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.
21 package jalview.project;
23 import static jalview.math.RotatableMatrix.Axis.X;
24 import static jalview.math.RotatableMatrix.Axis.Y;
25 import static jalview.math.RotatableMatrix.Axis.Z;
27 import jalview.analysis.Conservation;
28 import jalview.analysis.PCA;
29 import jalview.analysis.scoremodels.ScoreModels;
30 import jalview.analysis.scoremodels.SimilarityParams;
31 import jalview.api.FeatureColourI;
32 import jalview.api.ViewStyleI;
33 import jalview.api.analysis.ScoreModelI;
34 import jalview.api.analysis.SimilarityParamsI;
35 import jalview.api.structures.JalviewStructureDisplayI;
36 import jalview.bin.Cache;
37 import jalview.datamodel.AlignedCodonFrame;
38 import jalview.datamodel.Alignment;
39 import jalview.datamodel.AlignmentAnnotation;
40 import jalview.datamodel.AlignmentI;
41 import jalview.datamodel.DBRefEntry;
42 import jalview.datamodel.GraphLine;
43 import jalview.datamodel.PDBEntry;
44 import jalview.datamodel.Point;
45 import jalview.datamodel.RnaViewerModel;
46 import jalview.datamodel.SequenceFeature;
47 import jalview.datamodel.SequenceGroup;
48 import jalview.datamodel.SequenceI;
49 import jalview.datamodel.StructureViewerModel;
50 import jalview.datamodel.StructureViewerModel.StructureData;
51 import jalview.datamodel.features.FeatureMatcher;
52 import jalview.datamodel.features.FeatureMatcherI;
53 import jalview.datamodel.features.FeatureMatcherSet;
54 import jalview.datamodel.features.FeatureMatcherSetI;
55 import jalview.ext.varna.RnaModel;
56 import jalview.gui.AlignFrame;
57 import jalview.gui.AlignViewport;
58 import jalview.gui.AlignmentPanel;
59 import jalview.gui.AppVarna;
60 import jalview.gui.ChimeraViewFrame;
61 import jalview.gui.Desktop;
62 import jalview.gui.FeatureRenderer;
63 import jalview.gui.JvOptionPane;
64 import jalview.gui.OOMWarning;
65 import jalview.gui.PCAPanel;
66 import jalview.gui.PaintRefresher;
67 import jalview.gui.SplitFrame;
68 import jalview.gui.StructureViewer;
69 import jalview.gui.StructureViewer.ViewerType;
70 import jalview.gui.StructureViewerBase;
71 import jalview.gui.TreePanel;
72 import jalview.io.BackupFiles;
73 import jalview.io.DataSourceType;
74 import jalview.io.FileFormat;
75 import jalview.io.NewickFile;
76 import jalview.math.Matrix;
77 import jalview.math.MatrixI;
78 import jalview.renderer.ResidueShaderI;
79 import jalview.schemes.AnnotationColourGradient;
80 import jalview.schemes.ColourSchemeI;
81 import jalview.schemes.ColourSchemeProperty;
82 import jalview.schemes.FeatureColour;
83 import jalview.schemes.ResidueProperties;
84 import jalview.schemes.UserColourScheme;
85 import jalview.structures.models.AAStructureBindingModel;
86 import jalview.util.Format;
87 import jalview.util.MessageManager;
88 import jalview.util.Platform;
89 import jalview.util.StringUtils;
90 import jalview.util.jarInputStreamProvider;
91 import jalview.util.matcher.Condition;
92 import jalview.viewmodel.AlignmentViewport;
93 import jalview.viewmodel.PCAModel;
94 import jalview.viewmodel.ViewportRanges;
95 import jalview.viewmodel.seqfeatures.FeatureRendererSettings;
96 import jalview.viewmodel.seqfeatures.FeaturesDisplayed;
97 import jalview.ws.jws2.Jws2Discoverer;
98 import jalview.ws.jws2.dm.AAConSettings;
99 import jalview.ws.jws2.jabaws2.Jws2Instance;
100 import jalview.ws.params.ArgumentI;
101 import jalview.ws.params.AutoCalcSetting;
102 import jalview.ws.params.WsParamSetI;
103 import jalview.xml.binding.jalview.AlcodonFrame;
104 import jalview.xml.binding.jalview.AlcodonFrame.AlcodMap;
105 import jalview.xml.binding.jalview.Annotation;
106 import jalview.xml.binding.jalview.Annotation.ThresholdLine;
107 import jalview.xml.binding.jalview.AnnotationColourScheme;
108 import jalview.xml.binding.jalview.AnnotationElement;
109 import jalview.xml.binding.jalview.DoubleMatrix;
110 import jalview.xml.binding.jalview.DoubleVector;
111 import jalview.xml.binding.jalview.Feature;
112 import jalview.xml.binding.jalview.Feature.OtherData;
113 import jalview.xml.binding.jalview.FeatureMatcherSet.CompoundMatcher;
114 import jalview.xml.binding.jalview.FilterBy;
115 import jalview.xml.binding.jalview.JalviewModel;
116 import jalview.xml.binding.jalview.JalviewModel.FeatureSettings;
117 import jalview.xml.binding.jalview.JalviewModel.FeatureSettings.Group;
118 import jalview.xml.binding.jalview.JalviewModel.FeatureSettings.Setting;
119 import jalview.xml.binding.jalview.JalviewModel.JGroup;
120 import jalview.xml.binding.jalview.JalviewModel.JSeq;
121 import jalview.xml.binding.jalview.JalviewModel.JSeq.Pdbids;
122 import jalview.xml.binding.jalview.JalviewModel.JSeq.Pdbids.StructureState;
123 import jalview.xml.binding.jalview.JalviewModel.JSeq.RnaViewer;
124 import jalview.xml.binding.jalview.JalviewModel.JSeq.RnaViewer.SecondaryStructure;
125 import jalview.xml.binding.jalview.JalviewModel.PcaViewer;
126 import jalview.xml.binding.jalview.JalviewModel.PcaViewer.Axis;
127 import jalview.xml.binding.jalview.JalviewModel.PcaViewer.SeqPointMax;
128 import jalview.xml.binding.jalview.JalviewModel.PcaViewer.SeqPointMin;
129 import jalview.xml.binding.jalview.JalviewModel.PcaViewer.SequencePoint;
130 import jalview.xml.binding.jalview.JalviewModel.Tree;
131 import jalview.xml.binding.jalview.JalviewModel.UserColours;
132 import jalview.xml.binding.jalview.JalviewModel.Viewport;
133 import jalview.xml.binding.jalview.JalviewModel.Viewport.CalcIdParam;
134 import jalview.xml.binding.jalview.JalviewModel.Viewport.HiddenColumns;
135 import jalview.xml.binding.jalview.JalviewUserColours;
136 import jalview.xml.binding.jalview.JalviewUserColours.Colour;
137 import jalview.xml.binding.jalview.MapListType.MapListFrom;
138 import jalview.xml.binding.jalview.MapListType.MapListTo;
139 import jalview.xml.binding.jalview.Mapping;
140 import jalview.xml.binding.jalview.NoValueColour;
141 import jalview.xml.binding.jalview.ObjectFactory;
142 import jalview.xml.binding.jalview.PcaDataType;
143 import jalview.xml.binding.jalview.Pdbentry.Property;
144 import jalview.xml.binding.jalview.Sequence;
145 import jalview.xml.binding.jalview.Sequence.DBRef;
146 import jalview.xml.binding.jalview.SequenceSet;
147 import jalview.xml.binding.jalview.SequenceSet.SequenceSetProperties;
148 import jalview.xml.binding.jalview.ThresholdType;
149 import jalview.xml.binding.jalview.VAMSAS;
151 import java.awt.Color;
152 import java.awt.Font;
153 import java.awt.Rectangle;
154 import java.io.BufferedReader;
155 import java.io.ByteArrayInputStream;
156 import java.io.DataInputStream;
157 import java.io.DataOutputStream;
159 import java.io.FileInputStream;
160 import java.io.FileOutputStream;
161 import java.io.IOException;
162 import java.io.InputStreamReader;
163 import java.io.OutputStreamWriter;
164 import java.io.PrintWriter;
165 import java.lang.reflect.InvocationTargetException;
166 import java.math.BigInteger;
167 import java.net.MalformedURLException;
169 import java.util.ArrayList;
170 import java.util.Arrays;
171 import java.util.Collections;
172 import java.util.Enumeration;
173 import java.util.GregorianCalendar;
174 import java.util.HashMap;
175 import java.util.HashSet;
176 import java.util.Hashtable;
177 import java.util.IdentityHashMap;
178 import java.util.Iterator;
179 import java.util.LinkedHashMap;
180 import java.util.List;
181 import java.util.Map;
182 import java.util.Map.Entry;
183 import java.util.Set;
184 import java.util.Vector;
185 import java.util.jar.JarEntry;
186 import java.util.jar.JarInputStream;
187 import java.util.jar.JarOutputStream;
189 import javax.swing.JInternalFrame;
190 import javax.swing.SwingUtilities;
191 import javax.xml.bind.JAXBContext;
192 import javax.xml.bind.JAXBElement;
193 import javax.xml.bind.Marshaller;
194 import javax.xml.datatype.DatatypeConfigurationException;
195 import javax.xml.datatype.DatatypeFactory;
196 import javax.xml.datatype.XMLGregorianCalendar;
197 import javax.xml.stream.XMLInputFactory;
198 import javax.xml.stream.XMLStreamReader;
201 * Write out the current jalview desktop state as a Jalview XML stream.
203 * Note: the vamsas objects referred to here are primitive versions of the
204 * VAMSAS project schema elements - they are not the same and most likely never
208 * @version $Revision: 1.134 $
210 public class Jalview2XML
213 // BH 2018 we add the .jvp binary extension to J2S so that
214 // it will declare that binary when we do the file save from the browser
218 Platform.addJ2SBinaryType(".jvp?");
221 private static final String VIEWER_PREFIX = "viewer_";
223 private static final String RNA_PREFIX = "rna_";
225 private static final String UTF_8 = "UTF-8";
228 * prefix for recovering datasets for alignments with multiple views where
229 * non-existent dataset IDs were written for some views
231 private static final String UNIQSEQSETID = "uniqueSeqSetId.";
233 // use this with nextCounter() to make unique names for entities
234 private int counter = 0;
237 * SequenceI reference -> XML ID string in jalview XML. Populated as XML reps
238 * of sequence objects are created.
240 IdentityHashMap<SequenceI, String> seqsToIds = null;
243 * jalview XML Sequence ID to jalview sequence object reference (both dataset
244 * and alignment sequences. Populated as XML reps of sequence objects are
247 Map<String, SequenceI> seqRefIds = null;
249 Map<String, SequenceI> incompleteSeqs = null;
251 List<SeqFref> frefedSequence = null;
253 boolean raiseGUI = true; // whether errors are raised in dialog boxes or not
256 * Map of reconstructed AlignFrame objects that appear to have come from
257 * SplitFrame objects (have a dna/protein complement view).
259 private Map<Viewport, AlignFrame> splitFrameCandidates = new HashMap<>();
262 * Map from displayed rna structure models to their saved session state jar
265 private Map<RnaModel, String> rnaSessions = new HashMap<>();
268 * A helper method for safely using the value of an optional attribute that
269 * may be null if not present in the XML. Answers the boolean value, or false
275 public static boolean safeBoolean(Boolean b)
277 return b == null ? false : b.booleanValue();
281 * A helper method for safely using the value of an optional attribute that
282 * may be null if not present in the XML. Answers the integer value, or zero
288 public static int safeInt(Integer i)
290 return i == null ? 0 : i.intValue();
294 * A helper method for safely using the value of an optional attribute that
295 * may be null if not present in the XML. Answers the float value, or zero if
301 public static float safeFloat(Float f)
303 return f == null ? 0f : f.floatValue();
307 * create/return unique hash string for sq
310 * @return new or existing unique string for sq
312 String seqHash(SequenceI sq)
314 if (seqsToIds == null)
318 if (seqsToIds.containsKey(sq))
320 return seqsToIds.get(sq);
324 // create sequential key
325 String key = "sq" + (seqsToIds.size() + 1);
326 key = makeHashCode(sq, key); // check we don't have an external reference
328 seqsToIds.put(sq, key);
335 if (seqsToIds == null)
337 seqsToIds = new IdentityHashMap<>();
339 if (seqRefIds == null)
341 seqRefIds = new HashMap<>();
343 if (incompleteSeqs == null)
345 incompleteSeqs = new HashMap<>();
347 if (frefedSequence == null)
349 frefedSequence = new ArrayList<>();
357 public Jalview2XML(boolean raiseGUI)
359 this.raiseGUI = raiseGUI;
363 * base class for resolving forward references to sequences by their ID
368 abstract class SeqFref
374 public SeqFref(String _sref, String type)
380 public String getSref()
385 public SequenceI getSrefSeq()
387 return seqRefIds.get(sref);
390 public boolean isResolvable()
392 return seqRefIds.get(sref) != null;
395 public SequenceI getSrefDatasetSeq()
397 SequenceI sq = seqRefIds.get(sref);
400 while (sq.getDatasetSequence() != null)
402 sq = sq.getDatasetSequence();
409 * @return true if the forward reference was fully resolved
411 abstract boolean resolve();
414 public String toString()
416 return type + " reference to " + sref;
421 * create forward reference for a mapping
427 public SeqFref newMappingRef(final String sref,
428 final jalview.datamodel.Mapping _jmap)
430 SeqFref fref = new SeqFref(sref, "Mapping")
432 public jalview.datamodel.Mapping jmap = _jmap;
437 SequenceI seq = getSrefDatasetSeq();
449 public SeqFref newAlcodMapRef(final String sref,
450 final AlignedCodonFrame _cf,
451 final jalview.datamodel.Mapping _jmap)
454 SeqFref fref = new SeqFref(sref, "Codon Frame")
456 AlignedCodonFrame cf = _cf;
458 public jalview.datamodel.Mapping mp = _jmap;
461 public boolean isResolvable()
463 return super.isResolvable() && mp.getTo() != null;
469 SequenceI seq = getSrefDatasetSeq();
474 cf.addMap(seq, mp.getTo(), mp.getMap());
481 public void resolveFrefedSequences()
483 Iterator<SeqFref> nextFref = frefedSequence.iterator();
484 int toresolve = frefedSequence.size();
485 int unresolved = 0, failedtoresolve = 0;
486 while (nextFref.hasNext())
488 SeqFref ref = nextFref.next();
489 if (ref.isResolvable())
501 } catch (Exception x)
504 "IMPLEMENTATION ERROR: Failed to resolve forward reference for sequence "
517 System.err.println("Jalview Project Import: There were " + unresolved
518 + " forward references left unresolved on the stack.");
520 if (failedtoresolve > 0)
522 System.err.println("SERIOUS! " + failedtoresolve
523 + " resolvable forward references failed to resolve.");
525 if (incompleteSeqs != null && incompleteSeqs.size() > 0)
528 "Jalview Project Import: There are " + incompleteSeqs.size()
529 + " sequences which may have incomplete metadata.");
530 if (incompleteSeqs.size() < 10)
532 for (SequenceI s : incompleteSeqs.values())
534 System.err.println(s.toString());
540 "Too many to report. Skipping output of incomplete sequences.");
546 * This maintains a map of viewports, the key being the seqSetId. Important to
547 * set historyItem and redoList for multiple views
549 Map<String, AlignViewport> viewportsAdded = new HashMap<>();
551 Map<String, AlignmentAnnotation> annotationIds = new HashMap<>();
553 String uniqueSetSuffix = "";
556 * List of pdbfiles added to Jar
558 List<String> pdbfiles = null;
560 // SAVES SEVERAL ALIGNMENT WINDOWS TO SAME JARFILE
561 public void saveState(File statefile)
563 FileOutputStream fos = null;
568 fos = new FileOutputStream(statefile);
570 JarOutputStream jout = new JarOutputStream(fos);
574 } catch (Exception e)
576 Cache.log.error("Couln't write Jalview state to " + statefile, e);
577 // TODO: inform user of the problem - they need to know if their data was
579 if (errorMessage == null)
581 errorMessage = "Did't write Jalview Archive to output file '"
582 + statefile + "' - See console error log for details";
586 errorMessage += "(Didn't write Jalview Archive to output file '"
597 } catch (IOException e)
607 * Writes a jalview project archive to the given Jar output stream.
611 public void saveState(JarOutputStream jout)
613 AlignFrame[] frames = Desktop.getAlignFrames();
619 saveAllFrames(Arrays.asList(frames), jout);
623 * core method for storing state for a set of AlignFrames.
626 * - frames involving all data to be exported (including containing
629 * - project output stream
631 private void saveAllFrames(List<AlignFrame> frames, JarOutputStream jout)
633 Hashtable<String, AlignFrame> dsses = new Hashtable<>();
636 * ensure cached data is clear before starting
638 // todo tidy up seqRefIds, seqsToIds initialisation / reset
640 splitFrameCandidates.clear();
645 // NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS
646 // //////////////////////////////////////////////////
648 List<String> shortNames = new ArrayList<>();
649 List<String> viewIds = new ArrayList<>();
652 for (int i = frames.size() - 1; i > -1; i--)
654 AlignFrame af = frames.get(i);
656 if (skipList != null && skipList
657 .containsKey(af.getViewport().getSequenceSetId()))
662 String shortName = makeFilename(af, shortNames);
664 int apSize = af.getAlignPanels().size();
666 for (int ap = 0; ap < apSize; ap++)
668 AlignmentPanel apanel = (AlignmentPanel) af.getAlignPanels()
670 String fileName = apSize == 1 ? shortName : ap + shortName;
671 if (!fileName.endsWith(".xml"))
673 fileName = fileName + ".xml";
676 saveState(apanel, fileName, jout, viewIds);
678 String dssid = getDatasetIdRef(
679 af.getViewport().getAlignment().getDataset());
680 if (!dsses.containsKey(dssid))
682 dsses.put(dssid, af);
687 writeDatasetFor(dsses, "" + jout.hashCode() + " " + uniqueSetSuffix,
693 } catch (Exception foo)
697 } catch (Exception ex)
699 // TODO: inform user of the problem - they need to know if their data was
701 if (errorMessage == null)
703 errorMessage = "Couldn't write Jalview Archive - see error output for details";
705 ex.printStackTrace();
710 * Generates a distinct file name, based on the title of the AlignFrame, by
711 * appending _n for increasing n until an unused name is generated. The new
712 * name (without its extension) is added to the list.
716 * @return the generated name, with .xml extension
718 protected String makeFilename(AlignFrame af, List<String> namesUsed)
720 String shortName = af.getTitle();
722 if (shortName.indexOf(File.separatorChar) > -1)
724 shortName = shortName
725 .substring(shortName.lastIndexOf(File.separatorChar) + 1);
730 while (namesUsed.contains(shortName))
732 if (shortName.endsWith("_" + (count - 1)))
734 shortName = shortName.substring(0, shortName.lastIndexOf("_"));
737 shortName = shortName.concat("_" + count);
741 namesUsed.add(shortName);
743 if (!shortName.endsWith(".xml"))
745 shortName = shortName + ".xml";
750 // USE THIS METHOD TO SAVE A SINGLE ALIGNMENT WINDOW
751 public boolean saveAlignment(AlignFrame af, String jarFile,
756 // create backupfiles object and get new temp filename destination
757 boolean doBackup = BackupFiles.getEnabled();
758 BackupFiles backupfiles = doBackup ? new BackupFiles(jarFile) : null;
759 FileOutputStream fos = new FileOutputStream(doBackup ?
760 backupfiles.getTempFilePath() : jarFile);
762 JarOutputStream jout = new JarOutputStream(fos);
763 List<AlignFrame> frames = new ArrayList<>();
765 // resolve splitframes
766 if (af.getViewport().getCodingComplement() != null)
768 frames = ((SplitFrame) af.getSplitViewContainer()).getAlignFrames();
774 saveAllFrames(frames, jout);
778 } catch (Exception foo)
782 boolean success = true;
786 backupfiles.setWriteSuccess(success);
787 success = backupfiles.rollBackupsAndRenameTempFile();
791 } catch (Exception ex)
793 errorMessage = "Couldn't Write alignment view to Jalview Archive - see error output for details";
794 ex.printStackTrace();
799 private void writeDatasetFor(Hashtable<String, AlignFrame> dsses,
800 String fileName, JarOutputStream jout)
803 // BH: Question: What is this Dataset for, as it seems to
804 // duplicate the actual XML file data.
806 for (String dssids : dsses.keySet())
808 AlignFrame _af = dsses.get(dssids);
809 String jfileName = fileName + " Dataset for " + _af.getTitle();
810 if (!jfileName.endsWith(".xml"))
812 jfileName = jfileName + ".xml";
814 saveState(_af.alignPanel, jfileName, true, jout, null);
819 * create a JalviewModel from an alignment view and marshall it to a
823 * panel to create jalview model for
825 * name of alignment panel written to output stream
832 public JalviewModel saveState(AlignmentPanel ap, String fileName,
833 JarOutputStream jout, List<String> viewIds)
835 return saveState(ap, fileName, false, jout, viewIds);
839 * create a JalviewModel from an alignment view and marshall it to a
843 * panel to create jalview model for
845 * name of alignment panel written to output stream
847 * when true, only write the dataset for the alignment, not the data
848 * associated with the view.
854 public JalviewModel saveState(AlignmentPanel ap, String fileName,
855 boolean storeDS, JarOutputStream jout, List<String> viewIds)
859 viewIds = new ArrayList<>();
864 List<UserColourScheme> userColours = new ArrayList<>();
866 AlignViewport av = ap.av;
867 ViewportRanges vpRanges = av.getRanges();
869 final ObjectFactory objectFactory = new ObjectFactory();
870 JalviewModel object = objectFactory.createJalviewModel();
871 object.setVamsasModel(new VAMSAS());
873 // object.setCreationDate(new java.util.Date(System.currentTimeMillis()));
876 GregorianCalendar c = new GregorianCalendar();
877 DatatypeFactory datatypeFactory = DatatypeFactory.newInstance();
878 XMLGregorianCalendar now = datatypeFactory.newXMLGregorianCalendar(c);// gregorianCalendar);
879 object.setCreationDate(now);
880 } catch (DatatypeConfigurationException e)
882 System.err.println("error writing date: " + e.toString());
885 jalview.bin.Cache.getDefault("VERSION", "Development Build"));
888 * rjal is full height alignment, jal is actual alignment with full metadata
889 * but excludes hidden sequences.
891 jalview.datamodel.AlignmentI rjal = av.getAlignment(), jal = rjal;
893 if (av.hasHiddenRows())
895 rjal = jal.getHiddenSequences().getFullAlignment();
898 SequenceSet vamsasSet = new SequenceSet();
900 // JalviewModelSequence jms = new JalviewModelSequence();
902 vamsasSet.setGapChar(jal.getGapCharacter() + "");
904 if (jal.getDataset() != null)
906 // dataset id is the dataset's hashcode
907 vamsasSet.setDatasetId(getDatasetIdRef(jal.getDataset()));
910 // switch jal and the dataset
911 jal = jal.getDataset();
915 if (jal.getProperties() != null)
917 Enumeration en = jal.getProperties().keys();
918 while (en.hasMoreElements())
920 String key = en.nextElement().toString();
921 SequenceSetProperties ssp = new SequenceSetProperties();
923 ssp.setValue(jal.getProperties().get(key).toString());
924 // vamsasSet.addSequenceSetProperties(ssp);
925 vamsasSet.getSequenceSetProperties().add(ssp);
930 Set<String> calcIdSet = new HashSet<>();
931 // record the set of vamsas sequence XML POJO we create.
932 HashMap<String, Sequence> vamsasSetIds = new HashMap<>();
934 for (final SequenceI jds : rjal.getSequences())
936 final SequenceI jdatasq = jds.getDatasetSequence() == null ? jds
937 : jds.getDatasetSequence();
938 String id = seqHash(jds);
939 if (vamsasSetIds.get(id) == null)
941 if (seqRefIds.get(id) != null && !storeDS)
943 // This happens for two reasons: 1. multiple views are being
945 // 2. the hashCode has collided with another sequence's code. This
947 // HAPPEN! (PF00072.15.stk does this)
948 // JBPNote: Uncomment to debug writing out of files that do not read
949 // back in due to ArrayOutOfBoundExceptions.
950 // System.err.println("vamsasSeq backref: "+id+"");
951 // System.err.println(jds.getName()+"
952 // "+jds.getStart()+"-"+jds.getEnd()+" "+jds.getSequenceAsString());
953 // System.err.println("Hashcode: "+seqHash(jds));
954 // SequenceI rsq = (SequenceI) seqRefIds.get(id + "");
955 // System.err.println(rsq.getName()+"
956 // "+rsq.getStart()+"-"+rsq.getEnd()+" "+rsq.getSequenceAsString());
957 // System.err.println("Hashcode: "+seqHash(rsq));
961 vamsasSeq = createVamsasSequence(id, jds);
962 // vamsasSet.addSequence(vamsasSeq);
963 vamsasSet.getSequence().add(vamsasSeq);
964 vamsasSetIds.put(id, vamsasSeq);
965 seqRefIds.put(id, jds);
969 jseq.setStart(jds.getStart());
970 jseq.setEnd(jds.getEnd());
971 jseq.setColour(av.getSequenceColour(jds).getRGB());
973 jseq.setId(id); // jseq id should be a string not a number
976 // Store any sequences this sequence represents
977 if (av.hasHiddenRows())
979 // use rjal, contains the full height alignment
981 av.getAlignment().getHiddenSequences().isHidden(jds));
983 if (av.isHiddenRepSequence(jds))
985 jalview.datamodel.SequenceI[] reps = av
986 .getRepresentedSequences(jds).getSequencesInOrder(rjal);
988 for (int h = 0; h < reps.length; h++)
992 // jseq.addHiddenSequences(rjal.findIndex(reps[h]));
993 jseq.getHiddenSequences().add(rjal.findIndex(reps[h]));
998 // mark sequence as reference - if it is the reference for this view
1001 jseq.setViewreference(jds == jal.getSeqrep());
1005 // TODO: omit sequence features from each alignment view's XML dump if we
1006 // are storing dataset
1007 List<SequenceFeature> sfs = jds.getSequenceFeatures();
1008 for (SequenceFeature sf : sfs)
1010 // Features features = new Features();
1011 Feature features = new Feature();
1013 features.setBegin(sf.getBegin());
1014 features.setEnd(sf.getEnd());
1015 features.setDescription(sf.getDescription());
1016 features.setType(sf.getType());
1017 features.setFeatureGroup(sf.getFeatureGroup());
1018 features.setScore(sf.getScore());
1019 if (sf.links != null)
1021 for (int l = 0; l < sf.links.size(); l++)
1023 OtherData keyValue = new OtherData();
1024 keyValue.setKey("LINK_" + l);
1025 keyValue.setValue(sf.links.elementAt(l).toString());
1026 // features.addOtherData(keyValue);
1027 features.getOtherData().add(keyValue);
1030 if (sf.otherDetails != null)
1033 * save feature attributes, which may be simple strings or
1034 * map valued (have sub-attributes)
1036 for (Entry<String, Object> entry : sf.otherDetails.entrySet())
1038 String key = entry.getKey();
1039 Object value = entry.getValue();
1040 if (value instanceof Map<?, ?>)
1042 for (Entry<String, Object> subAttribute : ((Map<String, Object>) value)
1045 OtherData otherData = new OtherData();
1046 otherData.setKey(key);
1047 otherData.setKey2(subAttribute.getKey());
1048 otherData.setValue(subAttribute.getValue().toString());
1049 // features.addOtherData(otherData);
1050 features.getOtherData().add(otherData);
1055 OtherData otherData = new OtherData();
1056 otherData.setKey(key);
1057 otherData.setValue(value.toString());
1058 // features.addOtherData(otherData);
1059 features.getOtherData().add(otherData);
1064 // jseq.addFeatures(features);
1065 jseq.getFeatures().add(features);
1068 if (jdatasq.getAllPDBEntries() != null)
1070 Enumeration<PDBEntry> en = jdatasq.getAllPDBEntries().elements();
1071 while (en.hasMoreElements())
1073 Pdbids pdb = new Pdbids();
1074 jalview.datamodel.PDBEntry entry = en.nextElement();
1076 String pdbId = entry.getId();
1078 pdb.setType(entry.getType());
1081 * Store any structure views associated with this sequence. This
1082 * section copes with duplicate entries in the project, so a dataset
1083 * only view *should* be coped with sensibly.
1085 // This must have been loaded, is it still visible?
1086 JInternalFrame[] frames = Desktop.getDesktopPane().getAllFrames();
1087 String matchedFile = null;
1088 for (int f = frames.length - 1; f > -1; f--)
1090 if (frames[f] instanceof StructureViewerBase)
1092 StructureViewerBase viewFrame = (StructureViewerBase) frames[f];
1093 matchedFile = saveStructureState(ap, jds, pdb, entry, viewIds,
1094 matchedFile, viewFrame);
1096 * Only store each structure viewer's state once in the project
1097 * jar. First time through only (storeDS==false)
1099 String viewId = viewFrame.getViewId();
1100 if (!storeDS && !viewIds.contains(viewId))
1102 viewIds.add(viewId);
1105 String viewerState = viewFrame.getStateInfo();
1106 writeJarEntry(jout, getViewerJarEntryName(viewId),
1107 viewerState.getBytes());
1108 } catch (IOException e)
1111 "Error saving viewer state: " + e.getMessage());
1117 if (matchedFile != null || entry.getFile() != null)
1119 if (entry.getFile() != null)
1122 matchedFile = entry.getFile();
1124 pdb.setFile(matchedFile); // entry.getFile());
1125 if (pdbfiles == null)
1127 pdbfiles = new ArrayList<>();
1130 if (!pdbfiles.contains(pdbId))
1132 pdbfiles.add(pdbId);
1133 copyFileToJar(jout, matchedFile, pdbId);
1137 Enumeration<String> props = entry.getProperties();
1138 if (props.hasMoreElements())
1140 // PdbentryItem item = new PdbentryItem();
1141 while (props.hasMoreElements())
1143 Property prop = new Property();
1144 String key = props.nextElement();
1146 prop.setValue(entry.getProperty(key).toString());
1147 // item.addProperty(prop);
1148 pdb.getProperty().add(prop);
1150 // pdb.addPdbentryItem(item);
1153 // jseq.addPdbids(pdb);
1154 jseq.getPdbids().add(pdb);
1158 saveRnaViewers(jout, jseq, jds, viewIds, ap, storeDS);
1160 // jms.addJSeq(jseq);
1161 object.getJSeq().add(jseq);
1164 if (!storeDS && av.hasHiddenRows())
1166 jal = av.getAlignment();
1170 if (storeDS && jal.getCodonFrames() != null)
1172 List<AlignedCodonFrame> jac = jal.getCodonFrames();
1173 for (AlignedCodonFrame acf : jac)
1175 AlcodonFrame alc = new AlcodonFrame();
1176 if (acf.getProtMappings() != null
1177 && acf.getProtMappings().length > 0)
1179 boolean hasMap = false;
1180 SequenceI[] dnas = acf.getdnaSeqs();
1181 jalview.datamodel.Mapping[] pmaps = acf.getProtMappings();
1182 for (int m = 0; m < pmaps.length; m++)
1184 AlcodMap alcmap = new AlcodMap();
1185 alcmap.setDnasq(seqHash(dnas[m]));
1187 createVamsasMapping(pmaps[m], dnas[m], null, false));
1188 // alc.addAlcodMap(alcmap);
1189 alc.getAlcodMap().add(alcmap);
1194 // vamsasSet.addAlcodonFrame(alc);
1195 vamsasSet.getAlcodonFrame().add(alc);
1198 // TODO: delete this ? dead code from 2.8.3->2.9 ?
1200 // AlcodonFrame alc = new AlcodonFrame();
1201 // vamsasSet.addAlcodonFrame(alc);
1202 // for (int p = 0; p < acf.aaWidth; p++)
1204 // Alcodon cmap = new Alcodon();
1205 // if (acf.codons[p] != null)
1207 // // Null codons indicate a gapped column in the translated peptide
1209 // cmap.setPos1(acf.codons[p][0]);
1210 // cmap.setPos2(acf.codons[p][1]);
1211 // cmap.setPos3(acf.codons[p][2]);
1213 // alc.addAlcodon(cmap);
1215 // if (acf.getProtMappings() != null
1216 // && acf.getProtMappings().length > 0)
1218 // SequenceI[] dnas = acf.getdnaSeqs();
1219 // jalview.datamodel.Mapping[] pmaps = acf.getProtMappings();
1220 // for (int m = 0; m < pmaps.length; m++)
1222 // AlcodMap alcmap = new AlcodMap();
1223 // alcmap.setDnasq(seqHash(dnas[m]));
1224 // alcmap.setMapping(createVamsasMapping(pmaps[m], dnas[m], null,
1226 // alc.addAlcodMap(alcmap);
1233 // /////////////////////////////////
1234 if (!storeDS && av.getCurrentTree() != null)
1236 // FIND ANY ASSOCIATED TREES
1237 // NOT IMPLEMENTED FOR HEADLESS STATE AT PRESENT
1238 if (Desktop.getDesktopPane() != null)
1240 JInternalFrame[] frames = Desktop.getDesktopPane().getAllFrames();
1242 for (int t = 0; t < frames.length; t++)
1244 if (frames[t] instanceof TreePanel)
1246 TreePanel tp = (TreePanel) frames[t];
1248 if (tp.getTreeCanvas().getViewport().getAlignment() == jal)
1250 JalviewModel.Tree tree = new JalviewModel.Tree();
1251 tree.setTitle(tp.getTitle());
1252 tree.setCurrentTree((av.getCurrentTree() == tp.getTree()));
1253 tree.setNewick(tp.getTree().print());
1254 tree.setThreshold(tp.getTreeCanvas().getThreshold());
1256 tree.setFitToWindow(tp.fitToWindow.getState());
1257 tree.setFontName(tp.getTreeFont().getName());
1258 tree.setFontSize(tp.getTreeFont().getSize());
1259 tree.setFontStyle(tp.getTreeFont().getStyle());
1260 tree.setMarkUnlinked(tp.placeholdersMenu.getState());
1262 tree.setShowBootstrap(tp.bootstrapMenu.getState());
1263 tree.setShowDistances(tp.distanceMenu.getState());
1265 tree.setHeight(tp.getHeight());
1266 tree.setWidth(tp.getWidth());
1267 tree.setXpos(tp.getX());
1268 tree.setYpos(tp.getY());
1269 tree.setId(makeHashCode(tp, null));
1270 tree.setLinkToAllViews(
1271 tp.getTreeCanvas().isApplyToAllViews());
1273 // jms.addTree(tree);
1274 object.getTree().add(tree);
1284 if (!storeDS && Desktop.getDesktopPane() != null)
1286 for (JInternalFrame frame : Desktop.getDesktopPane().getAllFrames())
1288 if (frame instanceof PCAPanel)
1290 PCAPanel panel = (PCAPanel) frame;
1291 if (panel.getAlignViewport().getAlignment() == jal)
1293 savePCA(panel, object);
1301 * store forward refs from an annotationRow to any groups
1303 IdentityHashMap<SequenceGroup, String> groupRefs = new IdentityHashMap<>();
1306 for (SequenceI sq : jal.getSequences())
1308 // Store annotation on dataset sequences only
1309 AlignmentAnnotation[] aa = sq.getAnnotation();
1310 if (aa != null && aa.length > 0)
1312 storeAlignmentAnnotation(aa, groupRefs, av, calcIdSet, storeDS,
1319 if (jal.getAlignmentAnnotation() != null)
1321 // Store the annotation shown on the alignment.
1322 AlignmentAnnotation[] aa = jal.getAlignmentAnnotation();
1323 storeAlignmentAnnotation(aa, groupRefs, av, calcIdSet, storeDS,
1328 if (jal.getGroups() != null)
1330 JGroup[] groups = new JGroup[jal.getGroups().size()];
1332 for (jalview.datamodel.SequenceGroup sg : jal.getGroups())
1334 JGroup jGroup = new JGroup();
1335 groups[++i] = jGroup;
1337 jGroup.setStart(sg.getStartRes());
1338 jGroup.setEnd(sg.getEndRes());
1339 jGroup.setName(sg.getName());
1340 if (groupRefs.containsKey(sg))
1342 // group has references so set its ID field
1343 jGroup.setId(groupRefs.get(sg));
1345 ColourSchemeI colourScheme = sg.getColourScheme();
1346 if (colourScheme != null)
1348 ResidueShaderI groupColourScheme = sg.getGroupColourScheme();
1349 if (groupColourScheme.conservationApplied())
1351 jGroup.setConsThreshold(groupColourScheme.getConservationInc());
1353 if (colourScheme instanceof jalview.schemes.UserColourScheme)
1356 setUserColourScheme(colourScheme, userColours,
1361 jGroup.setColour(colourScheme.getSchemeName());
1364 else if (colourScheme instanceof jalview.schemes.AnnotationColourGradient)
1366 jGroup.setColour("AnnotationColourGradient");
1367 jGroup.setAnnotationColours(constructAnnotationColours(
1368 (jalview.schemes.AnnotationColourGradient) colourScheme,
1369 userColours, object));
1371 else if (colourScheme instanceof jalview.schemes.UserColourScheme)
1374 setUserColourScheme(colourScheme, userColours, object));
1378 jGroup.setColour(colourScheme.getSchemeName());
1381 jGroup.setPidThreshold(groupColourScheme.getThreshold());
1384 jGroup.setOutlineColour(sg.getOutlineColour().getRGB());
1385 jGroup.setDisplayBoxes(sg.getDisplayBoxes());
1386 jGroup.setDisplayText(sg.getDisplayText());
1387 jGroup.setColourText(sg.getColourText());
1388 jGroup.setTextCol1(sg.textColour.getRGB());
1389 jGroup.setTextCol2(sg.textColour2.getRGB());
1390 jGroup.setTextColThreshold(sg.thresholdTextColour);
1391 jGroup.setShowUnconserved(sg.getShowNonconserved());
1392 jGroup.setIgnoreGapsinConsensus(sg.getIgnoreGapsConsensus());
1393 jGroup.setShowConsensusHistogram(sg.isShowConsensusHistogram());
1394 jGroup.setShowSequenceLogo(sg.isShowSequenceLogo());
1395 jGroup.setNormaliseSequenceLogo(sg.isNormaliseSequenceLogo());
1396 for (SequenceI seq : sg.getSequences())
1398 // jGroup.addSeq(seqHash(seq));
1399 jGroup.getSeq().add(seqHash(seq));
1403 //jms.setJGroup(groups);
1405 for (JGroup grp : groups)
1407 object.getJGroup().add(grp);
1412 // /////////SAVE VIEWPORT
1413 Viewport view = new Viewport();
1414 view.setTitle(ap.alignFrame.getTitle());
1415 view.setSequenceSetId(
1416 makeHashCode(av.getSequenceSetId(), av.getSequenceSetId()));
1417 view.setId(av.getViewId());
1418 if (av.getCodingComplement() != null)
1420 view.setComplementId(av.getCodingComplement().getViewId());
1422 view.setViewName(av.getViewName());
1423 view.setGatheredViews(av.isGatherViewsHere());
1425 Rectangle size = ap.av.getExplodedGeometry();
1426 Rectangle position = size;
1429 size = ap.alignFrame.getBounds();
1430 if (av.getCodingComplement() != null)
1432 position = ((SplitFrame) ap.alignFrame.getSplitViewContainer())
1440 view.setXpos(position.x);
1441 view.setYpos(position.y);
1443 view.setWidth(size.width);
1444 view.setHeight(size.height);
1446 view.setStartRes(vpRanges.getStartRes());
1447 view.setStartSeq(vpRanges.getStartSeq());
1449 if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme)
1451 view.setBgColour(setUserColourScheme(av.getGlobalColourScheme(),
1452 userColours, object));
1455 .getGlobalColourScheme() instanceof jalview.schemes.AnnotationColourGradient)
1457 AnnotationColourScheme ac = constructAnnotationColours(
1458 (jalview.schemes.AnnotationColourGradient) av
1459 .getGlobalColourScheme(),
1460 userColours, object);
1462 view.setAnnotationColours(ac);
1463 view.setBgColour("AnnotationColourGradient");
1467 view.setBgColour(ColourSchemeProperty
1468 .getColourName(av.getGlobalColourScheme()));
1471 ResidueShaderI vcs = av.getResidueShading();
1472 ColourSchemeI cs = av.getGlobalColourScheme();
1476 if (vcs.conservationApplied())
1478 view.setConsThreshold(vcs.getConservationInc());
1479 if (cs instanceof jalview.schemes.UserColourScheme)
1481 view.setBgColour(setUserColourScheme(cs, userColours, object));
1484 view.setPidThreshold(vcs.getThreshold());
1487 view.setConservationSelected(av.getConservationSelected());
1488 view.setPidSelected(av.getAbovePIDThreshold());
1489 final Font font = av.getFont();
1490 view.setFontName(font.getName());
1491 view.setFontSize(font.getSize());
1492 view.setFontStyle(font.getStyle());
1493 view.setScaleProteinAsCdna(av.getViewStyle().isScaleProteinAsCdna());
1494 view.setRenderGaps(av.isRenderGaps());
1495 view.setShowAnnotation(av.isShowAnnotation());
1496 view.setShowBoxes(av.getShowBoxes());
1497 view.setShowColourText(av.getColourText());
1498 view.setShowFullId(av.getShowJVSuffix());
1499 view.setRightAlignIds(av.isRightAlignIds());
1500 view.setShowSequenceFeatures(av.isShowSequenceFeatures());
1501 view.setShowText(av.getShowText());
1502 view.setShowUnconserved(av.getShowUnconserved());
1503 view.setWrapAlignment(av.getWrapAlignment());
1504 view.setTextCol1(av.getTextColour().getRGB());
1505 view.setTextCol2(av.getTextColour2().getRGB());
1506 view.setTextColThreshold(av.getThresholdTextColour());
1507 view.setShowConsensusHistogram(av.isShowConsensusHistogram());
1508 view.setShowSequenceLogo(av.isShowSequenceLogo());
1509 view.setNormaliseSequenceLogo(av.isNormaliseSequenceLogo());
1510 view.setShowGroupConsensus(av.isShowGroupConsensus());
1511 view.setShowGroupConservation(av.isShowGroupConservation());
1512 view.setShowNPfeatureTooltip(av.isShowNPFeats());
1513 view.setShowDbRefTooltip(av.isShowDBRefs());
1514 view.setFollowHighlight(av.isFollowHighlight());
1515 view.setFollowSelection(av.followSelection);
1516 view.setIgnoreGapsinConsensus(av.isIgnoreGapsConsensus());
1517 if (av.getFeaturesDisplayed() != null)
1519 FeatureSettings fs = new FeatureSettings();
1521 FeatureRenderer fr = ap.getSeqPanel().seqCanvas
1522 .getFeatureRenderer();
1523 String[] renderOrder = fr.getRenderOrder().toArray(new String[0]);
1525 Vector<String> settingsAdded = new Vector<>();
1526 if (renderOrder != null)
1528 for (String featureType : renderOrder)
1530 FeatureSettings.Setting setting = new FeatureSettings.Setting();
1531 setting.setType(featureType);
1534 * save any filter for the feature type
1536 FeatureMatcherSetI filter = fr.getFeatureFilter(featureType);
1537 if (filter != null) {
1538 Iterator<FeatureMatcherI> filters = filter.getMatchers().iterator();
1539 FeatureMatcherI firstFilter = filters.next();
1540 setting.setMatcherSet(Jalview2XML.marshalFilter(
1541 firstFilter, filters, filter.isAnded()));
1545 * save colour scheme for the feature type
1547 FeatureColourI fcol = fr.getFeatureStyle(featureType);
1548 if (!fcol.isSimpleColour())
1550 setting.setColour(fcol.getMaxColour().getRGB());
1551 setting.setMincolour(fcol.getMinColour().getRGB());
1552 setting.setMin(fcol.getMin());
1553 setting.setMax(fcol.getMax());
1554 setting.setColourByLabel(fcol.isColourByLabel());
1555 if (fcol.isColourByAttribute())
1557 String[] attName = fcol.getAttributeName();
1558 setting.getAttributeName().add(attName[0]);
1559 if (attName.length > 1)
1561 setting.getAttributeName().add(attName[1]);
1564 setting.setAutoScale(fcol.isAutoScaled());
1565 setting.setThreshold(fcol.getThreshold());
1566 Color noColour = fcol.getNoColour();
1567 if (noColour == null)
1569 setting.setNoValueColour(NoValueColour.NONE);
1571 else if (noColour.equals(fcol.getMaxColour()))
1573 setting.setNoValueColour(NoValueColour.MAX);
1577 setting.setNoValueColour(NoValueColour.MIN);
1579 // -1 = No threshold, 0 = Below, 1 = Above
1580 setting.setThreshstate(fcol.isAboveThreshold() ? 1
1581 : (fcol.isBelowThreshold() ? 0 : -1));
1585 setting.setColour(fcol.getColour().getRGB());
1589 av.getFeaturesDisplayed().isVisible(featureType));
1591 .getOrder(featureType);
1594 setting.setOrder(rorder);
1596 /// fs.addSetting(setting);
1597 fs.getSetting().add(setting);
1598 settingsAdded.addElement(featureType);
1602 // is groups actually supposed to be a map here ?
1603 Iterator<String> en = fr.getFeatureGroups().iterator();
1604 Vector<String> groupsAdded = new Vector<>();
1605 while (en.hasNext())
1607 String grp = en.next();
1608 if (groupsAdded.contains(grp))
1612 Group g = new Group();
1614 g.setDisplay(((Boolean) fr.checkGroupVisibility(grp, false))
1617 fs.getGroup().add(g);
1618 groupsAdded.addElement(grp);
1620 // jms.setFeatureSettings(fs);
1621 object.setFeatureSettings(fs);
1624 if (av.hasHiddenColumns())
1626 jalview.datamodel.HiddenColumns hidden = av.getAlignment()
1627 .getHiddenColumns();
1630 warn("REPORT BUG: avoided null columnselection bug (DMAM reported). Please contact Jim about this.");
1634 Iterator<int[]> hiddenRegions = hidden.iterator();
1635 while (hiddenRegions.hasNext())
1637 int[] region = hiddenRegions.next();
1638 HiddenColumns hc = new HiddenColumns();
1639 hc.setStart(region[0]);
1640 hc.setEnd(region[1]);
1641 // view.addHiddenColumns(hc);
1642 view.getHiddenColumns().add(hc);
1646 if (calcIdSet.size() > 0)
1648 for (String calcId : calcIdSet)
1650 if (calcId.trim().length() > 0)
1652 CalcIdParam cidp = createCalcIdParam(calcId, av);
1653 // Some calcIds have no parameters.
1656 // view.addCalcIdParam(cidp);
1657 view.getCalcIdParam().add(cidp);
1663 // jms.addViewport(view);
1664 object.getViewport().add(view);
1666 // object.setJalviewModelSequence(jms);
1667 // object.getVamsasModel().addSequenceSet(vamsasSet);
1668 object.getVamsasModel().getSequenceSet().add(vamsasSet);
1670 if (jout != null && fileName != null)
1672 // We may not want to write the object to disk,
1673 // eg we can copy the alignViewport to a new view object
1674 // using save and then load
1677 fileName = fileName.replace('\\', '/');
1678 System.out.println("Writing jar entry " + fileName);
1679 JarEntry entry = new JarEntry(fileName);
1680 jout.putNextEntry(entry);
1681 PrintWriter pout = new PrintWriter(
1682 new OutputStreamWriter(jout, UTF_8));
1683 JAXBContext jaxbContext = JAXBContext
1684 .newInstance(JalviewModel.class);
1685 Marshaller jaxbMarshaller = jaxbContext.createMarshaller();
1687 // output pretty printed
1688 // jaxbMarshaller.setProperty(Marshaller.JAXB_FORMATTED_OUTPUT, true);
1689 jaxbMarshaller.marshal(
1690 new ObjectFactory().createJalviewModel(object), pout);
1692 // jaxbMarshaller.marshal(object, pout);
1693 // marshaller.marshal(object);
1696 } catch (Exception ex)
1698 // TODO: raise error in GUI if marshalling failed.
1699 System.err.println("Error writing Jalview project");
1700 ex.printStackTrace();
1707 * Writes PCA viewer attributes and computed values to an XML model object and
1708 * adds it to the JalviewModel. Any exceptions are reported by logging.
1710 protected void savePCA(PCAPanel panel, JalviewModel object)
1714 PcaViewer viewer = new PcaViewer();
1715 viewer.setHeight(panel.getHeight());
1716 viewer.setWidth(panel.getWidth());
1717 viewer.setXpos(panel.getX());
1718 viewer.setYpos(panel.getY());
1719 viewer.setTitle(panel.getTitle());
1720 PCAModel pcaModel = panel.getPcaModel();
1721 viewer.setScoreModelName(pcaModel.getScoreModelName());
1722 viewer.setXDim(panel.getSelectedDimensionIndex(X));
1723 viewer.setYDim(panel.getSelectedDimensionIndex(Y));
1724 viewer.setZDim(panel.getSelectedDimensionIndex(Z));
1726 panel.getRotatableCanvas().getBackgroundColour().getRGB());
1727 viewer.setScaleFactor(panel.getRotatableCanvas().getScaleFactor());
1728 float[] spMin = panel.getRotatableCanvas().getSeqMin();
1729 SeqPointMin spmin = new SeqPointMin();
1730 spmin.setXPos(spMin[0]);
1731 spmin.setYPos(spMin[1]);
1732 spmin.setZPos(spMin[2]);
1733 viewer.setSeqPointMin(spmin);
1734 float[] spMax = panel.getRotatableCanvas().getSeqMax();
1735 SeqPointMax spmax = new SeqPointMax();
1736 spmax.setXPos(spMax[0]);
1737 spmax.setYPos(spMax[1]);
1738 spmax.setZPos(spMax[2]);
1739 viewer.setSeqPointMax(spmax);
1740 viewer.setShowLabels(panel.getRotatableCanvas().isShowLabels());
1741 viewer.setLinkToAllViews(
1742 panel.getRotatableCanvas().isApplyToAllViews());
1743 SimilarityParamsI sp = pcaModel.getSimilarityParameters();
1744 viewer.setIncludeGaps(sp.includeGaps());
1745 viewer.setMatchGaps(sp.matchGaps());
1746 viewer.setIncludeGappedColumns(sp.includeGappedColumns());
1747 viewer.setDenominateByShortestLength(sp.denominateByShortestLength());
1750 * sequence points on display
1752 for (jalview.datamodel.SequencePoint spt : pcaModel
1753 .getSequencePoints())
1755 SequencePoint point = new SequencePoint();
1756 point.setSequenceRef(seqHash(spt.getSequence()));
1757 point.setXPos(spt.coord.x);
1758 point.setYPos(spt.coord.y);
1759 point.setZPos(spt.coord.z);
1760 viewer.getSequencePoint().add(point);
1764 * (end points of) axes on display
1766 for (Point p : panel.getRotatableCanvas().getAxisEndPoints())
1769 Axis axis = new Axis();
1773 viewer.getAxis().add(axis);
1777 * raw PCA data (note we are not restoring PCA inputs here -
1778 * alignment view, score model, similarity parameters)
1780 PcaDataType data = new PcaDataType();
1781 viewer.setPcaData(data);
1782 PCA pca = pcaModel.getPcaData();
1784 DoubleMatrix pm = new DoubleMatrix();
1785 saveDoubleMatrix(pca.getPairwiseScores(), pm);
1786 data.setPairwiseMatrix(pm);
1788 DoubleMatrix tm = new DoubleMatrix();
1789 saveDoubleMatrix(pca.getTridiagonal(), tm);
1790 data.setTridiagonalMatrix(tm);
1792 DoubleMatrix eigenMatrix = new DoubleMatrix();
1793 data.setEigenMatrix(eigenMatrix);
1794 saveDoubleMatrix(pca.getEigenmatrix(), eigenMatrix);
1796 object.getPcaViewer().add(viewer);
1797 } catch (Throwable t)
1799 Cache.log.error("Error saving PCA: " + t.getMessage());
1804 * Stores values from a matrix into an XML element, including (if present) the
1809 * @see #loadDoubleMatrix(DoubleMatrix)
1811 protected void saveDoubleMatrix(MatrixI m, DoubleMatrix xmlMatrix)
1813 xmlMatrix.setRows(m.height());
1814 xmlMatrix.setColumns(m.width());
1815 for (int i = 0; i < m.height(); i++)
1817 DoubleVector row = new DoubleVector();
1818 for (int j = 0; j < m.width(); j++)
1820 row.getV().add(m.getValue(i, j));
1822 xmlMatrix.getRow().add(row);
1824 if (m.getD() != null)
1826 DoubleVector dVector = new DoubleVector();
1827 for (double d : m.getD())
1829 dVector.getV().add(d);
1831 xmlMatrix.setD(dVector);
1833 if (m.getE() != null)
1835 DoubleVector eVector = new DoubleVector();
1836 for (double e : m.getE())
1838 eVector.getV().add(e);
1840 xmlMatrix.setE(eVector);
1845 * Loads XML matrix data into a new Matrix object, including the D and/or E
1846 * vectors (if present)
1850 * @see Jalview2XML#saveDoubleMatrix(MatrixI, DoubleMatrix)
1852 protected MatrixI loadDoubleMatrix(DoubleMatrix mData)
1854 int rows = mData.getRows();
1855 double[][] vals = new double[rows][];
1857 for (int i = 0; i < rows; i++)
1859 List<Double> dVector = mData.getRow().get(i).getV();
1860 vals[i] = new double[dVector.size()];
1862 for (Double d : dVector)
1868 MatrixI m = new Matrix(vals);
1870 if (mData.getD() != null)
1872 List<Double> dVector = mData.getD().getV();
1873 double[] vec = new double[dVector.size()];
1875 for (Double d : dVector)
1881 if (mData.getE() != null)
1883 List<Double> dVector = mData.getE().getV();
1884 double[] vec = new double[dVector.size()];
1886 for (Double d : dVector)
1897 * Save any Varna viewers linked to this sequence. Writes an rnaViewer element
1898 * for each viewer, with
1900 * <li>viewer geometry (position, size, split pane divider location)</li>
1901 * <li>index of the selected structure in the viewer (currently shows gapped
1903 * <li>the id of the annotation holding RNA secondary structure</li>
1904 * <li>(currently only one SS is shown per viewer, may be more in future)</li>
1906 * Varna viewer state is also written out (in native Varna XML) to separate
1907 * project jar entries. A separate entry is written for each RNA structure
1908 * displayed, with the naming convention
1910 * <li>rna_viewId_sequenceId_annotationId_[gapped|trimmed]</li>
1918 * @param storeDataset
1920 protected void saveRnaViewers(JarOutputStream jout, JSeq jseq,
1921 final SequenceI jds, List<String> viewIds, AlignmentPanel ap,
1922 boolean storeDataset)
1924 if (Desktop.getDesktopPane() == null)
1928 JInternalFrame[] frames = Desktop.getDesktopPane().getAllFrames();
1929 for (int f = frames.length - 1; f > -1; f--)
1931 if (frames[f] instanceof AppVarna)
1933 AppVarna varna = (AppVarna) frames[f];
1935 * link the sequence to every viewer that is showing it and is linked to
1936 * its alignment panel
1938 if (varna.isListeningFor(jds) && ap == varna.getAlignmentPanel())
1940 String viewId = varna.getViewId();
1941 RnaViewer rna = new RnaViewer();
1942 rna.setViewId(viewId);
1943 rna.setTitle(varna.getTitle());
1944 rna.setXpos(varna.getX());
1945 rna.setYpos(varna.getY());
1946 rna.setWidth(varna.getWidth());
1947 rna.setHeight(varna.getHeight());
1948 rna.setDividerLocation(varna.getDividerLocation());
1949 rna.setSelectedRna(varna.getSelectedIndex());
1950 // jseq.addRnaViewer(rna);
1951 jseq.getRnaViewer().add(rna);
1954 * Store each Varna panel's state once in the project per sequence.
1955 * First time through only (storeDataset==false)
1957 // boolean storeSessions = false;
1958 // String sequenceViewId = viewId + seqsToIds.get(jds);
1959 // if (!storeDataset && !viewIds.contains(sequenceViewId))
1961 // viewIds.add(sequenceViewId);
1962 // storeSessions = true;
1964 for (RnaModel model : varna.getModels())
1966 if (model.seq == jds)
1969 * VARNA saves each view (sequence or alignment secondary
1970 * structure, gapped or trimmed) as a separate XML file
1972 String jarEntryName = rnaSessions.get(model);
1973 if (jarEntryName == null)
1976 String varnaStateFile = varna.getStateInfo(model.rna);
1977 jarEntryName = RNA_PREFIX + viewId + "_" + nextCounter();
1978 copyFileToJar(jout, varnaStateFile, jarEntryName);
1979 rnaSessions.put(model, jarEntryName);
1981 SecondaryStructure ss = new SecondaryStructure();
1982 String annotationId = varna.getAnnotation(jds).annotationId;
1983 ss.setAnnotationId(annotationId);
1984 ss.setViewerState(jarEntryName);
1985 ss.setGapped(model.gapped);
1986 ss.setTitle(model.title);
1987 // rna.addSecondaryStructure(ss);
1988 rna.getSecondaryStructure().add(ss);
1997 * Copy the contents of a file to a new entry added to the output jar
2001 * @param jarEntryName
2003 protected void copyFileToJar(JarOutputStream jout, String infilePath,
2004 String jarEntryName)
2006 DataInputStream dis = null;
2009 File file = new File(infilePath);
2010 if (file.exists() && jout != null)
2012 dis = new DataInputStream(new FileInputStream(file));
2013 byte[] data = new byte[(int) file.length()];
2014 dis.readFully(data);
2015 writeJarEntry(jout, jarEntryName, data);
2017 } catch (Exception ex)
2019 ex.printStackTrace();
2027 } catch (IOException e)
2036 * Write the data to a new entry of given name in the output jar file
2039 * @param jarEntryName
2041 * @throws IOException
2043 protected void writeJarEntry(JarOutputStream jout, String jarEntryName,
2044 byte[] data) throws IOException
2048 jarEntryName = jarEntryName.replace('\\','/');
2049 System.out.println("Writing jar entry " + jarEntryName);
2050 jout.putNextEntry(new JarEntry(jarEntryName));
2051 DataOutputStream dout = new DataOutputStream(jout);
2052 dout.write(data, 0, data.length);
2059 * Save the state of a structure viewer
2064 * the archive XML element under which to save the state
2067 * @param matchedFile
2071 protected String saveStructureState(AlignmentPanel ap, SequenceI jds,
2072 Pdbids pdb, PDBEntry entry, List<String> viewIds,
2073 String matchedFile, StructureViewerBase viewFrame)
2075 final AAStructureBindingModel bindingModel = viewFrame.getBinding();
2078 * Look for any bindings for this viewer to the PDB file of interest
2079 * (including part matches excluding chain id)
2081 for (int peid = 0; peid < bindingModel.getPdbCount(); peid++)
2083 final PDBEntry pdbentry = bindingModel.getPdbEntry(peid);
2084 final String pdbId = pdbentry.getId();
2085 if (!pdbId.equals(entry.getId())
2086 && !(entry.getId().length() > 4 && entry.getId().toLowerCase()
2087 .startsWith(pdbId.toLowerCase())))
2090 * not interested in a binding to a different PDB entry here
2094 if (matchedFile == null)
2096 matchedFile = pdbentry.getFile();
2098 else if (!matchedFile.equals(pdbentry.getFile()))
2101 "Probably lost some PDB-Sequence mappings for this structure file (which apparently has same PDB Entry code): "
2102 + pdbentry.getFile());
2106 // can get at it if the ID
2107 // match is ambiguous (e.g.
2110 for (int smap = 0; smap < viewFrame.getBinding()
2111 .getSequence()[peid].length; smap++)
2113 // if (jal.findIndex(jmol.jmb.sequence[peid][smap]) > -1)
2114 if (jds == viewFrame.getBinding().getSequence()[peid][smap])
2116 StructureState state = new StructureState();
2117 state.setVisible(true);
2118 state.setXpos(viewFrame.getX());
2119 state.setYpos(viewFrame.getY());
2120 state.setWidth(viewFrame.getWidth());
2121 state.setHeight(viewFrame.getHeight());
2122 final String viewId = viewFrame.getViewId();
2123 state.setViewId(viewId);
2124 state.setAlignwithAlignPanel(viewFrame.isUsedforaligment(ap));
2125 state.setColourwithAlignPanel(viewFrame.isUsedforcolourby(ap));
2126 state.setColourByJmol(viewFrame.isColouredByViewer());
2127 state.setType(viewFrame.getViewerType().toString());
2128 // pdb.addStructureState(state);
2129 pdb.getStructureState().add(state);
2137 * Populates the AnnotationColourScheme xml for save. This captures the
2138 * settings of the options in the 'Colour by Annotation' dialog.
2141 * @param userColours
2145 private AnnotationColourScheme constructAnnotationColours(
2146 AnnotationColourGradient acg, List<UserColourScheme> userColours,
2149 AnnotationColourScheme ac = new AnnotationColourScheme();
2150 ac.setAboveThreshold(acg.getAboveThreshold());
2151 ac.setThreshold(acg.getAnnotationThreshold());
2152 // 2.10.2 save annotationId (unique) not annotation label
2153 ac.setAnnotation(acg.getAnnotation().annotationId);
2154 if (acg.getBaseColour() instanceof UserColourScheme)
2157 setUserColourScheme(acg.getBaseColour(), userColours, jm));
2162 ColourSchemeProperty.getColourName(acg.getBaseColour()));
2165 ac.setMaxColour(acg.getMaxColour().getRGB());
2166 ac.setMinColour(acg.getMinColour().getRGB());
2167 ac.setPerSequence(acg.isSeqAssociated());
2168 ac.setPredefinedColours(acg.isPredefinedColours());
2172 private void storeAlignmentAnnotation(AlignmentAnnotation[] aa,
2173 IdentityHashMap<SequenceGroup, String> groupRefs,
2174 AlignmentViewport av, Set<String> calcIdSet, boolean storeDS,
2175 SequenceSet vamsasSet)
2178 for (int i = 0; i < aa.length; i++)
2180 Annotation an = new Annotation();
2182 AlignmentAnnotation annotation = aa[i];
2183 if (annotation.annotationId != null)
2185 annotationIds.put(annotation.annotationId, annotation);
2188 an.setId(annotation.annotationId);
2190 an.setVisible(annotation.visible);
2192 an.setDescription(annotation.description);
2194 if (annotation.sequenceRef != null)
2196 // 2.9 JAL-1781 xref on sequence id rather than name
2197 an.setSequenceRef(seqsToIds.get(annotation.sequenceRef));
2199 if (annotation.groupRef != null)
2201 String groupIdr = groupRefs.get(annotation.groupRef);
2202 if (groupIdr == null)
2204 // make a locally unique String
2205 groupRefs.put(annotation.groupRef,
2206 groupIdr = ("" + System.currentTimeMillis()
2207 + annotation.groupRef.getName()
2208 + groupRefs.size()));
2210 an.setGroupRef(groupIdr.toString());
2213 // store all visualization attributes for annotation
2214 an.setGraphHeight(annotation.graphHeight);
2215 an.setCentreColLabels(annotation.centreColLabels);
2216 an.setScaleColLabels(annotation.scaleColLabel);
2217 an.setShowAllColLabels(annotation.showAllColLabels);
2218 an.setBelowAlignment(annotation.belowAlignment);
2220 if (annotation.graph > 0)
2223 an.setGraphType(annotation.graph);
2224 an.setGraphGroup(annotation.graphGroup);
2225 if (annotation.getThreshold() != null)
2227 ThresholdLine line = new ThresholdLine();
2228 line.setLabel(annotation.getThreshold().label);
2229 line.setValue(annotation.getThreshold().value);
2230 line.setColour(annotation.getThreshold().colour.getRGB());
2231 an.setThresholdLine(line);
2239 an.setLabel(annotation.label);
2241 if (annotation == av.getAlignmentQualityAnnot()
2242 || annotation == av.getAlignmentConservationAnnotation()
2243 || annotation == av.getAlignmentConsensusAnnotation()
2244 || annotation.autoCalculated)
2246 // new way of indicating autocalculated annotation -
2247 an.setAutoCalculated(annotation.autoCalculated);
2249 if (annotation.hasScore())
2251 an.setScore(annotation.getScore());
2254 if (annotation.getCalcId() != null)
2256 calcIdSet.add(annotation.getCalcId());
2257 an.setCalcId(annotation.getCalcId());
2259 if (annotation.hasProperties())
2261 for (String pr : annotation.getProperties())
2263 jalview.xml.binding.jalview.Annotation.Property prop = new jalview.xml.binding.jalview.Annotation.Property();
2265 prop.setValue(annotation.getProperty(pr));
2266 // an.addProperty(prop);
2267 an.getProperty().add(prop);
2271 AnnotationElement ae;
2272 if (annotation.annotations != null)
2274 an.setScoreOnly(false);
2275 for (int a = 0; a < annotation.annotations.length; a++)
2277 if ((annotation == null) || (annotation.annotations[a] == null))
2282 ae = new AnnotationElement();
2283 if (annotation.annotations[a].description != null)
2285 ae.setDescription(annotation.annotations[a].description);
2287 if (annotation.annotations[a].displayCharacter != null)
2289 ae.setDisplayCharacter(
2290 annotation.annotations[a].displayCharacter);
2293 if (!Float.isNaN(annotation.annotations[a].value))
2295 ae.setValue(annotation.annotations[a].value);
2299 if (annotation.annotations[a].secondaryStructure > ' ')
2301 ae.setSecondaryStructure(
2302 annotation.annotations[a].secondaryStructure + "");
2305 if (annotation.annotations[a].colour != null
2306 && annotation.annotations[a].colour != java.awt.Color.black)
2308 ae.setColour(annotation.annotations[a].colour.getRGB());
2311 // an.addAnnotationElement(ae);
2312 an.getAnnotationElement().add(ae);
2313 if (annotation.autoCalculated)
2315 // only write one non-null entry into the annotation row -
2316 // sufficient to get the visualization attributes necessary to
2324 an.setScoreOnly(true);
2326 if (!storeDS || (storeDS && !annotation.autoCalculated))
2328 // skip autocalculated annotation - these are only provided for
2330 // vamsasSet.addAnnotation(an);
2331 vamsasSet.getAnnotation().add(an);
2337 private CalcIdParam createCalcIdParam(String calcId, AlignViewport av)
2339 AutoCalcSetting settings = av.getCalcIdSettingsFor(calcId);
2340 if (settings != null)
2342 CalcIdParam vCalcIdParam = new CalcIdParam();
2343 vCalcIdParam.setCalcId(calcId);
2344 // vCalcIdParam.addServiceURL(settings.getServiceURI());
2345 vCalcIdParam.getServiceURL().add(settings.getServiceURI());
2346 // generic URI allowing a third party to resolve another instance of the
2347 // service used for this calculation
2348 for (String url : settings.getServiceURLs())
2350 // vCalcIdParam.addServiceURL(urls);
2351 vCalcIdParam.getServiceURL().add(url);
2353 vCalcIdParam.setVersion("1.0");
2354 if (settings.getPreset() != null)
2356 WsParamSetI setting = settings.getPreset();
2357 vCalcIdParam.setName(setting.getName());
2358 vCalcIdParam.setDescription(setting.getDescription());
2362 vCalcIdParam.setName("");
2363 vCalcIdParam.setDescription("Last used parameters");
2365 // need to be able to recover 1) settings 2) user-defined presets or
2366 // recreate settings from preset 3) predefined settings provided by
2367 // service - or settings that can be transferred (or discarded)
2368 vCalcIdParam.setParameters(
2369 settings.getWsParamFile().replace("\n", "|\\n|"));
2370 vCalcIdParam.setAutoUpdate(settings.isAutoUpdate());
2371 // todo - decide if updateImmediately is needed for any projects.
2373 return vCalcIdParam;
2378 private boolean recoverCalcIdParam(CalcIdParam calcIdParam,
2381 if (calcIdParam.getVersion().equals("1.0"))
2383 final String[] calcIds = calcIdParam.getServiceURL().toArray(new String[0]);
2384 Jws2Instance service = Jws2Discoverer.getInstance()
2385 .getPreferredServiceFor(calcIds);
2386 if (service != null)
2388 WsParamSetI parmSet = null;
2391 parmSet = service.getParamStore().parseServiceParameterFile(
2392 calcIdParam.getName(), calcIdParam.getDescription(),
2394 calcIdParam.getParameters().replace("|\\n|", "\n"));
2395 } catch (IOException x)
2397 warn("Couldn't parse parameter data for "
2398 + calcIdParam.getCalcId(), x);
2401 List<ArgumentI> argList = null;
2402 if (calcIdParam.getName().length() > 0)
2404 parmSet = service.getParamStore()
2405 .getPreset(calcIdParam.getName());
2406 if (parmSet != null)
2408 // TODO : check we have a good match with settings in AACon -
2409 // otherwise we'll need to create a new preset
2414 argList = parmSet.getArguments();
2417 AAConSettings settings = new AAConSettings(
2418 calcIdParam.isAutoUpdate(), service, parmSet, argList);
2419 av.setCalcIdSettingsFor(calcIdParam.getCalcId(), settings,
2420 calcIdParam.isNeedsUpdate());
2425 warn("Cannot resolve a service for the parameters used in this project. Try configuring a JABAWS server.");
2429 throw new Error(MessageManager.formatMessage(
2430 "error.unsupported_version_calcIdparam", new Object[]
2431 { calcIdParam.toString() }));
2435 * External mapping between jalview objects and objects yielding a valid and
2436 * unique object ID string. This is null for normal Jalview project IO, but
2437 * non-null when a jalview project is being read or written as part of a
2440 IdentityHashMap jv2vobj = null;
2443 * Construct a unique ID for jvobj using either existing bindings or if none
2444 * exist, the result of the hashcode call for the object.
2447 * jalview data object
2448 * @return unique ID for referring to jvobj
2450 private String makeHashCode(Object jvobj, String altCode)
2452 if (jv2vobj != null)
2454 Object id = jv2vobj.get(jvobj);
2457 return id.toString();
2459 // check string ID mappings
2460 if (jvids2vobj != null && jvobj instanceof String)
2462 id = jvids2vobj.get(jvobj);
2466 return id.toString();
2468 // give up and warn that something has gone wrong
2469 warn("Cannot find ID for object in external mapping : " + jvobj);
2475 * return local jalview object mapped to ID, if it exists
2479 * @return null or object bound to idcode
2481 private Object retrieveExistingObj(String idcode)
2483 if (idcode != null && vobj2jv != null)
2485 return vobj2jv.get(idcode);
2491 * binding from ID strings from external mapping table to jalview data model
2494 private Hashtable vobj2jv;
2496 private Sequence createVamsasSequence(String id, SequenceI jds)
2498 return createVamsasSequence(true, id, jds, null);
2501 private Sequence createVamsasSequence(boolean recurse, String id,
2502 SequenceI jds, SequenceI parentseq)
2504 Sequence vamsasSeq = new Sequence();
2505 vamsasSeq.setId(id);
2506 vamsasSeq.setName(jds.getName());
2507 vamsasSeq.setSequence(jds.getSequenceAsString());
2508 vamsasSeq.setDescription(jds.getDescription());
2509 List<DBRefEntry> dbrefs = null;
2510 if (jds.getDatasetSequence() != null)
2512 vamsasSeq.setDsseqid(seqHash(jds.getDatasetSequence()));
2516 // seqId==dsseqid so we can tell which sequences really are
2517 // dataset sequences only
2518 vamsasSeq.setDsseqid(id);
2519 dbrefs = jds.getDBRefs();
2520 if (parentseq == null)
2527 for (int d = 0, nd = dbrefs.size(); d < nd; d++)
2529 DBRef dbref = new DBRef();
2530 DBRefEntry ref = dbrefs.get(d);
2531 dbref.setSource(ref.getSource());
2532 dbref.setVersion(ref.getVersion());
2533 dbref.setAccessionId(ref.getAccessionId());
2536 Mapping mp = createVamsasMapping(ref.getMap(), parentseq,
2538 dbref.setMapping(mp);
2540 // vamsasSeq.addDBRef(dbref);
2541 vamsasSeq.getDBRef().add(dbref);
2547 private Mapping createVamsasMapping(jalview.datamodel.Mapping jmp,
2548 SequenceI parentseq, SequenceI jds, boolean recurse)
2551 if (jmp.getMap() != null)
2555 jalview.util.MapList mlst = jmp.getMap();
2556 List<int[]> r = mlst.getFromRanges();
2557 for (int[] range : r)
2559 MapListFrom mfrom = new MapListFrom();
2560 mfrom.setStart(range[0]);
2561 mfrom.setEnd(range[1]);
2562 // mp.addMapListFrom(mfrom);
2563 mp.getMapListFrom().add(mfrom);
2565 r = mlst.getToRanges();
2566 for (int[] range : r)
2568 MapListTo mto = new MapListTo();
2569 mto.setStart(range[0]);
2570 mto.setEnd(range[1]);
2571 // mp.addMapListTo(mto);
2572 mp.getMapListTo().add(mto);
2574 mp.setMapFromUnit(BigInteger.valueOf(mlst.getFromRatio()));
2575 mp.setMapToUnit(BigInteger.valueOf(mlst.getToRatio()));
2576 if (jmp.getTo() != null)
2578 // MappingChoice mpc = new MappingChoice();
2580 // check/create ID for the sequence referenced by getTo()
2583 SequenceI ps = null;
2584 if (parentseq != jmp.getTo()
2585 && parentseq.getDatasetSequence() != jmp.getTo())
2587 // chaining dbref rather than a handshaking one
2588 jmpid = seqHash(ps = jmp.getTo());
2592 jmpid = seqHash(ps = parentseq);
2594 // mpc.setDseqFor(jmpid);
2595 mp.setDseqFor(jmpid);
2596 if (!seqRefIds.containsKey(jmpid))
2598 jalview.bin.Cache.log.debug("creatign new DseqFor ID");
2599 seqRefIds.put(jmpid, ps);
2603 jalview.bin.Cache.log.debug("reusing DseqFor ID");
2606 // mp.setMappingChoice(mpc);
2612 String setUserColourScheme(jalview.schemes.ColourSchemeI cs,
2613 List<UserColourScheme> userColours, JalviewModel jm)
2616 jalview.schemes.UserColourScheme ucs = (jalview.schemes.UserColourScheme) cs;
2617 boolean newucs = false;
2618 if (!userColours.contains(ucs))
2620 userColours.add(ucs);
2623 id = "ucs" + userColours.indexOf(ucs);
2626 // actually create the scheme's entry in the XML model
2627 java.awt.Color[] colours = ucs.getColours();
2628 UserColours uc = new UserColours();
2629 // UserColourScheme jbucs = new UserColourScheme();
2630 JalviewUserColours jbucs = new JalviewUserColours();
2632 for (int i = 0; i < colours.length; i++)
2634 Colour col = new Colour();
2635 col.setName(ResidueProperties.aa[i]);
2636 col.setRGB(jalview.util.Format.getHexString(colours[i]));
2637 // jbucs.addColour(col);
2638 jbucs.getColour().add(col);
2640 if (ucs.getLowerCaseColours() != null)
2642 colours = ucs.getLowerCaseColours();
2643 for (int i = 0; i < colours.length; i++)
2645 Colour col = new Colour();
2646 col.setName(ResidueProperties.aa[i].toLowerCase());
2647 col.setRGB(jalview.util.Format.getHexString(colours[i]));
2648 // jbucs.addColour(col);
2649 jbucs.getColour().add(col);
2654 uc.setUserColourScheme(jbucs);
2655 // jm.addUserColours(uc);
2656 jm.getUserColours().add(uc);
2662 jalview.schemes.UserColourScheme getUserColourScheme(
2663 JalviewModel jm, String id)
2665 List<UserColours> uc = jm.getUserColours();
2666 UserColours colours = null;
2668 for (int i = 0; i < uc.length; i++)
2670 if (uc[i].getId().equals(id))
2677 for (UserColours c : uc)
2679 if (c.getId().equals(id))
2686 java.awt.Color[] newColours = new java.awt.Color[24];
2688 for (int i = 0; i < 24; i++)
2690 newColours[i] = new java.awt.Color(Integer.parseInt(
2691 // colours.getUserColourScheme().getColour(i).getRGB(), 16));
2692 colours.getUserColourScheme().getColour().get(i).getRGB(),
2696 jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(
2699 if (colours.getUserColourScheme().getColour().size()/*Count()*/ > 24)
2701 newColours = new java.awt.Color[23];
2702 for (int i = 0; i < 23; i++)
2704 newColours[i] = new java.awt.Color(Integer.parseInt(
2705 colours.getUserColourScheme().getColour().get(i + 24)
2709 ucs.setLowerCaseColours(newColours);
2716 * contains last error message (if any) encountered by XML loader.
2718 String errorMessage = null;
2721 * flag to control whether the Jalview2XML_V1 parser should be deferred to if
2722 * exceptions are raised during project XML parsing
2724 public boolean attemptversion1parse = false;
2727 * Load a jalview project archive from a jar file
2730 * - HTTP URL or filename
2732 public AlignFrame loadJalviewAlign(final Object file)
2735 jalview.gui.AlignFrame af = null;
2739 // create list to store references for any new Jmol viewers created
2740 newStructureViewers = new Vector<>();
2741 // UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
2742 // Workaround is to make sure caller implements the JarInputStreamProvider
2744 // so we can re-open the jar input stream for each entry.
2746 jarInputStreamProvider jprovider = createjarInputStreamProvider(file);
2747 af = loadJalviewAlign(jprovider);
2750 af.setMenusForViewport();
2752 } catch (MalformedURLException e)
2754 errorMessage = "Invalid URL format for '" + file + "'";
2760 SwingUtilities.invokeAndWait(new Runnable()
2765 setLoadingFinishedForNewStructureViewers();
2768 } catch (Exception x)
2770 System.err.println("Error loading alignment: " + x.getMessage());
2776 @SuppressWarnings("unused")
2777 private jarInputStreamProvider createjarInputStreamProvider(final Object ofile) throws MalformedURLException {
2779 // BH 2018 allow for bytes already attached to File object
2781 String file = (ofile instanceof File ? ((File) ofile).getCanonicalPath() : ofile.toString());
2782 byte[] bytes = Platform.isJS() ? Platform.getFileBytes((File) ofile)
2785 errorMessage = null;
2786 uniqueSetSuffix = null;
2788 viewportsAdded.clear();
2789 frefedSequence = null;
2791 if (file.startsWith("http://")) {
2792 url = new URL(file);
2794 final URL _url = url;
2795 return new jarInputStreamProvider() {
2798 public JarInputStream getJarInputStream() throws IOException {
2799 if (bytes != null) {
2800 // System.out.println("Jalview2XML: opening byte jarInputStream for bytes.length=" + bytes.length);
2801 return new JarInputStream(new ByteArrayInputStream(bytes));
2804 // System.out.println("Jalview2XML: opening url jarInputStream for " + _url);
2805 return new JarInputStream(_url.openStream());
2807 // System.out.println("Jalview2XML: opening file jarInputStream for " + file);
2808 return new JarInputStream(new FileInputStream(file));
2813 public String getFilename() {
2817 } catch (IOException e) {
2818 e.printStackTrace();
2824 * Recover jalview session from a jalview project archive. Caller may
2825 * initialise uniqueSetSuffix, seqRefIds, viewportsAdded and frefedSequence
2826 * themselves. Any null fields will be initialised with default values,
2827 * non-null fields are left alone.
2832 public AlignFrame loadJalviewAlign(final jarInputStreamProvider jprovider)
2834 errorMessage = null;
2835 if (uniqueSetSuffix == null)
2837 uniqueSetSuffix = System.currentTimeMillis() % 100000 + "";
2839 if (seqRefIds == null)
2843 AlignFrame af = null, _af = null;
2844 IdentityHashMap<AlignmentI, AlignmentI> importedDatasets = new IdentityHashMap<>();
2845 Map<String, AlignFrame> gatherToThisFrame = new HashMap<>();
2846 final String file = jprovider.getFilename();
2849 JarInputStream jin = null;
2850 JarEntry jarentry = null;
2855 jin = jprovider.getJarInputStream();
2856 for (int i = 0; i < entryCount; i++)
2858 jarentry = jin.getNextJarEntry();
2860 String name = (jarentry == null ? null : jarentry.getName());
2861 if (name != null && name.endsWith(".xml")
2862 // The question here is what to do with the two
2863 // .xml files in the jvp file. They are identical?
2864 // && name.indexOf(" Dataset for ") < 0 // BH 2019.05.21
2867 JAXBContext jc = JAXBContext
2868 .newInstance("jalview.xml.binding.jalview");
2869 XMLStreamReader streamReader = XMLInputFactory.newInstance()
2870 .createXMLStreamReader(jin);
2871 javax.xml.bind.Unmarshaller um = jc.createUnmarshaller();
2872 JAXBElement<JalviewModel> jbe = um
2873 .unmarshal(streamReader, JalviewModel.class);
2874 JalviewModel object = jbe.getValue();
2876 if (true) // !skipViewport(object))
2878 _af = loadFromObject(object, file, true, jprovider);
2879 if (_af != null && object.getViewport().size() > 0)
2880 // getJalviewModelSequence().getViewportCount() > 0)
2884 // store a reference to the first view
2887 if (_af.getViewport().isGatherViewsHere())
2889 // if this is a gathered view, keep its reference since
2890 // after gathering views, only this frame will remain
2892 gatherToThisFrame.put(_af.getViewport().getSequenceSetId(),
2895 // Save dataset to register mappings once all resolved
2896 importedDatasets.put(
2897 af.getViewport().getAlignment().getDataset(),
2898 af.getViewport().getAlignment().getDataset());
2903 else if (jarentry != null)
2905 // Some other file here.
2908 } while (jarentry != null);
2909 resolveFrefedSequences();
2910 } catch (IOException ex)
2912 ex.printStackTrace();
2913 errorMessage = "Couldn't locate Jalview XML file : " + file;
2915 "Exception whilst loading jalview XML file : " + ex + "\n");
2916 } catch (Exception ex)
2918 System.err.println("Parsing as Jalview Version 2 file failed.");
2919 ex.printStackTrace(System.err);
2920 if (attemptversion1parse)
2922 // used to attempt to parse as V1 castor-generated xml
2924 if (Desktop.getInstance() != null)
2926 Desktop.getInstance().stopLoading();
2930 System.out.println("Successfully loaded archive file");
2933 ex.printStackTrace();
2936 "Exception whilst loading jalview XML file : " + ex + "\n");
2937 } catch (OutOfMemoryError e)
2939 // Don't use the OOM Window here
2940 errorMessage = "Out of memory loading jalview XML file";
2941 System.err.println("Out of memory whilst loading jalview XML file");
2942 e.printStackTrace();
2946 * Regather multiple views (with the same sequence set id) to the frame (if
2947 * any) that is flagged as the one to gather to, i.e. convert them to tabbed
2948 * views instead of separate frames. Note this doesn't restore a state where
2949 * some expanded views in turn have tabbed views - the last "first tab" read
2950 * in will play the role of gatherer for all.
2952 for (AlignFrame fr : gatherToThisFrame.values())
2954 Desktop.getInstance().gatherViews(fr);
2957 restoreSplitFrames();
2958 for (AlignmentI ds : importedDatasets.keySet())
2960 if (ds.getCodonFrames() != null)
2962 Desktop.getInstance().getStructureSelectionManager()
2963 .registerMappings(ds.getCodonFrames());
2966 if (errorMessage != null)
2971 if (Desktop.getInstance() != null)
2973 Desktop.getInstance().stopLoading();
2980 * Try to reconstruct and display SplitFrame windows, where each contains
2981 * complementary dna and protein alignments. Done by pairing up AlignFrame
2982 * objects (created earlier) which have complementary viewport ids associated.
2984 protected void restoreSplitFrames()
2986 List<SplitFrame> gatherTo = new ArrayList<>();
2987 List<AlignFrame> addedToSplitFrames = new ArrayList<>();
2988 Map<String, AlignFrame> dna = new HashMap<>();
2991 * Identify the DNA alignments
2993 for (Entry<Viewport, AlignFrame> candidate : splitFrameCandidates
2996 AlignFrame af = candidate.getValue();
2997 if (af.getViewport().getAlignment().isNucleotide())
2999 dna.put(candidate.getKey().getId(), af);
3004 * Try to match up the protein complements
3006 for (Entry<Viewport, AlignFrame> candidate : splitFrameCandidates
3009 AlignFrame af = candidate.getValue();
3010 if (!af.getViewport().getAlignment().isNucleotide())
3012 String complementId = candidate.getKey().getComplementId();
3013 // only non-null complements should be in the Map
3014 if (complementId != null && dna.containsKey(complementId))
3016 final AlignFrame dnaFrame = dna.get(complementId);
3017 SplitFrame sf = createSplitFrame(dnaFrame, af);
3018 addedToSplitFrames.add(dnaFrame);
3019 addedToSplitFrames.add(af);
3020 dnaFrame.setMenusForViewport();
3021 af.setMenusForViewport();
3022 if (af.getViewport().isGatherViewsHere())
3031 * Open any that we failed to pair up (which shouldn't happen!) as
3032 * standalone AlignFrame's.
3034 for (Entry<Viewport, AlignFrame> candidate : splitFrameCandidates
3037 AlignFrame af = candidate.getValue();
3038 if (!addedToSplitFrames.contains(af))
3040 Viewport view = candidate.getKey();
3041 Desktop.addInternalFrame(af, view.getTitle(),
3042 safeInt(view.getWidth()), safeInt(view.getHeight()));
3043 af.setMenusForViewport();
3044 System.err.println("Failed to restore view " + view.getTitle()
3045 + " to split frame");
3050 * Gather back into tabbed views as flagged.
3052 for (SplitFrame sf : gatherTo)
3054 Desktop.getInstance().gatherViews(sf);
3057 splitFrameCandidates.clear();
3061 * Construct and display one SplitFrame holding DNA and protein alignments.
3064 * @param proteinFrame
3067 protected SplitFrame createSplitFrame(AlignFrame dnaFrame,
3068 AlignFrame proteinFrame)
3070 SplitFrame splitFrame = new SplitFrame(dnaFrame, proteinFrame);
3071 String title = MessageManager.getString("label.linked_view_title");
3072 int width = (int) dnaFrame.getBounds().getWidth();
3073 int height = (int) (dnaFrame.getBounds().getHeight()
3074 + proteinFrame.getBounds().getHeight() + 50);
3077 * SplitFrame location is saved to both enclosed frames
3079 splitFrame.setLocation(dnaFrame.getX(), dnaFrame.getY());
3080 Desktop.addInternalFrame(splitFrame, title, width, height);
3083 * And compute cDNA consensus (couldn't do earlier with consensus as
3084 * mappings were not yet present)
3086 proteinFrame.getViewport().alignmentChanged(proteinFrame.alignPanel);
3092 * check errorMessage for a valid error message and raise an error box in the
3093 * GUI or write the current errorMessage to stderr and then clear the error
3096 protected void reportErrors()
3098 reportErrors(false);
3101 protected void reportErrors(final boolean saving)
3103 if (errorMessage != null)
3105 final String finalErrorMessage = errorMessage;
3108 javax.swing.SwingUtilities.invokeLater(new Runnable()
3113 JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(),
3115 "Error " + (saving ? "saving" : "loading")
3117 JvOptionPane.WARNING_MESSAGE);
3123 System.err.println("Problem loading Jalview file: " + errorMessage);
3126 errorMessage = null;
3129 Map<String, String> alreadyLoadedPDB = new HashMap<>();
3132 * when set, local views will be updated from view stored in JalviewXML
3133 * Currently (28th Sep 2008) things will go horribly wrong in vamsas document
3134 * sync if this is set to true.
3136 private final boolean updateLocalViews = false;
3139 * Returns the path to a temporary file holding the PDB file for the given PDB
3140 * id. The first time of asking, searches for a file of that name in the
3141 * Jalview project jar, and copies it to a new temporary file. Any repeat
3142 * requests just return the path to the file previously created.
3148 String loadPDBFile(jarInputStreamProvider jprovider, String pdbId,
3151 if (alreadyLoadedPDB.containsKey(pdbId))
3153 return alreadyLoadedPDB.get(pdbId).toString();
3156 String tempFile = copyJarEntry(jprovider, pdbId, "jalview_pdb",
3158 if (tempFile != null)
3160 alreadyLoadedPDB.put(pdbId, tempFile);
3166 * Copies the jar entry of given name to a new temporary file and returns the
3167 * path to the file, or null if the entry is not found.
3170 * @param jarEntryName
3172 * a prefix for the temporary file name, must be at least three
3175 * null or original file - so new file can be given the same suffix
3179 protected String copyJarEntry(jarInputStreamProvider jprovider,
3180 String jarEntryName, String prefix, String origFile)
3182 BufferedReader in = null;
3183 PrintWriter out = null;
3184 String suffix = ".tmp";
3185 if (origFile == null)
3187 origFile = jarEntryName;
3189 int sfpos = origFile.lastIndexOf(".");
3190 if (sfpos > -1 && sfpos < (origFile.length() - 3))
3192 suffix = "." + origFile.substring(sfpos + 1);
3196 JarInputStream jin = jprovider.getJarInputStream();
3198 * if (jprovider.startsWith("http://")) { jin = new JarInputStream(new
3199 * URL(jprovider).openStream()); } else { jin = new JarInputStream(new
3200 * FileInputStream(jprovider)); }
3203 JarEntry entry = null;
3206 entry = jin.getNextJarEntry();
3207 } while (entry != null && !entry.getName().equals(jarEntryName));
3210 in = new BufferedReader(new InputStreamReader(jin, UTF_8));
3211 File outFile = File.createTempFile(prefix, suffix);
3212 outFile.deleteOnExit();
3213 out = new PrintWriter(new FileOutputStream(outFile));
3216 while ((data = in.readLine()) != null)
3221 String t = outFile.getAbsolutePath();
3226 warn("Couldn't find entry in Jalview Jar for " + jarEntryName);
3228 } catch (Exception ex)
3230 ex.printStackTrace();
3238 } catch (IOException e)
3252 private class JvAnnotRow
3254 public JvAnnotRow(int i, AlignmentAnnotation jaa)
3261 * persisted version of annotation row from which to take vis properties
3263 public jalview.datamodel.AlignmentAnnotation template;
3266 * original position of the annotation row in the alignment
3272 * Load alignment frame from jalview XML DOM object
3274 * @param jalviewModel
3277 * filename source string
3278 * @param loadTreesAndStructures
3279 * when false only create Viewport
3281 * data source provider
3282 * @return alignment frame created from view stored in DOM
3284 AlignFrame loadFromObject(JalviewModel jalviewModel, String file,
3285 boolean loadTreesAndStructures, jarInputStreamProvider jprovider)
3287 SequenceSet vamsasSet = jalviewModel.getVamsasModel().getSequenceSet().get(0);
3288 List<Sequence> vamsasSeqs = vamsasSet.getSequence();
3290 // JalviewModelSequence jms = object.getJalviewModelSequence();
3292 // Viewport view = (jms.getViewportCount() > 0) ? jms.getViewport(0)
3294 Viewport view = (jalviewModel.getViewport().size() > 0)
3295 ? jalviewModel.getViewport().get(0)
3298 // ////////////////////////////////
3299 // INITIALISE ALIGNMENT SEQUENCESETID AND VIEWID
3302 // If we just load in the same jar file again, the sequenceSetId
3303 // will be the same, and we end up with multiple references
3304 // to the same sequenceSet. We must modify this id on load
3305 // so that each load of the file gives a unique id
3308 * used to resolve correct alignment dataset for alignments with multiple
3311 String uniqueSeqSetId = null;
3312 String viewId = null;
3315 uniqueSeqSetId = view.getSequenceSetId() + uniqueSetSuffix;
3316 viewId = (view.getId() == null ? null
3317 : view.getId() + uniqueSetSuffix);
3320 // ////////////////////////////////
3323 List<SequenceI> hiddenSeqs = null;
3325 List<SequenceI> tmpseqs = new ArrayList<>();
3327 boolean multipleView = false;
3328 SequenceI referenceseqForView = null;
3329 // JSeq[] jseqs = object.getJalviewModelSequence().getJSeq();
3330 List<JSeq> jseqs = jalviewModel.getJSeq();
3331 int vi = 0; // counter in vamsasSeq array
3332 for (int i = 0; i < jseqs.size(); i++)
3334 JSeq jseq = jseqs.get(i);
3335 String seqId = jseq.getId();
3337 SequenceI tmpSeq = seqRefIds.get(seqId);
3340 if (!incompleteSeqs.containsKey(seqId))
3342 // may not need this check, but keep it for at least 2.9,1 release
3343 if (tmpSeq.getStart() != jseq.getStart()
3344 || tmpSeq.getEnd() != jseq.getEnd())
3347 "Warning JAL-2154 regression: updating start/end for sequence "
3348 + tmpSeq.toString() + " to " + jseq);
3353 incompleteSeqs.remove(seqId);
3355 if (vamsasSeqs.size() > vi
3356 && vamsasSeqs.get(vi).getId().equals(seqId))
3358 // most likely we are reading a dataset XML document so
3359 // update from vamsasSeq section of XML for this sequence
3360 tmpSeq.setName(vamsasSeqs.get(vi).getName());
3361 tmpSeq.setDescription(vamsasSeqs.get(vi).getDescription());
3362 tmpSeq.setSequence(vamsasSeqs.get(vi).getSequence());
3367 // reading multiple views, so vamsasSeq set is a subset of JSeq
3368 multipleView = true;
3370 tmpSeq.setStart(jseq.getStart());
3371 tmpSeq.setEnd(jseq.getEnd());
3372 tmpseqs.add(tmpSeq);
3376 Sequence vamsasSeq = vamsasSeqs.get(vi);
3377 tmpSeq = new jalview.datamodel.Sequence(vamsasSeq.getName(),
3378 vamsasSeq.getSequence());
3379 tmpSeq.setDescription(vamsasSeq.getDescription());
3380 tmpSeq.setStart(jseq.getStart());
3381 tmpSeq.setEnd(jseq.getEnd());
3382 tmpSeq.setVamsasId(uniqueSetSuffix + seqId);
3383 seqRefIds.put(vamsasSeq.getId(), tmpSeq);
3384 tmpseqs.add(tmpSeq);
3388 if (safeBoolean(jseq.isViewreference()))
3390 referenceseqForView = tmpseqs.get(tmpseqs.size() - 1);
3393 if (jseq.isHidden() != null && jseq.isHidden().booleanValue())
3395 if (hiddenSeqs == null)
3397 hiddenSeqs = new ArrayList<>();
3400 hiddenSeqs.add(tmpSeq);
3405 // Create the alignment object from the sequence set
3406 // ///////////////////////////////
3407 SequenceI[] orderedSeqs = tmpseqs
3408 .toArray(new SequenceI[tmpseqs.size()]);
3410 AlignmentI al = null;
3411 // so we must create or recover the dataset alignment before going further
3412 // ///////////////////////////////
3413 if (vamsasSet.getDatasetId() == null || vamsasSet.getDatasetId() == "")
3415 // older jalview projects do not have a dataset - so creat alignment and
3417 al = new Alignment(orderedSeqs);
3418 al.setDataset(null);
3422 boolean isdsal = jalviewModel.getViewport().isEmpty();
3425 // we are importing a dataset record, so
3426 // recover reference to an alignment already materialsed as dataset
3427 al = getDatasetFor(vamsasSet.getDatasetId());
3431 // materialse the alignment
3432 al = new Alignment(orderedSeqs);
3436 addDatasetRef(vamsasSet.getDatasetId(), al);
3439 // finally, verify all data in vamsasSet is actually present in al
3440 // passing on flag indicating if it is actually a stored dataset
3441 recoverDatasetFor(vamsasSet, al, isdsal, uniqueSeqSetId);
3444 if (referenceseqForView != null)
3446 al.setSeqrep(referenceseqForView);
3448 // / Add the alignment properties
3449 for (int i = 0; i < vamsasSet.getSequenceSetProperties().size(); i++)
3451 SequenceSetProperties ssp = vamsasSet.getSequenceSetProperties()
3453 al.setProperty(ssp.getKey(), ssp.getValue());
3456 // ///////////////////////////////
3458 Hashtable pdbloaded = new Hashtable(); // TODO nothing writes to this??
3461 // load sequence features, database references and any associated PDB
3462 // structures for the alignment
3464 // prior to 2.10, this part would only be executed the first time a
3465 // sequence was encountered, but not afterwards.
3466 // now, for 2.10 projects, this is also done if the xml doc includes
3467 // dataset sequences not actually present in any particular view.
3469 for (int i = 0; i < vamsasSeqs.size(); i++)
3471 JSeq jseq = jseqs.get(i);
3472 if (jseq.getFeatures().size() > 0)
3474 List<Feature> features = jseq.getFeatures();
3475 for (int f = 0; f < features.size(); f++)
3477 Feature feat = features.get(f);
3478 SequenceFeature sf = new SequenceFeature(feat.getType(),
3479 feat.getDescription(), feat.getBegin(), feat.getEnd(),
3480 safeFloat(feat.getScore()), feat.getFeatureGroup());
3481 sf.setStatus(feat.getStatus());
3484 * load any feature attributes - include map-valued attributes
3486 Map<String, Map<String, String>> mapAttributes = new HashMap<>();
3487 for (int od = 0; od < feat.getOtherData().size(); od++)
3489 OtherData keyValue = feat.getOtherData().get(od);
3490 String attributeName = keyValue.getKey();
3491 String attributeValue = keyValue.getValue();
3492 if (attributeName.startsWith("LINK"))
3494 sf.addLink(attributeValue);
3498 String subAttribute = keyValue.getKey2();
3499 if (subAttribute == null)
3501 // simple string-valued attribute
3502 sf.setValue(attributeName, attributeValue);
3506 // attribute 'key' has sub-attribute 'key2'
3507 if (!mapAttributes.containsKey(attributeName))
3509 mapAttributes.put(attributeName, new HashMap<>());
3511 mapAttributes.get(attributeName).put(subAttribute,
3516 for (Entry<String, Map<String, String>> mapAttribute : mapAttributes
3519 sf.setValue(mapAttribute.getKey(), mapAttribute.getValue());
3522 // adds feature to datasequence's feature set (since Jalview 2.10)
3523 al.getSequenceAt(i).addSequenceFeature(sf);
3526 if (vamsasSeqs.get(i).getDBRef().size() > 0)
3528 // adds dbrefs to datasequence's set (since Jalview 2.10)
3530 al.getSequenceAt(i).getDatasetSequence() == null
3531 ? al.getSequenceAt(i)
3532 : al.getSequenceAt(i).getDatasetSequence(),
3535 if (jseq.getPdbids().size() > 0)
3537 List<Pdbids> ids = jseq.getPdbids();
3538 for (int p = 0; p < ids.size(); p++)
3540 Pdbids pdbid = ids.get(p);
3541 jalview.datamodel.PDBEntry entry = new jalview.datamodel.PDBEntry();
3542 entry.setId(pdbid.getId());
3543 if (pdbid.getType() != null)
3545 if (PDBEntry.Type.getType(pdbid.getType()) != null)
3547 entry.setType(PDBEntry.Type.getType(pdbid.getType()));
3551 entry.setType(PDBEntry.Type.FILE);
3554 // jprovider is null when executing 'New View'
3555 if (pdbid.getFile() != null && jprovider != null)
3557 if (!pdbloaded.containsKey(pdbid.getFile()))
3559 entry.setFile(loadPDBFile(jprovider, pdbid.getId(),
3564 entry.setFile(pdbloaded.get(pdbid.getId()).toString());
3568 if (pdbid.getPdbentryItem() != null)
3570 for (PdbentryItem item : pdbid.getPdbentryItem())
3572 for (Property pr : item.getProperty())
3574 entry.setProperty(pr.getName(), pr.getValue());
3579 for (Property prop : pdbid.getProperty())
3581 entry.setProperty(prop.getName(), prop.getValue());
3583 Desktop.getInstance().getStructureSelectionManager()
3584 .registerPDBEntry(entry);
3585 // adds PDBEntry to datasequence's set (since Jalview 2.10)
3586 if (al.getSequenceAt(i).getDatasetSequence() != null)
3588 al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
3592 al.getSequenceAt(i).addPDBId(entry);
3597 } // end !multipleview
3599 // ///////////////////////////////
3600 // LOAD SEQUENCE MAPPINGS
3602 if (vamsasSet.getAlcodonFrame().size() > 0)
3604 // TODO Potentially this should only be done once for all views of an
3606 List<AlcodonFrame> alc = vamsasSet.getAlcodonFrame();
3607 for (int i = 0; i < alc.size(); i++)
3609 AlignedCodonFrame cf = new AlignedCodonFrame();
3610 if (alc.get(i).getAlcodMap().size() > 0)
3612 List<AlcodMap> maps = alc.get(i).getAlcodMap();
3613 for (int m = 0; m < maps.size(); m++)
3615 AlcodMap map = maps.get(m);
3616 SequenceI dnaseq = seqRefIds.get(map.getDnasq());
3618 jalview.datamodel.Mapping mapping = null;
3619 // attach to dna sequence reference.
3620 if (map.getMapping() != null)
3622 mapping = addMapping(map.getMapping());
3623 if (dnaseq != null && mapping.getTo() != null)
3625 cf.addMap(dnaseq, mapping.getTo(), mapping.getMap());
3631 newAlcodMapRef(map.getDnasq(), cf, mapping));
3635 al.addCodonFrame(cf);
3640 // ////////////////////////////////
3642 List<JvAnnotRow> autoAlan = new ArrayList<>();
3645 * store any annotations which forward reference a group's ID
3647 Map<String, List<AlignmentAnnotation>> groupAnnotRefs = new Hashtable<>();
3649 if (vamsasSet.getAnnotation().size()/*Count()*/ > 0)
3651 List<Annotation> an = vamsasSet.getAnnotation();
3653 for (int i = 0; i < an.size(); i++)
3655 Annotation annotation = an.get(i);
3658 * test if annotation is automatically calculated for this view only
3660 boolean autoForView = false;
3661 if (annotation.getLabel().equals("Quality")
3662 || annotation.getLabel().equals("Conservation")
3663 || annotation.getLabel().equals("Consensus"))
3665 // Kludge for pre 2.5 projects which lacked the autocalculated flag
3667 // JAXB has no has() test; schema defaults value to false
3668 // if (!annotation.hasAutoCalculated())
3670 // annotation.setAutoCalculated(true);
3673 if (autoForView || annotation.isAutoCalculated())
3675 // remove ID - we don't recover annotation from other views for
3676 // view-specific annotation
3677 annotation.setId(null);
3680 // set visibility for other annotation in this view
3681 String annotationId = annotation.getId();
3682 if (annotationId != null && annotationIds.containsKey(annotationId))
3684 AlignmentAnnotation jda = annotationIds.get(annotationId);
3685 // in principle Visible should always be true for annotation displayed
3686 // in multiple views
3687 if (annotation.isVisible() != null)
3689 jda.visible = annotation.isVisible();
3692 al.addAnnotation(jda);
3696 // Construct new annotation from model.
3697 List<AnnotationElement> ae = annotation.getAnnotationElement();
3698 jalview.datamodel.Annotation[] anot = null;
3699 java.awt.Color firstColour = null;
3701 if (!annotation.isScoreOnly())
3703 anot = new jalview.datamodel.Annotation[al.getWidth()];
3704 for (int aa = 0; aa < ae.size() && aa < anot.length; aa++)
3706 AnnotationElement annElement = ae.get(aa);
3707 anpos = annElement.getPosition();
3709 if (anpos >= anot.length)
3714 float value = safeFloat(annElement.getValue());
3715 anot[anpos] = new jalview.datamodel.Annotation(
3716 annElement.getDisplayCharacter(),
3717 annElement.getDescription(),
3718 (annElement.getSecondaryStructure() == null
3719 || annElement.getSecondaryStructure()
3723 .getSecondaryStructure()
3726 anot[anpos].colour = new Color(safeInt(annElement.getColour()));
3727 if (firstColour == null)
3729 firstColour = anot[anpos].colour;
3733 jalview.datamodel.AlignmentAnnotation jaa = null;
3735 if (annotation.isGraph())
3737 float llim = 0, hlim = 0;
3738 // if (autoForView || an[i].isAutoCalculated()) {
3741 jaa = new jalview.datamodel.AlignmentAnnotation(
3742 annotation.getLabel(), annotation.getDescription(), anot,
3743 llim, hlim, safeInt(annotation.getGraphType()));
3745 jaa.graphGroup = safeInt(annotation.getGraphGroup());
3746 jaa._linecolour = firstColour;
3747 if (annotation.getThresholdLine() != null)
3749 jaa.setThreshold(new jalview.datamodel.GraphLine(
3750 safeFloat(annotation.getThresholdLine().getValue()),
3751 annotation.getThresholdLine().getLabel(),
3752 new java.awt.Color(safeInt(
3753 annotation.getThresholdLine().getColour()))));
3755 if (autoForView || annotation.isAutoCalculated())
3757 // Hardwire the symbol display line to ensure that labels for
3758 // histograms are displayed
3764 jaa = new jalview.datamodel.AlignmentAnnotation(
3765 annotation.getLabel(), annotation.getDescription(), anot);
3766 jaa._linecolour = firstColour;
3768 // register new annotation
3769 if (annotation.getId() != null)
3771 annotationIds.put(annotation.getId(), jaa);
3772 jaa.annotationId = annotation.getId();
3774 // recover sequence association
3775 String sequenceRef = annotation.getSequenceRef();
3776 if (sequenceRef != null)
3778 // from 2.9 sequenceRef is to sequence id (JAL-1781)
3779 SequenceI sequence = seqRefIds.get(sequenceRef);
3780 if (sequence == null)
3782 // in pre-2.9 projects sequence ref is to sequence name
3783 sequence = al.findName(sequenceRef);
3785 if (sequence != null)
3787 jaa.createSequenceMapping(sequence, 1, true);
3788 sequence.addAlignmentAnnotation(jaa);
3791 // and make a note of any group association
3792 if (annotation.getGroupRef() != null
3793 && annotation.getGroupRef().length() > 0)
3795 List<jalview.datamodel.AlignmentAnnotation> aal = groupAnnotRefs
3796 .get(annotation.getGroupRef());
3799 aal = new ArrayList<>();
3800 groupAnnotRefs.put(annotation.getGroupRef(), aal);
3805 if (annotation.getScore() != null)
3807 jaa.setScore(annotation.getScore().doubleValue());
3809 if (annotation.isVisible() != null)
3811 jaa.visible = annotation.isVisible().booleanValue();
3814 if (annotation.isCentreColLabels() != null)
3816 jaa.centreColLabels = annotation.isCentreColLabels()
3820 if (annotation.isScaleColLabels() != null)
3822 jaa.scaleColLabel = annotation.isScaleColLabels().booleanValue();
3824 if (annotation.isAutoCalculated())
3826 // newer files have an 'autoCalculated' flag and store calculation
3827 // state in viewport properties
3828 jaa.autoCalculated = true; // means annotation will be marked for
3829 // update at end of load.
3831 if (annotation.getGraphHeight() != null)
3833 jaa.graphHeight = annotation.getGraphHeight().intValue();
3835 jaa.belowAlignment = annotation.isBelowAlignment();
3836 jaa.setCalcId(annotation.getCalcId());
3837 if (annotation.getProperty().size() > 0)
3839 for (Annotation.Property prop : annotation
3842 jaa.setProperty(prop.getName(), prop.getValue());
3845 if (jaa.autoCalculated)
3847 autoAlan.add(new JvAnnotRow(i, jaa));
3850 // if (!autoForView)
3852 // add autocalculated group annotation and any user created annotation
3854 al.addAnnotation(jaa);
3858 // ///////////////////////
3860 // Create alignment markup and styles for this view
3861 if (jalviewModel.getJGroup().size() > 0)
3863 List<JGroup> groups = jalviewModel.getJGroup();
3864 boolean addAnnotSchemeGroup = false;
3865 for (int i = 0; i < groups.size(); i++)
3867 JGroup jGroup = groups.get(i);
3868 ColourSchemeI cs = null;
3869 if (jGroup.getColour() != null)
3871 if (jGroup.getColour().startsWith("ucs"))
3873 cs = getUserColourScheme(jalviewModel, jGroup.getColour());
3875 else if (jGroup.getColour().equals("AnnotationColourGradient")
3876 && jGroup.getAnnotationColours() != null)
3878 addAnnotSchemeGroup = true;
3882 cs = ColourSchemeProperty.getColourScheme(null, al,
3883 jGroup.getColour());
3886 int pidThreshold = safeInt(jGroup.getPidThreshold());
3888 Vector<SequenceI> seqs = new Vector<>();
3890 for (int s = 0; s < jGroup.getSeq().size(); s++)
3892 String seqId = jGroup.getSeq().get(s);
3893 SequenceI ts = seqRefIds.get(seqId);
3897 seqs.addElement(ts);
3901 if (seqs.size() < 1)
3906 SequenceGroup sg = new SequenceGroup(seqs, jGroup.getName(), cs,
3907 safeBoolean(jGroup.isDisplayBoxes()),
3908 safeBoolean(jGroup.isDisplayText()),
3909 safeBoolean(jGroup.isColourText()),
3910 safeInt(jGroup.getStart()), safeInt(jGroup.getEnd()));
3911 sg.getGroupColourScheme().setThreshold(pidThreshold, true);
3912 sg.getGroupColourScheme()
3913 .setConservationInc(safeInt(jGroup.getConsThreshold()));
3914 sg.setOutlineColour(new Color(safeInt(jGroup.getOutlineColour())));
3916 sg.textColour = new Color(safeInt(jGroup.getTextCol1()));
3917 sg.textColour2 = new Color(safeInt(jGroup.getTextCol2()));
3918 sg.setShowNonconserved(safeBoolean(jGroup.isShowUnconserved()));
3919 sg.thresholdTextColour = safeInt(jGroup.getTextColThreshold());
3920 // attributes with a default in the schema are never null
3921 sg.setShowConsensusHistogram(jGroup.isShowConsensusHistogram());
3922 sg.setshowSequenceLogo(jGroup.isShowSequenceLogo());
3923 sg.setNormaliseSequenceLogo(jGroup.isNormaliseSequenceLogo());
3924 sg.setIgnoreGapsConsensus(jGroup.isIgnoreGapsinConsensus());
3925 if (jGroup.getConsThreshold() != null
3926 && jGroup.getConsThreshold().intValue() != 0)
3928 Conservation c = new Conservation("All", sg.getSequences(null), 0,
3931 c.verdict(false, 25);
3932 sg.cs.setConservation(c);
3935 if (jGroup.getId() != null && groupAnnotRefs.size() > 0)
3937 // re-instate unique group/annotation row reference
3938 List<AlignmentAnnotation> jaal = groupAnnotRefs
3939 .get(jGroup.getId());
3942 for (AlignmentAnnotation jaa : jaal)
3945 if (jaa.autoCalculated)
3947 // match up and try to set group autocalc alignment row for this
3949 if (jaa.label.startsWith("Consensus for "))
3951 sg.setConsensus(jaa);
3953 // match up and try to set group autocalc alignment row for this
3955 if (jaa.label.startsWith("Conservation for "))
3957 sg.setConservationRow(jaa);
3964 if (addAnnotSchemeGroup)
3966 // reconstruct the annotation colourscheme
3967 sg.setColourScheme(constructAnnotationColour(
3968 jGroup.getAnnotationColours(), null, al, jalviewModel, false));
3974 // only dataset in this model, so just return.
3977 // ///////////////////////////////
3980 AlignFrame af = null;
3981 AlignViewport av = null;
3982 // now check to see if we really need to create a new viewport.
3983 if (multipleView && viewportsAdded.size() == 0)
3985 // We recovered an alignment for which a viewport already exists.
3986 // TODO: fix up any settings necessary for overlaying stored state onto
3987 // state recovered from another document. (may not be necessary).
3988 // we may need a binding from a viewport in memory to one recovered from
3990 // and then recover its containing af to allow the settings to be applied.
3991 // TODO: fix for vamsas demo
3993 "About to recover a viewport for existing alignment: Sequence set ID is "
3995 Object seqsetobj = retrieveExistingObj(uniqueSeqSetId);
3996 if (seqsetobj != null)
3998 if (seqsetobj instanceof String)
4000 uniqueSeqSetId = (String) seqsetobj;
4002 "Recovered extant sequence set ID mapping for ID : New Sequence set ID is "
4008 "Warning : Collision between sequence set ID string and existing jalview object mapping.");
4014 * indicate that annotation colours are applied across all groups (pre
4015 * Jalview 2.8.1 behaviour)
4017 boolean doGroupAnnColour = Jalview2XML.isVersionStringLaterThan("2.8.1",
4018 jalviewModel.getVersion());
4020 AlignmentPanel ap = null;
4021 boolean isnewview = true;
4024 // Check to see if this alignment already has a view id == viewId
4025 jalview.gui.AlignmentPanel views[] = Desktop
4026 .getAlignmentPanels(uniqueSeqSetId);
4027 if (views != null && views.length > 0)
4029 for (int v = 0; v < views.length; v++)
4031 if (views[v].av.getViewId().equalsIgnoreCase(viewId))
4033 // recover the existing alignpanel, alignframe, viewport
4034 af = views[v].alignFrame;
4037 // TODO: could even skip resetting view settings if we don't want to
4038 // change the local settings from other jalview processes
4047 af = loadViewport(file, jseqs, hiddenSeqs, al, jalviewModel, view,
4048 uniqueSeqSetId, viewId, autoAlan);
4049 av = af.getViewport();
4054 * Load any trees, PDB structures and viewers
4056 * Not done if flag is false (when this method is used for New View)
4058 if (loadTreesAndStructures)
4060 loadTrees(jalviewModel, view, af, av, ap);
4061 loadPCAViewers(jalviewModel, ap);
4062 loadPDBStructures(jprovider, jseqs, af, ap);
4063 loadRnaViewers(jprovider, jseqs, ap);
4065 // and finally return.
4070 * Instantiate and link any saved RNA (Varna) viewers. The state of the Varna
4071 * panel is restored from separate jar entries, two (gapped and trimmed) per
4072 * sequence and secondary structure.
4074 * Currently each viewer shows just one sequence and structure (gapped and
4075 * trimmed), however this method is designed to support multiple sequences or
4076 * structures in viewers if wanted in future.
4082 private void loadRnaViewers(jarInputStreamProvider jprovider,
4083 List<JSeq> jseqs, AlignmentPanel ap)
4086 * scan the sequences for references to viewers; create each one the first
4087 * time it is referenced, add Rna models to existing viewers
4089 for (JSeq jseq : jseqs)
4091 for (int i = 0; i < jseq.getRnaViewer().size(); i++)
4093 RnaViewer viewer = jseq.getRnaViewer().get(i);
4094 AppVarna appVarna = findOrCreateVarnaViewer(viewer, uniqueSetSuffix,
4097 for (int j = 0; j < viewer.getSecondaryStructure().size(); j++)
4099 SecondaryStructure ss = viewer.getSecondaryStructure().get(j);
4100 SequenceI seq = seqRefIds.get(jseq.getId());
4101 AlignmentAnnotation ann = this.annotationIds
4102 .get(ss.getAnnotationId());
4105 * add the structure to the Varna display (with session state copied
4106 * from the jar to a temporary file)
4108 boolean gapped = safeBoolean(ss.isGapped());
4109 String rnaTitle = ss.getTitle();
4110 String sessionState = ss.getViewerState();
4111 String tempStateFile = copyJarEntry(jprovider, sessionState,
4113 RnaModel rna = new RnaModel(rnaTitle, ann, seq, null, gapped);
4114 appVarna.addModelSession(rna, rnaTitle, tempStateFile);
4116 appVarna.setInitialSelection(safeInt(viewer.getSelectedRna()));
4122 * Locate and return an already instantiated matching AppVarna, or create one
4126 * @param viewIdSuffix
4130 protected AppVarna findOrCreateVarnaViewer(RnaViewer viewer,
4131 String viewIdSuffix, AlignmentPanel ap)
4134 * on each load a suffix is appended to the saved viewId, to avoid conflicts
4135 * if load is repeated
4137 String postLoadId = viewer.getViewId() + viewIdSuffix;
4138 for (JInternalFrame frame : getAllFrames())
4140 if (frame instanceof AppVarna)
4142 AppVarna varna = (AppVarna) frame;
4143 if (postLoadId.equals(varna.getViewId()))
4145 // this viewer is already instantiated
4146 // could in future here add ap as another 'parent' of the
4147 // AppVarna window; currently just 1-to-many
4154 * viewer not found - make it
4156 RnaViewerModel model = new RnaViewerModel(postLoadId, viewer.getTitle(),
4157 safeInt(viewer.getXpos()), safeInt(viewer.getYpos()),
4158 safeInt(viewer.getWidth()), safeInt(viewer.getHeight()),
4159 safeInt(viewer.getDividerLocation()));
4160 AppVarna varna = new AppVarna(model, ap);
4166 * Load any saved trees
4174 protected void loadTrees(JalviewModel jm, Viewport view,
4175 AlignFrame af, AlignViewport av, AlignmentPanel ap)
4177 // TODO result of automated refactoring - are all these parameters needed?
4180 for (int t = 0; t < jm.getTree().size(); t++)
4183 Tree tree = jm.getTree().get(t);
4185 TreePanel tp = (TreePanel) retrieveExistingObj(tree.getId());
4188 tp = af.showNewickTree(new NewickFile(tree.getNewick()),
4189 tree.getTitle(), safeInt(tree.getWidth()),
4190 safeInt(tree.getHeight()), safeInt(tree.getXpos()),
4191 safeInt(tree.getYpos()));
4192 if (tree.getId() != null)
4194 // perhaps bind the tree id to something ?
4199 // update local tree attributes ?
4200 // TODO: should check if tp has been manipulated by user - if so its
4201 // settings shouldn't be modified
4202 tp.setTitle(tree.getTitle());
4203 tp.setBounds(new Rectangle(safeInt(tree.getXpos()),
4204 safeInt(tree.getYpos()), safeInt(tree.getWidth()),
4205 safeInt(tree.getHeight())));
4206 tp.setViewport(av); // af.viewport;
4207 // TODO: verify 'associate with all views' works still
4208 tp.getTreeCanvas().setViewport(av); // af.viewport;
4209 tp.getTreeCanvas().setAssociatedPanel(ap); // af.alignPanel;
4211 tp.getTreeCanvas().setApplyToAllViews(tree.isLinkToAllViews());
4214 warn("There was a problem recovering stored Newick tree: \n"
4215 + tree.getNewick());
4219 tp.fitToWindow.setState(safeBoolean(tree.isFitToWindow()));
4220 tp.fitToWindow_actionPerformed(null);
4222 if (tree.getFontName() != null)
4225 new Font(tree.getFontName(), safeInt(tree.getFontStyle()),
4226 safeInt(tree.getFontSize())));
4231 new Font(view.getFontName(), safeInt(view.getFontStyle()),
4232 safeInt(view.getFontSize())));
4235 tp.showPlaceholders(safeBoolean(tree.isMarkUnlinked()));
4236 tp.showBootstrap(safeBoolean(tree.isShowBootstrap()));
4237 tp.showDistances(safeBoolean(tree.isShowDistances()));
4239 tp.getTreeCanvas().setThreshold(safeFloat(tree.getThreshold()));
4241 if (safeBoolean(tree.isCurrentTree()))
4243 af.getViewport().setCurrentTree(tp.getTree());
4247 } catch (Exception ex)
4249 ex.printStackTrace();
4254 * Load and link any saved structure viewers.
4261 protected void loadPDBStructures(jarInputStreamProvider jprovider,
4262 List<JSeq> jseqs, AlignFrame af, AlignmentPanel ap)
4265 * Run through all PDB ids on the alignment, and collect mappings between
4266 * distinct view ids and all sequences referring to that view.
4268 Map<String, StructureViewerModel> structureViewers = new LinkedHashMap<>();
4270 for (int i = 0; i < jseqs.size(); i++)
4272 JSeq jseq = jseqs.get(i);
4273 if (jseq.getPdbids().size() > 0)
4275 List<Pdbids> ids = jseq.getPdbids();
4276 for (int p = 0; p < ids.size(); p++)
4278 Pdbids pdbid = ids.get(p);
4279 final int structureStateCount = pdbid.getStructureState().size();
4280 for (int s = 0; s < structureStateCount; s++)
4282 // check to see if we haven't already created this structure view
4283 final StructureState structureState = pdbid
4284 .getStructureState().get(s);
4285 String sviewid = (structureState.getViewId() == null) ? null
4286 : structureState.getViewId() + uniqueSetSuffix;
4287 jalview.datamodel.PDBEntry jpdb = new jalview.datamodel.PDBEntry();
4288 // Originally : pdbid.getFile()
4289 // : TODO: verify external PDB file recovery still works in normal
4290 // jalview project load
4292 loadPDBFile(jprovider, pdbid.getId(), pdbid.getFile()));
4293 jpdb.setId(pdbid.getId());
4295 int x = safeInt(structureState.getXpos());
4296 int y = safeInt(structureState.getYpos());
4297 int width = safeInt(structureState.getWidth());
4298 int height = safeInt(structureState.getHeight());
4300 // Probably don't need to do this anymore...
4301 // Desktop.getDesktop().getComponentAt(x, y);
4302 // TODO: NOW: check that this recovers the PDB file correctly.
4303 String pdbFile = loadPDBFile(jprovider, pdbid.getId(),
4305 jalview.datamodel.SequenceI seq = seqRefIds
4306 .get(jseq.getId() + "");
4307 if (sviewid == null)
4309 sviewid = "_jalview_pre2_4_" + x + "," + y + "," + width + ","
4312 if (!structureViewers.containsKey(sviewid))
4314 structureViewers.put(sviewid,
4315 new StructureViewerModel(x, y, width, height, false,
4316 false, true, structureState.getViewId(),
4317 structureState.getType()));
4318 // Legacy pre-2.7 conversion JAL-823 :
4319 // do not assume any view has to be linked for colour by
4323 // assemble String[] { pdb files }, String[] { id for each
4324 // file }, orig_fileloc, SequenceI[][] {{ seqs_file 1 }, {
4325 // seqs_file 2}, boolean[] {
4326 // linkAlignPanel,superposeWithAlignpanel}} from hash
4327 StructureViewerModel jmoldat = structureViewers.get(sviewid);
4328 jmoldat.setAlignWithPanel(jmoldat.isAlignWithPanel()
4329 || structureState.isAlignwithAlignPanel());
4332 * Default colour by linked panel to false if not specified (e.g.
4333 * for pre-2.7 projects)
4335 boolean colourWithAlignPanel = jmoldat.isColourWithAlignPanel();
4336 colourWithAlignPanel |= structureState.isColourwithAlignPanel();
4337 jmoldat.setColourWithAlignPanel(colourWithAlignPanel);
4340 * Default colour by viewer to true if not specified (e.g. for
4343 boolean colourByViewer = jmoldat.isColourByViewer();
4344 colourByViewer &= structureState.isColourByJmol();
4345 jmoldat.setColourByViewer(colourByViewer);
4347 if (jmoldat.getStateData().length() < structureState
4348 .getValue()/*Content()*/.length())
4350 jmoldat.setStateData(structureState.getValue());// Content());
4352 if (pdbid.getFile() != null)
4354 File mapkey = new File(pdbid.getFile());
4355 StructureData seqstrmaps = jmoldat.getFileData().get(mapkey);
4356 if (seqstrmaps == null)
4358 jmoldat.getFileData().put(mapkey,
4359 seqstrmaps = jmoldat.new StructureData(pdbFile,
4362 if (!seqstrmaps.getSeqList().contains(seq))
4364 seqstrmaps.getSeqList().add(seq);
4370 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");
4377 // Instantiate the associated structure views
4378 for (Entry<String, StructureViewerModel> entry : structureViewers
4383 createOrLinkStructureViewer(entry, af, ap, jprovider);
4384 } catch (Exception e)
4387 "Error loading structure viewer: " + e.getMessage());
4388 // failed - try the next one
4400 protected void createOrLinkStructureViewer(
4401 Entry<String, StructureViewerModel> viewerData, AlignFrame af,
4402 AlignmentPanel ap, jarInputStreamProvider jprovider)
4404 final StructureViewerModel stateData = viewerData.getValue();
4407 * Search for any viewer windows already open from other alignment views
4408 * that exactly match the stored structure state
4410 StructureViewerBase comp = findMatchingViewer(viewerData);
4414 linkStructureViewer(ap, comp, stateData);
4419 * From 2.9: stateData.type contains JMOL or CHIMERA, data is in jar entry
4420 * "viewer_"+stateData.viewId
4422 if (ViewerType.CHIMERA.toString().equals(stateData.getType()))
4424 createChimeraViewer(viewerData, af, jprovider);
4429 * else Jmol (if pre-2.9, stateData contains JMOL state string)
4431 createJmolViewer(viewerData, af, jprovider);
4436 * Create a new Chimera viewer.
4442 protected void createChimeraViewer(
4443 Entry<String, StructureViewerModel> viewerData, AlignFrame af,
4444 jarInputStreamProvider jprovider)
4446 StructureViewerModel data = viewerData.getValue();
4447 String chimeraSessionFile = data.getStateData();
4450 * Copy Chimera session from jar entry "viewer_"+viewId to a temporary file
4452 * NB this is the 'saved' viewId as in the project file XML, _not_ the
4453 * 'uniquified' sviewid used to reconstruct the viewer here
4455 String viewerJarEntryName = getViewerJarEntryName(data.getViewId());
4456 chimeraSessionFile = copyJarEntry(jprovider, viewerJarEntryName,
4459 Set<Entry<File, StructureData>> fileData = data.getFileData()
4461 List<PDBEntry> pdbs = new ArrayList<>();
4462 List<SequenceI[]> allseqs = new ArrayList<>();
4463 for (Entry<File, StructureData> pdb : fileData)
4465 String filePath = pdb.getValue().getFilePath();
4466 String pdbId = pdb.getValue().getPdbId();
4467 // pdbs.add(new PDBEntry(filePath, pdbId));
4468 pdbs.add(new PDBEntry(pdbId, null, PDBEntry.Type.PDB, filePath));
4469 final List<SequenceI> seqList = pdb.getValue().getSeqList();
4470 SequenceI[] seqs = seqList.toArray(new SequenceI[seqList.size()]);
4474 boolean colourByChimera = data.isColourByViewer();
4475 boolean colourBySequence = data.isColourWithAlignPanel();
4477 // TODO use StructureViewer as a factory here, see JAL-1761
4478 final PDBEntry[] pdbArray = pdbs.toArray(new PDBEntry[pdbs.size()]);
4479 final SequenceI[][] seqsArray = allseqs
4480 .toArray(new SequenceI[allseqs.size()][]);
4481 String newViewId = viewerData.getKey();
4483 ChimeraViewFrame cvf = new ChimeraViewFrame(chimeraSessionFile,
4484 af.alignPanel, pdbArray, seqsArray, colourByChimera,
4485 colourBySequence, newViewId);
4486 cvf.setSize(data.getWidth(), data.getHeight());
4487 cvf.setLocation(data.getX(), data.getY());
4491 * Create a new Jmol window. First parse the Jmol state to translate filenames
4492 * loaded into the view, and record the order in which files are shown in the
4493 * Jmol view, so we can add the sequence mappings in same order.
4499 protected void createJmolViewer(
4500 final Entry<String, StructureViewerModel> viewerData,
4501 AlignFrame af, jarInputStreamProvider jprovider)
4503 final StructureViewerModel svattrib = viewerData.getValue();
4504 String state = svattrib.getStateData();
4507 * Pre-2.9: state element value is the Jmol state string
4509 * 2.9+: @type is "JMOL", state data is in a Jar file member named "viewer_"
4512 if (ViewerType.JMOL.toString().equals(svattrib.getType()))
4514 state = readJarEntry(jprovider,
4515 getViewerJarEntryName(svattrib.getViewId()));
4518 List<String> pdbfilenames = new ArrayList<>();
4519 List<SequenceI[]> seqmaps = new ArrayList<>();
4520 List<String> pdbids = new ArrayList<>();
4521 StringBuilder newFileLoc = new StringBuilder(64);
4522 int cp = 0, ncp, ecp;
4523 Map<File, StructureData> oldFiles = svattrib.getFileData();
4524 while ((ncp = state.indexOf("load ", cp)) > -1)
4528 // look for next filename in load statement
4529 newFileLoc.append(state.substring(cp,
4530 ncp = (state.indexOf("\"", ncp + 1) + 1)));
4531 String oldfilenam = state.substring(ncp,
4532 ecp = state.indexOf("\"", ncp));
4533 // recover the new mapping data for this old filename
4534 // have to normalize filename - since Jmol and jalview do
4536 // translation differently.
4537 StructureData filedat = oldFiles.get(new File(oldfilenam));
4538 if (filedat == null)
4540 String reformatedOldFilename = oldfilenam.replaceAll("/", "\\\\");
4541 filedat = oldFiles.get(new File(reformatedOldFilename));
4543 newFileLoc.append(Platform.escapeString(filedat.getFilePath()));
4544 pdbfilenames.add(filedat.getFilePath());
4545 pdbids.add(filedat.getPdbId());
4546 seqmaps.add(filedat.getSeqList().toArray(new SequenceI[0]));
4547 newFileLoc.append("\"");
4548 cp = ecp + 1; // advance beyond last \" and set cursor so we can
4549 // look for next file statement.
4550 } while ((ncp = state.indexOf("/*file*/", cp)) > -1);
4554 // just append rest of state
4555 newFileLoc.append(state.substring(cp));
4559 System.err.print("Ignoring incomplete Jmol state for PDB ids: ");
4560 newFileLoc = new StringBuilder(state);
4561 newFileLoc.append("; load append ");
4562 for (File id : oldFiles.keySet())
4564 // add this and any other pdb files that should be present in
4566 StructureData filedat = oldFiles.get(id);
4567 newFileLoc.append(filedat.getFilePath());
4568 pdbfilenames.add(filedat.getFilePath());
4569 pdbids.add(filedat.getPdbId());
4570 seqmaps.add(filedat.getSeqList().toArray(new SequenceI[0]));
4571 newFileLoc.append(" \"");
4572 newFileLoc.append(filedat.getFilePath());
4573 newFileLoc.append("\"");
4576 newFileLoc.append(";");
4579 if (newFileLoc.length() == 0)
4583 int histbug = newFileLoc.indexOf("history = ");
4587 * change "history = [true|false];" to "history = [1|0];"
4590 int diff = histbug == -1 ? -1 : newFileLoc.indexOf(";", histbug);
4591 String val = (diff == -1) ? null
4592 : newFileLoc.substring(histbug, diff);
4593 if (val != null && val.length() >= 4)
4595 if (val.contains("e")) // eh? what can it be?
4597 if (val.trim().equals("true"))
4605 newFileLoc.replace(histbug, diff, val);
4610 final String[] pdbf = pdbfilenames
4611 .toArray(new String[pdbfilenames.size()]);
4612 final String[] id = pdbids.toArray(new String[pdbids.size()]);
4613 final SequenceI[][] sq = seqmaps
4614 .toArray(new SequenceI[seqmaps.size()][]);
4615 final String fileloc = newFileLoc.toString();
4616 final String sviewid = viewerData.getKey();
4617 final AlignFrame alf = af;
4618 final Rectangle rect = new Rectangle(svattrib.getX(), svattrib.getY(),
4619 svattrib.getWidth(), svattrib.getHeight());
4622 javax.swing.SwingUtilities.invokeAndWait(new Runnable()
4627 JalviewStructureDisplayI sview = null;
4630 sview = new StructureViewer(
4631 alf.alignPanel.getStructureSelectionManager())
4632 .createView(StructureViewer.ViewerType.JMOL,
4633 pdbf, id, sq, alf.alignPanel, svattrib,
4634 fileloc, rect, sviewid);
4635 addNewStructureViewer(sview);
4636 } catch (OutOfMemoryError ex)
4638 new OOMWarning("restoring structure view for PDB id " + id,
4639 (OutOfMemoryError) ex.getCause());
4640 if (sview != null && sview.isVisible())
4642 sview.closeViewer(false);
4643 sview.setVisible(false);
4649 } catch (InvocationTargetException ex)
4651 warn("Unexpected error when opening Jmol view.", ex);
4653 } catch (InterruptedException e)
4655 // e.printStackTrace();
4661 * Generates a name for the entry in the project jar file to hold state
4662 * information for a structure viewer
4667 protected String getViewerJarEntryName(String viewId)
4669 return VIEWER_PREFIX + viewId;
4673 * Returns any open frame that matches given structure viewer data. The match
4674 * is based on the unique viewId, or (for older project versions) the frame's
4680 protected StructureViewerBase findMatchingViewer(
4681 Entry<String, StructureViewerModel> viewerData)
4683 final String sviewid = viewerData.getKey();
4684 final StructureViewerModel svattrib = viewerData.getValue();
4685 StructureViewerBase comp = null;
4686 JInternalFrame[] frames = getAllFrames();
4687 for (JInternalFrame frame : frames)
4689 if (frame instanceof StructureViewerBase)
4692 * Post jalview 2.4 schema includes structure view id
4694 if (sviewid != null && ((StructureViewerBase) frame).getViewId()
4697 comp = (StructureViewerBase) frame;
4698 break; // break added in 2.9
4701 * Otherwise test for matching position and size of viewer frame
4703 else if (frame.getX() == svattrib.getX()
4704 && frame.getY() == svattrib.getY()
4705 && frame.getHeight() == svattrib.getHeight()
4706 && frame.getWidth() == svattrib.getWidth())
4708 comp = (StructureViewerBase) frame;
4709 // no break in faint hope of an exact match on viewId
4717 * Link an AlignmentPanel to an existing structure viewer.
4722 * @param useinViewerSuperpos
4723 * @param usetoColourbyseq
4724 * @param viewerColouring
4726 protected void linkStructureViewer(AlignmentPanel ap,
4727 StructureViewerBase viewer, StructureViewerModel stateData)
4729 // NOTE: if the jalview project is part of a shared session then
4730 // view synchronization should/could be done here.
4732 final boolean useinViewerSuperpos = stateData.isAlignWithPanel();
4733 final boolean usetoColourbyseq = stateData.isColourWithAlignPanel();
4734 final boolean viewerColouring = stateData.isColourByViewer();
4735 Map<File, StructureData> oldFiles = stateData.getFileData();
4738 * Add mapping for sequences in this view to an already open viewer
4740 final AAStructureBindingModel binding = viewer.getBinding();
4741 for (File id : oldFiles.keySet())
4743 // add this and any other pdb files that should be present in the
4745 StructureData filedat = oldFiles.get(id);
4746 String pdbFile = filedat.getFilePath();
4747 SequenceI[] seq = filedat.getSeqList().toArray(new SequenceI[0]);
4748 binding.getSsm().setMapping(seq, null, pdbFile, DataSourceType.FILE,
4750 binding.addSequenceForStructFile(pdbFile, seq);
4752 // and add the AlignmentPanel's reference to the view panel
4753 viewer.addAlignmentPanel(ap);
4754 if (useinViewerSuperpos)
4756 viewer.useAlignmentPanelForSuperposition(ap);
4760 viewer.excludeAlignmentPanelForSuperposition(ap);
4762 if (usetoColourbyseq)
4764 viewer.useAlignmentPanelForColourbyseq(ap, !viewerColouring);
4768 viewer.excludeAlignmentPanelForColourbyseq(ap);
4773 * Get all frames within the Desktop.
4777 protected JInternalFrame[] getAllFrames()
4779 JInternalFrame[] frames = null;
4780 // TODO is this necessary - is it safe - risk of hanging?
4785 frames = Desktop.getDesktopPane().getAllFrames();
4786 } catch (ArrayIndexOutOfBoundsException e)
4788 // occasional No such child exceptions are thrown here...
4792 } catch (InterruptedException f)
4796 } while (frames == null);
4801 * Answers true if 'version' is equal to or later than 'supported', where each
4802 * is formatted as major/minor versions like "2.8.3" or "2.3.4b1" for bugfix
4803 * changes. Development and test values for 'version' are leniently treated
4807 * - minimum version we are comparing against
4809 * - version of data being processsed
4812 public static boolean isVersionStringLaterThan(String supported,
4815 if (supported == null || version == null
4816 || version.equalsIgnoreCase("DEVELOPMENT BUILD")
4817 || version.equalsIgnoreCase("Test")
4818 || version.equalsIgnoreCase("AUTOMATED BUILD"))
4820 System.err.println("Assuming project file with "
4821 + (version == null ? "null" : version)
4822 + " is compatible with Jalview version " + supported);
4827 return StringUtils.compareVersions(version, supported, "b") >= 0;
4831 Vector<JalviewStructureDisplayI> newStructureViewers = null;
4833 protected void addNewStructureViewer(JalviewStructureDisplayI sview)
4835 if (newStructureViewers != null)
4837 sview.getBinding().setFinishedLoadingFromArchive(false);
4838 newStructureViewers.add(sview);
4842 protected void setLoadingFinishedForNewStructureViewers()
4844 if (newStructureViewers != null)
4846 for (JalviewStructureDisplayI sview : newStructureViewers)
4848 sview.getBinding().setFinishedLoadingFromArchive(true);
4850 newStructureViewers.clear();
4851 newStructureViewers = null;
4855 AlignFrame loadViewport(String file, List<JSeq> JSEQ,
4856 List<SequenceI> hiddenSeqs, AlignmentI al,
4857 JalviewModel jm, Viewport view, String uniqueSeqSetId,
4858 String viewId, List<JvAnnotRow> autoAlan)
4860 AlignFrame af = null;
4861 af = new AlignFrame(al, safeInt(view.getWidth()),
4862 safeInt(view.getHeight()), uniqueSeqSetId, viewId)
4866 // protected void processKeyEvent(java.awt.event.KeyEvent e) {
4867 // System.out.println("Jalview2XML AF " + e);
4868 // super.processKeyEvent(e);
4875 af.setFileName(file, FileFormat.Jalview);
4877 final AlignViewport viewport = af.getViewport();
4878 for (int i = 0; i < JSEQ.size(); i++)
4880 int colour = safeInt(JSEQ.get(i).getColour());
4881 viewport.setSequenceColour(viewport.getAlignment().getSequenceAt(i),
4887 viewport.setColourByReferenceSeq(true);
4888 viewport.setDisplayReferenceSeq(true);
4891 viewport.setGatherViewsHere(safeBoolean(view.isGatheredViews()));
4893 if (view.getSequenceSetId() != null)
4895 AlignmentViewport av = viewportsAdded.get(uniqueSeqSetId);
4897 viewport.setSequenceSetId(uniqueSeqSetId);
4900 // propagate shared settings to this new view
4901 viewport.setHistoryList(av.getHistoryList());
4902 viewport.setRedoList(av.getRedoList());
4906 viewportsAdded.put(uniqueSeqSetId, viewport);
4908 // TODO: check if this method can be called repeatedly without
4909 // side-effects if alignpanel already registered.
4910 PaintRefresher.Register(af.alignPanel, uniqueSeqSetId);
4912 // apply Hidden regions to view.
4913 if (hiddenSeqs != null)
4915 for (int s = 0; s < JSEQ.size(); s++)
4917 SequenceGroup hidden = new SequenceGroup();
4918 boolean isRepresentative = false;
4919 for (int r = 0; r < JSEQ.get(s).getHiddenSequences().size(); r++)
4921 isRepresentative = true;
4922 SequenceI sequenceToHide = al
4923 .getSequenceAt(JSEQ.get(s).getHiddenSequences().get(r));
4924 hidden.addSequence(sequenceToHide, false);
4925 // remove from hiddenSeqs list so we don't try to hide it twice
4926 hiddenSeqs.remove(sequenceToHide);
4928 if (isRepresentative)
4930 SequenceI representativeSequence = al.getSequenceAt(s);
4931 hidden.addSequence(representativeSequence, false);
4932 viewport.hideRepSequences(representativeSequence, hidden);
4936 SequenceI[] hseqs = hiddenSeqs
4937 .toArray(new SequenceI[hiddenSeqs.size()]);
4938 viewport.hideSequence(hseqs);
4941 // recover view properties and display parameters
4943 viewport.setShowAnnotation(safeBoolean(view.isShowAnnotation()));
4944 viewport.setAbovePIDThreshold(safeBoolean(view.isPidSelected()));
4945 final int pidThreshold = safeInt(view.getPidThreshold());
4946 viewport.setThreshold(pidThreshold);
4948 viewport.setColourText(safeBoolean(view.isShowColourText()));
4951 .setConservationSelected(
4952 safeBoolean(view.isConservationSelected()));
4953 viewport.setIncrement(safeInt(view.getConsThreshold()));
4954 viewport.setShowJVSuffix(safeBoolean(view.isShowFullId()));
4955 viewport.setRightAlignIds(safeBoolean(view.isRightAlignIds()));
4956 viewport.setFont(new Font(view.getFontName(),
4957 safeInt(view.getFontStyle()), safeInt(view.getFontSize())),
4959 ViewStyleI vs = viewport.getViewStyle();
4960 vs.setScaleProteinAsCdna(view.isScaleProteinAsCdna());
4961 viewport.setViewStyle(vs);
4962 // TODO: allow custom charWidth/Heights to be restored by updating them
4963 // after setting font - which means set above to false
4964 viewport.setRenderGaps(safeBoolean(view.isRenderGaps()));
4965 viewport.setWrapAlignment(safeBoolean(view.isWrapAlignment()));
4966 viewport.setShowAnnotation(safeBoolean(view.isShowAnnotation()));
4968 viewport.setShowBoxes(safeBoolean(view.isShowBoxes()));
4970 viewport.setShowText(safeBoolean(view.isShowText()));
4972 viewport.setTextColour(new Color(safeInt(view.getTextCol1())));
4973 viewport.setTextColour2(new Color(safeInt(view.getTextCol2())));
4974 viewport.setThresholdTextColour(safeInt(view.getTextColThreshold()));
4975 viewport.setShowUnconserved(view.isShowUnconserved());
4976 viewport.getRanges().setStartRes(safeInt(view.getStartRes()));
4978 if (view.getViewName() != null)
4980 viewport.setViewName(view.getViewName());
4981 af.setInitialTabVisible();
4983 int x = safeInt(view.getXpos());
4984 int y = safeInt(view.getYpos());
4985 int w = safeInt(view.getWidth());
4986 int h = safeInt(view.getHeight());
4987 // // BH we cannot let the title bar go off the top
4988 // if (Platform.isJS())
4990 // x = Math.max(50 - w, x);
4991 // y = Math.max(0, y);
4994 af.setBounds(x, y, w, h);
4995 // startSeq set in af.alignPanel.updateLayout below
4996 af.alignPanel.updateLayout();
4997 ColourSchemeI cs = null;
4998 // apply colourschemes
4999 if (view.getBgColour() != null)
5001 if (view.getBgColour().startsWith("ucs"))
5003 cs = getUserColourScheme(jm, view.getBgColour());
5005 else if (view.getBgColour().startsWith("Annotation"))
5007 AnnotationColourScheme viewAnnColour = view.getAnnotationColours();
5008 cs = constructAnnotationColour(viewAnnColour, af, al, jm, true);
5015 cs = ColourSchemeProperty.getColourScheme(af.getViewport(), al,
5016 view.getBgColour());
5021 * turn off 'alignment colour applies to all groups'
5022 * while restoring global colour scheme
5024 viewport.setColourAppliesToAllGroups(false);
5025 viewport.setGlobalColourScheme(cs);
5026 viewport.getResidueShading().setThreshold(pidThreshold,
5027 view.isIgnoreGapsinConsensus());
5028 viewport.getResidueShading()
5029 .setConsensus(viewport.getSequenceConsensusHash());
5030 if (safeBoolean(view.isConservationSelected()) && cs != null)
5032 viewport.getResidueShading()
5033 .setConservationInc(safeInt(view.getConsThreshold()));
5035 af.changeColour(cs);
5036 viewport.setColourAppliesToAllGroups(true);
5039 .setShowSequenceFeatures(
5040 safeBoolean(view.isShowSequenceFeatures()));
5042 viewport.setCentreColumnLabels(view.isCentreColumnLabels());
5043 viewport.setIgnoreGapsConsensus(view.isIgnoreGapsinConsensus(), null);
5044 viewport.setFollowHighlight(view.isFollowHighlight());
5045 viewport.followSelection = view.isFollowSelection();
5046 viewport.setShowConsensusHistogram(view.isShowConsensusHistogram());
5047 viewport.setShowSequenceLogo(view.isShowSequenceLogo());
5048 viewport.setNormaliseSequenceLogo(view.isNormaliseSequenceLogo());
5049 viewport.setShowDBRefs(safeBoolean(view.isShowDbRefTooltip()));
5050 viewport.setShowNPFeats(safeBoolean(view.isShowNPfeatureTooltip()));
5051 viewport.setShowGroupConsensus(view.isShowGroupConsensus());
5052 viewport.setShowGroupConservation(view.isShowGroupConservation());
5054 // recover feature settings
5055 if (jm.getFeatureSettings() != null)
5057 FeatureRenderer fr = af.alignPanel.getSeqPanel().seqCanvas
5058 .getFeatureRenderer();
5059 FeaturesDisplayed fdi;
5060 viewport.setFeaturesDisplayed(fdi = new FeaturesDisplayed());
5061 String[] renderOrder = new String[jm.getFeatureSettings()
5062 .getSetting().size()];
5063 Map<String, FeatureColourI> featureColours = new Hashtable<>();
5064 Map<String, Float> featureOrder = new Hashtable<>();
5066 for (int fs = 0; fs < jm.getFeatureSettings()
5067 .getSetting().size(); fs++)
5069 Setting setting = jm.getFeatureSettings().getSetting().get(fs);
5070 String featureType = setting.getType();
5073 * restore feature filters (if any)
5075 jalview.xml.binding.jalview.FeatureMatcherSet filters = setting
5077 if (filters != null)
5079 FeatureMatcherSetI filter = Jalview2XML
5080 .parseFilter(featureType, filters);
5081 if (!filter.isEmpty())
5083 fr.setFeatureFilter(featureType, filter);
5088 * restore feature colour scheme
5090 Color maxColour = new Color(setting.getColour());
5091 if (setting.getMincolour() != null)
5094 * minColour is always set unless a simple colour
5095 * (including for colour by label though it doesn't use it)
5097 Color minColour = new Color(setting.getMincolour().intValue());
5098 Color noValueColour = minColour;
5099 NoValueColour noColour = setting.getNoValueColour();
5100 if (noColour == NoValueColour.NONE)
5102 noValueColour = null;
5104 else if (noColour == NoValueColour.MAX)
5106 noValueColour = maxColour;
5108 float min = safeFloat(safeFloat(setting.getMin()));
5109 float max = setting.getMax() == null ? 1f
5110 : setting.getMax().floatValue();
5111 FeatureColourI gc = new FeatureColour(maxColour, minColour,
5113 noValueColour, min, max);
5114 if (setting.getAttributeName().size() > 0)
5116 gc.setAttributeName(setting.getAttributeName().toArray(
5117 new String[setting.getAttributeName().size()]));
5119 if (setting.getThreshold() != null)
5121 gc.setThreshold(setting.getThreshold().floatValue());
5122 int threshstate = safeInt(setting.getThreshstate());
5123 // -1 = None, 0 = Below, 1 = Above threshold
5124 if (threshstate == 0)
5126 gc.setBelowThreshold(true);
5128 else if (threshstate == 1)
5130 gc.setAboveThreshold(true);
5133 gc.setAutoScaled(true); // default
5134 if (setting.isAutoScale() != null)
5136 gc.setAutoScaled(setting.isAutoScale());
5138 if (setting.isColourByLabel() != null)
5140 gc.setColourByLabel(setting.isColourByLabel());
5142 // and put in the feature colour table.
5143 featureColours.put(featureType, gc);
5147 featureColours.put(featureType,
5148 new FeatureColour(maxColour));
5150 renderOrder[fs] = featureType;
5151 if (setting.getOrder() != null)
5153 featureOrder.put(featureType, setting.getOrder().floatValue());
5157 featureOrder.put(featureType, new Float(
5158 fs / jm.getFeatureSettings().getSetting().size()));
5160 if (safeBoolean(setting.isDisplay()))
5162 fdi.setVisible(featureType);
5165 Map<String, Boolean> fgtable = new Hashtable<>();
5166 for (int gs = 0; gs < jm.getFeatureSettings().getGroup().size(); gs++)
5168 Group grp = jm.getFeatureSettings().getGroup().get(gs);
5169 fgtable.put(grp.getName(), new Boolean(grp.isDisplay()));
5171 // FeatureRendererSettings frs = new FeatureRendererSettings(renderOrder,
5172 // fgtable, featureColours, jms.getFeatureSettings().hasTransparency() ?
5173 // jms.getFeatureSettings().getTransparency() : 0.0, featureOrder);
5174 FeatureRendererSettings frs = new FeatureRendererSettings(renderOrder,
5175 fgtable, featureColours, 1.0f, featureOrder);
5176 fr.transferSettings(frs);
5179 if (view.getHiddenColumns().size() > 0)
5181 for (int c = 0; c < view.getHiddenColumns().size(); c++)
5183 final HiddenColumns hc = view.getHiddenColumns().get(c);
5184 viewport.hideColumns(safeInt(hc.getStart()),
5185 safeInt(hc.getEnd()) /* +1 */);
5188 if (view.getCalcIdParam() != null)
5190 for (CalcIdParam calcIdParam : view.getCalcIdParam())
5192 if (calcIdParam != null)
5194 if (recoverCalcIdParam(calcIdParam, viewport))
5199 warn("Couldn't recover parameters for "
5200 + calcIdParam.getCalcId());
5205 af.setMenusFromViewport(viewport);
5206 af.setTitle(view.getTitle());
5207 // TODO: we don't need to do this if the viewport is aready visible.
5209 * Add the AlignFrame to the desktop (it may be 'gathered' later), unless it
5210 * has a 'cdna/protein complement' view, in which case save it in order to
5211 * populate a SplitFrame once all views have been read in.
5213 String complementaryViewId = view.getComplementId();
5214 if (complementaryViewId == null)
5216 Desktop.addInternalFrame(af, view.getTitle(),
5217 safeInt(view.getWidth()), safeInt(view.getHeight()));
5218 // recompute any autoannotation
5219 af.alignPanel.updateAnnotation(false, true);
5220 reorderAutoannotation(af, al, autoAlan);
5221 af.alignPanel.alignmentChanged();
5225 splitFrameCandidates.put(view, af);
5231 * Reads saved data to restore Colour by Annotation settings
5233 * @param viewAnnColour
5237 * @param checkGroupAnnColour
5240 private ColourSchemeI constructAnnotationColour(
5241 AnnotationColourScheme viewAnnColour, AlignFrame af,
5242 AlignmentI al, JalviewModel model, boolean checkGroupAnnColour)
5244 boolean propagateAnnColour = false;
5245 AlignmentI annAlignment = af != null ? af.getViewport().getAlignment()
5247 if (checkGroupAnnColour && al.getGroups() != null
5248 && al.getGroups().size() > 0)
5250 // pre 2.8.1 behaviour
5251 // check to see if we should transfer annotation colours
5252 propagateAnnColour = true;
5253 for (SequenceGroup sg : al.getGroups())
5255 if (sg.getColourScheme() instanceof AnnotationColourGradient)
5257 propagateAnnColour = false;
5263 * 2.10.2- : saved annotationId is AlignmentAnnotation.annotationId
5265 String annotationId = viewAnnColour.getAnnotation();
5266 AlignmentAnnotation matchedAnnotation = annotationIds.get(annotationId);
5269 * pre 2.10.2: saved annotationId is AlignmentAnnotation.label
5271 if (matchedAnnotation == null
5272 && annAlignment.getAlignmentAnnotation() != null)
5274 for (int i = 0; i < annAlignment.getAlignmentAnnotation().length; i++)
5277 .equals(annAlignment.getAlignmentAnnotation()[i].label))
5279 matchedAnnotation = annAlignment.getAlignmentAnnotation()[i];
5284 if (matchedAnnotation == null)
5286 System.err.println("Failed to match annotation colour scheme for "
5290 if (matchedAnnotation.getThreshold() == null)
5292 matchedAnnotation.setThreshold(
5293 new GraphLine(safeFloat(viewAnnColour.getThreshold()),
5294 "Threshold", Color.black));
5297 AnnotationColourGradient cs = null;
5298 if (viewAnnColour.getColourScheme().equals("None"))
5300 cs = new AnnotationColourGradient(matchedAnnotation,
5301 new Color(safeInt(viewAnnColour.getMinColour())),
5302 new Color(safeInt(viewAnnColour.getMaxColour())),
5303 safeInt(viewAnnColour.getAboveThreshold()));
5305 else if (viewAnnColour.getColourScheme().startsWith("ucs"))
5307 cs = new AnnotationColourGradient(matchedAnnotation,
5308 getUserColourScheme(model, viewAnnColour.getColourScheme()),
5309 safeInt(viewAnnColour.getAboveThreshold()));
5313 cs = new AnnotationColourGradient(matchedAnnotation,
5314 ColourSchemeProperty.getColourScheme(af.getViewport(), al,
5315 viewAnnColour.getColourScheme()),
5316 safeInt(viewAnnColour.getAboveThreshold()));
5319 boolean perSequenceOnly = safeBoolean(viewAnnColour.isPerSequence());
5320 boolean useOriginalColours = safeBoolean(
5321 viewAnnColour.isPredefinedColours());
5322 cs.setSeqAssociated(perSequenceOnly);
5323 cs.setPredefinedColours(useOriginalColours);
5325 if (propagateAnnColour && al.getGroups() != null)
5327 // Also use these settings for all the groups
5328 for (int g = 0; g < al.getGroups().size(); g++)
5330 SequenceGroup sg = al.getGroups().get(g);
5331 if (sg.getGroupColourScheme() == null)
5336 AnnotationColourGradient groupScheme = new AnnotationColourGradient(
5337 matchedAnnotation, sg.getColourScheme(),
5338 safeInt(viewAnnColour.getAboveThreshold()));
5339 sg.setColourScheme(groupScheme);
5340 groupScheme.setSeqAssociated(perSequenceOnly);
5341 groupScheme.setPredefinedColours(useOriginalColours);
5347 private void reorderAutoannotation(AlignFrame af, AlignmentI al,
5348 List<JvAnnotRow> autoAlan)
5350 // copy over visualization settings for autocalculated annotation in the
5352 if (al.getAlignmentAnnotation() != null)
5355 * Kludge for magic autoannotation names (see JAL-811)
5357 String[] magicNames = new String[] { "Consensus", "Quality",
5359 JvAnnotRow nullAnnot = new JvAnnotRow(-1, null);
5360 Hashtable<String, JvAnnotRow> visan = new Hashtable<>();
5361 for (String nm : magicNames)
5363 visan.put(nm, nullAnnot);
5365 for (JvAnnotRow auan : autoAlan)
5367 visan.put(auan.template.label
5368 + (auan.template.getCalcId() == null ? ""
5369 : "\t" + auan.template.getCalcId()),
5372 int hSize = al.getAlignmentAnnotation().length;
5373 List<JvAnnotRow> reorder = new ArrayList<>();
5374 // work through any autoCalculated annotation already on the view
5375 // removing it if it should be placed in a different location on the
5376 // annotation panel.
5377 List<String> remains = new ArrayList<>(visan.keySet());
5378 for (int h = 0; h < hSize; h++)
5380 jalview.datamodel.AlignmentAnnotation jalan = al
5381 .getAlignmentAnnotation()[h];
5382 if (jalan.autoCalculated)
5385 JvAnnotRow valan = visan.get(k = jalan.label);
5386 if (jalan.getCalcId() != null)
5388 valan = visan.get(k = jalan.label + "\t" + jalan.getCalcId());
5393 // delete the auto calculated row from the alignment
5394 al.deleteAnnotation(jalan, false);
5398 if (valan != nullAnnot)
5400 if (jalan != valan.template)
5402 // newly created autoannotation row instance
5403 // so keep a reference to the visible annotation row
5404 // and copy over all relevant attributes
5405 if (valan.template.graphHeight >= 0)
5408 jalan.graphHeight = valan.template.graphHeight;
5410 jalan.visible = valan.template.visible;
5412 reorder.add(new JvAnnotRow(valan.order, jalan));
5417 // Add any (possibly stale) autocalculated rows that were not appended to
5418 // the view during construction
5419 for (String other : remains)
5421 JvAnnotRow othera = visan.get(other);
5422 if (othera != nullAnnot && othera.template.getCalcId() != null
5423 && othera.template.getCalcId().length() > 0)
5425 reorder.add(othera);
5428 // now put the automatic annotation in its correct place
5429 int s = 0, srt[] = new int[reorder.size()];
5430 JvAnnotRow[] rws = new JvAnnotRow[reorder.size()];
5431 for (JvAnnotRow jvar : reorder)
5434 srt[s++] = jvar.order;
5437 jalview.util.QuickSort.sort(srt, rws);
5438 // and re-insert the annotation at its correct position
5439 for (JvAnnotRow jvar : rws)
5441 al.addAnnotation(jvar.template, jvar.order);
5443 af.alignPanel.adjustAnnotationHeight();
5447 Hashtable skipList = null;
5450 * TODO remove this method
5453 * @return AlignFrame bound to sequenceSetId from view, if one exists. private
5454 * AlignFrame getSkippedFrame(Viewport view) { if (skipList==null) {
5455 * throw new Error("Implementation Error. No skipList defined for this
5456 * Jalview2XML instance."); } return (AlignFrame)
5457 * skipList.get(view.getSequenceSetId()); }
5461 * Check if the Jalview view contained in object should be skipped or not.
5464 * @return true if view's sequenceSetId is a key in skipList
5466 private boolean skipViewport(JalviewModel object)
5468 if (skipList == null)
5472 String id = object.getViewport().get(0).getSequenceSetId();
5473 if (skipList.containsKey(id))
5475 if (Cache.log != null && Cache.log.isDebugEnabled())
5477 Cache.log.debug("Skipping seuqence set id " + id);
5484 public void addToSkipList(AlignFrame af)
5486 if (skipList == null)
5488 skipList = new Hashtable();
5490 skipList.put(af.getViewport().getSequenceSetId(), af);
5493 public void clearSkipList()
5495 if (skipList != null)
5502 private void recoverDatasetFor(SequenceSet vamsasSet, AlignmentI al,
5503 boolean ignoreUnrefed, String uniqueSeqSetId)
5505 jalview.datamodel.AlignmentI ds = getDatasetFor(
5506 vamsasSet.getDatasetId());
5507 AlignmentI xtant_ds = ds;
5508 if (xtant_ds == null)
5510 // good chance we are about to create a new dataset, but check if we've
5511 // seen some of the dataset sequence IDs before.
5512 // TODO: skip this check if we are working with project generated by
5513 // version 2.11 or later
5514 xtant_ds = checkIfHasDataset(vamsasSet.getSequence());
5515 if (xtant_ds != null)
5518 addDatasetRef(vamsasSet.getDatasetId(), ds);
5521 Vector dseqs = null;
5524 // recovering an alignment View
5525 AlignmentI seqSetDS = getDatasetFor(UNIQSEQSETID + uniqueSeqSetId);
5526 if (seqSetDS != null)
5528 if (ds != null && ds != seqSetDS)
5530 warn("JAL-3171 regression: Overwriting a dataset reference for an alignment"
5531 + " - CDS/Protein crossreference data may be lost");
5532 if (xtant_ds != null)
5534 // This can only happen if the unique sequence set ID was bound to a
5535 // dataset that did not contain any of the sequences in the view
5536 // currently being restored.
5537 warn("JAL-3171 SERIOUS! TOTAL CONFUSION - please consider contacting the Jalview Development team so they can investigate why your project caused this message to be displayed.");
5541 addDatasetRef(vamsasSet.getDatasetId(), ds);
5546 // try even harder to restore dataset
5547 AlignmentI xtantDS = checkIfHasDataset(vamsasSet.getSequence());
5548 // create a list of new dataset sequences
5549 dseqs = new Vector();
5551 for (int i = 0, iSize = vamsasSet.getSequence().size(); i < iSize; i++)
5553 Sequence vamsasSeq = vamsasSet.getSequence().get(i);
5554 ensureJalviewDatasetSequence(vamsasSeq, ds, dseqs, ignoreUnrefed, i);
5556 // create a new dataset
5559 SequenceI[] dsseqs = new SequenceI[dseqs.size()];
5560 dseqs.copyInto(dsseqs);
5561 ds = new jalview.datamodel.Alignment(dsseqs);
5562 debug("Created new dataset " + vamsasSet.getDatasetId()
5563 + " for alignment " + System.identityHashCode(al));
5564 addDatasetRef(vamsasSet.getDatasetId(), ds);
5566 // set the dataset for the newly imported alignment.
5567 if (al.getDataset() == null && !ignoreUnrefed)
5570 // register dataset for the alignment's uniqueSeqSetId for legacy projects
5571 addDatasetRef(UNIQSEQSETID + uniqueSeqSetId, ds);
5573 updateSeqDatasetBinding(vamsasSet.getSequence(), ds);
5577 * XML dataset sequence ID to materialised dataset reference
5579 HashMap<String, AlignmentI> seqToDataset = new HashMap<>();
5582 * @return the first materialised dataset reference containing a dataset
5583 * sequence referenced in the given view
5585 * - sequences from the view
5587 AlignmentI checkIfHasDataset(List<Sequence> list)
5589 for (Sequence restoredSeq : list)
5591 AlignmentI datasetFor = seqToDataset.get(restoredSeq.getDsseqid());
5592 if (datasetFor != null)
5601 * Register ds as the containing dataset for the dataset sequences referenced
5602 * by sequences in list
5605 * - sequences in a view
5608 void updateSeqDatasetBinding(List<Sequence> list, AlignmentI ds)
5610 for (Sequence restoredSeq : list)
5612 AlignmentI prevDS = seqToDataset.put(restoredSeq.getDsseqid(), ds);
5613 if (prevDS != null && prevDS != ds)
5615 warn("Dataset sequence appears in many datasets: "
5616 + restoredSeq.getDsseqid());
5617 // TODO: try to merge!
5624 * sequence definition to create/merge dataset sequence for
5628 * vector to add new dataset sequence to
5629 * @param ignoreUnrefed
5630 * - when true, don't create new sequences from vamsasSeq if it's id
5631 * doesn't already have an asssociated Jalview sequence.
5633 * - used to reorder the sequence in the alignment according to the
5634 * vamsasSeq array ordering, to preserve ordering of dataset
5636 private void ensureJalviewDatasetSequence(Sequence vamsasSeq,
5637 AlignmentI ds, Vector dseqs, boolean ignoreUnrefed, int vseqpos)
5639 // JBP TODO: Check this is called for AlCodonFrames to support recovery of
5641 SequenceI sq = seqRefIds.get(vamsasSeq.getId());
5642 boolean reorder = false;
5643 SequenceI dsq = null;
5644 if (sq != null && sq.getDatasetSequence() != null)
5646 dsq = sq.getDatasetSequence();
5652 if (sq == null && ignoreUnrefed)
5656 String sqid = vamsasSeq.getDsseqid();
5659 // need to create or add a new dataset sequence reference to this sequence
5662 dsq = seqRefIds.get(sqid);
5667 // make a new dataset sequence
5668 dsq = sq.createDatasetSequence();
5671 // make up a new dataset reference for this sequence
5672 sqid = seqHash(dsq);
5674 dsq.setVamsasId(uniqueSetSuffix + sqid);
5675 seqRefIds.put(sqid, dsq);
5680 dseqs.addElement(dsq);
5685 ds.addSequence(dsq);
5691 { // make this dataset sequence sq's dataset sequence
5692 sq.setDatasetSequence(dsq);
5693 // and update the current dataset alignment
5698 if (!dseqs.contains(dsq))
5705 if (ds.findIndex(dsq) < 0)
5707 ds.addSequence(dsq);
5714 // TODO: refactor this as a merge dataset sequence function
5715 // now check that sq (the dataset sequence) sequence really is the union of
5716 // all references to it
5717 // boolean pre = sq.getStart() < dsq.getStart();
5718 // boolean post = sq.getEnd() > dsq.getEnd();
5722 // StringBuffer sb = new StringBuffer();
5723 String newres = jalview.analysis.AlignSeq.extractGaps(
5724 jalview.util.Comparison.GapChars, sq.getSequenceAsString());
5725 if (!newres.equalsIgnoreCase(dsq.getSequenceAsString())
5726 && newres.length() > dsq.getLength())
5728 // Update with the longer sequence.
5732 * if (pre) { sb.insert(0, newres .substring(0, dsq.getStart() -
5733 * sq.getStart())); dsq.setStart(sq.getStart()); } if (post) {
5734 * sb.append(newres.substring(newres.length() - sq.getEnd() -
5735 * dsq.getEnd())); dsq.setEnd(sq.getEnd()); }
5737 dsq.setSequence(newres);
5739 // TODO: merges will never happen if we 'know' we have the real dataset
5740 // sequence - this should be detected when id==dssid
5742 "DEBUG Notice: Merged dataset sequence (if you see this often, post at http://issues.jalview.org/browse/JAL-1474)"); // ("
5743 // + (pre ? "prepended" : "") + " "
5744 // + (post ? "appended" : ""));
5749 // sequence refs are identical. We may need to update the existing dataset
5750 // alignment with this one, though.
5751 if (ds != null && dseqs == null)
5753 int opos = ds.findIndex(dsq);
5754 SequenceI tseq = null;
5755 if (opos != -1 && vseqpos != opos)
5757 // remove from old position
5758 ds.deleteSequence(dsq);
5760 if (vseqpos < ds.getHeight())
5762 if (vseqpos != opos)
5764 // save sequence at destination position
5765 tseq = ds.getSequenceAt(vseqpos);
5766 ds.replaceSequenceAt(vseqpos, dsq);
5767 ds.addSequence(tseq);
5772 ds.addSequence(dsq);
5779 * TODO use AlignmentI here and in related methods - needs
5780 * AlignmentI.getDataset() changed to return AlignmentI instead of Alignment
5782 Hashtable<String, AlignmentI> datasetIds = null;
5784 IdentityHashMap<AlignmentI, String> dataset2Ids = null;
5786 private AlignmentI getDatasetFor(String datasetId)
5788 if (datasetIds == null)
5790 datasetIds = new Hashtable<>();
5793 if (datasetIds.containsKey(datasetId))
5795 return datasetIds.get(datasetId);
5800 private void addDatasetRef(String datasetId, AlignmentI dataset)
5802 if (datasetIds == null)
5804 datasetIds = new Hashtable<>();
5806 datasetIds.put(datasetId, dataset);
5810 * make a new dataset ID for this jalview dataset alignment
5815 private String getDatasetIdRef(AlignmentI dataset)
5817 if (dataset.getDataset() != null)
5819 warn("Serious issue! Dataset Object passed to getDatasetIdRef is not a Jalview DATASET alignment...");
5821 String datasetId = makeHashCode(dataset, null);
5822 if (datasetId == null)
5824 // make a new datasetId and record it
5825 if (dataset2Ids == null)
5827 dataset2Ids = new IdentityHashMap<>();
5831 datasetId = dataset2Ids.get(dataset);
5833 if (datasetId == null)
5835 datasetId = "ds" + dataset2Ids.size() + 1;
5836 dataset2Ids.put(dataset, datasetId);
5842 private void addDBRefs(SequenceI datasetSequence, Sequence sequence)
5844 for (int d = 0; d < sequence.getDBRef().size(); d++)
5846 DBRef dr = sequence.getDBRef().get(d);
5847 jalview.datamodel.DBRefEntry entry = new jalview.datamodel.DBRefEntry(
5848 dr.getSource(), dr.getVersion(), dr.getAccessionId());
5849 if (dr.getMapping() != null)
5851 entry.setMap(addMapping(dr.getMapping()));
5853 datasetSequence.addDBRef(entry);
5857 private jalview.datamodel.Mapping addMapping(Mapping m)
5859 SequenceI dsto = null;
5860 // Mapping m = dr.getMapping();
5861 int fr[] = new int[m.getMapListFrom().size() * 2];
5862 Iterator<MapListFrom> from = m.getMapListFrom().iterator();// enumerateMapListFrom();
5863 for (int _i = 0; from.hasNext(); _i += 2)
5865 MapListFrom mf = from.next();
5866 fr[_i] = mf.getStart();
5867 fr[_i + 1] = mf.getEnd();
5869 int fto[] = new int[m.getMapListTo().size() * 2];
5870 Iterator<MapListTo> to = m.getMapListTo().iterator();// enumerateMapListTo();
5871 for (int _i = 0; to.hasNext(); _i += 2)
5873 MapListTo mf = to.next();
5874 fto[_i] = mf.getStart();
5875 fto[_i + 1] = mf.getEnd();
5877 jalview.datamodel.Mapping jmap = new jalview.datamodel.Mapping(dsto, fr,
5878 fto, m.getMapFromUnit().intValue(),
5879 m.getMapToUnit().intValue());
5882 * (optional) choice of dseqFor or Sequence
5884 if (m.getDseqFor() != null)
5886 String dsfor = m.getDseqFor();
5887 if (seqRefIds.containsKey(dsfor))
5892 jmap.setTo(seqRefIds.get(dsfor));
5896 frefedSequence.add(newMappingRef(dsfor, jmap));
5899 else if (m.getSequence() != null)
5902 * local sequence definition
5904 Sequence ms = m.getSequence();
5905 SequenceI djs = null;
5906 String sqid = ms.getDsseqid();
5907 if (sqid != null && sqid.length() > 0)
5910 * recover dataset sequence
5912 djs = seqRefIds.get(sqid);
5917 "Warning - making up dataset sequence id for DbRef sequence map reference");
5918 sqid = ((Object) ms).toString(); // make up a new hascode for
5919 // undefined dataset sequence hash
5920 // (unlikely to happen)
5926 * make a new dataset sequence and add it to refIds hash
5928 djs = new jalview.datamodel.Sequence(ms.getName(),
5930 djs.setStart(jmap.getMap().getToLowest());
5931 djs.setEnd(jmap.getMap().getToHighest());
5932 djs.setVamsasId(uniqueSetSuffix + sqid);
5934 incompleteSeqs.put(sqid, djs);
5935 seqRefIds.put(sqid, djs);
5938 jalview.bin.Cache.log.debug("about to recurse on addDBRefs.");
5947 * Provides a 'copy' of an alignment view (on action New View) by 'saving' the
5948 * view as XML (but not to file), and then reloading it
5953 public AlignmentPanel copyAlignPanel(AlignmentPanel ap)
5956 JalviewModel jm = saveState(ap, null, null, null);
5959 jm.getVamsasModel().getSequenceSet().get(0).getDatasetId(),
5960 ap.getAlignment().getDataset());
5962 uniqueSetSuffix = "";
5963 // jm.getJalviewModelSequence().getViewport(0).setId(null);
5964 jm.getViewport().get(0).setId(null);
5965 // we don't overwrite the view we just copied
5967 if (this.frefedSequence == null)
5969 frefedSequence = new Vector<>();
5972 viewportsAdded.clear();
5974 AlignFrame af = loadFromObject(jm, null, false, null);
5975 af.getAlignPanels().clear();
5976 af.closeMenuItem_actionPerformed(true);
5979 * if(ap.av.getAlignment().getAlignmentAnnotation()!=null) { for(int i=0;
5980 * i<ap.av.getAlignment().getAlignmentAnnotation().length; i++) {
5981 * if(!ap.av.getAlignment().getAlignmentAnnotation()[i].autoCalculated) {
5982 * af.alignPanel.av.getAlignment().getAlignmentAnnotation()[i] =
5983 * ap.av.getAlignment().getAlignmentAnnotation()[i]; } } }
5986 return af.alignPanel;
5989 private Hashtable jvids2vobj;
5991 private void warn(String msg)
5996 private void warn(String msg, Exception e)
5998 if (Cache.log != null)
6002 Cache.log.warn(msg, e);
6006 Cache.log.warn(msg);
6011 System.err.println("Warning: " + msg);
6014 e.printStackTrace();
6019 private void debug(String string)
6021 debug(string, null);
6024 private void debug(String msg, Exception e)
6026 if (Cache.log != null)
6030 Cache.log.debug(msg, e);
6034 Cache.log.debug(msg);
6039 System.err.println("Warning: " + msg);
6042 e.printStackTrace();
6048 * set the object to ID mapping tables used to write/recover objects and XML
6049 * ID strings for the jalview project. If external tables are provided then
6050 * finalize and clearSeqRefs will not clear the tables when the Jalview2XML
6051 * object goes out of scope. - also populates the datasetIds hashtable with
6052 * alignment objects containing dataset sequences
6055 * Map from ID strings to jalview datamodel
6057 * Map from jalview datamodel to ID strings
6061 public void setObjectMappingTables(Hashtable vobj2jv,
6062 IdentityHashMap jv2vobj)
6064 this.jv2vobj = jv2vobj;
6065 this.vobj2jv = vobj2jv;
6066 Iterator ds = jv2vobj.keySet().iterator();
6068 while (ds.hasNext())
6070 Object jvobj = ds.next();
6071 id = jv2vobj.get(jvobj).toString();
6072 if (jvobj instanceof jalview.datamodel.Alignment)
6074 if (((jalview.datamodel.Alignment) jvobj).getDataset() == null)
6076 addDatasetRef(id, (jalview.datamodel.Alignment) jvobj);
6079 else if (jvobj instanceof jalview.datamodel.Sequence)
6081 // register sequence object so the XML parser can recover it.
6082 if (seqRefIds == null)
6084 seqRefIds = new HashMap<>();
6086 if (seqsToIds == null)
6088 seqsToIds = new IdentityHashMap<>();
6090 seqRefIds.put(jv2vobj.get(jvobj).toString(), (SequenceI) jvobj);
6091 seqsToIds.put((SequenceI) jvobj, id);
6093 else if (jvobj instanceof jalview.datamodel.AlignmentAnnotation)
6096 AlignmentAnnotation jvann = (AlignmentAnnotation) jvobj;
6097 annotationIds.put(anid = jv2vobj.get(jvobj).toString(), jvann);
6098 if (jvann.annotationId == null)
6100 jvann.annotationId = anid;
6102 if (!jvann.annotationId.equals(anid))
6104 // TODO verify that this is the correct behaviour
6105 this.warn("Overriding Annotation ID for " + anid
6106 + " from different id : " + jvann.annotationId);
6107 jvann.annotationId = anid;
6110 else if (jvobj instanceof String)
6112 if (jvids2vobj == null)
6114 jvids2vobj = new Hashtable();
6115 jvids2vobj.put(jvobj, jv2vobj.get(jvobj).toString());
6120 Cache.log.debug("Ignoring " + jvobj.getClass() + " (ID = " + id);
6126 * set the uniqueSetSuffix used to prefix/suffix object IDs for jalview
6127 * objects created from the project archive. If string is null (default for
6128 * construction) then suffix will be set automatically.
6132 public void setUniqueSetSuffix(String string)
6134 uniqueSetSuffix = string;
6139 * uses skipList2 as the skipList for skipping views on sequence sets
6140 * associated with keys in the skipList
6144 public void setSkipList(Hashtable skipList2)
6146 skipList = skipList2;
6150 * Reads the jar entry of given name and returns its contents, or null if the
6151 * entry is not found.
6154 * @param jarEntryName
6157 protected String readJarEntry(jarInputStreamProvider jprovider,
6158 String jarEntryName)
6160 String result = null;
6161 BufferedReader in = null;
6166 * Reopen the jar input stream and traverse its entries to find a matching
6169 JarInputStream jin = jprovider.getJarInputStream();
6170 JarEntry entry = null;
6173 entry = jin.getNextJarEntry();
6174 } while (entry != null && !entry.getName().equals(jarEntryName));
6178 StringBuilder out = new StringBuilder(256);
6179 in = new BufferedReader(new InputStreamReader(jin, UTF_8));
6182 while ((data = in.readLine()) != null)
6186 result = out.toString();
6190 warn("Couldn't find entry in Jalview Jar for " + jarEntryName);
6192 } catch (Exception ex)
6194 ex.printStackTrace();
6202 } catch (IOException e)
6213 * Returns an incrementing counter (0, 1, 2...)
6217 private synchronized int nextCounter()
6223 * Loads any saved PCA viewers
6228 protected void loadPCAViewers(JalviewModel model, AlignmentPanel ap)
6232 List<PcaViewer> pcaviewers = model.getPcaViewer();
6233 for (PcaViewer viewer : pcaviewers)
6235 String modelName = viewer.getScoreModelName();
6236 SimilarityParamsI params = new SimilarityParams(
6237 viewer.isIncludeGappedColumns(), viewer.isMatchGaps(),
6238 viewer.isIncludeGaps(),
6239 viewer.isDenominateByShortestLength());
6242 * create the panel (without computing the PCA)
6244 PCAPanel panel = new PCAPanel(ap, modelName, params);
6246 panel.setTitle(viewer.getTitle());
6247 panel.setBounds(new Rectangle(viewer.getXpos(), viewer.getYpos(),
6248 viewer.getWidth(), viewer.getHeight()));
6250 boolean showLabels = viewer.isShowLabels();
6251 panel.setShowLabels(showLabels);
6252 panel.getRotatableCanvas().setShowLabels(showLabels);
6253 panel.getRotatableCanvas()
6254 .setBgColour(new Color(viewer.getBgColour()));
6255 panel.getRotatableCanvas()
6256 .setApplyToAllViews(viewer.isLinkToAllViews());
6259 * load PCA output data
6261 ScoreModelI scoreModel = ScoreModels.getInstance()
6262 .getScoreModel(modelName, ap);
6263 PCA pca = new PCA(null, scoreModel, params);
6264 PcaDataType pcaData = viewer.getPcaData();
6266 MatrixI pairwise = loadDoubleMatrix(pcaData.getPairwiseMatrix());
6267 pca.setPairwiseScores(pairwise);
6269 MatrixI triDiag = loadDoubleMatrix(pcaData.getTridiagonalMatrix());
6270 pca.setTridiagonal(triDiag);
6272 MatrixI result = loadDoubleMatrix(pcaData.getEigenMatrix());
6273 pca.setEigenmatrix(result);
6275 panel.getPcaModel().setPCA(pca);
6278 * we haven't saved the input data! (JAL-2647 to do)
6280 panel.setInputData(null);
6283 * add the sequence points for the PCA display
6285 List<jalview.datamodel.SequencePoint> seqPoints = new ArrayList<>();
6286 for (SequencePoint sp : viewer.getSequencePoint())
6288 String seqId = sp.getSequenceRef();
6289 SequenceI seq = seqRefIds.get(seqId);
6292 throw new IllegalStateException(
6293 "Unmatched seqref for PCA: " + seqId);
6295 Point pt = new Point(sp.getXPos(), sp.getYPos(), sp.getZPos());
6296 jalview.datamodel.SequencePoint seqPoint = new jalview.datamodel.SequencePoint(
6298 seqPoints.add(seqPoint);
6300 panel.getRotatableCanvas().setPoints(seqPoints, seqPoints.size());
6303 * set min-max ranges and scale after setPoints (which recomputes them)
6305 panel.getRotatableCanvas().setScaleFactor(viewer.getScaleFactor());
6306 SeqPointMin spMin = viewer.getSeqPointMin();
6307 float[] min = new float[] { spMin.getXPos(), spMin.getYPos(),
6309 SeqPointMax spMax = viewer.getSeqPointMax();
6310 float[] max = new float[] { spMax.getXPos(), spMax.getYPos(),
6312 panel.getRotatableCanvas().setSeqMinMax(min, max);
6314 // todo: hold points list in PCAModel only
6315 panel.getPcaModel().setSequencePoints(seqPoints);
6317 panel.setSelectedDimensionIndex(viewer.getXDim(), X);
6318 panel.setSelectedDimensionIndex(viewer.getYDim(), Y);
6319 panel.setSelectedDimensionIndex(viewer.getZDim(), Z);
6321 // is this duplication needed?
6322 panel.setTop(seqPoints.size() - 1);
6323 panel.getPcaModel().setTop(seqPoints.size() - 1);
6326 * add the axes' end points for the display
6328 for (int i = 0; i < 3; i++)
6330 Axis axis = viewer.getAxis().get(i);
6331 panel.getRotatableCanvas().getAxisEndPoints()[i] = new Point(
6332 axis.getXPos(), axis.getYPos(), axis.getZPos());
6335 Desktop.addInternalFrame(panel, MessageManager.formatMessage(
6336 "label.calc_title", "PCA", modelName), 475, 450);
6338 } catch (Exception ex)
6340 Cache.log.error("Error loading PCA: " + ex.toString());
6345 * Populates an XML model of the feature colour scheme for one feature type
6347 * @param featureType
6351 public static Colour marshalColour(
6352 String featureType, FeatureColourI fcol)
6354 Colour col = new Colour();
6355 if (fcol.isSimpleColour())
6357 col.setRGB(Format.getHexString(fcol.getColour()));
6361 col.setRGB(Format.getHexString(fcol.getMaxColour()));
6362 col.setMin(fcol.getMin());
6363 col.setMax(fcol.getMax());
6364 col.setMinRGB(jalview.util.Format.getHexString(fcol.getMinColour()));
6365 col.setAutoScale(fcol.isAutoScaled());
6366 col.setThreshold(fcol.getThreshold());
6367 col.setColourByLabel(fcol.isColourByLabel());
6368 col.setThreshType(fcol.isAboveThreshold() ? ThresholdType.ABOVE
6369 : (fcol.isBelowThreshold() ? ThresholdType.BELOW
6370 : ThresholdType.NONE));
6371 if (fcol.isColourByAttribute())
6373 final String[] attName = fcol.getAttributeName();
6374 col.getAttributeName().add(attName[0]);
6375 if (attName.length > 1)
6377 col.getAttributeName().add(attName[1]);
6380 Color noColour = fcol.getNoColour();
6381 if (noColour == null)
6383 col.setNoValueColour(NoValueColour.NONE);
6385 else if (noColour == fcol.getMaxColour())
6387 col.setNoValueColour(NoValueColour.MAX);
6391 col.setNoValueColour(NoValueColour.MIN);
6394 col.setName(featureType);
6399 * Populates an XML model of the feature filter(s) for one feature type
6401 * @param firstMatcher
6402 * the first (or only) match condition)
6404 * remaining match conditions (if any)
6406 * if true, conditions are and-ed, else or-ed
6408 public static jalview.xml.binding.jalview.FeatureMatcherSet marshalFilter(
6409 FeatureMatcherI firstMatcher, Iterator<FeatureMatcherI> filters,
6412 jalview.xml.binding.jalview.FeatureMatcherSet result = new jalview.xml.binding.jalview.FeatureMatcherSet();
6414 if (filters.hasNext())
6419 CompoundMatcher compound = new CompoundMatcher();
6420 compound.setAnd(and);
6421 jalview.xml.binding.jalview.FeatureMatcherSet matcher1 = marshalFilter(
6422 firstMatcher, Collections.emptyIterator(), and);
6423 // compound.addMatcherSet(matcher1);
6424 compound.getMatcherSet().add(matcher1);
6425 FeatureMatcherI nextMatcher = filters.next();
6426 jalview.xml.binding.jalview.FeatureMatcherSet matcher2 = marshalFilter(
6427 nextMatcher, filters, and);
6428 // compound.addMatcherSet(matcher2);
6429 compound.getMatcherSet().add(matcher2);
6430 result.setCompoundMatcher(compound);
6435 * single condition matcher
6437 // MatchCondition matcherModel = new MatchCondition();
6438 jalview.xml.binding.jalview.FeatureMatcher matcherModel = new jalview.xml.binding.jalview.FeatureMatcher();
6439 matcherModel.setCondition(
6440 firstMatcher.getMatcher().getCondition().getStableName());
6441 matcherModel.setValue(firstMatcher.getMatcher().getPattern());
6442 if (firstMatcher.isByAttribute())
6444 matcherModel.setBy(FilterBy.BY_ATTRIBUTE);
6445 // matcherModel.setAttributeName(firstMatcher.getAttribute());
6446 String[] attName = firstMatcher.getAttribute();
6447 matcherModel.getAttributeName().add(attName[0]); // attribute
6448 if (attName.length > 1)
6450 matcherModel.getAttributeName().add(attName[1]); // sub-attribute
6453 else if (firstMatcher.isByLabel())
6455 matcherModel.setBy(FilterBy.BY_LABEL);
6457 else if (firstMatcher.isByScore())
6459 matcherModel.setBy(FilterBy.BY_SCORE);
6461 result.setMatchCondition(matcherModel);
6468 * Loads one XML model of a feature filter to a Jalview object
6470 * @param featureType
6471 * @param matcherSetModel
6474 public static FeatureMatcherSetI parseFilter(
6476 jalview.xml.binding.jalview.FeatureMatcherSet matcherSetModel)
6478 FeatureMatcherSetI result = new FeatureMatcherSet();
6481 parseFilterConditions(result, matcherSetModel, true);
6482 } catch (IllegalStateException e)
6484 // mixing AND and OR conditions perhaps
6486 String.format("Error reading filter conditions for '%s': %s",
6487 featureType, e.getMessage()));
6488 // return as much as was parsed up to the error
6495 * Adds feature match conditions to matcherSet as unmarshalled from XML
6496 * (possibly recursively for compound conditions)
6499 * @param matcherSetModel
6501 * if true, multiple conditions are AND-ed, else they are OR-ed
6502 * @throws IllegalStateException
6503 * if AND and OR conditions are mixed
6505 protected static void parseFilterConditions(
6506 FeatureMatcherSetI matcherSet,
6507 jalview.xml.binding.jalview.FeatureMatcherSet matcherSetModel,
6510 jalview.xml.binding.jalview.FeatureMatcher mc = matcherSetModel
6511 .getMatchCondition();
6517 FilterBy filterBy = mc.getBy();
6518 Condition cond = Condition.fromString(mc.getCondition());
6519 String pattern = mc.getValue();
6520 FeatureMatcherI matchCondition = null;
6521 if (filterBy == FilterBy.BY_LABEL)
6523 matchCondition = FeatureMatcher.byLabel(cond, pattern);
6525 else if (filterBy == FilterBy.BY_SCORE)
6527 matchCondition = FeatureMatcher.byScore(cond, pattern);
6530 else if (filterBy == FilterBy.BY_ATTRIBUTE)
6532 final List<String> attributeName = mc.getAttributeName();
6533 String[] attNames = attributeName
6534 .toArray(new String[attributeName.size()]);
6535 matchCondition = FeatureMatcher.byAttribute(cond, pattern,
6540 * note this throws IllegalStateException if AND-ing to a
6541 * previously OR-ed compound condition, or vice versa
6545 matcherSet.and(matchCondition);
6549 matcherSet.or(matchCondition);
6555 * compound condition
6557 List<jalview.xml.binding.jalview.FeatureMatcherSet> matchers = matcherSetModel
6558 .getCompoundMatcher().getMatcherSet();
6559 boolean anded = matcherSetModel.getCompoundMatcher().isAnd();
6560 if (matchers.size() == 2)
6562 parseFilterConditions(matcherSet, matchers.get(0), anded);
6563 parseFilterConditions(matcherSet, matchers.get(1), anded);
6567 System.err.println("Malformed compound filter condition");
6573 * Loads one XML model of a feature colour to a Jalview object
6575 * @param colourModel
6578 public static FeatureColourI parseColour(Colour colourModel)
6580 FeatureColourI colour = null;
6582 if (colourModel.getMax() != null)
6584 Color mincol = null;
6585 Color maxcol = null;
6586 Color noValueColour = null;
6590 mincol = new Color(Integer.parseInt(colourModel.getMinRGB(), 16));
6591 maxcol = new Color(Integer.parseInt(colourModel.getRGB(), 16));
6592 } catch (Exception e)
6594 Cache.log.warn("Couldn't parse out graduated feature color.", e);
6597 NoValueColour noCol = colourModel.getNoValueColour();
6598 if (noCol == NoValueColour.MIN)
6600 noValueColour = mincol;
6602 else if (noCol == NoValueColour.MAX)
6604 noValueColour = maxcol;
6607 colour = new FeatureColour(maxcol, mincol, maxcol, noValueColour,
6608 safeFloat(colourModel.getMin()),
6609 safeFloat(colourModel.getMax()));
6610 final List<String> attributeName = colourModel.getAttributeName();
6611 String[] attributes = attributeName
6612 .toArray(new String[attributeName.size()]);
6613 if (attributes != null && attributes.length > 0)
6615 colour.setAttributeName(attributes);
6617 if (colourModel.isAutoScale() != null)
6619 colour.setAutoScaled(colourModel.isAutoScale().booleanValue());
6621 if (colourModel.isColourByLabel() != null)
6623 colour.setColourByLabel(
6624 colourModel.isColourByLabel().booleanValue());
6626 if (colourModel.getThreshold() != null)
6628 colour.setThreshold(colourModel.getThreshold().floatValue());
6630 ThresholdType ttyp = colourModel.getThreshType();
6631 if (ttyp == ThresholdType.ABOVE)
6633 colour.setAboveThreshold(true);
6635 else if (ttyp == ThresholdType.BELOW)
6637 colour.setBelowThreshold(true);
6642 Color color = new Color(Integer.parseInt(colourModel.getRGB(), 16));
6643 colour = new FeatureColour(color);