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 java.util.Locale;
25 import static jalview.math.RotatableMatrix.Axis.X;
26 import static jalview.math.RotatableMatrix.Axis.Y;
27 import static jalview.math.RotatableMatrix.Axis.Z;
29 import java.awt.Color;
31 import java.awt.Rectangle;
32 import java.io.BufferedReader;
33 import java.io.ByteArrayInputStream;
35 import java.io.FileInputStream;
36 import java.io.FileOutputStream;
37 import java.io.IOException;
38 import java.io.InputStream;
39 import java.io.InputStreamReader;
40 import java.io.OutputStream;
41 import java.io.OutputStreamWriter;
42 import java.io.PrintWriter;
43 import java.lang.reflect.InvocationTargetException;
44 import java.math.BigInteger;
45 import java.net.MalformedURLException;
47 import java.util.ArrayList;
48 import java.util.Arrays;
49 import java.util.Collections;
50 import java.util.Enumeration;
51 import java.util.GregorianCalendar;
52 import java.util.HashMap;
53 import java.util.HashSet;
54 import java.util.Hashtable;
55 import java.util.IdentityHashMap;
56 import java.util.Iterator;
57 import java.util.LinkedHashMap;
58 import java.util.List;
60 import java.util.Map.Entry;
62 import java.util.Vector;
63 import java.util.jar.JarEntry;
64 import java.util.jar.JarInputStream;
65 import java.util.jar.JarOutputStream;
67 import javax.swing.JInternalFrame;
68 import javax.swing.SwingUtilities;
69 import javax.xml.bind.JAXBContext;
70 import javax.xml.bind.JAXBElement;
71 import javax.xml.bind.Marshaller;
72 import javax.xml.datatype.DatatypeConfigurationException;
73 import javax.xml.datatype.DatatypeFactory;
74 import javax.xml.datatype.XMLGregorianCalendar;
75 import javax.xml.stream.XMLInputFactory;
76 import javax.xml.stream.XMLStreamReader;
78 import jalview.analysis.Conservation;
79 import jalview.analysis.PCA;
80 import jalview.analysis.scoremodels.ScoreModels;
81 import jalview.analysis.scoremodels.SimilarityParams;
82 import jalview.api.FeatureColourI;
83 import jalview.api.ViewStyleI;
84 import jalview.api.analysis.ScoreModelI;
85 import jalview.api.analysis.SimilarityParamsI;
86 import jalview.api.structures.JalviewStructureDisplayI;
87 import jalview.bin.Cache;
88 import jalview.datamodel.AlignedCodonFrame;
89 import jalview.datamodel.Alignment;
90 import jalview.datamodel.AlignmentAnnotation;
91 import jalview.datamodel.AlignmentI;
92 import jalview.datamodel.DBRefEntry;
93 import jalview.datamodel.GeneLocus;
94 import jalview.datamodel.GraphLine;
95 import jalview.datamodel.PDBEntry;
96 import jalview.datamodel.Point;
97 import jalview.datamodel.RnaViewerModel;
98 import jalview.datamodel.SequenceFeature;
99 import jalview.datamodel.SequenceGroup;
100 import jalview.datamodel.SequenceI;
101 import jalview.datamodel.StructureViewerModel;
102 import jalview.datamodel.StructureViewerModel.StructureData;
103 import jalview.datamodel.features.FeatureMatcher;
104 import jalview.datamodel.features.FeatureMatcherI;
105 import jalview.datamodel.features.FeatureMatcherSet;
106 import jalview.datamodel.features.FeatureMatcherSetI;
107 import jalview.ext.varna.RnaModel;
108 import jalview.gui.AlignFrame;
109 import jalview.gui.AlignViewport;
110 import jalview.gui.AlignmentPanel;
111 import jalview.gui.AppVarna;
112 import jalview.gui.Desktop;
113 import jalview.gui.JvOptionPane;
114 import jalview.gui.OOMWarning;
115 import jalview.gui.PCAPanel;
116 import jalview.gui.PaintRefresher;
117 import jalview.gui.SplitFrame;
118 import jalview.gui.StructureViewer;
119 import jalview.gui.StructureViewer.ViewerType;
120 import jalview.gui.StructureViewerBase;
121 import jalview.gui.TreePanel;
122 import jalview.io.BackupFiles;
123 import jalview.io.DataSourceType;
124 import jalview.io.FileFormat;
125 import jalview.io.NewickFile;
126 import jalview.math.Matrix;
127 import jalview.math.MatrixI;
128 import jalview.renderer.ResidueShaderI;
129 import jalview.schemes.AnnotationColourGradient;
130 import jalview.schemes.ColourSchemeI;
131 import jalview.schemes.ColourSchemeProperty;
132 import jalview.schemes.FeatureColour;
133 import jalview.schemes.ResidueProperties;
134 import jalview.schemes.UserColourScheme;
135 import jalview.structure.StructureSelectionManager;
136 import jalview.structures.models.AAStructureBindingModel;
137 import jalview.util.Format;
138 import jalview.util.HttpUtils;
139 import jalview.util.MessageManager;
140 import jalview.util.Platform;
141 import jalview.util.StringUtils;
142 import jalview.util.jarInputStreamProvider;
143 import jalview.util.matcher.Condition;
144 import jalview.viewmodel.AlignmentViewport;
145 import jalview.viewmodel.PCAModel;
146 import jalview.viewmodel.ViewportRanges;
147 import jalview.viewmodel.seqfeatures.FeatureRendererModel;
148 import jalview.viewmodel.seqfeatures.FeatureRendererSettings;
149 import jalview.viewmodel.seqfeatures.FeaturesDisplayed;
150 import jalview.ws.jws2.Jws2Discoverer;
151 import jalview.ws.jws2.dm.AAConSettings;
152 import jalview.ws.jws2.jabaws2.Jws2Instance;
153 import jalview.ws.params.ArgumentI;
154 import jalview.ws.params.AutoCalcSetting;
155 import jalview.ws.params.WsParamSetI;
156 import jalview.xml.binding.jalview.AlcodonFrame;
157 import jalview.xml.binding.jalview.AlcodonFrame.AlcodMap;
158 import jalview.xml.binding.jalview.Annotation;
159 import jalview.xml.binding.jalview.Annotation.ThresholdLine;
160 import jalview.xml.binding.jalview.AnnotationColourScheme;
161 import jalview.xml.binding.jalview.AnnotationElement;
162 import jalview.xml.binding.jalview.DoubleMatrix;
163 import jalview.xml.binding.jalview.DoubleVector;
164 import jalview.xml.binding.jalview.Feature;
165 import jalview.xml.binding.jalview.Feature.OtherData;
166 import jalview.xml.binding.jalview.FeatureMatcherSet.CompoundMatcher;
167 import jalview.xml.binding.jalview.FilterBy;
168 import jalview.xml.binding.jalview.JalviewModel;
169 import jalview.xml.binding.jalview.JalviewModel.FeatureSettings;
170 import jalview.xml.binding.jalview.JalviewModel.FeatureSettings.Group;
171 import jalview.xml.binding.jalview.JalviewModel.FeatureSettings.Setting;
172 import jalview.xml.binding.jalview.JalviewModel.JGroup;
173 import jalview.xml.binding.jalview.JalviewModel.JSeq;
174 import jalview.xml.binding.jalview.JalviewModel.JSeq.Pdbids;
175 import jalview.xml.binding.jalview.JalviewModel.JSeq.Pdbids.StructureState;
176 import jalview.xml.binding.jalview.JalviewModel.JSeq.RnaViewer;
177 import jalview.xml.binding.jalview.JalviewModel.JSeq.RnaViewer.SecondaryStructure;
178 import jalview.xml.binding.jalview.JalviewModel.PcaViewer;
179 import jalview.xml.binding.jalview.JalviewModel.PcaViewer.Axis;
180 import jalview.xml.binding.jalview.JalviewModel.PcaViewer.SeqPointMax;
181 import jalview.xml.binding.jalview.JalviewModel.PcaViewer.SeqPointMin;
182 import jalview.xml.binding.jalview.JalviewModel.PcaViewer.SequencePoint;
183 import jalview.xml.binding.jalview.JalviewModel.Tree;
184 import jalview.xml.binding.jalview.JalviewModel.UserColours;
185 import jalview.xml.binding.jalview.JalviewModel.Viewport;
186 import jalview.xml.binding.jalview.JalviewModel.Viewport.CalcIdParam;
187 import jalview.xml.binding.jalview.JalviewModel.Viewport.HiddenColumns;
188 import jalview.xml.binding.jalview.JalviewUserColours;
189 import jalview.xml.binding.jalview.JalviewUserColours.Colour;
190 import jalview.xml.binding.jalview.MapListType.MapListFrom;
191 import jalview.xml.binding.jalview.MapListType.MapListTo;
192 import jalview.xml.binding.jalview.Mapping;
193 import jalview.xml.binding.jalview.NoValueColour;
194 import jalview.xml.binding.jalview.ObjectFactory;
195 import jalview.xml.binding.jalview.PcaDataType;
196 import jalview.xml.binding.jalview.Pdbentry.Property;
197 import jalview.xml.binding.jalview.Sequence;
198 import jalview.xml.binding.jalview.Sequence.DBRef;
199 import jalview.xml.binding.jalview.SequenceSet;
200 import jalview.xml.binding.jalview.SequenceSet.SequenceSetProperties;
201 import jalview.xml.binding.jalview.ThresholdType;
202 import jalview.xml.binding.jalview.VAMSAS;
205 * Write out the current jalview desktop state as a Jalview XML stream.
207 * Note: the vamsas objects referred to here are primitive versions of the
208 * VAMSAS project schema elements - they are not the same and most likely never
212 * @version $Revision: 1.134 $
214 public class Jalview2XML
217 // BH 2018 we add the .jvp binary extension to J2S so that
218 // it will declare that binary when we do the file save from the browser
222 Platform.addJ2SBinaryType(".jvp?");
225 private static final String VIEWER_PREFIX = "viewer_";
227 private static final String RNA_PREFIX = "rna_";
229 private static final String UTF_8 = "UTF-8";
232 * prefix for recovering datasets for alignments with multiple views where
233 * non-existent dataset IDs were written for some views
235 private static final String UNIQSEQSETID = "uniqueSeqSetId.";
237 // use this with nextCounter() to make unique names for entities
238 private int counter = 0;
241 * SequenceI reference -> XML ID string in jalview XML. Populated as XML reps
242 * of sequence objects are created.
244 IdentityHashMap<SequenceI, String> seqsToIds = null;
247 * jalview XML Sequence ID to jalview sequence object reference (both dataset
248 * and alignment sequences. Populated as XML reps of sequence objects are
251 Map<String, SequenceI> seqRefIds = null;
253 Map<String, SequenceI> incompleteSeqs = null;
255 List<SeqFref> frefedSequence = null;
257 boolean raiseGUI = true; // whether errors are raised in dialog boxes or not
260 * Map of reconstructed AlignFrame objects that appear to have come from
261 * SplitFrame objects (have a dna/protein complement view).
263 private Map<Viewport, AlignFrame> splitFrameCandidates = new HashMap<>();
266 * Map from displayed rna structure models to their saved session state jar
269 private Map<RnaModel, String> rnaSessions = new HashMap<>();
272 * A helper method for safely using the value of an optional attribute that
273 * may be null if not present in the XML. Answers the boolean value, or false
279 public static boolean safeBoolean(Boolean b)
281 return b == null ? false : b.booleanValue();
285 * A helper method for safely using the value of an optional attribute that
286 * may be null if not present in the XML. Answers the integer value, or zero
292 public static int safeInt(Integer i)
294 return i == null ? 0 : i.intValue();
298 * A helper method for safely using the value of an optional attribute that
299 * may be null if not present in the XML. Answers the float value, or zero if
305 public static float safeFloat(Float f)
307 return f == null ? 0f : f.floatValue();
311 * create/return unique hash string for sq
314 * @return new or existing unique string for sq
316 String seqHash(SequenceI sq)
318 if (seqsToIds == null)
322 if (seqsToIds.containsKey(sq))
324 return seqsToIds.get(sq);
328 // create sequential key
329 String key = "sq" + (seqsToIds.size() + 1);
330 key = makeHashCode(sq, key); // check we don't have an external reference
332 seqsToIds.put(sq, key);
339 if (seqsToIds == null)
341 seqsToIds = new IdentityHashMap<>();
343 if (seqRefIds == null)
345 seqRefIds = new HashMap<>();
347 if (incompleteSeqs == null)
349 incompleteSeqs = new HashMap<>();
351 if (frefedSequence == null)
353 frefedSequence = new ArrayList<>();
361 public Jalview2XML(boolean raiseGUI)
363 this.raiseGUI = raiseGUI;
367 * base class for resolving forward references to sequences by their ID
372 abstract class SeqFref
378 public SeqFref(String _sref, String type)
384 public String getSref()
389 public SequenceI getSrefSeq()
391 return seqRefIds.get(sref);
394 public boolean isResolvable()
396 return seqRefIds.get(sref) != null;
399 public SequenceI getSrefDatasetSeq()
401 SequenceI sq = seqRefIds.get(sref);
404 while (sq.getDatasetSequence() != null)
406 sq = sq.getDatasetSequence();
413 * @return true if the forward reference was fully resolved
415 abstract boolean resolve();
418 public String toString()
420 return type + " reference to " + sref;
425 * create forward reference for a mapping
431 public SeqFref newMappingRef(final String sref,
432 final jalview.datamodel.Mapping _jmap)
434 SeqFref fref = new SeqFref(sref, "Mapping")
436 public jalview.datamodel.Mapping jmap = _jmap;
441 SequenceI seq = getSrefDatasetSeq();
453 public SeqFref newAlcodMapRef(final String sref,
454 final AlignedCodonFrame _cf,
455 final jalview.datamodel.Mapping _jmap)
458 SeqFref fref = new SeqFref(sref, "Codon Frame")
460 AlignedCodonFrame cf = _cf;
462 public jalview.datamodel.Mapping mp = _jmap;
465 public boolean isResolvable()
467 return super.isResolvable() && mp.getTo() != null;
473 SequenceI seq = getSrefDatasetSeq();
478 cf.addMap(seq, mp.getTo(), mp.getMap());
485 public void resolveFrefedSequences()
487 Iterator<SeqFref> nextFref = frefedSequence.iterator();
488 int toresolve = frefedSequence.size();
489 int unresolved = 0, failedtoresolve = 0;
490 while (nextFref.hasNext())
492 SeqFref ref = nextFref.next();
493 if (ref.isResolvable())
505 } catch (Exception x)
508 "IMPLEMENTATION ERROR: Failed to resolve forward reference for sequence "
521 System.err.println("Jalview Project Import: There were " + unresolved
522 + " forward references left unresolved on the stack.");
524 if (failedtoresolve > 0)
526 System.err.println("SERIOUS! " + failedtoresolve
527 + " resolvable forward references failed to resolve.");
529 if (incompleteSeqs != null && incompleteSeqs.size() > 0)
532 "Jalview Project Import: There are " + incompleteSeqs.size()
533 + " sequences which may have incomplete metadata.");
534 if (incompleteSeqs.size() < 10)
536 for (SequenceI s : incompleteSeqs.values())
538 System.err.println(s.toString());
544 "Too many to report. Skipping output of incomplete sequences.");
550 * This maintains a map of viewports, the key being the seqSetId. Important to
551 * set historyItem and redoList for multiple views
553 Map<String, AlignViewport> viewportsAdded = new HashMap<>();
555 Map<String, AlignmentAnnotation> annotationIds = new HashMap<>();
557 String uniqueSetSuffix = "";
560 * List of pdbfiles added to Jar
562 List<String> pdbfiles = null;
564 // SAVES SEVERAL ALIGNMENT WINDOWS TO SAME JARFILE
565 public void saveState(File statefile)
567 FileOutputStream fos = null;
572 fos = new FileOutputStream(statefile);
574 JarOutputStream jout = new JarOutputStream(fos);
578 } catch (Exception e)
580 Cache.log.error("Couln't write Jalview state to " + statefile, e);
581 // TODO: inform user of the problem - they need to know if their data was
583 if (errorMessage == null)
585 errorMessage = "Did't write Jalview Archive to output file '"
586 + statefile + "' - See console error log for details";
590 errorMessage += "(Didn't write Jalview Archive to output file '"
601 } catch (IOException e)
611 * Writes a jalview project archive to the given Jar output stream.
615 public void saveState(JarOutputStream jout)
617 AlignFrame[] frames = Desktop.getAlignFrames();
623 saveAllFrames(Arrays.asList(frames), jout);
627 * core method for storing state for a set of AlignFrames.
630 * - frames involving all data to be exported (including containing
633 * - project output stream
635 private void saveAllFrames(List<AlignFrame> frames, JarOutputStream jout)
637 Hashtable<String, AlignFrame> dsses = new Hashtable<>();
640 * ensure cached data is clear before starting
642 // todo tidy up seqRefIds, seqsToIds initialisation / reset
644 splitFrameCandidates.clear();
649 // NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS
650 // //////////////////////////////////////////////////
652 List<String> shortNames = new ArrayList<>();
653 List<String> viewIds = new ArrayList<>();
656 for (int i = frames.size() - 1; i > -1; i--)
658 AlignFrame af = frames.get(i);
660 if (skipList != null && skipList
661 .containsKey(af.getViewport().getSequenceSetId()))
666 String shortName = makeFilename(af, shortNames);
668 int apSize = af.getAlignPanels().size();
670 for (int ap = 0; ap < apSize; ap++)
672 AlignmentPanel apanel = (AlignmentPanel) af.getAlignPanels()
674 String fileName = apSize == 1 ? shortName : ap + shortName;
675 if (!fileName.endsWith(".xml"))
677 fileName = fileName + ".xml";
680 saveState(apanel, fileName, jout, viewIds);
682 String dssid = getDatasetIdRef(
683 af.getViewport().getAlignment().getDataset());
684 if (!dsses.containsKey(dssid))
686 dsses.put(dssid, af);
691 writeDatasetFor(dsses, "" + jout.hashCode() + " " + uniqueSetSuffix,
697 } catch (Exception foo)
701 } catch (Exception ex)
703 // TODO: inform user of the problem - they need to know if their data was
705 if (errorMessage == null)
707 errorMessage = "Couldn't write Jalview Archive - see error output for details";
709 ex.printStackTrace();
714 * Generates a distinct file name, based on the title of the AlignFrame, by
715 * appending _n for increasing n until an unused name is generated. The new
716 * name (without its extension) is added to the list.
720 * @return the generated name, with .xml extension
722 protected String makeFilename(AlignFrame af, List<String> namesUsed)
724 String shortName = af.getTitle();
726 if (shortName.indexOf(File.separatorChar) > -1)
728 shortName = shortName
729 .substring(shortName.lastIndexOf(File.separatorChar) + 1);
734 while (namesUsed.contains(shortName))
736 if (shortName.endsWith("_" + (count - 1)))
738 shortName = shortName.substring(0, shortName.lastIndexOf("_"));
741 shortName = shortName.concat("_" + count);
745 namesUsed.add(shortName);
747 if (!shortName.endsWith(".xml"))
749 shortName = shortName + ".xml";
754 // USE THIS METHOD TO SAVE A SINGLE ALIGNMENT WINDOW
755 public boolean saveAlignment(AlignFrame af, String jarFile,
760 // create backupfiles object and get new temp filename destination
761 boolean doBackup = BackupFiles.getEnabled();
762 BackupFiles backupfiles = doBackup ? new BackupFiles(jarFile) : null;
763 FileOutputStream fos = new FileOutputStream(
764 doBackup ? backupfiles.getTempFilePath() : jarFile);
766 JarOutputStream jout = new JarOutputStream(fos);
767 List<AlignFrame> frames = new ArrayList<>();
769 // resolve splitframes
770 if (af.getViewport().getCodingComplement() != null)
772 frames = ((SplitFrame) af.getSplitViewContainer()).getAlignFrames();
778 saveAllFrames(frames, jout);
782 } catch (Exception foo)
786 boolean success = true;
790 backupfiles.setWriteSuccess(success);
791 success = backupfiles.rollBackupsAndRenameTempFile();
795 } catch (Exception ex)
797 errorMessage = "Couldn't Write alignment view to Jalview Archive - see error output for details";
798 ex.printStackTrace();
803 private void writeDatasetFor(Hashtable<String, AlignFrame> dsses,
804 String fileName, JarOutputStream jout)
807 for (String dssids : dsses.keySet())
809 AlignFrame _af = dsses.get(dssids);
810 String jfileName = fileName + " Dataset for " + _af.getTitle();
811 if (!jfileName.endsWith(".xml"))
813 jfileName = jfileName + ".xml";
815 saveState(_af.alignPanel, jfileName, true, jout, null);
820 * create a JalviewModel from an alignment view and marshall it to a
824 * panel to create jalview model for
826 * name of alignment panel written to output stream
833 public JalviewModel saveState(AlignmentPanel ap, String fileName,
834 JarOutputStream jout, List<String> viewIds)
836 return saveState(ap, fileName, false, jout, viewIds);
840 * create a JalviewModel from an alignment view and marshall it to a
844 * panel to create jalview model for
846 * name of alignment panel written to output stream
848 * when true, only write the dataset for the alignment, not the data
849 * associated with the view.
855 public JalviewModel saveState(AlignmentPanel ap, String fileName,
856 boolean storeDS, JarOutputStream jout, List<String> viewIds)
860 viewIds = new ArrayList<>();
865 List<UserColourScheme> userColours = new ArrayList<>();
867 AlignViewport av = ap.av;
868 ViewportRanges vpRanges = av.getRanges();
870 final ObjectFactory objectFactory = new ObjectFactory();
871 JalviewModel object = objectFactory.createJalviewModel();
872 object.setVamsasModel(new VAMSAS());
874 // object.setCreationDate(new java.util.Date(System.currentTimeMillis()));
877 GregorianCalendar c = new GregorianCalendar();
878 DatatypeFactory datatypeFactory = DatatypeFactory.newInstance();
879 XMLGregorianCalendar now = datatypeFactory.newXMLGregorianCalendar(c);// gregorianCalendar);
880 object.setCreationDate(now);
881 } catch (DatatypeConfigurationException e)
883 System.err.println("error writing date: " + e.toString());
886 jalview.bin.Cache.getDefault("VERSION", "Development Build"));
889 * rjal is full height alignment, jal is actual alignment with full metadata
890 * but excludes hidden sequences.
892 jalview.datamodel.AlignmentI rjal = av.getAlignment(), jal = rjal;
894 if (av.hasHiddenRows())
896 rjal = jal.getHiddenSequences().getFullAlignment();
899 SequenceSet vamsasSet = new SequenceSet();
901 // JalviewModelSequence jms = new JalviewModelSequence();
903 vamsasSet.setGapChar(jal.getGapCharacter() + "");
905 if (jal.getDataset() != null)
907 // dataset id is the dataset's hashcode
908 vamsasSet.setDatasetId(getDatasetIdRef(jal.getDataset()));
911 // switch jal and the dataset
912 jal = jal.getDataset();
916 if (jal.getProperties() != null)
918 Enumeration en = jal.getProperties().keys();
919 while (en.hasMoreElements())
921 String key = en.nextElement().toString();
922 SequenceSetProperties ssp = new SequenceSetProperties();
924 ssp.setValue(jal.getProperties().get(key).toString());
925 // vamsasSet.addSequenceSetProperties(ssp);
926 vamsasSet.getSequenceSetProperties().add(ssp);
931 Set<String> calcIdSet = new HashSet<>();
932 // record the set of vamsas sequence XML POJO we create.
933 HashMap<String, Sequence> vamsasSetIds = new HashMap<>();
935 for (final SequenceI jds : rjal.getSequences())
937 final SequenceI jdatasq = jds.getDatasetSequence() == null ? jds
938 : jds.getDatasetSequence();
939 String id = seqHash(jds);
940 if (vamsasSetIds.get(id) == null)
942 if (seqRefIds.get(id) != null && !storeDS)
944 // This happens for two reasons: 1. multiple views are being
946 // 2. the hashCode has collided with another sequence's code. This
948 // HAPPEN! (PF00072.15.stk does this)
949 // JBPNote: Uncomment to debug writing out of files that do not read
950 // back in due to ArrayOutOfBoundExceptions.
951 // System.err.println("vamsasSeq backref: "+id+"");
952 // System.err.println(jds.getName()+"
953 // "+jds.getStart()+"-"+jds.getEnd()+" "+jds.getSequenceAsString());
954 // System.err.println("Hashcode: "+seqHash(jds));
955 // SequenceI rsq = (SequenceI) seqRefIds.get(id + "");
956 // System.err.println(rsq.getName()+"
957 // "+rsq.getStart()+"-"+rsq.getEnd()+" "+rsq.getSequenceAsString());
958 // System.err.println("Hashcode: "+seqHash(rsq));
962 vamsasSeq = createVamsasSequence(id, jds);
963 // vamsasSet.addSequence(vamsasSeq);
964 vamsasSet.getSequence().add(vamsasSeq);
965 vamsasSetIds.put(id, vamsasSeq);
966 seqRefIds.put(id, jds);
970 jseq.setStart(jds.getStart());
971 jseq.setEnd(jds.getEnd());
972 jseq.setColour(av.getSequenceColour(jds).getRGB());
974 jseq.setId(id); // jseq id should be a string not a number
977 // Store any sequences this sequence represents
978 if (av.hasHiddenRows())
980 // use rjal, contains the full height alignment
982 av.getAlignment().getHiddenSequences().isHidden(jds));
984 if (av.isHiddenRepSequence(jds))
986 jalview.datamodel.SequenceI[] reps = av
987 .getRepresentedSequences(jds).getSequencesInOrder(rjal);
989 for (int h = 0; h < reps.length; h++)
993 // jseq.addHiddenSequences(rjal.findIndex(reps[h]));
994 jseq.getHiddenSequences().add(rjal.findIndex(reps[h]));
999 // mark sequence as reference - if it is the reference for this view
1000 if (jal.hasSeqrep())
1002 jseq.setViewreference(jds == jal.getSeqrep());
1006 // TODO: omit sequence features from each alignment view's XML dump if we
1007 // are storing dataset
1008 List<SequenceFeature> sfs = jds.getSequenceFeatures();
1009 for (SequenceFeature sf : sfs)
1011 // Features features = new Features();
1012 Feature features = new Feature();
1014 features.setBegin(sf.getBegin());
1015 features.setEnd(sf.getEnd());
1016 features.setDescription(sf.getDescription());
1017 features.setType(sf.getType());
1018 features.setFeatureGroup(sf.getFeatureGroup());
1019 features.setScore(sf.getScore());
1020 if (sf.links != null)
1022 for (int l = 0; l < sf.links.size(); l++)
1024 OtherData keyValue = new OtherData();
1025 keyValue.setKey("LINK_" + l);
1026 keyValue.setValue(sf.links.elementAt(l).toString());
1027 // features.addOtherData(keyValue);
1028 features.getOtherData().add(keyValue);
1031 if (sf.otherDetails != null)
1034 * save feature attributes, which may be simple strings or
1035 * map valued (have sub-attributes)
1037 for (Entry<String, Object> entry : sf.otherDetails.entrySet())
1039 String key = entry.getKey();
1040 Object value = entry.getValue();
1041 if (value instanceof Map<?, ?>)
1043 for (Entry<String, Object> subAttribute : ((Map<String, Object>) value)
1046 OtherData otherData = new OtherData();
1047 otherData.setKey(key);
1048 otherData.setKey2(subAttribute.getKey());
1049 otherData.setValue(subAttribute.getValue().toString());
1050 // features.addOtherData(otherData);
1051 features.getOtherData().add(otherData);
1056 OtherData otherData = new OtherData();
1057 otherData.setKey(key);
1058 otherData.setValue(value.toString());
1059 // features.addOtherData(otherData);
1060 features.getOtherData().add(otherData);
1065 // jseq.addFeatures(features);
1066 jseq.getFeatures().add(features);
1069 if (jdatasq.getAllPDBEntries() != null)
1071 Enumeration<PDBEntry> en = jdatasq.getAllPDBEntries().elements();
1072 while (en.hasMoreElements())
1074 Pdbids pdb = new Pdbids();
1075 jalview.datamodel.PDBEntry entry = en.nextElement();
1077 String pdbId = entry.getId();
1079 pdb.setType(entry.getType());
1082 * Store any structure views associated with this sequence. This
1083 * section copes with duplicate entries in the project, so a dataset
1084 * only view *should* be coped with sensibly.
1086 // This must have been loaded, is it still visible?
1087 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1088 String matchedFile = null;
1089 for (int f = frames.length - 1; f > -1; f--)
1091 if (frames[f] instanceof StructureViewerBase)
1093 StructureViewerBase viewFrame = (StructureViewerBase) frames[f];
1094 matchedFile = saveStructureViewer(ap, jds, pdb, entry,
1095 viewIds, matchedFile, viewFrame);
1097 * Only store each structure viewer's state once in the project
1098 * jar. First time through only (storeDS==false)
1100 String viewId = viewFrame.getViewId();
1101 String viewerType = viewFrame.getViewerType().toString();
1102 if (!storeDS && !viewIds.contains(viewId))
1104 viewIds.add(viewId);
1105 File viewerState = viewFrame.saveSession();
1106 if (viewerState != null)
1108 copyFileToJar(jout, viewerState.getPath(),
1109 getViewerJarEntryName(viewId), viewerType);
1114 "Failed to save viewer state for " + viewerType);
1120 if (matchedFile != null || entry.getFile() != null)
1122 if (entry.getFile() != null)
1125 matchedFile = entry.getFile();
1127 pdb.setFile(matchedFile); // entry.getFile());
1128 if (pdbfiles == null)
1130 pdbfiles = new ArrayList<>();
1133 if (!pdbfiles.contains(pdbId))
1135 pdbfiles.add(pdbId);
1136 copyFileToJar(jout, matchedFile, pdbId, pdbId);
1140 Enumeration<String> props = entry.getProperties();
1141 if (props.hasMoreElements())
1143 // PdbentryItem item = new PdbentryItem();
1144 while (props.hasMoreElements())
1146 Property prop = new Property();
1147 String key = props.nextElement();
1149 prop.setValue(entry.getProperty(key).toString());
1150 // item.addProperty(prop);
1151 pdb.getProperty().add(prop);
1153 // pdb.addPdbentryItem(item);
1156 // jseq.addPdbids(pdb);
1157 jseq.getPdbids().add(pdb);
1161 saveRnaViewers(jout, jseq, jds, viewIds, ap, storeDS);
1163 // jms.addJSeq(jseq);
1164 object.getJSeq().add(jseq);
1167 if (!storeDS && av.hasHiddenRows())
1169 jal = av.getAlignment();
1173 if (storeDS && jal.getCodonFrames() != null)
1175 List<AlignedCodonFrame> jac = jal.getCodonFrames();
1176 for (AlignedCodonFrame acf : jac)
1178 AlcodonFrame alc = new AlcodonFrame();
1179 if (acf.getProtMappings() != null
1180 && acf.getProtMappings().length > 0)
1182 boolean hasMap = false;
1183 SequenceI[] dnas = acf.getdnaSeqs();
1184 jalview.datamodel.Mapping[] pmaps = acf.getProtMappings();
1185 for (int m = 0; m < pmaps.length; m++)
1187 AlcodMap alcmap = new AlcodMap();
1188 alcmap.setDnasq(seqHash(dnas[m]));
1190 createVamsasMapping(pmaps[m], dnas[m], null, false));
1191 // alc.addAlcodMap(alcmap);
1192 alc.getAlcodMap().add(alcmap);
1197 // vamsasSet.addAlcodonFrame(alc);
1198 vamsasSet.getAlcodonFrame().add(alc);
1201 // TODO: delete this ? dead code from 2.8.3->2.9 ?
1203 // AlcodonFrame alc = new AlcodonFrame();
1204 // vamsasSet.addAlcodonFrame(alc);
1205 // for (int p = 0; p < acf.aaWidth; p++)
1207 // Alcodon cmap = new Alcodon();
1208 // if (acf.codons[p] != null)
1210 // // Null codons indicate a gapped column in the translated peptide
1212 // cmap.setPos1(acf.codons[p][0]);
1213 // cmap.setPos2(acf.codons[p][1]);
1214 // cmap.setPos3(acf.codons[p][2]);
1216 // alc.addAlcodon(cmap);
1218 // if (acf.getProtMappings() != null
1219 // && acf.getProtMappings().length > 0)
1221 // SequenceI[] dnas = acf.getdnaSeqs();
1222 // jalview.datamodel.Mapping[] pmaps = acf.getProtMappings();
1223 // for (int m = 0; m < pmaps.length; m++)
1225 // AlcodMap alcmap = new AlcodMap();
1226 // alcmap.setDnasq(seqHash(dnas[m]));
1227 // alcmap.setMapping(createVamsasMapping(pmaps[m], dnas[m], null,
1229 // alc.addAlcodMap(alcmap);
1236 // /////////////////////////////////
1237 if (!storeDS && av.getCurrentTree() != null)
1239 // FIND ANY ASSOCIATED TREES
1240 // NOT IMPLEMENTED FOR HEADLESS STATE AT PRESENT
1241 if (Desktop.desktop != null)
1243 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1245 for (int t = 0; t < frames.length; t++)
1247 if (frames[t] instanceof TreePanel)
1249 TreePanel tp = (TreePanel) frames[t];
1251 if (tp.getTreeCanvas().getViewport().getAlignment() == jal)
1253 JalviewModel.Tree tree = new JalviewModel.Tree();
1254 tree.setTitle(tp.getTitle());
1255 tree.setCurrentTree((av.getCurrentTree() == tp.getTree()));
1256 tree.setNewick(tp.getTree().print());
1257 tree.setThreshold(tp.getTreeCanvas().getThreshold());
1259 tree.setFitToWindow(tp.fitToWindow.getState());
1260 tree.setFontName(tp.getTreeFont().getName());
1261 tree.setFontSize(tp.getTreeFont().getSize());
1262 tree.setFontStyle(tp.getTreeFont().getStyle());
1263 tree.setMarkUnlinked(tp.placeholdersMenu.getState());
1265 tree.setShowBootstrap(tp.bootstrapMenu.getState());
1266 tree.setShowDistances(tp.distanceMenu.getState());
1268 tree.setHeight(tp.getHeight());
1269 tree.setWidth(tp.getWidth());
1270 tree.setXpos(tp.getX());
1271 tree.setYpos(tp.getY());
1272 tree.setId(makeHashCode(tp, null));
1273 tree.setLinkToAllViews(
1274 tp.getTreeCanvas().isApplyToAllViews());
1276 // jms.addTree(tree);
1277 object.getTree().add(tree);
1287 if (!storeDS && Desktop.desktop != null)
1289 for (JInternalFrame frame : Desktop.desktop.getAllFrames())
1291 if (frame instanceof PCAPanel)
1293 PCAPanel panel = (PCAPanel) frame;
1294 if (panel.getAlignViewport().getAlignment() == jal)
1296 savePCA(panel, object);
1304 * store forward refs from an annotationRow to any groups
1306 IdentityHashMap<SequenceGroup, String> groupRefs = new IdentityHashMap<>();
1309 for (SequenceI sq : jal.getSequences())
1311 // Store annotation on dataset sequences only
1312 AlignmentAnnotation[] aa = sq.getAnnotation();
1313 if (aa != null && aa.length > 0)
1315 storeAlignmentAnnotation(aa, groupRefs, av, calcIdSet, storeDS,
1322 if (jal.getAlignmentAnnotation() != null)
1324 // Store the annotation shown on the alignment.
1325 AlignmentAnnotation[] aa = jal.getAlignmentAnnotation();
1326 storeAlignmentAnnotation(aa, groupRefs, av, calcIdSet, storeDS,
1331 if (jal.getGroups() != null)
1333 JGroup[] groups = new JGroup[jal.getGroups().size()];
1335 for (jalview.datamodel.SequenceGroup sg : jal.getGroups())
1337 JGroup jGroup = new JGroup();
1338 groups[++i] = jGroup;
1340 jGroup.setStart(sg.getStartRes());
1341 jGroup.setEnd(sg.getEndRes());
1342 jGroup.setName(sg.getName());
1343 if (groupRefs.containsKey(sg))
1345 // group has references so set its ID field
1346 jGroup.setId(groupRefs.get(sg));
1348 ColourSchemeI colourScheme = sg.getColourScheme();
1349 if (colourScheme != null)
1351 ResidueShaderI groupColourScheme = sg.getGroupColourScheme();
1352 if (groupColourScheme.conservationApplied())
1354 jGroup.setConsThreshold(groupColourScheme.getConservationInc());
1356 if (colourScheme instanceof jalview.schemes.UserColourScheme)
1358 jGroup.setColour(setUserColourScheme(colourScheme,
1359 userColours, object));
1363 jGroup.setColour(colourScheme.getSchemeName());
1366 else if (colourScheme instanceof jalview.schemes.AnnotationColourGradient)
1368 jGroup.setColour("AnnotationColourGradient");
1369 jGroup.setAnnotationColours(constructAnnotationColours(
1370 (jalview.schemes.AnnotationColourGradient) colourScheme,
1371 userColours, object));
1373 else if (colourScheme instanceof jalview.schemes.UserColourScheme)
1376 setUserColourScheme(colourScheme, userColours, object));
1380 jGroup.setColour(colourScheme.getSchemeName());
1383 jGroup.setPidThreshold(groupColourScheme.getThreshold());
1386 jGroup.setOutlineColour(sg.getOutlineColour().getRGB());
1387 jGroup.setDisplayBoxes(sg.getDisplayBoxes());
1388 jGroup.setDisplayText(sg.getDisplayText());
1389 jGroup.setColourText(sg.getColourText());
1390 jGroup.setTextCol1(sg.textColour.getRGB());
1391 jGroup.setTextCol2(sg.textColour2.getRGB());
1392 jGroup.setTextColThreshold(sg.thresholdTextColour);
1393 jGroup.setShowUnconserved(sg.getShowNonconserved());
1394 jGroup.setIgnoreGapsinConsensus(sg.getIgnoreGapsConsensus());
1395 jGroup.setShowConsensusHistogram(sg.isShowConsensusHistogram());
1396 jGroup.setShowSequenceLogo(sg.isShowSequenceLogo());
1397 jGroup.setNormaliseSequenceLogo(sg.isNormaliseSequenceLogo());
1398 for (SequenceI seq : sg.getSequences())
1400 // jGroup.addSeq(seqHash(seq));
1401 jGroup.getSeq().add(seqHash(seq));
1405 // jms.setJGroup(groups);
1407 for (JGroup grp : groups)
1409 object.getJGroup().add(grp);
1414 // /////////SAVE VIEWPORT
1415 Viewport view = new Viewport();
1416 view.setTitle(ap.alignFrame.getTitle());
1417 view.setSequenceSetId(
1418 makeHashCode(av.getSequenceSetId(), av.getSequenceSetId()));
1419 view.setId(av.getViewId());
1420 if (av.getCodingComplement() != null)
1422 view.setComplementId(av.getCodingComplement().getViewId());
1424 view.setViewName(av.getViewName());
1425 view.setGatheredViews(av.isGatherViewsHere());
1427 Rectangle size = ap.av.getExplodedGeometry();
1428 Rectangle position = size;
1431 size = ap.alignFrame.getBounds();
1432 if (av.getCodingComplement() != null)
1434 position = ((SplitFrame) ap.alignFrame.getSplitViewContainer())
1442 view.setXpos(position.x);
1443 view.setYpos(position.y);
1445 view.setWidth(size.width);
1446 view.setHeight(size.height);
1448 view.setStartRes(vpRanges.getStartRes());
1449 view.setStartSeq(vpRanges.getStartSeq());
1451 if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme)
1453 view.setBgColour(setUserColourScheme(av.getGlobalColourScheme(),
1454 userColours, object));
1457 .getGlobalColourScheme() instanceof jalview.schemes.AnnotationColourGradient)
1459 AnnotationColourScheme ac = constructAnnotationColours(
1460 (jalview.schemes.AnnotationColourGradient) av
1461 .getGlobalColourScheme(),
1462 userColours, object);
1464 view.setAnnotationColours(ac);
1465 view.setBgColour("AnnotationColourGradient");
1469 view.setBgColour(ColourSchemeProperty
1470 .getColourName(av.getGlobalColourScheme()));
1473 ResidueShaderI vcs = av.getResidueShading();
1474 ColourSchemeI cs = av.getGlobalColourScheme();
1478 if (vcs.conservationApplied())
1480 view.setConsThreshold(vcs.getConservationInc());
1481 if (cs instanceof jalview.schemes.UserColourScheme)
1483 view.setBgColour(setUserColourScheme(cs, userColours, object));
1486 view.setPidThreshold(vcs.getThreshold());
1489 view.setConservationSelected(av.getConservationSelected());
1490 view.setPidSelected(av.getAbovePIDThreshold());
1491 final Font font = av.getFont();
1492 view.setFontName(font.getName());
1493 view.setFontSize(font.getSize());
1494 view.setFontStyle(font.getStyle());
1495 view.setScaleProteinAsCdna(av.getViewStyle().isScaleProteinAsCdna());
1496 view.setRenderGaps(av.isRenderGaps());
1497 view.setShowAnnotation(av.isShowAnnotation());
1498 view.setShowBoxes(av.getShowBoxes());
1499 view.setShowColourText(av.getColourText());
1500 view.setShowFullId(av.getShowJVSuffix());
1501 view.setRightAlignIds(av.isRightAlignIds());
1502 view.setShowSequenceFeatures(av.isShowSequenceFeatures());
1503 view.setShowText(av.getShowText());
1504 view.setShowUnconserved(av.getShowUnconserved());
1505 view.setWrapAlignment(av.getWrapAlignment());
1506 view.setTextCol1(av.getTextColour().getRGB());
1507 view.setTextCol2(av.getTextColour2().getRGB());
1508 view.setTextColThreshold(av.getThresholdTextColour());
1509 view.setShowConsensusHistogram(av.isShowConsensusHistogram());
1510 view.setShowSequenceLogo(av.isShowSequenceLogo());
1511 view.setNormaliseSequenceLogo(av.isNormaliseSequenceLogo());
1512 view.setShowGroupConsensus(av.isShowGroupConsensus());
1513 view.setShowGroupConservation(av.isShowGroupConservation());
1514 view.setShowNPfeatureTooltip(av.isShowNPFeats());
1515 view.setShowDbRefTooltip(av.isShowDBRefs());
1516 view.setFollowHighlight(av.isFollowHighlight());
1517 view.setFollowSelection(av.followSelection);
1518 view.setIgnoreGapsinConsensus(av.isIgnoreGapsConsensus());
1519 view.setShowComplementFeatures(av.isShowComplementFeatures());
1520 view.setShowComplementFeaturesOnTop(
1521 av.isShowComplementFeaturesOnTop());
1522 if (av.getFeaturesDisplayed() != null)
1524 FeatureSettings fs = new FeatureSettings();
1526 FeatureRendererModel fr = ap.getSeqPanel().seqCanvas
1527 .getFeatureRenderer();
1528 String[] renderOrder = fr.getRenderOrder().toArray(new String[0]);
1530 Vector<String> settingsAdded = new Vector<>();
1531 if (renderOrder != null)
1533 for (String featureType : renderOrder)
1535 FeatureSettings.Setting setting = new FeatureSettings.Setting();
1536 setting.setType(featureType);
1539 * save any filter for the feature type
1541 FeatureMatcherSetI filter = fr.getFeatureFilter(featureType);
1544 Iterator<FeatureMatcherI> filters = filter.getMatchers()
1546 FeatureMatcherI firstFilter = filters.next();
1547 setting.setMatcherSet(Jalview2XML.marshalFilter(firstFilter,
1548 filters, filter.isAnded()));
1552 * save colour scheme for the feature type
1554 FeatureColourI fcol = fr.getFeatureStyle(featureType);
1555 if (!fcol.isSimpleColour())
1557 setting.setColour(fcol.getMaxColour().getRGB());
1558 setting.setMincolour(fcol.getMinColour().getRGB());
1559 setting.setMin(fcol.getMin());
1560 setting.setMax(fcol.getMax());
1561 setting.setColourByLabel(fcol.isColourByLabel());
1562 if (fcol.isColourByAttribute())
1564 String[] attName = fcol.getAttributeName();
1565 setting.getAttributeName().add(attName[0]);
1566 if (attName.length > 1)
1568 setting.getAttributeName().add(attName[1]);
1571 setting.setAutoScale(fcol.isAutoScaled());
1572 setting.setThreshold(fcol.getThreshold());
1573 Color noColour = fcol.getNoColour();
1574 if (noColour == null)
1576 setting.setNoValueColour(NoValueColour.NONE);
1578 else if (noColour.equals(fcol.getMaxColour()))
1580 setting.setNoValueColour(NoValueColour.MAX);
1584 setting.setNoValueColour(NoValueColour.MIN);
1586 // -1 = No threshold, 0 = Below, 1 = Above
1587 setting.setThreshstate(fcol.isAboveThreshold() ? 1
1588 : (fcol.isBelowThreshold() ? 0 : -1));
1592 setting.setColour(fcol.getColour().getRGB());
1596 av.getFeaturesDisplayed().isVisible(featureType));
1597 float rorder = fr.getOrder(featureType);
1600 setting.setOrder(rorder);
1602 /// fs.addSetting(setting);
1603 fs.getSetting().add(setting);
1604 settingsAdded.addElement(featureType);
1608 // is groups actually supposed to be a map here ?
1609 Iterator<String> en = fr.getFeatureGroups().iterator();
1610 Vector<String> groupsAdded = new Vector<>();
1611 while (en.hasNext())
1613 String grp = en.next();
1614 if (groupsAdded.contains(grp))
1618 Group g = new Group();
1620 g.setDisplay(((Boolean) fr.checkGroupVisibility(grp, false))
1623 fs.getGroup().add(g);
1624 groupsAdded.addElement(grp);
1626 // jms.setFeatureSettings(fs);
1627 object.setFeatureSettings(fs);
1630 if (av.hasHiddenColumns())
1632 jalview.datamodel.HiddenColumns hidden = av.getAlignment()
1633 .getHiddenColumns();
1636 warn("REPORT BUG: avoided null columnselection bug (DMAM reported). Please contact Jim about this.");
1640 Iterator<int[]> hiddenRegions = hidden.iterator();
1641 while (hiddenRegions.hasNext())
1643 int[] region = hiddenRegions.next();
1644 HiddenColumns hc = new HiddenColumns();
1645 hc.setStart(region[0]);
1646 hc.setEnd(region[1]);
1647 // view.addHiddenColumns(hc);
1648 view.getHiddenColumns().add(hc);
1652 if (calcIdSet.size() > 0)
1654 for (String calcId : calcIdSet)
1656 if (calcId.trim().length() > 0)
1658 CalcIdParam cidp = createCalcIdParam(calcId, av);
1659 // Some calcIds have no parameters.
1662 // view.addCalcIdParam(cidp);
1663 view.getCalcIdParam().add(cidp);
1669 // jms.addViewport(view);
1670 object.getViewport().add(view);
1672 // object.setJalviewModelSequence(jms);
1673 // object.getVamsasModel().addSequenceSet(vamsasSet);
1674 object.getVamsasModel().getSequenceSet().add(vamsasSet);
1676 if (jout != null && fileName != null)
1678 // We may not want to write the object to disk,
1679 // eg we can copy the alignViewport to a new view object
1680 // using save and then load
1683 fileName = fileName.replace('\\', '/');
1684 System.out.println("Writing jar entry " + fileName);
1685 JarEntry entry = new JarEntry(fileName);
1686 jout.putNextEntry(entry);
1687 PrintWriter pout = new PrintWriter(
1688 new OutputStreamWriter(jout, UTF_8));
1689 JAXBContext jaxbContext = JAXBContext
1690 .newInstance(JalviewModel.class);
1691 Marshaller jaxbMarshaller = jaxbContext.createMarshaller();
1693 // output pretty printed
1694 // jaxbMarshaller.setProperty(Marshaller.JAXB_FORMATTED_OUTPUT, true);
1695 jaxbMarshaller.marshal(
1696 new ObjectFactory().createJalviewModel(object), pout);
1698 // jaxbMarshaller.marshal(object, pout);
1699 // marshaller.marshal(object);
1702 } catch (Exception ex)
1704 // TODO: raise error in GUI if marshalling failed.
1705 System.err.println("Error writing Jalview project");
1706 ex.printStackTrace();
1713 * Writes PCA viewer attributes and computed values to an XML model object and
1714 * adds it to the JalviewModel. Any exceptions are reported by logging.
1716 protected void savePCA(PCAPanel panel, JalviewModel object)
1720 PcaViewer viewer = new PcaViewer();
1721 viewer.setHeight(panel.getHeight());
1722 viewer.setWidth(panel.getWidth());
1723 viewer.setXpos(panel.getX());
1724 viewer.setYpos(panel.getY());
1725 viewer.setTitle(panel.getTitle());
1726 PCAModel pcaModel = panel.getPcaModel();
1727 viewer.setScoreModelName(pcaModel.getScoreModelName());
1728 viewer.setXDim(panel.getSelectedDimensionIndex(X));
1729 viewer.setYDim(panel.getSelectedDimensionIndex(Y));
1730 viewer.setZDim(panel.getSelectedDimensionIndex(Z));
1732 panel.getRotatableCanvas().getBackgroundColour().getRGB());
1733 viewer.setScaleFactor(panel.getRotatableCanvas().getScaleFactor());
1734 float[] spMin = panel.getRotatableCanvas().getSeqMin();
1735 SeqPointMin spmin = new SeqPointMin();
1736 spmin.setXPos(spMin[0]);
1737 spmin.setYPos(spMin[1]);
1738 spmin.setZPos(spMin[2]);
1739 viewer.setSeqPointMin(spmin);
1740 float[] spMax = panel.getRotatableCanvas().getSeqMax();
1741 SeqPointMax spmax = new SeqPointMax();
1742 spmax.setXPos(spMax[0]);
1743 spmax.setYPos(spMax[1]);
1744 spmax.setZPos(spMax[2]);
1745 viewer.setSeqPointMax(spmax);
1746 viewer.setShowLabels(panel.getRotatableCanvas().isShowLabels());
1747 viewer.setLinkToAllViews(
1748 panel.getRotatableCanvas().isApplyToAllViews());
1749 SimilarityParamsI sp = pcaModel.getSimilarityParameters();
1750 viewer.setIncludeGaps(sp.includeGaps());
1751 viewer.setMatchGaps(sp.matchGaps());
1752 viewer.setIncludeGappedColumns(sp.includeGappedColumns());
1753 viewer.setDenominateByShortestLength(sp.denominateByShortestLength());
1756 * sequence points on display
1758 for (jalview.datamodel.SequencePoint spt : pcaModel
1759 .getSequencePoints())
1761 SequencePoint point = new SequencePoint();
1762 point.setSequenceRef(seqHash(spt.getSequence()));
1763 point.setXPos(spt.coord.x);
1764 point.setYPos(spt.coord.y);
1765 point.setZPos(spt.coord.z);
1766 viewer.getSequencePoint().add(point);
1770 * (end points of) axes on display
1772 for (Point p : panel.getRotatableCanvas().getAxisEndPoints())
1775 Axis axis = new Axis();
1779 viewer.getAxis().add(axis);
1783 * raw PCA data (note we are not restoring PCA inputs here -
1784 * alignment view, score model, similarity parameters)
1786 PcaDataType data = new PcaDataType();
1787 viewer.setPcaData(data);
1788 PCA pca = pcaModel.getPcaData();
1790 DoubleMatrix pm = new DoubleMatrix();
1791 saveDoubleMatrix(pca.getPairwiseScores(), pm);
1792 data.setPairwiseMatrix(pm);
1794 DoubleMatrix tm = new DoubleMatrix();
1795 saveDoubleMatrix(pca.getTridiagonal(), tm);
1796 data.setTridiagonalMatrix(tm);
1798 DoubleMatrix eigenMatrix = new DoubleMatrix();
1799 data.setEigenMatrix(eigenMatrix);
1800 saveDoubleMatrix(pca.getEigenmatrix(), eigenMatrix);
1802 object.getPcaViewer().add(viewer);
1803 } catch (Throwable t)
1805 Cache.log.error("Error saving PCA: " + t.getMessage());
1810 * Stores values from a matrix into an XML element, including (if present) the
1815 * @see #loadDoubleMatrix(DoubleMatrix)
1817 protected void saveDoubleMatrix(MatrixI m, DoubleMatrix xmlMatrix)
1819 xmlMatrix.setRows(m.height());
1820 xmlMatrix.setColumns(m.width());
1821 for (int i = 0; i < m.height(); i++)
1823 DoubleVector row = new DoubleVector();
1824 for (int j = 0; j < m.width(); j++)
1826 row.getV().add(m.getValue(i, j));
1828 xmlMatrix.getRow().add(row);
1830 if (m.getD() != null)
1832 DoubleVector dVector = new DoubleVector();
1833 for (double d : m.getD())
1835 dVector.getV().add(d);
1837 xmlMatrix.setD(dVector);
1839 if (m.getE() != null)
1841 DoubleVector eVector = new DoubleVector();
1842 for (double e : m.getE())
1844 eVector.getV().add(e);
1846 xmlMatrix.setE(eVector);
1851 * Loads XML matrix data into a new Matrix object, including the D and/or E
1852 * vectors (if present)
1856 * @see Jalview2XML#saveDoubleMatrix(MatrixI, DoubleMatrix)
1858 protected MatrixI loadDoubleMatrix(DoubleMatrix mData)
1860 int rows = mData.getRows();
1861 double[][] vals = new double[rows][];
1863 for (int i = 0; i < rows; i++)
1865 List<Double> dVector = mData.getRow().get(i).getV();
1866 vals[i] = new double[dVector.size()];
1868 for (Double d : dVector)
1874 MatrixI m = new Matrix(vals);
1876 if (mData.getD() != null)
1878 List<Double> dVector = mData.getD().getV();
1879 double[] vec = new double[dVector.size()];
1881 for (Double d : dVector)
1887 if (mData.getE() != null)
1889 List<Double> dVector = mData.getE().getV();
1890 double[] vec = new double[dVector.size()];
1892 for (Double d : dVector)
1903 * Save any Varna viewers linked to this sequence. Writes an rnaViewer element
1904 * for each viewer, with
1906 * <li>viewer geometry (position, size, split pane divider location)</li>
1907 * <li>index of the selected structure in the viewer (currently shows gapped
1909 * <li>the id of the annotation holding RNA secondary structure</li>
1910 * <li>(currently only one SS is shown per viewer, may be more in future)</li>
1912 * Varna viewer state is also written out (in native Varna XML) to separate
1913 * project jar entries. A separate entry is written for each RNA structure
1914 * displayed, with the naming convention
1916 * <li>rna_viewId_sequenceId_annotationId_[gapped|trimmed]</li>
1924 * @param storeDataset
1926 protected void saveRnaViewers(JarOutputStream jout, JSeq jseq,
1927 final SequenceI jds, List<String> viewIds, AlignmentPanel ap,
1928 boolean storeDataset)
1930 if (Desktop.desktop == null)
1934 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1935 for (int f = frames.length - 1; f > -1; f--)
1937 if (frames[f] instanceof AppVarna)
1939 AppVarna varna = (AppVarna) frames[f];
1941 * link the sequence to every viewer that is showing it and is linked to
1942 * its alignment panel
1944 if (varna.isListeningFor(jds) && ap == varna.getAlignmentPanel())
1946 String viewId = varna.getViewId();
1947 RnaViewer rna = new RnaViewer();
1948 rna.setViewId(viewId);
1949 rna.setTitle(varna.getTitle());
1950 rna.setXpos(varna.getX());
1951 rna.setYpos(varna.getY());
1952 rna.setWidth(varna.getWidth());
1953 rna.setHeight(varna.getHeight());
1954 rna.setDividerLocation(varna.getDividerLocation());
1955 rna.setSelectedRna(varna.getSelectedIndex());
1956 // jseq.addRnaViewer(rna);
1957 jseq.getRnaViewer().add(rna);
1960 * Store each Varna panel's state once in the project per sequence.
1961 * First time through only (storeDataset==false)
1963 // boolean storeSessions = false;
1964 // String sequenceViewId = viewId + seqsToIds.get(jds);
1965 // if (!storeDataset && !viewIds.contains(sequenceViewId))
1967 // viewIds.add(sequenceViewId);
1968 // storeSessions = true;
1970 for (RnaModel model : varna.getModels())
1972 if (model.seq == jds)
1975 * VARNA saves each view (sequence or alignment secondary
1976 * structure, gapped or trimmed) as a separate XML file
1978 String jarEntryName = rnaSessions.get(model);
1979 if (jarEntryName == null)
1982 String varnaStateFile = varna.getStateInfo(model.rna);
1983 jarEntryName = RNA_PREFIX + viewId + "_" + nextCounter();
1984 copyFileToJar(jout, varnaStateFile, jarEntryName, "Varna");
1985 rnaSessions.put(model, jarEntryName);
1987 SecondaryStructure ss = new SecondaryStructure();
1988 String annotationId = varna.getAnnotation(jds).annotationId;
1989 ss.setAnnotationId(annotationId);
1990 ss.setViewerState(jarEntryName);
1991 ss.setGapped(model.gapped);
1992 ss.setTitle(model.title);
1993 // rna.addSecondaryStructure(ss);
1994 rna.getSecondaryStructure().add(ss);
2003 * Copy the contents of a file to a new entry added to the output jar
2007 * @param jarEntryName
2009 * additional identifying info to log to the console
2011 protected void copyFileToJar(JarOutputStream jout, String infilePath,
2012 String jarEntryName, String msg)
2014 try (InputStream is = new FileInputStream(infilePath))
2016 File file = new File(infilePath);
2017 if (file.exists() && jout != null)
2020 "Writing jar entry " + jarEntryName + " (" + msg + ")");
2021 jout.putNextEntry(new JarEntry(jarEntryName));
2024 // dis = new DataInputStream(new FileInputStream(file));
2025 // byte[] data = new byte[(int) file.length()];
2026 // dis.readFully(data);
2027 // writeJarEntry(jout, jarEntryName, data);
2029 } catch (Exception ex)
2031 ex.printStackTrace();
2036 * Copies input to output, in 4K buffers; handles any data (text or binary)
2040 * @throws IOException
2042 protected void copyAll(InputStream in, OutputStream out)
2045 byte[] buffer = new byte[4096];
2047 while ((bytesRead = in.read(buffer)) != -1)
2049 out.write(buffer, 0, bytesRead);
2054 * Save the state of a structure viewer
2059 * the archive XML element under which to save the state
2062 * @param matchedFile
2066 protected String saveStructureViewer(AlignmentPanel ap, SequenceI jds,
2067 Pdbids pdb, PDBEntry entry, List<String> viewIds,
2068 String matchedFile, StructureViewerBase viewFrame)
2070 final AAStructureBindingModel bindingModel = viewFrame.getBinding();
2073 * Look for any bindings for this viewer to the PDB file of interest
2074 * (including part matches excluding chain id)
2076 for (int peid = 0; peid < bindingModel.getPdbCount(); peid++)
2078 final PDBEntry pdbentry = bindingModel.getPdbEntry(peid);
2079 final String pdbId = pdbentry.getId();
2080 if (!pdbId.equals(entry.getId())
2081 && !(entry.getId().length() > 4 && entry.getId().toLowerCase(Locale.ROOT)
2082 .startsWith(pdbId.toLowerCase(Locale.ROOT))))
2085 * not interested in a binding to a different PDB entry here
2089 if (matchedFile == null)
2091 matchedFile = pdbentry.getFile();
2093 else if (!matchedFile.equals(pdbentry.getFile()))
2096 "Probably lost some PDB-Sequence mappings for this structure file (which apparently has same PDB Entry code): "
2097 + pdbentry.getFile());
2101 // can get at it if the ID
2102 // match is ambiguous (e.g.
2105 for (int smap = 0; smap < viewFrame.getBinding()
2106 .getSequence()[peid].length; smap++)
2108 // if (jal.findIndex(jmol.jmb.sequence[peid][smap]) > -1)
2109 if (jds == viewFrame.getBinding().getSequence()[peid][smap])
2111 StructureState state = new StructureState();
2112 state.setVisible(true);
2113 state.setXpos(viewFrame.getX());
2114 state.setYpos(viewFrame.getY());
2115 state.setWidth(viewFrame.getWidth());
2116 state.setHeight(viewFrame.getHeight());
2117 final String viewId = viewFrame.getViewId();
2118 state.setViewId(viewId);
2119 state.setAlignwithAlignPanel(viewFrame.isUsedforaligment(ap));
2120 state.setColourwithAlignPanel(viewFrame.isUsedForColourBy(ap));
2121 state.setColourByJmol(viewFrame.isColouredByViewer());
2122 state.setType(viewFrame.getViewerType().toString());
2123 // pdb.addStructureState(state);
2124 pdb.getStructureState().add(state);
2132 * Populates the AnnotationColourScheme xml for save. This captures the
2133 * settings of the options in the 'Colour by Annotation' dialog.
2136 * @param userColours
2140 private AnnotationColourScheme constructAnnotationColours(
2141 AnnotationColourGradient acg, List<UserColourScheme> userColours,
2144 AnnotationColourScheme ac = new AnnotationColourScheme();
2145 ac.setAboveThreshold(acg.getAboveThreshold());
2146 ac.setThreshold(acg.getAnnotationThreshold());
2147 // 2.10.2 save annotationId (unique) not annotation label
2148 ac.setAnnotation(acg.getAnnotation().annotationId);
2149 if (acg.getBaseColour() instanceof UserColourScheme)
2152 setUserColourScheme(acg.getBaseColour(), userColours, jm));
2157 ColourSchemeProperty.getColourName(acg.getBaseColour()));
2160 ac.setMaxColour(acg.getMaxColour().getRGB());
2161 ac.setMinColour(acg.getMinColour().getRGB());
2162 ac.setPerSequence(acg.isSeqAssociated());
2163 ac.setPredefinedColours(acg.isPredefinedColours());
2167 private void storeAlignmentAnnotation(AlignmentAnnotation[] aa,
2168 IdentityHashMap<SequenceGroup, String> groupRefs,
2169 AlignmentViewport av, Set<String> calcIdSet, boolean storeDS,
2170 SequenceSet vamsasSet)
2173 for (int i = 0; i < aa.length; i++)
2175 Annotation an = new Annotation();
2177 AlignmentAnnotation annotation = aa[i];
2178 if (annotation.annotationId != null)
2180 annotationIds.put(annotation.annotationId, annotation);
2183 an.setId(annotation.annotationId);
2185 an.setVisible(annotation.visible);
2187 an.setDescription(annotation.description);
2189 if (annotation.sequenceRef != null)
2191 // 2.9 JAL-1781 xref on sequence id rather than name
2192 an.setSequenceRef(seqsToIds.get(annotation.sequenceRef));
2194 if (annotation.groupRef != null)
2196 String groupIdr = groupRefs.get(annotation.groupRef);
2197 if (groupIdr == null)
2199 // make a locally unique String
2200 groupRefs.put(annotation.groupRef,
2201 groupIdr = ("" + System.currentTimeMillis()
2202 + annotation.groupRef.getName()
2203 + groupRefs.size()));
2205 an.setGroupRef(groupIdr.toString());
2208 // store all visualization attributes for annotation
2209 an.setGraphHeight(annotation.graphHeight);
2210 an.setCentreColLabels(annotation.centreColLabels);
2211 an.setScaleColLabels(annotation.scaleColLabel);
2212 an.setShowAllColLabels(annotation.showAllColLabels);
2213 an.setBelowAlignment(annotation.belowAlignment);
2215 if (annotation.graph > 0)
2218 an.setGraphType(annotation.graph);
2219 an.setGraphGroup(annotation.graphGroup);
2220 if (annotation.getThreshold() != null)
2222 ThresholdLine line = new ThresholdLine();
2223 line.setLabel(annotation.getThreshold().label);
2224 line.setValue(annotation.getThreshold().value);
2225 line.setColour(annotation.getThreshold().colour.getRGB());
2226 an.setThresholdLine(line);
2234 an.setLabel(annotation.label);
2236 if (annotation == av.getAlignmentQualityAnnot()
2237 || annotation == av.getAlignmentConservationAnnotation()
2238 || annotation == av.getAlignmentConsensusAnnotation()
2239 || annotation.autoCalculated)
2241 // new way of indicating autocalculated annotation -
2242 an.setAutoCalculated(annotation.autoCalculated);
2244 if (annotation.hasScore())
2246 an.setScore(annotation.getScore());
2249 if (annotation.getCalcId() != null)
2251 calcIdSet.add(annotation.getCalcId());
2252 an.setCalcId(annotation.getCalcId());
2254 if (annotation.hasProperties())
2256 for (String pr : annotation.getProperties())
2258 jalview.xml.binding.jalview.Annotation.Property prop = new jalview.xml.binding.jalview.Annotation.Property();
2260 prop.setValue(annotation.getProperty(pr));
2261 // an.addProperty(prop);
2262 an.getProperty().add(prop);
2266 AnnotationElement ae;
2267 if (annotation.annotations != null)
2269 an.setScoreOnly(false);
2270 for (int a = 0; a < annotation.annotations.length; a++)
2272 if ((annotation == null) || (annotation.annotations[a] == null))
2277 ae = new AnnotationElement();
2278 if (annotation.annotations[a].description != null)
2280 ae.setDescription(annotation.annotations[a].description);
2282 if (annotation.annotations[a].displayCharacter != null)
2284 ae.setDisplayCharacter(
2285 annotation.annotations[a].displayCharacter);
2288 if (!Float.isNaN(annotation.annotations[a].value))
2290 ae.setValue(annotation.annotations[a].value);
2294 if (annotation.annotations[a].secondaryStructure > ' ')
2296 ae.setSecondaryStructure(
2297 annotation.annotations[a].secondaryStructure + "");
2300 if (annotation.annotations[a].colour != null
2301 && annotation.annotations[a].colour != java.awt.Color.black)
2303 ae.setColour(annotation.annotations[a].colour.getRGB());
2306 // an.addAnnotationElement(ae);
2307 an.getAnnotationElement().add(ae);
2308 if (annotation.autoCalculated)
2310 // only write one non-null entry into the annotation row -
2311 // sufficient to get the visualization attributes necessary to
2319 an.setScoreOnly(true);
2321 if (!storeDS || (storeDS && !annotation.autoCalculated))
2323 // skip autocalculated annotation - these are only provided for
2325 // vamsasSet.addAnnotation(an);
2326 vamsasSet.getAnnotation().add(an);
2332 private CalcIdParam createCalcIdParam(String calcId, AlignViewport av)
2334 AutoCalcSetting settings = av.getCalcIdSettingsFor(calcId);
2335 if (settings != null)
2337 CalcIdParam vCalcIdParam = new CalcIdParam();
2338 vCalcIdParam.setCalcId(calcId);
2339 // vCalcIdParam.addServiceURL(settings.getServiceURI());
2340 vCalcIdParam.getServiceURL().add(settings.getServiceURI());
2341 // generic URI allowing a third party to resolve another instance of the
2342 // service used for this calculation
2343 for (String url : settings.getServiceURLs())
2345 // vCalcIdParam.addServiceURL(urls);
2346 vCalcIdParam.getServiceURL().add(url);
2348 vCalcIdParam.setVersion("1.0");
2349 if (settings.getPreset() != null)
2351 WsParamSetI setting = settings.getPreset();
2352 vCalcIdParam.setName(setting.getName());
2353 vCalcIdParam.setDescription(setting.getDescription());
2357 vCalcIdParam.setName("");
2358 vCalcIdParam.setDescription("Last used parameters");
2360 // need to be able to recover 1) settings 2) user-defined presets or
2361 // recreate settings from preset 3) predefined settings provided by
2362 // service - or settings that can be transferred (or discarded)
2363 vCalcIdParam.setParameters(
2364 settings.getWsParamFile().replace("\n", "|\\n|"));
2365 vCalcIdParam.setAutoUpdate(settings.isAutoUpdate());
2366 // todo - decide if updateImmediately is needed for any projects.
2368 return vCalcIdParam;
2373 private boolean recoverCalcIdParam(CalcIdParam calcIdParam,
2376 if (calcIdParam.getVersion().equals("1.0"))
2378 final String[] calcIds = calcIdParam.getServiceURL()
2379 .toArray(new String[0]);
2380 Jws2Instance service = Jws2Discoverer.getDiscoverer()
2381 .getPreferredServiceFor(calcIds);
2382 if (service != null)
2384 WsParamSetI parmSet = null;
2387 parmSet = service.getParamStore().parseServiceParameterFile(
2388 calcIdParam.getName(), calcIdParam.getDescription(),
2390 calcIdParam.getParameters().replace("|\\n|", "\n"));
2391 } catch (IOException x)
2393 warn("Couldn't parse parameter data for "
2394 + calcIdParam.getCalcId(), x);
2397 List<ArgumentI> argList = null;
2398 if (calcIdParam.getName().length() > 0)
2400 parmSet = service.getParamStore()
2401 .getPreset(calcIdParam.getName());
2402 if (parmSet != null)
2404 // TODO : check we have a good match with settings in AACon -
2405 // otherwise we'll need to create a new preset
2410 argList = parmSet.getArguments();
2413 AAConSettings settings = new AAConSettings(
2414 calcIdParam.isAutoUpdate(), service, parmSet, argList);
2415 av.setCalcIdSettingsFor(calcIdParam.getCalcId(), settings,
2416 calcIdParam.isNeedsUpdate());
2421 warn("Cannot resolve a service for the parameters used in this project. Try configuring a JABAWS server.");
2425 throw new Error(MessageManager.formatMessage(
2426 "error.unsupported_version_calcIdparam", new Object[]
2427 { calcIdParam.toString() }));
2431 * External mapping between jalview objects and objects yielding a valid and
2432 * unique object ID string. This is null for normal Jalview project IO, but
2433 * non-null when a jalview project is being read or written as part of a
2436 IdentityHashMap jv2vobj = null;
2439 * Construct a unique ID for jvobj using either existing bindings or if none
2440 * exist, the result of the hashcode call for the object.
2443 * jalview data object
2444 * @return unique ID for referring to jvobj
2446 private String makeHashCode(Object jvobj, String altCode)
2448 if (jv2vobj != null)
2450 Object id = jv2vobj.get(jvobj);
2453 return id.toString();
2455 // check string ID mappings
2456 if (jvids2vobj != null && jvobj instanceof String)
2458 id = jvids2vobj.get(jvobj);
2462 return id.toString();
2464 // give up and warn that something has gone wrong
2465 warn("Cannot find ID for object in external mapping : " + jvobj);
2471 * return local jalview object mapped to ID, if it exists
2475 * @return null or object bound to idcode
2477 private Object retrieveExistingObj(String idcode)
2479 if (idcode != null && vobj2jv != null)
2481 return vobj2jv.get(idcode);
2487 * binding from ID strings from external mapping table to jalview data model
2490 private Hashtable vobj2jv;
2492 private Sequence createVamsasSequence(String id, SequenceI jds)
2494 return createVamsasSequence(true, id, jds, null);
2497 private Sequence createVamsasSequence(boolean recurse, String id,
2498 SequenceI jds, SequenceI parentseq)
2500 Sequence vamsasSeq = new Sequence();
2501 vamsasSeq.setId(id);
2502 vamsasSeq.setName(jds.getName());
2503 vamsasSeq.setSequence(jds.getSequenceAsString());
2504 vamsasSeq.setDescription(jds.getDescription());
2505 List<DBRefEntry> dbrefs = null;
2506 if (jds.getDatasetSequence() != null)
2508 vamsasSeq.setDsseqid(seqHash(jds.getDatasetSequence()));
2512 // seqId==dsseqid so we can tell which sequences really are
2513 // dataset sequences only
2514 vamsasSeq.setDsseqid(id);
2515 dbrefs = jds.getDBRefs();
2516 if (parentseq == null)
2523 * save any dbrefs; special subclass GeneLocus is flagged as 'locus'
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());
2534 dbref.setCanonical(ref.isCanonical());
2535 if (ref instanceof GeneLocus)
2537 dbref.setLocus(true);
2541 Mapping mp = createVamsasMapping(ref.getMap(), parentseq, jds,
2543 dbref.setMapping(mp);
2545 vamsasSeq.getDBRef().add(dbref);
2551 private Mapping createVamsasMapping(jalview.datamodel.Mapping jmp,
2552 SequenceI parentseq, SequenceI jds, boolean recurse)
2555 if (jmp.getMap() != null)
2559 jalview.util.MapList mlst = jmp.getMap();
2560 List<int[]> r = mlst.getFromRanges();
2561 for (int[] range : r)
2563 MapListFrom mfrom = new MapListFrom();
2564 mfrom.setStart(range[0]);
2565 mfrom.setEnd(range[1]);
2566 // mp.addMapListFrom(mfrom);
2567 mp.getMapListFrom().add(mfrom);
2569 r = mlst.getToRanges();
2570 for (int[] range : r)
2572 MapListTo mto = new MapListTo();
2573 mto.setStart(range[0]);
2574 mto.setEnd(range[1]);
2575 // mp.addMapListTo(mto);
2576 mp.getMapListTo().add(mto);
2578 mp.setMapFromUnit(BigInteger.valueOf(mlst.getFromRatio()));
2579 mp.setMapToUnit(BigInteger.valueOf(mlst.getToRatio()));
2580 if (jmp.getTo() != null)
2582 // MappingChoice mpc = new MappingChoice();
2584 // check/create ID for the sequence referenced by getTo()
2587 SequenceI ps = null;
2588 if (parentseq != jmp.getTo()
2589 && parentseq.getDatasetSequence() != jmp.getTo())
2591 // chaining dbref rather than a handshaking one
2592 jmpid = seqHash(ps = jmp.getTo());
2596 jmpid = seqHash(ps = parentseq);
2598 // mpc.setDseqFor(jmpid);
2599 mp.setDseqFor(jmpid);
2600 if (!seqRefIds.containsKey(jmpid))
2602 jalview.bin.Cache.log.debug("creatign new DseqFor ID");
2603 seqRefIds.put(jmpid, ps);
2607 jalview.bin.Cache.log.debug("reusing DseqFor ID");
2610 // mp.setMappingChoice(mpc);
2616 String setUserColourScheme(jalview.schemes.ColourSchemeI cs,
2617 List<UserColourScheme> userColours, JalviewModel jm)
2620 jalview.schemes.UserColourScheme ucs = (jalview.schemes.UserColourScheme) cs;
2621 boolean newucs = false;
2622 if (!userColours.contains(ucs))
2624 userColours.add(ucs);
2627 id = "ucs" + userColours.indexOf(ucs);
2630 // actually create the scheme's entry in the XML model
2631 java.awt.Color[] colours = ucs.getColours();
2632 UserColours uc = new UserColours();
2633 // UserColourScheme jbucs = new UserColourScheme();
2634 JalviewUserColours jbucs = new JalviewUserColours();
2636 for (int i = 0; i < colours.length; i++)
2638 Colour col = new Colour();
2639 col.setName(ResidueProperties.aa[i]);
2640 col.setRGB(jalview.util.Format.getHexString(colours[i]));
2641 // jbucs.addColour(col);
2642 jbucs.getColour().add(col);
2644 if (ucs.getLowerCaseColours() != null)
2646 colours = ucs.getLowerCaseColours();
2647 for (int i = 0; i < colours.length; i++)
2649 Colour col = new Colour();
2650 col.setName(ResidueProperties.aa[i].toLowerCase(Locale.ROOT));
2651 col.setRGB(jalview.util.Format.getHexString(colours[i]));
2652 // jbucs.addColour(col);
2653 jbucs.getColour().add(col);
2658 uc.setUserColourScheme(jbucs);
2659 // jm.addUserColours(uc);
2660 jm.getUserColours().add(uc);
2666 jalview.schemes.UserColourScheme getUserColourScheme(JalviewModel jm,
2669 List<UserColours> uc = jm.getUserColours();
2670 UserColours colours = null;
2672 for (int i = 0; i < uc.length; i++)
2674 if (uc[i].getId().equals(id))
2681 for (UserColours c : uc)
2683 if (c.getId().equals(id))
2690 java.awt.Color[] newColours = new java.awt.Color[24];
2692 for (int i = 0; i < 24; i++)
2694 newColours[i] = new java.awt.Color(Integer.parseInt(
2695 // colours.getUserColourScheme().getColour(i).getRGB(), 16));
2696 colours.getUserColourScheme().getColour().get(i).getRGB(),
2700 jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(
2703 if (colours.getUserColourScheme().getColour().size()/*Count()*/ > 24)
2705 newColours = new java.awt.Color[23];
2706 for (int i = 0; i < 23; i++)
2708 newColours[i] = new java.awt.Color(
2709 Integer.parseInt(colours.getUserColourScheme().getColour()
2710 .get(i + 24).getRGB(), 16));
2712 ucs.setLowerCaseColours(newColours);
2719 * contains last error message (if any) encountered by XML loader.
2721 String errorMessage = null;
2724 * flag to control whether the Jalview2XML_V1 parser should be deferred to if
2725 * exceptions are raised during project XML parsing
2727 public boolean attemptversion1parse = false;
2730 * Load a jalview project archive from a jar file
2733 * - HTTP URL or filename
2735 public AlignFrame loadJalviewAlign(final Object file)
2738 jalview.gui.AlignFrame af = null;
2742 // create list to store references for any new Jmol viewers created
2743 newStructureViewers = new Vector<>();
2744 // UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
2745 // Workaround is to make sure caller implements the JarInputStreamProvider
2747 // so we can re-open the jar input stream for each entry.
2749 jarInputStreamProvider jprovider = createjarInputStreamProvider(file);
2750 af = loadJalviewAlign(jprovider);
2753 af.setMenusForViewport();
2755 } catch (MalformedURLException e)
2757 errorMessage = "Invalid URL format for '" + file + "'";
2763 SwingUtilities.invokeAndWait(new Runnable()
2768 setLoadingFinishedForNewStructureViewers();
2771 } catch (Exception x)
2773 System.err.println("Error loading alignment: " + x.getMessage());
2779 @SuppressWarnings("unused")
2780 private jarInputStreamProvider createjarInputStreamProvider(
2781 final Object ofile) throws MalformedURLException
2784 // BH 2018 allow for bytes already attached to File object
2787 String file = (ofile instanceof File
2788 ? ((File) ofile).getCanonicalPath()
2789 : ofile.toString());
2790 byte[] bytes = Platform.isJS() ? Platform.getFileBytes((File) ofile)
2793 errorMessage = null;
2794 uniqueSetSuffix = null;
2796 viewportsAdded.clear();
2797 frefedSequence = null;
2799 if (HttpUtils.startsWithHttpOrHttps(file))
2801 url = new URL(file);
2803 final URL _url = url;
2804 return new jarInputStreamProvider()
2808 public JarInputStream getJarInputStream() throws IOException
2812 // System.out.println("Jalview2XML: opening byte jarInputStream for
2813 // bytes.length=" + bytes.length);
2814 return new JarInputStream(new ByteArrayInputStream(bytes));
2818 // System.out.println("Jalview2XML: opening url jarInputStream for "
2820 return new JarInputStream(_url.openStream());
2824 // System.out.println("Jalview2XML: opening file jarInputStream for
2826 return new JarInputStream(new FileInputStream(file));
2831 public String getFilename()
2836 } catch (IOException e)
2838 e.printStackTrace();
2844 * Recover jalview session from a jalview project archive. Caller may
2845 * initialise uniqueSetSuffix, seqRefIds, viewportsAdded and frefedSequence
2846 * themselves. Any null fields will be initialised with default values,
2847 * non-null fields are left alone.
2852 public AlignFrame loadJalviewAlign(final jarInputStreamProvider jprovider)
2854 errorMessage = null;
2855 if (uniqueSetSuffix == null)
2857 uniqueSetSuffix = System.currentTimeMillis() % 100000 + "";
2859 if (seqRefIds == null)
2863 AlignFrame af = null, _af = null;
2864 IdentityHashMap<AlignmentI, AlignmentI> importedDatasets = new IdentityHashMap<>();
2865 Map<String, AlignFrame> gatherToThisFrame = new HashMap<>();
2866 final String file = jprovider.getFilename();
2869 JarInputStream jin = null;
2870 JarEntry jarentry = null;
2875 jin = jprovider.getJarInputStream();
2876 for (int i = 0; i < entryCount; i++)
2878 jarentry = jin.getNextJarEntry();
2881 if (jarentry != null && jarentry.getName().endsWith(".xml"))
2883 JAXBContext jc = JAXBContext
2884 .newInstance("jalview.xml.binding.jalview");
2885 XMLStreamReader streamReader = XMLInputFactory.newInstance()
2886 .createXMLStreamReader(jin);
2887 javax.xml.bind.Unmarshaller um = jc.createUnmarshaller();
2888 JAXBElement<JalviewModel> jbe = um.unmarshal(streamReader,
2889 JalviewModel.class);
2890 JalviewModel object = jbe.getValue();
2892 if (true) // !skipViewport(object))
2894 _af = loadFromObject(object, file, true, jprovider);
2895 if (_af != null && object.getViewport().size() > 0)
2896 // getJalviewModelSequence().getViewportCount() > 0)
2900 // store a reference to the first view
2903 if (_af.getViewport().isGatherViewsHere())
2905 // if this is a gathered view, keep its reference since
2906 // after gathering views, only this frame will remain
2908 gatherToThisFrame.put(_af.getViewport().getSequenceSetId(),
2911 // Save dataset to register mappings once all resolved
2912 importedDatasets.put(
2913 af.getViewport().getAlignment().getDataset(),
2914 af.getViewport().getAlignment().getDataset());
2919 else if (jarentry != null)
2921 // Some other file here.
2924 } while (jarentry != null);
2925 resolveFrefedSequences();
2926 } catch (IOException ex)
2928 ex.printStackTrace();
2929 errorMessage = "Couldn't locate Jalview XML file : " + file;
2931 "Exception whilst loading jalview XML file : " + ex + "\n");
2932 } catch (Exception ex)
2934 System.err.println("Parsing as Jalview Version 2 file failed.");
2935 ex.printStackTrace(System.err);
2936 if (attemptversion1parse)
2938 // used to attempt to parse as V1 castor-generated xml
2940 if (Desktop.instance != null)
2942 Desktop.instance.stopLoading();
2946 System.out.println("Successfully loaded archive file");
2949 ex.printStackTrace();
2952 "Exception whilst loading jalview XML file : " + ex + "\n");
2953 } catch (OutOfMemoryError e)
2955 // Don't use the OOM Window here
2956 errorMessage = "Out of memory loading jalview XML file";
2957 System.err.println("Out of memory whilst loading jalview XML file");
2958 e.printStackTrace();
2962 * Regather multiple views (with the same sequence set id) to the frame (if
2963 * any) that is flagged as the one to gather to, i.e. convert them to tabbed
2964 * views instead of separate frames. Note this doesn't restore a state where
2965 * some expanded views in turn have tabbed views - the last "first tab" read
2966 * in will play the role of gatherer for all.
2968 for (AlignFrame fr : gatherToThisFrame.values())
2970 Desktop.instance.gatherViews(fr);
2973 restoreSplitFrames();
2974 for (AlignmentI ds : importedDatasets.keySet())
2976 if (ds.getCodonFrames() != null)
2978 StructureSelectionManager
2979 .getStructureSelectionManager(Desktop.instance)
2980 .registerMappings(ds.getCodonFrames());
2983 if (errorMessage != null)
2988 if (Desktop.instance != null)
2990 Desktop.instance.stopLoading();
2997 * Try to reconstruct and display SplitFrame windows, where each contains
2998 * complementary dna and protein alignments. Done by pairing up AlignFrame
2999 * objects (created earlier) which have complementary viewport ids associated.
3001 protected void restoreSplitFrames()
3003 List<SplitFrame> gatherTo = new ArrayList<>();
3004 List<AlignFrame> addedToSplitFrames = new ArrayList<>();
3005 Map<String, AlignFrame> dna = new HashMap<>();
3008 * Identify the DNA alignments
3010 for (Entry<Viewport, AlignFrame> candidate : splitFrameCandidates
3013 AlignFrame af = candidate.getValue();
3014 if (af.getViewport().getAlignment().isNucleotide())
3016 dna.put(candidate.getKey().getId(), af);
3021 * Try to match up the protein complements
3023 for (Entry<Viewport, AlignFrame> candidate : splitFrameCandidates
3026 AlignFrame af = candidate.getValue();
3027 if (!af.getViewport().getAlignment().isNucleotide())
3029 String complementId = candidate.getKey().getComplementId();
3030 // only non-null complements should be in the Map
3031 if (complementId != null && dna.containsKey(complementId))
3033 final AlignFrame dnaFrame = dna.get(complementId);
3034 SplitFrame sf = createSplitFrame(dnaFrame, af);
3035 addedToSplitFrames.add(dnaFrame);
3036 addedToSplitFrames.add(af);
3037 dnaFrame.setMenusForViewport();
3038 af.setMenusForViewport();
3039 if (af.getViewport().isGatherViewsHere())
3048 * Open any that we failed to pair up (which shouldn't happen!) as
3049 * standalone AlignFrame's.
3051 for (Entry<Viewport, AlignFrame> candidate : splitFrameCandidates
3054 AlignFrame af = candidate.getValue();
3055 if (!addedToSplitFrames.contains(af))
3057 Viewport view = candidate.getKey();
3058 Desktop.addInternalFrame(af, view.getTitle(),
3059 safeInt(view.getWidth()), safeInt(view.getHeight()));
3060 af.setMenusForViewport();
3061 System.err.println("Failed to restore view " + view.getTitle()
3062 + " to split frame");
3067 * Gather back into tabbed views as flagged.
3069 for (SplitFrame sf : gatherTo)
3071 Desktop.instance.gatherViews(sf);
3074 splitFrameCandidates.clear();
3078 * Construct and display one SplitFrame holding DNA and protein alignments.
3081 * @param proteinFrame
3084 protected SplitFrame createSplitFrame(AlignFrame dnaFrame,
3085 AlignFrame proteinFrame)
3087 SplitFrame splitFrame = new SplitFrame(dnaFrame, proteinFrame);
3088 String title = MessageManager.getString("label.linked_view_title");
3089 int width = (int) dnaFrame.getBounds().getWidth();
3090 int height = (int) (dnaFrame.getBounds().getHeight()
3091 + proteinFrame.getBounds().getHeight() + 50);
3094 * SplitFrame location is saved to both enclosed frames
3096 splitFrame.setLocation(dnaFrame.getX(), dnaFrame.getY());
3097 Desktop.addInternalFrame(splitFrame, title, width, height);
3100 * And compute cDNA consensus (couldn't do earlier with consensus as
3101 * mappings were not yet present)
3103 proteinFrame.getViewport().alignmentChanged(proteinFrame.alignPanel);
3109 * check errorMessage for a valid error message and raise an error box in the
3110 * GUI or write the current errorMessage to stderr and then clear the error
3113 protected void reportErrors()
3115 reportErrors(false);
3118 protected void reportErrors(final boolean saving)
3120 if (errorMessage != null)
3122 final String finalErrorMessage = errorMessage;
3125 javax.swing.SwingUtilities.invokeLater(new Runnable()
3130 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
3132 "Error " + (saving ? "saving" : "loading")
3134 JvOptionPane.WARNING_MESSAGE);
3140 System.err.println("Problem loading Jalview file: " + errorMessage);
3143 errorMessage = null;
3146 Map<String, String> alreadyLoadedPDB = new HashMap<>();
3149 * when set, local views will be updated from view stored in JalviewXML
3150 * Currently (28th Sep 2008) things will go horribly wrong in vamsas document
3151 * sync if this is set to true.
3153 private final boolean updateLocalViews = false;
3156 * Returns the path to a temporary file holding the PDB file for the given PDB
3157 * id. The first time of asking, searches for a file of that name in the
3158 * Jalview project jar, and copies it to a new temporary file. Any repeat
3159 * requests just return the path to the file previously created.
3165 String loadPDBFile(jarInputStreamProvider jprovider, String pdbId,
3168 if (alreadyLoadedPDB.containsKey(pdbId))
3170 return alreadyLoadedPDB.get(pdbId).toString();
3173 String tempFile = copyJarEntry(jprovider, pdbId, "jalview_pdb",
3175 if (tempFile != null)
3177 alreadyLoadedPDB.put(pdbId, tempFile);
3183 * Copies the jar entry of given name to a new temporary file and returns the
3184 * path to the file, or null if the entry is not found.
3187 * @param jarEntryName
3189 * a prefix for the temporary file name, must be at least three
3191 * @param suffixModel
3192 * null or original file - so new file can be given the same suffix
3196 protected String copyJarEntry(jarInputStreamProvider jprovider,
3197 String jarEntryName, String prefix, String suffixModel)
3199 String suffix = ".tmp";
3200 if (suffixModel == null)
3202 suffixModel = jarEntryName;
3204 int sfpos = suffixModel.lastIndexOf(".");
3205 if (sfpos > -1 && sfpos < (suffixModel.length() - 1))
3207 suffix = "." + suffixModel.substring(sfpos + 1);
3210 try (JarInputStream jin = jprovider.getJarInputStream())
3212 JarEntry entry = null;
3215 entry = jin.getNextJarEntry();
3216 } while (entry != null && !entry.getName().equals(jarEntryName));
3220 // in = new BufferedReader(new InputStreamReader(jin, UTF_8));
3221 File outFile = File.createTempFile(prefix, suffix);
3222 outFile.deleteOnExit();
3223 try (OutputStream os = new FileOutputStream(outFile))
3227 String t = outFile.getAbsolutePath();
3232 warn("Couldn't find entry in Jalview Jar for " + jarEntryName);
3234 } catch (Exception ex)
3236 ex.printStackTrace();
3242 private class JvAnnotRow
3244 public JvAnnotRow(int i, AlignmentAnnotation jaa)
3251 * persisted version of annotation row from which to take vis properties
3253 public jalview.datamodel.AlignmentAnnotation template;
3256 * original position of the annotation row in the alignment
3262 * Load alignment frame from jalview XML DOM object
3264 * @param jalviewModel
3267 * filename source string
3268 * @param loadTreesAndStructures
3269 * when false only create Viewport
3271 * data source provider
3272 * @return alignment frame created from view stored in DOM
3274 AlignFrame loadFromObject(JalviewModel jalviewModel, String file,
3275 boolean loadTreesAndStructures, jarInputStreamProvider jprovider)
3277 SequenceSet vamsasSet = jalviewModel.getVamsasModel().getSequenceSet()
3279 List<Sequence> vamsasSeqs = vamsasSet.getSequence();
3281 // JalviewModelSequence jms = object.getJalviewModelSequence();
3283 // Viewport view = (jms.getViewportCount() > 0) ? jms.getViewport(0)
3285 Viewport view = (jalviewModel.getViewport().size() > 0)
3286 ? jalviewModel.getViewport().get(0)
3289 // ////////////////////////////////
3290 // INITIALISE ALIGNMENT SEQUENCESETID AND VIEWID
3293 // If we just load in the same jar file again, the sequenceSetId
3294 // will be the same, and we end up with multiple references
3295 // to the same sequenceSet. We must modify this id on load
3296 // so that each load of the file gives a unique id
3299 * used to resolve correct alignment dataset for alignments with multiple
3302 String uniqueSeqSetId = null;
3303 String viewId = null;
3306 uniqueSeqSetId = view.getSequenceSetId() + uniqueSetSuffix;
3307 viewId = (view.getId() == null ? null
3308 : view.getId() + uniqueSetSuffix);
3311 // ////////////////////////////////
3314 List<SequenceI> hiddenSeqs = null;
3316 List<SequenceI> tmpseqs = new ArrayList<>();
3318 boolean multipleView = false;
3319 SequenceI referenceseqForView = null;
3320 // JSeq[] jseqs = object.getJalviewModelSequence().getJSeq();
3321 List<JSeq> jseqs = jalviewModel.getJSeq();
3322 int vi = 0; // counter in vamsasSeq array
3323 for (int i = 0; i < jseqs.size(); i++)
3325 JSeq jseq = jseqs.get(i);
3326 String seqId = jseq.getId();
3328 SequenceI tmpSeq = seqRefIds.get(seqId);
3331 if (!incompleteSeqs.containsKey(seqId))
3333 // may not need this check, but keep it for at least 2.9,1 release
3334 if (tmpSeq.getStart() != jseq.getStart()
3335 || tmpSeq.getEnd() != jseq.getEnd())
3337 System.err.println(String.format(
3338 "Warning JAL-2154 regression: updating start/end for sequence %s from %d/%d to %d/%d",
3339 tmpSeq.getName(), tmpSeq.getStart(), tmpSeq.getEnd(),
3340 jseq.getStart(), jseq.getEnd()));
3345 incompleteSeqs.remove(seqId);
3347 if (vamsasSeqs.size() > vi
3348 && vamsasSeqs.get(vi).getId().equals(seqId))
3350 // most likely we are reading a dataset XML document so
3351 // update from vamsasSeq section of XML for this sequence
3352 tmpSeq.setName(vamsasSeqs.get(vi).getName());
3353 tmpSeq.setDescription(vamsasSeqs.get(vi).getDescription());
3354 tmpSeq.setSequence(vamsasSeqs.get(vi).getSequence());
3359 // reading multiple views, so vamsasSeq set is a subset of JSeq
3360 multipleView = true;
3362 tmpSeq.setStart(jseq.getStart());
3363 tmpSeq.setEnd(jseq.getEnd());
3364 tmpseqs.add(tmpSeq);
3368 Sequence vamsasSeq = vamsasSeqs.get(vi);
3369 tmpSeq = new jalview.datamodel.Sequence(vamsasSeq.getName(),
3370 vamsasSeq.getSequence());
3371 tmpSeq.setDescription(vamsasSeq.getDescription());
3372 tmpSeq.setStart(jseq.getStart());
3373 tmpSeq.setEnd(jseq.getEnd());
3374 tmpSeq.setVamsasId(uniqueSetSuffix + seqId);
3375 seqRefIds.put(vamsasSeq.getId(), tmpSeq);
3376 tmpseqs.add(tmpSeq);
3380 if (safeBoolean(jseq.isViewreference()))
3382 referenceseqForView = tmpseqs.get(tmpseqs.size() - 1);
3385 if (jseq.isHidden() != null && jseq.isHidden().booleanValue())
3387 if (hiddenSeqs == null)
3389 hiddenSeqs = new ArrayList<>();
3392 hiddenSeqs.add(tmpSeq);
3397 // Create the alignment object from the sequence set
3398 // ///////////////////////////////
3399 SequenceI[] orderedSeqs = tmpseqs
3400 .toArray(new SequenceI[tmpseqs.size()]);
3402 AlignmentI al = null;
3403 // so we must create or recover the dataset alignment before going further
3404 // ///////////////////////////////
3405 if (vamsasSet.getDatasetId() == null || vamsasSet.getDatasetId() == "")
3407 // older jalview projects do not have a dataset - so creat alignment and
3409 al = new Alignment(orderedSeqs);
3410 al.setDataset(null);
3414 boolean isdsal = jalviewModel.getViewport().isEmpty();
3417 // we are importing a dataset record, so
3418 // recover reference to an alignment already materialsed as dataset
3419 al = getDatasetFor(vamsasSet.getDatasetId());
3423 // materialse the alignment
3424 al = new Alignment(orderedSeqs);
3428 addDatasetRef(vamsasSet.getDatasetId(), al);
3431 // finally, verify all data in vamsasSet is actually present in al
3432 // passing on flag indicating if it is actually a stored dataset
3433 recoverDatasetFor(vamsasSet, al, isdsal, uniqueSeqSetId);
3436 if (referenceseqForView != null)
3438 al.setSeqrep(referenceseqForView);
3440 // / Add the alignment properties
3441 for (int i = 0; i < vamsasSet.getSequenceSetProperties().size(); i++)
3443 SequenceSetProperties ssp = vamsasSet.getSequenceSetProperties()
3445 al.setProperty(ssp.getKey(), ssp.getValue());
3448 // ///////////////////////////////
3450 Hashtable pdbloaded = new Hashtable(); // TODO nothing writes to this??
3453 // load sequence features, database references and any associated PDB
3454 // structures for the alignment
3456 // prior to 2.10, this part would only be executed the first time a
3457 // sequence was encountered, but not afterwards.
3458 // now, for 2.10 projects, this is also done if the xml doc includes
3459 // dataset sequences not actually present in any particular view.
3461 for (int i = 0; i < vamsasSeqs.size(); i++)
3463 JSeq jseq = jseqs.get(i);
3464 if (jseq.getFeatures().size() > 0)
3466 List<Feature> features = jseq.getFeatures();
3467 for (int f = 0; f < features.size(); f++)
3469 Feature feat = features.get(f);
3470 SequenceFeature sf = new SequenceFeature(feat.getType(),
3471 feat.getDescription(), feat.getBegin(), feat.getEnd(),
3472 safeFloat(feat.getScore()), feat.getFeatureGroup());
3473 sf.setStatus(feat.getStatus());
3476 * load any feature attributes - include map-valued attributes
3478 Map<String, Map<String, String>> mapAttributes = new HashMap<>();
3479 for (int od = 0; od < feat.getOtherData().size(); od++)
3481 OtherData keyValue = feat.getOtherData().get(od);
3482 String attributeName = keyValue.getKey();
3483 String attributeValue = keyValue.getValue();
3484 if (attributeName.startsWith("LINK"))
3486 sf.addLink(attributeValue);
3490 String subAttribute = keyValue.getKey2();
3491 if (subAttribute == null)
3493 // simple string-valued attribute
3494 sf.setValue(attributeName, attributeValue);
3498 // attribute 'key' has sub-attribute 'key2'
3499 if (!mapAttributes.containsKey(attributeName))
3501 mapAttributes.put(attributeName, new HashMap<>());
3503 mapAttributes.get(attributeName).put(subAttribute,
3508 for (Entry<String, Map<String, String>> mapAttribute : mapAttributes
3511 sf.setValue(mapAttribute.getKey(), mapAttribute.getValue());
3514 // adds feature to datasequence's feature set (since Jalview 2.10)
3515 al.getSequenceAt(i).addSequenceFeature(sf);
3518 if (vamsasSeqs.get(i).getDBRef().size() > 0)
3520 // adds dbrefs to datasequence's set (since Jalview 2.10)
3522 al.getSequenceAt(i).getDatasetSequence() == null
3523 ? al.getSequenceAt(i)
3524 : al.getSequenceAt(i).getDatasetSequence(),
3527 if (jseq.getPdbids().size() > 0)
3529 List<Pdbids> ids = jseq.getPdbids();
3530 for (int p = 0; p < ids.size(); p++)
3532 Pdbids pdbid = ids.get(p);
3533 jalview.datamodel.PDBEntry entry = new jalview.datamodel.PDBEntry();
3534 entry.setId(pdbid.getId());
3535 if (pdbid.getType() != null)
3537 if (PDBEntry.Type.getType(pdbid.getType()) != null)
3539 entry.setType(PDBEntry.Type.getType(pdbid.getType()));
3543 entry.setType(PDBEntry.Type.FILE);
3546 // jprovider is null when executing 'New View'
3547 if (pdbid.getFile() != null && jprovider != null)
3549 if (!pdbloaded.containsKey(pdbid.getFile()))
3551 entry.setFile(loadPDBFile(jprovider, pdbid.getId(),
3556 entry.setFile(pdbloaded.get(pdbid.getId()).toString());
3560 if (pdbid.getPdbentryItem() != null)
3562 for (PdbentryItem item : pdbid.getPdbentryItem())
3564 for (Property pr : item.getProperty())
3566 entry.setProperty(pr.getName(), pr.getValue());
3571 for (Property prop : pdbid.getProperty())
3573 entry.setProperty(prop.getName(), prop.getValue());
3575 StructureSelectionManager
3576 .getStructureSelectionManager(Desktop.instance)
3577 .registerPDBEntry(entry);
3578 // adds PDBEntry to datasequence's set (since Jalview 2.10)
3579 if (al.getSequenceAt(i).getDatasetSequence() != null)
3581 al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
3585 al.getSequenceAt(i).addPDBId(entry);
3590 } // end !multipleview
3592 // ///////////////////////////////
3593 // LOAD SEQUENCE MAPPINGS
3595 if (vamsasSet.getAlcodonFrame().size() > 0)
3597 // TODO Potentially this should only be done once for all views of an
3599 List<AlcodonFrame> alc = vamsasSet.getAlcodonFrame();
3600 for (int i = 0; i < alc.size(); i++)
3602 AlignedCodonFrame cf = new AlignedCodonFrame();
3603 if (alc.get(i).getAlcodMap().size() > 0)
3605 List<AlcodMap> maps = alc.get(i).getAlcodMap();
3606 for (int m = 0; m < maps.size(); m++)
3608 AlcodMap map = maps.get(m);
3609 SequenceI dnaseq = seqRefIds.get(map.getDnasq());
3611 jalview.datamodel.Mapping mapping = null;
3612 // attach to dna sequence reference.
3613 if (map.getMapping() != null)
3615 mapping = addMapping(map.getMapping());
3616 if (dnaseq != null && mapping.getTo() != null)
3618 cf.addMap(dnaseq, mapping.getTo(), mapping.getMap());
3624 .add(newAlcodMapRef(map.getDnasq(), cf, mapping));
3628 al.addCodonFrame(cf);
3633 // ////////////////////////////////
3635 List<JvAnnotRow> autoAlan = new ArrayList<>();
3638 * store any annotations which forward reference a group's ID
3640 Map<String, List<AlignmentAnnotation>> groupAnnotRefs = new Hashtable<>();
3642 if (vamsasSet.getAnnotation().size()/*Count()*/ > 0)
3644 List<Annotation> an = vamsasSet.getAnnotation();
3646 for (int i = 0; i < an.size(); i++)
3648 Annotation annotation = an.get(i);
3651 * test if annotation is automatically calculated for this view only
3653 boolean autoForView = false;
3654 if (annotation.getLabel().equals("Quality")
3655 || annotation.getLabel().equals("Conservation")
3656 || annotation.getLabel().equals("Consensus"))
3658 // Kludge for pre 2.5 projects which lacked the autocalculated flag
3660 // JAXB has no has() test; schema defaults value to false
3661 // if (!annotation.hasAutoCalculated())
3663 // annotation.setAutoCalculated(true);
3666 if (autoForView || annotation.isAutoCalculated())
3668 // remove ID - we don't recover annotation from other views for
3669 // view-specific annotation
3670 annotation.setId(null);
3673 // set visibility for other annotation in this view
3674 String annotationId = annotation.getId();
3675 if (annotationId != null && annotationIds.containsKey(annotationId))
3677 AlignmentAnnotation jda = annotationIds.get(annotationId);
3678 // in principle Visible should always be true for annotation displayed
3679 // in multiple views
3680 if (annotation.isVisible() != null)
3682 jda.visible = annotation.isVisible();
3685 al.addAnnotation(jda);
3689 // Construct new annotation from model.
3690 List<AnnotationElement> ae = annotation.getAnnotationElement();
3691 jalview.datamodel.Annotation[] anot = null;
3692 java.awt.Color firstColour = null;
3694 if (!annotation.isScoreOnly())
3696 anot = new jalview.datamodel.Annotation[al.getWidth()];
3697 for (int aa = 0; aa < ae.size() && aa < anot.length; aa++)
3699 AnnotationElement annElement = ae.get(aa);
3700 anpos = annElement.getPosition();
3702 if (anpos >= anot.length)
3707 float value = safeFloat(annElement.getValue());
3708 anot[anpos] = new jalview.datamodel.Annotation(
3709 annElement.getDisplayCharacter(),
3710 annElement.getDescription(),
3711 (annElement.getSecondaryStructure() == null
3712 || annElement.getSecondaryStructure()
3716 .getSecondaryStructure()
3719 anot[anpos].colour = new Color(safeInt(annElement.getColour()));
3720 if (firstColour == null)
3722 firstColour = anot[anpos].colour;
3726 jalview.datamodel.AlignmentAnnotation jaa = null;
3728 if (annotation.isGraph())
3730 float llim = 0, hlim = 0;
3731 // if (autoForView || an[i].isAutoCalculated()) {
3734 jaa = new jalview.datamodel.AlignmentAnnotation(
3735 annotation.getLabel(), annotation.getDescription(), anot,
3736 llim, hlim, safeInt(annotation.getGraphType()));
3738 jaa.graphGroup = safeInt(annotation.getGraphGroup());
3739 jaa._linecolour = firstColour;
3740 if (annotation.getThresholdLine() != null)
3742 jaa.setThreshold(new jalview.datamodel.GraphLine(
3743 safeFloat(annotation.getThresholdLine().getValue()),
3744 annotation.getThresholdLine().getLabel(),
3745 new java.awt.Color(safeInt(
3746 annotation.getThresholdLine().getColour()))));
3748 if (autoForView || annotation.isAutoCalculated())
3750 // Hardwire the symbol display line to ensure that labels for
3751 // histograms are displayed
3757 jaa = new jalview.datamodel.AlignmentAnnotation(
3758 annotation.getLabel(), annotation.getDescription(), anot);
3759 jaa._linecolour = firstColour;
3761 // register new annotation
3762 if (annotation.getId() != null)
3764 annotationIds.put(annotation.getId(), jaa);
3765 jaa.annotationId = annotation.getId();
3767 // recover sequence association
3768 String sequenceRef = annotation.getSequenceRef();
3769 if (sequenceRef != null)
3771 // from 2.9 sequenceRef is to sequence id (JAL-1781)
3772 SequenceI sequence = seqRefIds.get(sequenceRef);
3773 if (sequence == null)
3775 // in pre-2.9 projects sequence ref is to sequence name
3776 sequence = al.findName(sequenceRef);
3778 if (sequence != null)
3780 jaa.createSequenceMapping(sequence, 1, true);
3781 sequence.addAlignmentAnnotation(jaa);
3784 // and make a note of any group association
3785 if (annotation.getGroupRef() != null
3786 && annotation.getGroupRef().length() > 0)
3788 List<jalview.datamodel.AlignmentAnnotation> aal = groupAnnotRefs
3789 .get(annotation.getGroupRef());
3792 aal = new ArrayList<>();
3793 groupAnnotRefs.put(annotation.getGroupRef(), aal);
3798 if (annotation.getScore() != null)
3800 jaa.setScore(annotation.getScore().doubleValue());
3802 if (annotation.isVisible() != null)
3804 jaa.visible = annotation.isVisible().booleanValue();
3807 if (annotation.isCentreColLabels() != null)
3809 jaa.centreColLabels = annotation.isCentreColLabels()
3813 if (annotation.isScaleColLabels() != null)
3815 jaa.scaleColLabel = annotation.isScaleColLabels().booleanValue();
3817 if (annotation.isAutoCalculated())
3819 // newer files have an 'autoCalculated' flag and store calculation
3820 // state in viewport properties
3821 jaa.autoCalculated = true; // means annotation will be marked for
3822 // update at end of load.
3824 if (annotation.getGraphHeight() != null)
3826 jaa.graphHeight = annotation.getGraphHeight().intValue();
3828 jaa.belowAlignment = annotation.isBelowAlignment();
3829 jaa.setCalcId(annotation.getCalcId());
3830 if (annotation.getProperty().size() > 0)
3832 for (Annotation.Property prop : annotation.getProperty())
3834 jaa.setProperty(prop.getName(), prop.getValue());
3837 if (jaa.autoCalculated)
3839 autoAlan.add(new JvAnnotRow(i, jaa));
3842 // if (!autoForView)
3844 // add autocalculated group annotation and any user created annotation
3846 al.addAnnotation(jaa);
3850 // ///////////////////////
3852 // Create alignment markup and styles for this view
3853 if (jalviewModel.getJGroup().size() > 0)
3855 List<JGroup> groups = jalviewModel.getJGroup();
3856 boolean addAnnotSchemeGroup = false;
3857 for (int i = 0; i < groups.size(); i++)
3859 JGroup jGroup = groups.get(i);
3860 ColourSchemeI cs = null;
3861 if (jGroup.getColour() != null)
3863 if (jGroup.getColour().startsWith("ucs"))
3865 cs = getUserColourScheme(jalviewModel, jGroup.getColour());
3867 else if (jGroup.getColour().equals("AnnotationColourGradient")
3868 && jGroup.getAnnotationColours() != null)
3870 addAnnotSchemeGroup = true;
3874 cs = ColourSchemeProperty.getColourScheme(null, al,
3875 jGroup.getColour());
3878 int pidThreshold = safeInt(jGroup.getPidThreshold());
3880 Vector<SequenceI> seqs = new Vector<>();
3882 for (int s = 0; s < jGroup.getSeq().size(); s++)
3884 String seqId = jGroup.getSeq().get(s);
3885 SequenceI ts = seqRefIds.get(seqId);
3889 seqs.addElement(ts);
3893 if (seqs.size() < 1)
3898 SequenceGroup sg = new SequenceGroup(seqs, jGroup.getName(), cs,
3899 safeBoolean(jGroup.isDisplayBoxes()),
3900 safeBoolean(jGroup.isDisplayText()),
3901 safeBoolean(jGroup.isColourText()),
3902 safeInt(jGroup.getStart()), safeInt(jGroup.getEnd()));
3903 sg.getGroupColourScheme().setThreshold(pidThreshold, true);
3904 sg.getGroupColourScheme()
3905 .setConservationInc(safeInt(jGroup.getConsThreshold()));
3906 sg.setOutlineColour(new Color(safeInt(jGroup.getOutlineColour())));
3908 sg.textColour = new Color(safeInt(jGroup.getTextCol1()));
3909 sg.textColour2 = new Color(safeInt(jGroup.getTextCol2()));
3910 sg.setShowNonconserved(safeBoolean(jGroup.isShowUnconserved()));
3911 sg.thresholdTextColour = safeInt(jGroup.getTextColThreshold());
3912 // attributes with a default in the schema are never null
3913 sg.setShowConsensusHistogram(jGroup.isShowConsensusHistogram());
3914 sg.setshowSequenceLogo(jGroup.isShowSequenceLogo());
3915 sg.setNormaliseSequenceLogo(jGroup.isNormaliseSequenceLogo());
3916 sg.setIgnoreGapsConsensus(jGroup.isIgnoreGapsinConsensus());
3917 if (jGroup.getConsThreshold() != null
3918 && jGroup.getConsThreshold().intValue() != 0)
3920 Conservation c = new Conservation("All", sg.getSequences(null), 0,
3923 c.verdict(false, 25);
3924 sg.cs.setConservation(c);
3927 if (jGroup.getId() != null && groupAnnotRefs.size() > 0)
3929 // re-instate unique group/annotation row reference
3930 List<AlignmentAnnotation> jaal = groupAnnotRefs
3931 .get(jGroup.getId());
3934 for (AlignmentAnnotation jaa : jaal)
3937 if (jaa.autoCalculated)
3939 // match up and try to set group autocalc alignment row for this
3941 if (jaa.label.startsWith("Consensus for "))
3943 sg.setConsensus(jaa);
3945 // match up and try to set group autocalc alignment row for this
3947 if (jaa.label.startsWith("Conservation for "))
3949 sg.setConservationRow(jaa);
3956 if (addAnnotSchemeGroup)
3958 // reconstruct the annotation colourscheme
3960 constructAnnotationColour(jGroup.getAnnotationColours(),
3961 null, al, jalviewModel, false));
3967 // only dataset in this model, so just return.
3970 // ///////////////////////////////
3973 AlignFrame af = null;
3974 AlignViewport av = null;
3975 // now check to see if we really need to create a new viewport.
3976 if (multipleView && viewportsAdded.size() == 0)
3978 // We recovered an alignment for which a viewport already exists.
3979 // TODO: fix up any settings necessary for overlaying stored state onto
3980 // state recovered from another document. (may not be necessary).
3981 // we may need a binding from a viewport in memory to one recovered from
3983 // and then recover its containing af to allow the settings to be applied.
3984 // TODO: fix for vamsas demo
3986 "About to recover a viewport for existing alignment: Sequence set ID is "
3988 Object seqsetobj = retrieveExistingObj(uniqueSeqSetId);
3989 if (seqsetobj != null)
3991 if (seqsetobj instanceof String)
3993 uniqueSeqSetId = (String) seqsetobj;
3995 "Recovered extant sequence set ID mapping for ID : New Sequence set ID is "
4001 "Warning : Collision between sequence set ID string and existing jalview object mapping.");
4007 * indicate that annotation colours are applied across all groups (pre
4008 * Jalview 2.8.1 behaviour)
4010 boolean doGroupAnnColour = Jalview2XML.isVersionStringLaterThan("2.8.1",
4011 jalviewModel.getVersion());
4013 AlignmentPanel ap = null;
4014 boolean isnewview = true;
4017 // Check to see if this alignment already has a view id == viewId
4018 jalview.gui.AlignmentPanel views[] = Desktop
4019 .getAlignmentPanels(uniqueSeqSetId);
4020 if (views != null && views.length > 0)
4022 for (int v = 0; v < views.length; v++)
4024 if (views[v].av.getViewId().equalsIgnoreCase(viewId))
4026 // recover the existing alignpanel, alignframe, viewport
4027 af = views[v].alignFrame;
4030 // TODO: could even skip resetting view settings if we don't want to
4031 // change the local settings from other jalview processes
4040 af = loadViewport(file, jseqs, hiddenSeqs, al, jalviewModel, view,
4041 uniqueSeqSetId, viewId, autoAlan);
4042 av = af.getViewport();
4047 * Load any trees, PDB structures and viewers
4049 * Not done if flag is false (when this method is used for New View)
4051 if (loadTreesAndStructures)
4053 loadTrees(jalviewModel, view, af, av, ap);
4054 loadPCAViewers(jalviewModel, ap);
4055 loadPDBStructures(jprovider, jseqs, af, ap);
4056 loadRnaViewers(jprovider, jseqs, ap);
4058 // and finally return.
4063 * Instantiate and link any saved RNA (Varna) viewers. The state of the Varna
4064 * panel is restored from separate jar entries, two (gapped and trimmed) per
4065 * sequence and secondary structure.
4067 * Currently each viewer shows just one sequence and structure (gapped and
4068 * trimmed), however this method is designed to support multiple sequences or
4069 * structures in viewers if wanted in future.
4075 private void loadRnaViewers(jarInputStreamProvider jprovider,
4076 List<JSeq> jseqs, AlignmentPanel ap)
4079 * scan the sequences for references to viewers; create each one the first
4080 * time it is referenced, add Rna models to existing viewers
4082 for (JSeq jseq : jseqs)
4084 for (int i = 0; i < jseq.getRnaViewer().size(); i++)
4086 RnaViewer viewer = jseq.getRnaViewer().get(i);
4087 AppVarna appVarna = findOrCreateVarnaViewer(viewer, uniqueSetSuffix,
4090 for (int j = 0; j < viewer.getSecondaryStructure().size(); j++)
4092 SecondaryStructure ss = viewer.getSecondaryStructure().get(j);
4093 SequenceI seq = seqRefIds.get(jseq.getId());
4094 AlignmentAnnotation ann = this.annotationIds
4095 .get(ss.getAnnotationId());
4098 * add the structure to the Varna display (with session state copied
4099 * from the jar to a temporary file)
4101 boolean gapped = safeBoolean(ss.isGapped());
4102 String rnaTitle = ss.getTitle();
4103 String sessionState = ss.getViewerState();
4104 String tempStateFile = copyJarEntry(jprovider, sessionState,
4106 RnaModel rna = new RnaModel(rnaTitle, ann, seq, null, gapped);
4107 appVarna.addModelSession(rna, rnaTitle, tempStateFile);
4109 appVarna.setInitialSelection(safeInt(viewer.getSelectedRna()));
4115 * Locate and return an already instantiated matching AppVarna, or create one
4119 * @param viewIdSuffix
4123 protected AppVarna findOrCreateVarnaViewer(RnaViewer viewer,
4124 String viewIdSuffix, AlignmentPanel ap)
4127 * on each load a suffix is appended to the saved viewId, to avoid conflicts
4128 * if load is repeated
4130 String postLoadId = viewer.getViewId() + viewIdSuffix;
4131 for (JInternalFrame frame : getAllFrames())
4133 if (frame instanceof AppVarna)
4135 AppVarna varna = (AppVarna) frame;
4136 if (postLoadId.equals(varna.getViewId()))
4138 // this viewer is already instantiated
4139 // could in future here add ap as another 'parent' of the
4140 // AppVarna window; currently just 1-to-many
4147 * viewer not found - make it
4149 RnaViewerModel model = new RnaViewerModel(postLoadId, viewer.getTitle(),
4150 safeInt(viewer.getXpos()), safeInt(viewer.getYpos()),
4151 safeInt(viewer.getWidth()), safeInt(viewer.getHeight()),
4152 safeInt(viewer.getDividerLocation()));
4153 AppVarna varna = new AppVarna(model, ap);
4159 * Load any saved trees
4167 protected void loadTrees(JalviewModel jm, Viewport view, AlignFrame af,
4168 AlignViewport av, AlignmentPanel ap)
4170 // TODO result of automated refactoring - are all these parameters needed?
4173 for (int t = 0; t < jm.getTree().size(); t++)
4176 Tree tree = jm.getTree().get(t);
4178 TreePanel tp = (TreePanel) retrieveExistingObj(tree.getId());
4181 tp = af.showNewickTree(new NewickFile(tree.getNewick()),
4182 tree.getTitle(), safeInt(tree.getWidth()),
4183 safeInt(tree.getHeight()), safeInt(tree.getXpos()),
4184 safeInt(tree.getYpos()));
4185 if (tree.getId() != null)
4187 // perhaps bind the tree id to something ?
4192 // update local tree attributes ?
4193 // TODO: should check if tp has been manipulated by user - if so its
4194 // settings shouldn't be modified
4195 tp.setTitle(tree.getTitle());
4196 tp.setBounds(new Rectangle(safeInt(tree.getXpos()),
4197 safeInt(tree.getYpos()), safeInt(tree.getWidth()),
4198 safeInt(tree.getHeight())));
4199 tp.setViewport(av); // af.viewport;
4200 // TODO: verify 'associate with all views' works still
4201 tp.getTreeCanvas().setViewport(av); // af.viewport;
4202 tp.getTreeCanvas().setAssociatedPanel(ap); // af.alignPanel;
4204 tp.getTreeCanvas().setApplyToAllViews(tree.isLinkToAllViews());
4207 warn("There was a problem recovering stored Newick tree: \n"
4208 + tree.getNewick());
4212 tp.fitToWindow.setState(safeBoolean(tree.isFitToWindow()));
4213 tp.fitToWindow_actionPerformed(null);
4215 if (tree.getFontName() != null)
4218 new Font(tree.getFontName(), safeInt(tree.getFontStyle()),
4219 safeInt(tree.getFontSize())));
4224 new Font(view.getFontName(), safeInt(view.getFontStyle()),
4225 safeInt(view.getFontSize())));
4228 tp.showPlaceholders(safeBoolean(tree.isMarkUnlinked()));
4229 tp.showBootstrap(safeBoolean(tree.isShowBootstrap()));
4230 tp.showDistances(safeBoolean(tree.isShowDistances()));
4232 tp.getTreeCanvas().setThreshold(safeFloat(tree.getThreshold()));
4234 if (safeBoolean(tree.isCurrentTree()))
4236 af.getViewport().setCurrentTree(tp.getTree());
4240 } catch (Exception ex)
4242 ex.printStackTrace();
4247 * Load and link any saved structure viewers.
4254 protected void loadPDBStructures(jarInputStreamProvider jprovider,
4255 List<JSeq> jseqs, AlignFrame af, AlignmentPanel ap)
4258 * Run through all PDB ids on the alignment, and collect mappings between
4259 * distinct view ids and all sequences referring to that view.
4261 Map<String, StructureViewerModel> structureViewers = new LinkedHashMap<>();
4263 for (int i = 0; i < jseqs.size(); i++)
4265 JSeq jseq = jseqs.get(i);
4266 if (jseq.getPdbids().size() > 0)
4268 List<Pdbids> ids = jseq.getPdbids();
4269 for (int p = 0; p < ids.size(); p++)
4271 Pdbids pdbid = ids.get(p);
4272 final int structureStateCount = pdbid.getStructureState().size();
4273 for (int s = 0; s < structureStateCount; s++)
4275 // check to see if we haven't already created this structure view
4276 final StructureState structureState = pdbid.getStructureState()
4278 String sviewid = (structureState.getViewId() == null) ? null
4279 : structureState.getViewId() + uniqueSetSuffix;
4280 jalview.datamodel.PDBEntry jpdb = new jalview.datamodel.PDBEntry();
4281 // Originally : pdbid.getFile()
4282 // : TODO: verify external PDB file recovery still works in normal
4283 // jalview project load
4285 loadPDBFile(jprovider, pdbid.getId(), pdbid.getFile()));
4286 jpdb.setId(pdbid.getId());
4288 int x = safeInt(structureState.getXpos());
4289 int y = safeInt(structureState.getYpos());
4290 int width = safeInt(structureState.getWidth());
4291 int height = safeInt(structureState.getHeight());
4293 // Probably don't need to do this anymore...
4294 // Desktop.desktop.getComponentAt(x, y);
4295 // TODO: NOW: check that this recovers the PDB file correctly.
4296 String pdbFile = loadPDBFile(jprovider, pdbid.getId(),
4298 jalview.datamodel.SequenceI seq = seqRefIds
4299 .get(jseq.getId() + "");
4300 if (sviewid == null)
4302 sviewid = "_jalview_pre2_4_" + x + "," + y + "," + width + ","
4305 if (!structureViewers.containsKey(sviewid))
4307 String viewerType = structureState.getType();
4308 if (viewerType == null) // pre Jalview 2.9
4310 viewerType = ViewerType.JMOL.toString();
4312 structureViewers.put(sviewid,
4313 new StructureViewerModel(x, y, width, height, false,
4314 false, true, structureState.getViewId(),
4316 // Legacy pre-2.7 conversion JAL-823 :
4317 // do not assume any view has to be linked for colour by
4321 // assemble String[] { pdb files }, String[] { id for each
4322 // file }, orig_fileloc, SequenceI[][] {{ seqs_file 1 }, {
4323 // seqs_file 2}, boolean[] {
4324 // linkAlignPanel,superposeWithAlignpanel}} from hash
4325 StructureViewerModel jmoldat = structureViewers.get(sviewid);
4326 jmoldat.setAlignWithPanel(jmoldat.isAlignWithPanel()
4327 || structureState.isAlignwithAlignPanel());
4330 * Default colour by linked panel to false if not specified (e.g.
4331 * for pre-2.7 projects)
4333 boolean colourWithAlignPanel = jmoldat.isColourWithAlignPanel();
4334 colourWithAlignPanel |= structureState.isColourwithAlignPanel();
4335 jmoldat.setColourWithAlignPanel(colourWithAlignPanel);
4338 * Default colour by viewer to true if not specified (e.g. for
4341 boolean colourByViewer = jmoldat.isColourByViewer();
4342 colourByViewer &= structureState.isColourByJmol();
4343 jmoldat.setColourByViewer(colourByViewer);
4345 if (jmoldat.getStateData().length() < structureState.getValue()
4346 /*Content()*/.length())
4348 jmoldat.setStateData(structureState.getValue());// Content());
4350 if (pdbid.getFile() != null)
4352 File mapkey = new File(pdbid.getFile());
4353 StructureData seqstrmaps = jmoldat.getFileData().get(mapkey);
4354 if (seqstrmaps == null)
4356 jmoldat.getFileData().put(mapkey,
4357 seqstrmaps = jmoldat.new StructureData(pdbFile,
4360 if (!seqstrmaps.getSeqList().contains(seq))
4362 seqstrmaps.getSeqList().add(seq);
4368 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");
4375 // Instantiate the associated structure views
4376 for (Entry<String, StructureViewerModel> entry : structureViewers
4381 createOrLinkStructureViewer(entry, af, ap, jprovider);
4382 } catch (Exception e)
4385 "Error loading structure viewer: " + e.getMessage());
4386 // failed - try the next one
4398 protected void createOrLinkStructureViewer(
4399 Entry<String, StructureViewerModel> viewerData, AlignFrame af,
4400 AlignmentPanel ap, jarInputStreamProvider jprovider)
4402 final StructureViewerModel stateData = viewerData.getValue();
4405 * Search for any viewer windows already open from other alignment views
4406 * that exactly match the stored structure state
4408 StructureViewerBase comp = findMatchingViewer(viewerData);
4412 linkStructureViewer(ap, comp, stateData);
4416 String type = stateData.getType();
4419 ViewerType viewerType = ViewerType.valueOf(type);
4420 createStructureViewer(viewerType, viewerData, af, jprovider);
4421 } catch (IllegalArgumentException | NullPointerException e)
4423 // TODO JAL-3619 show error dialog / offer an alternative viewer
4424 Cache.log.error("Invalid structure viewer type: " + type);
4429 * Generates a name for the entry in the project jar file to hold state
4430 * information for a structure viewer
4435 protected String getViewerJarEntryName(String viewId)
4437 return VIEWER_PREFIX + viewId;
4441 * Returns any open frame that matches given structure viewer data. The match
4442 * is based on the unique viewId, or (for older project versions) the frame's
4448 protected StructureViewerBase findMatchingViewer(
4449 Entry<String, StructureViewerModel> viewerData)
4451 final String sviewid = viewerData.getKey();
4452 final StructureViewerModel svattrib = viewerData.getValue();
4453 StructureViewerBase comp = null;
4454 JInternalFrame[] frames = getAllFrames();
4455 for (JInternalFrame frame : frames)
4457 if (frame instanceof StructureViewerBase)
4460 * Post jalview 2.4 schema includes structure view id
4462 if (sviewid != null && ((StructureViewerBase) frame).getViewId()
4465 comp = (StructureViewerBase) frame;
4466 break; // break added in 2.9
4469 * Otherwise test for matching position and size of viewer frame
4471 else if (frame.getX() == svattrib.getX()
4472 && frame.getY() == svattrib.getY()
4473 && frame.getHeight() == svattrib.getHeight()
4474 && frame.getWidth() == svattrib.getWidth())
4476 comp = (StructureViewerBase) frame;
4477 // no break in faint hope of an exact match on viewId
4485 * Link an AlignmentPanel to an existing structure viewer.
4490 * @param useinViewerSuperpos
4491 * @param usetoColourbyseq
4492 * @param viewerColouring
4494 protected void linkStructureViewer(AlignmentPanel ap,
4495 StructureViewerBase viewer, StructureViewerModel stateData)
4497 // NOTE: if the jalview project is part of a shared session then
4498 // view synchronization should/could be done here.
4500 final boolean useinViewerSuperpos = stateData.isAlignWithPanel();
4501 final boolean usetoColourbyseq = stateData.isColourWithAlignPanel();
4502 final boolean viewerColouring = stateData.isColourByViewer();
4503 Map<File, StructureData> oldFiles = stateData.getFileData();
4506 * Add mapping for sequences in this view to an already open viewer
4508 final AAStructureBindingModel binding = viewer.getBinding();
4509 for (File id : oldFiles.keySet())
4511 // add this and any other pdb files that should be present in the
4513 StructureData filedat = oldFiles.get(id);
4514 String pdbFile = filedat.getFilePath();
4515 SequenceI[] seq = filedat.getSeqList().toArray(new SequenceI[0]);
4516 binding.getSsm().setMapping(seq, null, pdbFile, DataSourceType.FILE,
4518 binding.addSequenceForStructFile(pdbFile, seq);
4520 // and add the AlignmentPanel's reference to the view panel
4521 viewer.addAlignmentPanel(ap);
4522 if (useinViewerSuperpos)
4524 viewer.useAlignmentPanelForSuperposition(ap);
4528 viewer.excludeAlignmentPanelForSuperposition(ap);
4530 if (usetoColourbyseq)
4532 viewer.useAlignmentPanelForColourbyseq(ap, !viewerColouring);
4536 viewer.excludeAlignmentPanelForColourbyseq(ap);
4541 * Get all frames within the Desktop.
4545 protected JInternalFrame[] getAllFrames()
4547 JInternalFrame[] frames = null;
4548 // TODO is this necessary - is it safe - risk of hanging?
4553 frames = Desktop.desktop.getAllFrames();
4554 } catch (ArrayIndexOutOfBoundsException e)
4556 // occasional No such child exceptions are thrown here...
4560 } catch (InterruptedException f)
4564 } while (frames == null);
4569 * Answers true if 'version' is equal to or later than 'supported', where each
4570 * is formatted as major/minor versions like "2.8.3" or "2.3.4b1" for bugfix
4571 * changes. Development and test values for 'version' are leniently treated
4575 * - minimum version we are comparing against
4577 * - version of data being processsed
4580 public static boolean isVersionStringLaterThan(String supported,
4583 if (supported == null || version == null
4584 || version.equalsIgnoreCase("DEVELOPMENT BUILD")
4585 || version.equalsIgnoreCase("Test")
4586 || version.equalsIgnoreCase("AUTOMATED BUILD"))
4588 System.err.println("Assuming project file with "
4589 + (version == null ? "null" : version)
4590 + " is compatible with Jalview version " + supported);
4595 return StringUtils.compareVersions(version, supported, "b") >= 0;
4599 Vector<JalviewStructureDisplayI> newStructureViewers = null;
4601 protected void addNewStructureViewer(JalviewStructureDisplayI sview)
4603 if (newStructureViewers != null)
4605 sview.getBinding().setFinishedLoadingFromArchive(false);
4606 newStructureViewers.add(sview);
4610 protected void setLoadingFinishedForNewStructureViewers()
4612 if (newStructureViewers != null)
4614 for (JalviewStructureDisplayI sview : newStructureViewers)
4616 sview.getBinding().setFinishedLoadingFromArchive(true);
4618 newStructureViewers.clear();
4619 newStructureViewers = null;
4623 AlignFrame loadViewport(String file, List<JSeq> JSEQ,
4624 List<SequenceI> hiddenSeqs, AlignmentI al, JalviewModel jm,
4625 Viewport view, String uniqueSeqSetId, String viewId,
4626 List<JvAnnotRow> autoAlan)
4628 AlignFrame af = null;
4629 af = new AlignFrame(al, safeInt(view.getWidth()),
4630 safeInt(view.getHeight()), uniqueSeqSetId, viewId)
4634 // protected void processKeyEvent(java.awt.event.KeyEvent e) {
4635 // System.out.println("Jalview2XML AF " + e);
4636 // super.processKeyEvent(e);
4643 af.setFileName(file, FileFormat.Jalview);
4645 final AlignViewport viewport = af.getViewport();
4646 for (int i = 0; i < JSEQ.size(); i++)
4648 int colour = safeInt(JSEQ.get(i).getColour());
4649 viewport.setSequenceColour(viewport.getAlignment().getSequenceAt(i),
4655 viewport.setColourByReferenceSeq(true);
4656 viewport.setDisplayReferenceSeq(true);
4659 viewport.setGatherViewsHere(safeBoolean(view.isGatheredViews()));
4661 if (view.getSequenceSetId() != null)
4663 AlignmentViewport av = viewportsAdded.get(uniqueSeqSetId);
4665 viewport.setSequenceSetId(uniqueSeqSetId);
4668 // propagate shared settings to this new view
4669 viewport.setHistoryList(av.getHistoryList());
4670 viewport.setRedoList(av.getRedoList());
4674 viewportsAdded.put(uniqueSeqSetId, viewport);
4676 // TODO: check if this method can be called repeatedly without
4677 // side-effects if alignpanel already registered.
4678 PaintRefresher.Register(af.alignPanel, uniqueSeqSetId);
4680 // apply Hidden regions to view.
4681 if (hiddenSeqs != null)
4683 for (int s = 0; s < JSEQ.size(); s++)
4685 SequenceGroup hidden = new SequenceGroup();
4686 boolean isRepresentative = false;
4687 for (int r = 0; r < JSEQ.get(s).getHiddenSequences().size(); r++)
4689 isRepresentative = true;
4690 SequenceI sequenceToHide = al
4691 .getSequenceAt(JSEQ.get(s).getHiddenSequences().get(r));
4692 hidden.addSequence(sequenceToHide, false);
4693 // remove from hiddenSeqs list so we don't try to hide it twice
4694 hiddenSeqs.remove(sequenceToHide);
4696 if (isRepresentative)
4698 SequenceI representativeSequence = al.getSequenceAt(s);
4699 hidden.addSequence(representativeSequence, false);
4700 viewport.hideRepSequences(representativeSequence, hidden);
4704 SequenceI[] hseqs = hiddenSeqs
4705 .toArray(new SequenceI[hiddenSeqs.size()]);
4706 viewport.hideSequence(hseqs);
4709 // recover view properties and display parameters
4711 viewport.setShowAnnotation(safeBoolean(view.isShowAnnotation()));
4712 viewport.setAbovePIDThreshold(safeBoolean(view.isPidSelected()));
4713 final int pidThreshold = safeInt(view.getPidThreshold());
4714 viewport.setThreshold(pidThreshold);
4716 viewport.setColourText(safeBoolean(view.isShowColourText()));
4718 viewport.setConservationSelected(
4719 safeBoolean(view.isConservationSelected()));
4720 viewport.setIncrement(safeInt(view.getConsThreshold()));
4721 viewport.setShowJVSuffix(safeBoolean(view.isShowFullId()));
4722 viewport.setRightAlignIds(safeBoolean(view.isRightAlignIds()));
4723 viewport.setFont(new Font(view.getFontName(),
4724 safeInt(view.getFontStyle()), safeInt(view.getFontSize())),
4726 ViewStyleI vs = viewport.getViewStyle();
4727 vs.setScaleProteinAsCdna(view.isScaleProteinAsCdna());
4728 viewport.setViewStyle(vs);
4729 // TODO: allow custom charWidth/Heights to be restored by updating them
4730 // after setting font - which means set above to false
4731 viewport.setRenderGaps(safeBoolean(view.isRenderGaps()));
4732 viewport.setWrapAlignment(safeBoolean(view.isWrapAlignment()));
4733 viewport.setShowAnnotation(safeBoolean(view.isShowAnnotation()));
4735 viewport.setShowBoxes(safeBoolean(view.isShowBoxes()));
4737 viewport.setShowText(safeBoolean(view.isShowText()));
4739 viewport.setTextColour(new Color(safeInt(view.getTextCol1())));
4740 viewport.setTextColour2(new Color(safeInt(view.getTextCol2())));
4741 viewport.setThresholdTextColour(safeInt(view.getTextColThreshold()));
4742 viewport.setShowUnconserved(view.isShowUnconserved());
4743 viewport.getRanges().setStartRes(safeInt(view.getStartRes()));
4745 if (view.getViewName() != null)
4747 viewport.setViewName(view.getViewName());
4748 af.setInitialTabVisible();
4750 af.setBounds(safeInt(view.getXpos()), safeInt(view.getYpos()),
4751 safeInt(view.getWidth()), safeInt(view.getHeight()));
4752 // startSeq set in af.alignPanel.updateLayout below
4753 af.alignPanel.updateLayout();
4754 ColourSchemeI cs = null;
4755 // apply colourschemes
4756 if (view.getBgColour() != null)
4758 if (view.getBgColour().startsWith("ucs"))
4760 cs = getUserColourScheme(jm, view.getBgColour());
4762 else if (view.getBgColour().startsWith("Annotation"))
4764 AnnotationColourScheme viewAnnColour = view.getAnnotationColours();
4765 cs = constructAnnotationColour(viewAnnColour, af, al, jm, true);
4772 cs = ColourSchemeProperty.getColourScheme(af.getViewport(), al,
4773 view.getBgColour());
4778 * turn off 'alignment colour applies to all groups'
4779 * while restoring global colour scheme
4781 viewport.setColourAppliesToAllGroups(false);
4782 viewport.setGlobalColourScheme(cs);
4783 viewport.getResidueShading().setThreshold(pidThreshold,
4784 view.isIgnoreGapsinConsensus());
4785 viewport.getResidueShading()
4786 .setConsensus(viewport.getSequenceConsensusHash());
4787 if (safeBoolean(view.isConservationSelected()) && cs != null)
4789 viewport.getResidueShading()
4790 .setConservationInc(safeInt(view.getConsThreshold()));
4792 af.changeColour(cs);
4793 viewport.setColourAppliesToAllGroups(true);
4795 viewport.setShowSequenceFeatures(
4796 safeBoolean(view.isShowSequenceFeatures()));
4798 viewport.setCentreColumnLabels(view.isCentreColumnLabels());
4799 viewport.setIgnoreGapsConsensus(view.isIgnoreGapsinConsensus(), null);
4800 viewport.setFollowHighlight(view.isFollowHighlight());
4801 viewport.followSelection = view.isFollowSelection();
4802 viewport.setShowConsensusHistogram(view.isShowConsensusHistogram());
4803 viewport.setShowSequenceLogo(view.isShowSequenceLogo());
4804 viewport.setNormaliseSequenceLogo(view.isNormaliseSequenceLogo());
4805 viewport.setShowDBRefs(safeBoolean(view.isShowDbRefTooltip()));
4806 viewport.setShowNPFeats(safeBoolean(view.isShowNPfeatureTooltip()));
4807 viewport.setShowGroupConsensus(view.isShowGroupConsensus());
4808 viewport.setShowGroupConservation(view.isShowGroupConservation());
4809 viewport.setShowComplementFeatures(view.isShowComplementFeatures());
4810 viewport.setShowComplementFeaturesOnTop(
4811 view.isShowComplementFeaturesOnTop());
4813 // recover feature settings
4814 if (jm.getFeatureSettings() != null)
4816 FeatureRendererModel fr = af.alignPanel.getSeqPanel().seqCanvas
4817 .getFeatureRenderer();
4818 FeaturesDisplayed fdi;
4819 viewport.setFeaturesDisplayed(fdi = new FeaturesDisplayed());
4820 String[] renderOrder = new String[jm.getFeatureSettings().getSetting()
4822 Map<String, FeatureColourI> featureColours = new Hashtable<>();
4823 Map<String, Float> featureOrder = new Hashtable<>();
4825 for (int fs = 0; fs < jm.getFeatureSettings().getSetting()
4828 Setting setting = jm.getFeatureSettings().getSetting().get(fs);
4829 String featureType = setting.getType();
4832 * restore feature filters (if any)
4834 jalview.xml.binding.jalview.FeatureMatcherSet filters = setting
4836 if (filters != null)
4838 FeatureMatcherSetI filter = Jalview2XML.parseFilter(featureType,
4840 if (!filter.isEmpty())
4842 fr.setFeatureFilter(featureType, filter);
4847 * restore feature colour scheme
4849 Color maxColour = new Color(setting.getColour());
4850 if (setting.getMincolour() != null)
4853 * minColour is always set unless a simple colour
4854 * (including for colour by label though it doesn't use it)
4856 Color minColour = new Color(setting.getMincolour().intValue());
4857 Color noValueColour = minColour;
4858 NoValueColour noColour = setting.getNoValueColour();
4859 if (noColour == NoValueColour.NONE)
4861 noValueColour = null;
4863 else if (noColour == NoValueColour.MAX)
4865 noValueColour = maxColour;
4867 float min = safeFloat(safeFloat(setting.getMin()));
4868 float max = setting.getMax() == null ? 1f
4869 : setting.getMax().floatValue();
4870 FeatureColourI gc = new FeatureColour(maxColour, minColour,
4871 maxColour, noValueColour, min, max);
4872 if (setting.getAttributeName().size() > 0)
4874 gc.setAttributeName(setting.getAttributeName().toArray(
4875 new String[setting.getAttributeName().size()]));
4877 if (setting.getThreshold() != null)
4879 gc.setThreshold(setting.getThreshold().floatValue());
4880 int threshstate = safeInt(setting.getThreshstate());
4881 // -1 = None, 0 = Below, 1 = Above threshold
4882 if (threshstate == 0)
4884 gc.setBelowThreshold(true);
4886 else if (threshstate == 1)
4888 gc.setAboveThreshold(true);
4891 gc.setAutoScaled(true); // default
4892 if (setting.isAutoScale() != null)
4894 gc.setAutoScaled(setting.isAutoScale());
4896 if (setting.isColourByLabel() != null)
4898 gc.setColourByLabel(setting.isColourByLabel());
4900 // and put in the feature colour table.
4901 featureColours.put(featureType, gc);
4905 featureColours.put(featureType, new FeatureColour(maxColour));
4907 renderOrder[fs] = featureType;
4908 if (setting.getOrder() != null)
4910 featureOrder.put(featureType, setting.getOrder().floatValue());
4914 featureOrder.put(featureType, Float.valueOf(
4915 fs / jm.getFeatureSettings().getSetting().size()));
4917 if (safeBoolean(setting.isDisplay()))
4919 fdi.setVisible(featureType);
4922 Map<String, Boolean> fgtable = new Hashtable<>();
4923 for (int gs = 0; gs < jm.getFeatureSettings().getGroup().size(); gs++)
4925 Group grp = jm.getFeatureSettings().getGroup().get(gs);
4926 fgtable.put(grp.getName(), Boolean.valueOf(grp.isDisplay()));
4928 // FeatureRendererSettings frs = new FeatureRendererSettings(renderOrder,
4929 // fgtable, featureColours, jms.getFeatureSettings().hasTransparency() ?
4930 // jms.getFeatureSettings().getTransparency() : 0.0, featureOrder);
4931 FeatureRendererSettings frs = new FeatureRendererSettings(renderOrder,
4932 fgtable, featureColours, 1.0f, featureOrder);
4933 fr.transferSettings(frs);
4936 if (view.getHiddenColumns().size() > 0)
4938 for (int c = 0; c < view.getHiddenColumns().size(); c++)
4940 final HiddenColumns hc = view.getHiddenColumns().get(c);
4941 viewport.hideColumns(safeInt(hc.getStart()),
4942 safeInt(hc.getEnd()) /* +1 */);
4945 if (view.getCalcIdParam() != null)
4947 for (CalcIdParam calcIdParam : view.getCalcIdParam())
4949 if (calcIdParam != null)
4951 if (recoverCalcIdParam(calcIdParam, viewport))
4956 warn("Couldn't recover parameters for "
4957 + calcIdParam.getCalcId());
4962 af.setMenusFromViewport(viewport);
4963 af.setTitle(view.getTitle());
4964 // TODO: we don't need to do this if the viewport is aready visible.
4966 * Add the AlignFrame to the desktop (it may be 'gathered' later), unless it
4967 * has a 'cdna/protein complement' view, in which case save it in order to
4968 * populate a SplitFrame once all views have been read in.
4970 String complementaryViewId = view.getComplementId();
4971 if (complementaryViewId == null)
4973 Desktop.addInternalFrame(af, view.getTitle(),
4974 safeInt(view.getWidth()), safeInt(view.getHeight()));
4975 // recompute any autoannotation
4976 af.alignPanel.updateAnnotation(false, true);
4977 reorderAutoannotation(af, al, autoAlan);
4978 af.alignPanel.alignmentChanged();
4982 splitFrameCandidates.put(view, af);
4988 * Reads saved data to restore Colour by Annotation settings
4990 * @param viewAnnColour
4994 * @param checkGroupAnnColour
4997 private ColourSchemeI constructAnnotationColour(
4998 AnnotationColourScheme viewAnnColour, AlignFrame af,
4999 AlignmentI al, JalviewModel model, boolean checkGroupAnnColour)
5001 boolean propagateAnnColour = false;
5002 AlignmentI annAlignment = af != null ? af.getViewport().getAlignment()
5004 if (checkGroupAnnColour && al.getGroups() != null
5005 && al.getGroups().size() > 0)
5007 // pre 2.8.1 behaviour
5008 // check to see if we should transfer annotation colours
5009 propagateAnnColour = true;
5010 for (SequenceGroup sg : al.getGroups())
5012 if (sg.getColourScheme() instanceof AnnotationColourGradient)
5014 propagateAnnColour = false;
5020 * 2.10.2- : saved annotationId is AlignmentAnnotation.annotationId
5022 String annotationId = viewAnnColour.getAnnotation();
5023 AlignmentAnnotation matchedAnnotation = annotationIds.get(annotationId);
5026 * pre 2.10.2: saved annotationId is AlignmentAnnotation.label
5028 if (matchedAnnotation == null
5029 && annAlignment.getAlignmentAnnotation() != null)
5031 for (int i = 0; i < annAlignment.getAlignmentAnnotation().length; i++)
5034 .equals(annAlignment.getAlignmentAnnotation()[i].label))
5036 matchedAnnotation = annAlignment.getAlignmentAnnotation()[i];
5041 if (matchedAnnotation == null)
5043 System.err.println("Failed to match annotation colour scheme for "
5047 if (matchedAnnotation.getThreshold() == null)
5049 matchedAnnotation.setThreshold(
5050 new GraphLine(safeFloat(viewAnnColour.getThreshold()),
5051 "Threshold", Color.black));
5054 AnnotationColourGradient cs = null;
5055 if (viewAnnColour.getColourScheme().equals("None"))
5057 cs = new AnnotationColourGradient(matchedAnnotation,
5058 new Color(safeInt(viewAnnColour.getMinColour())),
5059 new Color(safeInt(viewAnnColour.getMaxColour())),
5060 safeInt(viewAnnColour.getAboveThreshold()));
5062 else if (viewAnnColour.getColourScheme().startsWith("ucs"))
5064 cs = new AnnotationColourGradient(matchedAnnotation,
5065 getUserColourScheme(model, viewAnnColour.getColourScheme()),
5066 safeInt(viewAnnColour.getAboveThreshold()));
5070 cs = new AnnotationColourGradient(matchedAnnotation,
5071 ColourSchemeProperty.getColourScheme(af.getViewport(), al,
5072 viewAnnColour.getColourScheme()),
5073 safeInt(viewAnnColour.getAboveThreshold()));
5076 boolean perSequenceOnly = safeBoolean(viewAnnColour.isPerSequence());
5077 boolean useOriginalColours = safeBoolean(
5078 viewAnnColour.isPredefinedColours());
5079 cs.setSeqAssociated(perSequenceOnly);
5080 cs.setPredefinedColours(useOriginalColours);
5082 if (propagateAnnColour && al.getGroups() != null)
5084 // Also use these settings for all the groups
5085 for (int g = 0; g < al.getGroups().size(); g++)
5087 SequenceGroup sg = al.getGroups().get(g);
5088 if (sg.getGroupColourScheme() == null)
5093 AnnotationColourGradient groupScheme = new AnnotationColourGradient(
5094 matchedAnnotation, sg.getColourScheme(),
5095 safeInt(viewAnnColour.getAboveThreshold()));
5096 sg.setColourScheme(groupScheme);
5097 groupScheme.setSeqAssociated(perSequenceOnly);
5098 groupScheme.setPredefinedColours(useOriginalColours);
5104 private void reorderAutoannotation(AlignFrame af, AlignmentI al,
5105 List<JvAnnotRow> autoAlan)
5107 // copy over visualization settings for autocalculated annotation in the
5109 if (al.getAlignmentAnnotation() != null)
5112 * Kludge for magic autoannotation names (see JAL-811)
5114 String[] magicNames = new String[] { "Consensus", "Quality",
5116 JvAnnotRow nullAnnot = new JvAnnotRow(-1, null);
5117 Hashtable<String, JvAnnotRow> visan = new Hashtable<>();
5118 for (String nm : magicNames)
5120 visan.put(nm, nullAnnot);
5122 for (JvAnnotRow auan : autoAlan)
5124 visan.put(auan.template.label
5125 + (auan.template.getCalcId() == null ? ""
5126 : "\t" + auan.template.getCalcId()),
5129 int hSize = al.getAlignmentAnnotation().length;
5130 List<JvAnnotRow> reorder = new ArrayList<>();
5131 // work through any autoCalculated annotation already on the view
5132 // removing it if it should be placed in a different location on the
5133 // annotation panel.
5134 List<String> remains = new ArrayList<>(visan.keySet());
5135 for (int h = 0; h < hSize; h++)
5137 jalview.datamodel.AlignmentAnnotation jalan = al
5138 .getAlignmentAnnotation()[h];
5139 if (jalan.autoCalculated)
5142 JvAnnotRow valan = visan.get(k = jalan.label);
5143 if (jalan.getCalcId() != null)
5145 valan = visan.get(k = jalan.label + "\t" + jalan.getCalcId());
5150 // delete the auto calculated row from the alignment
5151 al.deleteAnnotation(jalan, false);
5155 if (valan != nullAnnot)
5157 if (jalan != valan.template)
5159 // newly created autoannotation row instance
5160 // so keep a reference to the visible annotation row
5161 // and copy over all relevant attributes
5162 if (valan.template.graphHeight >= 0)
5165 jalan.graphHeight = valan.template.graphHeight;
5167 jalan.visible = valan.template.visible;
5169 reorder.add(new JvAnnotRow(valan.order, jalan));
5174 // Add any (possibly stale) autocalculated rows that were not appended to
5175 // the view during construction
5176 for (String other : remains)
5178 JvAnnotRow othera = visan.get(other);
5179 if (othera != nullAnnot && othera.template.getCalcId() != null
5180 && othera.template.getCalcId().length() > 0)
5182 reorder.add(othera);
5185 // now put the automatic annotation in its correct place
5186 int s = 0, srt[] = new int[reorder.size()];
5187 JvAnnotRow[] rws = new JvAnnotRow[reorder.size()];
5188 for (JvAnnotRow jvar : reorder)
5191 srt[s++] = jvar.order;
5194 jalview.util.QuickSort.sort(srt, rws);
5195 // and re-insert the annotation at its correct position
5196 for (JvAnnotRow jvar : rws)
5198 al.addAnnotation(jvar.template, jvar.order);
5200 af.alignPanel.adjustAnnotationHeight();
5204 Hashtable skipList = null;
5207 * TODO remove this method
5210 * @return AlignFrame bound to sequenceSetId from view, if one exists. private
5211 * AlignFrame getSkippedFrame(Viewport view) { if (skipList==null) {
5212 * throw new Error("Implementation Error. No skipList defined for this
5213 * Jalview2XML instance."); } return (AlignFrame)
5214 * skipList.get(view.getSequenceSetId()); }
5218 * Check if the Jalview view contained in object should be skipped or not.
5221 * @return true if view's sequenceSetId is a key in skipList
5223 private boolean skipViewport(JalviewModel object)
5225 if (skipList == null)
5229 String id = object.getViewport().get(0).getSequenceSetId();
5230 if (skipList.containsKey(id))
5232 if (Cache.log != null && Cache.log.isDebugEnabled())
5234 Cache.log.debug("Skipping seuqence set id " + id);
5241 public void addToSkipList(AlignFrame af)
5243 if (skipList == null)
5245 skipList = new Hashtable();
5247 skipList.put(af.getViewport().getSequenceSetId(), af);
5250 public void clearSkipList()
5252 if (skipList != null)
5259 private void recoverDatasetFor(SequenceSet vamsasSet, AlignmentI al,
5260 boolean ignoreUnrefed, String uniqueSeqSetId)
5262 jalview.datamodel.AlignmentI ds = getDatasetFor(
5263 vamsasSet.getDatasetId());
5264 AlignmentI xtant_ds = ds;
5265 if (xtant_ds == null)
5267 // good chance we are about to create a new dataset, but check if we've
5268 // seen some of the dataset sequence IDs before.
5269 // TODO: skip this check if we are working with project generated by
5270 // version 2.11 or later
5271 xtant_ds = checkIfHasDataset(vamsasSet.getSequence());
5272 if (xtant_ds != null)
5275 addDatasetRef(vamsasSet.getDatasetId(), ds);
5278 Vector<SequenceI> dseqs = null;
5281 // recovering an alignment View
5282 AlignmentI seqSetDS = getDatasetFor(UNIQSEQSETID + uniqueSeqSetId);
5283 if (seqSetDS != null)
5285 if (ds != null && ds != seqSetDS)
5287 warn("JAL-3171 regression: Overwriting a dataset reference for an alignment"
5288 + " - CDS/Protein crossreference data may be lost");
5289 if (xtant_ds != null)
5291 // This can only happen if the unique sequence set ID was bound to a
5292 // dataset that did not contain any of the sequences in the view
5293 // currently being restored.
5294 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.");
5298 addDatasetRef(vamsasSet.getDatasetId(), ds);
5303 // try even harder to restore dataset
5304 AlignmentI xtantDS = checkIfHasDataset(vamsasSet.getSequence());
5305 // create a list of new dataset sequences
5306 dseqs = new Vector<>();
5308 for (int i = 0, iSize = vamsasSet.getSequence().size(); i < iSize; i++)
5310 Sequence vamsasSeq = vamsasSet.getSequence().get(i);
5311 ensureJalviewDatasetSequence(vamsasSeq, ds, dseqs, ignoreUnrefed, i);
5313 // create a new dataset
5316 SequenceI[] dsseqs = new SequenceI[dseqs.size()];
5317 dseqs.copyInto(dsseqs);
5318 ds = new jalview.datamodel.Alignment(dsseqs);
5319 debug("Created new dataset " + vamsasSet.getDatasetId()
5320 + " for alignment " + System.identityHashCode(al));
5321 addDatasetRef(vamsasSet.getDatasetId(), ds);
5323 // set the dataset for the newly imported alignment.
5324 if (al.getDataset() == null && !ignoreUnrefed)
5327 // register dataset for the alignment's uniqueSeqSetId for legacy projects
5328 addDatasetRef(UNIQSEQSETID + uniqueSeqSetId, ds);
5330 updateSeqDatasetBinding(vamsasSet.getSequence(), ds);
5334 * XML dataset sequence ID to materialised dataset reference
5336 HashMap<String, AlignmentI> seqToDataset = new HashMap<>();
5339 * @return the first materialised dataset reference containing a dataset
5340 * sequence referenced in the given view
5342 * - sequences from the view
5344 AlignmentI checkIfHasDataset(List<Sequence> list)
5346 for (Sequence restoredSeq : list)
5348 AlignmentI datasetFor = seqToDataset.get(restoredSeq.getDsseqid());
5349 if (datasetFor != null)
5358 * Register ds as the containing dataset for the dataset sequences referenced
5359 * by sequences in list
5362 * - sequences in a view
5365 void updateSeqDatasetBinding(List<Sequence> list, AlignmentI ds)
5367 for (Sequence restoredSeq : list)
5369 AlignmentI prevDS = seqToDataset.put(restoredSeq.getDsseqid(), ds);
5370 if (prevDS != null && prevDS != ds)
5372 warn("Dataset sequence appears in many datasets: "
5373 + restoredSeq.getDsseqid());
5374 // TODO: try to merge!
5382 * sequence definition to create/merge dataset sequence for
5386 * vector to add new dataset sequence to
5387 * @param ignoreUnrefed
5388 * - when true, don't create new sequences from vamsasSeq if it's id
5389 * doesn't already have an asssociated Jalview sequence.
5391 * - used to reorder the sequence in the alignment according to the
5392 * vamsasSeq array ordering, to preserve ordering of dataset
5394 private void ensureJalviewDatasetSequence(Sequence vamsasSeq,
5395 AlignmentI ds, Vector<SequenceI> dseqs, boolean ignoreUnrefed,
5398 // JBP TODO: Check this is called for AlCodonFrames to support recovery of
5400 SequenceI sq = seqRefIds.get(vamsasSeq.getId());
5401 boolean reorder = false;
5402 SequenceI dsq = null;
5403 if (sq != null && sq.getDatasetSequence() != null)
5405 dsq = sq.getDatasetSequence();
5411 if (sq == null && ignoreUnrefed)
5415 String sqid = vamsasSeq.getDsseqid();
5418 // need to create or add a new dataset sequence reference to this sequence
5421 dsq = seqRefIds.get(sqid);
5426 // make a new dataset sequence
5427 dsq = sq.createDatasetSequence();
5430 // make up a new dataset reference for this sequence
5431 sqid = seqHash(dsq);
5433 dsq.setVamsasId(uniqueSetSuffix + sqid);
5434 seqRefIds.put(sqid, dsq);
5439 dseqs.addElement(dsq);
5444 ds.addSequence(dsq);
5450 { // make this dataset sequence sq's dataset sequence
5451 sq.setDatasetSequence(dsq);
5452 // and update the current dataset alignment
5457 if (!dseqs.contains(dsq))
5464 if (ds.findIndex(dsq) < 0)
5466 ds.addSequence(dsq);
5473 // TODO: refactor this as a merge dataset sequence function
5474 // now check that sq (the dataset sequence) sequence really is the union of
5475 // all references to it
5476 // boolean pre = sq.getStart() < dsq.getStart();
5477 // boolean post = sq.getEnd() > dsq.getEnd();
5481 // StringBuffer sb = new StringBuffer();
5482 String newres = jalview.analysis.AlignSeq.extractGaps(
5483 jalview.util.Comparison.GapChars, sq.getSequenceAsString());
5484 if (!newres.equalsIgnoreCase(dsq.getSequenceAsString())
5485 && newres.length() > dsq.getLength())
5487 // Update with the longer sequence.
5491 * if (pre) { sb.insert(0, newres .substring(0, dsq.getStart() -
5492 * sq.getStart())); dsq.setStart(sq.getStart()); } if (post) {
5493 * sb.append(newres.substring(newres.length() - sq.getEnd() -
5494 * dsq.getEnd())); dsq.setEnd(sq.getEnd()); }
5496 dsq.setSequence(newres);
5498 // TODO: merges will never happen if we 'know' we have the real dataset
5499 // sequence - this should be detected when id==dssid
5501 "DEBUG Notice: Merged dataset sequence (if you see this often, post at http://issues.jalview.org/browse/JAL-1474)"); // ("
5502 // + (pre ? "prepended" : "") + " "
5503 // + (post ? "appended" : ""));
5508 // sequence refs are identical. We may need to update the existing dataset
5509 // alignment with this one, though.
5510 if (ds != null && dseqs == null)
5512 int opos = ds.findIndex(dsq);
5513 SequenceI tseq = null;
5514 if (opos != -1 && vseqpos != opos)
5516 // remove from old position
5517 ds.deleteSequence(dsq);
5519 if (vseqpos < ds.getHeight())
5521 if (vseqpos != opos)
5523 // save sequence at destination position
5524 tseq = ds.getSequenceAt(vseqpos);
5525 ds.replaceSequenceAt(vseqpos, dsq);
5526 ds.addSequence(tseq);
5531 ds.addSequence(dsq);
5538 * TODO use AlignmentI here and in related methods - needs
5539 * AlignmentI.getDataset() changed to return AlignmentI instead of Alignment
5541 Hashtable<String, AlignmentI> datasetIds = null;
5543 IdentityHashMap<AlignmentI, String> dataset2Ids = null;
5545 private AlignmentI getDatasetFor(String datasetId)
5547 if (datasetIds == null)
5549 datasetIds = new Hashtable<>();
5552 if (datasetIds.containsKey(datasetId))
5554 return datasetIds.get(datasetId);
5559 private void addDatasetRef(String datasetId, AlignmentI dataset)
5561 if (datasetIds == null)
5563 datasetIds = new Hashtable<>();
5565 datasetIds.put(datasetId, dataset);
5569 * make a new dataset ID for this jalview dataset alignment
5574 private String getDatasetIdRef(AlignmentI dataset)
5576 if (dataset.getDataset() != null)
5578 warn("Serious issue! Dataset Object passed to getDatasetIdRef is not a Jalview DATASET alignment...");
5580 String datasetId = makeHashCode(dataset, null);
5581 if (datasetId == null)
5583 // make a new datasetId and record it
5584 if (dataset2Ids == null)
5586 dataset2Ids = new IdentityHashMap<>();
5590 datasetId = dataset2Ids.get(dataset);
5592 if (datasetId == null)
5594 datasetId = "ds" + dataset2Ids.size() + 1;
5595 dataset2Ids.put(dataset, datasetId);
5602 * Add any saved DBRefEntry's to the sequence. An entry flagged as 'locus' is
5603 * constructed as a special subclass GeneLocus.
5605 * @param datasetSequence
5608 private void addDBRefs(SequenceI datasetSequence, Sequence sequence)
5610 for (int d = 0; d < sequence.getDBRef().size(); d++)
5612 DBRef dr = sequence.getDBRef().get(d);
5616 entry = new GeneLocus(dr.getSource(), dr.getVersion(),
5617 dr.getAccessionId());
5621 entry = new DBRefEntry(dr.getSource(), dr.getVersion(),
5622 dr.getAccessionId());
5624 if (dr.getMapping() != null)
5626 entry.setMap(addMapping(dr.getMapping()));
5628 entry.setCanonical(dr.isCanonical());
5629 datasetSequence.addDBRef(entry);
5633 private jalview.datamodel.Mapping addMapping(Mapping m)
5635 SequenceI dsto = null;
5636 // Mapping m = dr.getMapping();
5637 int fr[] = new int[m.getMapListFrom().size() * 2];
5638 Iterator<MapListFrom> from = m.getMapListFrom().iterator();// enumerateMapListFrom();
5639 for (int _i = 0; from.hasNext(); _i += 2)
5641 MapListFrom mf = from.next();
5642 fr[_i] = mf.getStart();
5643 fr[_i + 1] = mf.getEnd();
5645 int fto[] = new int[m.getMapListTo().size() * 2];
5646 Iterator<MapListTo> to = m.getMapListTo().iterator();// enumerateMapListTo();
5647 for (int _i = 0; to.hasNext(); _i += 2)
5649 MapListTo mf = to.next();
5650 fto[_i] = mf.getStart();
5651 fto[_i + 1] = mf.getEnd();
5653 jalview.datamodel.Mapping jmap = new jalview.datamodel.Mapping(dsto, fr,
5654 fto, m.getMapFromUnit().intValue(),
5655 m.getMapToUnit().intValue());
5658 * (optional) choice of dseqFor or Sequence
5660 if (m.getDseqFor() != null)
5662 String dsfor = m.getDseqFor();
5663 if (seqRefIds.containsKey(dsfor))
5668 jmap.setTo(seqRefIds.get(dsfor));
5672 frefedSequence.add(newMappingRef(dsfor, jmap));
5675 else if (m.getSequence() != null)
5678 * local sequence definition
5680 Sequence ms = m.getSequence();
5681 SequenceI djs = null;
5682 String sqid = ms.getDsseqid();
5683 if (sqid != null && sqid.length() > 0)
5686 * recover dataset sequence
5688 djs = seqRefIds.get(sqid);
5693 "Warning - making up dataset sequence id for DbRef sequence map reference");
5694 sqid = ((Object) ms).toString(); // make up a new hascode for
5695 // undefined dataset sequence hash
5696 // (unlikely to happen)
5702 * make a new dataset sequence and add it to refIds hash
5704 djs = new jalview.datamodel.Sequence(ms.getName(),
5706 djs.setStart(jmap.getMap().getToLowest());
5707 djs.setEnd(jmap.getMap().getToHighest());
5708 djs.setVamsasId(uniqueSetSuffix + sqid);
5710 incompleteSeqs.put(sqid, djs);
5711 seqRefIds.put(sqid, djs);
5714 jalview.bin.Cache.log.debug("about to recurse on addDBRefs.");
5723 * Provides a 'copy' of an alignment view (on action New View) by 'saving' the
5724 * view as XML (but not to file), and then reloading it
5729 public AlignmentPanel copyAlignPanel(AlignmentPanel ap)
5732 JalviewModel jm = saveState(ap, null, null, null);
5735 jm.getVamsasModel().getSequenceSet().get(0).getDatasetId(),
5736 ap.getAlignment().getDataset());
5738 uniqueSetSuffix = "";
5739 // jm.getJalviewModelSequence().getViewport(0).setId(null);
5740 jm.getViewport().get(0).setId(null);
5741 // we don't overwrite the view we just copied
5743 if (this.frefedSequence == null)
5745 frefedSequence = new Vector<>();
5748 viewportsAdded.clear();
5750 AlignFrame af = loadFromObject(jm, null, false, null);
5751 af.getAlignPanels().clear();
5752 af.closeMenuItem_actionPerformed(true);
5755 * if(ap.av.getAlignment().getAlignmentAnnotation()!=null) { for(int i=0;
5756 * i<ap.av.getAlignment().getAlignmentAnnotation().length; i++) {
5757 * if(!ap.av.getAlignment().getAlignmentAnnotation()[i].autoCalculated) {
5758 * af.alignPanel.av.getAlignment().getAlignmentAnnotation()[i] =
5759 * ap.av.getAlignment().getAlignmentAnnotation()[i]; } } }
5762 return af.alignPanel;
5765 private Hashtable jvids2vobj;
5767 private void warn(String msg)
5772 private void warn(String msg, Exception e)
5774 if (Cache.log != null)
5778 Cache.log.warn(msg, e);
5782 Cache.log.warn(msg);
5787 System.err.println("Warning: " + msg);
5790 e.printStackTrace();
5795 private void debug(String string)
5797 debug(string, null);
5800 private void debug(String msg, Exception e)
5802 if (Cache.log != null)
5806 Cache.log.debug(msg, e);
5810 Cache.log.debug(msg);
5815 System.err.println("Warning: " + msg);
5818 e.printStackTrace();
5824 * set the object to ID mapping tables used to write/recover objects and XML
5825 * ID strings for the jalview project. If external tables are provided then
5826 * finalize and clearSeqRefs will not clear the tables when the Jalview2XML
5827 * object goes out of scope. - also populates the datasetIds hashtable with
5828 * alignment objects containing dataset sequences
5831 * Map from ID strings to jalview datamodel
5833 * Map from jalview datamodel to ID strings
5837 public void setObjectMappingTables(Hashtable vobj2jv,
5838 IdentityHashMap jv2vobj)
5840 this.jv2vobj = jv2vobj;
5841 this.vobj2jv = vobj2jv;
5842 Iterator ds = jv2vobj.keySet().iterator();
5844 while (ds.hasNext())
5846 Object jvobj = ds.next();
5847 id = jv2vobj.get(jvobj).toString();
5848 if (jvobj instanceof jalview.datamodel.Alignment)
5850 if (((jalview.datamodel.Alignment) jvobj).getDataset() == null)
5852 addDatasetRef(id, (jalview.datamodel.Alignment) jvobj);
5855 else if (jvobj instanceof jalview.datamodel.Sequence)
5857 // register sequence object so the XML parser can recover it.
5858 if (seqRefIds == null)
5860 seqRefIds = new HashMap<>();
5862 if (seqsToIds == null)
5864 seqsToIds = new IdentityHashMap<>();
5866 seqRefIds.put(jv2vobj.get(jvobj).toString(), (SequenceI) jvobj);
5867 seqsToIds.put((SequenceI) jvobj, id);
5869 else if (jvobj instanceof jalview.datamodel.AlignmentAnnotation)
5872 AlignmentAnnotation jvann = (AlignmentAnnotation) jvobj;
5873 annotationIds.put(anid = jv2vobj.get(jvobj).toString(), jvann);
5874 if (jvann.annotationId == null)
5876 jvann.annotationId = anid;
5878 if (!jvann.annotationId.equals(anid))
5880 // TODO verify that this is the correct behaviour
5881 this.warn("Overriding Annotation ID for " + anid
5882 + " from different id : " + jvann.annotationId);
5883 jvann.annotationId = anid;
5886 else if (jvobj instanceof String)
5888 if (jvids2vobj == null)
5890 jvids2vobj = new Hashtable();
5891 jvids2vobj.put(jvobj, jv2vobj.get(jvobj).toString());
5896 Cache.log.debug("Ignoring " + jvobj.getClass() + " (ID = " + id);
5902 * set the uniqueSetSuffix used to prefix/suffix object IDs for jalview
5903 * objects created from the project archive. If string is null (default for
5904 * construction) then suffix will be set automatically.
5908 public void setUniqueSetSuffix(String string)
5910 uniqueSetSuffix = string;
5915 * uses skipList2 as the skipList for skipping views on sequence sets
5916 * associated with keys in the skipList
5920 public void setSkipList(Hashtable skipList2)
5922 skipList = skipList2;
5926 * Reads the jar entry of given name and returns its contents, or null if the
5927 * entry is not found.
5930 * @param jarEntryName
5933 protected String readJarEntry(jarInputStreamProvider jprovider,
5934 String jarEntryName)
5936 String result = null;
5937 BufferedReader in = null;
5942 * Reopen the jar input stream and traverse its entries to find a matching
5945 JarInputStream jin = jprovider.getJarInputStream();
5946 JarEntry entry = null;
5949 entry = jin.getNextJarEntry();
5950 } while (entry != null && !entry.getName().equals(jarEntryName));
5954 StringBuilder out = new StringBuilder(256);
5955 in = new BufferedReader(new InputStreamReader(jin, UTF_8));
5958 while ((data = in.readLine()) != null)
5962 result = out.toString();
5966 warn("Couldn't find entry in Jalview Jar for " + jarEntryName);
5968 } catch (Exception ex)
5970 ex.printStackTrace();
5978 } catch (IOException e)
5989 * Returns an incrementing counter (0, 1, 2...)
5993 private synchronized int nextCounter()
5999 * Loads any saved PCA viewers
6004 protected void loadPCAViewers(JalviewModel model, AlignmentPanel ap)
6008 List<PcaViewer> pcaviewers = model.getPcaViewer();
6009 for (PcaViewer viewer : pcaviewers)
6011 String modelName = viewer.getScoreModelName();
6012 SimilarityParamsI params = new SimilarityParams(
6013 viewer.isIncludeGappedColumns(), viewer.isMatchGaps(),
6014 viewer.isIncludeGaps(),
6015 viewer.isDenominateByShortestLength());
6018 * create the panel (without computing the PCA)
6020 PCAPanel panel = new PCAPanel(ap, modelName, params);
6022 panel.setTitle(viewer.getTitle());
6023 panel.setBounds(new Rectangle(viewer.getXpos(), viewer.getYpos(),
6024 viewer.getWidth(), viewer.getHeight()));
6026 boolean showLabels = viewer.isShowLabels();
6027 panel.setShowLabels(showLabels);
6028 panel.getRotatableCanvas().setShowLabels(showLabels);
6029 panel.getRotatableCanvas()
6030 .setBgColour(new Color(viewer.getBgColour()));
6031 panel.getRotatableCanvas()
6032 .setApplyToAllViews(viewer.isLinkToAllViews());
6035 * load PCA output data
6037 ScoreModelI scoreModel = ScoreModels.getInstance()
6038 .getScoreModel(modelName, ap);
6039 PCA pca = new PCA(null, scoreModel, params);
6040 PcaDataType pcaData = viewer.getPcaData();
6042 MatrixI pairwise = loadDoubleMatrix(pcaData.getPairwiseMatrix());
6043 pca.setPairwiseScores(pairwise);
6045 MatrixI triDiag = loadDoubleMatrix(pcaData.getTridiagonalMatrix());
6046 pca.setTridiagonal(triDiag);
6048 MatrixI result = loadDoubleMatrix(pcaData.getEigenMatrix());
6049 pca.setEigenmatrix(result);
6051 panel.getPcaModel().setPCA(pca);
6054 * we haven't saved the input data! (JAL-2647 to do)
6056 panel.setInputData(null);
6059 * add the sequence points for the PCA display
6061 List<jalview.datamodel.SequencePoint> seqPoints = new ArrayList<>();
6062 for (SequencePoint sp : viewer.getSequencePoint())
6064 String seqId = sp.getSequenceRef();
6065 SequenceI seq = seqRefIds.get(seqId);
6068 throw new IllegalStateException(
6069 "Unmatched seqref for PCA: " + seqId);
6071 Point pt = new Point(sp.getXPos(), sp.getYPos(), sp.getZPos());
6072 jalview.datamodel.SequencePoint seqPoint = new jalview.datamodel.SequencePoint(
6074 seqPoints.add(seqPoint);
6076 panel.getRotatableCanvas().setPoints(seqPoints, seqPoints.size());
6079 * set min-max ranges and scale after setPoints (which recomputes them)
6081 panel.getRotatableCanvas().setScaleFactor(viewer.getScaleFactor());
6082 SeqPointMin spMin = viewer.getSeqPointMin();
6083 float[] min = new float[] { spMin.getXPos(), spMin.getYPos(),
6085 SeqPointMax spMax = viewer.getSeqPointMax();
6086 float[] max = new float[] { spMax.getXPos(), spMax.getYPos(),
6088 panel.getRotatableCanvas().setSeqMinMax(min, max);
6090 // todo: hold points list in PCAModel only
6091 panel.getPcaModel().setSequencePoints(seqPoints);
6093 panel.setSelectedDimensionIndex(viewer.getXDim(), X);
6094 panel.setSelectedDimensionIndex(viewer.getYDim(), Y);
6095 panel.setSelectedDimensionIndex(viewer.getZDim(), Z);
6097 // is this duplication needed?
6098 panel.setTop(seqPoints.size() - 1);
6099 panel.getPcaModel().setTop(seqPoints.size() - 1);
6102 * add the axes' end points for the display
6104 for (int i = 0; i < 3; i++)
6106 Axis axis = viewer.getAxis().get(i);
6107 panel.getRotatableCanvas().getAxisEndPoints()[i] = new Point(
6108 axis.getXPos(), axis.getYPos(), axis.getZPos());
6111 Desktop.addInternalFrame(panel, MessageManager.formatMessage(
6112 "label.calc_title", "PCA", modelName), 475, 450);
6114 } catch (Exception ex)
6116 Cache.log.error("Error loading PCA: " + ex.toString());
6121 * Creates a new structure viewer window
6128 protected void createStructureViewer(ViewerType viewerType,
6129 final Entry<String, StructureViewerModel> viewerData,
6130 AlignFrame af, jarInputStreamProvider jprovider)
6132 final StructureViewerModel viewerModel = viewerData.getValue();
6133 String sessionFilePath = null;
6135 if (viewerType == ViewerType.JMOL)
6137 sessionFilePath = rewriteJmolSession(viewerModel, jprovider);
6141 String viewerJarEntryName = getViewerJarEntryName(
6142 viewerModel.getViewId());
6143 sessionFilePath = copyJarEntry(jprovider, viewerJarEntryName,
6144 "viewerSession", ".tmp");
6146 final String sessionPath = sessionFilePath;
6147 final String sviewid = viewerData.getKey();
6150 SwingUtilities.invokeAndWait(new Runnable()
6155 JalviewStructureDisplayI sview = null;
6158 sview = StructureViewer.createView(viewerType, af.alignPanel,
6159 viewerModel, sessionPath, sviewid);
6160 addNewStructureViewer(sview);
6161 } catch (OutOfMemoryError ex)
6163 new OOMWarning("Restoring structure view for " + viewerType,
6164 (OutOfMemoryError) ex.getCause());
6165 if (sview != null && sview.isVisible())
6167 sview.closeViewer(false);
6168 sview.setVisible(false);
6174 } catch (InvocationTargetException | InterruptedException ex)
6176 warn("Unexpected error when opening " + viewerType
6177 + " structure viewer", ex);
6182 * Rewrites a Jmol session script, saves it to a temporary file, and returns
6183 * the path of the file. "load file" commands are rewritten to change the
6184 * original PDB file names to those created as the Jalview project is loaded.
6190 private String rewriteJmolSession(StructureViewerModel svattrib,
6191 jarInputStreamProvider jprovider)
6193 String state = svattrib.getStateData(); // Jalview < 2.9
6194 if (state == null || state.isEmpty()) // Jalview >= 2.9
6196 String jarEntryName = getViewerJarEntryName(svattrib.getViewId());
6197 state = readJarEntry(jprovider, jarEntryName);
6199 // TODO or simpler? for each key in oldFiles,
6200 // replace key.getPath() in state with oldFiles.get(key).getFilePath()
6201 // (allowing for different path escapings)
6202 StringBuilder rewritten = new StringBuilder(state.length());
6203 int cp = 0, ncp, ecp;
6204 Map<File, StructureData> oldFiles = svattrib.getFileData();
6205 while ((ncp = state.indexOf("load ", cp)) > -1)
6209 // look for next filename in load statement
6210 rewritten.append(state.substring(cp,
6211 ncp = (state.indexOf("\"", ncp + 1) + 1)));
6212 String oldfilenam = state.substring(ncp,
6213 ecp = state.indexOf("\"", ncp));
6214 // recover the new mapping data for this old filename
6215 // have to normalize filename - since Jmol and jalview do
6216 // filename translation differently.
6217 StructureData filedat = oldFiles.get(new File(oldfilenam));
6218 if (filedat == null)
6220 String reformatedOldFilename = oldfilenam.replaceAll("/", "\\\\");
6221 filedat = oldFiles.get(new File(reformatedOldFilename));
6223 rewritten.append(Platform.escapeBackslashes(filedat.getFilePath()));
6224 rewritten.append("\"");
6225 cp = ecp + 1; // advance beyond last \" and set cursor so we can
6226 // look for next file statement.
6227 } while ((ncp = state.indexOf("/*file*/", cp)) > -1);
6231 // just append rest of state
6232 rewritten.append(state.substring(cp));
6236 System.err.print("Ignoring incomplete Jmol state for PDB ids: ");
6237 rewritten = new StringBuilder(state);
6238 rewritten.append("; load append ");
6239 for (File id : oldFiles.keySet())
6241 // add pdb files that should be present in the viewer
6242 StructureData filedat = oldFiles.get(id);
6243 rewritten.append(" \"").append(filedat.getFilePath()).append("\"");
6245 rewritten.append(";");
6248 if (rewritten.length() == 0)
6252 final String history = "history = ";
6253 int historyIndex = rewritten.indexOf(history);
6254 if (historyIndex > -1)
6257 * change "history = [true|false];" to "history = [1|0];"
6259 historyIndex += history.length();
6260 String val = rewritten.substring(historyIndex, historyIndex + 5);
6261 if (val.startsWith("true"))
6263 rewritten.replace(historyIndex, historyIndex + 4, "1");
6265 else if (val.startsWith("false"))
6267 rewritten.replace(historyIndex, historyIndex + 5, "0");
6273 File tmp = File.createTempFile("viewerSession", ".tmp");
6274 try (OutputStream os = new FileOutputStream(tmp))
6276 InputStream is = new ByteArrayInputStream(
6277 rewritten.toString().getBytes());
6279 return tmp.getAbsolutePath();
6281 } catch (IOException e)
6283 Cache.log.error("Error restoring Jmol session: " + e.toString());
6289 * Populates an XML model of the feature colour scheme for one feature type
6291 * @param featureType
6295 public static Colour marshalColour(String featureType,
6296 FeatureColourI fcol)
6298 Colour col = new Colour();
6299 if (fcol.isSimpleColour())
6301 col.setRGB(Format.getHexString(fcol.getColour()));
6305 col.setRGB(Format.getHexString(fcol.getMaxColour()));
6306 col.setMin(fcol.getMin());
6307 col.setMax(fcol.getMax());
6308 col.setMinRGB(jalview.util.Format.getHexString(fcol.getMinColour()));
6309 col.setAutoScale(fcol.isAutoScaled());
6310 col.setThreshold(fcol.getThreshold());
6311 col.setColourByLabel(fcol.isColourByLabel());
6312 col.setThreshType(fcol.isAboveThreshold() ? ThresholdType.ABOVE
6313 : (fcol.isBelowThreshold() ? ThresholdType.BELOW
6314 : ThresholdType.NONE));
6315 if (fcol.isColourByAttribute())
6317 final String[] attName = fcol.getAttributeName();
6318 col.getAttributeName().add(attName[0]);
6319 if (attName.length > 1)
6321 col.getAttributeName().add(attName[1]);
6324 Color noColour = fcol.getNoColour();
6325 if (noColour == null)
6327 col.setNoValueColour(NoValueColour.NONE);
6329 else if (noColour == fcol.getMaxColour())
6331 col.setNoValueColour(NoValueColour.MAX);
6335 col.setNoValueColour(NoValueColour.MIN);
6338 col.setName(featureType);
6343 * Populates an XML model of the feature filter(s) for one feature type
6345 * @param firstMatcher
6346 * the first (or only) match condition)
6348 * remaining match conditions (if any)
6350 * if true, conditions are and-ed, else or-ed
6352 public static jalview.xml.binding.jalview.FeatureMatcherSet marshalFilter(
6353 FeatureMatcherI firstMatcher, Iterator<FeatureMatcherI> filters,
6356 jalview.xml.binding.jalview.FeatureMatcherSet result = new jalview.xml.binding.jalview.FeatureMatcherSet();
6358 if (filters.hasNext())
6363 CompoundMatcher compound = new CompoundMatcher();
6364 compound.setAnd(and);
6365 jalview.xml.binding.jalview.FeatureMatcherSet matcher1 = marshalFilter(
6366 firstMatcher, Collections.emptyIterator(), and);
6367 // compound.addMatcherSet(matcher1);
6368 compound.getMatcherSet().add(matcher1);
6369 FeatureMatcherI nextMatcher = filters.next();
6370 jalview.xml.binding.jalview.FeatureMatcherSet matcher2 = marshalFilter(
6371 nextMatcher, filters, and);
6372 // compound.addMatcherSet(matcher2);
6373 compound.getMatcherSet().add(matcher2);
6374 result.setCompoundMatcher(compound);
6379 * single condition matcher
6381 // MatchCondition matcherModel = new MatchCondition();
6382 jalview.xml.binding.jalview.FeatureMatcher matcherModel = new jalview.xml.binding.jalview.FeatureMatcher();
6383 matcherModel.setCondition(
6384 firstMatcher.getMatcher().getCondition().getStableName());
6385 matcherModel.setValue(firstMatcher.getMatcher().getPattern());
6386 if (firstMatcher.isByAttribute())
6388 matcherModel.setBy(FilterBy.BY_ATTRIBUTE);
6389 // matcherModel.setAttributeName(firstMatcher.getAttribute());
6390 String[] attName = firstMatcher.getAttribute();
6391 matcherModel.getAttributeName().add(attName[0]); // attribute
6392 if (attName.length > 1)
6394 matcherModel.getAttributeName().add(attName[1]); // sub-attribute
6397 else if (firstMatcher.isByLabel())
6399 matcherModel.setBy(FilterBy.BY_LABEL);
6401 else if (firstMatcher.isByScore())
6403 matcherModel.setBy(FilterBy.BY_SCORE);
6405 result.setMatchCondition(matcherModel);
6412 * Loads one XML model of a feature filter to a Jalview object
6414 * @param featureType
6415 * @param matcherSetModel
6418 public static FeatureMatcherSetI parseFilter(String featureType,
6419 jalview.xml.binding.jalview.FeatureMatcherSet matcherSetModel)
6421 FeatureMatcherSetI result = new FeatureMatcherSet();
6424 parseFilterConditions(result, matcherSetModel, true);
6425 } catch (IllegalStateException e)
6427 // mixing AND and OR conditions perhaps
6429 String.format("Error reading filter conditions for '%s': %s",
6430 featureType, e.getMessage()));
6431 // return as much as was parsed up to the error
6438 * Adds feature match conditions to matcherSet as unmarshalled from XML
6439 * (possibly recursively for compound conditions)
6442 * @param matcherSetModel
6444 * if true, multiple conditions are AND-ed, else they are OR-ed
6445 * @throws IllegalStateException
6446 * if AND and OR conditions are mixed
6448 protected static void parseFilterConditions(FeatureMatcherSetI matcherSet,
6449 jalview.xml.binding.jalview.FeatureMatcherSet matcherSetModel,
6452 jalview.xml.binding.jalview.FeatureMatcher mc = matcherSetModel
6453 .getMatchCondition();
6459 FilterBy filterBy = mc.getBy();
6460 Condition cond = Condition.fromString(mc.getCondition());
6461 String pattern = mc.getValue();
6462 FeatureMatcherI matchCondition = null;
6463 if (filterBy == FilterBy.BY_LABEL)
6465 matchCondition = FeatureMatcher.byLabel(cond, pattern);
6467 else if (filterBy == FilterBy.BY_SCORE)
6469 matchCondition = FeatureMatcher.byScore(cond, pattern);
6472 else if (filterBy == FilterBy.BY_ATTRIBUTE)
6474 final List<String> attributeName = mc.getAttributeName();
6475 String[] attNames = attributeName
6476 .toArray(new String[attributeName.size()]);
6477 matchCondition = FeatureMatcher.byAttribute(cond, pattern,
6482 * note this throws IllegalStateException if AND-ing to a
6483 * previously OR-ed compound condition, or vice versa
6487 matcherSet.and(matchCondition);
6491 matcherSet.or(matchCondition);
6497 * compound condition
6499 List<jalview.xml.binding.jalview.FeatureMatcherSet> matchers = matcherSetModel
6500 .getCompoundMatcher().getMatcherSet();
6501 boolean anded = matcherSetModel.getCompoundMatcher().isAnd();
6502 if (matchers.size() == 2)
6504 parseFilterConditions(matcherSet, matchers.get(0), anded);
6505 parseFilterConditions(matcherSet, matchers.get(1), anded);
6509 System.err.println("Malformed compound filter condition");
6515 * Loads one XML model of a feature colour to a Jalview object
6517 * @param colourModel
6520 public static FeatureColourI parseColour(Colour colourModel)
6522 FeatureColourI colour = null;
6524 if (colourModel.getMax() != null)
6526 Color mincol = null;
6527 Color maxcol = null;
6528 Color noValueColour = null;
6532 mincol = new Color(Integer.parseInt(colourModel.getMinRGB(), 16));
6533 maxcol = new Color(Integer.parseInt(colourModel.getRGB(), 16));
6534 } catch (Exception e)
6536 Cache.log.warn("Couldn't parse out graduated feature color.", e);
6539 NoValueColour noCol = colourModel.getNoValueColour();
6540 if (noCol == NoValueColour.MIN)
6542 noValueColour = mincol;
6544 else if (noCol == NoValueColour.MAX)
6546 noValueColour = maxcol;
6549 colour = new FeatureColour(maxcol, mincol, maxcol, noValueColour,
6550 safeFloat(colourModel.getMin()),
6551 safeFloat(colourModel.getMax()));
6552 final List<String> attributeName = colourModel.getAttributeName();
6553 String[] attributes = attributeName
6554 .toArray(new String[attributeName.size()]);
6555 if (attributes != null && attributes.length > 0)
6557 colour.setAttributeName(attributes);
6559 if (colourModel.isAutoScale() != null)
6561 colour.setAutoScaled(colourModel.isAutoScale().booleanValue());
6563 if (colourModel.isColourByLabel() != null)
6565 colour.setColourByLabel(
6566 colourModel.isColourByLabel().booleanValue());
6568 if (colourModel.getThreshold() != null)
6570 colour.setThreshold(colourModel.getThreshold().floatValue());
6572 ThresholdType ttyp = colourModel.getThreshType();
6573 if (ttyp == ThresholdType.ABOVE)
6575 colour.setAboveThreshold(true);
6577 else if (ttyp == ThresholdType.BELOW)
6579 colour.setBelowThreshold(true);
6584 Color color = new Color(Integer.parseInt(colourModel.getRGB(), 16));
6585 colour = new FeatureColour(color);