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);
2298 af.setMenusForViewport();
2300 } catch (MalformedURLException e)
2302 errorMessage = "Invalid URL format for '" + file + "'";
2308 SwingUtilities.invokeAndWait(new Runnable()
2313 setLoadingFinishedForNewStructureViewers();
2316 } catch (Exception x)
2318 System.err.println("Error loading alignment: " + x.getMessage());
2324 private jarInputStreamProvider createjarInputStreamProvider(
2325 final String file) throws MalformedURLException
2328 errorMessage = null;
2329 uniqueSetSuffix = null;
2331 viewportsAdded.clear();
2332 frefedSequence = null;
2334 if (file.startsWith("http://"))
2336 url = new URL(file);
2338 final URL _url = url;
2339 return new jarInputStreamProvider()
2343 public JarInputStream getJarInputStream() throws IOException
2347 return new JarInputStream(_url.openStream());
2351 return new JarInputStream(new FileInputStream(file));
2356 public String getFilename()
2364 * Recover jalview session from a jalview project archive. Caller may
2365 * initialise uniqueSetSuffix, seqRefIds, viewportsAdded and frefedSequence
2366 * themselves. Any null fields will be initialised with default values,
2367 * non-null fields are left alone.
2372 public AlignFrame loadJalviewAlign(final jarInputStreamProvider jprovider)
2374 errorMessage = null;
2375 if (uniqueSetSuffix == null)
2377 uniqueSetSuffix = System.currentTimeMillis() % 100000 + "";
2379 if (seqRefIds == null)
2383 AlignFrame af = null, _af = null;
2384 IdentityHashMap<AlignmentI, AlignmentI> importedDatasets = new IdentityHashMap<>();
2385 Map<String, AlignFrame> gatherToThisFrame = new HashMap<>();
2386 final String file = jprovider.getFilename();
2389 JarInputStream jin = null;
2390 JarEntry jarentry = null;
2395 jin = jprovider.getJarInputStream();
2396 for (int i = 0; i < entryCount; i++)
2398 jarentry = jin.getNextJarEntry();
2401 if (jarentry != null && jarentry.getName().endsWith(".xml"))
2403 InputStreamReader in = new InputStreamReader(jin, UTF_8);
2404 JalviewModel object = new JalviewModel();
2406 Unmarshaller unmar = new Unmarshaller(object);
2407 unmar.setValidation(false);
2408 object = (JalviewModel) unmar.unmarshal(in);
2409 if (true) // !skipViewport(object))
2411 _af = loadFromObject(object, file, true, jprovider);
2412 if (_af != null && object.getJalviewModelSequence()
2413 .getViewportCount() > 0)
2417 // store a reference to the first view
2420 if (_af.viewport.isGatherViewsHere())
2422 // if this is a gathered view, keep its reference since
2423 // after gathering views, only this frame will remain
2425 gatherToThisFrame.put(_af.viewport.getSequenceSetId(), _af);
2427 // Save dataset to register mappings once all resolved
2428 importedDatasets.put(af.viewport.getAlignment().getDataset(),
2429 af.viewport.getAlignment().getDataset());
2434 else if (jarentry != null)
2436 // Some other file here.
2439 } while (jarentry != null);
2440 resolveFrefedSequences();
2441 } catch (IOException ex)
2443 ex.printStackTrace();
2444 errorMessage = "Couldn't locate Jalview XML file : " + file;
2446 "Exception whilst loading jalview XML file : " + ex + "\n");
2447 } catch (Exception ex)
2449 System.err.println("Parsing as Jalview Version 2 file failed.");
2450 ex.printStackTrace(System.err);
2451 if (attemptversion1parse)
2453 // Is Version 1 Jar file?
2456 af = new Jalview2XML_V1(raiseGUI).LoadJalviewAlign(jprovider);
2457 } catch (Exception ex2)
2459 System.err.println("Exception whilst loading as jalviewXMLV1:");
2460 ex2.printStackTrace();
2464 if (Desktop.instance != null)
2466 Desktop.instance.stopLoading();
2470 System.out.println("Successfully loaded archive file");
2473 ex.printStackTrace();
2476 "Exception whilst loading jalview XML file : " + ex + "\n");
2477 } catch (OutOfMemoryError e)
2479 // Don't use the OOM Window here
2480 errorMessage = "Out of memory loading jalview XML file";
2481 System.err.println("Out of memory whilst loading jalview XML file");
2482 e.printStackTrace();
2486 * Regather multiple views (with the same sequence set id) to the frame (if
2487 * any) that is flagged as the one to gather to, i.e. convert them to tabbed
2488 * views instead of separate frames. Note this doesn't restore a state where
2489 * some expanded views in turn have tabbed views - the last "first tab" read
2490 * in will play the role of gatherer for all.
2492 for (AlignFrame fr : gatherToThisFrame.values())
2494 Desktop.instance.gatherViews(fr);
2497 restoreSplitFrames();
2498 for (AlignmentI ds : importedDatasets.keySet())
2500 if (ds.getCodonFrames() != null)
2502 StructureSelectionManager
2503 .getStructureSelectionManager(Desktop.instance)
2504 .registerMappings(ds.getCodonFrames());
2507 if (errorMessage != null)
2512 if (Desktop.instance != null)
2514 Desktop.instance.stopLoading();
2521 * Try to reconstruct and display SplitFrame windows, where each contains
2522 * complementary dna and protein alignments. Done by pairing up AlignFrame
2523 * objects (created earlier) which have complementary viewport ids associated.
2525 protected void restoreSplitFrames()
2527 List<SplitFrame> gatherTo = new ArrayList<>();
2528 List<AlignFrame> addedToSplitFrames = new ArrayList<>();
2529 Map<String, AlignFrame> dna = new HashMap<>();
2532 * Identify the DNA alignments
2534 for (Entry<Viewport, AlignFrame> candidate : splitFrameCandidates
2537 AlignFrame af = candidate.getValue();
2538 if (af.getViewport().getAlignment().isNucleotide())
2540 dna.put(candidate.getKey().getId(), af);
2545 * Try to match up the protein complements
2547 for (Entry<Viewport, AlignFrame> candidate : splitFrameCandidates
2550 AlignFrame af = candidate.getValue();
2551 if (!af.getViewport().getAlignment().isNucleotide())
2553 String complementId = candidate.getKey().getComplementId();
2554 // only non-null complements should be in the Map
2555 if (complementId != null && dna.containsKey(complementId))
2557 final AlignFrame dnaFrame = dna.get(complementId);
2558 SplitFrame sf = createSplitFrame(dnaFrame, af);
2559 addedToSplitFrames.add(dnaFrame);
2560 addedToSplitFrames.add(af);
2561 dnaFrame.setMenusForViewport();
2562 af.setMenusForViewport();
2563 if (af.viewport.isGatherViewsHere())
2572 * Open any that we failed to pair up (which shouldn't happen!) as
2573 * standalone AlignFrame's.
2575 for (Entry<Viewport, AlignFrame> candidate : splitFrameCandidates
2578 AlignFrame af = candidate.getValue();
2579 if (!addedToSplitFrames.contains(af))
2581 Viewport view = candidate.getKey();
2582 Desktop.addInternalFrame(af, view.getTitle(), view.getWidth(),
2584 af.setMenusForViewport();
2585 System.err.println("Failed to restore view " + view.getTitle()
2586 + " to split frame");
2591 * Gather back into tabbed views as flagged.
2593 for (SplitFrame sf : gatherTo)
2595 Desktop.instance.gatherViews(sf);
2598 splitFrameCandidates.clear();
2602 * Construct and display one SplitFrame holding DNA and protein alignments.
2605 * @param proteinFrame
2608 protected SplitFrame createSplitFrame(AlignFrame dnaFrame,
2609 AlignFrame proteinFrame)
2611 SplitFrame splitFrame = new SplitFrame(dnaFrame, proteinFrame);
2612 String title = MessageManager.getString("label.linked_view_title");
2613 int width = (int) dnaFrame.getBounds().getWidth();
2614 int height = (int) (dnaFrame.getBounds().getHeight()
2615 + proteinFrame.getBounds().getHeight() + 50);
2618 * SplitFrame location is saved to both enclosed frames
2620 splitFrame.setLocation(dnaFrame.getX(), dnaFrame.getY());
2621 Desktop.addInternalFrame(splitFrame, title, width, height);
2624 * And compute cDNA consensus (couldn't do earlier with consensus as
2625 * mappings were not yet present)
2627 proteinFrame.viewport.alignmentChanged(proteinFrame.alignPanel);
2633 * check errorMessage for a valid error message and raise an error box in the
2634 * GUI or write the current errorMessage to stderr and then clear the error
2637 protected void reportErrors()
2639 reportErrors(false);
2642 protected void reportErrors(final boolean saving)
2644 if (errorMessage != null)
2646 final String finalErrorMessage = errorMessage;
2649 javax.swing.SwingUtilities.invokeLater(new Runnable()
2654 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
2656 "Error " + (saving ? "saving" : "loading")
2658 JvOptionPane.WARNING_MESSAGE);
2664 System.err.println("Problem loading Jalview file: " + errorMessage);
2667 errorMessage = null;
2670 Map<String, String> alreadyLoadedPDB = new HashMap<>();
2673 * when set, local views will be updated from view stored in JalviewXML
2674 * Currently (28th Sep 2008) things will go horribly wrong in vamsas document
2675 * sync if this is set to true.
2677 private final boolean updateLocalViews = false;
2680 * Returns the path to a temporary file holding the PDB file for the given PDB
2681 * id. The first time of asking, searches for a file of that name in the
2682 * Jalview project jar, and copies it to a new temporary file. Any repeat
2683 * requests just return the path to the file previously created.
2689 String loadPDBFile(jarInputStreamProvider jprovider, String pdbId,
2692 if (alreadyLoadedPDB.containsKey(pdbId))
2694 return alreadyLoadedPDB.get(pdbId).toString();
2697 String tempFile = copyJarEntry(jprovider, pdbId, "jalview_pdb",
2699 if (tempFile != null)
2701 alreadyLoadedPDB.put(pdbId, tempFile);
2707 * Copies the jar entry of given name to a new temporary file and returns the
2708 * path to the file, or null if the entry is not found.
2711 * @param jarEntryName
2713 * a prefix for the temporary file name, must be at least three
2716 * null or original file - so new file can be given the same suffix
2720 protected String copyJarEntry(jarInputStreamProvider jprovider,
2721 String jarEntryName, String prefix, String origFile)
2723 BufferedReader in = null;
2724 PrintWriter out = null;
2725 String suffix = ".tmp";
2726 if (origFile == null)
2728 origFile = jarEntryName;
2730 int sfpos = origFile.lastIndexOf(".");
2731 if (sfpos > -1 && sfpos < (origFile.length() - 3))
2733 suffix = "." + origFile.substring(sfpos + 1);
2737 JarInputStream jin = jprovider.getJarInputStream();
2739 * if (jprovider.startsWith("http://")) { jin = new JarInputStream(new
2740 * URL(jprovider).openStream()); } else { jin = new JarInputStream(new
2741 * FileInputStream(jprovider)); }
2744 JarEntry entry = null;
2747 entry = jin.getNextJarEntry();
2748 } while (entry != null && !entry.getName().equals(jarEntryName));
2751 in = new BufferedReader(new InputStreamReader(jin, UTF_8));
2752 File outFile = File.createTempFile(prefix, suffix);
2753 outFile.deleteOnExit();
2754 out = new PrintWriter(new FileOutputStream(outFile));
2757 while ((data = in.readLine()) != null)
2762 String t = outFile.getAbsolutePath();
2767 warn("Couldn't find entry in Jalview Jar for " + jarEntryName);
2769 } catch (Exception ex)
2771 ex.printStackTrace();
2779 } catch (IOException e)
2793 private class JvAnnotRow
2795 public JvAnnotRow(int i, AlignmentAnnotation jaa)
2802 * persisted version of annotation row from which to take vis properties
2804 public jalview.datamodel.AlignmentAnnotation template;
2807 * original position of the annotation row in the alignment
2813 * Load alignment frame from jalview XML DOM object
2818 * filename source string
2819 * @param loadTreesAndStructures
2820 * when false only create Viewport
2822 * data source provider
2823 * @return alignment frame created from view stored in DOM
2825 AlignFrame loadFromObject(JalviewModel object, String file,
2826 boolean loadTreesAndStructures, jarInputStreamProvider jprovider)
2828 SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);
2829 Sequence[] vamsasSeq = vamsasSet.getSequence();
2831 JalviewModelSequence jms = object.getJalviewModelSequence();
2833 Viewport view = (jms.getViewportCount() > 0) ? jms.getViewport(0)
2836 // ////////////////////////////////
2839 List<SequenceI> hiddenSeqs = null;
2841 List<SequenceI> tmpseqs = new ArrayList<>();
2843 boolean multipleView = false;
2844 SequenceI referenceseqForView = null;
2845 JSeq[] jseqs = object.getJalviewModelSequence().getJSeq();
2846 int vi = 0; // counter in vamsasSeq array
2847 for (int i = 0; i < jseqs.length; i++)
2849 String seqId = jseqs[i].getId();
2851 SequenceI tmpSeq = seqRefIds.get(seqId);
2854 if (!incompleteSeqs.containsKey(seqId))
2856 // may not need this check, but keep it for at least 2.9,1 release
2857 if (tmpSeq.getStart() != jseqs[i].getStart()
2858 || tmpSeq.getEnd() != jseqs[i].getEnd())
2861 "Warning JAL-2154 regression: updating start/end for sequence "
2862 + tmpSeq.toString() + " to " + jseqs[i]);
2867 incompleteSeqs.remove(seqId);
2869 if (vamsasSeq.length > vi && vamsasSeq[vi].getId().equals(seqId))
2871 // most likely we are reading a dataset XML document so
2872 // update from vamsasSeq section of XML for this sequence
2873 tmpSeq.setName(vamsasSeq[vi].getName());
2874 tmpSeq.setDescription(vamsasSeq[vi].getDescription());
2875 tmpSeq.setSequence(vamsasSeq[vi].getSequence());
2880 // reading multiple views, so vamsasSeq set is a subset of JSeq
2881 multipleView = true;
2883 tmpSeq.setStart(jseqs[i].getStart());
2884 tmpSeq.setEnd(jseqs[i].getEnd());
2885 tmpseqs.add(tmpSeq);
2889 tmpSeq = new jalview.datamodel.Sequence(vamsasSeq[vi].getName(),
2890 vamsasSeq[vi].getSequence());
2891 tmpSeq.setDescription(vamsasSeq[vi].getDescription());
2892 tmpSeq.setStart(jseqs[i].getStart());
2893 tmpSeq.setEnd(jseqs[i].getEnd());
2894 tmpSeq.setVamsasId(uniqueSetSuffix + seqId);
2895 seqRefIds.put(vamsasSeq[vi].getId(), tmpSeq);
2896 tmpseqs.add(tmpSeq);
2900 if (jseqs[i].hasViewreference() && jseqs[i].getViewreference())
2902 referenceseqForView = tmpseqs.get(tmpseqs.size() - 1);
2905 if (jseqs[i].getHidden())
2907 if (hiddenSeqs == null)
2909 hiddenSeqs = new ArrayList<>();
2912 hiddenSeqs.add(tmpSeq);
2917 // Create the alignment object from the sequence set
2918 // ///////////////////////////////
2919 SequenceI[] orderedSeqs = tmpseqs
2920 .toArray(new SequenceI[tmpseqs.size()]);
2922 AlignmentI al = null;
2923 // so we must create or recover the dataset alignment before going further
2924 // ///////////////////////////////
2925 if (vamsasSet.getDatasetId() == null || vamsasSet.getDatasetId() == "")
2927 // older jalview projects do not have a dataset - so creat alignment and
2929 al = new Alignment(orderedSeqs);
2930 al.setDataset(null);
2934 boolean isdsal = object.getJalviewModelSequence()
2935 .getViewportCount() == 0;
2938 // we are importing a dataset record, so
2939 // recover reference to an alignment already materialsed as dataset
2940 al = getDatasetFor(vamsasSet.getDatasetId());
2944 // materialse the alignment
2945 al = new Alignment(orderedSeqs);
2949 addDatasetRef(vamsasSet.getDatasetId(), al);
2952 // finally, verify all data in vamsasSet is actually present in al
2953 // passing on flag indicating if it is actually a stored dataset
2954 recoverDatasetFor(vamsasSet, al, isdsal);
2957 if (referenceseqForView != null)
2959 al.setSeqrep(referenceseqForView);
2961 // / Add the alignment properties
2962 for (int i = 0; i < vamsasSet.getSequenceSetPropertiesCount(); i++)
2964 SequenceSetProperties ssp = vamsasSet.getSequenceSetProperties(i);
2965 al.setProperty(ssp.getKey(), ssp.getValue());
2968 // ///////////////////////////////
2970 Hashtable pdbloaded = new Hashtable(); // TODO nothing writes to this??
2973 // load sequence features, database references and any associated PDB
2974 // structures for the alignment
2976 // prior to 2.10, this part would only be executed the first time a
2977 // sequence was encountered, but not afterwards.
2978 // now, for 2.10 projects, this is also done if the xml doc includes
2979 // dataset sequences not actually present in any particular view.
2981 for (int i = 0; i < vamsasSeq.length; i++)
2983 if (jseqs[i].getFeaturesCount() > 0)
2985 Features[] features = jseqs[i].getFeatures();
2986 for (int f = 0; f < features.length; f++)
2988 SequenceFeature sf = new SequenceFeature(features[f].getType(),
2989 features[f].getDescription(), features[f].getBegin(),
2990 features[f].getEnd(), features[f].getScore(),
2991 features[f].getFeatureGroup());
2992 sf.setStatus(features[f].getStatus());
2993 for (int od = 0; od < features[f].getOtherDataCount(); od++)
2995 OtherData keyValue = features[f].getOtherData(od);
2996 if (keyValue.getKey().startsWith("LINK"))
2998 sf.addLink(keyValue.getValue());
3002 sf.setValue(keyValue.getKey(), keyValue.getValue());
3006 // adds feature to datasequence's feature set (since Jalview 2.10)
3007 al.getSequenceAt(i).addSequenceFeature(sf);
3010 if (vamsasSeq[i].getDBRefCount() > 0)
3012 // adds dbrefs to datasequence's set (since Jalview 2.10)
3014 al.getSequenceAt(i).getDatasetSequence() == null
3015 ? al.getSequenceAt(i)
3016 : al.getSequenceAt(i).getDatasetSequence(),
3019 if (jseqs[i].getPdbidsCount() > 0)
3021 Pdbids[] ids = jseqs[i].getPdbids();
3022 for (int p = 0; p < ids.length; p++)
3024 jalview.datamodel.PDBEntry entry = new jalview.datamodel.PDBEntry();
3025 entry.setId(ids[p].getId());
3026 if (ids[p].getType() != null)
3028 if (PDBEntry.Type.getType(ids[p].getType()) != null)
3030 entry.setType(PDBEntry.Type.getType(ids[p].getType()));
3034 entry.setType(PDBEntry.Type.FILE);
3037 // jprovider is null when executing 'New View'
3038 if (ids[p].getFile() != null && jprovider != null)
3040 if (!pdbloaded.containsKey(ids[p].getFile()))
3042 entry.setFile(loadPDBFile(jprovider, ids[p].getId(),
3047 entry.setFile(pdbloaded.get(ids[p].getId()).toString());
3050 if (ids[p].getPdbentryItem() != null)
3052 for (PdbentryItem item : ids[p].getPdbentryItem())
3054 for (Property pr : item.getProperty())
3056 entry.setProperty(pr.getName(), pr.getValue());
3060 StructureSelectionManager
3061 .getStructureSelectionManager(Desktop.instance)
3062 .registerPDBEntry(entry);
3063 // adds PDBEntry to datasequence's set (since Jalview 2.10)
3064 if (al.getSequenceAt(i).getDatasetSequence() != null)
3066 al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
3070 al.getSequenceAt(i).addPDBId(entry);
3075 } // end !multipleview
3077 // ///////////////////////////////
3078 // LOAD SEQUENCE MAPPINGS
3080 if (vamsasSet.getAlcodonFrameCount() > 0)
3082 // TODO Potentially this should only be done once for all views of an
3084 AlcodonFrame[] alc = vamsasSet.getAlcodonFrame();
3085 for (int i = 0; i < alc.length; i++)
3087 AlignedCodonFrame cf = new AlignedCodonFrame();
3088 if (alc[i].getAlcodMapCount() > 0)
3090 AlcodMap[] maps = alc[i].getAlcodMap();
3091 for (int m = 0; m < maps.length; m++)
3093 SequenceI dnaseq = seqRefIds.get(maps[m].getDnasq());
3095 jalview.datamodel.Mapping mapping = null;
3096 // attach to dna sequence reference.
3097 if (maps[m].getMapping() != null)
3099 mapping = addMapping(maps[m].getMapping());
3100 if (dnaseq != null && mapping.getTo() != null)
3102 cf.addMap(dnaseq, mapping.getTo(), mapping.getMap());
3108 newAlcodMapRef(maps[m].getDnasq(), cf, mapping));
3112 al.addCodonFrame(cf);
3117 // ////////////////////////////////
3119 List<JvAnnotRow> autoAlan = new ArrayList<>();
3122 * store any annotations which forward reference a group's ID
3124 Map<String, List<AlignmentAnnotation>> groupAnnotRefs = new Hashtable<>();
3126 if (vamsasSet.getAnnotationCount() > 0)
3128 Annotation[] an = vamsasSet.getAnnotation();
3130 for (int i = 0; i < an.length; i++)
3132 Annotation annotation = an[i];
3135 * test if annotation is automatically calculated for this view only
3137 boolean autoForView = false;
3138 if (annotation.getLabel().equals("Quality")
3139 || annotation.getLabel().equals("Conservation")
3140 || annotation.getLabel().equals("Consensus"))
3142 // Kludge for pre 2.5 projects which lacked the autocalculated flag
3144 if (!annotation.hasAutoCalculated())
3146 annotation.setAutoCalculated(true);
3149 if (autoForView || (annotation.hasAutoCalculated()
3150 && annotation.isAutoCalculated()))
3152 // remove ID - we don't recover annotation from other views for
3153 // view-specific annotation
3154 annotation.setId(null);
3157 // set visiblity for other annotation in this view
3158 String annotationId = annotation.getId();
3159 if (annotationId != null && annotationIds.containsKey(annotationId))
3161 AlignmentAnnotation jda = annotationIds.get(annotationId);
3162 // in principle Visible should always be true for annotation displayed
3163 // in multiple views
3164 if (annotation.hasVisible())
3166 jda.visible = annotation.getVisible();
3169 al.addAnnotation(jda);
3173 // Construct new annotation from model.
3174 AnnotationElement[] ae = annotation.getAnnotationElement();
3175 jalview.datamodel.Annotation[] anot = null;
3176 java.awt.Color firstColour = null;
3178 if (!annotation.getScoreOnly())
3180 anot = new jalview.datamodel.Annotation[al.getWidth()];
3181 for (int aa = 0; aa < ae.length && aa < anot.length; aa++)
3183 anpos = ae[aa].getPosition();
3185 if (anpos >= anot.length)
3190 anot[anpos] = new jalview.datamodel.Annotation(
3192 ae[aa].getDisplayCharacter(), ae[aa].getDescription(),
3193 (ae[aa].getSecondaryStructure() == null
3194 || ae[aa].getSecondaryStructure().length() == 0)
3196 : ae[aa].getSecondaryStructure()
3201 // JBPNote: Consider verifying dataflow for IO of secondary
3202 // structure annotation read from Stockholm files
3203 // this was added to try to ensure that
3204 // if (anot[ae[aa].getPosition()].secondaryStructure>' ')
3206 // anot[ae[aa].getPosition()].displayCharacter = "";
3208 anot[anpos].colour = new java.awt.Color(ae[aa].getColour());
3209 if (firstColour == null)
3211 firstColour = anot[anpos].colour;
3215 jalview.datamodel.AlignmentAnnotation jaa = null;
3217 if (annotation.getGraph())
3219 float llim = 0, hlim = 0;
3220 // if (autoForView || an[i].isAutoCalculated()) {
3223 jaa = new jalview.datamodel.AlignmentAnnotation(
3224 annotation.getLabel(), annotation.getDescription(), anot,
3225 llim, hlim, annotation.getGraphType());
3227 jaa.graphGroup = annotation.getGraphGroup();
3228 jaa._linecolour = firstColour;
3229 if (annotation.getThresholdLine() != null)
3231 jaa.setThreshold(new jalview.datamodel.GraphLine(
3232 annotation.getThresholdLine().getValue(),
3233 annotation.getThresholdLine().getLabel(),
3235 annotation.getThresholdLine().getColour())));
3238 if (autoForView || annotation.isAutoCalculated())
3240 // Hardwire the symbol display line to ensure that labels for
3241 // histograms are displayed
3247 jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
3248 an[i].getDescription(), anot);
3249 jaa._linecolour = firstColour;
3251 // register new annotation
3252 if (an[i].getId() != null)
3254 annotationIds.put(an[i].getId(), jaa);
3255 jaa.annotationId = an[i].getId();
3257 // recover sequence association
3258 String sequenceRef = an[i].getSequenceRef();
3259 if (sequenceRef != null)
3261 // from 2.9 sequenceRef is to sequence id (JAL-1781)
3262 SequenceI sequence = seqRefIds.get(sequenceRef);
3263 if (sequence == null)
3265 // in pre-2.9 projects sequence ref is to sequence name
3266 sequence = al.findName(sequenceRef);
3268 if (sequence != null)
3270 jaa.createSequenceMapping(sequence, 1, true);
3271 sequence.addAlignmentAnnotation(jaa);
3274 // and make a note of any group association
3275 if (an[i].getGroupRef() != null && an[i].getGroupRef().length() > 0)
3277 List<jalview.datamodel.AlignmentAnnotation> aal = groupAnnotRefs
3278 .get(an[i].getGroupRef());
3281 aal = new ArrayList<>();
3282 groupAnnotRefs.put(an[i].getGroupRef(), aal);
3287 if (an[i].hasScore())
3289 jaa.setScore(an[i].getScore());
3291 if (an[i].hasVisible())
3293 jaa.visible = an[i].getVisible();
3296 if (an[i].hasCentreColLabels())
3298 jaa.centreColLabels = an[i].getCentreColLabels();
3301 if (an[i].hasScaleColLabels())
3303 jaa.scaleColLabel = an[i].getScaleColLabels();
3305 if (an[i].hasAutoCalculated() && an[i].isAutoCalculated())
3307 // newer files have an 'autoCalculated' flag and store calculation
3308 // state in viewport properties
3309 jaa.autoCalculated = true; // means annotation will be marked for
3310 // update at end of load.
3312 if (an[i].hasGraphHeight())
3314 jaa.graphHeight = an[i].getGraphHeight();
3316 if (an[i].hasBelowAlignment())
3318 jaa.belowAlignment = an[i].isBelowAlignment();
3320 jaa.setCalcId(an[i].getCalcId());
3321 if (an[i].getPropertyCount() > 0)
3323 for (jalview.schemabinding.version2.Property prop : an[i]
3326 jaa.setProperty(prop.getName(), prop.getValue());
3329 if (jaa.autoCalculated)
3331 autoAlan.add(new JvAnnotRow(i, jaa));
3334 // if (!autoForView)
3336 // add autocalculated group annotation and any user created annotation
3338 al.addAnnotation(jaa);
3342 // ///////////////////////
3344 // Create alignment markup and styles for this view
3345 if (jms.getJGroupCount() > 0)
3347 JGroup[] groups = jms.getJGroup();
3348 boolean addAnnotSchemeGroup = false;
3349 for (int i = 0; i < groups.length; i++)
3351 JGroup jGroup = groups[i];
3352 ColourSchemeI cs = null;
3353 if (jGroup.getColour() != null)
3355 if (jGroup.getColour().startsWith("ucs"))
3357 cs = getUserColourScheme(jms, jGroup.getColour());
3359 else if (jGroup.getColour().equals("AnnotationColourGradient")
3360 && jGroup.getAnnotationColours() != null)
3362 addAnnotSchemeGroup = true;
3366 cs = ColourSchemeProperty.getColourScheme(al,
3367 jGroup.getColour());
3370 int pidThreshold = jGroup.getPidThreshold();
3372 Vector<SequenceI> seqs = new Vector<>();
3374 for (int s = 0; s < jGroup.getSeqCount(); s++)
3376 String seqId = jGroup.getSeq(s) + "";
3377 SequenceI ts = seqRefIds.get(seqId);
3381 seqs.addElement(ts);
3385 if (seqs.size() < 1)
3390 SequenceGroup sg = new SequenceGroup(seqs, jGroup.getName(), cs,
3391 jGroup.getDisplayBoxes(), jGroup.getDisplayText(),
3392 jGroup.getColourText(), jGroup.getStart(), jGroup.getEnd());
3393 sg.getGroupColourScheme().setThreshold(pidThreshold, true);
3394 sg.getGroupColourScheme()
3395 .setConservationInc(jGroup.getConsThreshold());
3396 sg.setOutlineColour(new java.awt.Color(jGroup.getOutlineColour()));
3398 sg.textColour = new java.awt.Color(jGroup.getTextCol1());
3399 sg.textColour2 = new java.awt.Color(jGroup.getTextCol2());
3400 sg.setShowNonconserved(
3401 jGroup.hasShowUnconserved() ? jGroup.isShowUnconserved()
3403 sg.thresholdTextColour = jGroup.getTextColThreshold();
3404 if (jGroup.hasShowConsensusHistogram())
3406 sg.setShowConsensusHistogram(jGroup.isShowConsensusHistogram());
3409 if (jGroup.hasShowSequenceLogo())
3411 sg.setshowSequenceLogo(jGroup.isShowSequenceLogo());
3413 if (jGroup.hasNormaliseSequenceLogo())
3415 sg.setNormaliseSequenceLogo(jGroup.isNormaliseSequenceLogo());
3417 if (jGroup.hasIgnoreGapsinConsensus())
3419 sg.setIgnoreGapsConsensus(jGroup.getIgnoreGapsinConsensus());
3421 if (jGroup.getConsThreshold() != 0)
3423 Conservation c = new Conservation("All", sg.getSequences(null), 0,
3426 c.verdict(false, 25);
3427 sg.cs.setConservation(c);
3430 if (jGroup.getId() != null && groupAnnotRefs.size() > 0)
3432 // re-instate unique group/annotation row reference
3433 List<AlignmentAnnotation> jaal = groupAnnotRefs
3434 .get(jGroup.getId());
3437 for (AlignmentAnnotation jaa : jaal)
3440 if (jaa.autoCalculated)
3442 // match up and try to set group autocalc alignment row for this
3444 if (jaa.label.startsWith("Consensus for "))
3446 sg.setConsensus(jaa);
3448 // match up and try to set group autocalc alignment row for this
3450 if (jaa.label.startsWith("Conservation for "))
3452 sg.setConservationRow(jaa);
3459 if (addAnnotSchemeGroup)
3461 // reconstruct the annotation colourscheme
3462 sg.setColourScheme(constructAnnotationColour(
3463 jGroup.getAnnotationColours(), null, al, jms, false));
3469 // only dataset in this model, so just return.
3472 // ///////////////////////////////
3475 // If we just load in the same jar file again, the sequenceSetId
3476 // will be the same, and we end up with multiple references
3477 // to the same sequenceSet. We must modify this id on load
3478 // so that each load of the file gives a unique id
3479 String uniqueSeqSetId = view.getSequenceSetId() + uniqueSetSuffix;
3480 String viewId = (view.getId() == null ? null
3481 : view.getId() + uniqueSetSuffix);
3482 AlignFrame af = null;
3483 AlignViewport av = null;
3484 // now check to see if we really need to create a new viewport.
3485 if (multipleView && viewportsAdded.size() == 0)
3487 // We recovered an alignment for which a viewport already exists.
3488 // TODO: fix up any settings necessary for overlaying stored state onto
3489 // state recovered from another document. (may not be necessary).
3490 // we may need a binding from a viewport in memory to one recovered from
3492 // and then recover its containing af to allow the settings to be applied.
3493 // TODO: fix for vamsas demo
3495 "About to recover a viewport for existing alignment: Sequence set ID is "
3497 Object seqsetobj = retrieveExistingObj(uniqueSeqSetId);
3498 if (seqsetobj != null)
3500 if (seqsetobj instanceof String)
3502 uniqueSeqSetId = (String) seqsetobj;
3504 "Recovered extant sequence set ID mapping for ID : New Sequence set ID is "
3510 "Warning : Collision between sequence set ID string and existing jalview object mapping.");
3516 * indicate that annotation colours are applied across all groups (pre
3517 * Jalview 2.8.1 behaviour)
3519 boolean doGroupAnnColour = Jalview2XML.isVersionStringLaterThan("2.8.1",
3520 object.getVersion());
3522 AlignmentPanel ap = null;
3523 boolean isnewview = true;
3526 // Check to see if this alignment already has a view id == viewId
3527 jalview.gui.AlignmentPanel views[] = Desktop
3528 .getAlignmentPanels(uniqueSeqSetId);
3529 if (views != null && views.length > 0)
3531 for (int v = 0; v < views.length; v++)
3533 if (views[v].av.getViewId().equalsIgnoreCase(viewId))
3535 // recover the existing alignpanel, alignframe, viewport
3536 af = views[v].alignFrame;
3539 // TODO: could even skip resetting view settings if we don't want to
3540 // change the local settings from other jalview processes
3549 af = loadViewport(file, jseqs, hiddenSeqs, al, jms, view,
3550 uniqueSeqSetId, viewId, autoAlan);
3556 * Load any trees, PDB structures and viewers
3558 * Not done if flag is false (when this method is used for New View)
3560 if (loadTreesAndStructures)
3562 loadTrees(jms, view, af, av, ap);
3563 loadPDBStructures(jprovider, jseqs, af, ap);
3564 loadRnaViewers(jprovider, jseqs, ap);
3566 // and finally return.
3571 * Instantiate and link any saved RNA (Varna) viewers. The state of the Varna
3572 * panel is restored from separate jar entries, two (gapped and trimmed) per
3573 * sequence and secondary structure.
3575 * Currently each viewer shows just one sequence and structure (gapped and
3576 * trimmed), however this method is designed to support multiple sequences or
3577 * structures in viewers if wanted in future.
3583 private void loadRnaViewers(jarInputStreamProvider jprovider,
3584 JSeq[] jseqs, AlignmentPanel ap)
3587 * scan the sequences for references to viewers; create each one the first
3588 * time it is referenced, add Rna models to existing viewers
3590 for (JSeq jseq : jseqs)
3592 for (int i = 0; i < jseq.getRnaViewerCount(); i++)
3594 RnaViewer viewer = jseq.getRnaViewer(i);
3595 AppVarna appVarna = findOrCreateVarnaViewer(viewer, uniqueSetSuffix,
3598 for (int j = 0; j < viewer.getSecondaryStructureCount(); j++)
3600 SecondaryStructure ss = viewer.getSecondaryStructure(j);
3601 SequenceI seq = seqRefIds.get(jseq.getId());
3602 AlignmentAnnotation ann = this.annotationIds
3603 .get(ss.getAnnotationId());
3606 * add the structure to the Varna display (with session state copied
3607 * from the jar to a temporary file)
3609 boolean gapped = ss.isGapped();
3610 String rnaTitle = ss.getTitle();
3611 String sessionState = ss.getViewerState();
3612 String tempStateFile = copyJarEntry(jprovider, sessionState,
3614 RnaModel rna = new RnaModel(rnaTitle, ann, seq, null, gapped);
3615 appVarna.addModelSession(rna, rnaTitle, tempStateFile);
3617 appVarna.setInitialSelection(viewer.getSelectedRna());
3623 * Locate and return an already instantiated matching AppVarna, or create one
3627 * @param viewIdSuffix
3631 protected AppVarna findOrCreateVarnaViewer(RnaViewer viewer,
3632 String viewIdSuffix, AlignmentPanel ap)
3635 * on each load a suffix is appended to the saved viewId, to avoid conflicts
3636 * if load is repeated
3638 String postLoadId = viewer.getViewId() + viewIdSuffix;
3639 for (JInternalFrame frame : getAllFrames())
3641 if (frame instanceof AppVarna)
3643 AppVarna varna = (AppVarna) frame;
3644 if (postLoadId.equals(varna.getViewId()))
3646 // this viewer is already instantiated
3647 // could in future here add ap as another 'parent' of the
3648 // AppVarna window; currently just 1-to-many
3655 * viewer not found - make it
3657 RnaViewerModel model = new RnaViewerModel(postLoadId, viewer.getTitle(),
3658 viewer.getXpos(), viewer.getYpos(), viewer.getWidth(),
3659 viewer.getHeight(), viewer.getDividerLocation());
3660 AppVarna varna = new AppVarna(model, ap);
3666 * Load any saved trees
3674 protected void loadTrees(JalviewModelSequence jms, Viewport view,
3675 AlignFrame af, AlignViewport av, AlignmentPanel ap)
3677 // TODO result of automated refactoring - are all these parameters needed?
3680 for (int t = 0; t < jms.getTreeCount(); t++)
3683 Tree tree = jms.getTree(t);
3685 TreePanel tp = (TreePanel) retrieveExistingObj(tree.getId());
3688 tp = af.showNewickTree(
3689 new jalview.io.NewickFile(tree.getNewick()),
3690 tree.getTitle(), tree.getWidth(), tree.getHeight(),
3691 tree.getXpos(), tree.getYpos());
3692 if (tree.getId() != null)
3694 // perhaps bind the tree id to something ?
3699 // update local tree attributes ?
3700 // TODO: should check if tp has been manipulated by user - if so its
3701 // settings shouldn't be modified
3702 tp.setTitle(tree.getTitle());
3703 tp.setBounds(new Rectangle(tree.getXpos(), tree.getYpos(),
3704 tree.getWidth(), tree.getHeight()));
3705 tp.av = av; // af.viewport; // TODO: verify 'associate with all
3708 tp.treeCanvas.av = av; // af.viewport;
3709 tp.treeCanvas.ap = ap; // af.alignPanel;
3714 warn("There was a problem recovering stored Newick tree: \n"
3715 + tree.getNewick());
3719 tp.fitToWindow.setState(tree.getFitToWindow());
3720 tp.fitToWindow_actionPerformed(null);
3722 if (tree.getFontName() != null)
3724 tp.setTreeFont(new java.awt.Font(tree.getFontName(),
3725 tree.getFontStyle(), tree.getFontSize()));
3729 tp.setTreeFont(new java.awt.Font(view.getFontName(),
3730 view.getFontStyle(), tree.getFontSize()));
3733 tp.showPlaceholders(tree.getMarkUnlinked());
3734 tp.showBootstrap(tree.getShowBootstrap());
3735 tp.showDistances(tree.getShowDistances());
3737 tp.treeCanvas.threshold = tree.getThreshold();
3739 if (tree.getCurrentTree())
3741 af.viewport.setCurrentTree(tp.getTree());
3745 } catch (Exception ex)
3747 ex.printStackTrace();
3752 * Load and link any saved structure viewers.
3759 protected void loadPDBStructures(jarInputStreamProvider jprovider,
3760 JSeq[] jseqs, AlignFrame af, AlignmentPanel ap)
3763 * Run through all PDB ids on the alignment, and collect mappings between
3764 * distinct view ids and all sequences referring to that view.
3766 Map<String, StructureViewerModel> structureViewers = new LinkedHashMap<>();
3768 for (int i = 0; i < jseqs.length; i++)
3770 if (jseqs[i].getPdbidsCount() > 0)
3772 Pdbids[] ids = jseqs[i].getPdbids();
3773 for (int p = 0; p < ids.length; p++)
3775 final int structureStateCount = ids[p].getStructureStateCount();
3776 for (int s = 0; s < structureStateCount; s++)
3778 // check to see if we haven't already created this structure view
3779 final StructureState structureState = ids[p]
3780 .getStructureState(s);
3781 String sviewid = (structureState.getViewId() == null) ? null
3782 : structureState.getViewId() + uniqueSetSuffix;
3783 jalview.datamodel.PDBEntry jpdb = new jalview.datamodel.PDBEntry();
3784 // Originally : ids[p].getFile()
3785 // : TODO: verify external PDB file recovery still works in normal
3786 // jalview project load
3787 jpdb.setFile(loadPDBFile(jprovider, ids[p].getId(),
3789 jpdb.setId(ids[p].getId());
3791 int x = structureState.getXpos();
3792 int y = structureState.getYpos();
3793 int width = structureState.getWidth();
3794 int height = structureState.getHeight();
3796 // Probably don't need to do this anymore...
3797 // Desktop.desktop.getComponentAt(x, y);
3798 // TODO: NOW: check that this recovers the PDB file correctly.
3799 String pdbFile = loadPDBFile(jprovider, ids[p].getId(),
3801 jalview.datamodel.SequenceI seq = seqRefIds
3802 .get(jseqs[i].getId() + "");
3803 if (sviewid == null)
3805 sviewid = "_jalview_pre2_4_" + x + "," + y + "," + width + ","
3808 if (!structureViewers.containsKey(sviewid))
3810 structureViewers.put(sviewid,
3811 new StructureViewerModel(x, y, width, height, false,
3812 false, true, structureState.getViewId(),
3813 structureState.getType()));
3814 // Legacy pre-2.7 conversion JAL-823 :
3815 // do not assume any view has to be linked for colour by
3819 // assemble String[] { pdb files }, String[] { id for each
3820 // file }, orig_fileloc, SequenceI[][] {{ seqs_file 1 }, {
3821 // seqs_file 2}, boolean[] {
3822 // linkAlignPanel,superposeWithAlignpanel}} from hash
3823 StructureViewerModel jmoldat = structureViewers.get(sviewid);
3824 jmoldat.setAlignWithPanel(jmoldat.isAlignWithPanel()
3825 | (structureState.hasAlignwithAlignPanel()
3826 ? structureState.getAlignwithAlignPanel()
3830 * Default colour by linked panel to false if not specified (e.g.
3831 * for pre-2.7 projects)
3833 boolean colourWithAlignPanel = jmoldat.isColourWithAlignPanel();
3834 colourWithAlignPanel |= (structureState
3835 .hasColourwithAlignPanel()
3836 ? structureState.getColourwithAlignPanel()
3838 jmoldat.setColourWithAlignPanel(colourWithAlignPanel);
3841 * Default colour by viewer to true if not specified (e.g. for
3844 boolean colourByViewer = jmoldat.isColourByViewer();
3845 colourByViewer &= structureState.hasColourByJmol()
3846 ? structureState.getColourByJmol()
3848 jmoldat.setColourByViewer(colourByViewer);
3850 if (jmoldat.getStateData().length() < structureState
3851 .getContent().length())
3854 jmoldat.setStateData(structureState.getContent());
3857 if (ids[p].getFile() != null)
3859 File mapkey = new File(ids[p].getFile());
3860 StructureData seqstrmaps = jmoldat.getFileData().get(mapkey);
3861 if (seqstrmaps == null)
3863 jmoldat.getFileData().put(mapkey,
3864 seqstrmaps = jmoldat.new StructureData(pdbFile,
3867 if (!seqstrmaps.getSeqList().contains(seq))
3869 seqstrmaps.getSeqList().add(seq);
3875 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");
3882 // Instantiate the associated structure views
3883 for (Entry<String, StructureViewerModel> entry : structureViewers
3888 createOrLinkStructureViewer(entry, af, ap, jprovider);
3889 } catch (Exception e)
3892 "Error loading structure viewer: " + e.getMessage());
3893 // failed - try the next one
3905 protected void createOrLinkStructureViewer(
3906 Entry<String, StructureViewerModel> viewerData, AlignFrame af,
3907 AlignmentPanel ap, jarInputStreamProvider jprovider)
3909 final StructureViewerModel stateData = viewerData.getValue();
3912 * Search for any viewer windows already open from other alignment views
3913 * that exactly match the stored structure state
3915 StructureViewerBase comp = findMatchingViewer(viewerData);
3919 linkStructureViewer(ap, comp, stateData);
3924 * From 2.9: stateData.type contains JMOL or CHIMERA, data is in jar entry
3925 * "viewer_"+stateData.viewId
3927 if (ViewerType.CHIMERA.toString().equals(stateData.getType()))
3929 createChimeraViewer(viewerData, af, jprovider);
3934 * else Jmol (if pre-2.9, stateData contains JMOL state string)
3936 createJmolViewer(viewerData, af, jprovider);
3941 * Create a new Chimera viewer.
3947 protected void createChimeraViewer(
3948 Entry<String, StructureViewerModel> viewerData, AlignFrame af,
3949 jarInputStreamProvider jprovider)
3951 StructureViewerModel data = viewerData.getValue();
3952 String chimeraSessionFile = data.getStateData();
3955 * Copy Chimera session from jar entry "viewer_"+viewId to a temporary file
3957 * NB this is the 'saved' viewId as in the project file XML, _not_ the
3958 * 'uniquified' sviewid used to reconstruct the viewer here
3960 String viewerJarEntryName = getViewerJarEntryName(data.getViewId());
3961 chimeraSessionFile = copyJarEntry(jprovider, viewerJarEntryName,
3964 Set<Entry<File, StructureData>> fileData = data.getFileData()
3966 List<PDBEntry> pdbs = new ArrayList<>();
3967 List<SequenceI[]> allseqs = new ArrayList<>();
3968 for (Entry<File, StructureData> pdb : fileData)
3970 String filePath = pdb.getValue().getFilePath();
3971 String pdbId = pdb.getValue().getPdbId();
3972 // pdbs.add(new PDBEntry(filePath, pdbId));
3973 pdbs.add(new PDBEntry(pdbId, null, PDBEntry.Type.PDB, filePath));
3974 final List<SequenceI> seqList = pdb.getValue().getSeqList();
3975 SequenceI[] seqs = seqList.toArray(new SequenceI[seqList.size()]);
3979 boolean colourByChimera = data.isColourByViewer();
3980 boolean colourBySequence = data.isColourWithAlignPanel();
3982 // TODO use StructureViewer as a factory here, see JAL-1761
3983 final PDBEntry[] pdbArray = pdbs.toArray(new PDBEntry[pdbs.size()]);
3984 final SequenceI[][] seqsArray = allseqs
3985 .toArray(new SequenceI[allseqs.size()][]);
3986 String newViewId = viewerData.getKey();
3988 ChimeraViewFrame cvf = new ChimeraViewFrame(chimeraSessionFile,
3989 af.alignPanel, pdbArray, seqsArray, colourByChimera,
3990 colourBySequence, newViewId);
3991 cvf.setSize(data.getWidth(), data.getHeight());
3992 cvf.setLocation(data.getX(), data.getY());
3996 * Create a new Jmol window. First parse the Jmol state to translate filenames
3997 * loaded into the view, and record the order in which files are shown in the
3998 * Jmol view, so we can add the sequence mappings in same order.
4004 protected void createJmolViewer(
4005 final Entry<String, StructureViewerModel> viewerData,
4006 AlignFrame af, jarInputStreamProvider jprovider)
4008 final StructureViewerModel svattrib = viewerData.getValue();
4009 String state = svattrib.getStateData();
4012 * Pre-2.9: state element value is the Jmol state string
4014 * 2.9+: @type is "JMOL", state data is in a Jar file member named "viewer_"
4017 if (ViewerType.JMOL.toString().equals(svattrib.getType()))
4019 state = readJarEntry(jprovider,
4020 getViewerJarEntryName(svattrib.getViewId()));
4023 List<String> pdbfilenames = new ArrayList<>();
4024 List<SequenceI[]> seqmaps = new ArrayList<>();
4025 List<String> pdbids = new ArrayList<>();
4026 StringBuilder newFileLoc = new StringBuilder(64);
4027 int cp = 0, ncp, ecp;
4028 Map<File, StructureData> oldFiles = svattrib.getFileData();
4029 while ((ncp = state.indexOf("load ", cp)) > -1)
4033 // look for next filename in load statement
4034 newFileLoc.append(state.substring(cp,
4035 ncp = (state.indexOf("\"", ncp + 1) + 1)));
4036 String oldfilenam = state.substring(ncp,
4037 ecp = state.indexOf("\"", ncp));
4038 // recover the new mapping data for this old filename
4039 // have to normalize filename - since Jmol and jalview do
4041 // translation differently.
4042 StructureData filedat = oldFiles.get(new File(oldfilenam));
4043 if (filedat == null)
4045 String reformatedOldFilename = oldfilenam.replaceAll("/", "\\\\");
4046 filedat = oldFiles.get(new File(reformatedOldFilename));
4048 newFileLoc.append(Platform.escapeString(filedat.getFilePath()));
4049 pdbfilenames.add(filedat.getFilePath());
4050 pdbids.add(filedat.getPdbId());
4051 seqmaps.add(filedat.getSeqList().toArray(new SequenceI[0]));
4052 newFileLoc.append("\"");
4053 cp = ecp + 1; // advance beyond last \" and set cursor so we can
4054 // look for next file statement.
4055 } while ((ncp = state.indexOf("/*file*/", cp)) > -1);
4059 // just append rest of state
4060 newFileLoc.append(state.substring(cp));
4064 System.err.print("Ignoring incomplete Jmol state for PDB ids: ");
4065 newFileLoc = new StringBuilder(state);
4066 newFileLoc.append("; load append ");
4067 for (File id : oldFiles.keySet())
4069 // add this and any other pdb files that should be present in
4071 StructureData filedat = oldFiles.get(id);
4072 newFileLoc.append(filedat.getFilePath());
4073 pdbfilenames.add(filedat.getFilePath());
4074 pdbids.add(filedat.getPdbId());
4075 seqmaps.add(filedat.getSeqList().toArray(new SequenceI[0]));
4076 newFileLoc.append(" \"");
4077 newFileLoc.append(filedat.getFilePath());
4078 newFileLoc.append("\"");
4081 newFileLoc.append(";");
4084 if (newFileLoc.length() == 0)
4088 int histbug = newFileLoc.indexOf("history = ");
4092 * change "history = [true|false];" to "history = [1|0];"
4095 int diff = histbug == -1 ? -1 : newFileLoc.indexOf(";", histbug);
4096 String val = (diff == -1) ? null
4097 : newFileLoc.substring(histbug, diff);
4098 if (val != null && val.length() >= 4)
4100 if (val.contains("e")) // eh? what can it be?
4102 if (val.trim().equals("true"))
4110 newFileLoc.replace(histbug, diff, val);
4115 final String[] pdbf = pdbfilenames
4116 .toArray(new String[pdbfilenames.size()]);
4117 final String[] id = pdbids.toArray(new String[pdbids.size()]);
4118 final SequenceI[][] sq = seqmaps
4119 .toArray(new SequenceI[seqmaps.size()][]);
4120 final String fileloc = newFileLoc.toString();
4121 final String sviewid = viewerData.getKey();
4122 final AlignFrame alf = af;
4123 final Rectangle rect = new Rectangle(svattrib.getX(), svattrib.getY(),
4124 svattrib.getWidth(), svattrib.getHeight());
4127 javax.swing.SwingUtilities.invokeAndWait(new Runnable()
4132 JalviewStructureDisplayI sview = null;
4135 sview = new StructureViewer(
4136 alf.alignPanel.getStructureSelectionManager())
4137 .createView(StructureViewer.ViewerType.JMOL,
4138 pdbf, id, sq, alf.alignPanel, svattrib,
4139 fileloc, rect, sviewid);
4140 addNewStructureViewer(sview);
4141 } catch (OutOfMemoryError ex)
4143 new OOMWarning("restoring structure view for PDB id " + id,
4144 (OutOfMemoryError) ex.getCause());
4145 if (sview != null && sview.isVisible())
4147 sview.closeViewer(false);
4148 sview.setVisible(false);
4154 } catch (InvocationTargetException ex)
4156 warn("Unexpected error when opening Jmol view.", ex);
4158 } catch (InterruptedException e)
4160 // e.printStackTrace();
4166 * Generates a name for the entry in the project jar file to hold state
4167 * information for a structure viewer
4172 protected String getViewerJarEntryName(String viewId)
4174 return VIEWER_PREFIX + viewId;
4178 * Returns any open frame that matches given structure viewer data. The match
4179 * is based on the unique viewId, or (for older project versions) the frame's
4185 protected StructureViewerBase findMatchingViewer(
4186 Entry<String, StructureViewerModel> viewerData)
4188 final String sviewid = viewerData.getKey();
4189 final StructureViewerModel svattrib = viewerData.getValue();
4190 StructureViewerBase comp = null;
4191 JInternalFrame[] frames = getAllFrames();
4192 for (JInternalFrame frame : frames)
4194 if (frame instanceof StructureViewerBase)
4197 * Post jalview 2.4 schema includes structure view id
4199 if (sviewid != null && ((StructureViewerBase) frame).getViewId()
4202 comp = (StructureViewerBase) frame;
4203 break; // break added in 2.9
4206 * Otherwise test for matching position and size of viewer frame
4208 else if (frame.getX() == svattrib.getX()
4209 && frame.getY() == svattrib.getY()
4210 && frame.getHeight() == svattrib.getHeight()
4211 && frame.getWidth() == svattrib.getWidth())
4213 comp = (StructureViewerBase) frame;
4214 // no break in faint hope of an exact match on viewId
4222 * Link an AlignmentPanel to an existing structure viewer.
4227 * @param useinViewerSuperpos
4228 * @param usetoColourbyseq
4229 * @param viewerColouring
4231 protected void linkStructureViewer(AlignmentPanel ap,
4232 StructureViewerBase viewer, StructureViewerModel stateData)
4234 // NOTE: if the jalview project is part of a shared session then
4235 // view synchronization should/could be done here.
4237 final boolean useinViewerSuperpos = stateData.isAlignWithPanel();
4238 final boolean usetoColourbyseq = stateData.isColourWithAlignPanel();
4239 final boolean viewerColouring = stateData.isColourByViewer();
4240 Map<File, StructureData> oldFiles = stateData.getFileData();
4243 * Add mapping for sequences in this view to an already open viewer
4245 final AAStructureBindingModel binding = viewer.getBinding();
4246 for (File id : oldFiles.keySet())
4248 // add this and any other pdb files that should be present in the
4250 StructureData filedat = oldFiles.get(id);
4251 String pdbFile = filedat.getFilePath();
4252 SequenceI[] seq = filedat.getSeqList().toArray(new SequenceI[0]);
4253 binding.getSsm().setMapping(seq, null, pdbFile, DataSourceType.FILE);
4254 binding.addSequenceForStructFile(pdbFile, seq);
4256 // and add the AlignmentPanel's reference to the view panel
4257 viewer.addAlignmentPanel(ap);
4258 if (useinViewerSuperpos)
4260 viewer.useAlignmentPanelForSuperposition(ap);
4264 viewer.excludeAlignmentPanelForSuperposition(ap);
4266 if (usetoColourbyseq)
4268 viewer.useAlignmentPanelForColourbyseq(ap, !viewerColouring);
4272 viewer.excludeAlignmentPanelForColourbyseq(ap);
4277 * Get all frames within the Desktop.
4281 protected JInternalFrame[] getAllFrames()
4283 JInternalFrame[] frames = null;
4284 // TODO is this necessary - is it safe - risk of hanging?
4289 frames = Desktop.desktop.getAllFrames();
4290 } catch (ArrayIndexOutOfBoundsException e)
4292 // occasional No such child exceptions are thrown here...
4296 } catch (InterruptedException f)
4300 } while (frames == null);
4305 * Answers true if 'version' is equal to or later than 'supported', where each
4306 * is formatted as major/minor versions like "2.8.3" or "2.3.4b1" for bugfix
4307 * changes. Development and test values for 'version' are leniently treated
4311 * - minimum version we are comparing against
4313 * - version of data being processsed
4316 public static boolean isVersionStringLaterThan(String supported,
4319 if (supported == null || version == null
4320 || version.equalsIgnoreCase("DEVELOPMENT BUILD")
4321 || version.equalsIgnoreCase("Test")
4322 || version.equalsIgnoreCase("AUTOMATED BUILD"))
4324 System.err.println("Assuming project file with "
4325 + (version == null ? "null" : version)
4326 + " is compatible with Jalview version " + supported);
4331 return StringUtils.compareVersions(version, supported, "b") >= 0;
4335 Vector<JalviewStructureDisplayI> newStructureViewers = null;
4337 protected void addNewStructureViewer(JalviewStructureDisplayI sview)
4339 if (newStructureViewers != null)
4341 sview.getBinding().setFinishedLoadingFromArchive(false);
4342 newStructureViewers.add(sview);
4346 protected void setLoadingFinishedForNewStructureViewers()
4348 if (newStructureViewers != null)
4350 for (JalviewStructureDisplayI sview : newStructureViewers)
4352 sview.getBinding().setFinishedLoadingFromArchive(true);
4354 newStructureViewers.clear();
4355 newStructureViewers = null;
4359 AlignFrame loadViewport(String file, JSeq[] JSEQ,
4360 List<SequenceI> hiddenSeqs, AlignmentI al,
4361 JalviewModelSequence jms, Viewport view, String uniqueSeqSetId,
4362 String viewId, List<JvAnnotRow> autoAlan)
4364 AlignFrame af = null;
4365 af = new AlignFrame(al, view.getWidth(), view.getHeight(),
4366 uniqueSeqSetId, viewId);
4368 af.setFileName(file, FileFormat.Jalview);
4370 for (int i = 0; i < JSEQ.length; i++)
4372 af.viewport.setSequenceColour(
4373 af.viewport.getAlignment().getSequenceAt(i),
4374 new java.awt.Color(JSEQ[i].getColour()));
4379 af.getViewport().setColourByReferenceSeq(true);
4380 af.getViewport().setDisplayReferenceSeq(true);
4383 af.viewport.setGatherViewsHere(view.getGatheredViews());
4385 if (view.getSequenceSetId() != null)
4387 AlignmentViewport av = viewportsAdded.get(uniqueSeqSetId);
4389 af.viewport.setSequenceSetId(uniqueSeqSetId);
4392 // propagate shared settings to this new view
4393 af.viewport.setHistoryList(av.getHistoryList());
4394 af.viewport.setRedoList(av.getRedoList());
4398 viewportsAdded.put(uniqueSeqSetId, af.viewport);
4400 // TODO: check if this method can be called repeatedly without
4401 // side-effects if alignpanel already registered.
4402 PaintRefresher.Register(af.alignPanel, uniqueSeqSetId);
4404 // apply Hidden regions to view.
4405 if (hiddenSeqs != null)
4407 for (int s = 0; s < JSEQ.length; s++)
4409 SequenceGroup hidden = new SequenceGroup();
4410 boolean isRepresentative = false;
4411 for (int r = 0; r < JSEQ[s].getHiddenSequencesCount(); r++)
4413 isRepresentative = true;
4414 SequenceI sequenceToHide = al
4415 .getSequenceAt(JSEQ[s].getHiddenSequences(r));
4416 hidden.addSequence(sequenceToHide, false);
4417 // remove from hiddenSeqs list so we don't try to hide it twice
4418 hiddenSeqs.remove(sequenceToHide);
4420 if (isRepresentative)
4422 SequenceI representativeSequence = al.getSequenceAt(s);
4423 hidden.addSequence(representativeSequence, false);
4424 af.viewport.hideRepSequences(representativeSequence, hidden);
4428 SequenceI[] hseqs = hiddenSeqs
4429 .toArray(new SequenceI[hiddenSeqs.size()]);
4430 af.viewport.hideSequence(hseqs);
4433 // recover view properties and display parameters
4435 af.viewport.setShowAnnotation(view.getShowAnnotation());
4436 af.viewport.setAbovePIDThreshold(view.getPidSelected());
4437 af.viewport.setThreshold(view.getPidThreshold());
4439 af.viewport.setColourText(view.getShowColourText());
4441 af.viewport.setConservationSelected(view.getConservationSelected());
4442 af.viewport.setIncrement(view.getConsThreshold());
4443 af.viewport.setShowJVSuffix(view.getShowFullId());
4444 af.viewport.setRightAlignIds(view.getRightAlignIds());
4445 af.viewport.setFont(new java.awt.Font(view.getFontName(),
4446 view.getFontStyle(), view.getFontSize()), true);
4447 ViewStyleI vs = af.viewport.getViewStyle();
4448 vs.setScaleProteinAsCdna(view.isScaleProteinAsCdna());
4449 af.viewport.setViewStyle(vs);
4450 // TODO: allow custom charWidth/Heights to be restored by updating them
4451 // after setting font - which means set above to false
4452 af.viewport.setRenderGaps(view.getRenderGaps());
4453 af.viewport.setWrapAlignment(view.getWrapAlignment());
4454 af.viewport.setShowAnnotation(view.getShowAnnotation());
4456 af.viewport.setShowBoxes(view.getShowBoxes());
4458 af.viewport.setShowText(view.getShowText());
4460 af.viewport.setTextColour(new java.awt.Color(view.getTextCol1()));
4461 af.viewport.setTextColour2(new java.awt.Color(view.getTextCol2()));
4462 af.viewport.setThresholdTextColour(view.getTextColThreshold());
4463 af.viewport.setShowUnconserved(
4464 view.hasShowUnconserved() ? view.isShowUnconserved() : false);
4465 af.viewport.getRanges().setStartRes(view.getStartRes());
4467 if (view.getViewName() != null)
4469 af.viewport.viewName = view.getViewName();
4470 af.setInitialTabVisible();
4472 af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),
4474 // startSeq set in af.alignPanel.updateLayout below
4475 af.alignPanel.updateLayout();
4476 ColourSchemeI cs = null;
4477 // apply colourschemes
4478 if (view.getBgColour() != null)
4480 if (view.getBgColour().startsWith("ucs"))
4482 cs = getUserColourScheme(jms, view.getBgColour());
4484 else if (view.getBgColour().startsWith("Annotation"))
4486 AnnotationColours viewAnnColour = view.getAnnotationColours();
4487 cs = constructAnnotationColour(viewAnnColour, af, al, jms, true);
4494 cs = ColourSchemeProperty.getColourScheme(al, view.getBgColour());
4498 af.viewport.setGlobalColourScheme(cs);
4499 af.viewport.getResidueShading().setThreshold(view.getPidThreshold(),
4500 view.getIgnoreGapsinConsensus());
4501 af.viewport.getResidueShading()
4502 .setConsensus(af.viewport.getSequenceConsensusHash());
4503 af.viewport.setColourAppliesToAllGroups(false);
4505 if (view.getConservationSelected() && cs != null)
4507 af.viewport.getResidueShading()
4508 .setConservationInc(view.getConsThreshold());
4511 af.changeColour(cs);
4513 af.viewport.setColourAppliesToAllGroups(true);
4515 af.viewport.setShowSequenceFeatures(view.getShowSequenceFeatures());
4517 if (view.hasCentreColumnLabels())
4519 af.viewport.setCentreColumnLabels(view.getCentreColumnLabels());
4521 if (view.hasIgnoreGapsinConsensus())
4523 af.viewport.setIgnoreGapsConsensus(view.getIgnoreGapsinConsensus(),
4526 if (view.hasFollowHighlight())
4528 af.viewport.setFollowHighlight(view.getFollowHighlight());
4530 if (view.hasFollowSelection())
4532 af.viewport.followSelection = view.getFollowSelection();
4534 if (view.hasShowConsensusHistogram())
4537 .setShowConsensusHistogram(view.getShowConsensusHistogram());
4541 af.viewport.setShowConsensusHistogram(true);
4543 if (view.hasShowSequenceLogo())
4545 af.viewport.setShowSequenceLogo(view.getShowSequenceLogo());
4549 af.viewport.setShowSequenceLogo(false);
4551 if (view.hasNormaliseSequenceLogo())
4553 af.viewport.setNormaliseSequenceLogo(view.getNormaliseSequenceLogo());
4555 if (view.hasShowDbRefTooltip())
4557 af.viewport.setShowDBRefs(view.getShowDbRefTooltip());
4559 if (view.hasShowNPfeatureTooltip())
4561 af.viewport.setShowNPFeats(view.hasShowNPfeatureTooltip());
4563 if (view.hasShowGroupConsensus())
4565 af.viewport.setShowGroupConsensus(view.getShowGroupConsensus());
4569 af.viewport.setShowGroupConsensus(false);
4571 if (view.hasShowGroupConservation())
4573 af.viewport.setShowGroupConservation(view.getShowGroupConservation());
4577 af.viewport.setShowGroupConservation(false);
4580 // recover featre settings
4581 if (jms.getFeatureSettings() != null)
4583 FeaturesDisplayed fdi;
4584 af.viewport.setFeaturesDisplayed(fdi = new FeaturesDisplayed());
4585 String[] renderOrder = new String[jms.getFeatureSettings()
4586 .getSettingCount()];
4587 Map<String, FeatureColourI> featureColours = new Hashtable<>();
4588 Map<String, Float> featureOrder = new Hashtable<>();
4590 for (int fs = 0; fs < jms.getFeatureSettings()
4591 .getSettingCount(); fs++)
4593 Setting setting = jms.getFeatureSettings().getSetting(fs);
4594 if (setting.hasMincolour())
4596 FeatureColourI gc = setting.hasMin()
4597 ? new FeatureColour(new Color(setting.getMincolour()),
4598 new Color(setting.getColour()), setting.getMin(),
4600 : new FeatureColour(new Color(setting.getMincolour()),
4601 new Color(setting.getColour()), 0, 1);
4602 if (setting.hasThreshold())
4604 gc.setThreshold(setting.getThreshold());
4605 int threshstate = setting.getThreshstate();
4606 // -1 = None, 0 = Below, 1 = Above threshold
4607 if (threshstate == 0)
4609 gc.setBelowThreshold(true);
4611 else if (threshstate == 1)
4613 gc.setAboveThreshold(true);
4616 gc.setAutoScaled(true); // default
4617 if (setting.hasAutoScale())
4619 gc.setAutoScaled(setting.getAutoScale());
4621 if (setting.hasColourByLabel())
4623 gc.setColourByLabel(setting.getColourByLabel());
4625 // and put in the feature colour table.
4626 featureColours.put(setting.getType(), gc);
4630 featureColours.put(setting.getType(),
4631 new FeatureColour(new Color(setting.getColour())));
4633 renderOrder[fs] = setting.getType();
4634 if (setting.hasOrder())
4636 featureOrder.put(setting.getType(), setting.getOrder());
4640 featureOrder.put(setting.getType(), new Float(
4641 fs / jms.getFeatureSettings().getSettingCount()));
4643 if (setting.getDisplay())
4645 fdi.setVisible(setting.getType());
4648 Map<String, Boolean> fgtable = new Hashtable<>();
4649 for (int gs = 0; gs < jms.getFeatureSettings().getGroupCount(); gs++)
4651 Group grp = jms.getFeatureSettings().getGroup(gs);
4652 fgtable.put(grp.getName(), new Boolean(grp.getDisplay()));
4654 // FeatureRendererSettings frs = new FeatureRendererSettings(renderOrder,
4655 // fgtable, featureColours, jms.getFeatureSettings().hasTransparency() ?
4656 // jms.getFeatureSettings().getTransparency() : 0.0, featureOrder);
4657 FeatureRendererSettings frs = new FeatureRendererSettings(renderOrder,
4658 fgtable, featureColours, 1.0f, featureOrder);
4659 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
4660 .transferSettings(frs);
4664 if (view.getHiddenColumnsCount() > 0)
4666 for (int c = 0; c < view.getHiddenColumnsCount(); c++)
4668 af.viewport.hideColumns(view.getHiddenColumns(c).getStart(),
4669 view.getHiddenColumns(c).getEnd() // +1
4673 if (view.getCalcIdParam() != null)
4675 for (CalcIdParam calcIdParam : view.getCalcIdParam())
4677 if (calcIdParam != null)
4679 if (recoverCalcIdParam(calcIdParam, af.viewport))
4684 warn("Couldn't recover parameters for "
4685 + calcIdParam.getCalcId());
4690 af.setMenusFromViewport(af.viewport);
4691 af.setTitle(view.getTitle());
4692 // TODO: we don't need to do this if the viewport is aready visible.
4694 * Add the AlignFrame to the desktop (it may be 'gathered' later), unless it
4695 * has a 'cdna/protein complement' view, in which case save it in order to
4696 * populate a SplitFrame once all views have been read in.
4698 String complementaryViewId = view.getComplementId();
4699 if (complementaryViewId == null)
4701 Desktop.addInternalFrame(af, view.getTitle(), view.getWidth(),
4703 // recompute any autoannotation
4704 af.alignPanel.updateAnnotation(false, true);
4705 reorderAutoannotation(af, al, autoAlan);
4706 af.alignPanel.alignmentChanged();
4710 splitFrameCandidates.put(view, af);
4716 * Reads saved data to restore Colour by Annotation settings
4718 * @param viewAnnColour
4722 * @param checkGroupAnnColour
4725 private ColourSchemeI constructAnnotationColour(
4726 AnnotationColours viewAnnColour, AlignFrame af, AlignmentI al,
4727 JalviewModelSequence jms, boolean checkGroupAnnColour)
4729 boolean propagateAnnColour = false;
4730 AlignmentI annAlignment = af != null ? af.viewport.getAlignment() : al;
4731 if (checkGroupAnnColour && al.getGroups() != null
4732 && al.getGroups().size() > 0)
4734 // pre 2.8.1 behaviour
4735 // check to see if we should transfer annotation colours
4736 propagateAnnColour = true;
4737 for (SequenceGroup sg : al.getGroups())
4739 if (sg.getColourScheme() instanceof AnnotationColourGradient)
4741 propagateAnnColour = false;
4747 * 2.10.2- : saved annotationId is AlignmentAnnotation.annotationId
4749 String annotationId = viewAnnColour.getAnnotation();
4750 AlignmentAnnotation matchedAnnotation = annotationIds.get(annotationId);
4753 * pre 2.10.2: saved annotationId is AlignmentAnnotation.label
4755 if (matchedAnnotation == null
4756 && annAlignment.getAlignmentAnnotation() != null)
4758 for (int i = 0; i < annAlignment.getAlignmentAnnotation().length; i++)
4761 .equals(annAlignment.getAlignmentAnnotation()[i].label))
4763 matchedAnnotation = annAlignment.getAlignmentAnnotation()[i];
4768 if (matchedAnnotation == null)
4770 System.err.println("Failed to match annotation colour scheme for "
4774 if (matchedAnnotation.getThreshold() == null)
4776 matchedAnnotation.setThreshold(new GraphLine(
4777 viewAnnColour.getThreshold(), "Threshold", Color.black));
4780 AnnotationColourGradient cs = null;
4781 if (viewAnnColour.getColourScheme().equals("None"))
4783 cs = new AnnotationColourGradient(matchedAnnotation,
4784 new Color(viewAnnColour.getMinColour()),
4785 new Color(viewAnnColour.getMaxColour()),
4786 viewAnnColour.getAboveThreshold());
4788 else if (viewAnnColour.getColourScheme().startsWith("ucs"))
4790 cs = new AnnotationColourGradient(matchedAnnotation,
4791 getUserColourScheme(jms, viewAnnColour.getColourScheme()),
4792 viewAnnColour.getAboveThreshold());
4796 cs = new AnnotationColourGradient(matchedAnnotation,
4797 ColourSchemeProperty.getColourScheme(al,
4798 viewAnnColour.getColourScheme()),
4799 viewAnnColour.getAboveThreshold());
4802 boolean perSequenceOnly = viewAnnColour.isPerSequence();
4803 boolean useOriginalColours = viewAnnColour.isPredefinedColours();
4804 cs.setSeqAssociated(perSequenceOnly);
4805 cs.setPredefinedColours(useOriginalColours);
4807 if (propagateAnnColour && al.getGroups() != null)
4809 // Also use these settings for all the groups
4810 for (int g = 0; g < al.getGroups().size(); g++)
4812 SequenceGroup sg = al.getGroups().get(g);
4813 if (sg.getGroupColourScheme() == null)
4818 AnnotationColourGradient groupScheme = new AnnotationColourGradient(
4819 matchedAnnotation, sg.getColourScheme(),
4820 viewAnnColour.getAboveThreshold());
4821 sg.setColourScheme(groupScheme);
4822 groupScheme.setSeqAssociated(perSequenceOnly);
4823 groupScheme.setPredefinedColours(useOriginalColours);
4829 private void reorderAutoannotation(AlignFrame af, AlignmentI al,
4830 List<JvAnnotRow> autoAlan)
4832 // copy over visualization settings for autocalculated annotation in the
4834 if (al.getAlignmentAnnotation() != null)
4837 * Kludge for magic autoannotation names (see JAL-811)
4839 String[] magicNames = new String[] { "Consensus", "Quality",
4841 JvAnnotRow nullAnnot = new JvAnnotRow(-1, null);
4842 Hashtable<String, JvAnnotRow> visan = new Hashtable<>();
4843 for (String nm : magicNames)
4845 visan.put(nm, nullAnnot);
4847 for (JvAnnotRow auan : autoAlan)
4849 visan.put(auan.template.label
4850 + (auan.template.getCalcId() == null ? ""
4851 : "\t" + auan.template.getCalcId()),
4854 int hSize = al.getAlignmentAnnotation().length;
4855 List<JvAnnotRow> reorder = new ArrayList<>();
4856 // work through any autoCalculated annotation already on the view
4857 // removing it if it should be placed in a different location on the
4858 // annotation panel.
4859 List<String> remains = new ArrayList<>(visan.keySet());
4860 for (int h = 0; h < hSize; h++)
4862 jalview.datamodel.AlignmentAnnotation jalan = al
4863 .getAlignmentAnnotation()[h];
4864 if (jalan.autoCalculated)
4867 JvAnnotRow valan = visan.get(k = jalan.label);
4868 if (jalan.getCalcId() != null)
4870 valan = visan.get(k = jalan.label + "\t" + jalan.getCalcId());
4875 // delete the auto calculated row from the alignment
4876 al.deleteAnnotation(jalan, false);
4880 if (valan != nullAnnot)
4882 if (jalan != valan.template)
4884 // newly created autoannotation row instance
4885 // so keep a reference to the visible annotation row
4886 // and copy over all relevant attributes
4887 if (valan.template.graphHeight >= 0)
4890 jalan.graphHeight = valan.template.graphHeight;
4892 jalan.visible = valan.template.visible;
4894 reorder.add(new JvAnnotRow(valan.order, jalan));
4899 // Add any (possibly stale) autocalculated rows that were not appended to
4900 // the view during construction
4901 for (String other : remains)
4903 JvAnnotRow othera = visan.get(other);
4904 if (othera != nullAnnot && othera.template.getCalcId() != null
4905 && othera.template.getCalcId().length() > 0)
4907 reorder.add(othera);
4910 // now put the automatic annotation in its correct place
4911 int s = 0, srt[] = new int[reorder.size()];
4912 JvAnnotRow[] rws = new JvAnnotRow[reorder.size()];
4913 for (JvAnnotRow jvar : reorder)
4916 srt[s++] = jvar.order;
4919 jalview.util.QuickSort.sort(srt, rws);
4920 // and re-insert the annotation at its correct position
4921 for (JvAnnotRow jvar : rws)
4923 al.addAnnotation(jvar.template, jvar.order);
4925 af.alignPanel.adjustAnnotationHeight();
4929 Hashtable skipList = null;
4932 * TODO remove this method
4935 * @return AlignFrame bound to sequenceSetId from view, if one exists. private
4936 * AlignFrame getSkippedFrame(Viewport view) { if (skipList==null) {
4937 * throw new Error("Implementation Error. No skipList defined for this
4938 * Jalview2XML instance."); } return (AlignFrame)
4939 * skipList.get(view.getSequenceSetId()); }
4943 * Check if the Jalview view contained in object should be skipped or not.
4946 * @return true if view's sequenceSetId is a key in skipList
4948 private boolean skipViewport(JalviewModel object)
4950 if (skipList == null)
4955 if (skipList.containsKey(
4956 id = object.getJalviewModelSequence().getViewport()[0]
4957 .getSequenceSetId()))
4959 if (Cache.log != null && Cache.log.isDebugEnabled())
4961 Cache.log.debug("Skipping seuqence set id " + id);
4968 public void addToSkipList(AlignFrame af)
4970 if (skipList == null)
4972 skipList = new Hashtable();
4974 skipList.put(af.getViewport().getSequenceSetId(), af);
4977 public void clearSkipList()
4979 if (skipList != null)
4986 private void recoverDatasetFor(SequenceSet vamsasSet, AlignmentI al,
4987 boolean ignoreUnrefed)
4989 jalview.datamodel.AlignmentI ds = getDatasetFor(
4990 vamsasSet.getDatasetId());
4991 Vector dseqs = null;
4994 // create a list of new dataset sequences
4995 dseqs = new Vector();
4997 for (int i = 0, iSize = vamsasSet.getSequenceCount(); i < iSize; i++)
4999 Sequence vamsasSeq = vamsasSet.getSequence(i);
5000 ensureJalviewDatasetSequence(vamsasSeq, ds, dseqs, ignoreUnrefed, i);
5002 // create a new dataset
5005 SequenceI[] dsseqs = new SequenceI[dseqs.size()];
5006 dseqs.copyInto(dsseqs);
5007 ds = new jalview.datamodel.Alignment(dsseqs);
5008 debug("Created new dataset " + vamsasSet.getDatasetId()
5009 + " for alignment " + System.identityHashCode(al));
5010 addDatasetRef(vamsasSet.getDatasetId(), ds);
5012 // set the dataset for the newly imported alignment.
5013 if (al.getDataset() == null && !ignoreUnrefed)
5022 * sequence definition to create/merge dataset sequence for
5026 * vector to add new dataset sequence to
5027 * @param ignoreUnrefed
5028 * - when true, don't create new sequences from vamsasSeq if it's id
5029 * doesn't already have an asssociated Jalview sequence.
5031 * - used to reorder the sequence in the alignment according to the
5032 * vamsasSeq array ordering, to preserve ordering of dataset
5034 private void ensureJalviewDatasetSequence(Sequence vamsasSeq,
5035 AlignmentI ds, Vector dseqs, boolean ignoreUnrefed, int vseqpos)
5037 // JBP TODO: Check this is called for AlCodonFrames to support recovery of
5039 SequenceI sq = seqRefIds.get(vamsasSeq.getId());
5040 boolean reorder = false;
5041 SequenceI dsq = null;
5042 if (sq != null && sq.getDatasetSequence() != null)
5044 dsq = sq.getDatasetSequence();
5050 if (sq == null && ignoreUnrefed)
5054 String sqid = vamsasSeq.getDsseqid();
5057 // need to create or add a new dataset sequence reference to this sequence
5060 dsq = seqRefIds.get(sqid);
5065 // make a new dataset sequence
5066 dsq = sq.createDatasetSequence();
5069 // make up a new dataset reference for this sequence
5070 sqid = seqHash(dsq);
5072 dsq.setVamsasId(uniqueSetSuffix + sqid);
5073 seqRefIds.put(sqid, dsq);
5078 dseqs.addElement(dsq);
5083 ds.addSequence(dsq);
5089 { // make this dataset sequence sq's dataset sequence
5090 sq.setDatasetSequence(dsq);
5091 // and update the current dataset alignment
5096 if (!dseqs.contains(dsq))
5103 if (ds.findIndex(dsq) < 0)
5105 ds.addSequence(dsq);
5112 // TODO: refactor this as a merge dataset sequence function
5113 // now check that sq (the dataset sequence) sequence really is the union of
5114 // all references to it
5115 // boolean pre = sq.getStart() < dsq.getStart();
5116 // boolean post = sq.getEnd() > dsq.getEnd();
5120 // StringBuffer sb = new StringBuffer();
5121 String newres = jalview.analysis.AlignSeq.extractGaps(
5122 jalview.util.Comparison.GapChars, sq.getSequenceAsString());
5123 if (!newres.equalsIgnoreCase(dsq.getSequenceAsString())
5124 && newres.length() > dsq.getLength())
5126 // Update with the longer sequence.
5130 * if (pre) { sb.insert(0, newres .substring(0, dsq.getStart() -
5131 * sq.getStart())); dsq.setStart(sq.getStart()); } if (post) {
5132 * sb.append(newres.substring(newres.length() - sq.getEnd() -
5133 * dsq.getEnd())); dsq.setEnd(sq.getEnd()); }
5135 dsq.setSequence(newres);
5137 // TODO: merges will never happen if we 'know' we have the real dataset
5138 // sequence - this should be detected when id==dssid
5140 "DEBUG Notice: Merged dataset sequence (if you see this often, post at http://issues.jalview.org/browse/JAL-1474)"); // ("
5141 // + (pre ? "prepended" : "") + " "
5142 // + (post ? "appended" : ""));
5147 // sequence refs are identical. We may need to update the existing dataset
5148 // alignment with this one, though.
5149 if (ds != null && dseqs == null)
5151 int opos = ds.findIndex(dsq);
5152 SequenceI tseq = null;
5153 if (opos != -1 && vseqpos != opos)
5155 // remove from old position
5156 ds.deleteSequence(dsq);
5158 if (vseqpos < ds.getHeight())
5160 if (vseqpos != opos)
5162 // save sequence at destination position
5163 tseq = ds.getSequenceAt(vseqpos);
5164 ds.replaceSequenceAt(vseqpos, dsq);
5165 ds.addSequence(tseq);
5170 ds.addSequence(dsq);
5177 * TODO use AlignmentI here and in related methods - needs
5178 * AlignmentI.getDataset() changed to return AlignmentI instead of Alignment
5180 Hashtable<String, AlignmentI> datasetIds = null;
5182 IdentityHashMap<AlignmentI, String> dataset2Ids = null;
5184 private AlignmentI getDatasetFor(String datasetId)
5186 if (datasetIds == null)
5188 datasetIds = new Hashtable<>();
5191 if (datasetIds.containsKey(datasetId))
5193 return datasetIds.get(datasetId);
5198 private void addDatasetRef(String datasetId, AlignmentI dataset)
5200 if (datasetIds == null)
5202 datasetIds = new Hashtable<>();
5204 datasetIds.put(datasetId, dataset);
5208 * make a new dataset ID for this jalview dataset alignment
5213 private String getDatasetIdRef(AlignmentI dataset)
5215 if (dataset.getDataset() != null)
5217 warn("Serious issue! Dataset Object passed to getDatasetIdRef is not a Jalview DATASET alignment...");
5219 String datasetId = makeHashCode(dataset, null);
5220 if (datasetId == null)
5222 // make a new datasetId and record it
5223 if (dataset2Ids == null)
5225 dataset2Ids = new IdentityHashMap<>();
5229 datasetId = dataset2Ids.get(dataset);
5231 if (datasetId == null)
5233 datasetId = "ds" + dataset2Ids.size() + 1;
5234 dataset2Ids.put(dataset, datasetId);
5240 private void addDBRefs(SequenceI datasetSequence, Sequence sequence)
5242 for (int d = 0; d < sequence.getDBRefCount(); d++)
5244 DBRef dr = sequence.getDBRef(d);
5245 jalview.datamodel.DBRefEntry entry = new jalview.datamodel.DBRefEntry(
5246 sequence.getDBRef(d).getSource(),
5247 sequence.getDBRef(d).getVersion(),
5248 sequence.getDBRef(d).getAccessionId());
5249 if (dr.getMapping() != null)
5251 entry.setMap(addMapping(dr.getMapping()));
5253 datasetSequence.addDBRef(entry);
5257 private jalview.datamodel.Mapping addMapping(Mapping m)
5259 SequenceI dsto = null;
5260 // Mapping m = dr.getMapping();
5261 int fr[] = new int[m.getMapListFromCount() * 2];
5262 Enumeration f = m.enumerateMapListFrom();
5263 for (int _i = 0; f.hasMoreElements(); _i += 2)
5265 MapListFrom mf = (MapListFrom) f.nextElement();
5266 fr[_i] = mf.getStart();
5267 fr[_i + 1] = mf.getEnd();
5269 int fto[] = new int[m.getMapListToCount() * 2];
5270 f = m.enumerateMapListTo();
5271 for (int _i = 0; f.hasMoreElements(); _i += 2)
5273 MapListTo mf = (MapListTo) f.nextElement();
5274 fto[_i] = mf.getStart();
5275 fto[_i + 1] = mf.getEnd();
5277 jalview.datamodel.Mapping jmap = new jalview.datamodel.Mapping(dsto, fr,
5278 fto, (int) m.getMapFromUnit(), (int) m.getMapToUnit());
5279 if (m.getMappingChoice() != null)
5281 MappingChoice mc = m.getMappingChoice();
5282 if (mc.getDseqFor() != null)
5284 String dsfor = "" + mc.getDseqFor();
5285 if (seqRefIds.containsKey(dsfor))
5290 jmap.setTo(seqRefIds.get(dsfor));
5294 frefedSequence.add(newMappingRef(dsfor, jmap));
5300 * local sequence definition
5302 Sequence ms = mc.getSequence();
5303 SequenceI djs = null;
5304 String sqid = ms.getDsseqid();
5305 if (sqid != null && sqid.length() > 0)
5308 * recover dataset sequence
5310 djs = seqRefIds.get(sqid);
5315 "Warning - making up dataset sequence id for DbRef sequence map reference");
5316 sqid = ((Object) ms).toString(); // make up a new hascode for
5317 // undefined dataset sequence hash
5318 // (unlikely to happen)
5324 * make a new dataset sequence and add it to refIds hash
5326 djs = new jalview.datamodel.Sequence(ms.getName(),
5328 djs.setStart(jmap.getMap().getToLowest());
5329 djs.setEnd(jmap.getMap().getToHighest());
5330 djs.setVamsasId(uniqueSetSuffix + sqid);
5332 incompleteSeqs.put(sqid, djs);
5333 seqRefIds.put(sqid, djs);
5336 jalview.bin.Cache.log.debug("about to recurse on addDBRefs.");
5345 public jalview.gui.AlignmentPanel copyAlignPanel(AlignmentPanel ap,
5346 boolean keepSeqRefs)
5349 JalviewModel jm = saveState(ap, null, null, null);
5354 jm.getJalviewModelSequence().getViewport(0).setSequenceSetId(null);
5358 uniqueSetSuffix = "";
5359 jm.getJalviewModelSequence().getViewport(0).setId(null); // we don't
5364 if (this.frefedSequence == null)
5366 frefedSequence = new Vector();
5369 viewportsAdded.clear();
5371 AlignFrame af = loadFromObject(jm, null, false, null);
5372 af.alignPanels.clear();
5373 af.closeMenuItem_actionPerformed(true);
5376 * if(ap.av.getAlignment().getAlignmentAnnotation()!=null) { for(int i=0;
5377 * i<ap.av.getAlignment().getAlignmentAnnotation().length; i++) {
5378 * if(!ap.av.getAlignment().getAlignmentAnnotation()[i].autoCalculated) {
5379 * af.alignPanel.av.getAlignment().getAlignmentAnnotation()[i] =
5380 * ap.av.getAlignment().getAlignmentAnnotation()[i]; } } }
5383 return af.alignPanel;
5387 * flag indicating if hashtables should be cleared on finalization TODO this
5388 * flag may not be necessary
5390 private final boolean _cleartables = true;
5392 private Hashtable jvids2vobj;
5397 * @see java.lang.Object#finalize()
5400 protected void finalize() throws Throwable
5402 // really make sure we have no buried refs left.
5407 this.seqRefIds = null;
5408 this.seqsToIds = null;
5412 private void warn(String msg)
5417 private void warn(String msg, Exception e)
5419 if (Cache.log != null)
5423 Cache.log.warn(msg, e);
5427 Cache.log.warn(msg);
5432 System.err.println("Warning: " + msg);
5435 e.printStackTrace();
5440 private void debug(String string)
5442 debug(string, null);
5445 private void debug(String msg, Exception e)
5447 if (Cache.log != null)
5451 Cache.log.debug(msg, e);
5455 Cache.log.debug(msg);
5460 System.err.println("Warning: " + msg);
5463 e.printStackTrace();
5469 * set the object to ID mapping tables used to write/recover objects and XML
5470 * ID strings for the jalview project. If external tables are provided then
5471 * finalize and clearSeqRefs will not clear the tables when the Jalview2XML
5472 * object goes out of scope. - also populates the datasetIds hashtable with
5473 * alignment objects containing dataset sequences
5476 * Map from ID strings to jalview datamodel
5478 * Map from jalview datamodel to ID strings
5482 public void setObjectMappingTables(Hashtable vobj2jv,
5483 IdentityHashMap jv2vobj)
5485 this.jv2vobj = jv2vobj;
5486 this.vobj2jv = vobj2jv;
5487 Iterator ds = jv2vobj.keySet().iterator();
5489 while (ds.hasNext())
5491 Object jvobj = ds.next();
5492 id = jv2vobj.get(jvobj).toString();
5493 if (jvobj instanceof jalview.datamodel.Alignment)
5495 if (((jalview.datamodel.Alignment) jvobj).getDataset() == null)
5497 addDatasetRef(id, (jalview.datamodel.Alignment) jvobj);
5500 else if (jvobj instanceof jalview.datamodel.Sequence)
5502 // register sequence object so the XML parser can recover it.
5503 if (seqRefIds == null)
5505 seqRefIds = new HashMap<>();
5507 if (seqsToIds == null)
5509 seqsToIds = new IdentityHashMap<>();
5511 seqRefIds.put(jv2vobj.get(jvobj).toString(), (SequenceI) jvobj);
5512 seqsToIds.put((SequenceI) jvobj, id);
5514 else if (jvobj instanceof jalview.datamodel.AlignmentAnnotation)
5517 AlignmentAnnotation jvann = (AlignmentAnnotation) jvobj;
5518 annotationIds.put(anid = jv2vobj.get(jvobj).toString(), jvann);
5519 if (jvann.annotationId == null)
5521 jvann.annotationId = anid;
5523 if (!jvann.annotationId.equals(anid))
5525 // TODO verify that this is the correct behaviour
5526 this.warn("Overriding Annotation ID for " + anid
5527 + " from different id : " + jvann.annotationId);
5528 jvann.annotationId = anid;
5531 else if (jvobj instanceof String)
5533 if (jvids2vobj == null)
5535 jvids2vobj = new Hashtable();
5536 jvids2vobj.put(jvobj, jv2vobj.get(jvobj).toString());
5541 Cache.log.debug("Ignoring " + jvobj.getClass() + " (ID = " + id);
5547 * set the uniqueSetSuffix used to prefix/suffix object IDs for jalview
5548 * objects created from the project archive. If string is null (default for
5549 * construction) then suffix will be set automatically.
5553 public void setUniqueSetSuffix(String string)
5555 uniqueSetSuffix = string;
5560 * uses skipList2 as the skipList for skipping views on sequence sets
5561 * associated with keys in the skipList
5565 public void setSkipList(Hashtable skipList2)
5567 skipList = skipList2;
5571 * Reads the jar entry of given name and returns its contents, or null if the
5572 * entry is not found.
5575 * @param jarEntryName
5578 protected String readJarEntry(jarInputStreamProvider jprovider,
5579 String jarEntryName)
5581 String result = null;
5582 BufferedReader in = null;
5587 * Reopen the jar input stream and traverse its entries to find a matching
5590 JarInputStream jin = jprovider.getJarInputStream();
5591 JarEntry entry = null;
5594 entry = jin.getNextJarEntry();
5595 } while (entry != null && !entry.getName().equals(jarEntryName));
5599 StringBuilder out = new StringBuilder(256);
5600 in = new BufferedReader(new InputStreamReader(jin, UTF_8));
5603 while ((data = in.readLine()) != null)
5607 result = out.toString();
5611 warn("Couldn't find entry in Jalview Jar for " + jarEntryName);
5613 } catch (Exception ex)
5615 ex.printStackTrace();
5623 } catch (IOException e)
5634 * Returns an incrementing counter (0, 1, 2...)
5638 private synchronized int nextCounter()