResidueColourScheme)
1175 view.setPidThreshold(cs.getThreshold());
1179 view.setConservationSelected(av.getConservationSelected());
1180 view.setPidSelected(av.getAbovePIDThreshold());
1181 view.setFontName(av.font.getName());
1182 view.setFontSize(av.font.getSize());
1183 view.setFontStyle(av.font.getStyle());
1184 view.setScaleProteinAsCdna(av.getViewStyle().isScaleProteinAsCdna());
1185 view.setRenderGaps(av.isRenderGaps());
1186 view.setShowAnnotation(av.isShowAnnotation());
1187 view.setShowBoxes(av.getShowBoxes());
1188 view.setShowColourText(av.getColourText());
1189 view.setShowFullId(av.getShowJVSuffix());
1190 view.setRightAlignIds(av.isRightAlignIds());
1191 view.setShowSequenceFeatures(av.isShowSequenceFeatures());
1192 view.setShowText(av.getShowText());
1193 view.setShowUnconserved(av.getShowUnconserved());
1194 view.setWrapAlignment(av.getWrapAlignment());
1195 view.setTextCol1(av.getTextColour().getRGB());
1196 view.setTextCol2(av.getTextColour2().getRGB());
1197 view.setTextColThreshold(av.getThresholdTextColour());
1198 view.setShowConsensusHistogram(av.isShowConsensusHistogram());
1199 view.setShowSequenceLogo(av.isShowSequenceLogo());
1200 view.setNormaliseSequenceLogo(av.isNormaliseSequenceLogo());
1201 view.setShowGroupConsensus(av.isShowGroupConsensus());
1202 view.setShowGroupConservation(av.isShowGroupConservation());
1203 view.setShowNPfeatureTooltip(av.isShowNPFeats());
1204 view.setShowDbRefTooltip(av.isShowDBRefs());
1205 view.setFollowHighlight(av.isFollowHighlight());
1206 view.setFollowSelection(av.followSelection);
1207 view.setIgnoreGapsinConsensus(av.isIgnoreGapsConsensus());
1208 if (av.getFeaturesDisplayed() != null)
1210 jalview.schemabinding.version2.FeatureSettings fs = new jalview.schemabinding.version2.FeatureSettings();
1212 String[] renderOrder = ap.getSeqPanel().seqCanvas
1213 .getFeatureRenderer().getRenderOrder()
1214 .toArray(new String[0]);
1216 Vector<String> settingsAdded = new Vector<String>();
1217 if (renderOrder != null)
1219 for (String featureType : renderOrder)
1221 FeatureColourI fcol = ap.getSeqPanel().seqCanvas
1222 .getFeatureRenderer()
1223 .getFeatureStyle(featureType);
1224 Setting setting = new Setting();
1225 setting.setType(featureType);
1226 if (!fcol.isSimpleColour())
1228 setting.setColour(fcol.getMaxColour().getRGB());
1229 setting.setMincolour(fcol.getMinColour().getRGB());
1230 setting.setMin(fcol.getMin());
1231 setting.setMax(fcol.getMax());
1232 setting.setColourByLabel(fcol.isColourByLabel());
1233 setting.setAutoScale(fcol.isAutoScaled());
1234 setting.setThreshold(fcol.getThreshold());
1235 // -1 = No threshold, 0 = Below, 1 = Above
1236 setting.setThreshstate(fcol.isAboveThreshold() ? 1
1237 : (fcol.isBelowThreshold() ? 0 : -1));
1241 setting.setColour(fcol.getColour().getRGB());
1244 setting.setDisplay(av.getFeaturesDisplayed().isVisible(
1246 float rorder = ap.getSeqPanel().seqCanvas.getFeatureRenderer()
1247 .getOrder(featureType);
1250 setting.setOrder(rorder);
1252 fs.addSetting(setting);
1253 settingsAdded.addElement(featureType);
1257 // is groups actually supposed to be a map here ?
1258 Iterator<String> en = ap.getSeqPanel().seqCanvas
1259 .getFeatureRenderer()
1260 .getFeatureGroups().iterator();
1261 Vector<String> groupsAdded = new Vector<String>();
1262 while (en.hasNext())
1264 String grp = en.next();
1265 if (groupsAdded.contains(grp))
1269 Group g = new Group();
1271 g.setDisplay(((Boolean) ap.getSeqPanel().seqCanvas
1272 .getFeatureRenderer().checkGroupVisibility(grp, false))
1275 groupsAdded.addElement(grp);
1277 jms.setFeatureSettings(fs);
1280 if (av.hasHiddenColumns())
1282 if (av.getColumnSelection() == null
1283 || av.getColumnSelection().getHiddenColumns() == null)
1285 warn("REPORT BUG: avoided null columnselection bug (DMAM reported). Please contact Jim about this.");
1289 for (int c = 0; c < av.getColumnSelection().getHiddenColumns()
1292 int[] region = av.getColumnSelection().getHiddenColumns()
1294 HiddenColumns hc = new HiddenColumns();
1295 hc.setStart(region[0]);
1296 hc.setEnd(region[1]);
1297 view.addHiddenColumns(hc);
1301 if (calcIdSet.size() > 0)
1303 for (String calcId : calcIdSet)
1305 if (calcId.trim().length() > 0)
1307 CalcIdParam cidp = createCalcIdParam(calcId, av);
1308 // Some calcIds have no parameters.
1311 view.addCalcIdParam(cidp);
1317 jms.addViewport(view);
1319 object.setJalviewModelSequence(jms);
1320 object.getVamsasModel().addSequenceSet(vamsasSet);
1322 if (jout != null && fileName != null)
1324 // We may not want to write the object to disk,
1325 // eg we can copy the alignViewport to a new view object
1326 // using save and then load
1329 System.out.println("Writing jar entry " + fileName);
1330 JarEntry entry = new JarEntry(fileName);
1331 jout.putNextEntry(entry);
1332 PrintWriter pout = new PrintWriter(new OutputStreamWriter(jout,
1334 Marshaller marshaller = new Marshaller(pout);
1335 marshaller.marshal(object);
1338 } catch (Exception ex)
1340 // TODO: raise error in GUI if marshalling failed.
1341 ex.printStackTrace();
1348 * Save any Varna viewers linked to this sequence. Writes an rnaViewer element
1349 * for each viewer, with
1351 * <li>viewer geometry (position, size, split pane divider location)</li>
1352 * <li>index of the selected structure in the viewer (currently shows gapped
1354 * <li>the id of the annotation holding RNA secondary structure</li>
1355 * <li>(currently only one SS is shown per viewer, may be more in future)</li>
1357 * Varna viewer state is also written out (in native Varna XML) to separate
1358 * project jar entries. A separate entry is written for each RNA structure
1359 * displayed, with the naming convention
1361 * <li>rna_viewId_sequenceId_annotationId_[gapped|trimmed]</li>
1369 * @param storeDataset
1371 protected void saveRnaViewers(JarOutputStream jout, JSeq jseq,
1372 final SequenceI jds, List<String> viewIds, AlignmentPanel ap,
1373 boolean storeDataset)
1375 if (Desktop.desktop == null)
1379 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1380 for (int f = frames.length - 1; f > -1; f--)
1382 if (frames[f] instanceof AppVarna)
1384 AppVarna varna = (AppVarna) frames[f];
1386 * link the sequence to every viewer that is showing it and is linked to
1387 * its alignment panel
1389 if (varna.isListeningFor(jds) && ap == varna.getAlignmentPanel())
1391 String viewId = varna.getViewId();
1392 RnaViewer rna = new RnaViewer();
1393 rna.setViewId(viewId);
1394 rna.setTitle(varna.getTitle());
1395 rna.setXpos(varna.getX());
1396 rna.setYpos(varna.getY());
1397 rna.setWidth(varna.getWidth());
1398 rna.setHeight(varna.getHeight());
1399 rna.setDividerLocation(varna.getDividerLocation());
1400 rna.setSelectedRna(varna.getSelectedIndex());
1401 jseq.addRnaViewer(rna);
1404 * Store each Varna panel's state once in the project per sequence.
1405 * First time through only (storeDataset==false)
1407 // boolean storeSessions = false;
1408 // String sequenceViewId = viewId + seqsToIds.get(jds);
1409 // if (!storeDataset && !viewIds.contains(sequenceViewId))
1411 // viewIds.add(sequenceViewId);
1412 // storeSessions = true;
1414 for (RnaModel model : varna.getModels())
1416 if (model.seq == jds)
1419 * VARNA saves each view (sequence or alignment secondary
1420 * structure, gapped or trimmed) as a separate XML file
1422 String jarEntryName = rnaSessions.get(model);
1423 if (jarEntryName == null)
1426 String varnaStateFile = varna.getStateInfo(model.rna);
1427 jarEntryName = RNA_PREFIX + viewId + "_" + nextCounter();
1428 copyFileToJar(jout, varnaStateFile, jarEntryName);
1429 rnaSessions.put(model, jarEntryName);
1431 SecondaryStructure ss = new SecondaryStructure();
1432 String annotationId = varna.getAnnotation(jds).annotationId;
1433 ss.setAnnotationId(annotationId);
1434 ss.setViewerState(jarEntryName);
1435 ss.setGapped(model.gapped);
1436 ss.setTitle(model.title);
1437 rna.addSecondaryStructure(ss);
1446 * Copy the contents of a file to a new entry added to the output jar
1450 * @param jarEntryName
1452 protected void copyFileToJar(JarOutputStream jout, String infilePath,
1453 String jarEntryName)
1455 DataInputStream dis = null;
1458 File file = new File(infilePath);
1459 if (file.exists() && jout != null)
1461 dis = new DataInputStream(new FileInputStream(file));
1462 byte[] data = new byte[(int) file.length()];
1463 dis.readFully(data);
1464 writeJarEntry(jout, jarEntryName, data);
1466 } catch (Exception ex)
1468 ex.printStackTrace();
1476 } catch (IOException e)
1485 * Write the data to a new entry of given name in the output jar file
1488 * @param jarEntryName
1490 * @throws IOException
1492 protected void writeJarEntry(JarOutputStream jout, String jarEntryName,
1493 byte[] data) throws IOException
1497 System.out.println("Writing jar entry " + jarEntryName);
1498 jout.putNextEntry(new JarEntry(jarEntryName));
1499 DataOutputStream dout = new DataOutputStream(jout);
1500 dout.write(data, 0, data.length);
1507 * Save the state of a structure viewer
1512 * the archive XML element under which to save the state
1515 * @param matchedFile
1519 protected String saveStructureState(AlignmentPanel ap, SequenceI jds,
1520 Pdbids pdb, PDBEntry entry, List<String> viewIds,
1521 String matchedFile, StructureViewerBase viewFrame)
1523 final AAStructureBindingModel bindingModel = viewFrame.getBinding();
1526 * Look for any bindings for this viewer to the PDB file of interest
1527 * (including part matches excluding chain id)
1529 for (int peid = 0; peid < bindingModel.getPdbCount(); peid++)
1531 final PDBEntry pdbentry = bindingModel.getPdbEntry(peid);
1532 final String pdbId = pdbentry.getId();
1533 if (!pdbId.equals(entry.getId())
1534 && !(entry.getId().length() > 4 && entry.getId()
1535 .toLowerCase().startsWith(pdbId.toLowerCase())))
1538 * not interested in a binding to a different PDB entry here
1542 if (matchedFile == null)
1544 matchedFile = pdbentry.getFile();
1546 else if (!matchedFile.equals(pdbentry.getFile()))
1549 .warn("Probably lost some PDB-Sequence mappings for this structure file (which apparently has same PDB Entry code): "
1550 + pdbentry.getFile());
1554 // can get at it if the ID
1555 // match is ambiguous (e.g.
1558 for (int smap = 0; smap < viewFrame.getBinding().getSequence()[peid].length; smap++)
1560 // if (jal.findIndex(jmol.jmb.sequence[peid][smap]) > -1)
1561 if (jds == viewFrame.getBinding().getSequence()[peid][smap])
1563 StructureState state = new StructureState();
1564 state.setVisible(true);
1565 state.setXpos(viewFrame.getX());
1566 state.setYpos(viewFrame.getY());
1567 state.setWidth(viewFrame.getWidth());
1568 state.setHeight(viewFrame.getHeight());
1569 final String viewId = viewFrame.getViewId();
1570 state.setViewId(viewId);
1571 state.setAlignwithAlignPanel(viewFrame.isUsedforaligment(ap));
1572 state.setColourwithAlignPanel(viewFrame.isUsedforcolourby(ap));
1573 state.setColourByJmol(viewFrame.isColouredByViewer());
1574 state.setType(viewFrame.getViewerType().toString());
1575 pdb.addStructureState(state);
1582 private AnnotationColours constructAnnotationColours(
1583 AnnotationColourGradient acg, List<UserColourScheme> userColours,
1584 JalviewModelSequence jms)
1586 AnnotationColours ac = new AnnotationColours();
1587 ac.setAboveThreshold(acg.getAboveThreshold());
1588 ac.setThreshold(acg.getAnnotationThreshold());
1589 ac.setAnnotation(acg.getAnnotation());
1590 if (acg.getBaseColour() instanceof jalview.schemes.UserColourScheme)
1592 ac.setColourScheme(setUserColourScheme(acg.getBaseColour(),
1597 ac.setColourScheme(ColourSchemeProperty.getColourName(acg
1601 ac.setMaxColour(acg.getMaxColour().getRGB());
1602 ac.setMinColour(acg.getMinColour().getRGB());
1603 ac.setPerSequence(acg.isSeqAssociated());
1604 ac.setPredefinedColours(acg.isPredefinedColours());
1608 private void storeAlignmentAnnotation(AlignmentAnnotation[] aa,
1609 IdentityHashMap<SequenceGroup, String> groupRefs,
1610 AlignmentViewport av, Set<String> calcIdSet, boolean storeDS,
1611 SequenceSet vamsasSet)
1614 for (int i = 0; i < aa.length; i++)
1616 Annotation an = new Annotation();
1618 AlignmentAnnotation annotation = aa[i];
1619 if (annotation.annotationId != null)
1621 annotationIds.put(annotation.annotationId, annotation);
1624 an.setId(annotation.annotationId);
1626 an.setVisible(annotation.visible);
1628 an.setDescription(annotation.description);
1630 if (annotation.sequenceRef != null)
1632 // 2.9 JAL-1781 xref on sequence id rather than name
1633 an.setSequenceRef(seqsToIds.get(annotation.sequenceRef));
1635 if (annotation.groupRef != null)
1637 String groupIdr = groupRefs.get(annotation.groupRef);
1638 if (groupIdr == null)
1640 // make a locally unique String
1642 annotation.groupRef,
1643 groupIdr = ("" + System.currentTimeMillis()
1644 + annotation.groupRef.getName() + groupRefs
1647 an.setGroupRef(groupIdr.toString());
1650 // store all visualization attributes for annotation
1651 an.setGraphHeight(annotation.graphHeight);
1652 an.setCentreColLabels(annotation.centreColLabels);
1653 an.setScaleColLabels(annotation.scaleColLabel);
1654 an.setShowAllColLabels(annotation.showAllColLabels);
1655 an.setBelowAlignment(annotation.belowAlignment);
1657 if (annotation.graph > 0)
1660 an.setGraphType(annotation.graph);
1661 an.setGraphGroup(annotation.graphGroup);
1662 if (annotation.getThreshold() != null)
1664 ThresholdLine line = new ThresholdLine();
1665 line.setLabel(annotation.getThreshold().label);
1666 line.setValue(annotation.getThreshold().value);
1667 line.setColour(annotation.getThreshold().colour.getRGB());
1668 an.setThresholdLine(line);
1676 an.setLabel(annotation.label);
1678 if (annotation == av.getAlignmentQualityAnnot()
1679 || annotation == av.getAlignmentConservationAnnotation()
1680 || annotation == av.getAlignmentConsensusAnnotation()
1681 || annotation.autoCalculated)
1683 // new way of indicating autocalculated annotation -
1684 an.setAutoCalculated(annotation.autoCalculated);
1686 if (annotation.hasScore())
1688 an.setScore(annotation.getScore());
1691 if (annotation.getCalcId() != null)
1693 calcIdSet.add(annotation.getCalcId());
1694 an.setCalcId(annotation.getCalcId());
1696 if (annotation.hasProperties())
1698 for (String pr : annotation.getProperties())
1700 Property prop = new Property();
1702 prop.setValue(annotation.getProperty(pr));
1703 an.addProperty(prop);
1707 AnnotationElement ae;
1708 if (annotation.annotations != null)
1710 an.setScoreOnly(false);
1711 for (int a = 0; a < annotation.annotations.length; a++)
1713 if ((annotation == null) || (annotation.annotations[a] == null))
1718 ae = new AnnotationElement();
1719 if (annotation.annotations[a].description != null)
1721 ae.setDescription(annotation.annotations[a].description);
1723 if (annotation.annotations[a].displayCharacter != null)
1725 ae.setDisplayCharacter(annotation.annotations[a].displayCharacter);
1728 if (!Float.isNaN(annotation.annotations[a].value))
1730 ae.setValue(annotation.annotations[a].value);
1734 if (annotation.annotations[a].secondaryStructure > ' ')
1736 ae.setSecondaryStructure(annotation.annotations[a].secondaryStructure
1740 if (annotation.annotations[a].colour != null
1741 && annotation.annotations[a].colour != java.awt.Color.black)
1743 ae.setColour(annotation.annotations[a].colour.getRGB());
1746 an.addAnnotationElement(ae);
1747 if (annotation.autoCalculated)
1749 // only write one non-null entry into the annotation row -
1750 // sufficient to get the visualization attributes necessary to
1758 an.setScoreOnly(true);
1760 if (!storeDS || (storeDS && !annotation.autoCalculated))
1762 // skip autocalculated annotation - these are only provided for
1764 vamsasSet.addAnnotation(an);
1770 private CalcIdParam createCalcIdParam(String calcId, AlignViewport av)
1772 AutoCalcSetting settings = av.getCalcIdSettingsFor(calcId);
1773 if (settings != null)
1775 CalcIdParam vCalcIdParam = new CalcIdParam();
1776 vCalcIdParam.setCalcId(calcId);
1777 vCalcIdParam.addServiceURL(settings.getServiceURI());
1778 // generic URI allowing a third party to resolve another instance of the
1779 // service used for this calculation
1780 for (String urls : settings.getServiceURLs())
1782 vCalcIdParam.addServiceURL(urls);
1784 vCalcIdParam.setVersion("1.0");
1785 if (settings.getPreset() != null)
1787 WsParamSetI setting = settings.getPreset();
1788 vCalcIdParam.setName(setting.getName());
1789 vCalcIdParam.setDescription(setting.getDescription());
1793 vCalcIdParam.setName("");
1794 vCalcIdParam.setDescription("Last used parameters");
1796 // need to be able to recover 1) settings 2) user-defined presets or
1797 // recreate settings from preset 3) predefined settings provided by
1798 // service - or settings that can be transferred (or discarded)
1799 vCalcIdParam.setParameters(settings.getWsParamFile().replace("\n",
1801 vCalcIdParam.setAutoUpdate(settings.isAutoUpdate());
1802 // todo - decide if updateImmediately is needed for any projects.
1804 return vCalcIdParam;
1809 private boolean recoverCalcIdParam(CalcIdParam calcIdParam,
1812 if (calcIdParam.getVersion().equals("1.0"))
1814 Jws2Instance service = Jws2Discoverer.getDiscoverer()
1815 .getPreferredServiceFor(calcIdParam.getServiceURL());
1816 if (service != null)
1818 WsParamSetI parmSet = null;
1821 parmSet = service.getParamStore().parseServiceParameterFile(
1822 calcIdParam.getName(), calcIdParam.getDescription(),
1823 calcIdParam.getServiceURL(),
1824 calcIdParam.getParameters().replace("|\\n|", "\n"));
1825 } catch (IOException x)
1827 warn("Couldn't parse parameter data for "
1828 + calcIdParam.getCalcId(), x);
1831 List<ArgumentI> argList = null;
1832 if (calcIdParam.getName().length() > 0)
1834 parmSet = service.getParamStore()
1835 .getPreset(calcIdParam.getName());
1836 if (parmSet != null)
1838 // TODO : check we have a good match with settings in AACon -
1839 // otherwise we'll need to create a new preset
1844 argList = parmSet.getArguments();
1847 AAConSettings settings = new AAConSettings(
1848 calcIdParam.isAutoUpdate(), service, parmSet, argList);
1849 av.setCalcIdSettingsFor(calcIdParam.getCalcId(), settings,
1850 calcIdParam.isNeedsUpdate());
1855 warn("Cannot resolve a service for the parameters used in this project. Try configuring a JABAWS server.");
1859 throw new Error(MessageManager.formatMessage(
1860 "error.unsupported_version_calcIdparam",
1861 new Object[] { calcIdParam.toString() }));
1865 * External mapping between jalview objects and objects yielding a valid and
1866 * unique object ID string. This is null for normal Jalview project IO, but
1867 * non-null when a jalview project is being read or written as part of a
1870 IdentityHashMap jv2vobj = null;
1873 * Construct a unique ID for jvobj using either existing bindings or if none
1874 * exist, the result of the hashcode call for the object.
1877 * jalview data object
1878 * @return unique ID for referring to jvobj
1880 private String makeHashCode(Object jvobj, String altCode)
1882 if (jv2vobj != null)
1884 Object id = jv2vobj.get(jvobj);
1887 return id.toString();
1889 // check string ID mappings
1890 if (jvids2vobj != null && jvobj instanceof String)
1892 id = jvids2vobj.get(jvobj);
1896 return id.toString();
1898 // give up and warn that something has gone wrong
1899 warn("Cannot find ID for object in external mapping : " + jvobj);
1905 * return local jalview object mapped to ID, if it exists
1909 * @return null or object bound to idcode
1911 private Object retrieveExistingObj(String idcode)
1913 if (idcode != null && vobj2jv != null)
1915 return vobj2jv.get(idcode);
1921 * binding from ID strings from external mapping table to jalview data model
1924 private Hashtable vobj2jv;
1926 private Sequence createVamsasSequence(String id, SequenceI jds)
1928 return createVamsasSequence(true, id, jds, null);
1931 private Sequence createVamsasSequence(boolean recurse, String id,
1932 SequenceI jds, SequenceI parentseq)
1934 Sequence vamsasSeq = new Sequence();
1935 vamsasSeq.setId(id);
1936 vamsasSeq.setName(jds.getName());
1937 vamsasSeq.setSequence(jds.getSequenceAsString());
1938 vamsasSeq.setDescription(jds.getDescription());
1939 jalview.datamodel.DBRefEntry[] dbrefs = null;
1940 if (jds.getDatasetSequence() != null)
1942 vamsasSeq.setDsseqid(seqHash(jds.getDatasetSequence()));
1943 if (jds.getDatasetSequence().getDBRefs() != null)
1945 dbrefs = jds.getDatasetSequence().getDBRefs();
1950 vamsasSeq.setDsseqid(id); // so we can tell which sequences really are
1951 // dataset sequences only
1952 dbrefs = jds.getDBRefs();
1956 for (int d = 0; d < dbrefs.length; d++)
1958 DBRef dbref = new DBRef();
1959 dbref.setSource(dbrefs[d].getSource());
1960 dbref.setVersion(dbrefs[d].getVersion());
1961 dbref.setAccessionId(dbrefs[d].getAccessionId());
1962 if (dbrefs[d].hasMap())
1964 Mapping mp = createVamsasMapping(dbrefs[d].getMap(), parentseq,
1966 dbref.setMapping(mp);
1968 vamsasSeq.addDBRef(dbref);
1974 private Mapping createVamsasMapping(jalview.datamodel.Mapping jmp,
1975 SequenceI parentseq, SequenceI jds, boolean recurse)
1978 if (jmp.getMap() != null)
1982 jalview.util.MapList mlst = jmp.getMap();
1983 List<int[]> r = mlst.getFromRanges();
1984 for (int[] range : r)
1986 MapListFrom mfrom = new MapListFrom();
1987 mfrom.setStart(range[0]);
1988 mfrom.setEnd(range[1]);
1989 mp.addMapListFrom(mfrom);
1991 r = mlst.getToRanges();
1992 for (int[] range : r)
1994 MapListTo mto = new MapListTo();
1995 mto.setStart(range[0]);
1996 mto.setEnd(range[1]);
1997 mp.addMapListTo(mto);
1999 mp.setMapFromUnit(mlst.getFromRatio());
2000 mp.setMapToUnit(mlst.getToRatio());
2001 if (jmp.getTo() != null)
2003 MappingChoice mpc = new MappingChoice();
2005 && (parentseq != jmp.getTo() || parentseq
2006 .getDatasetSequence() != jmp.getTo()))
2008 mpc.setSequence(createVamsasSequence(false, seqHash(jmp.getTo()),
2014 SequenceI ps = null;
2015 if (parentseq != jmp.getTo()
2016 && parentseq.getDatasetSequence() != jmp.getTo())
2018 // chaining dbref rather than a handshaking one
2019 jmpid = seqHash(ps = jmp.getTo());
2023 jmpid = seqHash(ps = parentseq);
2025 mpc.setDseqFor(jmpid);
2026 if (!seqRefIds.containsKey(mpc.getDseqFor()))
2028 jalview.bin.Cache.log.debug("creatign new DseqFor ID");
2029 seqRefIds.put(mpc.getDseqFor(), ps);
2033 jalview.bin.Cache.log.debug("reusing DseqFor ID");
2036 mp.setMappingChoice(mpc);
2042 String setUserColourScheme(jalview.schemes.ColourSchemeI cs,
2043 List<UserColourScheme> userColours, JalviewModelSequence jms)
2046 jalview.schemes.UserColourScheme ucs = (jalview.schemes.UserColourScheme) cs;
2047 boolean newucs = false;
2048 if (!userColours.contains(ucs))
2050 userColours.add(ucs);
2053 id = "ucs" + userColours.indexOf(ucs);
2056 // actually create the scheme's entry in the XML model
2057 java.awt.Color[] colours = ucs.getColours();
2058 jalview.schemabinding.version2.UserColours uc = new jalview.schemabinding.version2.UserColours();
2059 jalview.schemabinding.version2.UserColourScheme jbucs = new jalview.schemabinding.version2.UserColourScheme();
2061 for (int i = 0; i < colours.length; i++)
2063 jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();
2064 col.setName(ResidueProperties.aa[i]);
2065 col.setRGB(jalview.util.Format.getHexString(colours[i]));
2066 jbucs.addColour(col);
2068 if (ucs.getLowerCaseColours() != null)
2070 colours = ucs.getLowerCaseColours();
2071 for (int i = 0; i < colours.length; i++)
2073 jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();
2074 col.setName(ResidueProperties.aa[i].toLowerCase());
2075 col.setRGB(jalview.util.Format.getHexString(colours[i]));
2076 jbucs.addColour(col);
2081 uc.setUserColourScheme(jbucs);
2082 jms.addUserColours(uc);
2088 jalview.schemes.UserColourScheme getUserColourScheme(
2089 JalviewModelSequence jms, String id)
2091 UserColours[] uc = jms.getUserColours();
2092 UserColours colours = null;
2094 for (int i = 0; i < uc.length; i++)
2096 if (uc[i].getId().equals(id))
2104 java.awt.Color[] newColours = new java.awt.Color[24];
2106 for (int i = 0; i < 24; i++)
2108 newColours[i] = new java.awt.Color(Integer.parseInt(colours
2109 .getUserColourScheme().getColour(i).getRGB(), 16));
2112 jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(
2115 if (colours.getUserColourScheme().getColourCount() > 24)
2117 newColours = new java.awt.Color[23];
2118 for (int i = 0; i < 23; i++)
2120 newColours[i] = new java.awt.Color(Integer.parseInt(colours
2121 .getUserColourScheme().getColour(i + 24).getRGB(), 16));
2123 ucs.setLowerCaseColours(newColours);
2130 * contains last error message (if any) encountered by XML loader.
2132 String errorMessage = null;
2135 * flag to control whether the Jalview2XML_V1 parser should be deferred to if
2136 * exceptions are raised during project XML parsing
2138 public boolean attemptversion1parse = true;
2141 * Load a jalview project archive from a jar file
2144 * - HTTP URL or filename
2146 public AlignFrame loadJalviewAlign(final String file)
2149 jalview.gui.AlignFrame af = null;
2153 // create list to store references for any new Jmol viewers created
2154 newStructureViewers = new Vector<JalviewStructureDisplayI>();
2155 // UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
2156 // Workaround is to make sure caller implements the JarInputStreamProvider
2158 // so we can re-open the jar input stream for each entry.
2160 jarInputStreamProvider jprovider = createjarInputStreamProvider(file);
2161 af = loadJalviewAlign(jprovider);
2163 } catch (MalformedURLException e)
2165 errorMessage = "Invalid URL format for '" + file + "'";
2171 SwingUtilities.invokeAndWait(new Runnable()
2176 setLoadingFinishedForNewStructureViewers();
2179 } catch (Exception x)
2181 System.err.println("Error loading alignment: " + x.getMessage());
2187 private jarInputStreamProvider createjarInputStreamProvider(
2188 final String file) throws MalformedURLException
2191 errorMessage = null;
2192 uniqueSetSuffix = null;
2194 viewportsAdded.clear();
2195 frefedSequence = null;
2197 if (file.startsWith("http://"))
2199 url = new URL(file);
2201 final URL _url = url;
2202 return new jarInputStreamProvider()
2206 public JarInputStream getJarInputStream() throws IOException
2210 return new JarInputStream(_url.openStream());
2214 return new JarInputStream(new FileInputStream(file));
2219 public String getFilename()
2227 * Recover jalview session from a jalview project archive. Caller may
2228 * initialise uniqueSetSuffix, seqRefIds, viewportsAdded and frefedSequence
2229 * themselves. Any null fields will be initialised with default values,
2230 * non-null fields are left alone.
2235 public AlignFrame loadJalviewAlign(final jarInputStreamProvider jprovider)
2237 errorMessage = null;
2238 if (uniqueSetSuffix == null)
2240 uniqueSetSuffix = System.currentTimeMillis() % 100000 + "";
2242 if (seqRefIds == null)
2244 seqRefIds = new HashMap<String, SequenceI>();
2246 if (frefedSequence == null)
2248 frefedSequence = new Vector<Object[]>();
2251 AlignFrame af = null, _af = null;
2252 Map<String, AlignFrame> gatherToThisFrame = new HashMap<String, AlignFrame>();
2253 final String file = jprovider.getFilename();
2256 JarInputStream jin = null;
2257 JarEntry jarentry = null;
2262 jin = jprovider.getJarInputStream();
2263 for (int i = 0; i < entryCount; i++)
2265 jarentry = jin.getNextJarEntry();
2268 if (jarentry != null && jarentry.getName().endsWith(".xml"))
2270 InputStreamReader in = new InputStreamReader(jin, UTF_8);
2271 JalviewModel object = new JalviewModel();
2273 Unmarshaller unmar = new Unmarshaller(object);
2274 unmar.setValidation(false);
2275 object = (JalviewModel) unmar.unmarshal(in);
2276 if (true) // !skipViewport(object))
2278 _af = loadFromObject(object, file, true, jprovider);
2279 if (object.getJalviewModelSequence().getViewportCount() > 0)
2282 if (af.viewport.isGatherViewsHere())
2284 gatherToThisFrame.put(af.viewport.getSequenceSetId(), af);
2290 else if (jarentry != null)
2292 // Some other file here.
2295 } while (jarentry != null);
2296 resolveFrefedSequences();
2297 } catch (IOException ex)
2299 ex.printStackTrace();
2300 errorMessage = "Couldn't locate Jalview XML file : " + file;
2301 System.err.println("Exception whilst loading jalview XML file : "
2303 } catch (Exception ex)
2305 System.err.println("Parsing as Jalview Version 2 file failed.");
2306 ex.printStackTrace(System.err);
2307 if (attemptversion1parse)
2309 // Is Version 1 Jar file?
2312 af = new Jalview2XML_V1(raiseGUI).LoadJalviewAlign(jprovider);
2313 } catch (Exception ex2)
2315 System.err.println("Exception whilst loading as jalviewXMLV1:");
2316 ex2.printStackTrace();
2320 if (Desktop.instance != null)
2322 Desktop.instance.stopLoading();
2326 System.out.println("Successfully loaded archive file");
2329 ex.printStackTrace();
2331 System.err.println("Exception whilst loading jalview XML file : "
2333 } catch (OutOfMemoryError e)
2335 // Don't use the OOM Window here
2336 errorMessage = "Out of memory loading jalview XML file";
2337 System.err.println("Out of memory whilst loading jalview XML file");
2338 e.printStackTrace();
2341 if (Desktop.instance != null)
2343 Desktop.instance.stopLoading();
2347 * Regather multiple views (with the same sequence set id) to the frame (if
2348 * any) that is flagged as the one to gather to, i.e. convert them to tabbed
2349 * views instead of separate frames. Note this doesn't restore a state where
2350 * some expanded views in turn have tabbed views - the last "first tab" read
2351 * in will play the role of gatherer for all.
2353 for (AlignFrame fr : gatherToThisFrame.values())
2355 Desktop.instance.gatherViews(fr);
2358 restoreSplitFrames();
2360 if (errorMessage != null)
2368 * Try to reconstruct and display SplitFrame windows, where each contains
2369 * complementary dna and protein alignments. Done by pairing up AlignFrame
2370 * objects (created earlier) which have complementary viewport ids associated.
2372 protected void restoreSplitFrames()
2374 List<SplitFrame> gatherTo = new ArrayList<SplitFrame>();
2375 List<AlignFrame> addedToSplitFrames = new ArrayList<AlignFrame>();
2376 Map<String, AlignFrame> dna = new HashMap<String, AlignFrame>();
2379 * Identify the DNA alignments
2381 for (Entry<Viewport, AlignFrame> candidate : splitFrameCandidates
2384 AlignFrame af = candidate.getValue();
2385 if (af.getViewport().getAlignment().isNucleotide())
2387 dna.put(candidate.getKey().getId(), af);
2392 * Try to match up the protein complements
2394 for (Entry<Viewport, AlignFrame> candidate : splitFrameCandidates
2397 AlignFrame af = candidate.getValue();
2398 if (!af.getViewport().getAlignment().isNucleotide())
2400 String complementId = candidate.getKey().getComplementId();
2401 // only non-null complements should be in the Map
2402 if (complementId != null && dna.containsKey(complementId))
2404 final AlignFrame dnaFrame = dna.get(complementId);
2405 SplitFrame sf = createSplitFrame(dnaFrame, af);
2406 addedToSplitFrames.add(dnaFrame);
2407 addedToSplitFrames.add(af);
2408 if (af.viewport.isGatherViewsHere())
2417 * Open any that we failed to pair up (which shouldn't happen!) as
2418 * standalone AlignFrame's.
2420 for (Entry<Viewport, AlignFrame> candidate : splitFrameCandidates
2423 AlignFrame af = candidate.getValue();
2424 if (!addedToSplitFrames.contains(af))
2426 Viewport view = candidate.getKey();
2427 Desktop.addInternalFrame(af, view.getTitle(), view.getWidth(),
2429 System.err.println("Failed to restore view " + view.getTitle()
2430 + " to split frame");
2435 * Gather back into tabbed views as flagged.
2437 for (SplitFrame sf : gatherTo)
2439 Desktop.instance.gatherViews(sf);
2442 splitFrameCandidates.clear();
2446 * Construct and display one SplitFrame holding DNA and protein alignments.
2449 * @param proteinFrame
2452 protected SplitFrame createSplitFrame(AlignFrame dnaFrame,
2453 AlignFrame proteinFrame)
2455 SplitFrame splitFrame = new SplitFrame(dnaFrame, proteinFrame);
2456 String title = MessageManager.getString("label.linked_view_title");
2457 int width = (int) dnaFrame.getBounds().getWidth();
2458 int height = (int) (dnaFrame.getBounds().getHeight()
2459 + proteinFrame.getBounds().getHeight() + 50);
2462 * SplitFrame location is saved to both enclosed frames
2464 splitFrame.setLocation(dnaFrame.getX(), dnaFrame.getY());
2465 Desktop.addInternalFrame(splitFrame, title, width, height);
2468 * And compute cDNA consensus (couldn't do earlier with consensus as
2469 * mappings were not yet present)
2471 proteinFrame.viewport.alignmentChanged(proteinFrame.alignPanel);
2477 * check errorMessage for a valid error message and raise an error box in the
2478 * GUI or write the current errorMessage to stderr and then clear the error
2481 protected void reportErrors()
2483 reportErrors(false);
2486 protected void reportErrors(final boolean saving)
2488 if (errorMessage != null)
2490 final String finalErrorMessage = errorMessage;
2493 javax.swing.SwingUtilities.invokeLater(new Runnable()
2498 JOptionPane.showInternalMessageDialog(Desktop.desktop,
2499 finalErrorMessage, "Error "
2500 + (saving ? "saving" : "loading")
2501 + " Jalview file", JOptionPane.WARNING_MESSAGE);
2507 System.err.println("Problem loading Jalview file: " + errorMessage);
2510 errorMessage = null;
2513 Map<String, String> alreadyLoadedPDB = new HashMap<String, String>();
2516 * when set, local views will be updated from view stored in JalviewXML
2517 * Currently (28th Sep 2008) things will go horribly wrong in vamsas document
2518 * sync if this is set to true.
2520 private final boolean updateLocalViews = false;
2523 * Returns the path to a temporary file holding the PDB file for the given PDB
2524 * id. The first time of asking, searches for a file of that name in the
2525 * Jalview project jar, and copies it to a new temporary file. Any repeat
2526 * requests just return the path to the file previously created.
2532 String loadPDBFile(jarInputStreamProvider jprovider, String pdbId)
2534 if (alreadyLoadedPDB.containsKey(pdbId))
2536 return alreadyLoadedPDB.get(pdbId).toString();
2539 String tempFile = copyJarEntry(jprovider, pdbId, "jalview_pdb");
2540 if (tempFile != null)
2542 alreadyLoadedPDB.put(pdbId, tempFile);
2548 * Copies the jar entry of given name to a new temporary file and returns the
2549 * path to the file, or null if the entry is not found.
2552 * @param jarEntryName
2554 * a prefix for the temporary file name, must be at least three
2558 protected String copyJarEntry(jarInputStreamProvider jprovider,
2559 String jarEntryName, String prefix)
2561 BufferedReader in = null;
2562 PrintWriter out = null;
2566 JarInputStream jin = jprovider.getJarInputStream();
2568 * if (jprovider.startsWith("http://")) { jin = new JarInputStream(new
2569 * URL(jprovider).openStream()); } else { jin = new JarInputStream(new
2570 * FileInputStream(jprovider)); }
2573 JarEntry entry = null;
2576 entry = jin.getNextJarEntry();
2577 } while (entry != null && !entry.getName().equals(jarEntryName));
2580 in = new BufferedReader(new InputStreamReader(jin, UTF_8));
2581 File outFile = File.createTempFile(prefix, ".tmp");
2582 outFile.deleteOnExit();
2583 out = new PrintWriter(new FileOutputStream(outFile));
2586 while ((data = in.readLine()) != null)
2591 String t = outFile.getAbsolutePath();
2596 warn("Couldn't find entry in Jalview Jar for " + jarEntryName);
2598 } catch (Exception ex)
2600 ex.printStackTrace();
2608 } catch (IOException e)
2622 private class JvAnnotRow
2624 public JvAnnotRow(int i, AlignmentAnnotation jaa)
2631 * persisted version of annotation row from which to take vis properties
2633 public jalview.datamodel.AlignmentAnnotation template;
2636 * original position of the annotation row in the alignment
2642 * Load alignment frame from jalview XML DOM object
2647 * filename source string
2648 * @param loadTreesAndStructures
2649 * when false only create Viewport
2651 * data source provider
2652 * @return alignment frame created from view stored in DOM
2654 AlignFrame loadFromObject(JalviewModel object, String file,
2655 boolean loadTreesAndStructures, jarInputStreamProvider jprovider)
2657 SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);
2658 Sequence[] vamsasSeq = vamsasSet.getSequence();
2660 JalviewModelSequence jms = object.getJalviewModelSequence();
2662 Viewport view = (jms.getViewportCount() > 0) ? jms.getViewport(0)
2665 // ////////////////////////////////
2668 List<SequenceI> hiddenSeqs = null;
2669 jalview.datamodel.Sequence jseq;
2671 List<SequenceI> tmpseqs = new ArrayList<SequenceI>();
2673 boolean multipleView = false;
2674 SequenceI referenceseqForView = null;
2675 JSeq[] jseqs = object.getJalviewModelSequence().getJSeq();
2676 int vi = 0; // counter in vamsasSeq array
2677 for (int i = 0; i < jseqs.length; i++)
2679 String seqId = jseqs[i].getId();
2681 if (seqRefIds.get(seqId) != null)
2683 tmpseqs.add(seqRefIds.get(seqId));
2684 multipleView = true;
2688 jseq = new jalview.datamodel.Sequence(vamsasSeq[vi].getName(),
2689 vamsasSeq[vi].getSequence());
2690 jseq.setDescription(vamsasSeq[vi].getDescription());
2691 jseq.setStart(jseqs[i].getStart());
2692 jseq.setEnd(jseqs[i].getEnd());
2693 jseq.setVamsasId(uniqueSetSuffix + seqId);
2694 seqRefIds.put(vamsasSeq[vi].getId(), jseq);
2699 if (jseqs[i].hasViewreference() && jseqs[i].getViewreference())
2701 referenceseqForView = tmpseqs.get(tmpseqs.size() - 1);
2704 if (jseqs[i].getHidden())
2706 if (hiddenSeqs == null)
2708 hiddenSeqs = new ArrayList<SequenceI>();
2711 hiddenSeqs.add(seqRefIds.get(seqId));
2716 // Create the alignment object from the sequence set
2717 // ///////////////////////////////
2718 SequenceI[] orderedSeqs = tmpseqs
2719 .toArray(new SequenceI[tmpseqs.size()]);
2721 AlignmentI al = new Alignment(orderedSeqs);
2723 if (referenceseqForView != null)
2725 al.setSeqrep(referenceseqForView);
2727 // / Add the alignment properties
2728 for (int i = 0; i < vamsasSet.getSequenceSetPropertiesCount(); i++)
2730 SequenceSetProperties ssp = vamsasSet.getSequenceSetProperties(i);
2731 al.setProperty(ssp.getKey(), ssp.getValue());
2735 // SequenceFeatures are added to the DatasetSequence,
2736 // so we must create or recover the dataset before loading features
2737 // ///////////////////////////////
2738 if (vamsasSet.getDatasetId() == null || vamsasSet.getDatasetId() == "")
2740 // older jalview projects do not have a dataset id.
2741 al.setDataset(null);
2745 // recover dataset - passing on flag indicating if this a 'viewless'
2746 // sequence set (a.k.a. a stored dataset for the project)
2747 recoverDatasetFor(vamsasSet, al, object.getJalviewModelSequence()
2748 .getViewportCount() == 0);
2750 // ///////////////////////////////
2752 Hashtable pdbloaded = new Hashtable(); // TODO nothing writes to this??
2755 // load sequence features, database references and any associated PDB
2756 // structures for the alignment
2757 for (int i = 0; i < vamsasSeq.length; i++)
2759 if (jseqs[i].getFeaturesCount() > 0)
2761 Features[] features = jseqs[i].getFeatures();
2762 for (int f = 0; f < features.length; f++)
2764 jalview.datamodel.SequenceFeature sf = new jalview.datamodel.SequenceFeature(
2765 features[f].getType(), features[f].getDescription(),
2766 features[f].getStatus(), features[f].getBegin(),
2767 features[f].getEnd(), features[f].getFeatureGroup());
2769 sf.setScore(features[f].getScore());
2770 for (int od = 0; od < features[f].getOtherDataCount(); od++)
2772 OtherData keyValue = features[f].getOtherData(od);
2773 if (keyValue.getKey().startsWith("LINK"))
2775 sf.addLink(keyValue.getValue());
2779 sf.setValue(keyValue.getKey(), keyValue.getValue());
2784 al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf);
2787 if (vamsasSeq[i].getDBRefCount() > 0)
2789 addDBRefs(al.getSequenceAt(i).getDatasetSequence(), vamsasSeq[i]);
2791 if (jseqs[i].getPdbidsCount() > 0)
2793 Pdbids[] ids = jseqs[i].getPdbids();
2794 for (int p = 0; p < ids.length; p++)
2796 jalview.datamodel.PDBEntry entry = new jalview.datamodel.PDBEntry();
2797 entry.setId(ids[p].getId());
2798 if (ids[p].getType() != null)
2800 if (ids[p].getType().equalsIgnoreCase("PDB"))
2802 entry.setType(PDBEntry.Type.PDB);
2806 entry.setType(PDBEntry.Type.FILE);
2809 if (ids[p].getFile() != null)
2811 if (!pdbloaded.containsKey(ids[p].getFile()))
2813 entry.setFile(loadPDBFile(jprovider, ids[p].getId()));
2817 entry.setFile(pdbloaded.get(ids[p].getId()).toString());
2820 StructureSelectionManager.getStructureSelectionManager(
2821 Desktop.instance).registerPDBEntry(entry);
2822 al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
2826 } // end !multipleview
2828 // ///////////////////////////////
2829 // LOAD SEQUENCE MAPPINGS
2831 if (vamsasSet.getAlcodonFrameCount() > 0)
2833 // TODO Potentially this should only be done once for all views of an
2835 AlcodonFrame[] alc = vamsasSet.getAlcodonFrame();
2836 for (int i = 0; i < alc.length; i++)
2838 AlignedCodonFrame cf = new AlignedCodonFrame();
2839 if (alc[i].getAlcodMapCount() > 0)
2841 AlcodMap[] maps = alc[i].getAlcodMap();
2842 for (int m = 0; m < maps.length; m++)
2844 SequenceI dnaseq = seqRefIds.get(maps[m].getDnasq());
2846 jalview.datamodel.Mapping mapping = null;
2847 // attach to dna sequence reference.
2848 if (maps[m].getMapping() != null)
2850 mapping = addMapping(maps[m].getMapping());
2852 if (dnaseq != null && mapping.getTo() != null)
2854 cf.addMap(dnaseq, mapping.getTo(), mapping.getMap());
2859 frefedSequence.add(new Object[] { maps[m].getDnasq(), cf,
2863 al.addCodonFrame(cf);
2868 // ////////////////////////////////
2870 List<JvAnnotRow> autoAlan = new ArrayList<JvAnnotRow>();
2873 * store any annotations which forward reference a group's ID
2875 Map<String, List<AlignmentAnnotation>> groupAnnotRefs = new Hashtable<String, List<AlignmentAnnotation>>();
2877 if (vamsasSet.getAnnotationCount() > 0)
2879 Annotation[] an = vamsasSet.getAnnotation();
2881 for (int i = 0; i < an.length; i++)
2883 Annotation annotation = an[i];
2886 * test if annotation is automatically calculated for this view only
2888 boolean autoForView = false;
2889 if (annotation.getLabel().equals("Quality")
2890 || annotation.getLabel().equals("Conservation")
2891 || annotation.getLabel().equals("Consensus"))
2893 // Kludge for pre 2.5 projects which lacked the autocalculated flag
2895 if (!annotation.hasAutoCalculated())
2897 annotation.setAutoCalculated(true);
2901 || (annotation.hasAutoCalculated() && annotation
2902 .isAutoCalculated()))
2904 // remove ID - we don't recover annotation from other views for
2905 // view-specific annotation
2906 annotation.setId(null);
2909 // set visiblity for other annotation in this view
2910 String annotationId = annotation.getId();
2911 if (annotationId != null && annotationIds.containsKey(annotationId))
2913 AlignmentAnnotation jda = annotationIds.get(annotationId);
2914 // in principle Visible should always be true for annotation displayed
2915 // in multiple views
2916 if (annotation.hasVisible())
2918 jda.visible = annotation.getVisible();
2921 al.addAnnotation(jda);
2925 // Construct new annotation from model.
2926 AnnotationElement[] ae = annotation.getAnnotationElement();
2927 jalview.datamodel.Annotation[] anot = null;
2928 java.awt.Color firstColour = null;
2930 if (!annotation.getScoreOnly())
2932 anot = new jalview.datamodel.Annotation[al.getWidth()];
2933 for (int aa = 0; aa < ae.length && aa < anot.length; aa++)
2935 anpos = ae[aa].getPosition();
2937 if (anpos >= anot.length)
2942 anot[anpos] = new jalview.datamodel.Annotation(
2944 ae[aa].getDisplayCharacter(), ae[aa].getDescription(),
2945 (ae[aa].getSecondaryStructure() == null || ae[aa]
2946 .getSecondaryStructure().length() == 0) ? ' '
2947 : ae[aa].getSecondaryStructure().charAt(0),
2951 // JBPNote: Consider verifying dataflow for IO of secondary
2952 // structure annotation read from Stockholm files
2953 // this was added to try to ensure that
2954 // if (anot[ae[aa].getPosition()].secondaryStructure>' ')
2956 // anot[ae[aa].getPosition()].displayCharacter = "";
2958 anot[anpos].colour = new java.awt.Color(ae[aa].getColour());
2959 if (firstColour == null)
2961 firstColour = anot[anpos].colour;
2965 jalview.datamodel.AlignmentAnnotation jaa = null;
2967 if (annotation.getGraph())
2969 float llim = 0, hlim = 0;
2970 // if (autoForView || an[i].isAutoCalculated()) {
2973 jaa = new jalview.datamodel.AlignmentAnnotation(
2974 annotation.getLabel(), annotation.getDescription(), anot,
2975 llim, hlim, annotation.getGraphType());
2977 jaa.graphGroup = annotation.getGraphGroup();
2978 jaa._linecolour = firstColour;
2979 if (annotation.getThresholdLine() != null)
2981 jaa.setThreshold(new jalview.datamodel.GraphLine(annotation
2982 .getThresholdLine().getValue(), annotation
2983 .getThresholdLine().getLabel(), new java.awt.Color(
2984 annotation.getThresholdLine().getColour())));
2987 if (autoForView || annotation.isAutoCalculated())
2989 // Hardwire the symbol display line to ensure that labels for
2990 // histograms are displayed
2996 jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
2997 an[i].getDescription(), anot);
2998 jaa._linecolour = firstColour;
3000 // register new annotation
3001 if (an[i].getId() != null)
3003 annotationIds.put(an[i].getId(), jaa);
3004 jaa.annotationId = an[i].getId();
3006 // recover sequence association
3007 String sequenceRef = an[i].getSequenceRef();
3008 if (sequenceRef != null)
3010 // from 2.9 sequenceRef is to sequence id (JAL-1781)
3011 SequenceI sequence = seqRefIds.get(sequenceRef);
3012 if (sequence == null)
3014 // in pre-2.9 projects sequence ref is to sequence name
3015 sequence = al.findName(sequenceRef);
3017 if (sequence != null)
3019 jaa.createSequenceMapping(sequence, 1, true);
3020 sequence.addAlignmentAnnotation(jaa);
3023 // and make a note of any group association
3024 if (an[i].getGroupRef() != null && an[i].getGroupRef().length() > 0)
3026 List<jalview.datamodel.AlignmentAnnotation> aal = groupAnnotRefs
3027 .get(an[i].getGroupRef());
3030 aal = new ArrayList<jalview.datamodel.AlignmentAnnotation>();
3031 groupAnnotRefs.put(an[i].getGroupRef(), aal);
3036 if (an[i].hasScore())
3038 jaa.setScore(an[i].getScore());
3040 if (an[i].hasVisible())
3042 jaa.visible = an[i].getVisible();
3045 if (an[i].hasCentreColLabels())
3047 jaa.centreColLabels = an[i].getCentreColLabels();
3050 if (an[i].hasScaleColLabels())
3052 jaa.scaleColLabel = an[i].getScaleColLabels();
3054 if (an[i].hasAutoCalculated() && an[i].isAutoCalculated())
3056 // newer files have an 'autoCalculated' flag and store calculation
3057 // state in viewport properties
3058 jaa.autoCalculated = true; // means annotation will be marked for
3059 // update at end of load.
3061 if (an[i].hasGraphHeight())
3063 jaa.graphHeight = an[i].getGraphHeight();
3065 if (an[i].hasBelowAlignment())
3067 jaa.belowAlignment = an[i].isBelowAlignment();
3069 jaa.setCalcId(an[i].getCalcId());
3070 if (an[i].getPropertyCount() > 0)
3072 for (jalview.schemabinding.version2.Property prop : an[i]
3075 jaa.setProperty(prop.getName(), prop.getValue());
3078 if (jaa.autoCalculated)
3080 autoAlan.add(new JvAnnotRow(i, jaa));
3083 // if (!autoForView)
3085 // add autocalculated group annotation and any user created annotation
3087 al.addAnnotation(jaa);
3091 // ///////////////////////
3093 // Create alignment markup and styles for this view
3094 if (jms.getJGroupCount() > 0)
3096 JGroup[] groups = jms.getJGroup();
3097 boolean addAnnotSchemeGroup = false;
3098 for (int i = 0; i < groups.length; i++)
3100 JGroup jGroup = groups[i];
3101 ColourSchemeI cs = null;
3102 if (jGroup.getColour() != null)
3104 if (jGroup.getColour().startsWith("ucs"))
3106 cs = getUserColourScheme(jms, jGroup.getColour());
3108 else if (jGroup.getColour().equals("AnnotationColourGradient")
3109 && jGroup.getAnnotationColours() != null)
3111 addAnnotSchemeGroup = true;
3116 cs = ColourSchemeProperty.getColour(al, jGroup.getColour());
3121 cs.setThreshold(jGroup.getPidThreshold(), true);
3125 Vector<SequenceI> seqs = new Vector<SequenceI>();
3127 for (int s = 0; s < jGroup.getSeqCount(); s++)
3129 String seqId = jGroup.getSeq(s) + "";
3130 SequenceI ts = seqRefIds.get(seqId);
3134 seqs.addElement(ts);
3138 if (seqs.size() < 1)
3143 SequenceGroup sg = new SequenceGroup(seqs, jGroup.getName(), cs,
3144 jGroup.getDisplayBoxes(), jGroup.getDisplayText(),
3145 jGroup.getColourText(), jGroup.getStart(), jGroup.getEnd());
3147 sg.setOutlineColour(new java.awt.Color(jGroup.getOutlineColour()));
3149 sg.textColour = new java.awt.Color(jGroup.getTextCol1());
3150 sg.textColour2 = new java.awt.Color(jGroup.getTextCol2());
3151 sg.setShowNonconserved(jGroup.hasShowUnconserved() ? jGroup
3152 .isShowUnconserved() : false);
3153 sg.thresholdTextColour = jGroup.getTextColThreshold();
3154 if (jGroup.hasShowConsensusHistogram())
3156 sg.setShowConsensusHistogram(jGroup.isShowConsensusHistogram());
3159 if (jGroup.hasShowSequenceLogo())
3161 sg.setshowSequenceLogo(jGroup.isShowSequenceLogo());
3163 if (jGroup.hasNormaliseSequenceLogo())
3165 sg.setNormaliseSequenceLogo(jGroup.isNormaliseSequenceLogo());
3167 if (jGroup.hasIgnoreGapsinConsensus())
3169 sg.setIgnoreGapsConsensus(jGroup.getIgnoreGapsinConsensus());
3171 if (jGroup.getConsThreshold() != 0)
3173 jalview.analysis.Conservation c = new jalview.analysis.Conservation(
3174 "All", ResidueProperties.propHash, 3,
3175 sg.getSequences(null), 0, sg.getWidth() - 1);
3177 c.verdict(false, 25);
3178 sg.cs.setConservation(c);
3181 if (jGroup.getId() != null && groupAnnotRefs.size() > 0)
3183 // re-instate unique group/annotation row reference
3184 List<AlignmentAnnotation> jaal = groupAnnotRefs.get(jGroup
3188 for (AlignmentAnnotation jaa : jaal)
3191 if (jaa.autoCalculated)
3193 // match up and try to set group autocalc alignment row for this
3195 if (jaa.label.startsWith("Consensus for "))
3197 sg.setConsensus(jaa);
3199 // match up and try to set group autocalc alignment row for this
3201 if (jaa.label.startsWith("Conservation for "))
3203 sg.setConservationRow(jaa);
3210 if (addAnnotSchemeGroup)
3212 // reconstruct the annotation colourscheme
3213 sg.cs = constructAnnotationColour(jGroup.getAnnotationColours(),
3214 null, al, jms, false);
3220 // only dataset in this model, so just return.
3223 // ///////////////////////////////
3226 // If we just load in the same jar file again, the sequenceSetId
3227 // will be the same, and we end up with multiple references
3228 // to the same sequenceSet. We must modify this id on load
3229 // so that each load of the file gives a unique id
3230 String uniqueSeqSetId = view.getSequenceSetId() + uniqueSetSuffix;
3231 String viewId = (view.getId() == null ? null : view.getId()
3233 AlignFrame af = null;
3234 AlignViewport av = null;
3235 // now check to see if we really need to create a new viewport.
3236 if (multipleView && viewportsAdded.size() == 0)
3238 // We recovered an alignment for which a viewport already exists.
3239 // TODO: fix up any settings necessary for overlaying stored state onto
3240 // state recovered from another document. (may not be necessary).
3241 // we may need a binding from a viewport in memory to one recovered from
3243 // and then recover its containing af to allow the settings to be applied.
3244 // TODO: fix for vamsas demo
3246 .println("About to recover a viewport for existing alignment: Sequence set ID is "
3248 Object seqsetobj = retrieveExistingObj(uniqueSeqSetId);
3249 if (seqsetobj != null)
3251 if (seqsetobj instanceof String)
3253 uniqueSeqSetId = (String) seqsetobj;
3255 .println("Recovered extant sequence set ID mapping for ID : New Sequence set ID is "
3261 .println("Warning : Collision between sequence set ID string and existing jalview object mapping.");
3267 * indicate that annotation colours are applied across all groups (pre
3268 * Jalview 2.8.1 behaviour)
3270 boolean doGroupAnnColour = Jalview2XML.isVersionStringLaterThan(
3271 "2.8.1", object.getVersion());
3273 AlignmentPanel ap = null;
3274 boolean isnewview = true;
3277 // Check to see if this alignment already has a view id == viewId
3278 jalview.gui.AlignmentPanel views[] = Desktop
3279 .getAlignmentPanels(uniqueSeqSetId);
3280 if (views != null && views.length > 0)
3282 for (int v = 0; v < views.length; v++)
3284 if (views[v].av.getViewId().equalsIgnoreCase(viewId))
3286 // recover the existing alignpanel, alignframe, viewport
3287 af = views[v].alignFrame;
3290 // TODO: could even skip resetting view settings if we don't want to
3291 // change the local settings from other jalview processes
3300 af = loadViewport(file, jseqs, hiddenSeqs, al, jms, view,
3301 uniqueSeqSetId, viewId, autoAlan);
3307 * Load any trees, PDB structures and viewers
3309 * Not done if flag is false (when this method is used for New View)
3311 if (loadTreesAndStructures)
3313 loadTrees(jms, view, af, av, ap);
3314 loadPDBStructures(jprovider, jseqs, af, ap);
3315 loadRnaViewers(jprovider, jseqs, ap);
3317 // and finally return.
3322 * Instantiate and link any saved RNA (Varna) viewers. The state of the Varna
3323 * panel is restored from separate jar entries, two (gapped and trimmed) per
3324 * sequence and secondary structure.
3326 * Currently each viewer shows just one sequence and structure (gapped and
3327 * trimmed), however this method is designed to support multiple sequences or
3328 * structures in viewers if wanted in future.
3334 private void loadRnaViewers(jarInputStreamProvider jprovider,
3335 JSeq[] jseqs, AlignmentPanel ap)
3338 * scan the sequences for references to viewers; create each one the first
3339 * time it is referenced, add Rna models to existing viewers
3341 for (JSeq jseq : jseqs)
3343 for (int i = 0; i < jseq.getRnaViewerCount(); i++)
3345 RnaViewer viewer = jseq.getRnaViewer(i);
3346 AppVarna appVarna = findOrCreateVarnaViewer(viewer,
3347 uniqueSetSuffix, ap);
3349 for (int j = 0; j < viewer.getSecondaryStructureCount(); j++)
3351 SecondaryStructure ss = viewer.getSecondaryStructure(j);
3352 SequenceI seq = seqRefIds.get(jseq.getId());
3353 AlignmentAnnotation ann = this.annotationIds.get(ss
3354 .getAnnotationId());
3357 * add the structure to the Varna display (with session state copied
3358 * from the jar to a temporary file)
3360 boolean gapped = ss.isGapped();
3361 String rnaTitle = ss.getTitle();
3362 String sessionState = ss.getViewerState();
3363 String tempStateFile = copyJarEntry(jprovider, sessionState,
3365 RnaModel rna = new RnaModel(rnaTitle, ann, seq, null, gapped);
3366 appVarna.addModelSession(rna, rnaTitle, tempStateFile);
3368 appVarna.setInitialSelection(viewer.getSelectedRna());
3374 * Locate and return an already instantiated matching AppVarna, or create one
3378 * @param viewIdSuffix
3382 protected AppVarna findOrCreateVarnaViewer(RnaViewer viewer,
3383 String viewIdSuffix, AlignmentPanel ap)
3386 * on each load a suffix is appended to the saved viewId, to avoid conflicts
3387 * if load is repeated
3389 String postLoadId = viewer.getViewId() + viewIdSuffix;
3390 for (JInternalFrame frame : getAllFrames())
3392 if (frame instanceof AppVarna)
3394 AppVarna varna = (AppVarna) frame;
3395 if (postLoadId.equals(varna.getViewId()))
3397 // this viewer is already instantiated
3398 // could in future here add ap as another 'parent' of the
3399 // AppVarna window; currently just 1-to-many
3406 * viewer not found - make it
3408 RnaViewerModel model = new RnaViewerModel(postLoadId,
3409 viewer.getTitle(), viewer.getXpos(), viewer.getYpos(),
3410 viewer.getWidth(), viewer.getHeight(),
3411 viewer.getDividerLocation());
3412 AppVarna varna = new AppVarna(model, ap);
3418 * Load any saved trees
3426 protected void loadTrees(JalviewModelSequence jms, Viewport view,
3427 AlignFrame af, AlignViewport av, AlignmentPanel ap)
3429 // TODO result of automated refactoring - are all these parameters needed?
3432 for (int t = 0; t < jms.getTreeCount(); t++)
3435 Tree tree = jms.getTree(t);
3437 TreePanel tp = (TreePanel) retrieveExistingObj(tree.getId());
3440 tp = af.ShowNewickTree(
3441 new jalview.io.NewickFile(tree.getNewick()),
3442 tree.getTitle(), tree.getWidth(), tree.getHeight(),
3443 tree.getXpos(), tree.getYpos());
3444 if (tree.getId() != null)
3446 // perhaps bind the tree id to something ?
3451 // update local tree attributes ?
3452 // TODO: should check if tp has been manipulated by user - if so its
3453 // settings shouldn't be modified
3454 tp.setTitle(tree.getTitle());
3455 tp.setBounds(new Rectangle(tree.getXpos(), tree.getYpos(), tree
3456 .getWidth(), tree.getHeight()));
3457 tp.av = av; // af.viewport; // TODO: verify 'associate with all
3460 tp.treeCanvas.av = av; // af.viewport;
3461 tp.treeCanvas.ap = ap; // af.alignPanel;
3466 warn("There was a problem recovering stored Newick tree: \n"
3467 + tree.getNewick());
3471 tp.fitToWindow.setState(tree.getFitToWindow());
3472 tp.fitToWindow_actionPerformed(null);
3474 if (tree.getFontName() != null)
3476 tp.setTreeFont(new java.awt.Font(tree.getFontName(), tree
3477 .getFontStyle(), tree.getFontSize()));
3481 tp.setTreeFont(new java.awt.Font(view.getFontName(), view
3482 .getFontStyle(), tree.getFontSize()));
3485 tp.showPlaceholders(tree.getMarkUnlinked());
3486 tp.showBootstrap(tree.getShowBootstrap());
3487 tp.showDistances(tree.getShowDistances());
3489 tp.treeCanvas.threshold = tree.getThreshold();
3491 if (tree.getCurrentTree())
3493 af.viewport.setCurrentTree(tp.getTree());
3497 } catch (Exception ex)
3499 ex.printStackTrace();
3504 * Load and link any saved structure viewers.
3511 protected void loadPDBStructures(jarInputStreamProvider jprovider,
3512 JSeq[] jseqs, AlignFrame af, AlignmentPanel ap)
3515 * Run through all PDB ids on the alignment, and collect mappings between
3516 * distinct view ids and all sequences referring to that view.
3518 Map<String, StructureViewerModel> structureViewers = new LinkedHashMap<String, StructureViewerModel>();
3520 for (int i = 0; i < jseqs.length; i++)
3522 if (jseqs[i].getPdbidsCount() > 0)
3524 Pdbids[] ids = jseqs[i].getPdbids();
3525 for (int p = 0; p < ids.length; p++)
3527 final int structureStateCount = ids[p].getStructureStateCount();
3528 for (int s = 0; s < structureStateCount; s++)
3530 // check to see if we haven't already created this structure view
3531 final StructureState structureState = ids[p]
3532 .getStructureState(s);
3533 String sviewid = (structureState.getViewId() == null) ? null
3534 : structureState.getViewId() + uniqueSetSuffix;
3535 jalview.datamodel.PDBEntry jpdb = new jalview.datamodel.PDBEntry();
3536 // Originally : ids[p].getFile()
3537 // : TODO: verify external PDB file recovery still works in normal
3538 // jalview project load
3539 jpdb.setFile(loadPDBFile(jprovider, ids[p].getId()));
3540 jpdb.setId(ids[p].getId());
3542 int x = structureState.getXpos();
3543 int y = structureState.getYpos();
3544 int width = structureState.getWidth();
3545 int height = structureState.getHeight();
3547 // Probably don't need to do this anymore...
3548 // Desktop.desktop.getComponentAt(x, y);
3549 // TODO: NOW: check that this recovers the PDB file correctly.
3550 String pdbFile = loadPDBFile(jprovider, ids[p].getId());
3551 jalview.datamodel.SequenceI seq = seqRefIds.get(jseqs[i]
3553 if (sviewid == null)
3555 sviewid = "_jalview_pre2_4_" + x + "," + y + "," + width
3558 if (!structureViewers.containsKey(sviewid))
3560 structureViewers.put(sviewid,
3561 new StructureViewerModel(x, y, width, height, false,
3562 false, true, structureState.getViewId(),
3563 structureState.getType()));
3564 // Legacy pre-2.7 conversion JAL-823 :
3565 // do not assume any view has to be linked for colour by
3569 // assemble String[] { pdb files }, String[] { id for each
3570 // file }, orig_fileloc, SequenceI[][] {{ seqs_file 1 }, {
3571 // seqs_file 2}, boolean[] {
3572 // linkAlignPanel,superposeWithAlignpanel}} from hash
3573 StructureViewerModel jmoldat = structureViewers.get(sviewid);
3574 jmoldat.setAlignWithPanel(jmoldat.isAlignWithPanel()
3575 | (structureState.hasAlignwithAlignPanel() ? structureState
3576 .getAlignwithAlignPanel() : false));
3579 * Default colour by linked panel to false if not specified (e.g.
3580 * for pre-2.7 projects)
3582 boolean colourWithAlignPanel = jmoldat.isColourWithAlignPanel();
3583 colourWithAlignPanel |= (structureState
3584 .hasColourwithAlignPanel() ? structureState
3585 .getColourwithAlignPanel() : false);
3586 jmoldat.setColourWithAlignPanel(colourWithAlignPanel);
3589 * Default colour by viewer to true if not specified (e.g. for
3592 boolean colourByViewer = jmoldat.isColourByViewer();
3593 colourByViewer &= structureState.hasColourByJmol() ? structureState
3594 .getColourByJmol() : true;
3595 jmoldat.setColourByViewer(colourByViewer);
3597 if (jmoldat.getStateData().length() < structureState
3598 .getContent().length())
3601 jmoldat.setStateData(structureState.getContent());
3604 if (ids[p].getFile() != null)
3606 File mapkey = new File(ids[p].getFile());
3607 StructureData seqstrmaps = jmoldat.getFileData().get(mapkey);
3608 if (seqstrmaps == null)
3610 jmoldat.getFileData().put(
3612 seqstrmaps = jmoldat.new StructureData(pdbFile,
3615 if (!seqstrmaps.getSeqList().contains(seq))
3617 seqstrmaps.getSeqList().add(seq);
3623 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");
3630 // Instantiate the associated structure views
3631 for (Entry<String, StructureViewerModel> entry : structureViewers
3636 createOrLinkStructureViewer(entry, af, ap, jprovider);
3637 } catch (Exception e)
3639 System.err.println("Error loading structure viewer: "
3641 // failed - try the next one
3653 protected void createOrLinkStructureViewer(
3654 Entry<String, StructureViewerModel> viewerData, AlignFrame af,
3655 AlignmentPanel ap, jarInputStreamProvider jprovider)
3657 final StructureViewerModel stateData = viewerData.getValue();
3660 * Search for any viewer windows already open from other alignment views
3661 * that exactly match the stored structure state
3663 StructureViewerBase comp = findMatchingViewer(viewerData);
3667 linkStructureViewer(ap, comp, stateData);
3672 * From 2.9: stateData.type contains JMOL or CHIMERA, data is in jar entry
3673 * "viewer_"+stateData.viewId
3675 if (ViewerType.CHIMERA.toString().equals(stateData.getType()))
3677 createChimeraViewer(viewerData, af, jprovider);
3682 * else Jmol (if pre-2.9, stateData contains JMOL state string)
3684 createJmolViewer(viewerData, af, jprovider);
3689 * Create a new Chimera viewer.
3695 protected void createChimeraViewer(
3696 Entry<String, StructureViewerModel> viewerData, AlignFrame af,
3697 jarInputStreamProvider jprovider)
3699 StructureViewerModel data = viewerData.getValue();
3700 String chimeraSessionFile = data.getStateData();
3703 * Copy Chimera session from jar entry "viewer_"+viewId to a temporary file
3705 * NB this is the 'saved' viewId as in the project file XML, _not_ the
3706 * 'uniquified' sviewid used to reconstruct the viewer here
3708 String viewerJarEntryName = getViewerJarEntryName(data.getViewId());
3709 chimeraSessionFile = copyJarEntry(jprovider, viewerJarEntryName,
3712 Set<Entry<File, StructureData>> fileData = data.getFileData()
3714 List<PDBEntry> pdbs = new ArrayList<PDBEntry>();
3715 List<SequenceI[]> allseqs = new ArrayList<SequenceI[]>();
3716 for (Entry<File, StructureData> pdb : fileData)
3718 String filePath = pdb.getValue().getFilePath();
3719 String pdbId = pdb.getValue().getPdbId();
3720 // pdbs.add(new PDBEntry(filePath, pdbId));
3721 pdbs.add(new PDBEntry(pdbId, null, PDBEntry.Type.PDB, filePath));
3722 final List<SequenceI> seqList = pdb.getValue().getSeqList();
3723 SequenceI[] seqs = seqList.toArray(new SequenceI[seqList.size()]);
3727 boolean colourByChimera = data.isColourByViewer();
3728 boolean colourBySequence = data.isColourWithAlignPanel();
3730 // TODO use StructureViewer as a factory here, see JAL-1761
3731 final PDBEntry[] pdbArray = pdbs.toArray(new PDBEntry[pdbs.size()]);
3732 final SequenceI[][] seqsArray = allseqs.toArray(new SequenceI[allseqs
3734 String newViewId = viewerData.getKey();
3736 ChimeraViewFrame cvf = new ChimeraViewFrame(chimeraSessionFile,
3737 af.alignPanel, pdbArray, seqsArray, colourByChimera,
3738 colourBySequence, newViewId);
3739 cvf.setSize(data.getWidth(), data.getHeight());
3740 cvf.setLocation(data.getX(), data.getY());
3744 * Create a new Jmol window. First parse the Jmol state to translate filenames
3745 * loaded into the view, and record the order in which files are shown in the
3746 * Jmol view, so we can add the sequence mappings in same order.
3752 protected void createJmolViewer(
3753 final Entry<String, StructureViewerModel> viewerData,
3754 AlignFrame af, jarInputStreamProvider jprovider)
3756 final StructureViewerModel svattrib = viewerData.getValue();
3757 String state = svattrib.getStateData();
3760 * Pre-2.9: state element value is the Jmol state string
3762 * 2.9+: @type is "JMOL", state data is in a Jar file member named "viewer_"
3765 if (ViewerType.JMOL.toString().equals(svattrib.getType()))
3767 state = readJarEntry(jprovider,
3768 getViewerJarEntryName(svattrib.getViewId()));
3771 List<String> pdbfilenames = new ArrayList<String>();
3772 List<SequenceI[]> seqmaps = new ArrayList<SequenceI[]>();
3773 List<String> pdbids = new ArrayList<String>();
3774 StringBuilder newFileLoc = new StringBuilder(64);
3775 int cp = 0, ncp, ecp;
3776 Map<File, StructureData> oldFiles = svattrib.getFileData();
3777 while ((ncp = state.indexOf("load ", cp)) > -1)
3781 // look for next filename in load statement
3782 newFileLoc.append(state.substring(cp,
3783 ncp = (state.indexOf("\"", ncp + 1) + 1)));
3784 String oldfilenam = state.substring(ncp,
3785 ecp = state.indexOf("\"", ncp));
3786 // recover the new mapping data for this old filename
3787 // have to normalize filename - since Jmol and jalview do
3789 // translation differently.
3790 StructureData filedat = oldFiles.get(new File(oldfilenam));
3791 newFileLoc.append(Platform.escapeString(filedat.getFilePath()));
3792 pdbfilenames.add(filedat.getFilePath());
3793 pdbids.add(filedat.getPdbId());
3794 seqmaps.add(filedat.getSeqList().toArray(new SequenceI[0]));
3795 newFileLoc.append("\"");
3796 cp = ecp + 1; // advance beyond last \" and set cursor so we can
3797 // look for next file statement.
3798 } while ((ncp = state.indexOf("/*file*/", cp)) > -1);
3802 // just append rest of state
3803 newFileLoc.append(state.substring(cp));
3807 System.err.print("Ignoring incomplete Jmol state for PDB ids: ");
3808 newFileLoc = new StringBuilder(state);
3809 newFileLoc.append("; load append ");
3810 for (File id : oldFiles.keySet())
3812 // add this and any other pdb files that should be present in
3814 StructureData filedat = oldFiles.get(id);
3815 newFileLoc.append(filedat.getFilePath());
3816 pdbfilenames.add(filedat.getFilePath());
3817 pdbids.add(filedat.getPdbId());
3818 seqmaps.add(filedat.getSeqList().toArray(new SequenceI[0]));
3819 newFileLoc.append(" \"");
3820 newFileLoc.append(filedat.getFilePath());
3821 newFileLoc.append("\"");
3824 newFileLoc.append(";");
3827 if (newFileLoc.length() == 0)
3831 int histbug = newFileLoc.indexOf("history = ");
3835 * change "history = [true|false];" to "history = [1|0];"
3838 int diff = histbug == -1 ? -1 : newFileLoc.indexOf(";", histbug);
3839 String val = (diff == -1) ? null : newFileLoc
3840 .substring(histbug, diff);
3841 if (val != null && val.length() >= 4)
3843 if (val.contains("e")) // eh? what can it be?
3845 if (val.trim().equals("true"))
3853 newFileLoc.replace(histbug, diff, val);
3858 final String[] pdbf = pdbfilenames.toArray(new String[pdbfilenames
3860 final String[] id = pdbids.toArray(new String[pdbids.size()]);
3861 final SequenceI[][] sq = seqmaps
3862 .toArray(new SequenceI[seqmaps.size()][]);
3863 final String fileloc = newFileLoc.toString();
3864 final String sviewid = viewerData.getKey();
3865 final AlignFrame alf = af;
3866 final Rectangle rect = new Rectangle(svattrib.getX(), svattrib.getY(),
3867 svattrib.getWidth(), svattrib.getHeight());
3870 javax.swing.SwingUtilities.invokeAndWait(new Runnable()
3875 JalviewStructureDisplayI sview = null;
3878 sview = new StructureViewer(alf.alignPanel
3879 .getStructureSelectionManager()).createView(
3880 StructureViewer.ViewerType.JMOL, pdbf, id, sq,
3881 alf.alignPanel, svattrib, fileloc, rect, sviewid);
3882 addNewStructureViewer(sview);
3883 } catch (OutOfMemoryError ex)
3885 new OOMWarning("restoring structure view for PDB id " + id,
3886 (OutOfMemoryError) ex.getCause());
3887 if (sview != null && sview.isVisible())
3889 sview.closeViewer(false);
3890 sview.setVisible(false);
3896 } catch (InvocationTargetException ex)
3898 warn("Unexpected error when opening Jmol view.", ex);
3900 } catch (InterruptedException e)
3902 // e.printStackTrace();
3908 * Generates a name for the entry in the project jar file to hold state
3909 * information for a structure viewer
3914 protected String getViewerJarEntryName(String viewId)
3916 return VIEWER_PREFIX + viewId;
3920 * Returns any open frame that matches given structure viewer data. The match
3921 * is based on the unique viewId, or (for older project versions) the frame's
3927 protected StructureViewerBase findMatchingViewer(
3928 Entry<String, StructureViewerModel> viewerData)
3930 final String sviewid = viewerData.getKey();
3931 final StructureViewerModel svattrib = viewerData.getValue();
3932 StructureViewerBase comp = null;
3933 JInternalFrame[] frames = getAllFrames();
3934 for (JInternalFrame frame : frames)
3936 if (frame instanceof StructureViewerBase)
3939 * Post jalview 2.4 schema includes structure view id
3942 && ((StructureViewerBase) frame).getViewId()
3945 comp = (StructureViewerBase) frame;
3946 break; // break added in 2.9
3949 * Otherwise test for matching position and size of viewer frame
3951 else if (frame.getX() == svattrib.getX()
3952 && frame.getY() == svattrib.getY()
3953 && frame.getHeight() == svattrib.getHeight()
3954 && frame.getWidth() == svattrib.getWidth())
3956 comp = (StructureViewerBase) frame;
3957 // no break in faint hope of an exact match on viewId
3965 * Link an AlignmentPanel to an existing structure viewer.
3970 * @param useinViewerSuperpos
3971 * @param usetoColourbyseq
3972 * @param viewerColouring
3974 protected void linkStructureViewer(AlignmentPanel ap,
3975 StructureViewerBase viewer, StructureViewerModel stateData)
3977 // NOTE: if the jalview project is part of a shared session then
3978 // view synchronization should/could be done here.
3980 final boolean useinViewerSuperpos = stateData.isAlignWithPanel();
3981 final boolean usetoColourbyseq = stateData.isColourWithAlignPanel();
3982 final boolean viewerColouring = stateData.isColourByViewer();
3983 Map<File, StructureData> oldFiles = stateData.getFileData();
3986 * Add mapping for sequences in this view to an already open viewer
3988 final AAStructureBindingModel binding = viewer.getBinding();
3989 for (File id : oldFiles.keySet())
3991 // add this and any other pdb files that should be present in the
3993 StructureData filedat = oldFiles.get(id);
3994 String pdbFile = filedat.getFilePath();
3995 SequenceI[] seq = filedat.getSeqList().toArray(new SequenceI[0]);
3996 binding.getSsm().setMapping(seq, null, pdbFile,
3997 jalview.io.AppletFormatAdapter.FILE);
3998 binding.addSequenceForStructFile(pdbFile, seq);
4000 // and add the AlignmentPanel's reference to the view panel
4001 viewer.addAlignmentPanel(ap);
4002 if (useinViewerSuperpos)
4004 viewer.useAlignmentPanelForSuperposition(ap);
4008 viewer.excludeAlignmentPanelForSuperposition(ap);
4010 if (usetoColourbyseq)
4012 viewer.useAlignmentPanelForColourbyseq(ap, !viewerColouring);
4016 viewer.excludeAlignmentPanelForColourbyseq(ap);
4021 * Get all frames within the Desktop.
4025 protected JInternalFrame[] getAllFrames()
4027 JInternalFrame[] frames = null;
4028 // TODO is this necessary - is it safe - risk of hanging?
4033 frames = Desktop.desktop.getAllFrames();
4034 } catch (ArrayIndexOutOfBoundsException e)
4036 // occasional No such child exceptions are thrown here...
4040 } catch (InterruptedException f)
4044 } while (frames == null);
4049 * Answers true if 'version' is equal to or later than 'supported', where each
4050 * is formatted as major/minor versions like "2.8.3" or "2.3.4b1" for bugfix
4051 * changes. Development and test values for 'version' are leniently treated
4055 * - minimum version we are comparing against
4057 * - version of data being processsed
4060 public static boolean isVersionStringLaterThan(String supported,
4063 if (supported == null || version == null
4064 || version.equalsIgnoreCase("DEVELOPMENT BUILD")
4065 || version.equalsIgnoreCase("Test")
4066 || version.equalsIgnoreCase("AUTOMATED BUILD"))
4068 System.err.println("Assuming project file with "
4069 + (version == null ? "null" : version)
4070 + " is compatible with Jalview version " + supported);
4075 return StringUtils.compareVersions(version, supported, "b") >= 0;
4079 Vector<JalviewStructureDisplayI> newStructureViewers = null;
4081 protected void addNewStructureViewer(JalviewStructureDisplayI sview)
4083 if (newStructureViewers != null)
4085 sview.getBinding().setFinishedLoadingFromArchive(false);
4086 newStructureViewers.add(sview);
4090 protected void setLoadingFinishedForNewStructureViewers()
4092 if (newStructureViewers != null)
4094 for (JalviewStructureDisplayI sview : newStructureViewers)
4096 sview.getBinding().setFinishedLoadingFromArchive(true);
4098 newStructureViewers.clear();
4099 newStructureViewers = null;
4103 AlignFrame loadViewport(String file, JSeq[] JSEQ,
4104 List<SequenceI> hiddenSeqs, AlignmentI al,
4105 JalviewModelSequence jms, Viewport view, String uniqueSeqSetId,
4106 String viewId, List<JvAnnotRow> autoAlan)
4108 AlignFrame af = null;
4109 af = new AlignFrame(al, view.getWidth(), view.getHeight(),
4110 uniqueSeqSetId, viewId);
4112 af.setFileName(file, "Jalview");
4114 for (int i = 0; i < JSEQ.length; i++)
4116 af.viewport.setSequenceColour(af.viewport.getAlignment()
4117 .getSequenceAt(i), new java.awt.Color(JSEQ[i].getColour()));
4122 af.getViewport().setColourByReferenceSeq(true);
4123 af.getViewport().setDisplayReferenceSeq(true);
4126 af.viewport.setGatherViewsHere(view.getGatheredViews());
4128 if (view.getSequenceSetId() != null)
4130 AlignmentViewport av = viewportsAdded.get(uniqueSeqSetId);
4132 af.viewport.setSequenceSetId(uniqueSeqSetId);
4135 // propagate shared settings to this new view
4136 af.viewport.setHistoryList(av.getHistoryList());
4137 af.viewport.setRedoList(av.getRedoList());
4141 viewportsAdded.put(uniqueSeqSetId, af.viewport);
4143 // TODO: check if this method can be called repeatedly without
4144 // side-effects if alignpanel already registered.
4145 PaintRefresher.Register(af.alignPanel, uniqueSeqSetId);
4147 // apply Hidden regions to view.
4148 if (hiddenSeqs != null)
4150 for (int s = 0; s < JSEQ.length; s++)
4152 SequenceGroup hidden = new SequenceGroup();
4153 boolean isRepresentative = false;
4154 for (int r = 0; r < JSEQ[s].getHiddenSequencesCount(); r++)
4156 isRepresentative = true;
4157 SequenceI sequenceToHide = al.getSequenceAt(JSEQ[s]
4158 .getHiddenSequences(r));
4159 hidden.addSequence(sequenceToHide, false);
4160 // remove from hiddenSeqs list so we don't try to hide it twice
4161 hiddenSeqs.remove(sequenceToHide);
4163 if (isRepresentative)
4165 SequenceI representativeSequence = al.getSequenceAt(s);
4166 hidden.addSequence(representativeSequence, false);
4167 af.viewport.hideRepSequences(representativeSequence, hidden);
4171 SequenceI[] hseqs = hiddenSeqs.toArray(new SequenceI[hiddenSeqs
4173 af.viewport.hideSequence(hseqs);
4176 // recover view properties and display parameters
4177 if (view.getViewName() != null)
4179 af.viewport.viewName = view.getViewName();
4180 af.setInitialTabVisible();
4182 af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),
4185 af.viewport.setShowAnnotation(view.getShowAnnotation());
4186 af.viewport.setAbovePIDThreshold(view.getPidSelected());
4188 af.viewport.setColourText(view.getShowColourText());
4190 af.viewport.setConservationSelected(view.getConservationSelected());
4191 af.viewport.setShowJVSuffix(view.getShowFullId());
4192 af.viewport.setRightAlignIds(view.getRightAlignIds());
4193 af.viewport.setFont(
4194 new java.awt.Font(view.getFontName(), view.getFontStyle(), view
4195 .getFontSize()), true);
4196 ViewStyleI vs = af.viewport.getViewStyle();
4197 vs.setScaleProteinAsCdna(view.isScaleProteinAsCdna());
4198 af.viewport.setViewStyle(vs);
4199 // TODO: allow custom charWidth/Heights to be restored by updating them
4200 // after setting font - which means set above to false
4201 af.viewport.setRenderGaps(view.getRenderGaps());
4202 af.viewport.setWrapAlignment(view.getWrapAlignment());
4203 af.viewport.setShowAnnotation(view.getShowAnnotation());
4205 af.viewport.setShowBoxes(view.getShowBoxes());
4207 af.viewport.setShowText(view.getShowText());
4209 af.viewport.setTextColour(new java.awt.Color(view.getTextCol1()));
4210 af.viewport.setTextColour2(new java.awt.Color(view.getTextCol2()));
4211 af.viewport.setThresholdTextColour(view.getTextColThreshold());
4212 af.viewport.setShowUnconserved(view.hasShowUnconserved() ? view
4213 .isShowUnconserved() : false);
4214 af.viewport.setStartRes(view.getStartRes());
4215 af.viewport.setStartSeq(view.getStartSeq());
4216 af.alignPanel.updateLayout();
4217 ColourSchemeI cs = null;
4218 // apply colourschemes
4219 if (view.getBgColour() != null)
4221 if (view.getBgColour().startsWith("ucs"))
4223 cs = getUserColourScheme(jms, view.getBgColour());
4225 else if (view.getBgColour().startsWith("Annotation"))
4227 AnnotationColours viewAnnColour = view.getAnnotationColours();
4228 cs = constructAnnotationColour(viewAnnColour, af, al, jms, true);
4235 cs = ColourSchemeProperty.getColour(al, view.getBgColour());
4240 cs.setThreshold(view.getPidThreshold(), true);
4241 cs.setConsensus(af.viewport.getSequenceConsensusHash());
4245 af.viewport.setGlobalColourScheme(cs);
4246 af.viewport.setColourAppliesToAllGroups(false);
4248 if (view.getConservationSelected() && cs != null)
4250 cs.setConservationInc(view.getConsThreshold());
4253 af.changeColour(cs);
4255 af.viewport.setColourAppliesToAllGroups(true);
4257 af.viewport.setShowSequenceFeatures(view.getShowSequenceFeatures());
4259 if (view.hasCentreColumnLabels())
4261 af.viewport.setCentreColumnLabels(view.getCentreColumnLabels());
4263 if (view.hasIgnoreGapsinConsensus())
4265 af.viewport.setIgnoreGapsConsensus(view.getIgnoreGapsinConsensus(),
4268 if (view.hasFollowHighlight())
4270 af.viewport.setFollowHighlight(view.getFollowHighlight());
4272 if (view.hasFollowSelection())
4274 af.viewport.followSelection = view.getFollowSelection();
4276 if (view.hasShowConsensusHistogram())
4278 af.viewport.setShowConsensusHistogram(view
4279 .getShowConsensusHistogram());
4283 af.viewport.setShowConsensusHistogram(true);
4285 if (view.hasShowSequenceLogo())
4287 af.viewport.setShowSequenceLogo(view.getShowSequenceLogo());
4291 af.viewport.setShowSequenceLogo(false);
4293 if (view.hasNormaliseSequenceLogo())
4295 af.viewport.setNormaliseSequenceLogo(view.getNormaliseSequenceLogo());
4297 if (view.hasShowDbRefTooltip())
4299 af.viewport.setShowDBRefs(view.getShowDbRefTooltip());
4301 if (view.hasShowNPfeatureTooltip())
4303 af.viewport.setShowNPFeats(view.hasShowNPfeatureTooltip());
4305 if (view.hasShowGroupConsensus())
4307 af.viewport.setShowGroupConsensus(view.getShowGroupConsensus());
4311 af.viewport.setShowGroupConsensus(false);
4313 if (view.hasShowGroupConservation())
4315 af.viewport.setShowGroupConservation(view.getShowGroupConservation());
4319 af.viewport.setShowGroupConservation(false);
4322 // recover featre settings
4323 if (jms.getFeatureSettings() != null)
4325 FeaturesDisplayed fdi;
4326 af.viewport.setFeaturesDisplayed(fdi = new FeaturesDisplayed());
4327 String[] renderOrder = new String[jms.getFeatureSettings()
4328 .getSettingCount()];
4329 Map<String, FeatureColourI> featureColours = new Hashtable<String, FeatureColourI>();
4330 Map<String, Float> featureOrder = new Hashtable<String, Float>();
4332 for (int fs = 0; fs < jms.getFeatureSettings().getSettingCount(); fs++)
4334 Setting setting = jms.getFeatureSettings().getSetting(fs);
4335 if (setting.hasMincolour())
4337 FeatureColourI gc = setting.hasMin() ? new FeatureColour(
4338 new Color(setting.getMincolour()), new Color(
4339 setting.getColour()), setting.getMin(),
4340 setting.getMax()) : new FeatureColour(new Color(
4341 setting.getMincolour()), new Color(setting.getColour()),
4343 if (setting.hasThreshold())
4345 gc.setThreshold(setting.getThreshold());
4346 int threshstate = setting.getThreshstate();
4347 // -1 = None, 0 = Below, 1 = Above threshold
4348 if (threshstate == 0)
4350 gc.setBelowThreshold(true);
4352 else if (threshstate == 1)
4354 gc.setAboveThreshold(true);
4357 gc.setAutoScaled(true); // default
4358 if (setting.hasAutoScale())
4360 gc.setAutoScaled(setting.getAutoScale());
4362 if (setting.hasColourByLabel())
4364 gc.setColourByLabel(setting.getColourByLabel());
4366 // and put in the feature colour table.
4367 featureColours.put(setting.getType(), gc);
4371 featureColours.put(setting.getType(), new FeatureColour(
4372 new Color(setting.getColour())));
4374 renderOrder[fs] = setting.getType();
4375 if (setting.hasOrder())
4377 featureOrder.put(setting.getType(), setting.getOrder());
4381 featureOrder.put(setting.getType(), new Float(fs
4382 / jms.getFeatureSettings().getSettingCount()));
4384 if (setting.getDisplay())
4386 fdi.setVisible(setting.getType());
4389 Map<String, Boolean> fgtable = new Hashtable<String, Boolean>();
4390 for (int gs = 0; gs < jms.getFeatureSettings().getGroupCount(); gs++)
4392 Group grp = jms.getFeatureSettings().getGroup(gs);
4393 fgtable.put(grp.getName(), new Boolean(grp.getDisplay()));
4395 // FeatureRendererSettings frs = new FeatureRendererSettings(renderOrder,
4396 // fgtable, featureColours, jms.getFeatureSettings().hasTransparency() ?
4397 // jms.getFeatureSettings().getTransparency() : 0.0, featureOrder);
4398 FeatureRendererSettings frs = new FeatureRendererSettings(
4399 renderOrder, fgtable, featureColours, 1.0f, featureOrder);
4400 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
4401 .transferSettings(frs);
4405 if (view.getHiddenColumnsCount() > 0)
4407 for (int c = 0; c < view.getHiddenColumnsCount(); c++)
4409 af.viewport.hideColumns(view.getHiddenColumns(c).getStart(), view
4410 .getHiddenColumns(c).getEnd() // +1
4414 if (view.getCalcIdParam() != null)
4416 for (CalcIdParam calcIdParam : view.getCalcIdParam())
4418 if (calcIdParam != null)
4420 if (recoverCalcIdParam(calcIdParam, af.viewport))
4425 warn("Couldn't recover parameters for "
4426 + calcIdParam.getCalcId());
4431 af.setMenusFromViewport(af.viewport);
4433 // TODO: we don't need to do this if the viewport is aready visible.
4435 * Add the AlignFrame to the desktop (it may be 'gathered' later), unless it
4436 * has a 'cdna/protein complement' view, in which case save it in order to
4437 * populate a SplitFrame once all views have been read in.
4439 String complementaryViewId = view.getComplementId();
4440 if (complementaryViewId == null)
4442 Desktop.addInternalFrame(af, view.getTitle(), view.getWidth(),
4444 // recompute any autoannotation
4445 af.alignPanel.updateAnnotation(false, true);
4446 reorderAutoannotation(af, al, autoAlan);
4447 af.alignPanel.alignmentChanged();
4451 splitFrameCandidates.put(view, af);
4456 private ColourSchemeI constructAnnotationColour(
4457 AnnotationColours viewAnnColour, AlignFrame af, AlignmentI al,
4458 JalviewModelSequence jms, boolean checkGroupAnnColour)
4460 boolean propagateAnnColour = false;
4461 ColourSchemeI cs = null;
4462 AlignmentI annAlignment = af != null ? af.viewport.getAlignment() : al;
4463 if (checkGroupAnnColour && al.getGroups() != null
4464 && al.getGroups().size() > 0)
4466 // pre 2.8.1 behaviour
4467 // check to see if we should transfer annotation colours
4468 propagateAnnColour = true;
4469 for (jalview.datamodel.SequenceGroup sg : al.getGroups())
4471 if (sg.cs instanceof AnnotationColourGradient)
4473 propagateAnnColour = false;
4477 // int find annotation
4478 if (annAlignment.getAlignmentAnnotation() != null)
4480 for (int i = 0; i < annAlignment.getAlignmentAnnotation().length; i++)
4482 if (annAlignment.getAlignmentAnnotation()[i].label
4483 .equals(viewAnnColour.getAnnotation()))
4485 if (annAlignment.getAlignmentAnnotation()[i].getThreshold() == null)
4487 annAlignment.getAlignmentAnnotation()[i]
4488 .setThreshold(new jalview.datamodel.GraphLine(
4489 viewAnnColour.getThreshold(), "Threshold",
4490 java.awt.Color.black)
4495 if (viewAnnColour.getColourScheme().equals("None"))
4497 cs = new AnnotationColourGradient(
4498 annAlignment.getAlignmentAnnotation()[i],
4499 new java.awt.Color(viewAnnColour.getMinColour()),
4500 new java.awt.Color(viewAnnColour.getMaxColour()),
4501 viewAnnColour.getAboveThreshold());
4503 else if (viewAnnColour.getColourScheme().startsWith("ucs"))
4505 cs = new AnnotationColourGradient(
4506 annAlignment.getAlignmentAnnotation()[i],
4507 getUserColourScheme(jms,
4508 viewAnnColour.getColourScheme()),
4509 viewAnnColour.getAboveThreshold());
4513 cs = new AnnotationColourGradient(
4514 annAlignment.getAlignmentAnnotation()[i],
4515 ColourSchemeProperty.getColour(al,
4516 viewAnnColour.getColourScheme()),
4517 viewAnnColour.getAboveThreshold());
4519 if (viewAnnColour.hasPerSequence())
4521 ((AnnotationColourGradient) cs).setSeqAssociated(viewAnnColour
4524 if (viewAnnColour.hasPredefinedColours())
4526 ((AnnotationColourGradient) cs)
4527 .setPredefinedColours(viewAnnColour
4528 .isPredefinedColours());
4530 if (propagateAnnColour && al.getGroups() != null)
4532 // Also use these settings for all the groups
4533 for (int g = 0; g < al.getGroups().size(); g++)
4535 jalview.datamodel.SequenceGroup sg = al.getGroups().get(g);
4543 * if (viewAnnColour.getColourScheme().equals("None" )) { sg.cs =
4544 * new AnnotationColourGradient(
4545 * annAlignment.getAlignmentAnnotation()[i], new
4546 * java.awt.Color(viewAnnColour. getMinColour()), new
4547 * java.awt.Color(viewAnnColour. getMaxColour()),
4548 * viewAnnColour.getAboveThreshold()); } else
4551 sg.cs = new AnnotationColourGradient(
4552 annAlignment.getAlignmentAnnotation()[i], sg.cs,
4553 viewAnnColour.getAboveThreshold());
4554 if (cs instanceof AnnotationColourGradient)
4556 if (viewAnnColour.hasPerSequence())
4558 ((AnnotationColourGradient) cs)
4559 .setSeqAssociated(viewAnnColour.isPerSequence());
4561 if (viewAnnColour.hasPredefinedColours())
4563 ((AnnotationColourGradient) cs)
4564 .setPredefinedColours(viewAnnColour
4565 .isPredefinedColours());
4581 private void reorderAutoannotation(AlignFrame af, AlignmentI al,
4582 List<JvAnnotRow> autoAlan)
4584 // copy over visualization settings for autocalculated annotation in the
4586 if (al.getAlignmentAnnotation() != null)
4589 * Kludge for magic autoannotation names (see JAL-811)
4591 String[] magicNames = new String[] { "Consensus", "Quality",
4593 JvAnnotRow nullAnnot = new JvAnnotRow(-1, null);
4594 Hashtable<String, JvAnnotRow> visan = new Hashtable<String, JvAnnotRow>();
4595 for (String nm : magicNames)
4597 visan.put(nm, nullAnnot);
4599 for (JvAnnotRow auan : autoAlan)
4601 visan.put(auan.template.label
4602 + (auan.template.getCalcId() == null ? "" : "\t"
4603 + auan.template.getCalcId()), auan);
4605 int hSize = al.getAlignmentAnnotation().length;
4606 List<JvAnnotRow> reorder = new ArrayList<JvAnnotRow>();
4607 // work through any autoCalculated annotation already on the view
4608 // removing it if it should be placed in a different location on the
4609 // annotation panel.
4610 List<String> remains = new ArrayList<String>(visan.keySet());
4611 for (int h = 0; h < hSize; h++)
4613 jalview.datamodel.AlignmentAnnotation jalan = al
4614 .getAlignmentAnnotation()[h];
4615 if (jalan.autoCalculated)
4618 JvAnnotRow valan = visan.get(k = jalan.label);
4619 if (jalan.getCalcId() != null)
4621 valan = visan.get(k = jalan.label + "\t" + jalan.getCalcId());
4626 // delete the auto calculated row from the alignment
4627 al.deleteAnnotation(jalan, false);
4631 if (valan != nullAnnot)
4633 if (jalan != valan.template)
4635 // newly created autoannotation row instance
4636 // so keep a reference to the visible annotation row
4637 // and copy over all relevant attributes
4638 if (valan.template.graphHeight >= 0)
4641 jalan.graphHeight = valan.template.graphHeight;
4643 jalan.visible = valan.template.visible;
4645 reorder.add(new JvAnnotRow(valan.order, jalan));
4650 // Add any (possibly stale) autocalculated rows that were not appended to
4651 // the view during construction
4652 for (String other : remains)
4654 JvAnnotRow othera = visan.get(other);
4655 if (othera != nullAnnot && othera.template.getCalcId() != null
4656 && othera.template.getCalcId().length() > 0)
4658 reorder.add(othera);
4661 // now put the automatic annotation in its correct place
4662 int s = 0, srt[] = new int[reorder.size()];
4663 JvAnnotRow[] rws = new JvAnnotRow[reorder.size()];
4664 for (JvAnnotRow jvar : reorder)
4667 srt[s++] = jvar.order;
4670 jalview.util.QuickSort.sort(srt, rws);
4671 // and re-insert the annotation at its correct position
4672 for (JvAnnotRow jvar : rws)
4674 al.addAnnotation(jvar.template, jvar.order);
4676 af.alignPanel.adjustAnnotationHeight();
4680 Hashtable skipList = null;
4683 * TODO remove this method
4686 * @return AlignFrame bound to sequenceSetId from view, if one exists. private
4687 * AlignFrame getSkippedFrame(Viewport view) { if (skipList==null) {
4688 * throw new Error("Implementation Error. No skipList defined for this
4689 * Jalview2XML instance."); } return (AlignFrame)
4690 * skipList.get(view.getSequenceSetId()); }
4694 * Check if the Jalview view contained in object should be skipped or not.
4697 * @return true if view's sequenceSetId is a key in skipList
4699 private boolean skipViewport(JalviewModel object)
4701 if (skipList == null)
4706 if (skipList.containsKey(id = object.getJalviewModelSequence()
4707 .getViewport()[0].getSequenceSetId()))
4709 if (Cache.log != null && Cache.log.isDebugEnabled())
4711 Cache.log.debug("Skipping seuqence set id " + id);
4718 public void addToSkipList(AlignFrame af)
4720 if (skipList == null)
4722 skipList = new Hashtable();
4724 skipList.put(af.getViewport().getSequenceSetId(), af);
4727 public void clearSkipList()
4729 if (skipList != null)
4736 private void recoverDatasetFor(SequenceSet vamsasSet, AlignmentI al,
4737 boolean ignoreUnrefed)
4739 jalview.datamodel.AlignmentI ds = getDatasetFor(vamsasSet
4741 Vector dseqs = null;
4744 // create a list of new dataset sequences
4745 dseqs = new Vector();
4747 for (int i = 0, iSize = vamsasSet.getSequenceCount(); i < iSize; i++)
4749 Sequence vamsasSeq = vamsasSet.getSequence(i);
4750 ensureJalviewDatasetSequence(vamsasSeq, ds, dseqs, ignoreUnrefed);
4752 // create a new dataset
4755 SequenceI[] dsseqs = new SequenceI[dseqs.size()];
4756 dseqs.copyInto(dsseqs);
4757 ds = new jalview.datamodel.Alignment(dsseqs);
4758 debug("Created new dataset " + vamsasSet.getDatasetId()
4759 + " for alignment " + System.identityHashCode(al));
4760 addDatasetRef(vamsasSet.getDatasetId(), ds);
4762 // set the dataset for the newly imported alignment.
4763 if (al.getDataset() == null && !ignoreUnrefed)
4772 * sequence definition to create/merge dataset sequence for
4776 * vector to add new dataset sequence to
4778 private void ensureJalviewDatasetSequence(Sequence vamsasSeq,
4779 AlignmentI ds, Vector dseqs, boolean ignoreUnrefed)
4781 // JBP TODO: Check this is called for AlCodonFrames to support recovery of
4783 SequenceI sq = seqRefIds.get(vamsasSeq.getId());
4784 SequenceI dsq = null;
4785 if (sq != null && sq.getDatasetSequence() != null)
4787 dsq = sq.getDatasetSequence();
4789 if (sq == null && ignoreUnrefed)
4793 String sqid = vamsasSeq.getDsseqid();
4796 // need to create or add a new dataset sequence reference to this sequence
4799 dsq = seqRefIds.get(sqid);
4804 // make a new dataset sequence
4805 dsq = sq.createDatasetSequence();
4808 // make up a new dataset reference for this sequence
4809 sqid = seqHash(dsq);
4811 dsq.setVamsasId(uniqueSetSuffix + sqid);
4812 seqRefIds.put(sqid, dsq);
4817 dseqs.addElement(dsq);
4822 ds.addSequence(dsq);
4828 { // make this dataset sequence sq's dataset sequence
4829 sq.setDatasetSequence(dsq);
4830 // and update the current dataset alignment
4835 if (!dseqs.contains(dsq))
4842 if (ds.findIndex(dsq) < 0)
4844 ds.addSequence(dsq);
4851 // TODO: refactor this as a merge dataset sequence function
4852 // now check that sq (the dataset sequence) sequence really is the union of
4853 // all references to it
4854 // boolean pre = sq.getStart() < dsq.getStart();
4855 // boolean post = sq.getEnd() > dsq.getEnd();
4859 // StringBuffer sb = new StringBuffer();
4860 String newres = jalview.analysis.AlignSeq.extractGaps(
4861 jalview.util.Comparison.GapChars, sq.getSequenceAsString());
4862 if (!newres.equalsIgnoreCase(dsq.getSequenceAsString())
4863 && newres.length() > dsq.getLength())
4865 // Update with the longer sequence.
4869 * if (pre) { sb.insert(0, newres .substring(0, dsq.getStart() -
4870 * sq.getStart())); dsq.setStart(sq.getStart()); } if (post) {
4871 * sb.append(newres.substring(newres.length() - sq.getEnd() -
4872 * dsq.getEnd())); dsq.setEnd(sq.getEnd()); }
4874 dsq.setSequence(newres);
4876 // TODO: merges will never happen if we 'know' we have the real dataset
4877 // sequence - this should be detected when id==dssid
4879 .println("DEBUG Notice: Merged dataset sequence (if you see this often, post at http://issues.jalview.org/browse/JAL-1474)"); // ("
4880 // + (pre ? "prepended" : "") + " "
4881 // + (post ? "appended" : ""));
4887 * TODO use AlignmentI here and in related methods - needs
4888 * AlignmentI.getDataset() changed to return AlignmentI instead of Alignment
4890 Hashtable<String, AlignmentI> datasetIds = null;
4892 IdentityHashMap<AlignmentI, String> dataset2Ids = null;
4894 private AlignmentI getDatasetFor(String datasetId)
4896 if (datasetIds == null)
4898 datasetIds = new Hashtable<String, AlignmentI>();
4901 if (datasetIds.containsKey(datasetId))
4903 return datasetIds.get(datasetId);
4908 private void addDatasetRef(String datasetId, AlignmentI dataset)
4910 if (datasetIds == null)
4912 datasetIds = new Hashtable<String, AlignmentI>();
4914 datasetIds.put(datasetId, dataset);
4918 * make a new dataset ID for this jalview dataset alignment
4923 private String getDatasetIdRef(AlignmentI dataset)
4925 if (dataset.getDataset() != null)
4927 warn("Serious issue! Dataset Object passed to getDatasetIdRef is not a Jalview DATASET alignment...");
4929 String datasetId = makeHashCode(dataset, null);
4930 if (datasetId == null)
4932 // make a new datasetId and record it
4933 if (dataset2Ids == null)
4935 dataset2Ids = new IdentityHashMap<AlignmentI, String>();
4939 datasetId = dataset2Ids.get(dataset);
4941 if (datasetId == null)
4943 datasetId = "ds" + dataset2Ids.size() + 1;
4944 dataset2Ids.put(dataset, datasetId);
4950 private void addDBRefs(SequenceI datasetSequence, Sequence sequence)
4952 for (int d = 0; d < sequence.getDBRefCount(); d++)
4954 DBRef dr = sequence.getDBRef(d);
4955 jalview.datamodel.DBRefEntry entry = new jalview.datamodel.DBRefEntry(
4956 sequence.getDBRef(d).getSource(), sequence.getDBRef(d)
4957 .getVersion(), sequence.getDBRef(d).getAccessionId());
4958 if (dr.getMapping() != null)
4960 entry.setMap(addMapping(dr.getMapping()));
4962 datasetSequence.addDBRef(entry);
4966 private jalview.datamodel.Mapping addMapping(Mapping m)
4968 SequenceI dsto = null;
4969 // Mapping m = dr.getMapping();
4970 int fr[] = new int[m.getMapListFromCount() * 2];
4971 Enumeration f = m.enumerateMapListFrom();
4972 for (int _i = 0; f.hasMoreElements(); _i += 2)
4974 MapListFrom mf = (MapListFrom) f.nextElement();
4975 fr[_i] = mf.getStart();
4976 fr[_i + 1] = mf.getEnd();
4978 int fto[] = new int[m.getMapListToCount() * 2];
4979 f = m.enumerateMapListTo();
4980 for (int _i = 0; f.hasMoreElements(); _i += 2)
4982 MapListTo mf = (MapListTo) f.nextElement();
4983 fto[_i] = mf.getStart();
4984 fto[_i + 1] = mf.getEnd();
4986 jalview.datamodel.Mapping jmap = new jalview.datamodel.Mapping(dsto,
4987 fr, fto, (int) m.getMapFromUnit(), (int) m.getMapToUnit());
4988 if (m.getMappingChoice() != null)
4990 MappingChoice mc = m.getMappingChoice();
4991 if (mc.getDseqFor() != null)
4993 String dsfor = "" + mc.getDseqFor();
4994 if (seqRefIds.containsKey(dsfor))
4999 jmap.setTo(seqRefIds.get(dsfor));
5003 frefedSequence.add(new Object[] { dsfor, jmap });
5009 * local sequence definition
5011 Sequence ms = mc.getSequence();
5012 SequenceI djs = null;
5013 String sqid = ms.getDsseqid();
5014 if (sqid != null && sqid.length() > 0)
5017 * recover dataset sequence
5019 djs = seqRefIds.get(sqid);
5024 .println("Warning - making up dataset sequence id for DbRef sequence map reference");
5025 sqid = ((Object) ms).toString(); // make up a new hascode for
5026 // undefined dataset sequence hash
5027 // (unlikely to happen)
5033 * make a new dataset sequence and add it to refIds hash
5035 djs = new jalview.datamodel.Sequence(ms.getName(),
5037 djs.setStart(jmap.getMap().getToLowest());
5038 djs.setEnd(jmap.getMap().getToHighest());
5039 djs.setVamsasId(uniqueSetSuffix + sqid);
5041 seqRefIds.put(sqid, djs);
5044 jalview.bin.Cache.log.debug("about to recurse on addDBRefs.");
5053 public jalview.gui.AlignmentPanel copyAlignPanel(AlignmentPanel ap,
5054 boolean keepSeqRefs)
5057 JalviewModel jm = saveState(ap, null, null, null);
5062 jm.getJalviewModelSequence().getViewport(0).setSequenceSetId(null);
5066 uniqueSetSuffix = "";
5067 jm.getJalviewModelSequence().getViewport(0).setId(null); // we don't
5072 if (this.frefedSequence == null)
5074 frefedSequence = new Vector();
5077 viewportsAdded.clear();
5079 AlignFrame af = loadFromObject(jm, null, false, null);
5080 af.alignPanels.clear();
5081 af.closeMenuItem_actionPerformed(true);
5084 * if(ap.av.getAlignment().getAlignmentAnnotation()!=null) { for(int i=0;
5085 * i<ap.av.getAlignment().getAlignmentAnnotation().length; i++) {
5086 * if(!ap.av.getAlignment().getAlignmentAnnotation()[i].autoCalculated) {
5087 * af.alignPanel.av.getAlignment().getAlignmentAnnotation()[i] =
5088 * ap.av.getAlignment().getAlignmentAnnotation()[i]; } } }
5091 return af.alignPanel;
5095 * flag indicating if hashtables should be cleared on finalization TODO this
5096 * flag may not be necessary
5098 private final boolean _cleartables = true;
5100 private Hashtable jvids2vobj;
5105 * @see java.lang.Object#finalize()
5108 protected void finalize() throws Throwable
5110 // really make sure we have no buried refs left.
5115 this.seqRefIds = null;
5116 this.seqsToIds = null;
5120 private void warn(String msg)
5125 private void warn(String msg, Exception e)
5127 if (Cache.log != null)
5131 Cache.log.warn(msg, e);
5135 Cache.log.warn(msg);
5140 System.err.println("Warning: " + msg);
5143 e.printStackTrace();
5148 private void debug(String string)
5150 debug(string, null);
5153 private void debug(String msg, Exception e)
5155 if (Cache.log != null)
5159 Cache.log.debug(msg, e);
5163 Cache.log.debug(msg);
5168 System.err.println("Warning: " + msg);
5171 e.printStackTrace();
5177 * set the object to ID mapping tables used to write/recover objects and XML
5178 * ID strings for the jalview project. If external tables are provided then
5179 * finalize and clearSeqRefs will not clear the tables when the Jalview2XML
5180 * object goes out of scope. - also populates the datasetIds hashtable with
5181 * alignment objects containing dataset sequences
5184 * Map from ID strings to jalview datamodel
5186 * Map from jalview datamodel to ID strings
5190 public void setObjectMappingTables(Hashtable vobj2jv,
5191 IdentityHashMap jv2vobj)
5193 this.jv2vobj = jv2vobj;
5194 this.vobj2jv = vobj2jv;
5195 Iterator ds = jv2vobj.keySet().iterator();
5197 while (ds.hasNext())
5199 Object jvobj = ds.next();
5200 id = jv2vobj.get(jvobj).toString();
5201 if (jvobj instanceof jalview.datamodel.Alignment)
5203 if (((jalview.datamodel.Alignment) jvobj).getDataset() == null)
5205 addDatasetRef(id, (jalview.datamodel.Alignment) jvobj);
5208 else if (jvobj instanceof jalview.datamodel.Sequence)
5210 // register sequence object so the XML parser can recover it.
5211 if (seqRefIds == null)
5213 seqRefIds = new HashMap<String, SequenceI>();
5215 if (seqsToIds == null)
5217 seqsToIds = new IdentityHashMap<SequenceI, String>();
5219 seqRefIds.put(jv2vobj.get(jvobj).toString(), (SequenceI) jvobj);
5220 seqsToIds.put((SequenceI) jvobj, id);
5222 else if (jvobj instanceof jalview.datamodel.AlignmentAnnotation)
5225 AlignmentAnnotation jvann = (AlignmentAnnotation) jvobj;
5226 annotationIds.put(anid = jv2vobj.get(jvobj).toString(), jvann);
5227 if (jvann.annotationId == null)
5229 jvann.annotationId = anid;
5231 if (!jvann.annotationId.equals(anid))
5233 // TODO verify that this is the correct behaviour
5234 this.warn("Overriding Annotation ID for " + anid
5235 + " from different id : " + jvann.annotationId);
5236 jvann.annotationId = anid;
5239 else if (jvobj instanceof String)
5241 if (jvids2vobj == null)
5243 jvids2vobj = new Hashtable();
5244 jvids2vobj.put(jvobj, jv2vobj.get(jvobj).toString());
5249 Cache.log.debug("Ignoring " + jvobj.getClass() + " (ID = " + id);
5255 * set the uniqueSetSuffix used to prefix/suffix object IDs for jalview
5256 * objects created from the project archive. If string is null (default for
5257 * construction) then suffix will be set automatically.
5261 public void setUniqueSetSuffix(String string)
5263 uniqueSetSuffix = string;
5268 * uses skipList2 as the skipList for skipping views on sequence sets
5269 * associated with keys in the skipList
5273 public void setSkipList(Hashtable skipList2)
5275 skipList = skipList2;
5279 * Reads the jar entry of given name and returns its contents, or null if the
5280 * entry is not found.
5283 * @param jarEntryName
5286 protected String readJarEntry(jarInputStreamProvider jprovider,
5287 String jarEntryName)
5289 String result = null;
5290 BufferedReader in = null;
5295 * Reopen the jar input stream and traverse its entries to find a matching
5298 JarInputStream jin = jprovider.getJarInputStream();
5299 JarEntry entry = null;
5302 entry = jin.getNextJarEntry();
5303 } while (entry != null && !entry.getName().equals(jarEntryName));
5307 StringBuilder out = new StringBuilder(256);
5308 in = new BufferedReader(new InputStreamReader(jin, UTF_8));
5311 while ((data = in.readLine()) != null)
5315 result = out.toString();
5319 warn("Couldn't find entry in Jalview Jar for " + jarEntryName);
5321 } catch (Exception ex)
5323 ex.printStackTrace();
5331 } catch (IOException e)
5342 * Returns an incrementing counter (0, 1, 2...)
5346 private synchronized int nextCounter()