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.analysis.Conservation;
24 import jalview.api.FeatureColourI;
25 import jalview.api.ViewStyleI;
26 import jalview.api.structures.JalviewStructureDisplayI;
27 import jalview.bin.Cache;
28 import jalview.datamodel.AlignedCodonFrame;
29 import jalview.datamodel.Alignment;
30 import jalview.datamodel.AlignmentAnnotation;
31 import jalview.datamodel.AlignmentI;
32 import jalview.datamodel.GraphLine;
33 import jalview.datamodel.PDBEntry;
34 import jalview.datamodel.RnaViewerModel;
35 import jalview.datamodel.SequenceFeature;
36 import jalview.datamodel.SequenceGroup;
37 import jalview.datamodel.SequenceI;
38 import jalview.datamodel.StructureViewerModel;
39 import jalview.datamodel.StructureViewerModel.StructureData;
40 import jalview.ext.varna.RnaModel;
41 import jalview.gui.StructureViewer.ViewerType;
42 import jalview.io.DataSourceType;
43 import jalview.io.FileFormat;
44 import jalview.renderer.ResidueShaderI;
45 import jalview.schemabinding.version2.AlcodMap;
46 import jalview.schemabinding.version2.AlcodonFrame;
47 import jalview.schemabinding.version2.Annotation;
48 import jalview.schemabinding.version2.AnnotationColours;
49 import jalview.schemabinding.version2.AnnotationElement;
50 import jalview.schemabinding.version2.CalcIdParam;
51 import jalview.schemabinding.version2.DBRef;
52 import jalview.schemabinding.version2.Features;
53 import jalview.schemabinding.version2.Group;
54 import jalview.schemabinding.version2.HiddenColumns;
55 import jalview.schemabinding.version2.JGroup;
56 import jalview.schemabinding.version2.JSeq;
57 import jalview.schemabinding.version2.JalviewModel;
58 import jalview.schemabinding.version2.JalviewModelSequence;
59 import jalview.schemabinding.version2.MapListFrom;
60 import jalview.schemabinding.version2.MapListTo;
61 import jalview.schemabinding.version2.Mapping;
62 import jalview.schemabinding.version2.MappingChoice;
63 import jalview.schemabinding.version2.OtherData;
64 import jalview.schemabinding.version2.PdbentryItem;
65 import jalview.schemabinding.version2.Pdbids;
66 import jalview.schemabinding.version2.Property;
67 import jalview.schemabinding.version2.RnaViewer;
68 import jalview.schemabinding.version2.SecondaryStructure;
69 import jalview.schemabinding.version2.Sequence;
70 import jalview.schemabinding.version2.SequenceSet;
71 import jalview.schemabinding.version2.SequenceSetProperties;
72 import jalview.schemabinding.version2.Setting;
73 import jalview.schemabinding.version2.StructureState;
74 import jalview.schemabinding.version2.ThresholdLine;
75 import jalview.schemabinding.version2.Tree;
76 import jalview.schemabinding.version2.UserColours;
77 import jalview.schemabinding.version2.Viewport;
78 import jalview.schemes.AnnotationColourGradient;
79 import jalview.schemes.ColourSchemeI;
80 import jalview.schemes.ColourSchemeProperty;
81 import jalview.schemes.FeatureColour;
82 import jalview.schemes.ResidueProperties;
83 import jalview.schemes.UserColourScheme;
84 import jalview.structure.StructureSelectionManager;
85 import jalview.structures.models.AAStructureBindingModel;
86 import jalview.util.MessageManager;
87 import jalview.util.Platform;
88 import jalview.util.StringUtils;
89 import jalview.util.jarInputStreamProvider;
90 import jalview.viewmodel.AlignmentViewport;
91 import jalview.viewmodel.ViewportRanges;
92 import jalview.viewmodel.seqfeatures.FeatureRendererSettings;
93 import jalview.viewmodel.seqfeatures.FeaturesDisplayed;
94 import jalview.ws.jws2.Jws2Discoverer;
95 import jalview.ws.jws2.dm.AAConSettings;
96 import jalview.ws.jws2.jabaws2.Jws2Instance;
97 import jalview.ws.params.ArgumentI;
98 import jalview.ws.params.AutoCalcSetting;
99 import jalview.ws.params.WsParamSetI;
101 import java.awt.Color;
102 import java.awt.Rectangle;
103 import java.io.BufferedReader;
104 import java.io.DataInputStream;
105 import java.io.DataOutputStream;
107 import java.io.FileInputStream;
108 import java.io.FileOutputStream;
109 import java.io.IOException;
110 import java.io.InputStreamReader;
111 import java.io.OutputStreamWriter;
112 import java.io.PrintWriter;
113 import java.lang.reflect.InvocationTargetException;
114 import java.net.MalformedURLException;
116 import java.util.ArrayList;
117 import java.util.Arrays;
118 import java.util.Enumeration;
119 import java.util.HashMap;
120 import java.util.HashSet;
121 import java.util.Hashtable;
122 import java.util.IdentityHashMap;
123 import java.util.Iterator;
124 import java.util.LinkedHashMap;
125 import java.util.List;
126 import java.util.Map;
127 import java.util.Map.Entry;
128 import java.util.Set;
129 import java.util.Vector;
130 import java.util.jar.JarEntry;
131 import java.util.jar.JarInputStream;
132 import java.util.jar.JarOutputStream;
134 import javax.swing.JInternalFrame;
135 import javax.swing.SwingUtilities;
137 import org.exolab.castor.xml.Marshaller;
138 import org.exolab.castor.xml.Unmarshaller;
141 * Write out the current jalview desktop state as a Jalview XML stream.
143 * Note: the vamsas objects referred to here are primitive versions of the
144 * VAMSAS project schema elements - they are not the same and most likely never
148 * @version $Revision: 1.134 $
150 public class Jalview2XML
152 private static final String VIEWER_PREFIX = "viewer_";
154 private static final String RNA_PREFIX = "rna_";
156 private static final String UTF_8 = "UTF-8";
158 // use this with nextCounter() to make unique names for entities
159 private int counter = 0;
162 * SequenceI reference -> XML ID string in jalview XML. Populated as XML reps
163 * of sequence objects are created.
165 IdentityHashMap<SequenceI, String> seqsToIds = null;
168 * jalview XML Sequence ID to jalview sequence object reference (both dataset
169 * and alignment sequences. Populated as XML reps of sequence objects are
172 Map<String, SequenceI> seqRefIds = null;
174 Map<String, SequenceI> incompleteSeqs = null;
176 List<SeqFref> frefedSequence = null;
178 boolean raiseGUI = true; // whether errors are raised in dialog boxes or not
181 * Map of reconstructed AlignFrame objects that appear to have come from
182 * SplitFrame objects (have a dna/protein complement view).
184 private Map<Viewport, AlignFrame> splitFrameCandidates = new HashMap<>();
187 * Map from displayed rna structure models to their saved session state jar
190 private Map<RnaModel, String> rnaSessions = new HashMap<>();
193 * create/return unique hash string for sq
196 * @return new or existing unique string for sq
198 String seqHash(SequenceI sq)
200 if (seqsToIds == null)
204 if (seqsToIds.containsKey(sq))
206 return seqsToIds.get(sq);
210 // create sequential key
211 String key = "sq" + (seqsToIds.size() + 1);
212 key = makeHashCode(sq, key); // check we don't have an external reference
214 seqsToIds.put(sq, key);
223 if (seqRefIds != null)
227 if (seqsToIds != null)
231 if (incompleteSeqs != null)
233 incompleteSeqs.clear();
241 warn("clearSeqRefs called when _cleartables was not set. Doing nothing.");
242 // seqRefIds = new Hashtable();
243 // seqsToIds = new IdentityHashMap();
249 if (seqsToIds == null)
251 seqsToIds = new IdentityHashMap<>();
253 if (seqRefIds == null)
255 seqRefIds = new HashMap<>();
257 if (incompleteSeqs == null)
259 incompleteSeqs = new HashMap<>();
261 if (frefedSequence == null)
263 frefedSequence = new ArrayList<>();
271 public Jalview2XML(boolean raiseGUI)
273 this.raiseGUI = raiseGUI;
277 * base class for resolving forward references to sequences by their ID
282 abstract class SeqFref
288 public SeqFref(String _sref, String type)
294 public String getSref()
299 public SequenceI getSrefSeq()
301 return seqRefIds.get(sref);
304 public boolean isResolvable()
306 return seqRefIds.get(sref) != null;
309 public SequenceI getSrefDatasetSeq()
311 SequenceI sq = seqRefIds.get(sref);
314 while (sq.getDatasetSequence() != null)
316 sq = sq.getDatasetSequence();
323 * @return true if the forward reference was fully resolved
325 abstract boolean resolve();
328 public String toString()
330 return type + " reference to " + sref;
335 * create forward reference for a mapping
341 public SeqFref newMappingRef(final String sref,
342 final jalview.datamodel.Mapping _jmap)
344 SeqFref fref = new SeqFref(sref, "Mapping")
346 public jalview.datamodel.Mapping jmap = _jmap;
351 SequenceI seq = getSrefDatasetSeq();
363 public SeqFref newAlcodMapRef(final String sref,
364 final AlignedCodonFrame _cf,
365 final jalview.datamodel.Mapping _jmap)
368 SeqFref fref = new SeqFref(sref, "Codon Frame")
370 AlignedCodonFrame cf = _cf;
372 public jalview.datamodel.Mapping mp = _jmap;
375 public boolean isResolvable()
377 return super.isResolvable() && mp.getTo() != null;
383 SequenceI seq = getSrefDatasetSeq();
388 cf.addMap(seq, mp.getTo(), mp.getMap());
395 public void resolveFrefedSequences()
397 Iterator<SeqFref> nextFref = frefedSequence.iterator();
398 int toresolve = frefedSequence.size();
399 int unresolved = 0, failedtoresolve = 0;
400 while (nextFref.hasNext())
402 SeqFref ref = nextFref.next();
403 if (ref.isResolvable())
415 } catch (Exception x)
418 "IMPLEMENTATION ERROR: Failed to resolve forward reference for sequence "
431 System.err.println("Jalview Project Import: There were " + unresolved
432 + " forward references left unresolved on the stack.");
434 if (failedtoresolve > 0)
436 System.err.println("SERIOUS! " + failedtoresolve
437 + " resolvable forward references failed to resolve.");
439 if (incompleteSeqs != null && incompleteSeqs.size() > 0)
442 "Jalview Project Import: There are " + incompleteSeqs.size()
443 + " sequences which may have incomplete metadata.");
444 if (incompleteSeqs.size() < 10)
446 for (SequenceI s : incompleteSeqs.values())
448 System.err.println(s.toString());
454 "Too many to report. Skipping output of incomplete sequences.");
460 * This maintains a map of viewports, the key being the seqSetId. Important to
461 * set historyItem and redoList for multiple views
463 Map<String, AlignViewport> viewportsAdded = new HashMap<>();
465 Map<String, AlignmentAnnotation> annotationIds = new HashMap<>();
467 String uniqueSetSuffix = "";
470 * List of pdbfiles added to Jar
472 List<String> pdbfiles = null;
474 // SAVES SEVERAL ALIGNMENT WINDOWS TO SAME JARFILE
475 public void saveState(File statefile)
477 FileOutputStream fos = null;
480 fos = new FileOutputStream(statefile);
481 JarOutputStream jout = new JarOutputStream(fos);
484 } catch (Exception e)
486 // TODO: inform user of the problem - they need to know if their data was
488 if (errorMessage == null)
490 errorMessage = "Couldn't write Jalview Archive to output file '"
491 + statefile + "' - See console error log for details";
495 errorMessage += "(output file was '" + statefile + "')";
505 } catch (IOException e)
515 * Writes a jalview project archive to the given Jar output stream.
519 public void saveState(JarOutputStream jout)
521 AlignFrame[] frames = Desktop.getAlignFrames();
527 saveAllFrames(Arrays.asList(frames), jout);
531 * core method for storing state for a set of AlignFrames.
534 * - frames involving all data to be exported (including containing
537 * - project output stream
539 private void saveAllFrames(List<AlignFrame> frames, JarOutputStream jout)
541 Hashtable<String, AlignFrame> dsses = new Hashtable<>();
544 * ensure cached data is clear before starting
546 // todo tidy up seqRefIds, seqsToIds initialisation / reset
548 splitFrameCandidates.clear();
553 // NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS
554 // //////////////////////////////////////////////////
556 List<String> shortNames = new ArrayList<>();
557 List<String> viewIds = new ArrayList<>();
560 for (int i = frames.size() - 1; i > -1; i--)
562 AlignFrame af = frames.get(i);
564 if (skipList != null && skipList
565 .containsKey(af.getViewport().getSequenceSetId()))
570 String shortName = makeFilename(af, shortNames);
572 int ap, apSize = af.alignPanels.size();
574 for (ap = 0; ap < apSize; ap++)
576 AlignmentPanel apanel = af.alignPanels.get(ap);
577 String fileName = apSize == 1 ? shortName : ap + shortName;
578 if (!fileName.endsWith(".xml"))
580 fileName = fileName + ".xml";
583 saveState(apanel, fileName, jout, viewIds);
585 String dssid = getDatasetIdRef(
586 af.getViewport().getAlignment().getDataset());
587 if (!dsses.containsKey(dssid))
589 dsses.put(dssid, af);
594 writeDatasetFor(dsses, "" + jout.hashCode() + " " + uniqueSetSuffix,
600 } catch (Exception foo)
605 } catch (Exception ex)
607 // TODO: inform user of the problem - they need to know if their data was
609 if (errorMessage == null)
611 errorMessage = "Couldn't write Jalview Archive - see error output for details";
613 ex.printStackTrace();
618 * Generates a distinct file name, based on the title of the AlignFrame, by
619 * appending _n for increasing n until an unused name is generated. The new
620 * name (without its extension) is added to the list.
624 * @return the generated name, with .xml extension
626 protected String makeFilename(AlignFrame af, List<String> namesUsed)
628 String shortName = af.getTitle();
630 if (shortName.indexOf(File.separatorChar) > -1)
632 shortName = shortName
633 .substring(shortName.lastIndexOf(File.separatorChar) + 1);
638 while (namesUsed.contains(shortName))
640 if (shortName.endsWith("_" + (count - 1)))
642 shortName = shortName.substring(0, shortName.lastIndexOf("_"));
645 shortName = shortName.concat("_" + count);
649 namesUsed.add(shortName);
651 if (!shortName.endsWith(".xml"))
653 shortName = shortName + ".xml";
658 // USE THIS METHOD TO SAVE A SINGLE ALIGNMENT WINDOW
659 public boolean saveAlignment(AlignFrame af, String jarFile,
664 FileOutputStream fos = new FileOutputStream(jarFile);
665 JarOutputStream jout = new JarOutputStream(fos);
666 List<AlignFrame> frames = new ArrayList<>();
668 // resolve splitframes
669 if (af.getViewport().getCodingComplement() != null)
671 frames = ((SplitFrame) af.getSplitViewContainer()).getAlignFrames();
677 saveAllFrames(frames, jout);
681 } catch (Exception foo)
687 } catch (Exception ex)
689 errorMessage = "Couldn't Write alignment view to Jalview Archive - see error output for details";
690 ex.printStackTrace();
695 private void writeDatasetFor(Hashtable<String, AlignFrame> dsses,
696 String fileName, JarOutputStream jout)
699 for (String dssids : dsses.keySet())
701 AlignFrame _af = dsses.get(dssids);
702 String jfileName = fileName + " Dataset for " + _af.getTitle();
703 if (!jfileName.endsWith(".xml"))
705 jfileName = jfileName + ".xml";
707 saveState(_af.alignPanel, jfileName, true, jout, null);
712 * create a JalviewModel from an alignment view and marshall it to a
716 * panel to create jalview model for
718 * name of alignment panel written to output stream
725 public JalviewModel saveState(AlignmentPanel ap, String fileName,
726 JarOutputStream jout, List<String> viewIds)
728 return saveState(ap, fileName, false, jout, viewIds);
732 * create a JalviewModel from an alignment view and marshall it to a
736 * panel to create jalview model for
738 * name of alignment panel written to output stream
740 * when true, only write the dataset for the alignment, not the data
741 * associated with the view.
747 public JalviewModel saveState(AlignmentPanel ap, String fileName,
748 boolean storeDS, JarOutputStream jout, List<String> viewIds)
752 viewIds = new ArrayList<>();
757 List<UserColourScheme> userColours = new ArrayList<>();
759 AlignViewport av = ap.av;
760 ViewportRanges vpRanges = av.getRanges();
762 JalviewModel object = new JalviewModel();
763 object.setVamsasModel(new jalview.schemabinding.version2.VamsasModel());
765 object.setCreationDate(new java.util.Date(System.currentTimeMillis()));
767 jalview.bin.Cache.getDefault("VERSION", "Development Build"));
770 * rjal is full height alignment, jal is actual alignment with full metadata
771 * but excludes hidden sequences.
773 jalview.datamodel.AlignmentI rjal = av.getAlignment(), jal = rjal;
775 if (av.hasHiddenRows())
777 rjal = jal.getHiddenSequences().getFullAlignment();
780 SequenceSet vamsasSet = new SequenceSet();
782 JalviewModelSequence jms = new JalviewModelSequence();
784 vamsasSet.setGapChar(jal.getGapCharacter() + "");
786 if (jal.getDataset() != null)
788 // dataset id is the dataset's hashcode
789 vamsasSet.setDatasetId(getDatasetIdRef(jal.getDataset()));
792 // switch jal and the dataset
793 jal = jal.getDataset();
797 if (jal.getProperties() != null)
799 Enumeration en = jal.getProperties().keys();
800 while (en.hasMoreElements())
802 String key = en.nextElement().toString();
803 SequenceSetProperties ssp = new SequenceSetProperties();
805 ssp.setValue(jal.getProperties().get(key).toString());
806 vamsasSet.addSequenceSetProperties(ssp);
811 Set<String> calcIdSet = new HashSet<>();
812 // record the set of vamsas sequence XML POJO we create.
813 HashMap<String, Sequence> vamsasSetIds = new HashMap<>();
815 for (final SequenceI jds : rjal.getSequences())
817 final SequenceI jdatasq = jds.getDatasetSequence() == null ? jds
818 : jds.getDatasetSequence();
819 String id = seqHash(jds);
820 if (vamsasSetIds.get(id) == null)
822 if (seqRefIds.get(id) != null && !storeDS)
824 // This happens for two reasons: 1. multiple views are being
826 // 2. the hashCode has collided with another sequence's code. This
828 // HAPPEN! (PF00072.15.stk does this)
829 // JBPNote: Uncomment to debug writing out of files that do not read
830 // back in due to ArrayOutOfBoundExceptions.
831 // System.err.println("vamsasSeq backref: "+id+"");
832 // System.err.println(jds.getName()+"
833 // "+jds.getStart()+"-"+jds.getEnd()+" "+jds.getSequenceAsString());
834 // System.err.println("Hashcode: "+seqHash(jds));
835 // SequenceI rsq = (SequenceI) seqRefIds.get(id + "");
836 // System.err.println(rsq.getName()+"
837 // "+rsq.getStart()+"-"+rsq.getEnd()+" "+rsq.getSequenceAsString());
838 // System.err.println("Hashcode: "+seqHash(rsq));
842 vamsasSeq = createVamsasSequence(id, jds);
843 vamsasSet.addSequence(vamsasSeq);
844 vamsasSetIds.put(id, vamsasSeq);
845 seqRefIds.put(id, jds);
849 jseq.setStart(jds.getStart());
850 jseq.setEnd(jds.getEnd());
851 jseq.setColour(av.getSequenceColour(jds).getRGB());
853 jseq.setId(id); // jseq id should be a string not a number
856 // Store any sequences this sequence represents
857 if (av.hasHiddenRows())
859 // use rjal, contains the full height alignment
861 av.getAlignment().getHiddenSequences().isHidden(jds));
863 if (av.isHiddenRepSequence(jds))
865 jalview.datamodel.SequenceI[] reps = av
866 .getRepresentedSequences(jds).getSequencesInOrder(rjal);
868 for (int h = 0; h < reps.length; h++)
872 jseq.addHiddenSequences(rjal.findIndex(reps[h]));
877 // mark sequence as reference - if it is the reference for this view
880 jseq.setViewreference(jds == jal.getSeqrep());
884 // TODO: omit sequence features from each alignment view's XML dump if we
885 // are storing dataset
886 List<jalview.datamodel.SequenceFeature> sfs = jds
887 .getSequenceFeatures();
888 for (SequenceFeature sf : sfs)
890 Features features = new Features();
892 features.setBegin(sf.getBegin());
893 features.setEnd(sf.getEnd());
894 features.setDescription(sf.getDescription());
895 features.setType(sf.getType());
896 features.setFeatureGroup(sf.getFeatureGroup());
897 features.setScore(sf.getScore());
898 if (sf.links != null)
900 for (int l = 0; l < sf.links.size(); l++)
902 OtherData keyValue = new OtherData();
903 keyValue.setKey("LINK_" + l);
904 keyValue.setValue(sf.links.elementAt(l).toString());
905 features.addOtherData(keyValue);
908 if (sf.otherDetails != null)
911 Iterator<String> keys = sf.otherDetails.keySet().iterator();
912 while (keys.hasNext())
915 OtherData keyValue = new OtherData();
916 keyValue.setKey(key);
917 keyValue.setValue(sf.otherDetails.get(key).toString());
918 features.addOtherData(keyValue);
922 jseq.addFeatures(features);
925 if (jdatasq.getAllPDBEntries() != null)
927 Enumeration en = jdatasq.getAllPDBEntries().elements();
928 while (en.hasMoreElements())
930 Pdbids pdb = new Pdbids();
931 jalview.datamodel.PDBEntry entry = (jalview.datamodel.PDBEntry) en
934 String pdbId = entry.getId();
936 pdb.setType(entry.getType());
939 * Store any structure views associated with this sequence. This
940 * section copes with duplicate entries in the project, so a dataset
941 * only view *should* be coped with sensibly.
943 // This must have been loaded, is it still visible?
944 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
945 String matchedFile = null;
946 for (int f = frames.length - 1; f > -1; f--)
948 if (frames[f] instanceof StructureViewerBase)
950 StructureViewerBase viewFrame = (StructureViewerBase) frames[f];
951 matchedFile = saveStructureState(ap, jds, pdb, entry, viewIds,
952 matchedFile, viewFrame);
954 * Only store each structure viewer's state once in the project
955 * jar. First time through only (storeDS==false)
957 String viewId = viewFrame.getViewId();
958 if (!storeDS && !viewIds.contains(viewId))
963 String viewerState = viewFrame.getStateInfo();
964 writeJarEntry(jout, getViewerJarEntryName(viewId),
965 viewerState.getBytes());
966 } catch (IOException e)
969 "Error saving viewer state: " + e.getMessage());
975 if (matchedFile != null || entry.getFile() != null)
977 if (entry.getFile() != null)
980 matchedFile = entry.getFile();
982 pdb.setFile(matchedFile); // entry.getFile());
983 if (pdbfiles == null)
985 pdbfiles = new ArrayList<>();
988 if (!pdbfiles.contains(pdbId))
991 copyFileToJar(jout, matchedFile, pdbId);
995 Enumeration<String> props = entry.getProperties();
996 if (props.hasMoreElements())
998 PdbentryItem item = new PdbentryItem();
999 while (props.hasMoreElements())
1001 Property prop = new Property();
1002 String key = props.nextElement();
1004 prop.setValue(entry.getProperty(key).toString());
1005 item.addProperty(prop);
1007 pdb.addPdbentryItem(item);
1010 jseq.addPdbids(pdb);
1014 saveRnaViewers(jout, jseq, jds, viewIds, ap, storeDS);
1019 if (!storeDS && av.hasHiddenRows())
1021 jal = av.getAlignment();
1025 if (storeDS && jal.getCodonFrames() != null)
1027 List<AlignedCodonFrame> jac = jal.getCodonFrames();
1028 for (AlignedCodonFrame acf : jac)
1030 AlcodonFrame alc = new AlcodonFrame();
1031 if (acf.getProtMappings() != null
1032 && acf.getProtMappings().length > 0)
1034 boolean hasMap = false;
1035 SequenceI[] dnas = acf.getdnaSeqs();
1036 jalview.datamodel.Mapping[] pmaps = acf.getProtMappings();
1037 for (int m = 0; m < pmaps.length; m++)
1039 AlcodMap alcmap = new AlcodMap();
1040 alcmap.setDnasq(seqHash(dnas[m]));
1042 createVamsasMapping(pmaps[m], dnas[m], null, false));
1043 alc.addAlcodMap(alcmap);
1048 vamsasSet.addAlcodonFrame(alc);
1051 // TODO: delete this ? dead code from 2.8.3->2.9 ?
1053 // AlcodonFrame alc = new AlcodonFrame();
1054 // vamsasSet.addAlcodonFrame(alc);
1055 // for (int p = 0; p < acf.aaWidth; p++)
1057 // Alcodon cmap = new Alcodon();
1058 // if (acf.codons[p] != null)
1060 // // Null codons indicate a gapped column in the translated peptide
1062 // cmap.setPos1(acf.codons[p][0]);
1063 // cmap.setPos2(acf.codons[p][1]);
1064 // cmap.setPos3(acf.codons[p][2]);
1066 // alc.addAlcodon(cmap);
1068 // if (acf.getProtMappings() != null
1069 // && acf.getProtMappings().length > 0)
1071 // SequenceI[] dnas = acf.getdnaSeqs();
1072 // jalview.datamodel.Mapping[] pmaps = acf.getProtMappings();
1073 // for (int m = 0; m < pmaps.length; m++)
1075 // AlcodMap alcmap = new AlcodMap();
1076 // alcmap.setDnasq(seqHash(dnas[m]));
1077 // alcmap.setMapping(createVamsasMapping(pmaps[m], dnas[m], null,
1079 // alc.addAlcodMap(alcmap);
1086 // /////////////////////////////////
1087 if (!storeDS && av.currentTree != null)
1089 // FIND ANY ASSOCIATED TREES
1090 // NOT IMPLEMENTED FOR HEADLESS STATE AT PRESENT
1091 if (Desktop.desktop != null)
1093 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1095 for (int t = 0; t < frames.length; t++)
1097 if (frames[t] instanceof TreePanel)
1099 TreePanel tp = (TreePanel) frames[t];
1101 if (tp.treeCanvas.av.getAlignment() == jal)
1103 Tree tree = new Tree();
1104 tree.setTitle(tp.getTitle());
1105 tree.setCurrentTree((av.currentTree == tp.getTree()));
1106 tree.setNewick(tp.getTree().print());
1107 tree.setThreshold(tp.treeCanvas.threshold);
1109 tree.setFitToWindow(tp.fitToWindow.getState());
1110 tree.setFontName(tp.getTreeFont().getName());
1111 tree.setFontSize(tp.getTreeFont().getSize());
1112 tree.setFontStyle(tp.getTreeFont().getStyle());
1113 tree.setMarkUnlinked(tp.placeholdersMenu.getState());
1115 tree.setShowBootstrap(tp.bootstrapMenu.getState());
1116 tree.setShowDistances(tp.distanceMenu.getState());
1118 tree.setHeight(tp.getHeight());
1119 tree.setWidth(tp.getWidth());
1120 tree.setXpos(tp.getX());
1121 tree.setYpos(tp.getY());
1122 tree.setId(makeHashCode(tp, null));
1132 * store forward refs from an annotationRow to any groups
1134 IdentityHashMap<SequenceGroup, String> groupRefs = new IdentityHashMap<>();
1137 for (SequenceI sq : jal.getSequences())
1139 // Store annotation on dataset sequences only
1140 AlignmentAnnotation[] aa = sq.getAnnotation();
1141 if (aa != null && aa.length > 0)
1143 storeAlignmentAnnotation(aa, groupRefs, av, calcIdSet, storeDS,
1150 if (jal.getAlignmentAnnotation() != null)
1152 // Store the annotation shown on the alignment.
1153 AlignmentAnnotation[] aa = jal.getAlignmentAnnotation();
1154 storeAlignmentAnnotation(aa, groupRefs, av, calcIdSet, storeDS,
1159 if (jal.getGroups() != null)
1161 JGroup[] groups = new JGroup[jal.getGroups().size()];
1163 for (jalview.datamodel.SequenceGroup sg : jal.getGroups())
1165 JGroup jGroup = new JGroup();
1166 groups[++i] = jGroup;
1168 jGroup.setStart(sg.getStartRes());
1169 jGroup.setEnd(sg.getEndRes());
1170 jGroup.setName(sg.getName());
1171 if (groupRefs.containsKey(sg))
1173 // group has references so set its ID field
1174 jGroup.setId(groupRefs.get(sg));
1176 ColourSchemeI colourScheme = sg.getColourScheme();
1177 if (colourScheme != null)
1179 ResidueShaderI groupColourScheme = sg.getGroupColourScheme();
1180 if (groupColourScheme.conservationApplied())
1182 jGroup.setConsThreshold(groupColourScheme.getConservationInc());
1184 if (colourScheme instanceof jalview.schemes.UserColourScheme)
1187 setUserColourScheme(colourScheme, userColours, jms));
1191 jGroup.setColour(colourScheme.getSchemeName());
1194 else if (colourScheme instanceof jalview.schemes.AnnotationColourGradient)
1196 jGroup.setColour("AnnotationColourGradient");
1197 jGroup.setAnnotationColours(constructAnnotationColours(
1198 (jalview.schemes.AnnotationColourGradient) colourScheme,
1201 else if (colourScheme instanceof jalview.schemes.UserColourScheme)
1204 setUserColourScheme(colourScheme, userColours, jms));
1208 jGroup.setColour(colourScheme.getSchemeName());
1211 jGroup.setPidThreshold(groupColourScheme.getThreshold());
1214 jGroup.setOutlineColour(sg.getOutlineColour().getRGB());
1215 jGroup.setDisplayBoxes(sg.getDisplayBoxes());
1216 jGroup.setDisplayText(sg.getDisplayText());
1217 jGroup.setColourText(sg.getColourText());
1218 jGroup.setTextCol1(sg.textColour.getRGB());
1219 jGroup.setTextCol2(sg.textColour2.getRGB());
1220 jGroup.setTextColThreshold(sg.thresholdTextColour);
1221 jGroup.setShowUnconserved(sg.getShowNonconserved());
1222 jGroup.setIgnoreGapsinConsensus(sg.getIgnoreGapsConsensus());
1223 jGroup.setShowConsensusHistogram(sg.isShowConsensusHistogram());
1224 jGroup.setShowSequenceLogo(sg.isShowSequenceLogo());
1225 jGroup.setNormaliseSequenceLogo(sg.isNormaliseSequenceLogo());
1226 for (SequenceI seq : sg.getSequences())
1228 jGroup.addSeq(seqHash(seq));
1232 jms.setJGroup(groups);
1236 // /////////SAVE VIEWPORT
1237 Viewport view = new Viewport();
1238 view.setTitle(ap.alignFrame.getTitle());
1239 view.setSequenceSetId(
1240 makeHashCode(av.getSequenceSetId(), av.getSequenceSetId()));
1241 view.setId(av.getViewId());
1242 if (av.getCodingComplement() != null)
1244 view.setComplementId(av.getCodingComplement().getViewId());
1246 view.setViewName(av.viewName);
1247 view.setGatheredViews(av.isGatherViewsHere());
1249 Rectangle size = ap.av.getExplodedGeometry();
1250 Rectangle position = size;
1253 size = ap.alignFrame.getBounds();
1254 if (av.getCodingComplement() != null)
1256 position = ((SplitFrame) ap.alignFrame.getSplitViewContainer())
1264 view.setXpos(position.x);
1265 view.setYpos(position.y);
1267 view.setWidth(size.width);
1268 view.setHeight(size.height);
1270 view.setStartRes(vpRanges.getStartRes());
1271 view.setStartSeq(vpRanges.getStartSeq());
1273 if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme)
1275 view.setBgColour(setUserColourScheme(av.getGlobalColourScheme(),
1279 .getGlobalColourScheme() instanceof jalview.schemes.AnnotationColourGradient)
1281 AnnotationColours ac = constructAnnotationColours(
1282 (jalview.schemes.AnnotationColourGradient) av
1283 .getGlobalColourScheme(),
1286 view.setAnnotationColours(ac);
1287 view.setBgColour("AnnotationColourGradient");
1291 view.setBgColour(ColourSchemeProperty
1292 .getColourName(av.getGlobalColourScheme()));
1295 ResidueShaderI vcs = av.getResidueShading();
1296 ColourSchemeI cs = av.getGlobalColourScheme();
1300 if (vcs.conservationApplied())
1302 view.setConsThreshold(vcs.getConservationInc());
1303 if (cs instanceof jalview.schemes.UserColourScheme)
1305 view.setBgColour(setUserColourScheme(cs, userColours, jms));
1308 view.setPidThreshold(vcs.getThreshold());
1311 view.setConservationSelected(av.getConservationSelected());
1312 view.setPidSelected(av.getAbovePIDThreshold());
1313 view.setFontName(av.font.getName());
1314 view.setFontSize(av.font.getSize());
1315 view.setFontStyle(av.font.getStyle());
1316 view.setScaleProteinAsCdna(av.getViewStyle().isScaleProteinAsCdna());
1317 view.setRenderGaps(av.isRenderGaps());
1318 view.setShowAnnotation(av.isShowAnnotation());
1319 view.setShowBoxes(av.getShowBoxes());
1320 view.setShowColourText(av.getColourText());
1321 view.setShowFullId(av.getShowJVSuffix());
1322 view.setRightAlignIds(av.isRightAlignIds());
1323 view.setShowSequenceFeatures(av.isShowSequenceFeatures());
1324 view.setShowText(av.getShowText());
1325 view.setShowUnconserved(av.getShowUnconserved());
1326 view.setWrapAlignment(av.getWrapAlignment());
1327 view.setTextCol1(av.getTextColour().getRGB());
1328 view.setTextCol2(av.getTextColour2().getRGB());
1329 view.setTextColThreshold(av.getThresholdTextColour());
1330 view.setShowConsensusHistogram(av.isShowConsensusHistogram());
1331 view.setShowSequenceLogo(av.isShowSequenceLogo());
1332 view.setNormaliseSequenceLogo(av.isNormaliseSequenceLogo());
1333 view.setShowGroupConsensus(av.isShowGroupConsensus());
1334 view.setShowGroupConservation(av.isShowGroupConservation());
1335 view.setShowNPfeatureTooltip(av.isShowNPFeats());
1336 view.setShowDbRefTooltip(av.isShowDBRefs());
1337 view.setFollowHighlight(av.isFollowHighlight());
1338 view.setFollowSelection(av.followSelection);
1339 view.setIgnoreGapsinConsensus(av.isIgnoreGapsConsensus());
1340 if (av.getFeaturesDisplayed() != null)
1342 jalview.schemabinding.version2.FeatureSettings fs = new jalview.schemabinding.version2.FeatureSettings();
1344 String[] renderOrder = ap.getSeqPanel().seqCanvas
1345 .getFeatureRenderer().getRenderOrder()
1346 .toArray(new String[0]);
1348 Vector<String> settingsAdded = new Vector<>();
1349 if (renderOrder != null)
1351 for (String featureType : renderOrder)
1353 FeatureColourI fcol = ap.getSeqPanel().seqCanvas
1354 .getFeatureRenderer().getFeatureStyle(featureType);
1355 Setting setting = new Setting();
1356 setting.setType(featureType);
1357 if (!fcol.isSimpleColour())
1359 setting.setColour(fcol.getMaxColour().getRGB());
1360 setting.setMincolour(fcol.getMinColour().getRGB());
1361 setting.setMin(fcol.getMin());
1362 setting.setMax(fcol.getMax());
1363 setting.setColourByLabel(fcol.isColourByLabel());
1364 setting.setAutoScale(fcol.isAutoScaled());
1365 setting.setThreshold(fcol.getThreshold());
1366 // -1 = No threshold, 0 = Below, 1 = Above
1367 setting.setThreshstate(fcol.isAboveThreshold() ? 1
1368 : (fcol.isBelowThreshold() ? 0 : -1));
1372 setting.setColour(fcol.getColour().getRGB());
1376 av.getFeaturesDisplayed().isVisible(featureType));
1377 float rorder = ap.getSeqPanel().seqCanvas.getFeatureRenderer()
1378 .getOrder(featureType);
1381 setting.setOrder(rorder);
1383 fs.addSetting(setting);
1384 settingsAdded.addElement(featureType);
1388 // is groups actually supposed to be a map here ?
1389 Iterator<String> en = ap.getSeqPanel().seqCanvas
1390 .getFeatureRenderer().getFeatureGroups().iterator();
1391 Vector<String> groupsAdded = new Vector<>();
1392 while (en.hasNext())
1394 String grp = en.next();
1395 if (groupsAdded.contains(grp))
1399 Group g = new Group();
1401 g.setDisplay(((Boolean) ap.getSeqPanel().seqCanvas
1402 .getFeatureRenderer().checkGroupVisibility(grp, false))
1405 groupsAdded.addElement(grp);
1407 jms.setFeatureSettings(fs);
1410 if (av.hasHiddenColumns())
1412 jalview.datamodel.HiddenColumns hidden = av.getAlignment()
1413 .getHiddenColumns();
1416 warn("REPORT BUG: avoided null columnselection bug (DMAM reported). Please contact Jim about this.");
1420 ArrayList<int[]> hiddenRegions = hidden.getHiddenColumnsCopy();
1421 for (int[] region : hiddenRegions)
1423 HiddenColumns hc = new HiddenColumns();
1424 hc.setStart(region[0]);
1425 hc.setEnd(region[1]);
1426 view.addHiddenColumns(hc);
1430 if (calcIdSet.size() > 0)
1432 for (String calcId : calcIdSet)
1434 if (calcId.trim().length() > 0)
1436 CalcIdParam cidp = createCalcIdParam(calcId, av);
1437 // Some calcIds have no parameters.
1440 view.addCalcIdParam(cidp);
1446 jms.addViewport(view);
1448 object.setJalviewModelSequence(jms);
1449 object.getVamsasModel().addSequenceSet(vamsasSet);
1451 if (jout != null && fileName != null)
1453 // We may not want to write the object to disk,
1454 // eg we can copy the alignViewport to a new view object
1455 // using save and then load
1458 System.out.println("Writing jar entry " + fileName);
1459 JarEntry entry = new JarEntry(fileName);
1460 jout.putNextEntry(entry);
1461 PrintWriter pout = new PrintWriter(
1462 new OutputStreamWriter(jout, UTF_8));
1463 Marshaller marshaller = new Marshaller(pout);
1464 marshaller.marshal(object);
1467 } catch (Exception ex)
1469 // TODO: raise error in GUI if marshalling failed.
1470 ex.printStackTrace();
1477 * Save any Varna viewers linked to this sequence. Writes an rnaViewer element
1478 * for each viewer, with
1480 * <li>viewer geometry (position, size, split pane divider location)</li>
1481 * <li>index of the selected structure in the viewer (currently shows gapped
1483 * <li>the id of the annotation holding RNA secondary structure</li>
1484 * <li>(currently only one SS is shown per viewer, may be more in future)</li>
1486 * Varna viewer state is also written out (in native Varna XML) to separate
1487 * project jar entries. A separate entry is written for each RNA structure
1488 * displayed, with the naming convention
1490 * <li>rna_viewId_sequenceId_annotationId_[gapped|trimmed]</li>
1498 * @param storeDataset
1500 protected void saveRnaViewers(JarOutputStream jout, JSeq jseq,
1501 final SequenceI jds, List<String> viewIds, AlignmentPanel ap,
1502 boolean storeDataset)
1504 if (Desktop.desktop == null)
1508 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1509 for (int f = frames.length - 1; f > -1; f--)
1511 if (frames[f] instanceof AppVarna)
1513 AppVarna varna = (AppVarna) frames[f];
1515 * link the sequence to every viewer that is showing it and is linked to
1516 * its alignment panel
1518 if (varna.isListeningFor(jds) && ap == varna.getAlignmentPanel())
1520 String viewId = varna.getViewId();
1521 RnaViewer rna = new RnaViewer();
1522 rna.setViewId(viewId);
1523 rna.setTitle(varna.getTitle());
1524 rna.setXpos(varna.getX());
1525 rna.setYpos(varna.getY());
1526 rna.setWidth(varna.getWidth());
1527 rna.setHeight(varna.getHeight());
1528 rna.setDividerLocation(varna.getDividerLocation());
1529 rna.setSelectedRna(varna.getSelectedIndex());
1530 jseq.addRnaViewer(rna);
1533 * Store each Varna panel's state once in the project per sequence.
1534 * First time through only (storeDataset==false)
1536 // boolean storeSessions = false;
1537 // String sequenceViewId = viewId + seqsToIds.get(jds);
1538 // if (!storeDataset && !viewIds.contains(sequenceViewId))
1540 // viewIds.add(sequenceViewId);
1541 // storeSessions = true;
1543 for (RnaModel model : varna.getModels())
1545 if (model.seq == jds)
1548 * VARNA saves each view (sequence or alignment secondary
1549 * structure, gapped or trimmed) as a separate XML file
1551 String jarEntryName = rnaSessions.get(model);
1552 if (jarEntryName == null)
1555 String varnaStateFile = varna.getStateInfo(model.rna);
1556 jarEntryName = RNA_PREFIX + viewId + "_" + nextCounter();
1557 copyFileToJar(jout, varnaStateFile, jarEntryName);
1558 rnaSessions.put(model, jarEntryName);
1560 SecondaryStructure ss = new SecondaryStructure();
1561 String annotationId = varna.getAnnotation(jds).annotationId;
1562 ss.setAnnotationId(annotationId);
1563 ss.setViewerState(jarEntryName);
1564 ss.setGapped(model.gapped);
1565 ss.setTitle(model.title);
1566 rna.addSecondaryStructure(ss);
1575 * Copy the contents of a file to a new entry added to the output jar
1579 * @param jarEntryName
1581 protected void copyFileToJar(JarOutputStream jout, String infilePath,
1582 String jarEntryName)
1584 DataInputStream dis = null;
1587 File file = new File(infilePath);
1588 if (file.exists() && jout != null)
1590 dis = new DataInputStream(new FileInputStream(file));
1591 byte[] data = new byte[(int) file.length()];
1592 dis.readFully(data);
1593 writeJarEntry(jout, jarEntryName, data);
1595 } catch (Exception ex)
1597 ex.printStackTrace();
1605 } catch (IOException e)
1614 * Write the data to a new entry of given name in the output jar file
1617 * @param jarEntryName
1619 * @throws IOException
1621 protected void writeJarEntry(JarOutputStream jout, String jarEntryName,
1622 byte[] data) throws IOException
1626 System.out.println("Writing jar entry " + jarEntryName);
1627 jout.putNextEntry(new JarEntry(jarEntryName));
1628 DataOutputStream dout = new DataOutputStream(jout);
1629 dout.write(data, 0, data.length);
1636 * Save the state of a structure viewer
1641 * the archive XML element under which to save the state
1644 * @param matchedFile
1648 protected String saveStructureState(AlignmentPanel ap, SequenceI jds,
1649 Pdbids pdb, PDBEntry entry, List<String> viewIds,
1650 String matchedFile, StructureViewerBase viewFrame)
1652 final AAStructureBindingModel bindingModel = viewFrame.getBinding();
1655 * Look for any bindings for this viewer to the PDB file of interest
1656 * (including part matches excluding chain id)
1658 for (int peid = 0; peid < bindingModel.getPdbCount(); peid++)
1660 final PDBEntry pdbentry = bindingModel.getPdbEntry(peid);
1661 final String pdbId = pdbentry.getId();
1662 if (!pdbId.equals(entry.getId())
1663 && !(entry.getId().length() > 4 && entry.getId().toLowerCase()
1664 .startsWith(pdbId.toLowerCase())))
1667 * not interested in a binding to a different PDB entry here
1671 if (matchedFile == null)
1673 matchedFile = pdbentry.getFile();
1675 else if (!matchedFile.equals(pdbentry.getFile()))
1678 "Probably lost some PDB-Sequence mappings for this structure file (which apparently has same PDB Entry code): "
1679 + pdbentry.getFile());
1683 // can get at it if the ID
1684 // match is ambiguous (e.g.
1687 for (int smap = 0; smap < viewFrame.getBinding()
1688 .getSequence()[peid].length; smap++)
1690 // if (jal.findIndex(jmol.jmb.sequence[peid][smap]) > -1)
1691 if (jds == viewFrame.getBinding().getSequence()[peid][smap])
1693 StructureState state = new StructureState();
1694 state.setVisible(true);
1695 state.setXpos(viewFrame.getX());
1696 state.setYpos(viewFrame.getY());
1697 state.setWidth(viewFrame.getWidth());
1698 state.setHeight(viewFrame.getHeight());
1699 final String viewId = viewFrame.getViewId();
1700 state.setViewId(viewId);
1701 state.setAlignwithAlignPanel(viewFrame.isUsedforaligment(ap));
1702 state.setColourwithAlignPanel(viewFrame.isUsedforcolourby(ap));
1703 state.setColourByJmol(viewFrame.isColouredByViewer());
1704 state.setType(viewFrame.getViewerType().toString());
1705 pdb.addStructureState(state);
1713 * Populates the AnnotationColours xml for save. This captures the settings of
1714 * the options in the 'Colour by Annotation' dialog.
1717 * @param userColours
1721 private AnnotationColours constructAnnotationColours(
1722 AnnotationColourGradient acg, List<UserColourScheme> userColours,
1723 JalviewModelSequence jms)
1725 AnnotationColours ac = new AnnotationColours();
1726 ac.setAboveThreshold(acg.getAboveThreshold());
1727 ac.setThreshold(acg.getAnnotationThreshold());
1728 // 2.10.2 save annotationId (unique) not annotation label
1729 ac.setAnnotation(acg.getAnnotation().annotationId);
1730 if (acg.getBaseColour() instanceof UserColourScheme)
1733 setUserColourScheme(acg.getBaseColour(), userColours, jms));
1738 ColourSchemeProperty.getColourName(acg.getBaseColour()));
1741 ac.setMaxColour(acg.getMaxColour().getRGB());
1742 ac.setMinColour(acg.getMinColour().getRGB());
1743 ac.setPerSequence(acg.isSeqAssociated());
1744 ac.setPredefinedColours(acg.isPredefinedColours());
1748 private void storeAlignmentAnnotation(AlignmentAnnotation[] aa,
1749 IdentityHashMap<SequenceGroup, String> groupRefs,
1750 AlignmentViewport av, Set<String> calcIdSet, boolean storeDS,
1751 SequenceSet vamsasSet)
1754 for (int i = 0; i < aa.length; i++)
1756 Annotation an = new Annotation();
1758 AlignmentAnnotation annotation = aa[i];
1759 if (annotation.annotationId != null)
1761 annotationIds.put(annotation.annotationId, annotation);
1764 an.setId(annotation.annotationId);
1766 an.setVisible(annotation.visible);
1768 an.setDescription(annotation.description);
1770 if (annotation.sequenceRef != null)
1772 // 2.9 JAL-1781 xref on sequence id rather than name
1773 an.setSequenceRef(seqsToIds.get(annotation.sequenceRef));
1775 if (annotation.groupRef != null)
1777 String groupIdr = groupRefs.get(annotation.groupRef);
1778 if (groupIdr == null)
1780 // make a locally unique String
1781 groupRefs.put(annotation.groupRef,
1782 groupIdr = ("" + System.currentTimeMillis()
1783 + annotation.groupRef.getName()
1784 + groupRefs.size()));
1786 an.setGroupRef(groupIdr.toString());
1789 // store all visualization attributes for annotation
1790 an.setGraphHeight(annotation.graphHeight);
1791 an.setCentreColLabels(annotation.centreColLabels);
1792 an.setScaleColLabels(annotation.scaleColLabel);
1793 an.setShowAllColLabels(annotation.showAllColLabels);
1794 an.setBelowAlignment(annotation.belowAlignment);
1796 if (annotation.graph > 0)
1799 an.setGraphType(annotation.graph);
1800 an.setGraphGroup(annotation.graphGroup);
1801 if (annotation.getThreshold() != null)
1803 ThresholdLine line = new ThresholdLine();
1804 line.setLabel(annotation.getThreshold().label);
1805 line.setValue(annotation.getThreshold().value);
1806 line.setColour(annotation.getThreshold().colour.getRGB());
1807 an.setThresholdLine(line);
1815 an.setLabel(annotation.label);
1817 if (annotation == av.getAlignmentQualityAnnot()
1818 || annotation == av.getAlignmentConservationAnnotation()
1819 || annotation == av.getAlignmentConsensusAnnotation()
1820 || annotation.autoCalculated)
1822 // new way of indicating autocalculated annotation -
1823 an.setAutoCalculated(annotation.autoCalculated);
1825 if (annotation.hasScore())
1827 an.setScore(annotation.getScore());
1830 if (annotation.getCalcId() != null)
1832 calcIdSet.add(annotation.getCalcId());
1833 an.setCalcId(annotation.getCalcId());
1835 if (annotation.hasProperties())
1837 for (String pr : annotation.getProperties())
1839 Property prop = new Property();
1841 prop.setValue(annotation.getProperty(pr));
1842 an.addProperty(prop);
1846 AnnotationElement ae;
1847 if (annotation.annotations != null)
1849 an.setScoreOnly(false);
1850 for (int a = 0; a < annotation.annotations.length; a++)
1852 if ((annotation == null) || (annotation.annotations[a] == null))
1857 ae = new AnnotationElement();
1858 if (annotation.annotations[a].description != null)
1860 ae.setDescription(annotation.annotations[a].description);
1862 if (annotation.annotations[a].displayCharacter != null)
1864 ae.setDisplayCharacter(
1865 annotation.annotations[a].displayCharacter);
1868 if (!Float.isNaN(annotation.annotations[a].value))
1870 ae.setValue(annotation.annotations[a].value);
1874 if (annotation.annotations[a].secondaryStructure > ' ')
1876 ae.setSecondaryStructure(
1877 annotation.annotations[a].secondaryStructure + "");
1880 if (annotation.annotations[a].colour != null
1881 && annotation.annotations[a].colour != java.awt.Color.black)
1883 ae.setColour(annotation.annotations[a].colour.getRGB());
1886 an.addAnnotationElement(ae);
1887 if (annotation.autoCalculated)
1889 // only write one non-null entry into the annotation row -
1890 // sufficient to get the visualization attributes necessary to
1898 an.setScoreOnly(true);
1900 if (!storeDS || (storeDS && !annotation.autoCalculated))
1902 // skip autocalculated annotation - these are only provided for
1904 vamsasSet.addAnnotation(an);
1910 private CalcIdParam createCalcIdParam(String calcId, AlignViewport av)
1912 AutoCalcSetting settings = av.getCalcIdSettingsFor(calcId);
1913 if (settings != null)
1915 CalcIdParam vCalcIdParam = new CalcIdParam();
1916 vCalcIdParam.setCalcId(calcId);
1917 vCalcIdParam.addServiceURL(settings.getServiceURI());
1918 // generic URI allowing a third party to resolve another instance of the
1919 // service used for this calculation
1920 for (String urls : settings.getServiceURLs())
1922 vCalcIdParam.addServiceURL(urls);
1924 vCalcIdParam.setVersion("1.0");
1925 if (settings.getPreset() != null)
1927 WsParamSetI setting = settings.getPreset();
1928 vCalcIdParam.setName(setting.getName());
1929 vCalcIdParam.setDescription(setting.getDescription());
1933 vCalcIdParam.setName("");
1934 vCalcIdParam.setDescription("Last used parameters");
1936 // need to be able to recover 1) settings 2) user-defined presets or
1937 // recreate settings from preset 3) predefined settings provided by
1938 // service - or settings that can be transferred (or discarded)
1939 vCalcIdParam.setParameters(
1940 settings.getWsParamFile().replace("\n", "|\\n|"));
1941 vCalcIdParam.setAutoUpdate(settings.isAutoUpdate());
1942 // todo - decide if updateImmediately is needed for any projects.
1944 return vCalcIdParam;
1949 private boolean recoverCalcIdParam(CalcIdParam calcIdParam,
1952 if (calcIdParam.getVersion().equals("1.0"))
1954 Jws2Instance service = Jws2Discoverer.getDiscoverer()
1955 .getPreferredServiceFor(calcIdParam.getServiceURL());
1956 if (service != null)
1958 WsParamSetI parmSet = null;
1961 parmSet = service.getParamStore().parseServiceParameterFile(
1962 calcIdParam.getName(), calcIdParam.getDescription(),
1963 calcIdParam.getServiceURL(),
1964 calcIdParam.getParameters().replace("|\\n|", "\n"));
1965 } catch (IOException x)
1967 warn("Couldn't parse parameter data for "
1968 + calcIdParam.getCalcId(), x);
1971 List<ArgumentI> argList = null;
1972 if (calcIdParam.getName().length() > 0)
1974 parmSet = service.getParamStore()
1975 .getPreset(calcIdParam.getName());
1976 if (parmSet != null)
1978 // TODO : check we have a good match with settings in AACon -
1979 // otherwise we'll need to create a new preset
1984 argList = parmSet.getArguments();
1987 AAConSettings settings = new AAConSettings(
1988 calcIdParam.isAutoUpdate(), service, parmSet, argList);
1989 av.setCalcIdSettingsFor(calcIdParam.getCalcId(), settings,
1990 calcIdParam.isNeedsUpdate());
1995 warn("Cannot resolve a service for the parameters used in this project. Try configuring a JABAWS server.");
1999 throw new Error(MessageManager.formatMessage(
2000 "error.unsupported_version_calcIdparam", new Object[]
2001 { calcIdParam.toString() }));
2005 * External mapping between jalview objects and objects yielding a valid and
2006 * unique object ID string. This is null for normal Jalview project IO, but
2007 * non-null when a jalview project is being read or written as part of a
2010 IdentityHashMap jv2vobj = null;
2013 * Construct a unique ID for jvobj using either existing bindings or if none
2014 * exist, the result of the hashcode call for the object.
2017 * jalview data object
2018 * @return unique ID for referring to jvobj
2020 private String makeHashCode(Object jvobj, String altCode)
2022 if (jv2vobj != null)
2024 Object id = jv2vobj.get(jvobj);
2027 return id.toString();
2029 // check string ID mappings
2030 if (jvids2vobj != null && jvobj instanceof String)
2032 id = jvids2vobj.get(jvobj);
2036 return id.toString();
2038 // give up and warn that something has gone wrong
2039 warn("Cannot find ID for object in external mapping : " + jvobj);
2045 * return local jalview object mapped to ID, if it exists
2049 * @return null or object bound to idcode
2051 private Object retrieveExistingObj(String idcode)
2053 if (idcode != null && vobj2jv != null)
2055 return vobj2jv.get(idcode);
2061 * binding from ID strings from external mapping table to jalview data model
2064 private Hashtable vobj2jv;
2066 private Sequence createVamsasSequence(String id, SequenceI jds)
2068 return createVamsasSequence(true, id, jds, null);
2071 private Sequence createVamsasSequence(boolean recurse, String id,
2072 SequenceI jds, SequenceI parentseq)
2074 Sequence vamsasSeq = new Sequence();
2075 vamsasSeq.setId(id);
2076 vamsasSeq.setName(jds.getName());
2077 vamsasSeq.setSequence(jds.getSequenceAsString());
2078 vamsasSeq.setDescription(jds.getDescription());
2079 jalview.datamodel.DBRefEntry[] dbrefs = null;
2080 if (jds.getDatasetSequence() != null)
2082 vamsasSeq.setDsseqid(seqHash(jds.getDatasetSequence()));
2086 // seqId==dsseqid so we can tell which sequences really are
2087 // dataset sequences only
2088 vamsasSeq.setDsseqid(id);
2089 dbrefs = jds.getDBRefs();
2090 if (parentseq == null)
2097 for (int d = 0; d < dbrefs.length; d++)
2099 DBRef dbref = new DBRef();
2100 dbref.setSource(dbrefs[d].getSource());
2101 dbref.setVersion(dbrefs[d].getVersion());
2102 dbref.setAccessionId(dbrefs[d].getAccessionId());
2103 if (dbrefs[d].hasMap())
2105 Mapping mp = createVamsasMapping(dbrefs[d].getMap(), parentseq,
2107 dbref.setMapping(mp);
2109 vamsasSeq.addDBRef(dbref);
2115 private Mapping createVamsasMapping(jalview.datamodel.Mapping jmp,
2116 SequenceI parentseq, SequenceI jds, boolean recurse)
2119 if (jmp.getMap() != null)
2123 jalview.util.MapList mlst = jmp.getMap();
2124 List<int[]> r = mlst.getFromRanges();
2125 for (int[] range : r)
2127 MapListFrom mfrom = new MapListFrom();
2128 mfrom.setStart(range[0]);
2129 mfrom.setEnd(range[1]);
2130 mp.addMapListFrom(mfrom);
2132 r = mlst.getToRanges();
2133 for (int[] range : r)
2135 MapListTo mto = new MapListTo();
2136 mto.setStart(range[0]);
2137 mto.setEnd(range[1]);
2138 mp.addMapListTo(mto);
2140 mp.setMapFromUnit(mlst.getFromRatio());
2141 mp.setMapToUnit(mlst.getToRatio());
2142 if (jmp.getTo() != null)
2144 MappingChoice mpc = new MappingChoice();
2146 // check/create ID for the sequence referenced by getTo()
2149 SequenceI ps = null;
2150 if (parentseq != jmp.getTo()
2151 && parentseq.getDatasetSequence() != jmp.getTo())
2153 // chaining dbref rather than a handshaking one
2154 jmpid = seqHash(ps = jmp.getTo());
2158 jmpid = seqHash(ps = parentseq);
2160 mpc.setDseqFor(jmpid);
2161 if (!seqRefIds.containsKey(mpc.getDseqFor()))
2163 jalview.bin.Cache.log.debug("creatign new DseqFor ID");
2164 seqRefIds.put(mpc.getDseqFor(), ps);
2168 jalview.bin.Cache.log.debug("reusing DseqFor ID");
2171 mp.setMappingChoice(mpc);
2177 String setUserColourScheme(jalview.schemes.ColourSchemeI cs,
2178 List<UserColourScheme> userColours, JalviewModelSequence jms)
2181 jalview.schemes.UserColourScheme ucs = (jalview.schemes.UserColourScheme) cs;
2182 boolean newucs = false;
2183 if (!userColours.contains(ucs))
2185 userColours.add(ucs);
2188 id = "ucs" + userColours.indexOf(ucs);
2191 // actually create the scheme's entry in the XML model
2192 java.awt.Color[] colours = ucs.getColours();
2193 jalview.schemabinding.version2.UserColours uc = new jalview.schemabinding.version2.UserColours();
2194 jalview.schemabinding.version2.UserColourScheme jbucs = new jalview.schemabinding.version2.UserColourScheme();
2196 for (int i = 0; i < colours.length; i++)
2198 jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();
2199 col.setName(ResidueProperties.aa[i]);
2200 col.setRGB(jalview.util.Format.getHexString(colours[i]));
2201 jbucs.addColour(col);
2203 if (ucs.getLowerCaseColours() != null)
2205 colours = ucs.getLowerCaseColours();
2206 for (int i = 0; i < colours.length; i++)
2208 jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();
2209 col.setName(ResidueProperties.aa[i].toLowerCase());
2210 col.setRGB(jalview.util.Format.getHexString(colours[i]));
2211 jbucs.addColour(col);
2216 uc.setUserColourScheme(jbucs);
2217 jms.addUserColours(uc);
2223 jalview.schemes.UserColourScheme getUserColourScheme(
2224 JalviewModelSequence jms, String id)
2226 UserColours[] uc = jms.getUserColours();
2227 UserColours colours = null;
2229 for (int i = 0; i < uc.length; i++)
2231 if (uc[i].getId().equals(id))
2239 java.awt.Color[] newColours = new java.awt.Color[24];
2241 for (int i = 0; i < 24; i++)
2243 newColours[i] = new java.awt.Color(Integer.parseInt(
2244 colours.getUserColourScheme().getColour(i).getRGB(), 16));
2247 jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(
2250 if (colours.getUserColourScheme().getColourCount() > 24)
2252 newColours = new java.awt.Color[23];
2253 for (int i = 0; i < 23; i++)
2255 newColours[i] = new java.awt.Color(Integer.parseInt(
2256 colours.getUserColourScheme().getColour(i + 24).getRGB(),
2259 ucs.setLowerCaseColours(newColours);
2266 * contains last error message (if any) encountered by XML loader.
2268 String errorMessage = null;
2271 * flag to control whether the Jalview2XML_V1 parser should be deferred to if
2272 * exceptions are raised during project XML parsing
2274 public boolean attemptversion1parse = true;
2277 * Load a jalview project archive from a jar file
2280 * - HTTP URL or filename
2282 public AlignFrame loadJalviewAlign(final String file)
2285 jalview.gui.AlignFrame af = null;
2289 // create list to store references for any new Jmol viewers created
2290 newStructureViewers = new Vector<>();
2291 // UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
2292 // Workaround is to make sure caller implements the JarInputStreamProvider
2294 // so we can re-open the jar input stream for each entry.
2296 jarInputStreamProvider jprovider = createjarInputStreamProvider(file);
2297 af = loadJalviewAlign(jprovider);
2299 } catch (MalformedURLException e)
2301 errorMessage = "Invalid URL format for '" + file + "'";
2307 SwingUtilities.invokeAndWait(new Runnable()
2312 setLoadingFinishedForNewStructureViewers();
2315 } catch (Exception x)
2317 System.err.println("Error loading alignment: " + x.getMessage());
2323 private jarInputStreamProvider createjarInputStreamProvider(
2324 final String file) throws MalformedURLException
2327 errorMessage = null;
2328 uniqueSetSuffix = null;
2330 viewportsAdded.clear();
2331 frefedSequence = null;
2333 if (file.startsWith("http://"))
2335 url = new URL(file);
2337 final URL _url = url;
2338 return new jarInputStreamProvider()
2342 public JarInputStream getJarInputStream() throws IOException
2346 return new JarInputStream(_url.openStream());
2350 return new JarInputStream(new FileInputStream(file));
2355 public String getFilename()
2363 * Recover jalview session from a jalview project archive. Caller may
2364 * initialise uniqueSetSuffix, seqRefIds, viewportsAdded and frefedSequence
2365 * themselves. Any null fields will be initialised with default values,
2366 * non-null fields are left alone.
2371 public AlignFrame loadJalviewAlign(final jarInputStreamProvider jprovider)
2373 errorMessage = null;
2374 if (uniqueSetSuffix == null)
2376 uniqueSetSuffix = System.currentTimeMillis() % 100000 + "";
2378 if (seqRefIds == null)
2382 AlignFrame af = null, _af = null;
2383 IdentityHashMap<AlignmentI, AlignmentI> importedDatasets = new IdentityHashMap<>();
2384 Map<String, AlignFrame> gatherToThisFrame = new HashMap<>();
2385 final String file = jprovider.getFilename();
2388 JarInputStream jin = null;
2389 JarEntry jarentry = null;
2394 jin = jprovider.getJarInputStream();
2395 for (int i = 0; i < entryCount; i++)
2397 jarentry = jin.getNextJarEntry();
2400 if (jarentry != null && jarentry.getName().endsWith(".xml"))
2402 InputStreamReader in = new InputStreamReader(jin, UTF_8);
2403 JalviewModel object = new JalviewModel();
2405 Unmarshaller unmar = new Unmarshaller(object);
2406 unmar.setValidation(false);
2407 object = (JalviewModel) unmar.unmarshal(in);
2408 if (true) // !skipViewport(object))
2410 _af = loadFromObject(object, file, true, jprovider);
2411 if (_af != null && object.getJalviewModelSequence()
2412 .getViewportCount() > 0)
2416 // store a reference to the first view
2419 if (_af.viewport.isGatherViewsHere())
2421 // if this is a gathered view, keep its reference since
2422 // after gathering views, only this frame will remain
2424 gatherToThisFrame.put(_af.viewport.getSequenceSetId(), _af);
2426 // Save dataset to register mappings once all resolved
2427 importedDatasets.put(af.viewport.getAlignment().getDataset(),
2428 af.viewport.getAlignment().getDataset());
2433 else if (jarentry != null)
2435 // Some other file here.
2438 } while (jarentry != null);
2439 resolveFrefedSequences();
2440 } catch (IOException ex)
2442 ex.printStackTrace();
2443 errorMessage = "Couldn't locate Jalview XML file : " + file;
2445 "Exception whilst loading jalview XML file : " + ex + "\n");
2446 } catch (Exception ex)
2448 System.err.println("Parsing as Jalview Version 2 file failed.");
2449 ex.printStackTrace(System.err);
2450 if (attemptversion1parse)
2452 // Is Version 1 Jar file?
2455 af = new Jalview2XML_V1(raiseGUI).LoadJalviewAlign(jprovider);
2456 } catch (Exception ex2)
2458 System.err.println("Exception whilst loading as jalviewXMLV1:");
2459 ex2.printStackTrace();
2463 if (Desktop.instance != null)
2465 Desktop.instance.stopLoading();
2469 System.out.println("Successfully loaded archive file");
2472 ex.printStackTrace();
2475 "Exception whilst loading jalview XML file : " + ex + "\n");
2476 } catch (OutOfMemoryError e)
2478 // Don't use the OOM Window here
2479 errorMessage = "Out of memory loading jalview XML file";
2480 System.err.println("Out of memory whilst loading jalview XML file");
2481 e.printStackTrace();
2485 * Regather multiple views (with the same sequence set id) to the frame (if
2486 * any) that is flagged as the one to gather to, i.e. convert them to tabbed
2487 * views instead of separate frames. Note this doesn't restore a state where
2488 * some expanded views in turn have tabbed views - the last "first tab" read
2489 * in will play the role of gatherer for all.
2491 for (AlignFrame fr : gatherToThisFrame.values())
2493 Desktop.instance.gatherViews(fr);
2496 restoreSplitFrames();
2497 for (AlignmentI ds : importedDatasets.keySet())
2499 if (ds.getCodonFrames() != null)
2501 StructureSelectionManager
2502 .getStructureSelectionManager(Desktop.instance)
2503 .registerMappings(ds.getCodonFrames());
2506 if (errorMessage != null)
2511 if (Desktop.instance != null)
2513 Desktop.instance.stopLoading();
2520 * Try to reconstruct and display SplitFrame windows, where each contains
2521 * complementary dna and protein alignments. Done by pairing up AlignFrame
2522 * objects (created earlier) which have complementary viewport ids associated.
2524 protected void restoreSplitFrames()
2526 List<SplitFrame> gatherTo = new ArrayList<>();
2527 List<AlignFrame> addedToSplitFrames = new ArrayList<>();
2528 Map<String, AlignFrame> dna = new HashMap<>();
2531 * Identify the DNA alignments
2533 for (Entry<Viewport, AlignFrame> candidate : splitFrameCandidates
2536 AlignFrame af = candidate.getValue();
2537 if (af.getViewport().getAlignment().isNucleotide())
2539 dna.put(candidate.getKey().getId(), af);
2544 * Try to match up the protein complements
2546 for (Entry<Viewport, AlignFrame> candidate : splitFrameCandidates
2549 AlignFrame af = candidate.getValue();
2550 if (!af.getViewport().getAlignment().isNucleotide())
2552 String complementId = candidate.getKey().getComplementId();
2553 // only non-null complements should be in the Map
2554 if (complementId != null && dna.containsKey(complementId))
2556 final AlignFrame dnaFrame = dna.get(complementId);
2557 SplitFrame sf = createSplitFrame(dnaFrame, af);
2558 addedToSplitFrames.add(dnaFrame);
2559 addedToSplitFrames.add(af);
2560 dnaFrame.setMenusForViewport();
2561 af.setMenusForViewport();
2562 if (af.viewport.isGatherViewsHere())
2571 * Open any that we failed to pair up (which shouldn't happen!) as
2572 * standalone AlignFrame's.
2574 for (Entry<Viewport, AlignFrame> candidate : splitFrameCandidates
2577 AlignFrame af = candidate.getValue();
2578 if (!addedToSplitFrames.contains(af))
2580 Viewport view = candidate.getKey();
2581 Desktop.addInternalFrame(af, view.getTitle(), view.getWidth(),
2583 af.setMenusForViewport();
2584 System.err.println("Failed to restore view " + view.getTitle()
2585 + " to split frame");
2590 * Gather back into tabbed views as flagged.
2592 for (SplitFrame sf : gatherTo)
2594 Desktop.instance.gatherViews(sf);
2597 splitFrameCandidates.clear();
2601 * Construct and display one SplitFrame holding DNA and protein alignments.
2604 * @param proteinFrame
2607 protected SplitFrame createSplitFrame(AlignFrame dnaFrame,
2608 AlignFrame proteinFrame)
2610 SplitFrame splitFrame = new SplitFrame(dnaFrame, proteinFrame);
2611 String title = MessageManager.getString("label.linked_view_title");
2612 int width = (int) dnaFrame.getBounds().getWidth();
2613 int height = (int) (dnaFrame.getBounds().getHeight()
2614 + proteinFrame.getBounds().getHeight() + 50);
2617 * SplitFrame location is saved to both enclosed frames
2619 splitFrame.setLocation(dnaFrame.getX(), dnaFrame.getY());
2620 Desktop.addInternalFrame(splitFrame, title, width, height);
2623 * And compute cDNA consensus (couldn't do earlier with consensus as
2624 * mappings were not yet present)
2626 proteinFrame.viewport.alignmentChanged(proteinFrame.alignPanel);
2632 * check errorMessage for a valid error message and raise an error box in the
2633 * GUI or write the current errorMessage to stderr and then clear the error
2636 protected void reportErrors()
2638 reportErrors(false);
2641 protected void reportErrors(final boolean saving)
2643 if (errorMessage != null)
2645 final String finalErrorMessage = errorMessage;
2648 javax.swing.SwingUtilities.invokeLater(new Runnable()
2653 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
2655 "Error " + (saving ? "saving" : "loading")
2657 JvOptionPane.WARNING_MESSAGE);
2663 System.err.println("Problem loading Jalview file: " + errorMessage);
2666 errorMessage = null;
2669 Map<String, String> alreadyLoadedPDB = new HashMap<>();
2672 * when set, local views will be updated from view stored in JalviewXML
2673 * Currently (28th Sep 2008) things will go horribly wrong in vamsas document
2674 * sync if this is set to true.
2676 private final boolean updateLocalViews = false;
2679 * Returns the path to a temporary file holding the PDB file for the given PDB
2680 * id. The first time of asking, searches for a file of that name in the
2681 * Jalview project jar, and copies it to a new temporary file. Any repeat
2682 * requests just return the path to the file previously created.
2688 String loadPDBFile(jarInputStreamProvider jprovider, String pdbId,
2691 if (alreadyLoadedPDB.containsKey(pdbId))
2693 return alreadyLoadedPDB.get(pdbId).toString();
2696 String tempFile = copyJarEntry(jprovider, pdbId, "jalview_pdb",
2698 if (tempFile != null)
2700 alreadyLoadedPDB.put(pdbId, tempFile);
2706 * Copies the jar entry of given name to a new temporary file and returns the
2707 * path to the file, or null if the entry is not found.
2710 * @param jarEntryName
2712 * a prefix for the temporary file name, must be at least three
2715 * null or original file - so new file can be given the same suffix
2719 protected String copyJarEntry(jarInputStreamProvider jprovider,
2720 String jarEntryName, String prefix, String origFile)
2722 BufferedReader in = null;
2723 PrintWriter out = null;
2724 String suffix = ".tmp";
2725 if (origFile == null)
2727 origFile = jarEntryName;
2729 int sfpos = origFile.lastIndexOf(".");
2730 if (sfpos > -1 && sfpos < (origFile.length() - 3))
2732 suffix = "." + origFile.substring(sfpos + 1);
2736 JarInputStream jin = jprovider.getJarInputStream();
2738 * if (jprovider.startsWith("http://")) { jin = new JarInputStream(new
2739 * URL(jprovider).openStream()); } else { jin = new JarInputStream(new
2740 * FileInputStream(jprovider)); }
2743 JarEntry entry = null;
2746 entry = jin.getNextJarEntry();
2747 } while (entry != null && !entry.getName().equals(jarEntryName));
2750 in = new BufferedReader(new InputStreamReader(jin, UTF_8));
2751 File outFile = File.createTempFile(prefix, suffix);
2752 outFile.deleteOnExit();
2753 out = new PrintWriter(new FileOutputStream(outFile));
2756 while ((data = in.readLine()) != null)
2761 String t = outFile.getAbsolutePath();
2766 warn("Couldn't find entry in Jalview Jar for " + jarEntryName);
2768 } catch (Exception ex)
2770 ex.printStackTrace();
2778 } catch (IOException e)
2792 private class JvAnnotRow
2794 public JvAnnotRow(int i, AlignmentAnnotation jaa)
2801 * persisted version of annotation row from which to take vis properties
2803 public jalview.datamodel.AlignmentAnnotation template;
2806 * original position of the annotation row in the alignment
2812 * Load alignment frame from jalview XML DOM object
2817 * filename source string
2818 * @param loadTreesAndStructures
2819 * when false only create Viewport
2821 * data source provider
2822 * @return alignment frame created from view stored in DOM
2824 AlignFrame loadFromObject(JalviewModel object, String file,
2825 boolean loadTreesAndStructures, jarInputStreamProvider jprovider)
2827 SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);
2828 Sequence[] vamsasSeq = vamsasSet.getSequence();
2830 JalviewModelSequence jms = object.getJalviewModelSequence();
2832 Viewport view = (jms.getViewportCount() > 0) ? jms.getViewport(0)
2835 // ////////////////////////////////
2838 List<SequenceI> hiddenSeqs = null;
2840 List<SequenceI> tmpseqs = new ArrayList<>();
2842 boolean multipleView = false;
2843 SequenceI referenceseqForView = null;
2844 JSeq[] jseqs = object.getJalviewModelSequence().getJSeq();
2845 int vi = 0; // counter in vamsasSeq array
2846 for (int i = 0; i < jseqs.length; i++)
2848 String seqId = jseqs[i].getId();
2850 SequenceI tmpSeq = seqRefIds.get(seqId);
2853 if (!incompleteSeqs.containsKey(seqId))
2855 // may not need this check, but keep it for at least 2.9,1 release
2856 if (tmpSeq.getStart() != jseqs[i].getStart()
2857 || tmpSeq.getEnd() != jseqs[i].getEnd())
2860 "Warning JAL-2154 regression: updating start/end for sequence "
2861 + tmpSeq.toString() + " to " + jseqs[i]);
2866 incompleteSeqs.remove(seqId);
2868 if (vamsasSeq.length > vi && vamsasSeq[vi].getId().equals(seqId))
2870 // most likely we are reading a dataset XML document so
2871 // update from vamsasSeq section of XML for this sequence
2872 tmpSeq.setName(vamsasSeq[vi].getName());
2873 tmpSeq.setDescription(vamsasSeq[vi].getDescription());
2874 tmpSeq.setSequence(vamsasSeq[vi].getSequence());
2879 // reading multiple views, so vamsasSeq set is a subset of JSeq
2880 multipleView = true;
2882 tmpSeq.setStart(jseqs[i].getStart());
2883 tmpSeq.setEnd(jseqs[i].getEnd());
2884 tmpseqs.add(tmpSeq);
2888 tmpSeq = new jalview.datamodel.Sequence(vamsasSeq[vi].getName(),
2889 vamsasSeq[vi].getSequence());
2890 tmpSeq.setDescription(vamsasSeq[vi].getDescription());
2891 tmpSeq.setStart(jseqs[i].getStart());
2892 tmpSeq.setEnd(jseqs[i].getEnd());
2893 tmpSeq.setVamsasId(uniqueSetSuffix + seqId);
2894 seqRefIds.put(vamsasSeq[vi].getId(), tmpSeq);
2895 tmpseqs.add(tmpSeq);
2899 if (jseqs[i].hasViewreference() && jseqs[i].getViewreference())
2901 referenceseqForView = tmpseqs.get(tmpseqs.size() - 1);
2904 if (jseqs[i].getHidden())
2906 if (hiddenSeqs == null)
2908 hiddenSeqs = new ArrayList<>();
2911 hiddenSeqs.add(tmpSeq);
2916 // Create the alignment object from the sequence set
2917 // ///////////////////////////////
2918 SequenceI[] orderedSeqs = tmpseqs
2919 .toArray(new SequenceI[tmpseqs.size()]);
2921 AlignmentI al = null;
2922 // so we must create or recover the dataset alignment before going further
2923 // ///////////////////////////////
2924 if (vamsasSet.getDatasetId() == null || vamsasSet.getDatasetId() == "")
2926 // older jalview projects do not have a dataset - so creat alignment and
2928 al = new Alignment(orderedSeqs);
2929 al.setDataset(null);
2933 boolean isdsal = object.getJalviewModelSequence()
2934 .getViewportCount() == 0;
2937 // we are importing a dataset record, so
2938 // recover reference to an alignment already materialsed as dataset
2939 al = getDatasetFor(vamsasSet.getDatasetId());
2943 // materialse the alignment
2944 al = new Alignment(orderedSeqs);
2948 addDatasetRef(vamsasSet.getDatasetId(), al);
2951 // finally, verify all data in vamsasSet is actually present in al
2952 // passing on flag indicating if it is actually a stored dataset
2953 recoverDatasetFor(vamsasSet, al, isdsal);
2956 if (referenceseqForView != null)
2958 al.setSeqrep(referenceseqForView);
2960 // / Add the alignment properties
2961 for (int i = 0; i < vamsasSet.getSequenceSetPropertiesCount(); i++)
2963 SequenceSetProperties ssp = vamsasSet.getSequenceSetProperties(i);
2964 al.setProperty(ssp.getKey(), ssp.getValue());
2967 // ///////////////////////////////
2969 Hashtable pdbloaded = new Hashtable(); // TODO nothing writes to this??
2972 // load sequence features, database references and any associated PDB
2973 // structures for the alignment
2975 // prior to 2.10, this part would only be executed the first time a
2976 // sequence was encountered, but not afterwards.
2977 // now, for 2.10 projects, this is also done if the xml doc includes
2978 // dataset sequences not actually present in any particular view.
2980 for (int i = 0; i < vamsasSeq.length; i++)
2982 if (jseqs[i].getFeaturesCount() > 0)
2984 Features[] features = jseqs[i].getFeatures();
2985 for (int f = 0; f < features.length; f++)
2987 SequenceFeature sf = new SequenceFeature(features[f].getType(),
2988 features[f].getDescription(), features[f].getBegin(),
2989 features[f].getEnd(), features[f].getScore(),
2990 features[f].getFeatureGroup());
2991 sf.setStatus(features[f].getStatus());
2992 for (int od = 0; od < features[f].getOtherDataCount(); od++)
2994 OtherData keyValue = features[f].getOtherData(od);
2995 if (keyValue.getKey().startsWith("LINK"))
2997 sf.addLink(keyValue.getValue());
3001 sf.setValue(keyValue.getKey(), keyValue.getValue());
3005 // adds feature to datasequence's feature set (since Jalview 2.10)
3006 al.getSequenceAt(i).addSequenceFeature(sf);
3009 if (vamsasSeq[i].getDBRefCount() > 0)
3011 // adds dbrefs to datasequence's set (since Jalview 2.10)
3013 al.getSequenceAt(i).getDatasetSequence() == null
3014 ? al.getSequenceAt(i)
3015 : al.getSequenceAt(i).getDatasetSequence(),
3018 if (jseqs[i].getPdbidsCount() > 0)
3020 Pdbids[] ids = jseqs[i].getPdbids();
3021 for (int p = 0; p < ids.length; p++)
3023 jalview.datamodel.PDBEntry entry = new jalview.datamodel.PDBEntry();
3024 entry.setId(ids[p].getId());
3025 if (ids[p].getType() != null)
3027 if (PDBEntry.Type.getType(ids[p].getType()) != null)
3029 entry.setType(PDBEntry.Type.getType(ids[p].getType()));
3033 entry.setType(PDBEntry.Type.FILE);
3036 // jprovider is null when executing 'New View'
3037 if (ids[p].getFile() != null && jprovider != null)
3039 if (!pdbloaded.containsKey(ids[p].getFile()))
3041 entry.setFile(loadPDBFile(jprovider, ids[p].getId(),
3046 entry.setFile(pdbloaded.get(ids[p].getId()).toString());
3049 if (ids[p].getPdbentryItem() != null)
3051 for (PdbentryItem item : ids[p].getPdbentryItem())
3053 for (Property pr : item.getProperty())
3055 entry.setProperty(pr.getName(), pr.getValue());
3059 StructureSelectionManager
3060 .getStructureSelectionManager(Desktop.instance)
3061 .registerPDBEntry(entry);
3062 // adds PDBEntry to datasequence's set (since Jalview 2.10)
3063 if (al.getSequenceAt(i).getDatasetSequence() != null)
3065 al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
3069 al.getSequenceAt(i).addPDBId(entry);
3074 } // end !multipleview
3076 // ///////////////////////////////
3077 // LOAD SEQUENCE MAPPINGS
3079 if (vamsasSet.getAlcodonFrameCount() > 0)
3081 // TODO Potentially this should only be done once for all views of an
3083 AlcodonFrame[] alc = vamsasSet.getAlcodonFrame();
3084 for (int i = 0; i < alc.length; i++)
3086 AlignedCodonFrame cf = new AlignedCodonFrame();
3087 if (alc[i].getAlcodMapCount() > 0)
3089 AlcodMap[] maps = alc[i].getAlcodMap();
3090 for (int m = 0; m < maps.length; m++)
3092 SequenceI dnaseq = seqRefIds.get(maps[m].getDnasq());
3094 jalview.datamodel.Mapping mapping = null;
3095 // attach to dna sequence reference.
3096 if (maps[m].getMapping() != null)
3098 mapping = addMapping(maps[m].getMapping());
3099 if (dnaseq != null && mapping.getTo() != null)
3101 cf.addMap(dnaseq, mapping.getTo(), mapping.getMap());
3107 newAlcodMapRef(maps[m].getDnasq(), cf, mapping));
3111 al.addCodonFrame(cf);
3116 // ////////////////////////////////
3118 List<JvAnnotRow> autoAlan = new ArrayList<>();
3121 * store any annotations which forward reference a group's ID
3123 Map<String, List<AlignmentAnnotation>> groupAnnotRefs = new Hashtable<>();
3125 if (vamsasSet.getAnnotationCount() > 0)
3127 Annotation[] an = vamsasSet.getAnnotation();
3129 for (int i = 0; i < an.length; i++)
3131 Annotation annotation = an[i];
3134 * test if annotation is automatically calculated for this view only
3136 boolean autoForView = false;
3137 if (annotation.getLabel().equals("Quality")
3138 || annotation.getLabel().equals("Conservation")
3139 || annotation.getLabel().equals("Consensus"))
3141 // Kludge for pre 2.5 projects which lacked the autocalculated flag
3143 if (!annotation.hasAutoCalculated())
3145 annotation.setAutoCalculated(true);
3148 if (autoForView || (annotation.hasAutoCalculated()
3149 && annotation.isAutoCalculated()))
3151 // remove ID - we don't recover annotation from other views for
3152 // view-specific annotation
3153 annotation.setId(null);
3156 // set visiblity for other annotation in this view
3157 String annotationId = annotation.getId();
3158 if (annotationId != null && annotationIds.containsKey(annotationId))
3160 AlignmentAnnotation jda = annotationIds.get(annotationId);
3161 // in principle Visible should always be true for annotation displayed
3162 // in multiple views
3163 if (annotation.hasVisible())
3165 jda.visible = annotation.getVisible();
3168 al.addAnnotation(jda);
3172 // Construct new annotation from model.
3173 AnnotationElement[] ae = annotation.getAnnotationElement();
3174 jalview.datamodel.Annotation[] anot = null;
3175 java.awt.Color firstColour = null;
3177 if (!annotation.getScoreOnly())
3179 anot = new jalview.datamodel.Annotation[al.getWidth()];
3180 for (int aa = 0; aa < ae.length && aa < anot.length; aa++)
3182 anpos = ae[aa].getPosition();
3184 if (anpos >= anot.length)
3189 anot[anpos] = new jalview.datamodel.Annotation(
3191 ae[aa].getDisplayCharacter(), ae[aa].getDescription(),
3192 (ae[aa].getSecondaryStructure() == null
3193 || ae[aa].getSecondaryStructure().length() == 0)
3195 : ae[aa].getSecondaryStructure()
3200 // JBPNote: Consider verifying dataflow for IO of secondary
3201 // structure annotation read from Stockholm files
3202 // this was added to try to ensure that
3203 // if (anot[ae[aa].getPosition()].secondaryStructure>' ')
3205 // anot[ae[aa].getPosition()].displayCharacter = "";
3207 anot[anpos].colour = new java.awt.Color(ae[aa].getColour());
3208 if (firstColour == null)
3210 firstColour = anot[anpos].colour;
3214 jalview.datamodel.AlignmentAnnotation jaa = null;
3216 if (annotation.getGraph())
3218 float llim = 0, hlim = 0;
3219 // if (autoForView || an[i].isAutoCalculated()) {
3222 jaa = new jalview.datamodel.AlignmentAnnotation(
3223 annotation.getLabel(), annotation.getDescription(), anot,
3224 llim, hlim, annotation.getGraphType());
3226 jaa.graphGroup = annotation.getGraphGroup();
3227 jaa._linecolour = firstColour;
3228 if (annotation.getThresholdLine() != null)
3230 jaa.setThreshold(new jalview.datamodel.GraphLine(
3231 annotation.getThresholdLine().getValue(),
3232 annotation.getThresholdLine().getLabel(),
3234 annotation.getThresholdLine().getColour())));
3237 if (autoForView || annotation.isAutoCalculated())
3239 // Hardwire the symbol display line to ensure that labels for
3240 // histograms are displayed
3246 jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
3247 an[i].getDescription(), anot);
3248 jaa._linecolour = firstColour;
3250 // register new annotation
3251 if (an[i].getId() != null)
3253 annotationIds.put(an[i].getId(), jaa);
3254 jaa.annotationId = an[i].getId();
3256 // recover sequence association
3257 String sequenceRef = an[i].getSequenceRef();
3258 if (sequenceRef != null)
3260 // from 2.9 sequenceRef is to sequence id (JAL-1781)
3261 SequenceI sequence = seqRefIds.get(sequenceRef);
3262 if (sequence == null)
3264 // in pre-2.9 projects sequence ref is to sequence name
3265 sequence = al.findName(sequenceRef);
3267 if (sequence != null)
3269 jaa.createSequenceMapping(sequence, 1, true);
3270 sequence.addAlignmentAnnotation(jaa);
3273 // and make a note of any group association
3274 if (an[i].getGroupRef() != null && an[i].getGroupRef().length() > 0)
3276 List<jalview.datamodel.AlignmentAnnotation> aal = groupAnnotRefs
3277 .get(an[i].getGroupRef());
3280 aal = new ArrayList<>();
3281 groupAnnotRefs.put(an[i].getGroupRef(), aal);
3286 if (an[i].hasScore())
3288 jaa.setScore(an[i].getScore());
3290 if (an[i].hasVisible())
3292 jaa.visible = an[i].getVisible();
3295 if (an[i].hasCentreColLabels())
3297 jaa.centreColLabels = an[i].getCentreColLabels();
3300 if (an[i].hasScaleColLabels())
3302 jaa.scaleColLabel = an[i].getScaleColLabels();
3304 if (an[i].hasAutoCalculated() && an[i].isAutoCalculated())
3306 // newer files have an 'autoCalculated' flag and store calculation
3307 // state in viewport properties
3308 jaa.autoCalculated = true; // means annotation will be marked for
3309 // update at end of load.
3311 if (an[i].hasGraphHeight())
3313 jaa.graphHeight = an[i].getGraphHeight();
3315 if (an[i].hasBelowAlignment())
3317 jaa.belowAlignment = an[i].isBelowAlignment();
3319 jaa.setCalcId(an[i].getCalcId());
3320 if (an[i].getPropertyCount() > 0)
3322 for (jalview.schemabinding.version2.Property prop : an[i]
3325 jaa.setProperty(prop.getName(), prop.getValue());
3328 if (jaa.autoCalculated)
3330 autoAlan.add(new JvAnnotRow(i, jaa));
3333 // if (!autoForView)
3335 // add autocalculated group annotation and any user created annotation
3337 al.addAnnotation(jaa);
3341 // ///////////////////////
3343 // Create alignment markup and styles for this view
3344 if (jms.getJGroupCount() > 0)
3346 JGroup[] groups = jms.getJGroup();
3347 boolean addAnnotSchemeGroup = false;
3348 for (int i = 0; i < groups.length; i++)
3350 JGroup jGroup = groups[i];
3351 ColourSchemeI cs = null;
3352 if (jGroup.getColour() != null)
3354 if (jGroup.getColour().startsWith("ucs"))
3356 cs = getUserColourScheme(jms, jGroup.getColour());
3358 else if (jGroup.getColour().equals("AnnotationColourGradient")
3359 && jGroup.getAnnotationColours() != null)
3361 addAnnotSchemeGroup = true;
3365 cs = ColourSchemeProperty.getColourScheme(al,
3366 jGroup.getColour());
3369 int pidThreshold = jGroup.getPidThreshold();
3371 Vector<SequenceI> seqs = new Vector<>();
3373 for (int s = 0; s < jGroup.getSeqCount(); s++)
3375 String seqId = jGroup.getSeq(s) + "";
3376 SequenceI ts = seqRefIds.get(seqId);
3380 seqs.addElement(ts);
3384 if (seqs.size() < 1)
3389 SequenceGroup sg = new SequenceGroup(seqs, jGroup.getName(), cs,
3390 jGroup.getDisplayBoxes(), jGroup.getDisplayText(),
3391 jGroup.getColourText(), jGroup.getStart(), jGroup.getEnd());
3392 sg.getGroupColourScheme().setThreshold(pidThreshold, true);
3393 sg.getGroupColourScheme()
3394 .setConservationInc(jGroup.getConsThreshold());
3395 sg.setOutlineColour(new java.awt.Color(jGroup.getOutlineColour()));
3397 sg.textColour = new java.awt.Color(jGroup.getTextCol1());
3398 sg.textColour2 = new java.awt.Color(jGroup.getTextCol2());
3399 sg.setShowNonconserved(
3400 jGroup.hasShowUnconserved() ? jGroup.isShowUnconserved()
3402 sg.thresholdTextColour = jGroup.getTextColThreshold();
3403 if (jGroup.hasShowConsensusHistogram())
3405 sg.setShowConsensusHistogram(jGroup.isShowConsensusHistogram());
3408 if (jGroup.hasShowSequenceLogo())
3410 sg.setshowSequenceLogo(jGroup.isShowSequenceLogo());
3412 if (jGroup.hasNormaliseSequenceLogo())
3414 sg.setNormaliseSequenceLogo(jGroup.isNormaliseSequenceLogo());
3416 if (jGroup.hasIgnoreGapsinConsensus())
3418 sg.setIgnoreGapsConsensus(jGroup.getIgnoreGapsinConsensus());
3420 if (jGroup.getConsThreshold() != 0)
3422 Conservation c = new Conservation("All", sg.getSequences(null), 0,
3425 c.verdict(false, 25);
3426 sg.cs.setConservation(c);
3429 if (jGroup.getId() != null && groupAnnotRefs.size() > 0)
3431 // re-instate unique group/annotation row reference
3432 List<AlignmentAnnotation> jaal = groupAnnotRefs
3433 .get(jGroup.getId());
3436 for (AlignmentAnnotation jaa : jaal)
3439 if (jaa.autoCalculated)
3441 // match up and try to set group autocalc alignment row for this
3443 if (jaa.label.startsWith("Consensus for "))
3445 sg.setConsensus(jaa);
3447 // match up and try to set group autocalc alignment row for this
3449 if (jaa.label.startsWith("Conservation for "))
3451 sg.setConservationRow(jaa);
3458 if (addAnnotSchemeGroup)
3460 // reconstruct the annotation colourscheme
3461 sg.setColourScheme(constructAnnotationColour(
3462 jGroup.getAnnotationColours(), null, al, jms, false));
3468 // only dataset in this model, so just return.
3471 // ///////////////////////////////
3474 // If we just load in the same jar file again, the sequenceSetId
3475 // will be the same, and we end up with multiple references
3476 // to the same sequenceSet. We must modify this id on load
3477 // so that each load of the file gives a unique id
3478 String uniqueSeqSetId = view.getSequenceSetId() + uniqueSetSuffix;
3479 String viewId = (view.getId() == null ? null
3480 : view.getId() + uniqueSetSuffix);
3481 AlignFrame af = null;
3482 AlignViewport av = null;
3483 // now check to see if we really need to create a new viewport.
3484 if (multipleView && viewportsAdded.size() == 0)
3486 // We recovered an alignment for which a viewport already exists.
3487 // TODO: fix up any settings necessary for overlaying stored state onto
3488 // state recovered from another document. (may not be necessary).
3489 // we may need a binding from a viewport in memory to one recovered from
3491 // and then recover its containing af to allow the settings to be applied.
3492 // TODO: fix for vamsas demo
3494 "About to recover a viewport for existing alignment: Sequence set ID is "
3496 Object seqsetobj = retrieveExistingObj(uniqueSeqSetId);
3497 if (seqsetobj != null)
3499 if (seqsetobj instanceof String)
3501 uniqueSeqSetId = (String) seqsetobj;
3503 "Recovered extant sequence set ID mapping for ID : New Sequence set ID is "
3509 "Warning : Collision between sequence set ID string and existing jalview object mapping.");
3515 * indicate that annotation colours are applied across all groups (pre
3516 * Jalview 2.8.1 behaviour)
3518 boolean doGroupAnnColour = Jalview2XML.isVersionStringLaterThan("2.8.1",
3519 object.getVersion());
3521 AlignmentPanel ap = null;
3522 boolean isnewview = true;
3525 // Check to see if this alignment already has a view id == viewId
3526 jalview.gui.AlignmentPanel views[] = Desktop
3527 .getAlignmentPanels(uniqueSeqSetId);
3528 if (views != null && views.length > 0)
3530 for (int v = 0; v < views.length; v++)
3532 if (views[v].av.getViewId().equalsIgnoreCase(viewId))
3534 // recover the existing alignpanel, alignframe, viewport
3535 af = views[v].alignFrame;
3538 // TODO: could even skip resetting view settings if we don't want to
3539 // change the local settings from other jalview processes
3548 af = loadViewport(file, jseqs, hiddenSeqs, al, jms, view,
3549 uniqueSeqSetId, viewId, autoAlan);
3555 * Load any trees, PDB structures and viewers
3557 * Not done if flag is false (when this method is used for New View)
3559 if (loadTreesAndStructures)
3561 loadTrees(jms, view, af, av, ap);
3562 loadPDBStructures(jprovider, jseqs, af, ap);
3563 loadRnaViewers(jprovider, jseqs, ap);
3565 // and finally return.
3570 * Instantiate and link any saved RNA (Varna) viewers. The state of the Varna
3571 * panel is restored from separate jar entries, two (gapped and trimmed) per
3572 * sequence and secondary structure.
3574 * Currently each viewer shows just one sequence and structure (gapped and
3575 * trimmed), however this method is designed to support multiple sequences or
3576 * structures in viewers if wanted in future.
3582 private void loadRnaViewers(jarInputStreamProvider jprovider,
3583 JSeq[] jseqs, AlignmentPanel ap)
3586 * scan the sequences for references to viewers; create each one the first
3587 * time it is referenced, add Rna models to existing viewers
3589 for (JSeq jseq : jseqs)
3591 for (int i = 0; i < jseq.getRnaViewerCount(); i++)
3593 RnaViewer viewer = jseq.getRnaViewer(i);
3594 AppVarna appVarna = findOrCreateVarnaViewer(viewer, uniqueSetSuffix,
3597 for (int j = 0; j < viewer.getSecondaryStructureCount(); j++)
3599 SecondaryStructure ss = viewer.getSecondaryStructure(j);
3600 SequenceI seq = seqRefIds.get(jseq.getId());
3601 AlignmentAnnotation ann = this.annotationIds
3602 .get(ss.getAnnotationId());
3605 * add the structure to the Varna display (with session state copied
3606 * from the jar to a temporary file)
3608 boolean gapped = ss.isGapped();
3609 String rnaTitle = ss.getTitle();
3610 String sessionState = ss.getViewerState();
3611 String tempStateFile = copyJarEntry(jprovider, sessionState,
3613 RnaModel rna = new RnaModel(rnaTitle, ann, seq, null, gapped);
3614 appVarna.addModelSession(rna, rnaTitle, tempStateFile);
3616 appVarna.setInitialSelection(viewer.getSelectedRna());
3622 * Locate and return an already instantiated matching AppVarna, or create one
3626 * @param viewIdSuffix
3630 protected AppVarna findOrCreateVarnaViewer(RnaViewer viewer,
3631 String viewIdSuffix, AlignmentPanel ap)
3634 * on each load a suffix is appended to the saved viewId, to avoid conflicts
3635 * if load is repeated
3637 String postLoadId = viewer.getViewId() + viewIdSuffix;
3638 for (JInternalFrame frame : getAllFrames())
3640 if (frame instanceof AppVarna)
3642 AppVarna varna = (AppVarna) frame;
3643 if (postLoadId.equals(varna.getViewId()))
3645 // this viewer is already instantiated
3646 // could in future here add ap as another 'parent' of the
3647 // AppVarna window; currently just 1-to-many
3654 * viewer not found - make it
3656 RnaViewerModel model = new RnaViewerModel(postLoadId, viewer.getTitle(),
3657 viewer.getXpos(), viewer.getYpos(), viewer.getWidth(),
3658 viewer.getHeight(), viewer.getDividerLocation());
3659 AppVarna varna = new AppVarna(model, ap);
3665 * Load any saved trees
3673 protected void loadTrees(JalviewModelSequence jms, Viewport view,
3674 AlignFrame af, AlignViewport av, AlignmentPanel ap)
3676 // TODO result of automated refactoring - are all these parameters needed?
3679 for (int t = 0; t < jms.getTreeCount(); t++)
3682 Tree tree = jms.getTree(t);
3684 TreePanel tp = (TreePanel) retrieveExistingObj(tree.getId());
3687 tp = af.showNewickTree(
3688 new jalview.io.NewickFile(tree.getNewick()),
3689 tree.getTitle(), tree.getWidth(), tree.getHeight(),
3690 tree.getXpos(), tree.getYpos());
3691 if (tree.getId() != null)
3693 // perhaps bind the tree id to something ?
3698 // update local tree attributes ?
3699 // TODO: should check if tp has been manipulated by user - if so its
3700 // settings shouldn't be modified
3701 tp.setTitle(tree.getTitle());
3702 tp.setBounds(new Rectangle(tree.getXpos(), tree.getYpos(),
3703 tree.getWidth(), tree.getHeight()));
3704 tp.av = av; // af.viewport; // TODO: verify 'associate with all
3707 tp.treeCanvas.av = av; // af.viewport;
3708 tp.treeCanvas.ap = ap; // af.alignPanel;
3713 warn("There was a problem recovering stored Newick tree: \n"
3714 + tree.getNewick());
3718 tp.fitToWindow.setState(tree.getFitToWindow());
3719 tp.fitToWindow_actionPerformed(null);
3721 if (tree.getFontName() != null)
3723 tp.setTreeFont(new java.awt.Font(tree.getFontName(),
3724 tree.getFontStyle(), tree.getFontSize()));
3728 tp.setTreeFont(new java.awt.Font(view.getFontName(),
3729 view.getFontStyle(), tree.getFontSize()));
3732 tp.showPlaceholders(tree.getMarkUnlinked());
3733 tp.showBootstrap(tree.getShowBootstrap());
3734 tp.showDistances(tree.getShowDistances());
3736 tp.treeCanvas.threshold = tree.getThreshold();
3738 if (tree.getCurrentTree())
3740 af.viewport.setCurrentTree(tp.getTree());
3744 } catch (Exception ex)
3746 ex.printStackTrace();
3751 * Load and link any saved structure viewers.
3758 protected void loadPDBStructures(jarInputStreamProvider jprovider,
3759 JSeq[] jseqs, AlignFrame af, AlignmentPanel ap)
3762 * Run through all PDB ids on the alignment, and collect mappings between
3763 * distinct view ids and all sequences referring to that view.
3765 Map<String, StructureViewerModel> structureViewers = new LinkedHashMap<>();
3767 for (int i = 0; i < jseqs.length; i++)
3769 if (jseqs[i].getPdbidsCount() > 0)
3771 Pdbids[] ids = jseqs[i].getPdbids();
3772 for (int p = 0; p < ids.length; p++)
3774 final int structureStateCount = ids[p].getStructureStateCount();
3775 for (int s = 0; s < structureStateCount; s++)
3777 // check to see if we haven't already created this structure view
3778 final StructureState structureState = ids[p]
3779 .getStructureState(s);
3780 String sviewid = (structureState.getViewId() == null) ? null
3781 : structureState.getViewId() + uniqueSetSuffix;
3782 jalview.datamodel.PDBEntry jpdb = new jalview.datamodel.PDBEntry();
3783 // Originally : ids[p].getFile()
3784 // : TODO: verify external PDB file recovery still works in normal
3785 // jalview project load
3786 jpdb.setFile(loadPDBFile(jprovider, ids[p].getId(),
3788 jpdb.setId(ids[p].getId());
3790 int x = structureState.getXpos();
3791 int y = structureState.getYpos();
3792 int width = structureState.getWidth();
3793 int height = structureState.getHeight();
3795 // Probably don't need to do this anymore...
3796 // Desktop.desktop.getComponentAt(x, y);
3797 // TODO: NOW: check that this recovers the PDB file correctly.
3798 String pdbFile = loadPDBFile(jprovider, ids[p].getId(),
3800 jalview.datamodel.SequenceI seq = seqRefIds
3801 .get(jseqs[i].getId() + "");
3802 if (sviewid == null)
3804 sviewid = "_jalview_pre2_4_" + x + "," + y + "," + width + ","
3807 if (!structureViewers.containsKey(sviewid))
3809 structureViewers.put(sviewid,
3810 new StructureViewerModel(x, y, width, height, false,
3811 false, true, structureState.getViewId(),
3812 structureState.getType()));
3813 // Legacy pre-2.7 conversion JAL-823 :
3814 // do not assume any view has to be linked for colour by
3818 // assemble String[] { pdb files }, String[] { id for each
3819 // file }, orig_fileloc, SequenceI[][] {{ seqs_file 1 }, {
3820 // seqs_file 2}, boolean[] {
3821 // linkAlignPanel,superposeWithAlignpanel}} from hash
3822 StructureViewerModel jmoldat = structureViewers.get(sviewid);
3823 jmoldat.setAlignWithPanel(jmoldat.isAlignWithPanel()
3824 | (structureState.hasAlignwithAlignPanel()
3825 ? structureState.getAlignwithAlignPanel()
3829 * Default colour by linked panel to false if not specified (e.g.
3830 * for pre-2.7 projects)
3832 boolean colourWithAlignPanel = jmoldat.isColourWithAlignPanel();
3833 colourWithAlignPanel |= (structureState
3834 .hasColourwithAlignPanel()
3835 ? structureState.getColourwithAlignPanel()
3837 jmoldat.setColourWithAlignPanel(colourWithAlignPanel);
3840 * Default colour by viewer to true if not specified (e.g. for
3843 boolean colourByViewer = jmoldat.isColourByViewer();
3844 colourByViewer &= structureState.hasColourByJmol()
3845 ? structureState.getColourByJmol()
3847 jmoldat.setColourByViewer(colourByViewer);
3849 if (jmoldat.getStateData().length() < structureState
3850 .getContent().length())
3853 jmoldat.setStateData(structureState.getContent());
3856 if (ids[p].getFile() != null)
3858 File mapkey = new File(ids[p].getFile());
3859 StructureData seqstrmaps = jmoldat.getFileData().get(mapkey);
3860 if (seqstrmaps == null)
3862 jmoldat.getFileData().put(mapkey,
3863 seqstrmaps = jmoldat.new StructureData(pdbFile,
3866 if (!seqstrmaps.getSeqList().contains(seq))
3868 seqstrmaps.getSeqList().add(seq);
3874 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");
3881 // Instantiate the associated structure views
3882 for (Entry<String, StructureViewerModel> entry : structureViewers
3887 createOrLinkStructureViewer(entry, af, ap, jprovider);
3888 } catch (Exception e)
3891 "Error loading structure viewer: " + e.getMessage());
3892 // failed - try the next one
3904 protected void createOrLinkStructureViewer(
3905 Entry<String, StructureViewerModel> viewerData, AlignFrame af,
3906 AlignmentPanel ap, jarInputStreamProvider jprovider)
3908 final StructureViewerModel stateData = viewerData.getValue();
3911 * Search for any viewer windows already open from other alignment views
3912 * that exactly match the stored structure state
3914 StructureViewerBase comp = findMatchingViewer(viewerData);
3918 linkStructureViewer(ap, comp, stateData);
3923 * From 2.9: stateData.type contains JMOL or CHIMERA, data is in jar entry
3924 * "viewer_"+stateData.viewId
3926 if (ViewerType.CHIMERA.toString().equals(stateData.getType()))
3928 createChimeraViewer(viewerData, af, jprovider);
3933 * else Jmol (if pre-2.9, stateData contains JMOL state string)
3935 createJmolViewer(viewerData, af, jprovider);
3940 * Create a new Chimera viewer.
3946 protected void createChimeraViewer(
3947 Entry<String, StructureViewerModel> viewerData, AlignFrame af,
3948 jarInputStreamProvider jprovider)
3950 StructureViewerModel data = viewerData.getValue();
3951 String chimeraSessionFile = data.getStateData();
3954 * Copy Chimera session from jar entry "viewer_"+viewId to a temporary file
3956 * NB this is the 'saved' viewId as in the project file XML, _not_ the
3957 * 'uniquified' sviewid used to reconstruct the viewer here
3959 String viewerJarEntryName = getViewerJarEntryName(data.getViewId());
3960 chimeraSessionFile = copyJarEntry(jprovider, viewerJarEntryName,
3963 Set<Entry<File, StructureData>> fileData = data.getFileData()
3965 List<PDBEntry> pdbs = new ArrayList<>();
3966 List<SequenceI[]> allseqs = new ArrayList<>();
3967 for (Entry<File, StructureData> pdb : fileData)
3969 String filePath = pdb.getValue().getFilePath();
3970 String pdbId = pdb.getValue().getPdbId();
3971 // pdbs.add(new PDBEntry(filePath, pdbId));
3972 pdbs.add(new PDBEntry(pdbId, null, PDBEntry.Type.PDB, filePath));
3973 final List<SequenceI> seqList = pdb.getValue().getSeqList();
3974 SequenceI[] seqs = seqList.toArray(new SequenceI[seqList.size()]);
3978 boolean colourByChimera = data.isColourByViewer();
3979 boolean colourBySequence = data.isColourWithAlignPanel();
3981 // TODO use StructureViewer as a factory here, see JAL-1761
3982 final PDBEntry[] pdbArray = pdbs.toArray(new PDBEntry[pdbs.size()]);
3983 final SequenceI[][] seqsArray = allseqs
3984 .toArray(new SequenceI[allseqs.size()][]);
3985 String newViewId = viewerData.getKey();
3987 ChimeraViewFrame cvf = new ChimeraViewFrame(chimeraSessionFile,
3988 af.alignPanel, pdbArray, seqsArray, colourByChimera,
3989 colourBySequence, newViewId);
3990 cvf.setSize(data.getWidth(), data.getHeight());
3991 cvf.setLocation(data.getX(), data.getY());
3995 * Create a new Jmol window. First parse the Jmol state to translate filenames
3996 * loaded into the view, and record the order in which files are shown in the
3997 * Jmol view, so we can add the sequence mappings in same order.
4003 protected void createJmolViewer(
4004 final Entry<String, StructureViewerModel> viewerData,
4005 AlignFrame af, jarInputStreamProvider jprovider)
4007 final StructureViewerModel svattrib = viewerData.getValue();
4008 String state = svattrib.getStateData();
4011 * Pre-2.9: state element value is the Jmol state string
4013 * 2.9+: @type is "JMOL", state data is in a Jar file member named "viewer_"
4016 if (ViewerType.JMOL.toString().equals(svattrib.getType()))
4018 state = readJarEntry(jprovider,
4019 getViewerJarEntryName(svattrib.getViewId()));
4022 List<String> pdbfilenames = new ArrayList<>();
4023 List<SequenceI[]> seqmaps = new ArrayList<>();
4024 List<String> pdbids = new ArrayList<>();
4025 StringBuilder newFileLoc = new StringBuilder(64);
4026 int cp = 0, ncp, ecp;
4027 Map<File, StructureData> oldFiles = svattrib.getFileData();
4028 while ((ncp = state.indexOf("load ", cp)) > -1)
4032 // look for next filename in load statement
4033 newFileLoc.append(state.substring(cp,
4034 ncp = (state.indexOf("\"", ncp + 1) + 1)));
4035 String oldfilenam = state.substring(ncp,
4036 ecp = state.indexOf("\"", ncp));
4037 // recover the new mapping data for this old filename
4038 // have to normalize filename - since Jmol and jalview do
4040 // translation differently.
4041 StructureData filedat = oldFiles.get(new File(oldfilenam));
4042 if (filedat == null)
4044 String reformatedOldFilename = oldfilenam.replaceAll("/", "\\\\");
4045 filedat = oldFiles.get(new File(reformatedOldFilename));
4047 newFileLoc.append(Platform.escapeString(filedat.getFilePath()));
4048 pdbfilenames.add(filedat.getFilePath());
4049 pdbids.add(filedat.getPdbId());
4050 seqmaps.add(filedat.getSeqList().toArray(new SequenceI[0]));
4051 newFileLoc.append("\"");
4052 cp = ecp + 1; // advance beyond last \" and set cursor so we can
4053 // look for next file statement.
4054 } while ((ncp = state.indexOf("/*file*/", cp)) > -1);
4058 // just append rest of state
4059 newFileLoc.append(state.substring(cp));
4063 System.err.print("Ignoring incomplete Jmol state for PDB ids: ");
4064 newFileLoc = new StringBuilder(state);
4065 newFileLoc.append("; load append ");
4066 for (File id : oldFiles.keySet())
4068 // add this and any other pdb files that should be present in
4070 StructureData filedat = oldFiles.get(id);
4071 newFileLoc.append(filedat.getFilePath());
4072 pdbfilenames.add(filedat.getFilePath());
4073 pdbids.add(filedat.getPdbId());
4074 seqmaps.add(filedat.getSeqList().toArray(new SequenceI[0]));
4075 newFileLoc.append(" \"");
4076 newFileLoc.append(filedat.getFilePath());
4077 newFileLoc.append("\"");
4080 newFileLoc.append(";");
4083 if (newFileLoc.length() == 0)
4087 int histbug = newFileLoc.indexOf("history = ");
4091 * change "history = [true|false];" to "history = [1|0];"
4094 int diff = histbug == -1 ? -1 : newFileLoc.indexOf(";", histbug);
4095 String val = (diff == -1) ? null
4096 : newFileLoc.substring(histbug, diff);
4097 if (val != null && val.length() >= 4)
4099 if (val.contains("e")) // eh? what can it be?
4101 if (val.trim().equals("true"))
4109 newFileLoc.replace(histbug, diff, val);
4114 final String[] pdbf = pdbfilenames
4115 .toArray(new String[pdbfilenames.size()]);
4116 final String[] id = pdbids.toArray(new String[pdbids.size()]);
4117 final SequenceI[][] sq = seqmaps
4118 .toArray(new SequenceI[seqmaps.size()][]);
4119 final String fileloc = newFileLoc.toString();
4120 final String sviewid = viewerData.getKey();
4121 final AlignFrame alf = af;
4122 final Rectangle rect = new Rectangle(svattrib.getX(), svattrib.getY(),
4123 svattrib.getWidth(), svattrib.getHeight());
4126 javax.swing.SwingUtilities.invokeAndWait(new Runnable()
4131 JalviewStructureDisplayI sview = null;
4134 sview = new StructureViewer(
4135 alf.alignPanel.getStructureSelectionManager())
4136 .createView(StructureViewer.ViewerType.JMOL,
4137 pdbf, id, sq, alf.alignPanel, svattrib,
4138 fileloc, rect, sviewid);
4139 addNewStructureViewer(sview);
4140 } catch (OutOfMemoryError ex)
4142 new OOMWarning("restoring structure view for PDB id " + id,
4143 (OutOfMemoryError) ex.getCause());
4144 if (sview != null && sview.isVisible())
4146 sview.closeViewer(false);
4147 sview.setVisible(false);
4153 } catch (InvocationTargetException ex)
4155 warn("Unexpected error when opening Jmol view.", ex);
4157 } catch (InterruptedException e)
4159 // e.printStackTrace();
4165 * Generates a name for the entry in the project jar file to hold state
4166 * information for a structure viewer
4171 protected String getViewerJarEntryName(String viewId)
4173 return VIEWER_PREFIX + viewId;
4177 * Returns any open frame that matches given structure viewer data. The match
4178 * is based on the unique viewId, or (for older project versions) the frame's
4184 protected StructureViewerBase findMatchingViewer(
4185 Entry<String, StructureViewerModel> viewerData)
4187 final String sviewid = viewerData.getKey();
4188 final StructureViewerModel svattrib = viewerData.getValue();
4189 StructureViewerBase comp = null;
4190 JInternalFrame[] frames = getAllFrames();
4191 for (JInternalFrame frame : frames)
4193 if (frame instanceof StructureViewerBase)
4196 * Post jalview 2.4 schema includes structure view id
4198 if (sviewid != null && ((StructureViewerBase) frame).getViewId()
4201 comp = (StructureViewerBase) frame;
4202 break; // break added in 2.9
4205 * Otherwise test for matching position and size of viewer frame
4207 else if (frame.getX() == svattrib.getX()
4208 && frame.getY() == svattrib.getY()
4209 && frame.getHeight() == svattrib.getHeight()
4210 && frame.getWidth() == svattrib.getWidth())
4212 comp = (StructureViewerBase) frame;
4213 // no break in faint hope of an exact match on viewId
4221 * Link an AlignmentPanel to an existing structure viewer.
4226 * @param useinViewerSuperpos
4227 * @param usetoColourbyseq
4228 * @param viewerColouring
4230 protected void linkStructureViewer(AlignmentPanel ap,
4231 StructureViewerBase viewer, StructureViewerModel stateData)
4233 // NOTE: if the jalview project is part of a shared session then
4234 // view synchronization should/could be done here.
4236 final boolean useinViewerSuperpos = stateData.isAlignWithPanel();
4237 final boolean usetoColourbyseq = stateData.isColourWithAlignPanel();
4238 final boolean viewerColouring = stateData.isColourByViewer();
4239 Map<File, StructureData> oldFiles = stateData.getFileData();
4242 * Add mapping for sequences in this view to an already open viewer
4244 final AAStructureBindingModel binding = viewer.getBinding();
4245 for (File id : oldFiles.keySet())
4247 // add this and any other pdb files that should be present in the
4249 StructureData filedat = oldFiles.get(id);
4250 String pdbFile = filedat.getFilePath();
4251 SequenceI[] seq = filedat.getSeqList().toArray(new SequenceI[0]);
4252 binding.getSsm().setMapping(seq, null, pdbFile, DataSourceType.FILE);
4253 binding.addSequenceForStructFile(pdbFile, seq);
4255 // and add the AlignmentPanel's reference to the view panel
4256 viewer.addAlignmentPanel(ap);
4257 if (useinViewerSuperpos)
4259 viewer.useAlignmentPanelForSuperposition(ap);
4263 viewer.excludeAlignmentPanelForSuperposition(ap);
4265 if (usetoColourbyseq)
4267 viewer.useAlignmentPanelForColourbyseq(ap, !viewerColouring);
4271 viewer.excludeAlignmentPanelForColourbyseq(ap);
4276 * Get all frames within the Desktop.
4280 protected JInternalFrame[] getAllFrames()
4282 JInternalFrame[] frames = null;
4283 // TODO is this necessary - is it safe - risk of hanging?
4288 frames = Desktop.desktop.getAllFrames();
4289 } catch (ArrayIndexOutOfBoundsException e)
4291 // occasional No such child exceptions are thrown here...
4295 } catch (InterruptedException f)
4299 } while (frames == null);
4304 * Answers true if 'version' is equal to or later than 'supported', where each
4305 * is formatted as major/minor versions like "2.8.3" or "2.3.4b1" for bugfix
4306 * changes. Development and test values for 'version' are leniently treated
4310 * - minimum version we are comparing against
4312 * - version of data being processsed
4315 public static boolean isVersionStringLaterThan(String supported,
4318 if (supported == null || version == null
4319 || version.equalsIgnoreCase("DEVELOPMENT BUILD")
4320 || version.equalsIgnoreCase("Test")
4321 || version.equalsIgnoreCase("AUTOMATED BUILD"))
4323 System.err.println("Assuming project file with "
4324 + (version == null ? "null" : version)
4325 + " is compatible with Jalview version " + supported);
4330 return StringUtils.compareVersions(version, supported, "b") >= 0;
4334 Vector<JalviewStructureDisplayI> newStructureViewers = null;
4336 protected void addNewStructureViewer(JalviewStructureDisplayI sview)
4338 if (newStructureViewers != null)
4340 sview.getBinding().setFinishedLoadingFromArchive(false);
4341 newStructureViewers.add(sview);
4345 protected void setLoadingFinishedForNewStructureViewers()
4347 if (newStructureViewers != null)
4349 for (JalviewStructureDisplayI sview : newStructureViewers)
4351 sview.getBinding().setFinishedLoadingFromArchive(true);
4353 newStructureViewers.clear();
4354 newStructureViewers = null;
4358 AlignFrame loadViewport(String file, JSeq[] JSEQ,
4359 List<SequenceI> hiddenSeqs, AlignmentI al,
4360 JalviewModelSequence jms, Viewport view, String uniqueSeqSetId,
4361 String viewId, List<JvAnnotRow> autoAlan)
4363 AlignFrame af = null;
4364 af = new AlignFrame(al, view.getWidth(), view.getHeight(),
4365 uniqueSeqSetId, viewId);
4367 af.setFileName(file, FileFormat.Jalview);
4369 for (int i = 0; i < JSEQ.length; i++)
4371 af.viewport.setSequenceColour(
4372 af.viewport.getAlignment().getSequenceAt(i),
4373 new java.awt.Color(JSEQ[i].getColour()));
4378 af.getViewport().setColourByReferenceSeq(true);
4379 af.getViewport().setDisplayReferenceSeq(true);
4382 af.viewport.setGatherViewsHere(view.getGatheredViews());
4384 if (view.getSequenceSetId() != null)
4386 AlignmentViewport av = viewportsAdded.get(uniqueSeqSetId);
4388 af.viewport.setSequenceSetId(uniqueSeqSetId);
4391 // propagate shared settings to this new view
4392 af.viewport.setHistoryList(av.getHistoryList());
4393 af.viewport.setRedoList(av.getRedoList());
4397 viewportsAdded.put(uniqueSeqSetId, af.viewport);
4399 // TODO: check if this method can be called repeatedly without
4400 // side-effects if alignpanel already registered.
4401 PaintRefresher.Register(af.alignPanel, uniqueSeqSetId);
4403 // apply Hidden regions to view.
4404 if (hiddenSeqs != null)
4406 for (int s = 0; s < JSEQ.length; s++)
4408 SequenceGroup hidden = new SequenceGroup();
4409 boolean isRepresentative = false;
4410 for (int r = 0; r < JSEQ[s].getHiddenSequencesCount(); r++)
4412 isRepresentative = true;
4413 SequenceI sequenceToHide = al
4414 .getSequenceAt(JSEQ[s].getHiddenSequences(r));
4415 hidden.addSequence(sequenceToHide, false);
4416 // remove from hiddenSeqs list so we don't try to hide it twice
4417 hiddenSeqs.remove(sequenceToHide);
4419 if (isRepresentative)
4421 SequenceI representativeSequence = al.getSequenceAt(s);
4422 hidden.addSequence(representativeSequence, false);
4423 af.viewport.hideRepSequences(representativeSequence, hidden);
4427 SequenceI[] hseqs = hiddenSeqs
4428 .toArray(new SequenceI[hiddenSeqs.size()]);
4429 af.viewport.hideSequence(hseqs);
4432 // recover view properties and display parameters
4434 af.viewport.setShowAnnotation(view.getShowAnnotation());
4435 af.viewport.setAbovePIDThreshold(view.getPidSelected());
4436 af.viewport.setThreshold(view.getPidThreshold());
4438 af.viewport.setColourText(view.getShowColourText());
4440 af.viewport.setConservationSelected(view.getConservationSelected());
4441 af.viewport.setIncrement(view.getConsThreshold());
4442 af.viewport.setShowJVSuffix(view.getShowFullId());
4443 af.viewport.setRightAlignIds(view.getRightAlignIds());
4444 af.viewport.setFont(new java.awt.Font(view.getFontName(),
4445 view.getFontStyle(), view.getFontSize()), true);
4446 ViewStyleI vs = af.viewport.getViewStyle();
4447 vs.setScaleProteinAsCdna(view.isScaleProteinAsCdna());
4448 af.viewport.setViewStyle(vs);
4449 // TODO: allow custom charWidth/Heights to be restored by updating them
4450 // after setting font - which means set above to false
4451 af.viewport.setRenderGaps(view.getRenderGaps());
4452 af.viewport.setWrapAlignment(view.getWrapAlignment());
4453 af.viewport.setShowAnnotation(view.getShowAnnotation());
4455 af.viewport.setShowBoxes(view.getShowBoxes());
4457 af.viewport.setShowText(view.getShowText());
4459 af.viewport.setTextColour(new java.awt.Color(view.getTextCol1()));
4460 af.viewport.setTextColour2(new java.awt.Color(view.getTextCol2()));
4461 af.viewport.setThresholdTextColour(view.getTextColThreshold());
4462 af.viewport.setShowUnconserved(
4463 view.hasShowUnconserved() ? view.isShowUnconserved() : false);
4464 af.viewport.getRanges().setStartRes(view.getStartRes());
4466 if (view.getViewName() != null)
4468 af.viewport.viewName = view.getViewName();
4469 af.setInitialTabVisible();
4471 af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),
4473 // startSeq set in af.alignPanel.updateLayout below
4474 af.alignPanel.updateLayout();
4475 ColourSchemeI cs = null;
4476 // apply colourschemes
4477 if (view.getBgColour() != null)
4479 if (view.getBgColour().startsWith("ucs"))
4481 cs = getUserColourScheme(jms, view.getBgColour());
4483 else if (view.getBgColour().startsWith("Annotation"))
4485 AnnotationColours viewAnnColour = view.getAnnotationColours();
4486 cs = constructAnnotationColour(viewAnnColour, af, al, jms, true);
4493 cs = ColourSchemeProperty.getColourScheme(al, view.getBgColour());
4497 af.viewport.setGlobalColourScheme(cs);
4498 af.viewport.getResidueShading().setThreshold(view.getPidThreshold(),
4499 view.getIgnoreGapsinConsensus());
4500 af.viewport.getResidueShading()
4501 .setConsensus(af.viewport.getSequenceConsensusHash());
4502 af.viewport.setColourAppliesToAllGroups(false);
4504 if (view.getConservationSelected() && cs != null)
4506 af.viewport.getResidueShading()
4507 .setConservationInc(view.getConsThreshold());
4510 af.changeColour(cs);
4512 af.viewport.setColourAppliesToAllGroups(true);
4514 af.viewport.setShowSequenceFeatures(view.getShowSequenceFeatures());
4516 if (view.hasCentreColumnLabels())
4518 af.viewport.setCentreColumnLabels(view.getCentreColumnLabels());
4520 if (view.hasIgnoreGapsinConsensus())
4522 af.viewport.setIgnoreGapsConsensus(view.getIgnoreGapsinConsensus(),
4525 if (view.hasFollowHighlight())
4527 af.viewport.setFollowHighlight(view.getFollowHighlight());
4529 if (view.hasFollowSelection())
4531 af.viewport.followSelection = view.getFollowSelection();
4533 if (view.hasShowConsensusHistogram())
4536 .setShowConsensusHistogram(view.getShowConsensusHistogram());
4540 af.viewport.setShowConsensusHistogram(true);
4542 if (view.hasShowSequenceLogo())
4544 af.viewport.setShowSequenceLogo(view.getShowSequenceLogo());
4548 af.viewport.setShowSequenceLogo(false);
4550 if (view.hasNormaliseSequenceLogo())
4552 af.viewport.setNormaliseSequenceLogo(view.getNormaliseSequenceLogo());
4554 if (view.hasShowDbRefTooltip())
4556 af.viewport.setShowDBRefs(view.getShowDbRefTooltip());
4558 if (view.hasShowNPfeatureTooltip())
4560 af.viewport.setShowNPFeats(view.hasShowNPfeatureTooltip());
4562 if (view.hasShowGroupConsensus())
4564 af.viewport.setShowGroupConsensus(view.getShowGroupConsensus());
4568 af.viewport.setShowGroupConsensus(false);
4570 if (view.hasShowGroupConservation())
4572 af.viewport.setShowGroupConservation(view.getShowGroupConservation());
4576 af.viewport.setShowGroupConservation(false);
4579 // recover featre settings
4580 if (jms.getFeatureSettings() != null)
4582 FeaturesDisplayed fdi;
4583 af.viewport.setFeaturesDisplayed(fdi = new FeaturesDisplayed());
4584 String[] renderOrder = new String[jms.getFeatureSettings()
4585 .getSettingCount()];
4586 Map<String, FeatureColourI> featureColours = new Hashtable<>();
4587 Map<String, Float> featureOrder = new Hashtable<>();
4589 for (int fs = 0; fs < jms.getFeatureSettings()
4590 .getSettingCount(); fs++)
4592 Setting setting = jms.getFeatureSettings().getSetting(fs);
4593 if (setting.hasMincolour())
4595 FeatureColourI gc = setting.hasMin()
4596 ? new FeatureColour(new Color(setting.getMincolour()),
4597 new Color(setting.getColour()), setting.getMin(),
4599 : new FeatureColour(new Color(setting.getMincolour()),
4600 new Color(setting.getColour()), 0, 1);
4601 if (setting.hasThreshold())
4603 gc.setThreshold(setting.getThreshold());
4604 int threshstate = setting.getThreshstate();
4605 // -1 = None, 0 = Below, 1 = Above threshold
4606 if (threshstate == 0)
4608 gc.setBelowThreshold(true);
4610 else if (threshstate == 1)
4612 gc.setAboveThreshold(true);
4615 gc.setAutoScaled(true); // default
4616 if (setting.hasAutoScale())
4618 gc.setAutoScaled(setting.getAutoScale());
4620 if (setting.hasColourByLabel())
4622 gc.setColourByLabel(setting.getColourByLabel());
4624 // and put in the feature colour table.
4625 featureColours.put(setting.getType(), gc);
4629 featureColours.put(setting.getType(),
4630 new FeatureColour(new Color(setting.getColour())));
4632 renderOrder[fs] = setting.getType();
4633 if (setting.hasOrder())
4635 featureOrder.put(setting.getType(), setting.getOrder());
4639 featureOrder.put(setting.getType(), new Float(
4640 fs / jms.getFeatureSettings().getSettingCount()));
4642 if (setting.getDisplay())
4644 fdi.setVisible(setting.getType());
4647 Map<String, Boolean> fgtable = new Hashtable<>();
4648 for (int gs = 0; gs < jms.getFeatureSettings().getGroupCount(); gs++)
4650 Group grp = jms.getFeatureSettings().getGroup(gs);
4651 fgtable.put(grp.getName(), new Boolean(grp.getDisplay()));
4653 // FeatureRendererSettings frs = new FeatureRendererSettings(renderOrder,
4654 // fgtable, featureColours, jms.getFeatureSettings().hasTransparency() ?
4655 // jms.getFeatureSettings().getTransparency() : 0.0, featureOrder);
4656 FeatureRendererSettings frs = new FeatureRendererSettings(renderOrder,
4657 fgtable, featureColours, 1.0f, featureOrder);
4658 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
4659 .transferSettings(frs);
4663 if (view.getHiddenColumnsCount() > 0)
4665 for (int c = 0; c < view.getHiddenColumnsCount(); c++)
4667 af.viewport.hideColumns(view.getHiddenColumns(c).getStart(),
4668 view.getHiddenColumns(c).getEnd() // +1
4672 if (view.getCalcIdParam() != null)
4674 for (CalcIdParam calcIdParam : view.getCalcIdParam())
4676 if (calcIdParam != null)
4678 if (recoverCalcIdParam(calcIdParam, af.viewport))
4683 warn("Couldn't recover parameters for "
4684 + calcIdParam.getCalcId());
4689 af.setMenusFromViewport(af.viewport);
4690 af.setTitle(view.getTitle());
4691 // TODO: we don't need to do this if the viewport is aready visible.
4693 * Add the AlignFrame to the desktop (it may be 'gathered' later), unless it
4694 * has a 'cdna/protein complement' view, in which case save it in order to
4695 * populate a SplitFrame once all views have been read in.
4697 String complementaryViewId = view.getComplementId();
4698 if (complementaryViewId == null)
4700 Desktop.addInternalFrame(af, view.getTitle(), view.getWidth(),
4702 // recompute any autoannotation
4703 af.alignPanel.updateAnnotation(false, true);
4704 reorderAutoannotation(af, al, autoAlan);
4705 af.alignPanel.alignmentChanged();
4709 splitFrameCandidates.put(view, af);
4715 * Reads saved data to restore Colour by Annotation settings
4717 * @param viewAnnColour
4721 * @param checkGroupAnnColour
4724 private ColourSchemeI constructAnnotationColour(
4725 AnnotationColours viewAnnColour, AlignFrame af, AlignmentI al,
4726 JalviewModelSequence jms, boolean checkGroupAnnColour)
4728 boolean propagateAnnColour = false;
4729 AlignmentI annAlignment = af != null ? af.viewport.getAlignment() : al;
4730 if (checkGroupAnnColour && al.getGroups() != null
4731 && al.getGroups().size() > 0)
4733 // pre 2.8.1 behaviour
4734 // check to see if we should transfer annotation colours
4735 propagateAnnColour = true;
4736 for (SequenceGroup sg : al.getGroups())
4738 if (sg.getColourScheme() instanceof AnnotationColourGradient)
4740 propagateAnnColour = false;
4746 * 2.10.2- : saved annotationId is AlignmentAnnotation.annotationId
4748 String annotationId = viewAnnColour.getAnnotation();
4749 AlignmentAnnotation matchedAnnotation = annotationIds.get(annotationId);
4752 * pre 2.10.2: saved annotationId is AlignmentAnnotation.label
4754 if (matchedAnnotation == null
4755 && annAlignment.getAlignmentAnnotation() != null)
4757 for (int i = 0; i < annAlignment.getAlignmentAnnotation().length; i++)
4760 .equals(annAlignment.getAlignmentAnnotation()[i].label))
4762 matchedAnnotation = annAlignment.getAlignmentAnnotation()[i];
4767 if (matchedAnnotation == null)
4769 System.err.println("Failed to match annotation colour scheme for "
4773 if (matchedAnnotation.getThreshold() == null)
4775 matchedAnnotation.setThreshold(new GraphLine(
4776 viewAnnColour.getThreshold(), "Threshold", Color.black));
4779 AnnotationColourGradient cs = null;
4780 if (viewAnnColour.getColourScheme().equals("None"))
4782 cs = new AnnotationColourGradient(matchedAnnotation,
4783 new Color(viewAnnColour.getMinColour()),
4784 new Color(viewAnnColour.getMaxColour()),
4785 viewAnnColour.getAboveThreshold());
4787 else if (viewAnnColour.getColourScheme().startsWith("ucs"))
4789 cs = new AnnotationColourGradient(matchedAnnotation,
4790 getUserColourScheme(jms, viewAnnColour.getColourScheme()),
4791 viewAnnColour.getAboveThreshold());
4795 cs = new AnnotationColourGradient(matchedAnnotation,
4796 ColourSchemeProperty.getColourScheme(al,
4797 viewAnnColour.getColourScheme()),
4798 viewAnnColour.getAboveThreshold());
4801 boolean perSequenceOnly = viewAnnColour.isPerSequence();
4802 boolean useOriginalColours = viewAnnColour.isPredefinedColours();
4803 cs.setSeqAssociated(perSequenceOnly);
4804 cs.setPredefinedColours(useOriginalColours);
4806 if (propagateAnnColour && al.getGroups() != null)
4808 // Also use these settings for all the groups
4809 for (int g = 0; g < al.getGroups().size(); g++)
4811 SequenceGroup sg = al.getGroups().get(g);
4812 if (sg.getGroupColourScheme() == null)
4817 AnnotationColourGradient groupScheme = new AnnotationColourGradient(
4818 matchedAnnotation, sg.getColourScheme(),
4819 viewAnnColour.getAboveThreshold());
4820 sg.setColourScheme(groupScheme);
4821 groupScheme.setSeqAssociated(perSequenceOnly);
4822 groupScheme.setPredefinedColours(useOriginalColours);
4828 private void reorderAutoannotation(AlignFrame af, AlignmentI al,
4829 List<JvAnnotRow> autoAlan)
4831 // copy over visualization settings for autocalculated annotation in the
4833 if (al.getAlignmentAnnotation() != null)
4836 * Kludge for magic autoannotation names (see JAL-811)
4838 String[] magicNames = new String[] { "Consensus", "Quality",
4840 JvAnnotRow nullAnnot = new JvAnnotRow(-1, null);
4841 Hashtable<String, JvAnnotRow> visan = new Hashtable<>();
4842 for (String nm : magicNames)
4844 visan.put(nm, nullAnnot);
4846 for (JvAnnotRow auan : autoAlan)
4848 visan.put(auan.template.label
4849 + (auan.template.getCalcId() == null ? ""
4850 : "\t" + auan.template.getCalcId()),
4853 int hSize = al.getAlignmentAnnotation().length;
4854 List<JvAnnotRow> reorder = new ArrayList<>();
4855 // work through any autoCalculated annotation already on the view
4856 // removing it if it should be placed in a different location on the
4857 // annotation panel.
4858 List<String> remains = new ArrayList<>(visan.keySet());
4859 for (int h = 0; h < hSize; h++)
4861 jalview.datamodel.AlignmentAnnotation jalan = al
4862 .getAlignmentAnnotation()[h];
4863 if (jalan.autoCalculated)
4866 JvAnnotRow valan = visan.get(k = jalan.label);
4867 if (jalan.getCalcId() != null)
4869 valan = visan.get(k = jalan.label + "\t" + jalan.getCalcId());
4874 // delete the auto calculated row from the alignment
4875 al.deleteAnnotation(jalan, false);
4879 if (valan != nullAnnot)
4881 if (jalan != valan.template)
4883 // newly created autoannotation row instance
4884 // so keep a reference to the visible annotation row
4885 // and copy over all relevant attributes
4886 if (valan.template.graphHeight >= 0)
4889 jalan.graphHeight = valan.template.graphHeight;
4891 jalan.visible = valan.template.visible;
4893 reorder.add(new JvAnnotRow(valan.order, jalan));
4898 // Add any (possibly stale) autocalculated rows that were not appended to
4899 // the view during construction
4900 for (String other : remains)
4902 JvAnnotRow othera = visan.get(other);
4903 if (othera != nullAnnot && othera.template.getCalcId() != null
4904 && othera.template.getCalcId().length() > 0)
4906 reorder.add(othera);
4909 // now put the automatic annotation in its correct place
4910 int s = 0, srt[] = new int[reorder.size()];
4911 JvAnnotRow[] rws = new JvAnnotRow[reorder.size()];
4912 for (JvAnnotRow jvar : reorder)
4915 srt[s++] = jvar.order;
4918 jalview.util.QuickSort.sort(srt, rws);
4919 // and re-insert the annotation at its correct position
4920 for (JvAnnotRow jvar : rws)
4922 al.addAnnotation(jvar.template, jvar.order);
4924 af.alignPanel.adjustAnnotationHeight();
4928 Hashtable skipList = null;
4931 * TODO remove this method
4934 * @return AlignFrame bound to sequenceSetId from view, if one exists. private
4935 * AlignFrame getSkippedFrame(Viewport view) { if (skipList==null) {
4936 * throw new Error("Implementation Error. No skipList defined for this
4937 * Jalview2XML instance."); } return (AlignFrame)
4938 * skipList.get(view.getSequenceSetId()); }
4942 * Check if the Jalview view contained in object should be skipped or not.
4945 * @return true if view's sequenceSetId is a key in skipList
4947 private boolean skipViewport(JalviewModel object)
4949 if (skipList == null)
4954 if (skipList.containsKey(
4955 id = object.getJalviewModelSequence().getViewport()[0]
4956 .getSequenceSetId()))
4958 if (Cache.log != null && Cache.log.isDebugEnabled())
4960 Cache.log.debug("Skipping seuqence set id " + id);
4967 public void addToSkipList(AlignFrame af)
4969 if (skipList == null)
4971 skipList = new Hashtable();
4973 skipList.put(af.getViewport().getSequenceSetId(), af);
4976 public void clearSkipList()
4978 if (skipList != null)
4985 private void recoverDatasetFor(SequenceSet vamsasSet, AlignmentI al,
4986 boolean ignoreUnrefed)
4988 jalview.datamodel.AlignmentI ds = getDatasetFor(
4989 vamsasSet.getDatasetId());
4990 Vector dseqs = null;
4993 // create a list of new dataset sequences
4994 dseqs = new Vector();
4996 for (int i = 0, iSize = vamsasSet.getSequenceCount(); i < iSize; i++)
4998 Sequence vamsasSeq = vamsasSet.getSequence(i);
4999 ensureJalviewDatasetSequence(vamsasSeq, ds, dseqs, ignoreUnrefed, i);
5001 // create a new dataset
5004 SequenceI[] dsseqs = new SequenceI[dseqs.size()];
5005 dseqs.copyInto(dsseqs);
5006 ds = new jalview.datamodel.Alignment(dsseqs);
5007 debug("Created new dataset " + vamsasSet.getDatasetId()
5008 + " for alignment " + System.identityHashCode(al));
5009 addDatasetRef(vamsasSet.getDatasetId(), ds);
5011 // set the dataset for the newly imported alignment.
5012 if (al.getDataset() == null && !ignoreUnrefed)
5021 * sequence definition to create/merge dataset sequence for
5025 * vector to add new dataset sequence to
5026 * @param ignoreUnrefed
5027 * - when true, don't create new sequences from vamsasSeq if it's id
5028 * doesn't already have an asssociated Jalview sequence.
5030 * - used to reorder the sequence in the alignment according to the
5031 * vamsasSeq array ordering, to preserve ordering of dataset
5033 private void ensureJalviewDatasetSequence(Sequence vamsasSeq,
5034 AlignmentI ds, Vector dseqs, boolean ignoreUnrefed, int vseqpos)
5036 // JBP TODO: Check this is called for AlCodonFrames to support recovery of
5038 SequenceI sq = seqRefIds.get(vamsasSeq.getId());
5039 boolean reorder = false;
5040 SequenceI dsq = null;
5041 if (sq != null && sq.getDatasetSequence() != null)
5043 dsq = sq.getDatasetSequence();
5049 if (sq == null && ignoreUnrefed)
5053 String sqid = vamsasSeq.getDsseqid();
5056 // need to create or add a new dataset sequence reference to this sequence
5059 dsq = seqRefIds.get(sqid);
5064 // make a new dataset sequence
5065 dsq = sq.createDatasetSequence();
5068 // make up a new dataset reference for this sequence
5069 sqid = seqHash(dsq);
5071 dsq.setVamsasId(uniqueSetSuffix + sqid);
5072 seqRefIds.put(sqid, dsq);
5077 dseqs.addElement(dsq);
5082 ds.addSequence(dsq);
5088 { // make this dataset sequence sq's dataset sequence
5089 sq.setDatasetSequence(dsq);
5090 // and update the current dataset alignment
5095 if (!dseqs.contains(dsq))
5102 if (ds.findIndex(dsq) < 0)
5104 ds.addSequence(dsq);
5111 // TODO: refactor this as a merge dataset sequence function
5112 // now check that sq (the dataset sequence) sequence really is the union of
5113 // all references to it
5114 // boolean pre = sq.getStart() < dsq.getStart();
5115 // boolean post = sq.getEnd() > dsq.getEnd();
5119 // StringBuffer sb = new StringBuffer();
5120 String newres = jalview.analysis.AlignSeq.extractGaps(
5121 jalview.util.Comparison.GapChars, sq.getSequenceAsString());
5122 if (!newres.equalsIgnoreCase(dsq.getSequenceAsString())
5123 && newres.length() > dsq.getLength())
5125 // Update with the longer sequence.
5129 * if (pre) { sb.insert(0, newres .substring(0, dsq.getStart() -
5130 * sq.getStart())); dsq.setStart(sq.getStart()); } if (post) {
5131 * sb.append(newres.substring(newres.length() - sq.getEnd() -
5132 * dsq.getEnd())); dsq.setEnd(sq.getEnd()); }
5134 dsq.setSequence(newres);
5136 // TODO: merges will never happen if we 'know' we have the real dataset
5137 // sequence - this should be detected when id==dssid
5139 "DEBUG Notice: Merged dataset sequence (if you see this often, post at http://issues.jalview.org/browse/JAL-1474)"); // ("
5140 // + (pre ? "prepended" : "") + " "
5141 // + (post ? "appended" : ""));
5146 // sequence refs are identical. We may need to update the existing dataset
5147 // alignment with this one, though.
5148 if (ds != null && dseqs == null)
5150 int opos = ds.findIndex(dsq);
5151 SequenceI tseq = null;
5152 if (opos != -1 && vseqpos != opos)
5154 // remove from old position
5155 ds.deleteSequence(dsq);
5157 if (vseqpos < ds.getHeight())
5159 if (vseqpos != opos)
5161 // save sequence at destination position
5162 tseq = ds.getSequenceAt(vseqpos);
5163 ds.replaceSequenceAt(vseqpos, dsq);
5164 ds.addSequence(tseq);
5169 ds.addSequence(dsq);
5176 * TODO use AlignmentI here and in related methods - needs
5177 * AlignmentI.getDataset() changed to return AlignmentI instead of Alignment
5179 Hashtable<String, AlignmentI> datasetIds = null;
5181 IdentityHashMap<AlignmentI, String> dataset2Ids = null;
5183 private AlignmentI getDatasetFor(String datasetId)
5185 if (datasetIds == null)
5187 datasetIds = new Hashtable<>();
5190 if (datasetIds.containsKey(datasetId))
5192 return datasetIds.get(datasetId);
5197 private void addDatasetRef(String datasetId, AlignmentI dataset)
5199 if (datasetIds == null)
5201 datasetIds = new Hashtable<>();
5203 datasetIds.put(datasetId, dataset);
5207 * make a new dataset ID for this jalview dataset alignment
5212 private String getDatasetIdRef(AlignmentI dataset)
5214 if (dataset.getDataset() != null)
5216 warn("Serious issue! Dataset Object passed to getDatasetIdRef is not a Jalview DATASET alignment...");
5218 String datasetId = makeHashCode(dataset, null);
5219 if (datasetId == null)
5221 // make a new datasetId and record it
5222 if (dataset2Ids == null)
5224 dataset2Ids = new IdentityHashMap<>();
5228 datasetId = dataset2Ids.get(dataset);
5230 if (datasetId == null)
5232 datasetId = "ds" + dataset2Ids.size() + 1;
5233 dataset2Ids.put(dataset, datasetId);
5239 private void addDBRefs(SequenceI datasetSequence, Sequence sequence)
5241 for (int d = 0; d < sequence.getDBRefCount(); d++)
5243 DBRef dr = sequence.getDBRef(d);
5244 jalview.datamodel.DBRefEntry entry = new jalview.datamodel.DBRefEntry(
5245 sequence.getDBRef(d).getSource(),
5246 sequence.getDBRef(d).getVersion(),
5247 sequence.getDBRef(d).getAccessionId());
5248 if (dr.getMapping() != null)
5250 entry.setMap(addMapping(dr.getMapping()));
5252 datasetSequence.addDBRef(entry);
5256 private jalview.datamodel.Mapping addMapping(Mapping m)
5258 SequenceI dsto = null;
5259 // Mapping m = dr.getMapping();
5260 int fr[] = new int[m.getMapListFromCount() * 2];
5261 Enumeration f = m.enumerateMapListFrom();
5262 for (int _i = 0; f.hasMoreElements(); _i += 2)
5264 MapListFrom mf = (MapListFrom) f.nextElement();
5265 fr[_i] = mf.getStart();
5266 fr[_i + 1] = mf.getEnd();
5268 int fto[] = new int[m.getMapListToCount() * 2];
5269 f = m.enumerateMapListTo();
5270 for (int _i = 0; f.hasMoreElements(); _i += 2)
5272 MapListTo mf = (MapListTo) f.nextElement();
5273 fto[_i] = mf.getStart();
5274 fto[_i + 1] = mf.getEnd();
5276 jalview.datamodel.Mapping jmap = new jalview.datamodel.Mapping(dsto, fr,
5277 fto, (int) m.getMapFromUnit(), (int) m.getMapToUnit());
5278 if (m.getMappingChoice() != null)
5280 MappingChoice mc = m.getMappingChoice();
5281 if (mc.getDseqFor() != null)
5283 String dsfor = "" + mc.getDseqFor();
5284 if (seqRefIds.containsKey(dsfor))
5289 jmap.setTo(seqRefIds.get(dsfor));
5293 frefedSequence.add(newMappingRef(dsfor, jmap));
5299 * local sequence definition
5301 Sequence ms = mc.getSequence();
5302 SequenceI djs = null;
5303 String sqid = ms.getDsseqid();
5304 if (sqid != null && sqid.length() > 0)
5307 * recover dataset sequence
5309 djs = seqRefIds.get(sqid);
5314 "Warning - making up dataset sequence id for DbRef sequence map reference");
5315 sqid = ((Object) ms).toString(); // make up a new hascode for
5316 // undefined dataset sequence hash
5317 // (unlikely to happen)
5323 * make a new dataset sequence and add it to refIds hash
5325 djs = new jalview.datamodel.Sequence(ms.getName(),
5327 djs.setStart(jmap.getMap().getToLowest());
5328 djs.setEnd(jmap.getMap().getToHighest());
5329 djs.setVamsasId(uniqueSetSuffix + sqid);
5331 incompleteSeqs.put(sqid, djs);
5332 seqRefIds.put(sqid, djs);
5335 jalview.bin.Cache.log.debug("about to recurse on addDBRefs.");
5344 public jalview.gui.AlignmentPanel copyAlignPanel(AlignmentPanel ap,
5345 boolean keepSeqRefs)
5348 JalviewModel jm = saveState(ap, null, null, null);
5353 jm.getJalviewModelSequence().getViewport(0).setSequenceSetId(null);
5357 uniqueSetSuffix = "";
5358 jm.getJalviewModelSequence().getViewport(0).setId(null); // we don't
5363 if (this.frefedSequence == null)
5365 frefedSequence = new Vector();
5368 viewportsAdded.clear();
5370 AlignFrame af = loadFromObject(jm, null, false, null);
5371 af.alignPanels.clear();
5372 af.closeMenuItem_actionPerformed(true);
5375 * if(ap.av.getAlignment().getAlignmentAnnotation()!=null) { for(int i=0;
5376 * i<ap.av.getAlignment().getAlignmentAnnotation().length; i++) {
5377 * if(!ap.av.getAlignment().getAlignmentAnnotation()[i].autoCalculated) {
5378 * af.alignPanel.av.getAlignment().getAlignmentAnnotation()[i] =
5379 * ap.av.getAlignment().getAlignmentAnnotation()[i]; } } }
5382 return af.alignPanel;
5386 * flag indicating if hashtables should be cleared on finalization TODO this
5387 * flag may not be necessary
5389 private final boolean _cleartables = true;
5391 private Hashtable jvids2vobj;
5396 * @see java.lang.Object#finalize()
5399 protected void finalize() throws Throwable
5401 // really make sure we have no buried refs left.
5406 this.seqRefIds = null;
5407 this.seqsToIds = null;
5411 private void warn(String msg)
5416 private void warn(String msg, Exception e)
5418 if (Cache.log != null)
5422 Cache.log.warn(msg, e);
5426 Cache.log.warn(msg);
5431 System.err.println("Warning: " + msg);
5434 e.printStackTrace();
5439 private void debug(String string)
5441 debug(string, null);
5444 private void debug(String msg, Exception e)
5446 if (Cache.log != null)
5450 Cache.log.debug(msg, e);
5454 Cache.log.debug(msg);
5459 System.err.println("Warning: " + msg);
5462 e.printStackTrace();
5468 * set the object to ID mapping tables used to write/recover objects and XML
5469 * ID strings for the jalview project. If external tables are provided then
5470 * finalize and clearSeqRefs will not clear the tables when the Jalview2XML
5471 * object goes out of scope. - also populates the datasetIds hashtable with
5472 * alignment objects containing dataset sequences
5475 * Map from ID strings to jalview datamodel
5477 * Map from jalview datamodel to ID strings
5481 public void setObjectMappingTables(Hashtable vobj2jv,
5482 IdentityHashMap jv2vobj)
5484 this.jv2vobj = jv2vobj;
5485 this.vobj2jv = vobj2jv;
5486 Iterator ds = jv2vobj.keySet().iterator();
5488 while (ds.hasNext())
5490 Object jvobj = ds.next();
5491 id = jv2vobj.get(jvobj).toString();
5492 if (jvobj instanceof jalview.datamodel.Alignment)
5494 if (((jalview.datamodel.Alignment) jvobj).getDataset() == null)
5496 addDatasetRef(id, (jalview.datamodel.Alignment) jvobj);
5499 else if (jvobj instanceof jalview.datamodel.Sequence)
5501 // register sequence object so the XML parser can recover it.
5502 if (seqRefIds == null)
5504 seqRefIds = new HashMap<>();
5506 if (seqsToIds == null)
5508 seqsToIds = new IdentityHashMap<>();
5510 seqRefIds.put(jv2vobj.get(jvobj).toString(), (SequenceI) jvobj);
5511 seqsToIds.put((SequenceI) jvobj, id);
5513 else if (jvobj instanceof jalview.datamodel.AlignmentAnnotation)
5516 AlignmentAnnotation jvann = (AlignmentAnnotation) jvobj;
5517 annotationIds.put(anid = jv2vobj.get(jvobj).toString(), jvann);
5518 if (jvann.annotationId == null)
5520 jvann.annotationId = anid;
5522 if (!jvann.annotationId.equals(anid))
5524 // TODO verify that this is the correct behaviour
5525 this.warn("Overriding Annotation ID for " + anid
5526 + " from different id : " + jvann.annotationId);
5527 jvann.annotationId = anid;
5530 else if (jvobj instanceof String)
5532 if (jvids2vobj == null)
5534 jvids2vobj = new Hashtable();
5535 jvids2vobj.put(jvobj, jv2vobj.get(jvobj).toString());
5540 Cache.log.debug("Ignoring " + jvobj.getClass() + " (ID = " + id);
5546 * set the uniqueSetSuffix used to prefix/suffix object IDs for jalview
5547 * objects created from the project archive. If string is null (default for
5548 * construction) then suffix will be set automatically.
5552 public void setUniqueSetSuffix(String string)
5554 uniqueSetSuffix = string;
5559 * uses skipList2 as the skipList for skipping views on sequence sets
5560 * associated with keys in the skipList
5564 public void setSkipList(Hashtable skipList2)
5566 skipList = skipList2;
5570 * Reads the jar entry of given name and returns its contents, or null if the
5571 * entry is not found.
5574 * @param jarEntryName
5577 protected String readJarEntry(jarInputStreamProvider jprovider,
5578 String jarEntryName)
5580 String result = null;
5581 BufferedReader in = null;
5586 * Reopen the jar input stream and traverse its entries to find a matching
5589 JarInputStream jin = jprovider.getJarInputStream();
5590 JarEntry entry = null;
5593 entry = jin.getNextJarEntry();
5594 } while (entry != null && !entry.getName().equals(jarEntryName));
5598 StringBuilder out = new StringBuilder(256);
5599 in = new BufferedReader(new InputStreamReader(jin, UTF_8));
5602 while ((data = in.readLine()) != null)
5606 result = out.toString();
5610 warn("Couldn't find entry in Jalview Jar for " + jarEntryName);
5612 } catch (Exception ex)
5614 ex.printStackTrace();
5622 } catch (IOException e)
5633 * Returns an incrementing counter (0, 1, 2...)
5637 private synchronized int nextCounter()