2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 package jalview.project;
23 import static jalview.math.RotatableMatrix.Axis.X;
24 import static jalview.math.RotatableMatrix.Axis.Y;
25 import static jalview.math.RotatableMatrix.Axis.Z;
27 import java.awt.Color;
29 import java.awt.Rectangle;
30 import java.io.BufferedReader;
31 import java.io.DataOutputStream;
33 import java.io.FileInputStream;
34 import java.io.FileOutputStream;
35 import java.io.IOException;
36 import java.io.InputStream;
37 import java.io.InputStreamReader;
38 import java.io.OutputStream;
39 import java.io.OutputStreamWriter;
40 import java.io.PrintWriter;
41 import java.lang.reflect.InvocationTargetException;
42 import java.math.BigInteger;
43 import java.net.MalformedURLException;
45 import java.util.ArrayList;
46 import java.util.Arrays;
47 import java.util.Collections;
48 import java.util.Enumeration;
49 import java.util.GregorianCalendar;
50 import java.util.HashMap;
51 import java.util.HashSet;
52 import java.util.Hashtable;
53 import java.util.IdentityHashMap;
54 import java.util.Iterator;
55 import java.util.LinkedHashMap;
56 import java.util.List;
58 import java.util.Map.Entry;
60 import java.util.Vector;
61 import java.util.jar.JarEntry;
62 import java.util.jar.JarInputStream;
63 import java.util.jar.JarOutputStream;
65 import javax.swing.JInternalFrame;
66 import javax.swing.SwingUtilities;
67 import javax.xml.bind.JAXBContext;
68 import javax.xml.bind.JAXBElement;
69 import javax.xml.bind.Marshaller;
70 import javax.xml.datatype.DatatypeConfigurationException;
71 import javax.xml.datatype.DatatypeFactory;
72 import javax.xml.datatype.XMLGregorianCalendar;
73 import javax.xml.stream.XMLInputFactory;
74 import javax.xml.stream.XMLStreamReader;
76 import jalview.analysis.Conservation;
77 import jalview.analysis.PCA;
78 import jalview.analysis.scoremodels.ScoreModels;
79 import jalview.analysis.scoremodels.SimilarityParams;
80 import jalview.api.FeatureColourI;
81 import jalview.api.ViewStyleI;
82 import jalview.api.analysis.ScoreModelI;
83 import jalview.api.analysis.SimilarityParamsI;
84 import jalview.api.structures.JalviewStructureDisplayI;
85 import jalview.bin.Cache;
86 import jalview.datamodel.AlignedCodonFrame;
87 import jalview.datamodel.Alignment;
88 import jalview.datamodel.AlignmentAnnotation;
89 import jalview.datamodel.AlignmentI;
90 import jalview.datamodel.DBRefEntry;
91 import jalview.datamodel.GeneLocus;
92 import jalview.datamodel.GraphLine;
93 import jalview.datamodel.PDBEntry;
94 import jalview.datamodel.Point;
95 import jalview.datamodel.RnaViewerModel;
96 import jalview.datamodel.SequenceFeature;
97 import jalview.datamodel.SequenceGroup;
98 import jalview.datamodel.SequenceI;
99 import jalview.datamodel.StructureViewerModel;
100 import jalview.datamodel.StructureViewerModel.StructureData;
101 import jalview.datamodel.features.FeatureMatcher;
102 import jalview.datamodel.features.FeatureMatcherI;
103 import jalview.datamodel.features.FeatureMatcherSet;
104 import jalview.datamodel.features.FeatureMatcherSetI;
105 import jalview.ext.rbvi.chimera.JalviewChimeraBinding;
106 import jalview.ext.varna.RnaModel;
107 import jalview.gui.AlignFrame;
108 import jalview.gui.AlignViewport;
109 import jalview.gui.AlignmentPanel;
110 import jalview.gui.AppVarna;
111 import jalview.gui.ChimeraViewFrame;
112 import jalview.gui.ChimeraXViewFrame;
113 import jalview.gui.Desktop;
114 import jalview.gui.JalviewChimeraXBindingModel;
115 import jalview.gui.JvOptionPane;
116 import jalview.gui.OOMWarning;
117 import jalview.gui.PCAPanel;
118 import jalview.gui.PaintRefresher;
119 import jalview.gui.PymolViewer;
120 import jalview.gui.SplitFrame;
121 import jalview.gui.StructureViewer;
122 import jalview.gui.StructureViewer.ViewerType;
123 import jalview.gui.StructureViewerBase;
124 import jalview.gui.TreePanel;
125 import jalview.io.BackupFiles;
126 import jalview.io.DataSourceType;
127 import jalview.io.FileFormat;
128 import jalview.io.NewickFile;
129 import jalview.math.Matrix;
130 import jalview.math.MatrixI;
131 import jalview.renderer.ResidueShaderI;
132 import jalview.schemes.AnnotationColourGradient;
133 import jalview.schemes.ColourSchemeI;
134 import jalview.schemes.ColourSchemeProperty;
135 import jalview.schemes.FeatureColour;
136 import jalview.schemes.ResidueProperties;
137 import jalview.schemes.UserColourScheme;
138 import jalview.structure.StructureSelectionManager;
139 import jalview.structures.models.AAStructureBindingModel;
140 import jalview.util.Format;
141 import jalview.util.MessageManager;
142 import jalview.util.Platform;
143 import jalview.util.StringUtils;
144 import jalview.util.jarInputStreamProvider;
145 import jalview.util.matcher.Condition;
146 import jalview.viewmodel.AlignmentViewport;
147 import jalview.viewmodel.PCAModel;
148 import jalview.viewmodel.ViewportRanges;
149 import jalview.viewmodel.seqfeatures.FeatureRendererModel;
150 import jalview.viewmodel.seqfeatures.FeatureRendererSettings;
151 import jalview.viewmodel.seqfeatures.FeaturesDisplayed;
152 import jalview.ws.jws2.Jws2Discoverer;
153 import jalview.ws.jws2.dm.AAConSettings;
154 import jalview.ws.jws2.jabaws2.Jws2Instance;
155 import jalview.ws.params.ArgumentI;
156 import jalview.ws.params.AutoCalcSetting;
157 import jalview.ws.params.WsParamSetI;
158 import jalview.xml.binding.jalview.AlcodonFrame;
159 import jalview.xml.binding.jalview.AlcodonFrame.AlcodMap;
160 import jalview.xml.binding.jalview.Annotation;
161 import jalview.xml.binding.jalview.Annotation.ThresholdLine;
162 import jalview.xml.binding.jalview.AnnotationColourScheme;
163 import jalview.xml.binding.jalview.AnnotationElement;
164 import jalview.xml.binding.jalview.DoubleMatrix;
165 import jalview.xml.binding.jalview.DoubleVector;
166 import jalview.xml.binding.jalview.Feature;
167 import jalview.xml.binding.jalview.Feature.OtherData;
168 import jalview.xml.binding.jalview.FeatureMatcherSet.CompoundMatcher;
169 import jalview.xml.binding.jalview.FilterBy;
170 import jalview.xml.binding.jalview.JalviewModel;
171 import jalview.xml.binding.jalview.JalviewModel.FeatureSettings;
172 import jalview.xml.binding.jalview.JalviewModel.FeatureSettings.Group;
173 import jalview.xml.binding.jalview.JalviewModel.FeatureSettings.Setting;
174 import jalview.xml.binding.jalview.JalviewModel.JGroup;
175 import jalview.xml.binding.jalview.JalviewModel.JSeq;
176 import jalview.xml.binding.jalview.JalviewModel.JSeq.Pdbids;
177 import jalview.xml.binding.jalview.JalviewModel.JSeq.Pdbids.StructureState;
178 import jalview.xml.binding.jalview.JalviewModel.JSeq.RnaViewer;
179 import jalview.xml.binding.jalview.JalviewModel.JSeq.RnaViewer.SecondaryStructure;
180 import jalview.xml.binding.jalview.JalviewModel.PcaViewer;
181 import jalview.xml.binding.jalview.JalviewModel.PcaViewer.Axis;
182 import jalview.xml.binding.jalview.JalviewModel.PcaViewer.SeqPointMax;
183 import jalview.xml.binding.jalview.JalviewModel.PcaViewer.SeqPointMin;
184 import jalview.xml.binding.jalview.JalviewModel.PcaViewer.SequencePoint;
185 import jalview.xml.binding.jalview.JalviewModel.Tree;
186 import jalview.xml.binding.jalview.JalviewModel.UserColours;
187 import jalview.xml.binding.jalview.JalviewModel.Viewport;
188 import jalview.xml.binding.jalview.JalviewModel.Viewport.CalcIdParam;
189 import jalview.xml.binding.jalview.JalviewModel.Viewport.HiddenColumns;
190 import jalview.xml.binding.jalview.JalviewUserColours;
191 import jalview.xml.binding.jalview.JalviewUserColours.Colour;
192 import jalview.xml.binding.jalview.MapListType.MapListFrom;
193 import jalview.xml.binding.jalview.MapListType.MapListTo;
194 import jalview.xml.binding.jalview.Mapping;
195 import jalview.xml.binding.jalview.NoValueColour;
196 import jalview.xml.binding.jalview.ObjectFactory;
197 import jalview.xml.binding.jalview.PcaDataType;
198 import jalview.xml.binding.jalview.Pdbentry.Property;
199 import jalview.xml.binding.jalview.Sequence;
200 import jalview.xml.binding.jalview.Sequence.DBRef;
201 import jalview.xml.binding.jalview.SequenceSet;
202 import jalview.xml.binding.jalview.SequenceSet.SequenceSetProperties;
203 import jalview.xml.binding.jalview.ThresholdType;
204 import jalview.xml.binding.jalview.VAMSAS;
207 * Write out the current jalview desktop state as a Jalview XML stream.
209 * Note: the vamsas objects referred to here are primitive versions of the
210 * VAMSAS project schema elements - they are not the same and most likely never
214 * @version $Revision: 1.134 $
216 public class Jalview2XML
218 private static final String VIEWER_PREFIX = "viewer_";
220 private static final String RNA_PREFIX = "rna_";
222 private static final String UTF_8 = "UTF-8";
225 * prefix for recovering datasets for alignments with multiple views where
226 * non-existent dataset IDs were written for some views
228 private static final String UNIQSEQSETID = "uniqueSeqSetId.";
230 // use this with nextCounter() to make unique names for entities
231 private int counter = 0;
234 * SequenceI reference -> XML ID string in jalview XML. Populated as XML reps
235 * of sequence objects are created.
237 IdentityHashMap<SequenceI, String> seqsToIds = null;
240 * jalview XML Sequence ID to jalview sequence object reference (both dataset
241 * and alignment sequences. Populated as XML reps of sequence objects are
244 Map<String, SequenceI> seqRefIds = null;
246 Map<String, SequenceI> incompleteSeqs = null;
248 List<SeqFref> frefedSequence = null;
250 boolean raiseGUI = true; // whether errors are raised in dialog boxes or not
253 * Map of reconstructed AlignFrame objects that appear to have come from
254 * SplitFrame objects (have a dna/protein complement view).
256 private Map<Viewport, AlignFrame> splitFrameCandidates = new HashMap<>();
259 * Map from displayed rna structure models to their saved session state jar
262 private Map<RnaModel, String> rnaSessions = new HashMap<>();
265 * A helper method for safely using the value of an optional attribute that
266 * may be null if not present in the XML. Answers the boolean value, or false
272 public static boolean safeBoolean(Boolean b)
274 return b == null ? false : b.booleanValue();
278 * A helper method for safely using the value of an optional attribute that
279 * may be null if not present in the XML. Answers the integer value, or zero
285 public static int safeInt(Integer i)
287 return i == null ? 0 : i.intValue();
291 * A helper method for safely using the value of an optional attribute that
292 * may be null if not present in the XML. Answers the float value, or zero if
298 public static float safeFloat(Float f)
300 return f == null ? 0f : f.floatValue();
304 * create/return unique hash string for sq
307 * @return new or existing unique string for sq
309 String seqHash(SequenceI sq)
311 if (seqsToIds == null)
315 if (seqsToIds.containsKey(sq))
317 return seqsToIds.get(sq);
321 // create sequential key
322 String key = "sq" + (seqsToIds.size() + 1);
323 key = makeHashCode(sq, key); // check we don't have an external reference
325 seqsToIds.put(sq, key);
332 if (seqsToIds == null)
334 seqsToIds = new IdentityHashMap<>();
336 if (seqRefIds == null)
338 seqRefIds = new HashMap<>();
340 if (incompleteSeqs == null)
342 incompleteSeqs = new HashMap<>();
344 if (frefedSequence == null)
346 frefedSequence = new ArrayList<>();
354 public Jalview2XML(boolean raiseGUI)
356 this.raiseGUI = raiseGUI;
360 * base class for resolving forward references to sequences by their ID
365 abstract class SeqFref
371 public SeqFref(String _sref, String type)
377 public String getSref()
382 public SequenceI getSrefSeq()
384 return seqRefIds.get(sref);
387 public boolean isResolvable()
389 return seqRefIds.get(sref) != null;
392 public SequenceI getSrefDatasetSeq()
394 SequenceI sq = seqRefIds.get(sref);
397 while (sq.getDatasetSequence() != null)
399 sq = sq.getDatasetSequence();
406 * @return true if the forward reference was fully resolved
408 abstract boolean resolve();
411 public String toString()
413 return type + " reference to " + sref;
418 * create forward reference for a mapping
424 public SeqFref newMappingRef(final String sref,
425 final jalview.datamodel.Mapping _jmap)
427 SeqFref fref = new SeqFref(sref, "Mapping")
429 public jalview.datamodel.Mapping jmap = _jmap;
434 SequenceI seq = getSrefDatasetSeq();
446 public SeqFref newAlcodMapRef(final String sref,
447 final AlignedCodonFrame _cf,
448 final jalview.datamodel.Mapping _jmap)
451 SeqFref fref = new SeqFref(sref, "Codon Frame")
453 AlignedCodonFrame cf = _cf;
455 public jalview.datamodel.Mapping mp = _jmap;
458 public boolean isResolvable()
460 return super.isResolvable() && mp.getTo() != null;
466 SequenceI seq = getSrefDatasetSeq();
471 cf.addMap(seq, mp.getTo(), mp.getMap());
478 public void resolveFrefedSequences()
480 Iterator<SeqFref> nextFref = frefedSequence.iterator();
481 int toresolve = frefedSequence.size();
482 int unresolved = 0, failedtoresolve = 0;
483 while (nextFref.hasNext())
485 SeqFref ref = nextFref.next();
486 if (ref.isResolvable())
498 } catch (Exception x)
501 "IMPLEMENTATION ERROR: Failed to resolve forward reference for sequence "
514 System.err.println("Jalview Project Import: There were " + unresolved
515 + " forward references left unresolved on the stack.");
517 if (failedtoresolve > 0)
519 System.err.println("SERIOUS! " + failedtoresolve
520 + " resolvable forward references failed to resolve.");
522 if (incompleteSeqs != null && incompleteSeqs.size() > 0)
525 "Jalview Project Import: There are " + incompleteSeqs.size()
526 + " sequences which may have incomplete metadata.");
527 if (incompleteSeqs.size() < 10)
529 for (SequenceI s : incompleteSeqs.values())
531 System.err.println(s.toString());
537 "Too many to report. Skipping output of incomplete sequences.");
543 * This maintains a map of viewports, the key being the seqSetId. Important to
544 * set historyItem and redoList for multiple views
546 Map<String, AlignViewport> viewportsAdded = new HashMap<>();
548 Map<String, AlignmentAnnotation> annotationIds = new HashMap<>();
550 String uniqueSetSuffix = "";
553 * List of pdbfiles added to Jar
555 List<String> pdbfiles = null;
557 // SAVES SEVERAL ALIGNMENT WINDOWS TO SAME JARFILE
558 public void saveState(File statefile)
560 FileOutputStream fos = null;
565 fos = new FileOutputStream(statefile);
567 JarOutputStream jout = new JarOutputStream(fos);
571 } catch (Exception e)
573 Cache.log.error("Couln't write Jalview state to " + statefile, e);
574 // TODO: inform user of the problem - they need to know if their data was
576 if (errorMessage == null)
578 errorMessage = "Did't write Jalview Archive to output file '"
579 + statefile + "' - See console error log for details";
583 errorMessage += "(Didn't write Jalview Archive to output file '"
594 } catch (IOException e)
604 * Writes a jalview project archive to the given Jar output stream.
608 public void saveState(JarOutputStream jout)
610 AlignFrame[] frames = Desktop.getAlignFrames();
616 saveAllFrames(Arrays.asList(frames), jout);
620 * core method for storing state for a set of AlignFrames.
623 * - frames involving all data to be exported (including containing
626 * - project output stream
628 private void saveAllFrames(List<AlignFrame> frames, JarOutputStream jout)
630 Hashtable<String, AlignFrame> dsses = new Hashtable<>();
633 * ensure cached data is clear before starting
635 // todo tidy up seqRefIds, seqsToIds initialisation / reset
637 splitFrameCandidates.clear();
642 // NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS
643 // //////////////////////////////////////////////////
645 List<String> shortNames = new ArrayList<>();
646 List<String> viewIds = new ArrayList<>();
649 for (int i = frames.size() - 1; i > -1; i--)
651 AlignFrame af = frames.get(i);
653 if (skipList != null && skipList
654 .containsKey(af.getViewport().getSequenceSetId()))
659 String shortName = makeFilename(af, shortNames);
661 int apSize = af.getAlignPanels().size();
663 for (int ap = 0; ap < apSize; ap++)
665 AlignmentPanel apanel = (AlignmentPanel) af.getAlignPanels()
667 String fileName = apSize == 1 ? shortName : ap + shortName;
668 if (!fileName.endsWith(".xml"))
670 fileName = fileName + ".xml";
673 saveState(apanel, fileName, jout, viewIds);
675 String dssid = getDatasetIdRef(
676 af.getViewport().getAlignment().getDataset());
677 if (!dsses.containsKey(dssid))
679 dsses.put(dssid, af);
684 writeDatasetFor(dsses, "" + jout.hashCode() + " " + uniqueSetSuffix,
690 } catch (Exception foo)
695 } catch (Exception ex)
697 // TODO: inform user of the problem - they need to know if their data was
699 if (errorMessage == null)
701 errorMessage = "Couldn't write Jalview Archive - see error output for details";
703 ex.printStackTrace();
708 * Generates a distinct file name, based on the title of the AlignFrame, by
709 * appending _n for increasing n until an unused name is generated. The new
710 * name (without its extension) is added to the list.
714 * @return the generated name, with .xml extension
716 protected String makeFilename(AlignFrame af, List<String> namesUsed)
718 String shortName = af.getTitle();
720 if (shortName.indexOf(File.separatorChar) > -1)
722 shortName = shortName
723 .substring(shortName.lastIndexOf(File.separatorChar) + 1);
728 while (namesUsed.contains(shortName))
730 if (shortName.endsWith("_" + (count - 1)))
732 shortName = shortName.substring(0, shortName.lastIndexOf("_"));
735 shortName = shortName.concat("_" + count);
739 namesUsed.add(shortName);
741 if (!shortName.endsWith(".xml"))
743 shortName = shortName + ".xml";
748 // USE THIS METHOD TO SAVE A SINGLE ALIGNMENT WINDOW
749 public boolean saveAlignment(AlignFrame af, String jarFile,
754 // create backupfiles object and get new temp filename destination
755 BackupFiles backupfiles = new BackupFiles(jarFile);
756 FileOutputStream fos = new FileOutputStream(
757 backupfiles.getTempFilePath());
759 JarOutputStream jout = new JarOutputStream(fos);
760 List<AlignFrame> frames = new ArrayList<>();
762 // resolve splitframes
763 if (af.getViewport().getCodingComplement() != null)
765 frames = ((SplitFrame) af.getSplitViewContainer()).getAlignFrames();
771 saveAllFrames(frames, jout);
775 } catch (Exception foo)
780 boolean success = true;
782 backupfiles.setWriteSuccess(success);
783 success = backupfiles.rollBackupsAndRenameTempFile();
786 } catch (Exception ex)
788 errorMessage = "Couldn't Write alignment view to Jalview Archive - see error output for details";
789 ex.printStackTrace();
794 private void writeDatasetFor(Hashtable<String, AlignFrame> dsses,
795 String fileName, JarOutputStream jout)
798 for (String dssids : dsses.keySet())
800 AlignFrame _af = dsses.get(dssids);
801 String jfileName = fileName + " Dataset for " + _af.getTitle();
802 if (!jfileName.endsWith(".xml"))
804 jfileName = jfileName + ".xml";
806 saveState(_af.alignPanel, jfileName, true, jout, null);
811 * create a JalviewModel from an alignment view and marshall it to a
815 * panel to create jalview model for
817 * name of alignment panel written to output stream
824 public JalviewModel saveState(AlignmentPanel ap, String fileName,
825 JarOutputStream jout, List<String> viewIds)
827 return saveState(ap, fileName, false, jout, viewIds);
831 * create a JalviewModel from an alignment view and marshall it to a
835 * panel to create jalview model for
837 * name of alignment panel written to output stream
839 * when true, only write the dataset for the alignment, not the data
840 * associated with the view.
846 public JalviewModel saveState(AlignmentPanel ap, String fileName,
847 boolean storeDS, JarOutputStream jout, List<String> viewIds)
851 viewIds = new ArrayList<>();
856 List<UserColourScheme> userColours = new ArrayList<>();
858 AlignViewport av = ap.av;
859 ViewportRanges vpRanges = av.getRanges();
861 final ObjectFactory objectFactory = new ObjectFactory();
862 JalviewModel object = objectFactory.createJalviewModel();
863 object.setVamsasModel(new VAMSAS());
865 // object.setCreationDate(new java.util.Date(System.currentTimeMillis()));
868 GregorianCalendar c = new GregorianCalendar();
869 DatatypeFactory datatypeFactory = DatatypeFactory.newInstance();
870 XMLGregorianCalendar now = datatypeFactory.newXMLGregorianCalendar(c);// gregorianCalendar);
871 object.setCreationDate(now);
872 } catch (DatatypeConfigurationException e)
874 System.err.println("error writing date: " + e.toString());
877 jalview.bin.Cache.getDefault("VERSION", "Development Build"));
880 * rjal is full height alignment, jal is actual alignment with full metadata
881 * but excludes hidden sequences.
883 jalview.datamodel.AlignmentI rjal = av.getAlignment(), jal = rjal;
885 if (av.hasHiddenRows())
887 rjal = jal.getHiddenSequences().getFullAlignment();
890 SequenceSet vamsasSet = new SequenceSet();
892 // JalviewModelSequence jms = new JalviewModelSequence();
894 vamsasSet.setGapChar(jal.getGapCharacter() + "");
896 if (jal.getDataset() != null)
898 // dataset id is the dataset's hashcode
899 vamsasSet.setDatasetId(getDatasetIdRef(jal.getDataset()));
902 // switch jal and the dataset
903 jal = jal.getDataset();
907 if (jal.getProperties() != null)
909 Enumeration en = jal.getProperties().keys();
910 while (en.hasMoreElements())
912 String key = en.nextElement().toString();
913 SequenceSetProperties ssp = new SequenceSetProperties();
915 ssp.setValue(jal.getProperties().get(key).toString());
916 // vamsasSet.addSequenceSetProperties(ssp);
917 vamsasSet.getSequenceSetProperties().add(ssp);
922 Set<String> calcIdSet = new HashSet<>();
923 // record the set of vamsas sequence XML POJO we create.
924 HashMap<String, Sequence> vamsasSetIds = new HashMap<>();
926 for (final SequenceI jds : rjal.getSequences())
928 final SequenceI jdatasq = jds.getDatasetSequence() == null ? jds
929 : jds.getDatasetSequence();
930 String id = seqHash(jds);
931 if (vamsasSetIds.get(id) == null)
933 if (seqRefIds.get(id) != null && !storeDS)
935 // This happens for two reasons: 1. multiple views are being
937 // 2. the hashCode has collided with another sequence's code. This
939 // HAPPEN! (PF00072.15.stk does this)
940 // JBPNote: Uncomment to debug writing out of files that do not read
941 // back in due to ArrayOutOfBoundExceptions.
942 // System.err.println("vamsasSeq backref: "+id+"");
943 // System.err.println(jds.getName()+"
944 // "+jds.getStart()+"-"+jds.getEnd()+" "+jds.getSequenceAsString());
945 // System.err.println("Hashcode: "+seqHash(jds));
946 // SequenceI rsq = (SequenceI) seqRefIds.get(id + "");
947 // System.err.println(rsq.getName()+"
948 // "+rsq.getStart()+"-"+rsq.getEnd()+" "+rsq.getSequenceAsString());
949 // System.err.println("Hashcode: "+seqHash(rsq));
953 vamsasSeq = createVamsasSequence(id, jds);
954 // vamsasSet.addSequence(vamsasSeq);
955 vamsasSet.getSequence().add(vamsasSeq);
956 vamsasSetIds.put(id, vamsasSeq);
957 seqRefIds.put(id, jds);
961 jseq.setStart(jds.getStart());
962 jseq.setEnd(jds.getEnd());
963 jseq.setColour(av.getSequenceColour(jds).getRGB());
965 jseq.setId(id); // jseq id should be a string not a number
968 // Store any sequences this sequence represents
969 if (av.hasHiddenRows())
971 // use rjal, contains the full height alignment
973 av.getAlignment().getHiddenSequences().isHidden(jds));
975 if (av.isHiddenRepSequence(jds))
977 jalview.datamodel.SequenceI[] reps = av
978 .getRepresentedSequences(jds).getSequencesInOrder(rjal);
980 for (int h = 0; h < reps.length; h++)
984 // jseq.addHiddenSequences(rjal.findIndex(reps[h]));
985 jseq.getHiddenSequences().add(rjal.findIndex(reps[h]));
990 // mark sequence as reference - if it is the reference for this view
993 jseq.setViewreference(jds == jal.getSeqrep());
997 // TODO: omit sequence features from each alignment view's XML dump if we
998 // are storing dataset
999 List<SequenceFeature> sfs = jds.getSequenceFeatures();
1000 for (SequenceFeature sf : sfs)
1002 // Features features = new Features();
1003 Feature features = new Feature();
1005 features.setBegin(sf.getBegin());
1006 features.setEnd(sf.getEnd());
1007 features.setDescription(sf.getDescription());
1008 features.setType(sf.getType());
1009 features.setFeatureGroup(sf.getFeatureGroup());
1010 features.setScore(sf.getScore());
1011 if (sf.links != null)
1013 for (int l = 0; l < sf.links.size(); l++)
1015 OtherData keyValue = new OtherData();
1016 keyValue.setKey("LINK_" + l);
1017 keyValue.setValue(sf.links.elementAt(l).toString());
1018 // features.addOtherData(keyValue);
1019 features.getOtherData().add(keyValue);
1022 if (sf.otherDetails != null)
1025 * save feature attributes, which may be simple strings or
1026 * map valued (have sub-attributes)
1028 for (Entry<String, Object> entry : sf.otherDetails.entrySet())
1030 String key = entry.getKey();
1031 Object value = entry.getValue();
1032 if (value instanceof Map<?, ?>)
1034 for (Entry<String, Object> subAttribute : ((Map<String, Object>) value)
1037 OtherData otherData = new OtherData();
1038 otherData.setKey(key);
1039 otherData.setKey2(subAttribute.getKey());
1040 otherData.setValue(subAttribute.getValue().toString());
1041 // features.addOtherData(otherData);
1042 features.getOtherData().add(otherData);
1047 OtherData otherData = new OtherData();
1048 otherData.setKey(key);
1049 otherData.setValue(value.toString());
1050 // features.addOtherData(otherData);
1051 features.getOtherData().add(otherData);
1056 // jseq.addFeatures(features);
1057 jseq.getFeatures().add(features);
1060 if (jdatasq.getAllPDBEntries() != null)
1062 Enumeration<PDBEntry> en = jdatasq.getAllPDBEntries().elements();
1063 while (en.hasMoreElements())
1065 Pdbids pdb = new Pdbids();
1066 jalview.datamodel.PDBEntry entry = en.nextElement();
1068 String pdbId = entry.getId();
1070 pdb.setType(entry.getType());
1073 * Store any structure views associated with this sequence. This
1074 * section copes with duplicate entries in the project, so a dataset
1075 * only view *should* be coped with sensibly.
1077 // This must have been loaded, is it still visible?
1078 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1079 String matchedFile = null;
1080 for (int f = frames.length - 1; f > -1; f--)
1082 if (frames[f] instanceof StructureViewerBase)
1084 StructureViewerBase viewFrame = (StructureViewerBase) frames[f];
1085 matchedFile = saveStructureState(ap, jds, pdb, entry, viewIds,
1086 matchedFile, viewFrame);
1088 * Only store each structure viewer's state once in the project
1089 * jar. First time through only (storeDS==false)
1091 String viewId = viewFrame.getViewId();
1092 if (!storeDS && !viewIds.contains(viewId))
1094 viewIds.add(viewId);
1095 File viewerState = viewFrame.saveSession();
1096 if (viewerState != null)
1098 copyFileToJar(jout, viewerState.getPath(),
1099 getViewerJarEntryName(viewId));
1103 Cache.log.error("Failed to save viewer state for "
1105 viewFrame.getViewerType().toString());
1111 if (matchedFile != null || entry.getFile() != null)
1113 if (entry.getFile() != null)
1116 matchedFile = entry.getFile();
1118 pdb.setFile(matchedFile); // entry.getFile());
1119 if (pdbfiles == null)
1121 pdbfiles = new ArrayList<>();
1124 if (!pdbfiles.contains(pdbId))
1126 pdbfiles.add(pdbId);
1127 copyFileToJar(jout, matchedFile, pdbId);
1131 Enumeration<String> props = entry.getProperties();
1132 if (props.hasMoreElements())
1134 // PdbentryItem item = new PdbentryItem();
1135 while (props.hasMoreElements())
1137 Property prop = new Property();
1138 String key = props.nextElement();
1140 prop.setValue(entry.getProperty(key).toString());
1141 // item.addProperty(prop);
1142 pdb.getProperty().add(prop);
1144 // pdb.addPdbentryItem(item);
1147 // jseq.addPdbids(pdb);
1148 jseq.getPdbids().add(pdb);
1152 saveRnaViewers(jout, jseq, jds, viewIds, ap, storeDS);
1154 // jms.addJSeq(jseq);
1155 object.getJSeq().add(jseq);
1158 if (!storeDS && av.hasHiddenRows())
1160 jal = av.getAlignment();
1164 if (storeDS && jal.getCodonFrames() != null)
1166 List<AlignedCodonFrame> jac = jal.getCodonFrames();
1167 for (AlignedCodonFrame acf : jac)
1169 AlcodonFrame alc = new AlcodonFrame();
1170 if (acf.getProtMappings() != null
1171 && acf.getProtMappings().length > 0)
1173 boolean hasMap = false;
1174 SequenceI[] dnas = acf.getdnaSeqs();
1175 jalview.datamodel.Mapping[] pmaps = acf.getProtMappings();
1176 for (int m = 0; m < pmaps.length; m++)
1178 AlcodMap alcmap = new AlcodMap();
1179 alcmap.setDnasq(seqHash(dnas[m]));
1181 createVamsasMapping(pmaps[m], dnas[m], null, false));
1182 // alc.addAlcodMap(alcmap);
1183 alc.getAlcodMap().add(alcmap);
1188 // vamsasSet.addAlcodonFrame(alc);
1189 vamsasSet.getAlcodonFrame().add(alc);
1192 // TODO: delete this ? dead code from 2.8.3->2.9 ?
1194 // AlcodonFrame alc = new AlcodonFrame();
1195 // vamsasSet.addAlcodonFrame(alc);
1196 // for (int p = 0; p < acf.aaWidth; p++)
1198 // Alcodon cmap = new Alcodon();
1199 // if (acf.codons[p] != null)
1201 // // Null codons indicate a gapped column in the translated peptide
1203 // cmap.setPos1(acf.codons[p][0]);
1204 // cmap.setPos2(acf.codons[p][1]);
1205 // cmap.setPos3(acf.codons[p][2]);
1207 // alc.addAlcodon(cmap);
1209 // if (acf.getProtMappings() != null
1210 // && acf.getProtMappings().length > 0)
1212 // SequenceI[] dnas = acf.getdnaSeqs();
1213 // jalview.datamodel.Mapping[] pmaps = acf.getProtMappings();
1214 // for (int m = 0; m < pmaps.length; m++)
1216 // AlcodMap alcmap = new AlcodMap();
1217 // alcmap.setDnasq(seqHash(dnas[m]));
1218 // alcmap.setMapping(createVamsasMapping(pmaps[m], dnas[m], null,
1220 // alc.addAlcodMap(alcmap);
1227 // /////////////////////////////////
1228 if (!storeDS && av.getCurrentTree() != null)
1230 // FIND ANY ASSOCIATED TREES
1231 // NOT IMPLEMENTED FOR HEADLESS STATE AT PRESENT
1232 if (Desktop.desktop != null)
1234 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1236 for (int t = 0; t < frames.length; t++)
1238 if (frames[t] instanceof TreePanel)
1240 TreePanel tp = (TreePanel) frames[t];
1242 if (tp.getTreeCanvas().getViewport().getAlignment() == jal)
1244 JalviewModel.Tree tree = new JalviewModel.Tree();
1245 tree.setTitle(tp.getTitle());
1246 tree.setCurrentTree((av.getCurrentTree() == tp.getTree()));
1247 tree.setNewick(tp.getTree().print());
1248 tree.setThreshold(tp.getTreeCanvas().getThreshold());
1250 tree.setFitToWindow(tp.fitToWindow.getState());
1251 tree.setFontName(tp.getTreeFont().getName());
1252 tree.setFontSize(tp.getTreeFont().getSize());
1253 tree.setFontStyle(tp.getTreeFont().getStyle());
1254 tree.setMarkUnlinked(tp.placeholdersMenu.getState());
1256 tree.setShowBootstrap(tp.bootstrapMenu.getState());
1257 tree.setShowDistances(tp.distanceMenu.getState());
1259 tree.setHeight(tp.getHeight());
1260 tree.setWidth(tp.getWidth());
1261 tree.setXpos(tp.getX());
1262 tree.setYpos(tp.getY());
1263 tree.setId(makeHashCode(tp, null));
1264 tree.setLinkToAllViews(
1265 tp.getTreeCanvas().isApplyToAllViews());
1267 // jms.addTree(tree);
1268 object.getTree().add(tree);
1278 if (!storeDS && Desktop.desktop != null)
1280 for (JInternalFrame frame : Desktop.desktop.getAllFrames())
1282 if (frame instanceof PCAPanel)
1284 PCAPanel panel = (PCAPanel) frame;
1285 if (panel.getAlignViewport().getAlignment() == jal)
1287 savePCA(panel, object);
1295 * store forward refs from an annotationRow to any groups
1297 IdentityHashMap<SequenceGroup, String> groupRefs = new IdentityHashMap<>();
1300 for (SequenceI sq : jal.getSequences())
1302 // Store annotation on dataset sequences only
1303 AlignmentAnnotation[] aa = sq.getAnnotation();
1304 if (aa != null && aa.length > 0)
1306 storeAlignmentAnnotation(aa, groupRefs, av, calcIdSet, storeDS,
1313 if (jal.getAlignmentAnnotation() != null)
1315 // Store the annotation shown on the alignment.
1316 AlignmentAnnotation[] aa = jal.getAlignmentAnnotation();
1317 storeAlignmentAnnotation(aa, groupRefs, av, calcIdSet, storeDS,
1322 if (jal.getGroups() != null)
1324 JGroup[] groups = new JGroup[jal.getGroups().size()];
1326 for (jalview.datamodel.SequenceGroup sg : jal.getGroups())
1328 JGroup jGroup = new JGroup();
1329 groups[++i] = jGroup;
1331 jGroup.setStart(sg.getStartRes());
1332 jGroup.setEnd(sg.getEndRes());
1333 jGroup.setName(sg.getName());
1334 if (groupRefs.containsKey(sg))
1336 // group has references so set its ID field
1337 jGroup.setId(groupRefs.get(sg));
1339 ColourSchemeI colourScheme = sg.getColourScheme();
1340 if (colourScheme != null)
1342 ResidueShaderI groupColourScheme = sg.getGroupColourScheme();
1343 if (groupColourScheme.conservationApplied())
1345 jGroup.setConsThreshold(groupColourScheme.getConservationInc());
1347 if (colourScheme instanceof jalview.schemes.UserColourScheme)
1350 setUserColourScheme(colourScheme, userColours,
1355 jGroup.setColour(colourScheme.getSchemeName());
1358 else if (colourScheme instanceof jalview.schemes.AnnotationColourGradient)
1360 jGroup.setColour("AnnotationColourGradient");
1361 jGroup.setAnnotationColours(constructAnnotationColours(
1362 (jalview.schemes.AnnotationColourGradient) colourScheme,
1363 userColours, object));
1365 else if (colourScheme instanceof jalview.schemes.UserColourScheme)
1368 setUserColourScheme(colourScheme, userColours, object));
1372 jGroup.setColour(colourScheme.getSchemeName());
1375 jGroup.setPidThreshold(groupColourScheme.getThreshold());
1378 jGroup.setOutlineColour(sg.getOutlineColour().getRGB());
1379 jGroup.setDisplayBoxes(sg.getDisplayBoxes());
1380 jGroup.setDisplayText(sg.getDisplayText());
1381 jGroup.setColourText(sg.getColourText());
1382 jGroup.setTextCol1(sg.textColour.getRGB());
1383 jGroup.setTextCol2(sg.textColour2.getRGB());
1384 jGroup.setTextColThreshold(sg.thresholdTextColour);
1385 jGroup.setShowUnconserved(sg.getShowNonconserved());
1386 jGroup.setIgnoreGapsinConsensus(sg.getIgnoreGapsConsensus());
1387 jGroup.setShowConsensusHistogram(sg.isShowConsensusHistogram());
1388 jGroup.setShowSequenceLogo(sg.isShowSequenceLogo());
1389 jGroup.setNormaliseSequenceLogo(sg.isNormaliseSequenceLogo());
1390 for (SequenceI seq : sg.getSequences())
1392 // jGroup.addSeq(seqHash(seq));
1393 jGroup.getSeq().add(seqHash(seq));
1397 //jms.setJGroup(groups);
1399 for (JGroup grp : groups)
1401 object.getJGroup().add(grp);
1406 // /////////SAVE VIEWPORT
1407 Viewport view = new Viewport();
1408 view.setTitle(ap.alignFrame.getTitle());
1409 view.setSequenceSetId(
1410 makeHashCode(av.getSequenceSetId(), av.getSequenceSetId()));
1411 view.setId(av.getViewId());
1412 if (av.getCodingComplement() != null)
1414 view.setComplementId(av.getCodingComplement().getViewId());
1416 view.setViewName(av.getViewName());
1417 view.setGatheredViews(av.isGatherViewsHere());
1419 Rectangle size = ap.av.getExplodedGeometry();
1420 Rectangle position = size;
1423 size = ap.alignFrame.getBounds();
1424 if (av.getCodingComplement() != null)
1426 position = ((SplitFrame) ap.alignFrame.getSplitViewContainer())
1434 view.setXpos(position.x);
1435 view.setYpos(position.y);
1437 view.setWidth(size.width);
1438 view.setHeight(size.height);
1440 view.setStartRes(vpRanges.getStartRes());
1441 view.setStartSeq(vpRanges.getStartSeq());
1443 if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme)
1445 view.setBgColour(setUserColourScheme(av.getGlobalColourScheme(),
1446 userColours, object));
1449 .getGlobalColourScheme() instanceof jalview.schemes.AnnotationColourGradient)
1451 AnnotationColourScheme ac = constructAnnotationColours(
1452 (jalview.schemes.AnnotationColourGradient) av
1453 .getGlobalColourScheme(),
1454 userColours, object);
1456 view.setAnnotationColours(ac);
1457 view.setBgColour("AnnotationColourGradient");
1461 view.setBgColour(ColourSchemeProperty
1462 .getColourName(av.getGlobalColourScheme()));
1465 ResidueShaderI vcs = av.getResidueShading();
1466 ColourSchemeI cs = av.getGlobalColourScheme();
1470 if (vcs.conservationApplied())
1472 view.setConsThreshold(vcs.getConservationInc());
1473 if (cs instanceof jalview.schemes.UserColourScheme)
1475 view.setBgColour(setUserColourScheme(cs, userColours, object));
1478 view.setPidThreshold(vcs.getThreshold());
1481 view.setConservationSelected(av.getConservationSelected());
1482 view.setPidSelected(av.getAbovePIDThreshold());
1483 final Font font = av.getFont();
1484 view.setFontName(font.getName());
1485 view.setFontSize(font.getSize());
1486 view.setFontStyle(font.getStyle());
1487 view.setScaleProteinAsCdna(av.getViewStyle().isScaleProteinAsCdna());
1488 view.setRenderGaps(av.isRenderGaps());
1489 view.setShowAnnotation(av.isShowAnnotation());
1490 view.setShowBoxes(av.getShowBoxes());
1491 view.setShowColourText(av.getColourText());
1492 view.setShowFullId(av.getShowJVSuffix());
1493 view.setRightAlignIds(av.isRightAlignIds());
1494 view.setShowSequenceFeatures(av.isShowSequenceFeatures());
1495 view.setShowText(av.getShowText());
1496 view.setShowUnconserved(av.getShowUnconserved());
1497 view.setWrapAlignment(av.getWrapAlignment());
1498 view.setTextCol1(av.getTextColour().getRGB());
1499 view.setTextCol2(av.getTextColour2().getRGB());
1500 view.setTextColThreshold(av.getThresholdTextColour());
1501 view.setShowConsensusHistogram(av.isShowConsensusHistogram());
1502 view.setShowSequenceLogo(av.isShowSequenceLogo());
1503 view.setNormaliseSequenceLogo(av.isNormaliseSequenceLogo());
1504 view.setShowGroupConsensus(av.isShowGroupConsensus());
1505 view.setShowGroupConservation(av.isShowGroupConservation());
1506 view.setShowNPfeatureTooltip(av.isShowNPFeats());
1507 view.setShowDbRefTooltip(av.isShowDBRefs());
1508 view.setFollowHighlight(av.isFollowHighlight());
1509 view.setFollowSelection(av.followSelection);
1510 view.setIgnoreGapsinConsensus(av.isIgnoreGapsConsensus());
1511 view.setShowComplementFeatures(av.isShowComplementFeatures());
1512 view.setShowComplementFeaturesOnTop(
1513 av.isShowComplementFeaturesOnTop());
1514 if (av.getFeaturesDisplayed() != null)
1516 FeatureSettings fs = new FeatureSettings();
1518 FeatureRendererModel fr = ap.getSeqPanel().seqCanvas
1519 .getFeatureRenderer();
1520 String[] renderOrder = fr.getRenderOrder().toArray(new String[0]);
1522 Vector<String> settingsAdded = new Vector<>();
1523 if (renderOrder != null)
1525 for (String featureType : renderOrder)
1527 FeatureSettings.Setting setting = new FeatureSettings.Setting();
1528 setting.setType(featureType);
1531 * save any filter for the feature type
1533 FeatureMatcherSetI filter = fr.getFeatureFilter(featureType);
1534 if (filter != null) {
1535 Iterator<FeatureMatcherI> filters = filter.getMatchers().iterator();
1536 FeatureMatcherI firstFilter = filters.next();
1537 setting.setMatcherSet(Jalview2XML.marshalFilter(
1538 firstFilter, filters, filter.isAnded()));
1542 * save colour scheme for the feature type
1544 FeatureColourI fcol = fr.getFeatureStyle(featureType);
1545 if (!fcol.isSimpleColour())
1547 setting.setColour(fcol.getMaxColour().getRGB());
1548 setting.setMincolour(fcol.getMinColour().getRGB());
1549 setting.setMin(fcol.getMin());
1550 setting.setMax(fcol.getMax());
1551 setting.setColourByLabel(fcol.isColourByLabel());
1552 if (fcol.isColourByAttribute())
1554 String[] attName = fcol.getAttributeName();
1555 setting.getAttributeName().add(attName[0]);
1556 if (attName.length > 1)
1558 setting.getAttributeName().add(attName[1]);
1561 setting.setAutoScale(fcol.isAutoScaled());
1562 setting.setThreshold(fcol.getThreshold());
1563 Color noColour = fcol.getNoColour();
1564 if (noColour == null)
1566 setting.setNoValueColour(NoValueColour.NONE);
1568 else if (noColour.equals(fcol.getMaxColour()))
1570 setting.setNoValueColour(NoValueColour.MAX);
1574 setting.setNoValueColour(NoValueColour.MIN);
1576 // -1 = No threshold, 0 = Below, 1 = Above
1577 setting.setThreshstate(fcol.isAboveThreshold() ? 1
1578 : (fcol.isBelowThreshold() ? 0 : -1));
1582 setting.setColour(fcol.getColour().getRGB());
1586 av.getFeaturesDisplayed().isVisible(featureType));
1588 .getOrder(featureType);
1591 setting.setOrder(rorder);
1593 /// fs.addSetting(setting);
1594 fs.getSetting().add(setting);
1595 settingsAdded.addElement(featureType);
1599 // is groups actually supposed to be a map here ?
1600 Iterator<String> en = fr.getFeatureGroups().iterator();
1601 Vector<String> groupsAdded = new Vector<>();
1602 while (en.hasNext())
1604 String grp = en.next();
1605 if (groupsAdded.contains(grp))
1609 Group g = new Group();
1611 g.setDisplay(((Boolean) fr.checkGroupVisibility(grp, false))
1614 fs.getGroup().add(g);
1615 groupsAdded.addElement(grp);
1617 // jms.setFeatureSettings(fs);
1618 object.setFeatureSettings(fs);
1621 if (av.hasHiddenColumns())
1623 jalview.datamodel.HiddenColumns hidden = av.getAlignment()
1624 .getHiddenColumns();
1627 warn("REPORT BUG: avoided null columnselection bug (DMAM reported). Please contact Jim about this.");
1631 Iterator<int[]> hiddenRegions = hidden.iterator();
1632 while (hiddenRegions.hasNext())
1634 int[] region = hiddenRegions.next();
1635 HiddenColumns hc = new HiddenColumns();
1636 hc.setStart(region[0]);
1637 hc.setEnd(region[1]);
1638 // view.addHiddenColumns(hc);
1639 view.getHiddenColumns().add(hc);
1643 if (calcIdSet.size() > 0)
1645 for (String calcId : calcIdSet)
1647 if (calcId.trim().length() > 0)
1649 CalcIdParam cidp = createCalcIdParam(calcId, av);
1650 // Some calcIds have no parameters.
1653 // view.addCalcIdParam(cidp);
1654 view.getCalcIdParam().add(cidp);
1660 // jms.addViewport(view);
1661 object.getViewport().add(view);
1663 // object.setJalviewModelSequence(jms);
1664 // object.getVamsasModel().addSequenceSet(vamsasSet);
1665 object.getVamsasModel().getSequenceSet().add(vamsasSet);
1667 if (jout != null && fileName != null)
1669 // We may not want to write the object to disk,
1670 // eg we can copy the alignViewport to a new view object
1671 // using save and then load
1674 System.out.println("Writing jar entry " + fileName);
1675 JarEntry entry = new JarEntry(fileName);
1676 jout.putNextEntry(entry);
1677 PrintWriter pout = new PrintWriter(
1678 new OutputStreamWriter(jout, UTF_8));
1679 JAXBContext jaxbContext = JAXBContext
1680 .newInstance(JalviewModel.class);
1681 Marshaller jaxbMarshaller = jaxbContext.createMarshaller();
1683 // output pretty printed
1684 // jaxbMarshaller.setProperty(Marshaller.JAXB_FORMATTED_OUTPUT, true);
1685 jaxbMarshaller.marshal(
1686 new ObjectFactory().createJalviewModel(object), pout);
1688 // jaxbMarshaller.marshal(object, pout);
1689 // marshaller.marshal(object);
1692 } catch (Exception ex)
1694 // TODO: raise error in GUI if marshalling failed.
1695 System.err.println("Error writing Jalview project");
1696 ex.printStackTrace();
1703 * Writes PCA viewer attributes and computed values to an XML model object and
1704 * adds it to the JalviewModel. Any exceptions are reported by logging.
1706 protected void savePCA(PCAPanel panel, JalviewModel object)
1710 PcaViewer viewer = new PcaViewer();
1711 viewer.setHeight(panel.getHeight());
1712 viewer.setWidth(panel.getWidth());
1713 viewer.setXpos(panel.getX());
1714 viewer.setYpos(panel.getY());
1715 viewer.setTitle(panel.getTitle());
1716 PCAModel pcaModel = panel.getPcaModel();
1717 viewer.setScoreModelName(pcaModel.getScoreModelName());
1718 viewer.setXDim(panel.getSelectedDimensionIndex(X));
1719 viewer.setYDim(panel.getSelectedDimensionIndex(Y));
1720 viewer.setZDim(panel.getSelectedDimensionIndex(Z));
1722 panel.getRotatableCanvas().getBackgroundColour().getRGB());
1723 viewer.setScaleFactor(panel.getRotatableCanvas().getScaleFactor());
1724 float[] spMin = panel.getRotatableCanvas().getSeqMin();
1725 SeqPointMin spmin = new SeqPointMin();
1726 spmin.setXPos(spMin[0]);
1727 spmin.setYPos(spMin[1]);
1728 spmin.setZPos(spMin[2]);
1729 viewer.setSeqPointMin(spmin);
1730 float[] spMax = panel.getRotatableCanvas().getSeqMax();
1731 SeqPointMax spmax = new SeqPointMax();
1732 spmax.setXPos(spMax[0]);
1733 spmax.setYPos(spMax[1]);
1734 spmax.setZPos(spMax[2]);
1735 viewer.setSeqPointMax(spmax);
1736 viewer.setShowLabels(panel.getRotatableCanvas().isShowLabels());
1737 viewer.setLinkToAllViews(
1738 panel.getRotatableCanvas().isApplyToAllViews());
1739 SimilarityParamsI sp = pcaModel.getSimilarityParameters();
1740 viewer.setIncludeGaps(sp.includeGaps());
1741 viewer.setMatchGaps(sp.matchGaps());
1742 viewer.setIncludeGappedColumns(sp.includeGappedColumns());
1743 viewer.setDenominateByShortestLength(sp.denominateByShortestLength());
1746 * sequence points on display
1748 for (jalview.datamodel.SequencePoint spt : pcaModel
1749 .getSequencePoints())
1751 SequencePoint point = new SequencePoint();
1752 point.setSequenceRef(seqHash(spt.getSequence()));
1753 point.setXPos(spt.coord.x);
1754 point.setYPos(spt.coord.y);
1755 point.setZPos(spt.coord.z);
1756 viewer.getSequencePoint().add(point);
1760 * (end points of) axes on display
1762 for (Point p : panel.getRotatableCanvas().getAxisEndPoints())
1765 Axis axis = new Axis();
1769 viewer.getAxis().add(axis);
1773 * raw PCA data (note we are not restoring PCA inputs here -
1774 * alignment view, score model, similarity parameters)
1776 PcaDataType data = new PcaDataType();
1777 viewer.setPcaData(data);
1778 PCA pca = pcaModel.getPcaData();
1780 DoubleMatrix pm = new DoubleMatrix();
1781 saveDoubleMatrix(pca.getPairwiseScores(), pm);
1782 data.setPairwiseMatrix(pm);
1784 DoubleMatrix tm = new DoubleMatrix();
1785 saveDoubleMatrix(pca.getTridiagonal(), tm);
1786 data.setTridiagonalMatrix(tm);
1788 DoubleMatrix eigenMatrix = new DoubleMatrix();
1789 data.setEigenMatrix(eigenMatrix);
1790 saveDoubleMatrix(pca.getEigenmatrix(), eigenMatrix);
1792 object.getPcaViewer().add(viewer);
1793 } catch (Throwable t)
1795 Cache.log.error("Error saving PCA: " + t.getMessage());
1800 * Stores values from a matrix into an XML element, including (if present) the
1805 * @see #loadDoubleMatrix(DoubleMatrix)
1807 protected void saveDoubleMatrix(MatrixI m, DoubleMatrix xmlMatrix)
1809 xmlMatrix.setRows(m.height());
1810 xmlMatrix.setColumns(m.width());
1811 for (int i = 0; i < m.height(); i++)
1813 DoubleVector row = new DoubleVector();
1814 for (int j = 0; j < m.width(); j++)
1816 row.getV().add(m.getValue(i, j));
1818 xmlMatrix.getRow().add(row);
1820 if (m.getD() != null)
1822 DoubleVector dVector = new DoubleVector();
1823 for (double d : m.getD())
1825 dVector.getV().add(d);
1827 xmlMatrix.setD(dVector);
1829 if (m.getE() != null)
1831 DoubleVector eVector = new DoubleVector();
1832 for (double e : m.getE())
1834 eVector.getV().add(e);
1836 xmlMatrix.setE(eVector);
1841 * Loads XML matrix data into a new Matrix object, including the D and/or E
1842 * vectors (if present)
1846 * @see Jalview2XML#saveDoubleMatrix(MatrixI, DoubleMatrix)
1848 protected MatrixI loadDoubleMatrix(DoubleMatrix mData)
1850 int rows = mData.getRows();
1851 double[][] vals = new double[rows][];
1853 for (int i = 0; i < rows; i++)
1855 List<Double> dVector = mData.getRow().get(i).getV();
1856 vals[i] = new double[dVector.size()];
1858 for (Double d : dVector)
1864 MatrixI m = new Matrix(vals);
1866 if (mData.getD() != null)
1868 List<Double> dVector = mData.getD().getV();
1869 double[] vec = new double[dVector.size()];
1871 for (Double d : dVector)
1877 if (mData.getE() != null)
1879 List<Double> dVector = mData.getE().getV();
1880 double[] vec = new double[dVector.size()];
1882 for (Double d : dVector)
1893 * Save any Varna viewers linked to this sequence. Writes an rnaViewer element
1894 * for each viewer, with
1896 * <li>viewer geometry (position, size, split pane divider location)</li>
1897 * <li>index of the selected structure in the viewer (currently shows gapped
1899 * <li>the id of the annotation holding RNA secondary structure</li>
1900 * <li>(currently only one SS is shown per viewer, may be more in future)</li>
1902 * Varna viewer state is also written out (in native Varna XML) to separate
1903 * project jar entries. A separate entry is written for each RNA structure
1904 * displayed, with the naming convention
1906 * <li>rna_viewId_sequenceId_annotationId_[gapped|trimmed]</li>
1914 * @param storeDataset
1916 protected void saveRnaViewers(JarOutputStream jout, JSeq jseq,
1917 final SequenceI jds, List<String> viewIds, AlignmentPanel ap,
1918 boolean storeDataset)
1920 if (Desktop.desktop == null)
1924 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1925 for (int f = frames.length - 1; f > -1; f--)
1927 if (frames[f] instanceof AppVarna)
1929 AppVarna varna = (AppVarna) frames[f];
1931 * link the sequence to every viewer that is showing it and is linked to
1932 * its alignment panel
1934 if (varna.isListeningFor(jds) && ap == varna.getAlignmentPanel())
1936 String viewId = varna.getViewId();
1937 RnaViewer rna = new RnaViewer();
1938 rna.setViewId(viewId);
1939 rna.setTitle(varna.getTitle());
1940 rna.setXpos(varna.getX());
1941 rna.setYpos(varna.getY());
1942 rna.setWidth(varna.getWidth());
1943 rna.setHeight(varna.getHeight());
1944 rna.setDividerLocation(varna.getDividerLocation());
1945 rna.setSelectedRna(varna.getSelectedIndex());
1946 // jseq.addRnaViewer(rna);
1947 jseq.getRnaViewer().add(rna);
1950 * Store each Varna panel's state once in the project per sequence.
1951 * First time through only (storeDataset==false)
1953 // boolean storeSessions = false;
1954 // String sequenceViewId = viewId + seqsToIds.get(jds);
1955 // if (!storeDataset && !viewIds.contains(sequenceViewId))
1957 // viewIds.add(sequenceViewId);
1958 // storeSessions = true;
1960 for (RnaModel model : varna.getModels())
1962 if (model.seq == jds)
1965 * VARNA saves each view (sequence or alignment secondary
1966 * structure, gapped or trimmed) as a separate XML file
1968 String jarEntryName = rnaSessions.get(model);
1969 if (jarEntryName == null)
1972 String varnaStateFile = varna.getStateInfo(model.rna);
1973 jarEntryName = RNA_PREFIX + viewId + "_" + nextCounter();
1974 copyFileToJar(jout, varnaStateFile, jarEntryName);
1975 rnaSessions.put(model, jarEntryName);
1977 SecondaryStructure ss = new SecondaryStructure();
1978 String annotationId = varna.getAnnotation(jds).annotationId;
1979 ss.setAnnotationId(annotationId);
1980 ss.setViewerState(jarEntryName);
1981 ss.setGapped(model.gapped);
1982 ss.setTitle(model.title);
1983 // rna.addSecondaryStructure(ss);
1984 rna.getSecondaryStructure().add(ss);
1993 * Copy the contents of a file to a new entry added to the output jar
1997 * @param jarEntryName
1999 protected void copyFileToJar(JarOutputStream jout, String infilePath,
2000 String jarEntryName)
2002 try (InputStream is = new FileInputStream(infilePath))
2004 File file = new File(infilePath);
2005 if (file.exists() && jout != null)
2007 System.out.println("Writing jar entry " + jarEntryName);
2008 jout.putNextEntry(new JarEntry(jarEntryName));
2011 // dis = new DataInputStream(new FileInputStream(file));
2012 // byte[] data = new byte[(int) file.length()];
2013 // dis.readFully(data);
2014 // writeJarEntry(jout, jarEntryName, data);
2016 } catch (Exception ex)
2018 ex.printStackTrace();
2023 * Write the data to a new entry of given name in the output jar file
2026 * @param jarEntryName
2028 * @throws IOException
2030 protected void writeJarEntry(JarOutputStream jout, String jarEntryName,
2031 byte[] data) throws IOException
2035 System.out.println("Writing jar entry " + jarEntryName);
2036 jout.putNextEntry(new JarEntry(jarEntryName));
2037 DataOutputStream dout = new DataOutputStream(jout);
2038 dout.write(data, 0, data.length);
2045 * Copies input to output, in 4K buffers; handles any data (text or binary)
2049 * @throws IOException
2051 protected void copyAll(InputStream in, OutputStream out)
2054 byte[] buffer = new byte[4096];
2056 while ((bytesRead = in.read(buffer)) != -1)
2058 out.write(buffer, 0, bytesRead);
2063 * Save the state of a structure viewer
2068 * the archive XML element under which to save the state
2071 * @param matchedFile
2075 protected String saveStructureState(AlignmentPanel ap, SequenceI jds,
2076 Pdbids pdb, PDBEntry entry, List<String> viewIds,
2077 String matchedFile, StructureViewerBase viewFrame)
2079 final AAStructureBindingModel bindingModel = viewFrame.getBinding();
2082 * Look for any bindings for this viewer to the PDB file of interest
2083 * (including part matches excluding chain id)
2085 for (int peid = 0; peid < bindingModel.getPdbCount(); peid++)
2087 final PDBEntry pdbentry = bindingModel.getPdbEntry(peid);
2088 final String pdbId = pdbentry.getId();
2089 if (!pdbId.equals(entry.getId())
2090 && !(entry.getId().length() > 4 && entry.getId().toLowerCase()
2091 .startsWith(pdbId.toLowerCase())))
2094 * not interested in a binding to a different PDB entry here
2098 if (matchedFile == null)
2100 matchedFile = pdbentry.getFile();
2102 else if (!matchedFile.equals(pdbentry.getFile()))
2105 "Probably lost some PDB-Sequence mappings for this structure file (which apparently has same PDB Entry code): "
2106 + pdbentry.getFile());
2110 // can get at it if the ID
2111 // match is ambiguous (e.g.
2114 for (int smap = 0; smap < viewFrame.getBinding()
2115 .getSequence()[peid].length; smap++)
2117 // if (jal.findIndex(jmol.jmb.sequence[peid][smap]) > -1)
2118 if (jds == viewFrame.getBinding().getSequence()[peid][smap])
2120 StructureState state = new StructureState();
2121 state.setVisible(true);
2122 state.setXpos(viewFrame.getX());
2123 state.setYpos(viewFrame.getY());
2124 state.setWidth(viewFrame.getWidth());
2125 state.setHeight(viewFrame.getHeight());
2126 final String viewId = viewFrame.getViewId();
2127 state.setViewId(viewId);
2128 state.setAlignwithAlignPanel(viewFrame.isUsedforaligment(ap));
2129 state.setColourwithAlignPanel(viewFrame.isUsedForColourBy(ap));
2130 state.setColourByJmol(viewFrame.isColouredByViewer());
2131 state.setType(viewFrame.getViewerType().toString());
2132 // pdb.addStructureState(state);
2133 pdb.getStructureState().add(state);
2141 * Populates the AnnotationColourScheme xml for save. This captures the
2142 * settings of the options in the 'Colour by Annotation' dialog.
2145 * @param userColours
2149 private AnnotationColourScheme constructAnnotationColours(
2150 AnnotationColourGradient acg, List<UserColourScheme> userColours,
2153 AnnotationColourScheme ac = new AnnotationColourScheme();
2154 ac.setAboveThreshold(acg.getAboveThreshold());
2155 ac.setThreshold(acg.getAnnotationThreshold());
2156 // 2.10.2 save annotationId (unique) not annotation label
2157 ac.setAnnotation(acg.getAnnotation().annotationId);
2158 if (acg.getBaseColour() instanceof UserColourScheme)
2161 setUserColourScheme(acg.getBaseColour(), userColours, jm));
2166 ColourSchemeProperty.getColourName(acg.getBaseColour()));
2169 ac.setMaxColour(acg.getMaxColour().getRGB());
2170 ac.setMinColour(acg.getMinColour().getRGB());
2171 ac.setPerSequence(acg.isSeqAssociated());
2172 ac.setPredefinedColours(acg.isPredefinedColours());
2176 private void storeAlignmentAnnotation(AlignmentAnnotation[] aa,
2177 IdentityHashMap<SequenceGroup, String> groupRefs,
2178 AlignmentViewport av, Set<String> calcIdSet, boolean storeDS,
2179 SequenceSet vamsasSet)
2182 for (int i = 0; i < aa.length; i++)
2184 Annotation an = new Annotation();
2186 AlignmentAnnotation annotation = aa[i];
2187 if (annotation.annotationId != null)
2189 annotationIds.put(annotation.annotationId, annotation);
2192 an.setId(annotation.annotationId);
2194 an.setVisible(annotation.visible);
2196 an.setDescription(annotation.description);
2198 if (annotation.sequenceRef != null)
2200 // 2.9 JAL-1781 xref on sequence id rather than name
2201 an.setSequenceRef(seqsToIds.get(annotation.sequenceRef));
2203 if (annotation.groupRef != null)
2205 String groupIdr = groupRefs.get(annotation.groupRef);
2206 if (groupIdr == null)
2208 // make a locally unique String
2209 groupRefs.put(annotation.groupRef,
2210 groupIdr = ("" + System.currentTimeMillis()
2211 + annotation.groupRef.getName()
2212 + groupRefs.size()));
2214 an.setGroupRef(groupIdr.toString());
2217 // store all visualization attributes for annotation
2218 an.setGraphHeight(annotation.graphHeight);
2219 an.setCentreColLabels(annotation.centreColLabels);
2220 an.setScaleColLabels(annotation.scaleColLabel);
2221 an.setShowAllColLabels(annotation.showAllColLabels);
2222 an.setBelowAlignment(annotation.belowAlignment);
2224 if (annotation.graph > 0)
2227 an.setGraphType(annotation.graph);
2228 an.setGraphGroup(annotation.graphGroup);
2229 if (annotation.getThreshold() != null)
2231 ThresholdLine line = new ThresholdLine();
2232 line.setLabel(annotation.getThreshold().label);
2233 line.setValue(annotation.getThreshold().value);
2234 line.setColour(annotation.getThreshold().colour.getRGB());
2235 an.setThresholdLine(line);
2243 an.setLabel(annotation.label);
2245 if (annotation == av.getAlignmentQualityAnnot()
2246 || annotation == av.getAlignmentConservationAnnotation()
2247 || annotation == av.getAlignmentConsensusAnnotation()
2248 || annotation.autoCalculated)
2250 // new way of indicating autocalculated annotation -
2251 an.setAutoCalculated(annotation.autoCalculated);
2253 if (annotation.hasScore())
2255 an.setScore(annotation.getScore());
2258 if (annotation.getCalcId() != null)
2260 calcIdSet.add(annotation.getCalcId());
2261 an.setCalcId(annotation.getCalcId());
2263 if (annotation.hasProperties())
2265 for (String pr : annotation.getProperties())
2267 jalview.xml.binding.jalview.Annotation.Property prop = new jalview.xml.binding.jalview.Annotation.Property();
2269 prop.setValue(annotation.getProperty(pr));
2270 // an.addProperty(prop);
2271 an.getProperty().add(prop);
2275 AnnotationElement ae;
2276 if (annotation.annotations != null)
2278 an.setScoreOnly(false);
2279 for (int a = 0; a < annotation.annotations.length; a++)
2281 if ((annotation == null) || (annotation.annotations[a] == null))
2286 ae = new AnnotationElement();
2287 if (annotation.annotations[a].description != null)
2289 ae.setDescription(annotation.annotations[a].description);
2291 if (annotation.annotations[a].displayCharacter != null)
2293 ae.setDisplayCharacter(
2294 annotation.annotations[a].displayCharacter);
2297 if (!Float.isNaN(annotation.annotations[a].value))
2299 ae.setValue(annotation.annotations[a].value);
2303 if (annotation.annotations[a].secondaryStructure > ' ')
2305 ae.setSecondaryStructure(
2306 annotation.annotations[a].secondaryStructure + "");
2309 if (annotation.annotations[a].colour != null
2310 && annotation.annotations[a].colour != java.awt.Color.black)
2312 ae.setColour(annotation.annotations[a].colour.getRGB());
2315 // an.addAnnotationElement(ae);
2316 an.getAnnotationElement().add(ae);
2317 if (annotation.autoCalculated)
2319 // only write one non-null entry into the annotation row -
2320 // sufficient to get the visualization attributes necessary to
2328 an.setScoreOnly(true);
2330 if (!storeDS || (storeDS && !annotation.autoCalculated))
2332 // skip autocalculated annotation - these are only provided for
2334 // vamsasSet.addAnnotation(an);
2335 vamsasSet.getAnnotation().add(an);
2341 private CalcIdParam createCalcIdParam(String calcId, AlignViewport av)
2343 AutoCalcSetting settings = av.getCalcIdSettingsFor(calcId);
2344 if (settings != null)
2346 CalcIdParam vCalcIdParam = new CalcIdParam();
2347 vCalcIdParam.setCalcId(calcId);
2348 // vCalcIdParam.addServiceURL(settings.getServiceURI());
2349 vCalcIdParam.getServiceURL().add(settings.getServiceURI());
2350 // generic URI allowing a third party to resolve another instance of the
2351 // service used for this calculation
2352 for (String url : settings.getServiceURLs())
2354 // vCalcIdParam.addServiceURL(urls);
2355 vCalcIdParam.getServiceURL().add(url);
2357 vCalcIdParam.setVersion("1.0");
2358 if (settings.getPreset() != null)
2360 WsParamSetI setting = settings.getPreset();
2361 vCalcIdParam.setName(setting.getName());
2362 vCalcIdParam.setDescription(setting.getDescription());
2366 vCalcIdParam.setName("");
2367 vCalcIdParam.setDescription("Last used parameters");
2369 // need to be able to recover 1) settings 2) user-defined presets or
2370 // recreate settings from preset 3) predefined settings provided by
2371 // service - or settings that can be transferred (or discarded)
2372 vCalcIdParam.setParameters(
2373 settings.getWsParamFile().replace("\n", "|\\n|"));
2374 vCalcIdParam.setAutoUpdate(settings.isAutoUpdate());
2375 // todo - decide if updateImmediately is needed for any projects.
2377 return vCalcIdParam;
2382 private boolean recoverCalcIdParam(CalcIdParam calcIdParam,
2385 if (calcIdParam.getVersion().equals("1.0"))
2387 final String[] calcIds = calcIdParam.getServiceURL().toArray(new String[0]);
2388 Jws2Instance service = Jws2Discoverer.getDiscoverer()
2389 .getPreferredServiceFor(calcIds);
2390 if (service != null)
2392 WsParamSetI parmSet = null;
2395 parmSet = service.getParamStore().parseServiceParameterFile(
2396 calcIdParam.getName(), calcIdParam.getDescription(),
2398 calcIdParam.getParameters().replace("|\\n|", "\n"));
2399 } catch (IOException x)
2401 warn("Couldn't parse parameter data for "
2402 + calcIdParam.getCalcId(), x);
2405 List<ArgumentI> argList = null;
2406 if (calcIdParam.getName().length() > 0)
2408 parmSet = service.getParamStore()
2409 .getPreset(calcIdParam.getName());
2410 if (parmSet != null)
2412 // TODO : check we have a good match with settings in AACon -
2413 // otherwise we'll need to create a new preset
2418 argList = parmSet.getArguments();
2421 AAConSettings settings = new AAConSettings(
2422 calcIdParam.isAutoUpdate(), service, parmSet, argList);
2423 av.setCalcIdSettingsFor(calcIdParam.getCalcId(), settings,
2424 calcIdParam.isNeedsUpdate());
2429 warn("Cannot resolve a service for the parameters used in this project. Try configuring a JABAWS server.");
2433 throw new Error(MessageManager.formatMessage(
2434 "error.unsupported_version_calcIdparam", new Object[]
2435 { calcIdParam.toString() }));
2439 * External mapping between jalview objects and objects yielding a valid and
2440 * unique object ID string. This is null for normal Jalview project IO, but
2441 * non-null when a jalview project is being read or written as part of a
2444 IdentityHashMap jv2vobj = null;
2447 * Construct a unique ID for jvobj using either existing bindings or if none
2448 * exist, the result of the hashcode call for the object.
2451 * jalview data object
2452 * @return unique ID for referring to jvobj
2454 private String makeHashCode(Object jvobj, String altCode)
2456 if (jv2vobj != null)
2458 Object id = jv2vobj.get(jvobj);
2461 return id.toString();
2463 // check string ID mappings
2464 if (jvids2vobj != null && jvobj instanceof String)
2466 id = jvids2vobj.get(jvobj);
2470 return id.toString();
2472 // give up and warn that something has gone wrong
2473 warn("Cannot find ID for object in external mapping : " + jvobj);
2479 * return local jalview object mapped to ID, if it exists
2483 * @return null or object bound to idcode
2485 private Object retrieveExistingObj(String idcode)
2487 if (idcode != null && vobj2jv != null)
2489 return vobj2jv.get(idcode);
2495 * binding from ID strings from external mapping table to jalview data model
2498 private Hashtable vobj2jv;
2500 private Sequence createVamsasSequence(String id, SequenceI jds)
2502 return createVamsasSequence(true, id, jds, null);
2505 private Sequence createVamsasSequence(boolean recurse, String id,
2506 SequenceI jds, SequenceI parentseq)
2508 Sequence vamsasSeq = new Sequence();
2509 vamsasSeq.setId(id);
2510 vamsasSeq.setName(jds.getName());
2511 vamsasSeq.setSequence(jds.getSequenceAsString());
2512 vamsasSeq.setDescription(jds.getDescription());
2513 jalview.datamodel.DBRefEntry[] dbrefs = null;
2514 if (jds.getDatasetSequence() != null)
2516 vamsasSeq.setDsseqid(seqHash(jds.getDatasetSequence()));
2520 // seqId==dsseqid so we can tell which sequences really are
2521 // dataset sequences only
2522 vamsasSeq.setDsseqid(id);
2523 dbrefs = jds.getDBRefs();
2524 if (parentseq == null)
2531 * save any dbrefs; special subclass GeneLocus is flagged as 'locus'
2535 for (int d = 0; d < dbrefs.length; d++)
2537 DBRef dbref = new DBRef();
2538 DBRefEntry dbRefEntry = dbrefs[d];
2539 dbref.setSource(dbRefEntry.getSource());
2540 dbref.setVersion(dbRefEntry.getVersion());
2541 dbref.setAccessionId(dbRefEntry.getAccessionId());
2542 if (dbRefEntry instanceof GeneLocus)
2544 dbref.setLocus(true);
2546 if (dbRefEntry.hasMap())
2548 Mapping mp = createVamsasMapping(dbRefEntry.getMap(), parentseq,
2550 dbref.setMapping(mp);
2552 vamsasSeq.getDBRef().add(dbref);
2558 private Mapping createVamsasMapping(jalview.datamodel.Mapping jmp,
2559 SequenceI parentseq, SequenceI jds, boolean recurse)
2562 if (jmp.getMap() != null)
2566 jalview.util.MapList mlst = jmp.getMap();
2567 List<int[]> r = mlst.getFromRanges();
2568 for (int[] range : r)
2570 MapListFrom mfrom = new MapListFrom();
2571 mfrom.setStart(range[0]);
2572 mfrom.setEnd(range[1]);
2573 // mp.addMapListFrom(mfrom);
2574 mp.getMapListFrom().add(mfrom);
2576 r = mlst.getToRanges();
2577 for (int[] range : r)
2579 MapListTo mto = new MapListTo();
2580 mto.setStart(range[0]);
2581 mto.setEnd(range[1]);
2582 // mp.addMapListTo(mto);
2583 mp.getMapListTo().add(mto);
2585 mp.setMapFromUnit(BigInteger.valueOf(mlst.getFromRatio()));
2586 mp.setMapToUnit(BigInteger.valueOf(mlst.getToRatio()));
2587 if (jmp.getTo() != null)
2589 // MappingChoice mpc = new MappingChoice();
2591 // check/create ID for the sequence referenced by getTo()
2594 SequenceI ps = null;
2595 if (parentseq != jmp.getTo()
2596 && parentseq.getDatasetSequence() != jmp.getTo())
2598 // chaining dbref rather than a handshaking one
2599 jmpid = seqHash(ps = jmp.getTo());
2603 jmpid = seqHash(ps = parentseq);
2605 // mpc.setDseqFor(jmpid);
2606 mp.setDseqFor(jmpid);
2607 if (!seqRefIds.containsKey(jmpid))
2609 jalview.bin.Cache.log.debug("creatign new DseqFor ID");
2610 seqRefIds.put(jmpid, ps);
2614 jalview.bin.Cache.log.debug("reusing DseqFor ID");
2617 // mp.setMappingChoice(mpc);
2623 String setUserColourScheme(jalview.schemes.ColourSchemeI cs,
2624 List<UserColourScheme> userColours, JalviewModel jm)
2627 jalview.schemes.UserColourScheme ucs = (jalview.schemes.UserColourScheme) cs;
2628 boolean newucs = false;
2629 if (!userColours.contains(ucs))
2631 userColours.add(ucs);
2634 id = "ucs" + userColours.indexOf(ucs);
2637 // actually create the scheme's entry in the XML model
2638 java.awt.Color[] colours = ucs.getColours();
2639 UserColours uc = new UserColours();
2640 // UserColourScheme jbucs = new UserColourScheme();
2641 JalviewUserColours jbucs = new JalviewUserColours();
2643 for (int i = 0; i < colours.length; i++)
2645 Colour col = new Colour();
2646 col.setName(ResidueProperties.aa[i]);
2647 col.setRGB(jalview.util.Format.getHexString(colours[i]));
2648 // jbucs.addColour(col);
2649 jbucs.getColour().add(col);
2651 if (ucs.getLowerCaseColours() != null)
2653 colours = ucs.getLowerCaseColours();
2654 for (int i = 0; i < colours.length; i++)
2656 Colour col = new Colour();
2657 col.setName(ResidueProperties.aa[i].toLowerCase());
2658 col.setRGB(jalview.util.Format.getHexString(colours[i]));
2659 // jbucs.addColour(col);
2660 jbucs.getColour().add(col);
2665 uc.setUserColourScheme(jbucs);
2666 // jm.addUserColours(uc);
2667 jm.getUserColours().add(uc);
2673 jalview.schemes.UserColourScheme getUserColourScheme(
2674 JalviewModel jm, String id)
2676 List<UserColours> uc = jm.getUserColours();
2677 UserColours colours = null;
2679 for (int i = 0; i < uc.length; i++)
2681 if (uc[i].getId().equals(id))
2688 for (UserColours c : uc)
2690 if (c.getId().equals(id))
2697 java.awt.Color[] newColours = new java.awt.Color[24];
2699 for (int i = 0; i < 24; i++)
2701 newColours[i] = new java.awt.Color(Integer.parseInt(
2702 // colours.getUserColourScheme().getColour(i).getRGB(), 16));
2703 colours.getUserColourScheme().getColour().get(i).getRGB(),
2707 jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(
2710 if (colours.getUserColourScheme().getColour().size()/*Count()*/ > 24)
2712 newColours = new java.awt.Color[23];
2713 for (int i = 0; i < 23; i++)
2715 newColours[i] = new java.awt.Color(Integer.parseInt(
2716 colours.getUserColourScheme().getColour().get(i + 24)
2720 ucs.setLowerCaseColours(newColours);
2727 * contains last error message (if any) encountered by XML loader.
2729 String errorMessage = null;
2732 * flag to control whether the Jalview2XML_V1 parser should be deferred to if
2733 * exceptions are raised during project XML parsing
2735 public boolean attemptversion1parse = false;
2738 * Load a jalview project archive from a jar file
2741 * - HTTP URL or filename
2743 public AlignFrame loadJalviewAlign(final String file)
2746 jalview.gui.AlignFrame af = null;
2750 // create list to store references for any new Jmol viewers created
2751 newStructureViewers = new Vector<>();
2752 // UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
2753 // Workaround is to make sure caller implements the JarInputStreamProvider
2755 // so we can re-open the jar input stream for each entry.
2757 jarInputStreamProvider jprovider = createjarInputStreamProvider(file);
2758 af = loadJalviewAlign(jprovider);
2761 af.setMenusForViewport();
2763 } catch (MalformedURLException e)
2765 errorMessage = "Invalid URL format for '" + file + "'";
2771 SwingUtilities.invokeAndWait(new Runnable()
2776 setLoadingFinishedForNewStructureViewers();
2779 } catch (Exception x)
2781 System.err.println("Error loading alignment: " + x.getMessage());
2787 private jarInputStreamProvider createjarInputStreamProvider(
2788 final String file) throws MalformedURLException
2791 errorMessage = null;
2792 uniqueSetSuffix = null;
2794 viewportsAdded.clear();
2795 frefedSequence = null;
2797 if (file.startsWith("http://"))
2799 url = new URL(file);
2801 final URL _url = url;
2802 return new jarInputStreamProvider()
2806 public JarInputStream getJarInputStream() throws IOException
2810 return new JarInputStream(_url.openStream());
2814 return new JarInputStream(new FileInputStream(file));
2819 public String getFilename()
2827 * Recover jalview session from a jalview project archive. Caller may
2828 * initialise uniqueSetSuffix, seqRefIds, viewportsAdded and frefedSequence
2829 * themselves. Any null fields will be initialised with default values,
2830 * non-null fields are left alone.
2835 public AlignFrame loadJalviewAlign(final jarInputStreamProvider jprovider)
2837 errorMessage = null;
2838 if (uniqueSetSuffix == null)
2840 uniqueSetSuffix = System.currentTimeMillis() % 100000 + "";
2842 if (seqRefIds == null)
2846 AlignFrame af = null, _af = null;
2847 IdentityHashMap<AlignmentI, AlignmentI> importedDatasets = new IdentityHashMap<>();
2848 Map<String, AlignFrame> gatherToThisFrame = new HashMap<>();
2849 final String file = jprovider.getFilename();
2852 JarInputStream jin = null;
2853 JarEntry jarentry = null;
2858 jin = jprovider.getJarInputStream();
2859 for (int i = 0; i < entryCount; i++)
2861 jarentry = jin.getNextJarEntry();
2864 if (jarentry != null && jarentry.getName().endsWith(".xml"))
2866 InputStreamReader in = new InputStreamReader(jin, UTF_8);
2867 // JalviewModel object = new JalviewModel();
2869 JAXBContext jc = JAXBContext
2870 .newInstance("jalview.xml.binding.jalview");
2871 XMLStreamReader streamReader = XMLInputFactory.newInstance()
2872 .createXMLStreamReader(jin);
2873 javax.xml.bind.Unmarshaller um = jc.createUnmarshaller();
2874 JAXBElement<JalviewModel> jbe = um
2875 .unmarshal(streamReader, JalviewModel.class);
2876 JalviewModel object = jbe.getValue();
2879 Unmarshaller unmar = new Unmarshaller(object);
2880 unmar.setValidation(false);
2881 object = (JalviewModel) unmar.unmarshal(in);
2883 if (true) // !skipViewport(object))
2885 _af = loadFromObject(object, file, true, jprovider);
2886 if (_af != null && object.getViewport().size() > 0)
2887 // getJalviewModelSequence().getViewportCount() > 0)
2891 // store a reference to the first view
2894 if (_af.getViewport().isGatherViewsHere())
2896 // if this is a gathered view, keep its reference since
2897 // after gathering views, only this frame will remain
2899 gatherToThisFrame.put(_af.getViewport().getSequenceSetId(),
2902 // Save dataset to register mappings once all resolved
2903 importedDatasets.put(
2904 af.getViewport().getAlignment().getDataset(),
2905 af.getViewport().getAlignment().getDataset());
2910 else if (jarentry != null)
2912 // Some other file here.
2915 } while (jarentry != null);
2916 resolveFrefedSequences();
2917 } catch (IOException ex)
2919 ex.printStackTrace();
2920 errorMessage = "Couldn't locate Jalview XML file : " + file;
2922 "Exception whilst loading jalview XML file : " + ex + "\n");
2923 } catch (Exception ex)
2925 System.err.println("Parsing as Jalview Version 2 file failed.");
2926 ex.printStackTrace(System.err);
2927 if (attemptversion1parse)
2929 // used to attempt to parse as V1 castor-generated xml
2931 if (Desktop.instance != null)
2933 Desktop.instance.stopLoading();
2937 System.out.println("Successfully loaded archive file");
2940 ex.printStackTrace();
2943 "Exception whilst loading jalview XML file : " + ex + "\n");
2944 } catch (OutOfMemoryError e)
2946 // Don't use the OOM Window here
2947 errorMessage = "Out of memory loading jalview XML file";
2948 System.err.println("Out of memory whilst loading jalview XML file");
2949 e.printStackTrace();
2953 * Regather multiple views (with the same sequence set id) to the frame (if
2954 * any) that is flagged as the one to gather to, i.e. convert them to tabbed
2955 * views instead of separate frames. Note this doesn't restore a state where
2956 * some expanded views in turn have tabbed views - the last "first tab" read
2957 * in will play the role of gatherer for all.
2959 for (AlignFrame fr : gatherToThisFrame.values())
2961 Desktop.instance.gatherViews(fr);
2964 restoreSplitFrames();
2965 for (AlignmentI ds : importedDatasets.keySet())
2967 if (ds.getCodonFrames() != null)
2969 StructureSelectionManager
2970 .getStructureSelectionManager(Desktop.instance)
2971 .registerMappings(ds.getCodonFrames());
2974 if (errorMessage != null)
2979 if (Desktop.instance != null)
2981 Desktop.instance.stopLoading();
2988 * Try to reconstruct and display SplitFrame windows, where each contains
2989 * complementary dna and protein alignments. Done by pairing up AlignFrame
2990 * objects (created earlier) which have complementary viewport ids associated.
2992 protected void restoreSplitFrames()
2994 List<SplitFrame> gatherTo = new ArrayList<>();
2995 List<AlignFrame> addedToSplitFrames = new ArrayList<>();
2996 Map<String, AlignFrame> dna = new HashMap<>();
2999 * Identify the DNA alignments
3001 for (Entry<Viewport, AlignFrame> candidate : splitFrameCandidates
3004 AlignFrame af = candidate.getValue();
3005 if (af.getViewport().getAlignment().isNucleotide())
3007 dna.put(candidate.getKey().getId(), af);
3012 * Try to match up the protein complements
3014 for (Entry<Viewport, AlignFrame> candidate : splitFrameCandidates
3017 AlignFrame af = candidate.getValue();
3018 if (!af.getViewport().getAlignment().isNucleotide())
3020 String complementId = candidate.getKey().getComplementId();
3021 // only non-null complements should be in the Map
3022 if (complementId != null && dna.containsKey(complementId))
3024 final AlignFrame dnaFrame = dna.get(complementId);
3025 SplitFrame sf = createSplitFrame(dnaFrame, af);
3026 addedToSplitFrames.add(dnaFrame);
3027 addedToSplitFrames.add(af);
3028 dnaFrame.setMenusForViewport();
3029 af.setMenusForViewport();
3030 if (af.getViewport().isGatherViewsHere())
3039 * Open any that we failed to pair up (which shouldn't happen!) as
3040 * standalone AlignFrame's.
3042 for (Entry<Viewport, AlignFrame> candidate : splitFrameCandidates
3045 AlignFrame af = candidate.getValue();
3046 if (!addedToSplitFrames.contains(af))
3048 Viewport view = candidate.getKey();
3049 Desktop.addInternalFrame(af, view.getTitle(),
3050 safeInt(view.getWidth()), safeInt(view.getHeight()));
3051 af.setMenusForViewport();
3052 System.err.println("Failed to restore view " + view.getTitle()
3053 + " to split frame");
3058 * Gather back into tabbed views as flagged.
3060 for (SplitFrame sf : gatherTo)
3062 Desktop.instance.gatherViews(sf);
3065 splitFrameCandidates.clear();
3069 * Construct and display one SplitFrame holding DNA and protein alignments.
3072 * @param proteinFrame
3075 protected SplitFrame createSplitFrame(AlignFrame dnaFrame,
3076 AlignFrame proteinFrame)
3078 SplitFrame splitFrame = new SplitFrame(dnaFrame, proteinFrame);
3079 String title = MessageManager.getString("label.linked_view_title");
3080 int width = (int) dnaFrame.getBounds().getWidth();
3081 int height = (int) (dnaFrame.getBounds().getHeight()
3082 + proteinFrame.getBounds().getHeight() + 50);
3085 * SplitFrame location is saved to both enclosed frames
3087 splitFrame.setLocation(dnaFrame.getX(), dnaFrame.getY());
3088 Desktop.addInternalFrame(splitFrame, title, width, height);
3091 * And compute cDNA consensus (couldn't do earlier with consensus as
3092 * mappings were not yet present)
3094 proteinFrame.getViewport().alignmentChanged(proteinFrame.alignPanel);
3100 * check errorMessage for a valid error message and raise an error box in the
3101 * GUI or write the current errorMessage to stderr and then clear the error
3104 protected void reportErrors()
3106 reportErrors(false);
3109 protected void reportErrors(final boolean saving)
3111 if (errorMessage != null)
3113 final String finalErrorMessage = errorMessage;
3116 javax.swing.SwingUtilities.invokeLater(new Runnable()
3121 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
3123 "Error " + (saving ? "saving" : "loading")
3125 JvOptionPane.WARNING_MESSAGE);
3131 System.err.println("Problem loading Jalview file: " + errorMessage);
3134 errorMessage = null;
3137 Map<String, String> alreadyLoadedPDB = new HashMap<>();
3140 * when set, local views will be updated from view stored in JalviewXML
3141 * Currently (28th Sep 2008) things will go horribly wrong in vamsas document
3142 * sync if this is set to true.
3144 private final boolean updateLocalViews = false;
3147 * Returns the path to a temporary file holding the PDB file for the given PDB
3148 * id. The first time of asking, searches for a file of that name in the
3149 * Jalview project jar, and copies it to a new temporary file. Any repeat
3150 * requests just return the path to the file previously created.
3156 String loadPDBFile(jarInputStreamProvider jprovider, String pdbId,
3159 if (alreadyLoadedPDB.containsKey(pdbId))
3161 return alreadyLoadedPDB.get(pdbId).toString();
3164 String tempFile = copyJarEntry(jprovider, pdbId, "jalview_pdb",
3166 if (tempFile != null)
3168 alreadyLoadedPDB.put(pdbId, tempFile);
3174 * Copies the jar entry of given name to a new temporary file and returns the
3175 * path to the file, or null if the entry is not found.
3178 * @param jarEntryName
3180 * a prefix for the temporary file name, must be at least three
3182 * @param suffixModel
3183 * null or original file - so new file can be given the same suffix
3187 protected String copyJarEntry(jarInputStreamProvider jprovider,
3188 String jarEntryName, String prefix, String suffixModel)
3190 String suffix = ".tmp";
3191 if (suffixModel == null)
3193 suffixModel = jarEntryName;
3195 int sfpos = suffixModel.lastIndexOf(".");
3196 if (sfpos > -1 && sfpos < (suffixModel.length() - 1))
3198 suffix = "." + suffixModel.substring(sfpos + 1);
3201 try (JarInputStream jin = jprovider.getJarInputStream())
3203 JarEntry entry = null;
3206 entry = jin.getNextJarEntry();
3207 } while (entry != null && !entry.getName().equals(jarEntryName));
3211 // in = new BufferedReader(new InputStreamReader(jin, UTF_8));
3212 File outFile = File.createTempFile(prefix, suffix);
3213 outFile.deleteOnExit();
3214 try (OutputStream os = new FileOutputStream(outFile))
3218 String t = outFile.getAbsolutePath();
3223 warn("Couldn't find entry in Jalview Jar for " + jarEntryName);
3225 } catch (Exception ex)
3227 ex.printStackTrace();
3233 private class JvAnnotRow
3235 public JvAnnotRow(int i, AlignmentAnnotation jaa)
3242 * persisted version of annotation row from which to take vis properties
3244 public jalview.datamodel.AlignmentAnnotation template;
3247 * original position of the annotation row in the alignment
3253 * Load alignment frame from jalview XML DOM object
3255 * @param jalviewModel
3258 * filename source string
3259 * @param loadTreesAndStructures
3260 * when false only create Viewport
3262 * data source provider
3263 * @return alignment frame created from view stored in DOM
3265 AlignFrame loadFromObject(JalviewModel jalviewModel, String file,
3266 boolean loadTreesAndStructures, jarInputStreamProvider jprovider)
3268 SequenceSet vamsasSet = jalviewModel.getVamsasModel().getSequenceSet().get(0);
3269 List<Sequence> vamsasSeqs = vamsasSet.getSequence();
3271 // JalviewModelSequence jms = object.getJalviewModelSequence();
3273 // Viewport view = (jms.getViewportCount() > 0) ? jms.getViewport(0)
3275 Viewport view = (jalviewModel.getViewport().size() > 0)
3276 ? jalviewModel.getViewport().get(0)
3279 // ////////////////////////////////
3280 // INITIALISE ALIGNMENT SEQUENCESETID AND VIEWID
3283 // If we just load in the same jar file again, the sequenceSetId
3284 // will be the same, and we end up with multiple references
3285 // to the same sequenceSet. We must modify this id on load
3286 // so that each load of the file gives a unique id
3289 * used to resolve correct alignment dataset for alignments with multiple
3292 String uniqueSeqSetId = null;
3293 String viewId = null;
3296 uniqueSeqSetId = view.getSequenceSetId() + uniqueSetSuffix;
3297 viewId = (view.getId() == null ? null
3298 : view.getId() + uniqueSetSuffix);
3301 // ////////////////////////////////
3304 List<SequenceI> hiddenSeqs = null;
3306 List<SequenceI> tmpseqs = new ArrayList<>();
3308 boolean multipleView = false;
3309 SequenceI referenceseqForView = null;
3310 // JSeq[] jseqs = object.getJalviewModelSequence().getJSeq();
3311 List<JSeq> jseqs = jalviewModel.getJSeq();
3312 int vi = 0; // counter in vamsasSeq array
3313 for (int i = 0; i < jseqs.size(); i++)
3315 JSeq jseq = jseqs.get(i);
3316 String seqId = jseq.getId();
3318 SequenceI tmpSeq = seqRefIds.get(seqId);
3321 if (!incompleteSeqs.containsKey(seqId))
3323 // may not need this check, but keep it for at least 2.9,1 release
3324 if (tmpSeq.getStart() != jseq.getStart()
3325 || tmpSeq.getEnd() != jseq.getEnd())
3328 String.format("Warning JAL-2154 regression: updating start/end for sequence %s from %d/%d to %d/%d",
3329 tmpSeq.getName(), tmpSeq.getStart(),
3330 tmpSeq.getEnd(), jseq.getStart(),
3336 incompleteSeqs.remove(seqId);
3338 if (vamsasSeqs.size() > vi
3339 && vamsasSeqs.get(vi).getId().equals(seqId))
3341 // most likely we are reading a dataset XML document so
3342 // update from vamsasSeq section of XML for this sequence
3343 tmpSeq.setName(vamsasSeqs.get(vi).getName());
3344 tmpSeq.setDescription(vamsasSeqs.get(vi).getDescription());
3345 tmpSeq.setSequence(vamsasSeqs.get(vi).getSequence());
3350 // reading multiple views, so vamsasSeq set is a subset of JSeq
3351 multipleView = true;
3353 tmpSeq.setStart(jseq.getStart());
3354 tmpSeq.setEnd(jseq.getEnd());
3355 tmpseqs.add(tmpSeq);
3359 Sequence vamsasSeq = vamsasSeqs.get(vi);
3360 tmpSeq = new jalview.datamodel.Sequence(vamsasSeq.getName(),
3361 vamsasSeq.getSequence());
3362 tmpSeq.setDescription(vamsasSeq.getDescription());
3363 tmpSeq.setStart(jseq.getStart());
3364 tmpSeq.setEnd(jseq.getEnd());
3365 tmpSeq.setVamsasId(uniqueSetSuffix + seqId);
3366 seqRefIds.put(vamsasSeq.getId(), tmpSeq);
3367 tmpseqs.add(tmpSeq);
3371 if (safeBoolean(jseq.isViewreference()))
3373 referenceseqForView = tmpseqs.get(tmpseqs.size() - 1);
3376 if (jseq.isHidden() != null && jseq.isHidden().booleanValue())
3378 if (hiddenSeqs == null)
3380 hiddenSeqs = new ArrayList<>();
3383 hiddenSeqs.add(tmpSeq);
3388 // Create the alignment object from the sequence set
3389 // ///////////////////////////////
3390 SequenceI[] orderedSeqs = tmpseqs
3391 .toArray(new SequenceI[tmpseqs.size()]);
3393 AlignmentI al = null;
3394 // so we must create or recover the dataset alignment before going further
3395 // ///////////////////////////////
3396 if (vamsasSet.getDatasetId() == null || vamsasSet.getDatasetId() == "")
3398 // older jalview projects do not have a dataset - so creat alignment and
3400 al = new Alignment(orderedSeqs);
3401 al.setDataset(null);
3405 boolean isdsal = jalviewModel.getViewport().isEmpty();
3408 // we are importing a dataset record, so
3409 // recover reference to an alignment already materialsed as dataset
3410 al = getDatasetFor(vamsasSet.getDatasetId());
3414 // materialse the alignment
3415 al = new Alignment(orderedSeqs);
3419 addDatasetRef(vamsasSet.getDatasetId(), al);
3422 // finally, verify all data in vamsasSet is actually present in al
3423 // passing on flag indicating if it is actually a stored dataset
3424 recoverDatasetFor(vamsasSet, al, isdsal, uniqueSeqSetId);
3427 if (referenceseqForView != null)
3429 al.setSeqrep(referenceseqForView);
3431 // / Add the alignment properties
3432 for (int i = 0; i < vamsasSet.getSequenceSetProperties().size(); i++)
3434 SequenceSetProperties ssp = vamsasSet.getSequenceSetProperties()
3436 al.setProperty(ssp.getKey(), ssp.getValue());
3439 // ///////////////////////////////
3441 Hashtable pdbloaded = new Hashtable(); // TODO nothing writes to this??
3444 // load sequence features, database references and any associated PDB
3445 // structures for the alignment
3447 // prior to 2.10, this part would only be executed the first time a
3448 // sequence was encountered, but not afterwards.
3449 // now, for 2.10 projects, this is also done if the xml doc includes
3450 // dataset sequences not actually present in any particular view.
3452 for (int i = 0; i < vamsasSeqs.size(); i++)
3454 JSeq jseq = jseqs.get(i);
3455 if (jseq.getFeatures().size() > 0)
3457 List<Feature> features = jseq.getFeatures();
3458 for (int f = 0; f < features.size(); f++)
3460 Feature feat = features.get(f);
3461 SequenceFeature sf = new SequenceFeature(feat.getType(),
3462 feat.getDescription(), feat.getBegin(), feat.getEnd(),
3463 safeFloat(feat.getScore()), feat.getFeatureGroup());
3464 sf.setStatus(feat.getStatus());
3467 * load any feature attributes - include map-valued attributes
3469 Map<String, Map<String, String>> mapAttributes = new HashMap<>();
3470 for (int od = 0; od < feat.getOtherData().size(); od++)
3472 OtherData keyValue = feat.getOtherData().get(od);
3473 String attributeName = keyValue.getKey();
3474 String attributeValue = keyValue.getValue();
3475 if (attributeName.startsWith("LINK"))
3477 sf.addLink(attributeValue);
3481 String subAttribute = keyValue.getKey2();
3482 if (subAttribute == null)
3484 // simple string-valued attribute
3485 sf.setValue(attributeName, attributeValue);
3489 // attribute 'key' has sub-attribute 'key2'
3490 if (!mapAttributes.containsKey(attributeName))
3492 mapAttributes.put(attributeName, new HashMap<>());
3494 mapAttributes.get(attributeName).put(subAttribute,
3499 for (Entry<String, Map<String, String>> mapAttribute : mapAttributes
3502 sf.setValue(mapAttribute.getKey(), mapAttribute.getValue());
3505 // adds feature to datasequence's feature set (since Jalview 2.10)
3506 al.getSequenceAt(i).addSequenceFeature(sf);
3509 if (vamsasSeqs.get(i).getDBRef().size() > 0)
3511 // adds dbrefs to datasequence's set (since Jalview 2.10)
3513 al.getSequenceAt(i).getDatasetSequence() == null
3514 ? al.getSequenceAt(i)
3515 : al.getSequenceAt(i).getDatasetSequence(),
3518 if (jseq.getPdbids().size() > 0)
3520 List<Pdbids> ids = jseq.getPdbids();
3521 for (int p = 0; p < ids.size(); p++)
3523 Pdbids pdbid = ids.get(p);
3524 jalview.datamodel.PDBEntry entry = new jalview.datamodel.PDBEntry();
3525 entry.setId(pdbid.getId());
3526 if (pdbid.getType() != null)
3528 if (PDBEntry.Type.getType(pdbid.getType()) != null)
3530 entry.setType(PDBEntry.Type.getType(pdbid.getType()));
3534 entry.setType(PDBEntry.Type.FILE);
3537 // jprovider is null when executing 'New View'
3538 if (pdbid.getFile() != null && jprovider != null)
3540 if (!pdbloaded.containsKey(pdbid.getFile()))
3542 entry.setFile(loadPDBFile(jprovider, pdbid.getId(),
3547 entry.setFile(pdbloaded.get(pdbid.getId()).toString());
3551 if (pdbid.getPdbentryItem() != null)
3553 for (PdbentryItem item : pdbid.getPdbentryItem())
3555 for (Property pr : item.getProperty())
3557 entry.setProperty(pr.getName(), pr.getValue());
3562 for (Property prop : pdbid.getProperty())
3564 entry.setProperty(prop.getName(), prop.getValue());
3566 StructureSelectionManager
3567 .getStructureSelectionManager(Desktop.instance)
3568 .registerPDBEntry(entry);
3569 // adds PDBEntry to datasequence's set (since Jalview 2.10)
3570 if (al.getSequenceAt(i).getDatasetSequence() != null)
3572 al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
3576 al.getSequenceAt(i).addPDBId(entry);
3581 } // end !multipleview
3583 // ///////////////////////////////
3584 // LOAD SEQUENCE MAPPINGS
3586 if (vamsasSet.getAlcodonFrame().size() > 0)
3588 // TODO Potentially this should only be done once for all views of an
3590 List<AlcodonFrame> alc = vamsasSet.getAlcodonFrame();
3591 for (int i = 0; i < alc.size(); i++)
3593 AlignedCodonFrame cf = new AlignedCodonFrame();
3594 if (alc.get(i).getAlcodMap().size() > 0)
3596 List<AlcodMap> maps = alc.get(i).getAlcodMap();
3597 for (int m = 0; m < maps.size(); m++)
3599 AlcodMap map = maps.get(m);
3600 SequenceI dnaseq = seqRefIds.get(map.getDnasq());
3602 jalview.datamodel.Mapping mapping = null;
3603 // attach to dna sequence reference.
3604 if (map.getMapping() != null)
3606 mapping = addMapping(map.getMapping());
3607 if (dnaseq != null && mapping.getTo() != null)
3609 cf.addMap(dnaseq, mapping.getTo(), mapping.getMap());
3615 newAlcodMapRef(map.getDnasq(), cf, mapping));
3619 al.addCodonFrame(cf);
3624 // ////////////////////////////////
3626 List<JvAnnotRow> autoAlan = new ArrayList<>();
3629 * store any annotations which forward reference a group's ID
3631 Map<String, List<AlignmentAnnotation>> groupAnnotRefs = new Hashtable<>();
3633 if (vamsasSet.getAnnotation().size()/*Count()*/ > 0)
3635 List<Annotation> an = vamsasSet.getAnnotation();
3637 for (int i = 0; i < an.size(); i++)
3639 Annotation annotation = an.get(i);
3642 * test if annotation is automatically calculated for this view only
3644 boolean autoForView = false;
3645 if (annotation.getLabel().equals("Quality")
3646 || annotation.getLabel().equals("Conservation")
3647 || annotation.getLabel().equals("Consensus"))
3649 // Kludge for pre 2.5 projects which lacked the autocalculated flag
3651 // JAXB has no has() test; schema defaults value to false
3652 // if (!annotation.hasAutoCalculated())
3654 // annotation.setAutoCalculated(true);
3657 if (autoForView || annotation.isAutoCalculated())
3659 // remove ID - we don't recover annotation from other views for
3660 // view-specific annotation
3661 annotation.setId(null);
3664 // set visibility for other annotation in this view
3665 String annotationId = annotation.getId();
3666 if (annotationId != null && annotationIds.containsKey(annotationId))
3668 AlignmentAnnotation jda = annotationIds.get(annotationId);
3669 // in principle Visible should always be true for annotation displayed
3670 // in multiple views
3671 if (annotation.isVisible() != null)
3673 jda.visible = annotation.isVisible();
3676 al.addAnnotation(jda);
3680 // Construct new annotation from model.
3681 List<AnnotationElement> ae = annotation.getAnnotationElement();
3682 jalview.datamodel.Annotation[] anot = null;
3683 java.awt.Color firstColour = null;
3685 if (!annotation.isScoreOnly())
3687 anot = new jalview.datamodel.Annotation[al.getWidth()];
3688 for (int aa = 0; aa < ae.size() && aa < anot.length; aa++)
3690 AnnotationElement annElement = ae.get(aa);
3691 anpos = annElement.getPosition();
3693 if (anpos >= anot.length)
3698 float value = safeFloat(annElement.getValue());
3699 anot[anpos] = new jalview.datamodel.Annotation(
3700 annElement.getDisplayCharacter(),
3701 annElement.getDescription(),
3702 (annElement.getSecondaryStructure() == null
3703 || annElement.getSecondaryStructure()
3707 .getSecondaryStructure()
3710 anot[anpos].colour = new Color(safeInt(annElement.getColour()));
3711 if (firstColour == null)
3713 firstColour = anot[anpos].colour;
3717 jalview.datamodel.AlignmentAnnotation jaa = null;
3719 if (annotation.isGraph())
3721 float llim = 0, hlim = 0;
3722 // if (autoForView || an[i].isAutoCalculated()) {
3725 jaa = new jalview.datamodel.AlignmentAnnotation(
3726 annotation.getLabel(), annotation.getDescription(), anot,
3727 llim, hlim, safeInt(annotation.getGraphType()));
3729 jaa.graphGroup = safeInt(annotation.getGraphGroup());
3730 jaa._linecolour = firstColour;
3731 if (annotation.getThresholdLine() != null)
3733 jaa.setThreshold(new jalview.datamodel.GraphLine(
3734 safeFloat(annotation.getThresholdLine().getValue()),
3735 annotation.getThresholdLine().getLabel(),
3736 new java.awt.Color(safeInt(
3737 annotation.getThresholdLine().getColour()))));
3739 if (autoForView || annotation.isAutoCalculated())
3741 // Hardwire the symbol display line to ensure that labels for
3742 // histograms are displayed
3748 jaa = new jalview.datamodel.AlignmentAnnotation(
3749 annotation.getLabel(), annotation.getDescription(), anot);
3750 jaa._linecolour = firstColour;
3752 // register new annotation
3753 if (annotation.getId() != null)
3755 annotationIds.put(annotation.getId(), jaa);
3756 jaa.annotationId = annotation.getId();
3758 // recover sequence association
3759 String sequenceRef = annotation.getSequenceRef();
3760 if (sequenceRef != null)
3762 // from 2.9 sequenceRef is to sequence id (JAL-1781)
3763 SequenceI sequence = seqRefIds.get(sequenceRef);
3764 if (sequence == null)
3766 // in pre-2.9 projects sequence ref is to sequence name
3767 sequence = al.findName(sequenceRef);
3769 if (sequence != null)
3771 jaa.createSequenceMapping(sequence, 1, true);
3772 sequence.addAlignmentAnnotation(jaa);
3775 // and make a note of any group association
3776 if (annotation.getGroupRef() != null
3777 && annotation.getGroupRef().length() > 0)
3779 List<jalview.datamodel.AlignmentAnnotation> aal = groupAnnotRefs
3780 .get(annotation.getGroupRef());
3783 aal = new ArrayList<>();
3784 groupAnnotRefs.put(annotation.getGroupRef(), aal);
3789 if (annotation.getScore() != null)
3791 jaa.setScore(annotation.getScore().doubleValue());
3793 if (annotation.isVisible() != null)
3795 jaa.visible = annotation.isVisible().booleanValue();
3798 if (annotation.isCentreColLabels() != null)
3800 jaa.centreColLabels = annotation.isCentreColLabels()
3804 if (annotation.isScaleColLabels() != null)
3806 jaa.scaleColLabel = annotation.isScaleColLabels().booleanValue();
3808 if (annotation.isAutoCalculated())
3810 // newer files have an 'autoCalculated' flag and store calculation
3811 // state in viewport properties
3812 jaa.autoCalculated = true; // means annotation will be marked for
3813 // update at end of load.
3815 if (annotation.getGraphHeight() != null)
3817 jaa.graphHeight = annotation.getGraphHeight().intValue();
3819 jaa.belowAlignment = annotation.isBelowAlignment();
3820 jaa.setCalcId(annotation.getCalcId());
3821 if (annotation.getProperty().size() > 0)
3823 for (Annotation.Property prop : annotation
3826 jaa.setProperty(prop.getName(), prop.getValue());
3829 if (jaa.autoCalculated)
3831 autoAlan.add(new JvAnnotRow(i, jaa));
3834 // if (!autoForView)
3836 // add autocalculated group annotation and any user created annotation
3838 al.addAnnotation(jaa);
3842 // ///////////////////////
3844 // Create alignment markup and styles for this view
3845 if (jalviewModel.getJGroup().size() > 0)
3847 List<JGroup> groups = jalviewModel.getJGroup();
3848 boolean addAnnotSchemeGroup = false;
3849 for (int i = 0; i < groups.size(); i++)
3851 JGroup jGroup = groups.get(i);
3852 ColourSchemeI cs = null;
3853 if (jGroup.getColour() != null)
3855 if (jGroup.getColour().startsWith("ucs"))
3857 cs = getUserColourScheme(jalviewModel, jGroup.getColour());
3859 else if (jGroup.getColour().equals("AnnotationColourGradient")
3860 && jGroup.getAnnotationColours() != null)
3862 addAnnotSchemeGroup = true;
3866 cs = ColourSchemeProperty.getColourScheme(null, al,
3867 jGroup.getColour());
3870 int pidThreshold = safeInt(jGroup.getPidThreshold());
3872 Vector<SequenceI> seqs = new Vector<>();
3874 for (int s = 0; s < jGroup.getSeq().size(); s++)
3876 String seqId = jGroup.getSeq().get(s);
3877 SequenceI ts = seqRefIds.get(seqId);
3881 seqs.addElement(ts);
3885 if (seqs.size() < 1)
3890 SequenceGroup sg = new SequenceGroup(seqs, jGroup.getName(), cs,
3891 safeBoolean(jGroup.isDisplayBoxes()),
3892 safeBoolean(jGroup.isDisplayText()),
3893 safeBoolean(jGroup.isColourText()),
3894 safeInt(jGroup.getStart()), safeInt(jGroup.getEnd()));
3895 sg.getGroupColourScheme().setThreshold(pidThreshold, true);
3896 sg.getGroupColourScheme()
3897 .setConservationInc(safeInt(jGroup.getConsThreshold()));
3898 sg.setOutlineColour(new Color(safeInt(jGroup.getOutlineColour())));
3900 sg.textColour = new Color(safeInt(jGroup.getTextCol1()));
3901 sg.textColour2 = new Color(safeInt(jGroup.getTextCol2()));
3902 sg.setShowNonconserved(safeBoolean(jGroup.isShowUnconserved()));
3903 sg.thresholdTextColour = safeInt(jGroup.getTextColThreshold());
3904 // attributes with a default in the schema are never null
3905 sg.setShowConsensusHistogram(jGroup.isShowConsensusHistogram());
3906 sg.setshowSequenceLogo(jGroup.isShowSequenceLogo());
3907 sg.setNormaliseSequenceLogo(jGroup.isNormaliseSequenceLogo());
3908 sg.setIgnoreGapsConsensus(jGroup.isIgnoreGapsinConsensus());
3909 if (jGroup.getConsThreshold() != null
3910 && jGroup.getConsThreshold().intValue() != 0)
3912 Conservation c = new Conservation("All", sg.getSequences(null), 0,
3915 c.verdict(false, 25);
3916 sg.cs.setConservation(c);
3919 if (jGroup.getId() != null && groupAnnotRefs.size() > 0)
3921 // re-instate unique group/annotation row reference
3922 List<AlignmentAnnotation> jaal = groupAnnotRefs
3923 .get(jGroup.getId());
3926 for (AlignmentAnnotation jaa : jaal)
3929 if (jaa.autoCalculated)
3931 // match up and try to set group autocalc alignment row for this
3933 if (jaa.label.startsWith("Consensus for "))
3935 sg.setConsensus(jaa);
3937 // match up and try to set group autocalc alignment row for this
3939 if (jaa.label.startsWith("Conservation for "))
3941 sg.setConservationRow(jaa);
3948 if (addAnnotSchemeGroup)
3950 // reconstruct the annotation colourscheme
3951 sg.setColourScheme(constructAnnotationColour(
3952 jGroup.getAnnotationColours(), null, al, jalviewModel, false));
3958 // only dataset in this model, so just return.
3961 // ///////////////////////////////
3964 AlignFrame af = null;
3965 AlignViewport av = null;
3966 // now check to see if we really need to create a new viewport.
3967 if (multipleView && viewportsAdded.size() == 0)
3969 // We recovered an alignment for which a viewport already exists.
3970 // TODO: fix up any settings necessary for overlaying stored state onto
3971 // state recovered from another document. (may not be necessary).
3972 // we may need a binding from a viewport in memory to one recovered from
3974 // and then recover its containing af to allow the settings to be applied.
3975 // TODO: fix for vamsas demo
3977 "About to recover a viewport for existing alignment: Sequence set ID is "
3979 Object seqsetobj = retrieveExistingObj(uniqueSeqSetId);
3980 if (seqsetobj != null)
3982 if (seqsetobj instanceof String)
3984 uniqueSeqSetId = (String) seqsetobj;
3986 "Recovered extant sequence set ID mapping for ID : New Sequence set ID is "
3992 "Warning : Collision between sequence set ID string and existing jalview object mapping.");
3998 * indicate that annotation colours are applied across all groups (pre
3999 * Jalview 2.8.1 behaviour)
4001 boolean doGroupAnnColour = Jalview2XML.isVersionStringLaterThan("2.8.1",
4002 jalviewModel.getVersion());
4004 AlignmentPanel ap = null;
4005 boolean isnewview = true;
4008 // Check to see if this alignment already has a view id == viewId
4009 jalview.gui.AlignmentPanel views[] = Desktop
4010 .getAlignmentPanels(uniqueSeqSetId);
4011 if (views != null && views.length > 0)
4013 for (int v = 0; v < views.length; v++)
4015 if (views[v].av.getViewId().equalsIgnoreCase(viewId))
4017 // recover the existing alignpanel, alignframe, viewport
4018 af = views[v].alignFrame;
4021 // TODO: could even skip resetting view settings if we don't want to
4022 // change the local settings from other jalview processes
4031 af = loadViewport(file, jseqs, hiddenSeqs, al, jalviewModel, view,
4032 uniqueSeqSetId, viewId, autoAlan);
4033 av = af.getViewport();
4038 * Load any trees, PDB structures and viewers
4040 * Not done if flag is false (when this method is used for New View)
4042 if (loadTreesAndStructures)
4044 loadTrees(jalviewModel, view, af, av, ap);
4045 loadPCAViewers(jalviewModel, ap);
4046 loadPDBStructures(jprovider, jseqs, af, ap);
4047 loadRnaViewers(jprovider, jseqs, ap);
4049 // and finally return.
4054 * Instantiate and link any saved RNA (Varna) viewers. The state of the Varna
4055 * panel is restored from separate jar entries, two (gapped and trimmed) per
4056 * sequence and secondary structure.
4058 * Currently each viewer shows just one sequence and structure (gapped and
4059 * trimmed), however this method is designed to support multiple sequences or
4060 * structures in viewers if wanted in future.
4066 private void loadRnaViewers(jarInputStreamProvider jprovider,
4067 List<JSeq> jseqs, AlignmentPanel ap)
4070 * scan the sequences for references to viewers; create each one the first
4071 * time it is referenced, add Rna models to existing viewers
4073 for (JSeq jseq : jseqs)
4075 for (int i = 0; i < jseq.getRnaViewer().size(); i++)
4077 RnaViewer viewer = jseq.getRnaViewer().get(i);
4078 AppVarna appVarna = findOrCreateVarnaViewer(viewer, uniqueSetSuffix,
4081 for (int j = 0; j < viewer.getSecondaryStructure().size(); j++)
4083 SecondaryStructure ss = viewer.getSecondaryStructure().get(j);
4084 SequenceI seq = seqRefIds.get(jseq.getId());
4085 AlignmentAnnotation ann = this.annotationIds
4086 .get(ss.getAnnotationId());
4089 * add the structure to the Varna display (with session state copied
4090 * from the jar to a temporary file)
4092 boolean gapped = safeBoolean(ss.isGapped());
4093 String rnaTitle = ss.getTitle();
4094 String sessionState = ss.getViewerState();
4095 String tempStateFile = copyJarEntry(jprovider, sessionState,
4097 RnaModel rna = new RnaModel(rnaTitle, ann, seq, null, gapped);
4098 appVarna.addModelSession(rna, rnaTitle, tempStateFile);
4100 appVarna.setInitialSelection(safeInt(viewer.getSelectedRna()));
4106 * Locate and return an already instantiated matching AppVarna, or create one
4110 * @param viewIdSuffix
4114 protected AppVarna findOrCreateVarnaViewer(RnaViewer viewer,
4115 String viewIdSuffix, AlignmentPanel ap)
4118 * on each load a suffix is appended to the saved viewId, to avoid conflicts
4119 * if load is repeated
4121 String postLoadId = viewer.getViewId() + viewIdSuffix;
4122 for (JInternalFrame frame : getAllFrames())
4124 if (frame instanceof AppVarna)
4126 AppVarna varna = (AppVarna) frame;
4127 if (postLoadId.equals(varna.getViewId()))
4129 // this viewer is already instantiated
4130 // could in future here add ap as another 'parent' of the
4131 // AppVarna window; currently just 1-to-many
4138 * viewer not found - make it
4140 RnaViewerModel model = new RnaViewerModel(postLoadId, viewer.getTitle(),
4141 safeInt(viewer.getXpos()), safeInt(viewer.getYpos()),
4142 safeInt(viewer.getWidth()), safeInt(viewer.getHeight()),
4143 safeInt(viewer.getDividerLocation()));
4144 AppVarna varna = new AppVarna(model, ap);
4150 * Load any saved trees
4158 protected void loadTrees(JalviewModel jm, Viewport view,
4159 AlignFrame af, AlignViewport av, AlignmentPanel ap)
4161 // TODO result of automated refactoring - are all these parameters needed?
4164 for (int t = 0; t < jm.getTree().size(); t++)
4167 Tree tree = jm.getTree().get(t);
4169 TreePanel tp = (TreePanel) retrieveExistingObj(tree.getId());
4172 tp = af.showNewickTree(new NewickFile(tree.getNewick()),
4173 tree.getTitle(), safeInt(tree.getWidth()),
4174 safeInt(tree.getHeight()), safeInt(tree.getXpos()),
4175 safeInt(tree.getYpos()));
4176 if (tree.getId() != null)
4178 // perhaps bind the tree id to something ?
4183 // update local tree attributes ?
4184 // TODO: should check if tp has been manipulated by user - if so its
4185 // settings shouldn't be modified
4186 tp.setTitle(tree.getTitle());
4187 tp.setBounds(new Rectangle(safeInt(tree.getXpos()),
4188 safeInt(tree.getYpos()), safeInt(tree.getWidth()),
4189 safeInt(tree.getHeight())));
4190 tp.setViewport(av); // af.viewport;
4191 // TODO: verify 'associate with all views' works still
4192 tp.getTreeCanvas().setViewport(av); // af.viewport;
4193 tp.getTreeCanvas().setAssociatedPanel(ap); // af.alignPanel;
4195 tp.getTreeCanvas().setApplyToAllViews(tree.isLinkToAllViews());
4198 warn("There was a problem recovering stored Newick tree: \n"
4199 + tree.getNewick());
4203 tp.fitToWindow.setState(safeBoolean(tree.isFitToWindow()));
4204 tp.fitToWindow_actionPerformed(null);
4206 if (tree.getFontName() != null)
4209 new Font(tree.getFontName(), safeInt(tree.getFontStyle()),
4210 safeInt(tree.getFontSize())));
4215 new Font(view.getFontName(), safeInt(view.getFontStyle()),
4216 safeInt(view.getFontSize())));
4219 tp.showPlaceholders(safeBoolean(tree.isMarkUnlinked()));
4220 tp.showBootstrap(safeBoolean(tree.isShowBootstrap()));
4221 tp.showDistances(safeBoolean(tree.isShowDistances()));
4223 tp.getTreeCanvas().setThreshold(safeFloat(tree.getThreshold()));
4225 if (safeBoolean(tree.isCurrentTree()))
4227 af.getViewport().setCurrentTree(tp.getTree());
4231 } catch (Exception ex)
4233 ex.printStackTrace();
4238 * Load and link any saved structure viewers.
4245 protected void loadPDBStructures(jarInputStreamProvider jprovider,
4246 List<JSeq> jseqs, AlignFrame af, AlignmentPanel ap)
4249 * Run through all PDB ids on the alignment, and collect mappings between
4250 * distinct view ids and all sequences referring to that view.
4252 Map<String, StructureViewerModel> structureViewers = new LinkedHashMap<>();
4254 for (int i = 0; i < jseqs.size(); i++)
4256 JSeq jseq = jseqs.get(i);
4257 if (jseq.getPdbids().size() > 0)
4259 List<Pdbids> ids = jseq.getPdbids();
4260 for (int p = 0; p < ids.size(); p++)
4262 Pdbids pdbid = ids.get(p);
4263 final int structureStateCount = pdbid.getStructureState().size();
4264 for (int s = 0; s < structureStateCount; s++)
4266 // check to see if we haven't already created this structure view
4267 final StructureState structureState = pdbid
4268 .getStructureState().get(s);
4269 String sviewid = (structureState.getViewId() == null) ? null
4270 : structureState.getViewId() + uniqueSetSuffix;
4271 jalview.datamodel.PDBEntry jpdb = new jalview.datamodel.PDBEntry();
4272 // Originally : pdbid.getFile()
4273 // : TODO: verify external PDB file recovery still works in normal
4274 // jalview project load
4276 loadPDBFile(jprovider, pdbid.getId(), pdbid.getFile()));
4277 jpdb.setId(pdbid.getId());
4279 int x = safeInt(structureState.getXpos());
4280 int y = safeInt(structureState.getYpos());
4281 int width = safeInt(structureState.getWidth());
4282 int height = safeInt(structureState.getHeight());
4284 // Probably don't need to do this anymore...
4285 // Desktop.desktop.getComponentAt(x, y);
4286 // TODO: NOW: check that this recovers the PDB file correctly.
4287 String pdbFile = loadPDBFile(jprovider, pdbid.getId(),
4289 jalview.datamodel.SequenceI seq = seqRefIds
4290 .get(jseq.getId() + "");
4291 if (sviewid == null)
4293 sviewid = "_jalview_pre2_4_" + x + "," + y + "," + width + ","
4296 if (!structureViewers.containsKey(sviewid))
4298 structureViewers.put(sviewid,
4299 new StructureViewerModel(x, y, width, height, false,
4300 false, true, structureState.getViewId(),
4301 structureState.getType()));
4302 // Legacy pre-2.7 conversion JAL-823 :
4303 // do not assume any view has to be linked for colour by
4307 // assemble String[] { pdb files }, String[] { id for each
4308 // file }, orig_fileloc, SequenceI[][] {{ seqs_file 1 }, {
4309 // seqs_file 2}, boolean[] {
4310 // linkAlignPanel,superposeWithAlignpanel}} from hash
4311 StructureViewerModel jmoldat = structureViewers.get(sviewid);
4312 jmoldat.setAlignWithPanel(jmoldat.isAlignWithPanel()
4313 || structureState.isAlignwithAlignPanel());
4316 * Default colour by linked panel to false if not specified (e.g.
4317 * for pre-2.7 projects)
4319 boolean colourWithAlignPanel = jmoldat.isColourWithAlignPanel();
4320 colourWithAlignPanel |= structureState.isColourwithAlignPanel();
4321 jmoldat.setColourWithAlignPanel(colourWithAlignPanel);
4324 * Default colour by viewer to true if not specified (e.g. for
4327 boolean colourByViewer = jmoldat.isColourByViewer();
4328 colourByViewer &= structureState.isColourByJmol();
4329 jmoldat.setColourByViewer(colourByViewer);
4331 if (jmoldat.getStateData().length() < structureState
4332 .getValue()/*Content()*/.length())
4334 jmoldat.setStateData(structureState.getValue());// Content());
4336 if (pdbid.getFile() != null)
4338 File mapkey = new File(pdbid.getFile());
4339 StructureData seqstrmaps = jmoldat.getFileData().get(mapkey);
4340 if (seqstrmaps == null)
4342 jmoldat.getFileData().put(mapkey,
4343 seqstrmaps = jmoldat.new StructureData(pdbFile,
4346 if (!seqstrmaps.getSeqList().contains(seq))
4348 seqstrmaps.getSeqList().add(seq);
4354 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");
4361 // Instantiate the associated structure views
4362 for (Entry<String, StructureViewerModel> entry : structureViewers
4367 createOrLinkStructureViewer(entry, af, ap, jprovider);
4368 } catch (Exception e)
4371 "Error loading structure viewer: " + e.getMessage());
4372 // failed - try the next one
4384 protected void createOrLinkStructureViewer(
4385 Entry<String, StructureViewerModel> viewerData, AlignFrame af,
4386 AlignmentPanel ap, jarInputStreamProvider jprovider)
4388 final StructureViewerModel stateData = viewerData.getValue();
4391 * Search for any viewer windows already open from other alignment views
4392 * that exactly match the stored structure state
4394 StructureViewerBase comp = findMatchingViewer(viewerData);
4398 linkStructureViewer(ap, comp, stateData);
4403 * From 2.9: stateData.type contains JMOL or CHIMERA, data is in jar entry
4404 * "viewer_"+stateData.viewId
4406 String type = stateData.getType();
4409 type = ViewerType.JMOL.toString();
4413 ViewerType viewerType = ViewerType.valueOf(type);
4417 createChimeraViewer(viewerData, af, jprovider, false);
4420 createChimeraViewer(viewerData, af, jprovider, true);
4423 createPymolViewer(viewerData, af, jprovider);
4426 createJmolViewer(viewerData, af, jprovider);
4428 } catch (IllegalArgumentException | NullPointerException e)
4431 "Invalid structure viewer type: " + type);
4436 * Create a new Chimera or ChimeraX viewer
4443 protected void createChimeraViewer(
4444 Entry<String, StructureViewerModel> viewerData, AlignFrame af,
4445 jarInputStreamProvider jprovider, boolean isChimeraX)
4447 StructureViewerModel data = viewerData.getValue();
4448 String chimeraSessionFile = data.getStateData();
4451 * Copy Chimera session from jar entry "viewer_"+viewId to a temporary file
4453 * NB this is the 'saved' viewId as in the project file XML, _not_ the
4454 * 'uniquified' sviewid used to reconstruct the viewer here
4456 String viewerJarEntryName = getViewerJarEntryName(data.getViewId());
4457 String extension = isChimeraX
4458 ? JalviewChimeraXBindingModel.CHIMERAX_SESSION_EXTENSION
4459 : JalviewChimeraBinding.CHIMERA_SESSION_EXTENSION;
4460 chimeraSessionFile = copyJarEntry(jprovider, viewerJarEntryName,
4461 "chimera", extension);
4463 Set<Entry<File, StructureData>> fileData = data.getFileData()
4465 List<PDBEntry> pdbs = new ArrayList<>();
4466 List<SequenceI[]> allseqs = new ArrayList<>();
4467 for (Entry<File, StructureData> pdb : fileData)
4469 String filePath = pdb.getValue().getFilePath();
4470 String pdbId = pdb.getValue().getPdbId();
4471 // pdbs.add(new PDBEntry(filePath, pdbId));
4472 pdbs.add(new PDBEntry(pdbId, null, PDBEntry.Type.PDB, filePath));
4473 final List<SequenceI> seqList = pdb.getValue().getSeqList();
4474 SequenceI[] seqs = seqList.toArray(new SequenceI[seqList.size()]);
4478 boolean colourByChimera = data.isColourByViewer();
4479 boolean colourBySequence = data.isColourWithAlignPanel();
4481 // TODO use StructureViewer as a factory here, see JAL-1761
4482 final PDBEntry[] pdbArray = pdbs.toArray(new PDBEntry[pdbs.size()]);
4483 final SequenceI[][] seqsArray = allseqs
4484 .toArray(new SequenceI[allseqs.size()][]);
4485 String newViewId = viewerData.getKey();
4487 ChimeraViewFrame cvf = isChimeraX
4488 ? new ChimeraXViewFrame(chimeraSessionFile, af.alignPanel,
4489 pdbArray, seqsArray, colourByChimera, colourBySequence,
4491 : new ChimeraViewFrame(chimeraSessionFile, af.alignPanel,
4492 pdbArray, seqsArray, colourByChimera, colourBySequence,
4494 cvf.setSize(data.getWidth(), data.getHeight());
4495 cvf.setLocation(data.getX(), data.getY());
4499 * Create a new Jmol window. First parse the Jmol state to translate filenames
4500 * loaded into the view, and record the order in which files are shown in the
4501 * Jmol view, so we can add the sequence mappings in same order.
4507 protected void createJmolViewer(
4508 final Entry<String, StructureViewerModel> viewerData,
4509 AlignFrame af, jarInputStreamProvider jprovider)
4511 final StructureViewerModel svattrib = viewerData.getValue();
4512 String state = svattrib.getStateData();
4515 * Pre-2.9: state element value is the Jmol state string
4517 * 2.9+: @type is "JMOL", state data is in a Jar file member named "viewer_"
4520 if (ViewerType.JMOL.toString().equals(svattrib.getType()))
4522 state = readJarEntry(jprovider,
4523 getViewerJarEntryName(svattrib.getViewId()));
4526 List<String> pdbfilenames = new ArrayList<>();
4527 List<SequenceI[]> seqmaps = new ArrayList<>();
4528 List<String> pdbids = new ArrayList<>();
4529 StringBuilder newFileLoc = new StringBuilder(64);
4530 int cp = 0, ncp, ecp;
4531 Map<File, StructureData> oldFiles = svattrib.getFileData();
4532 while ((ncp = state.indexOf("load ", cp)) > -1)
4536 // look for next filename in load statement
4537 newFileLoc.append(state.substring(cp,
4538 ncp = (state.indexOf("\"", ncp + 1) + 1)));
4539 String oldfilenam = state.substring(ncp,
4540 ecp = state.indexOf("\"", ncp));
4541 // recover the new mapping data for this old filename
4542 // have to normalize filename - since Jmol and jalview do
4544 // translation differently.
4545 StructureData filedat = oldFiles.get(new File(oldfilenam));
4546 if (filedat == null)
4548 String reformatedOldFilename = oldfilenam.replaceAll("/", "\\\\");
4549 filedat = oldFiles.get(new File(reformatedOldFilename));
4551 newFileLoc.append(Platform.escapeBackslashes(filedat.getFilePath()));
4552 pdbfilenames.add(filedat.getFilePath());
4553 pdbids.add(filedat.getPdbId());
4554 seqmaps.add(filedat.getSeqList().toArray(new SequenceI[0]));
4555 newFileLoc.append("\"");
4556 cp = ecp + 1; // advance beyond last \" and set cursor so we can
4557 // look for next file statement.
4558 } while ((ncp = state.indexOf("/*file*/", cp)) > -1);
4562 // just append rest of state
4563 newFileLoc.append(state.substring(cp));
4567 System.err.print("Ignoring incomplete Jmol state for PDB ids: ");
4568 newFileLoc = new StringBuilder(state);
4569 newFileLoc.append("; load append ");
4570 for (File id : oldFiles.keySet())
4572 // add this and any other pdb files that should be present in
4574 StructureData filedat = oldFiles.get(id);
4575 newFileLoc.append(filedat.getFilePath());
4576 pdbfilenames.add(filedat.getFilePath());
4577 pdbids.add(filedat.getPdbId());
4578 seqmaps.add(filedat.getSeqList().toArray(new SequenceI[0]));
4579 newFileLoc.append(" \"");
4580 newFileLoc.append(filedat.getFilePath());
4581 newFileLoc.append("\"");
4584 newFileLoc.append(";");
4587 if (newFileLoc.length() == 0)
4591 int histbug = newFileLoc.indexOf("history = ");
4595 * change "history = [true|false];" to "history = [1|0];"
4598 int diff = histbug == -1 ? -1 : newFileLoc.indexOf(";", histbug);
4599 String val = (diff == -1) ? null
4600 : newFileLoc.substring(histbug, diff);
4601 if (val != null && val.length() >= 4)
4603 if (val.contains("e")) // eh? what can it be?
4605 if (val.trim().equals("true"))
4613 newFileLoc.replace(histbug, diff, val);
4618 final String[] pdbf = pdbfilenames
4619 .toArray(new String[pdbfilenames.size()]);
4620 final String[] id = pdbids.toArray(new String[pdbids.size()]);
4621 final SequenceI[][] sq = seqmaps
4622 .toArray(new SequenceI[seqmaps.size()][]);
4623 final String fileloc = newFileLoc.toString();
4624 final String sviewid = viewerData.getKey();
4625 final AlignFrame alf = af;
4626 final Rectangle rect = new Rectangle(svattrib.getX(), svattrib.getY(),
4627 svattrib.getWidth(), svattrib.getHeight());
4630 javax.swing.SwingUtilities.invokeAndWait(new Runnable()
4635 JalviewStructureDisplayI sview = null;
4638 sview = new StructureViewer(
4639 alf.alignPanel.getStructureSelectionManager())
4640 .createView(StructureViewer.ViewerType.JMOL,
4641 pdbf, id, sq, alf.alignPanel, svattrib,
4642 fileloc, rect, sviewid);
4643 addNewStructureViewer(sview);
4644 } catch (OutOfMemoryError ex)
4646 new OOMWarning("restoring structure view for PDB id " + id,
4647 (OutOfMemoryError) ex.getCause());
4648 if (sview != null && sview.isVisible())
4650 sview.closeViewer(false);
4651 sview.setVisible(false);
4657 } catch (InvocationTargetException ex)
4659 warn("Unexpected error when opening Jmol view.", ex);
4661 } catch (InterruptedException e)
4663 // e.printStackTrace();
4669 * Generates a name for the entry in the project jar file to hold state
4670 * information for a structure viewer
4675 protected String getViewerJarEntryName(String viewId)
4677 return VIEWER_PREFIX + viewId;
4681 * Returns any open frame that matches given structure viewer data. The match
4682 * is based on the unique viewId, or (for older project versions) the frame's
4688 protected StructureViewerBase findMatchingViewer(
4689 Entry<String, StructureViewerModel> viewerData)
4691 final String sviewid = viewerData.getKey();
4692 final StructureViewerModel svattrib = viewerData.getValue();
4693 StructureViewerBase comp = null;
4694 JInternalFrame[] frames = getAllFrames();
4695 for (JInternalFrame frame : frames)
4697 if (frame instanceof StructureViewerBase)
4700 * Post jalview 2.4 schema includes structure view id
4702 if (sviewid != null && ((StructureViewerBase) frame).getViewId()
4705 comp = (StructureViewerBase) frame;
4706 break; // break added in 2.9
4709 * Otherwise test for matching position and size of viewer frame
4711 else if (frame.getX() == svattrib.getX()
4712 && frame.getY() == svattrib.getY()
4713 && frame.getHeight() == svattrib.getHeight()
4714 && frame.getWidth() == svattrib.getWidth())
4716 comp = (StructureViewerBase) frame;
4717 // no break in faint hope of an exact match on viewId
4725 * Link an AlignmentPanel to an existing structure viewer.
4730 * @param useinViewerSuperpos
4731 * @param usetoColourbyseq
4732 * @param viewerColouring
4734 protected void linkStructureViewer(AlignmentPanel ap,
4735 StructureViewerBase viewer, StructureViewerModel stateData)
4737 // NOTE: if the jalview project is part of a shared session then
4738 // view synchronization should/could be done here.
4740 final boolean useinViewerSuperpos = stateData.isAlignWithPanel();
4741 final boolean usetoColourbyseq = stateData.isColourWithAlignPanel();
4742 final boolean viewerColouring = stateData.isColourByViewer();
4743 Map<File, StructureData> oldFiles = stateData.getFileData();
4746 * Add mapping for sequences in this view to an already open viewer
4748 final AAStructureBindingModel binding = viewer.getBinding();
4749 for (File id : oldFiles.keySet())
4751 // add this and any other pdb files that should be present in the
4753 StructureData filedat = oldFiles.get(id);
4754 String pdbFile = filedat.getFilePath();
4755 SequenceI[] seq = filedat.getSeqList().toArray(new SequenceI[0]);
4756 binding.getSsm().setMapping(seq, null, pdbFile, DataSourceType.FILE,
4758 binding.addSequenceForStructFile(pdbFile, seq);
4760 // and add the AlignmentPanel's reference to the view panel
4761 viewer.addAlignmentPanel(ap);
4762 if (useinViewerSuperpos)
4764 viewer.useAlignmentPanelForSuperposition(ap);
4768 viewer.excludeAlignmentPanelForSuperposition(ap);
4770 if (usetoColourbyseq)
4772 viewer.useAlignmentPanelForColourbyseq(ap, !viewerColouring);
4776 viewer.excludeAlignmentPanelForColourbyseq(ap);
4781 * Get all frames within the Desktop.
4785 protected JInternalFrame[] getAllFrames()
4787 JInternalFrame[] frames = null;
4788 // TODO is this necessary - is it safe - risk of hanging?
4793 frames = Desktop.desktop.getAllFrames();
4794 } catch (ArrayIndexOutOfBoundsException e)
4796 // occasional No such child exceptions are thrown here...
4800 } catch (InterruptedException f)
4804 } while (frames == null);
4809 * Answers true if 'version' is equal to or later than 'supported', where each
4810 * is formatted as major/minor versions like "2.8.3" or "2.3.4b1" for bugfix
4811 * changes. Development and test values for 'version' are leniently treated
4815 * - minimum version we are comparing against
4817 * - version of data being processsed
4820 public static boolean isVersionStringLaterThan(String supported,
4823 if (supported == null || version == null
4824 || version.equalsIgnoreCase("DEVELOPMENT BUILD")
4825 || version.equalsIgnoreCase("Test")
4826 || version.equalsIgnoreCase("AUTOMATED BUILD"))
4828 System.err.println("Assuming project file with "
4829 + (version == null ? "null" : version)
4830 + " is compatible with Jalview version " + supported);
4835 return StringUtils.compareVersions(version, supported, "b") >= 0;
4839 Vector<JalviewStructureDisplayI> newStructureViewers = null;
4841 protected void addNewStructureViewer(JalviewStructureDisplayI sview)
4843 if (newStructureViewers != null)
4845 sview.getBinding().setFinishedLoadingFromArchive(false);
4846 newStructureViewers.add(sview);
4850 protected void setLoadingFinishedForNewStructureViewers()
4852 if (newStructureViewers != null)
4854 for (JalviewStructureDisplayI sview : newStructureViewers)
4856 sview.getBinding().setFinishedLoadingFromArchive(true);
4858 newStructureViewers.clear();
4859 newStructureViewers = null;
4863 AlignFrame loadViewport(String file, List<JSeq> JSEQ,
4864 List<SequenceI> hiddenSeqs, AlignmentI al,
4865 JalviewModel jm, Viewport view, String uniqueSeqSetId,
4866 String viewId, List<JvAnnotRow> autoAlan)
4868 AlignFrame af = null;
4869 af = new AlignFrame(al, safeInt(view.getWidth()),
4870 safeInt(view.getHeight()), uniqueSeqSetId, viewId);
4872 af.setFileName(file, FileFormat.Jalview);
4874 final AlignViewport viewport = af.getViewport();
4875 for (int i = 0; i < JSEQ.size(); i++)
4877 int colour = safeInt(JSEQ.get(i).getColour());
4878 viewport.setSequenceColour(viewport.getAlignment().getSequenceAt(i),
4884 viewport.setColourByReferenceSeq(true);
4885 viewport.setDisplayReferenceSeq(true);
4888 viewport.setGatherViewsHere(safeBoolean(view.isGatheredViews()));
4890 if (view.getSequenceSetId() != null)
4892 AlignmentViewport av = viewportsAdded.get(uniqueSeqSetId);
4894 viewport.setSequenceSetId(uniqueSeqSetId);
4897 // propagate shared settings to this new view
4898 viewport.setHistoryList(av.getHistoryList());
4899 viewport.setRedoList(av.getRedoList());
4903 viewportsAdded.put(uniqueSeqSetId, viewport);
4905 // TODO: check if this method can be called repeatedly without
4906 // side-effects if alignpanel already registered.
4907 PaintRefresher.Register(af.alignPanel, uniqueSeqSetId);
4909 // apply Hidden regions to view.
4910 if (hiddenSeqs != null)
4912 for (int s = 0; s < JSEQ.size(); s++)
4914 SequenceGroup hidden = new SequenceGroup();
4915 boolean isRepresentative = false;
4916 for (int r = 0; r < JSEQ.get(s).getHiddenSequences().size(); r++)
4918 isRepresentative = true;
4919 SequenceI sequenceToHide = al
4920 .getSequenceAt(JSEQ.get(s).getHiddenSequences().get(r));
4921 hidden.addSequence(sequenceToHide, false);
4922 // remove from hiddenSeqs list so we don't try to hide it twice
4923 hiddenSeqs.remove(sequenceToHide);
4925 if (isRepresentative)
4927 SequenceI representativeSequence = al.getSequenceAt(s);
4928 hidden.addSequence(representativeSequence, false);
4929 viewport.hideRepSequences(representativeSequence, hidden);
4933 SequenceI[] hseqs = hiddenSeqs
4934 .toArray(new SequenceI[hiddenSeqs.size()]);
4935 viewport.hideSequence(hseqs);
4938 // recover view properties and display parameters
4940 viewport.setShowAnnotation(safeBoolean(view.isShowAnnotation()));
4941 viewport.setAbovePIDThreshold(safeBoolean(view.isPidSelected()));
4942 final int pidThreshold = safeInt(view.getPidThreshold());
4943 viewport.setThreshold(pidThreshold);
4945 viewport.setColourText(safeBoolean(view.isShowColourText()));
4948 .setConservationSelected(
4949 safeBoolean(view.isConservationSelected()));
4950 viewport.setIncrement(safeInt(view.getConsThreshold()));
4951 viewport.setShowJVSuffix(safeBoolean(view.isShowFullId()));
4952 viewport.setRightAlignIds(safeBoolean(view.isRightAlignIds()));
4953 viewport.setFont(new Font(view.getFontName(),
4954 safeInt(view.getFontStyle()), safeInt(view.getFontSize())),
4956 ViewStyleI vs = viewport.getViewStyle();
4957 vs.setScaleProteinAsCdna(view.isScaleProteinAsCdna());
4958 viewport.setViewStyle(vs);
4959 // TODO: allow custom charWidth/Heights to be restored by updating them
4960 // after setting font - which means set above to false
4961 viewport.setRenderGaps(safeBoolean(view.isRenderGaps()));
4962 viewport.setWrapAlignment(safeBoolean(view.isWrapAlignment()));
4963 viewport.setShowAnnotation(safeBoolean(view.isShowAnnotation()));
4965 viewport.setShowBoxes(safeBoolean(view.isShowBoxes()));
4967 viewport.setShowText(safeBoolean(view.isShowText()));
4969 viewport.setTextColour(new Color(safeInt(view.getTextCol1())));
4970 viewport.setTextColour2(new Color(safeInt(view.getTextCol2())));
4971 viewport.setThresholdTextColour(safeInt(view.getTextColThreshold()));
4972 viewport.setShowUnconserved(view.isShowUnconserved());
4973 viewport.getRanges().setStartRes(safeInt(view.getStartRes()));
4975 if (view.getViewName() != null)
4977 viewport.setViewName(view.getViewName());
4978 af.setInitialTabVisible();
4980 af.setBounds(safeInt(view.getXpos()), safeInt(view.getYpos()),
4981 safeInt(view.getWidth()), safeInt(view.getHeight()));
4982 // startSeq set in af.alignPanel.updateLayout below
4983 af.alignPanel.updateLayout();
4984 ColourSchemeI cs = null;
4985 // apply colourschemes
4986 if (view.getBgColour() != null)
4988 if (view.getBgColour().startsWith("ucs"))
4990 cs = getUserColourScheme(jm, view.getBgColour());
4992 else if (view.getBgColour().startsWith("Annotation"))
4994 AnnotationColourScheme viewAnnColour = view.getAnnotationColours();
4995 cs = constructAnnotationColour(viewAnnColour, af, al, jm, true);
5002 cs = ColourSchemeProperty.getColourScheme(af.getViewport(), al,
5003 view.getBgColour());
5008 * turn off 'alignment colour applies to all groups'
5009 * while restoring global colour scheme
5011 viewport.setColourAppliesToAllGroups(false);
5012 viewport.setGlobalColourScheme(cs);
5013 viewport.getResidueShading().setThreshold(pidThreshold,
5014 view.isIgnoreGapsinConsensus());
5015 viewport.getResidueShading()
5016 .setConsensus(viewport.getSequenceConsensusHash());
5017 if (safeBoolean(view.isConservationSelected()) && cs != null)
5019 viewport.getResidueShading()
5020 .setConservationInc(safeInt(view.getConsThreshold()));
5022 af.changeColour(cs);
5023 viewport.setColourAppliesToAllGroups(true);
5026 .setShowSequenceFeatures(
5027 safeBoolean(view.isShowSequenceFeatures()));
5029 viewport.setCentreColumnLabels(view.isCentreColumnLabels());
5030 viewport.setIgnoreGapsConsensus(view.isIgnoreGapsinConsensus(), null);
5031 viewport.setFollowHighlight(view.isFollowHighlight());
5032 viewport.followSelection = view.isFollowSelection();
5033 viewport.setShowConsensusHistogram(view.isShowConsensusHistogram());
5034 viewport.setShowSequenceLogo(view.isShowSequenceLogo());
5035 viewport.setNormaliseSequenceLogo(view.isNormaliseSequenceLogo());
5036 viewport.setShowDBRefs(safeBoolean(view.isShowDbRefTooltip()));
5037 viewport.setShowNPFeats(safeBoolean(view.isShowNPfeatureTooltip()));
5038 viewport.setShowGroupConsensus(view.isShowGroupConsensus());
5039 viewport.setShowGroupConservation(view.isShowGroupConservation());
5040 viewport.setShowComplementFeatures(view.isShowComplementFeatures());
5041 viewport.setShowComplementFeaturesOnTop(
5042 view.isShowComplementFeaturesOnTop());
5044 // recover feature settings
5045 if (jm.getFeatureSettings() != null)
5047 FeatureRendererModel fr = af.alignPanel.getSeqPanel().seqCanvas
5048 .getFeatureRenderer();
5049 FeaturesDisplayed fdi;
5050 viewport.setFeaturesDisplayed(fdi = new FeaturesDisplayed());
5051 String[] renderOrder = new String[jm.getFeatureSettings()
5052 .getSetting().size()];
5053 Map<String, FeatureColourI> featureColours = new Hashtable<>();
5054 Map<String, Float> featureOrder = new Hashtable<>();
5056 for (int fs = 0; fs < jm.getFeatureSettings()
5057 .getSetting().size(); fs++)
5059 Setting setting = jm.getFeatureSettings().getSetting().get(fs);
5060 String featureType = setting.getType();
5063 * restore feature filters (if any)
5065 jalview.xml.binding.jalview.FeatureMatcherSet filters = setting
5067 if (filters != null)
5069 FeatureMatcherSetI filter = Jalview2XML
5070 .parseFilter(featureType, filters);
5071 if (!filter.isEmpty())
5073 fr.setFeatureFilter(featureType, filter);
5078 * restore feature colour scheme
5080 Color maxColour = new Color(setting.getColour());
5081 if (setting.getMincolour() != null)
5084 * minColour is always set unless a simple colour
5085 * (including for colour by label though it doesn't use it)
5087 Color minColour = new Color(setting.getMincolour().intValue());
5088 Color noValueColour = minColour;
5089 NoValueColour noColour = setting.getNoValueColour();
5090 if (noColour == NoValueColour.NONE)
5092 noValueColour = null;
5094 else if (noColour == NoValueColour.MAX)
5096 noValueColour = maxColour;
5098 float min = safeFloat(safeFloat(setting.getMin()));
5099 float max = setting.getMax() == null ? 1f
5100 : setting.getMax().floatValue();
5101 FeatureColourI gc = new FeatureColour(maxColour, minColour,
5103 noValueColour, min, max);
5104 if (setting.getAttributeName().size() > 0)
5106 gc.setAttributeName(setting.getAttributeName().toArray(
5107 new String[setting.getAttributeName().size()]));
5109 if (setting.getThreshold() != null)
5111 gc.setThreshold(setting.getThreshold().floatValue());
5112 int threshstate = safeInt(setting.getThreshstate());
5113 // -1 = None, 0 = Below, 1 = Above threshold
5114 if (threshstate == 0)
5116 gc.setBelowThreshold(true);
5118 else if (threshstate == 1)
5120 gc.setAboveThreshold(true);
5123 gc.setAutoScaled(true); // default
5124 if (setting.isAutoScale() != null)
5126 gc.setAutoScaled(setting.isAutoScale());
5128 if (setting.isColourByLabel() != null)
5130 gc.setColourByLabel(setting.isColourByLabel());
5132 // and put in the feature colour table.
5133 featureColours.put(featureType, gc);
5137 featureColours.put(featureType,
5138 new FeatureColour(maxColour));
5140 renderOrder[fs] = featureType;
5141 if (setting.getOrder() != null)
5143 featureOrder.put(featureType, setting.getOrder().floatValue());
5147 featureOrder.put(featureType, Float.valueOf(
5148 fs / jm.getFeatureSettings().getSetting().size()));
5150 if (safeBoolean(setting.isDisplay()))
5152 fdi.setVisible(featureType);
5155 Map<String, Boolean> fgtable = new Hashtable<>();
5156 for (int gs = 0; gs < jm.getFeatureSettings().getGroup().size(); gs++)
5158 Group grp = jm.getFeatureSettings().getGroup().get(gs);
5159 fgtable.put(grp.getName(), Boolean.valueOf(grp.isDisplay()));
5161 // FeatureRendererSettings frs = new FeatureRendererSettings(renderOrder,
5162 // fgtable, featureColours, jms.getFeatureSettings().hasTransparency() ?
5163 // jms.getFeatureSettings().getTransparency() : 0.0, featureOrder);
5164 FeatureRendererSettings frs = new FeatureRendererSettings(renderOrder,
5165 fgtable, featureColours, 1.0f, featureOrder);
5166 fr.transferSettings(frs);
5169 if (view.getHiddenColumns().size() > 0)
5171 for (int c = 0; c < view.getHiddenColumns().size(); c++)
5173 final HiddenColumns hc = view.getHiddenColumns().get(c);
5174 viewport.hideColumns(safeInt(hc.getStart()),
5175 safeInt(hc.getEnd()) /* +1 */);
5178 if (view.getCalcIdParam() != null)
5180 for (CalcIdParam calcIdParam : view.getCalcIdParam())
5182 if (calcIdParam != null)
5184 if (recoverCalcIdParam(calcIdParam, viewport))
5189 warn("Couldn't recover parameters for "
5190 + calcIdParam.getCalcId());
5195 af.setMenusFromViewport(viewport);
5196 af.setTitle(view.getTitle());
5197 // TODO: we don't need to do this if the viewport is aready visible.
5199 * Add the AlignFrame to the desktop (it may be 'gathered' later), unless it
5200 * has a 'cdna/protein complement' view, in which case save it in order to
5201 * populate a SplitFrame once all views have been read in.
5203 String complementaryViewId = view.getComplementId();
5204 if (complementaryViewId == null)
5206 Desktop.addInternalFrame(af, view.getTitle(),
5207 safeInt(view.getWidth()), safeInt(view.getHeight()));
5208 // recompute any autoannotation
5209 af.alignPanel.updateAnnotation(false, true);
5210 reorderAutoannotation(af, al, autoAlan);
5211 af.alignPanel.alignmentChanged();
5215 splitFrameCandidates.put(view, af);
5221 * Reads saved data to restore Colour by Annotation settings
5223 * @param viewAnnColour
5227 * @param checkGroupAnnColour
5230 private ColourSchemeI constructAnnotationColour(
5231 AnnotationColourScheme viewAnnColour, AlignFrame af,
5232 AlignmentI al, JalviewModel model, boolean checkGroupAnnColour)
5234 boolean propagateAnnColour = false;
5235 AlignmentI annAlignment = af != null ? af.getViewport().getAlignment()
5237 if (checkGroupAnnColour && al.getGroups() != null
5238 && al.getGroups().size() > 0)
5240 // pre 2.8.1 behaviour
5241 // check to see if we should transfer annotation colours
5242 propagateAnnColour = true;
5243 for (SequenceGroup sg : al.getGroups())
5245 if (sg.getColourScheme() instanceof AnnotationColourGradient)
5247 propagateAnnColour = false;
5253 * 2.10.2- : saved annotationId is AlignmentAnnotation.annotationId
5255 String annotationId = viewAnnColour.getAnnotation();
5256 AlignmentAnnotation matchedAnnotation = annotationIds.get(annotationId);
5259 * pre 2.10.2: saved annotationId is AlignmentAnnotation.label
5261 if (matchedAnnotation == null
5262 && annAlignment.getAlignmentAnnotation() != null)
5264 for (int i = 0; i < annAlignment.getAlignmentAnnotation().length; i++)
5267 .equals(annAlignment.getAlignmentAnnotation()[i].label))
5269 matchedAnnotation = annAlignment.getAlignmentAnnotation()[i];
5274 if (matchedAnnotation == null)
5276 System.err.println("Failed to match annotation colour scheme for "
5280 if (matchedAnnotation.getThreshold() == null)
5282 matchedAnnotation.setThreshold(
5283 new GraphLine(safeFloat(viewAnnColour.getThreshold()),
5284 "Threshold", Color.black));
5287 AnnotationColourGradient cs = null;
5288 if (viewAnnColour.getColourScheme().equals("None"))
5290 cs = new AnnotationColourGradient(matchedAnnotation,
5291 new Color(safeInt(viewAnnColour.getMinColour())),
5292 new Color(safeInt(viewAnnColour.getMaxColour())),
5293 safeInt(viewAnnColour.getAboveThreshold()));
5295 else if (viewAnnColour.getColourScheme().startsWith("ucs"))
5297 cs = new AnnotationColourGradient(matchedAnnotation,
5298 getUserColourScheme(model, viewAnnColour.getColourScheme()),
5299 safeInt(viewAnnColour.getAboveThreshold()));
5303 cs = new AnnotationColourGradient(matchedAnnotation,
5304 ColourSchemeProperty.getColourScheme(af.getViewport(), al,
5305 viewAnnColour.getColourScheme()),
5306 safeInt(viewAnnColour.getAboveThreshold()));
5309 boolean perSequenceOnly = safeBoolean(viewAnnColour.isPerSequence());
5310 boolean useOriginalColours = safeBoolean(
5311 viewAnnColour.isPredefinedColours());
5312 cs.setSeqAssociated(perSequenceOnly);
5313 cs.setPredefinedColours(useOriginalColours);
5315 if (propagateAnnColour && al.getGroups() != null)
5317 // Also use these settings for all the groups
5318 for (int g = 0; g < al.getGroups().size(); g++)
5320 SequenceGroup sg = al.getGroups().get(g);
5321 if (sg.getGroupColourScheme() == null)
5326 AnnotationColourGradient groupScheme = new AnnotationColourGradient(
5327 matchedAnnotation, sg.getColourScheme(),
5328 safeInt(viewAnnColour.getAboveThreshold()));
5329 sg.setColourScheme(groupScheme);
5330 groupScheme.setSeqAssociated(perSequenceOnly);
5331 groupScheme.setPredefinedColours(useOriginalColours);
5337 private void reorderAutoannotation(AlignFrame af, AlignmentI al,
5338 List<JvAnnotRow> autoAlan)
5340 // copy over visualization settings for autocalculated annotation in the
5342 if (al.getAlignmentAnnotation() != null)
5345 * Kludge for magic autoannotation names (see JAL-811)
5347 String[] magicNames = new String[] { "Consensus", "Quality",
5349 JvAnnotRow nullAnnot = new JvAnnotRow(-1, null);
5350 Hashtable<String, JvAnnotRow> visan = new Hashtable<>();
5351 for (String nm : magicNames)
5353 visan.put(nm, nullAnnot);
5355 for (JvAnnotRow auan : autoAlan)
5357 visan.put(auan.template.label
5358 + (auan.template.getCalcId() == null ? ""
5359 : "\t" + auan.template.getCalcId()),
5362 int hSize = al.getAlignmentAnnotation().length;
5363 List<JvAnnotRow> reorder = new ArrayList<>();
5364 // work through any autoCalculated annotation already on the view
5365 // removing it if it should be placed in a different location on the
5366 // annotation panel.
5367 List<String> remains = new ArrayList<>(visan.keySet());
5368 for (int h = 0; h < hSize; h++)
5370 jalview.datamodel.AlignmentAnnotation jalan = al
5371 .getAlignmentAnnotation()[h];
5372 if (jalan.autoCalculated)
5375 JvAnnotRow valan = visan.get(k = jalan.label);
5376 if (jalan.getCalcId() != null)
5378 valan = visan.get(k = jalan.label + "\t" + jalan.getCalcId());
5383 // delete the auto calculated row from the alignment
5384 al.deleteAnnotation(jalan, false);
5388 if (valan != nullAnnot)
5390 if (jalan != valan.template)
5392 // newly created autoannotation row instance
5393 // so keep a reference to the visible annotation row
5394 // and copy over all relevant attributes
5395 if (valan.template.graphHeight >= 0)
5398 jalan.graphHeight = valan.template.graphHeight;
5400 jalan.visible = valan.template.visible;
5402 reorder.add(new JvAnnotRow(valan.order, jalan));
5407 // Add any (possibly stale) autocalculated rows that were not appended to
5408 // the view during construction
5409 for (String other : remains)
5411 JvAnnotRow othera = visan.get(other);
5412 if (othera != nullAnnot && othera.template.getCalcId() != null
5413 && othera.template.getCalcId().length() > 0)
5415 reorder.add(othera);
5418 // now put the automatic annotation in its correct place
5419 int s = 0, srt[] = new int[reorder.size()];
5420 JvAnnotRow[] rws = new JvAnnotRow[reorder.size()];
5421 for (JvAnnotRow jvar : reorder)
5424 srt[s++] = jvar.order;
5427 jalview.util.QuickSort.sort(srt, rws);
5428 // and re-insert the annotation at its correct position
5429 for (JvAnnotRow jvar : rws)
5431 al.addAnnotation(jvar.template, jvar.order);
5433 af.alignPanel.adjustAnnotationHeight();
5437 Hashtable skipList = null;
5440 * TODO remove this method
5443 * @return AlignFrame bound to sequenceSetId from view, if one exists. private
5444 * AlignFrame getSkippedFrame(Viewport view) { if (skipList==null) {
5445 * throw new Error("Implementation Error. No skipList defined for this
5446 * Jalview2XML instance."); } return (AlignFrame)
5447 * skipList.get(view.getSequenceSetId()); }
5451 * Check if the Jalview view contained in object should be skipped or not.
5454 * @return true if view's sequenceSetId is a key in skipList
5456 private boolean skipViewport(JalviewModel object)
5458 if (skipList == null)
5462 String id = object.getViewport().get(0).getSequenceSetId();
5463 if (skipList.containsKey(id))
5465 if (Cache.log != null && Cache.log.isDebugEnabled())
5467 Cache.log.debug("Skipping seuqence set id " + id);
5474 public void addToSkipList(AlignFrame af)
5476 if (skipList == null)
5478 skipList = new Hashtable();
5480 skipList.put(af.getViewport().getSequenceSetId(), af);
5483 public void clearSkipList()
5485 if (skipList != null)
5492 private void recoverDatasetFor(SequenceSet vamsasSet, AlignmentI al,
5493 boolean ignoreUnrefed, String uniqueSeqSetId)
5495 jalview.datamodel.AlignmentI ds = getDatasetFor(
5496 vamsasSet.getDatasetId());
5497 AlignmentI xtant_ds = ds;
5498 if (xtant_ds == null)
5500 // good chance we are about to create a new dataset, but check if we've
5501 // seen some of the dataset sequence IDs before.
5502 // TODO: skip this check if we are working with project generated by
5503 // version 2.11 or later
5504 xtant_ds = checkIfHasDataset(vamsasSet.getSequence());
5505 if (xtant_ds != null)
5508 addDatasetRef(vamsasSet.getDatasetId(), ds);
5511 Vector dseqs = null;
5514 // recovering an alignment View
5515 AlignmentI seqSetDS = getDatasetFor(UNIQSEQSETID + uniqueSeqSetId);
5516 if (seqSetDS != null)
5518 if (ds != null && ds != seqSetDS)
5520 warn("JAL-3171 regression: Overwriting a dataset reference for an alignment"
5521 + " - CDS/Protein crossreference data may be lost");
5522 if (xtant_ds != null)
5524 // This can only happen if the unique sequence set ID was bound to a
5525 // dataset that did not contain any of the sequences in the view
5526 // currently being restored.
5527 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.");
5531 addDatasetRef(vamsasSet.getDatasetId(), ds);
5536 // try even harder to restore dataset
5537 AlignmentI xtantDS = checkIfHasDataset(vamsasSet.getSequence());
5538 // create a list of new dataset sequences
5539 dseqs = new Vector();
5541 for (int i = 0, iSize = vamsasSet.getSequence().size(); i < iSize; i++)
5543 Sequence vamsasSeq = vamsasSet.getSequence().get(i);
5544 ensureJalviewDatasetSequence(vamsasSeq, ds, dseqs, ignoreUnrefed, i);
5546 // create a new dataset
5549 SequenceI[] dsseqs = new SequenceI[dseqs.size()];
5550 dseqs.copyInto(dsseqs);
5551 ds = new jalview.datamodel.Alignment(dsseqs);
5552 debug("Created new dataset " + vamsasSet.getDatasetId()
5553 + " for alignment " + System.identityHashCode(al));
5554 addDatasetRef(vamsasSet.getDatasetId(), ds);
5556 // set the dataset for the newly imported alignment.
5557 if (al.getDataset() == null && !ignoreUnrefed)
5560 // register dataset for the alignment's uniqueSeqSetId for legacy projects
5561 addDatasetRef(UNIQSEQSETID + uniqueSeqSetId, ds);
5563 updateSeqDatasetBinding(vamsasSet.getSequence(), ds);
5567 * XML dataset sequence ID to materialised dataset reference
5569 HashMap<String, AlignmentI> seqToDataset = new HashMap<>();
5572 * @return the first materialised dataset reference containing a dataset
5573 * sequence referenced in the given view
5575 * - sequences from the view
5577 AlignmentI checkIfHasDataset(List<Sequence> list)
5579 for (Sequence restoredSeq : list)
5581 AlignmentI datasetFor = seqToDataset.get(restoredSeq.getDsseqid());
5582 if (datasetFor != null)
5591 * Register ds as the containing dataset for the dataset sequences referenced
5592 * by sequences in list
5595 * - sequences in a view
5598 void updateSeqDatasetBinding(List<Sequence> list, AlignmentI ds)
5600 for (Sequence restoredSeq : list)
5602 AlignmentI prevDS = seqToDataset.put(restoredSeq.getDsseqid(), ds);
5603 if (prevDS != null && prevDS != ds)
5605 warn("Dataset sequence appears in many datasets: "
5606 + restoredSeq.getDsseqid());
5607 // TODO: try to merge!
5614 * sequence definition to create/merge dataset sequence for
5618 * vector to add new dataset sequence to
5619 * @param ignoreUnrefed
5620 * - when true, don't create new sequences from vamsasSeq if it's id
5621 * doesn't already have an asssociated Jalview sequence.
5623 * - used to reorder the sequence in the alignment according to the
5624 * vamsasSeq array ordering, to preserve ordering of dataset
5626 private void ensureJalviewDatasetSequence(Sequence vamsasSeq,
5627 AlignmentI ds, Vector dseqs, boolean ignoreUnrefed, int vseqpos)
5629 // JBP TODO: Check this is called for AlCodonFrames to support recovery of
5631 SequenceI sq = seqRefIds.get(vamsasSeq.getId());
5632 boolean reorder = false;
5633 SequenceI dsq = null;
5634 if (sq != null && sq.getDatasetSequence() != null)
5636 dsq = sq.getDatasetSequence();
5642 if (sq == null && ignoreUnrefed)
5646 String sqid = vamsasSeq.getDsseqid();
5649 // need to create or add a new dataset sequence reference to this sequence
5652 dsq = seqRefIds.get(sqid);
5657 // make a new dataset sequence
5658 dsq = sq.createDatasetSequence();
5661 // make up a new dataset reference for this sequence
5662 sqid = seqHash(dsq);
5664 dsq.setVamsasId(uniqueSetSuffix + sqid);
5665 seqRefIds.put(sqid, dsq);
5670 dseqs.addElement(dsq);
5675 ds.addSequence(dsq);
5681 { // make this dataset sequence sq's dataset sequence
5682 sq.setDatasetSequence(dsq);
5683 // and update the current dataset alignment
5688 if (!dseqs.contains(dsq))
5695 if (ds.findIndex(dsq) < 0)
5697 ds.addSequence(dsq);
5704 // TODO: refactor this as a merge dataset sequence function
5705 // now check that sq (the dataset sequence) sequence really is the union of
5706 // all references to it
5707 // boolean pre = sq.getStart() < dsq.getStart();
5708 // boolean post = sq.getEnd() > dsq.getEnd();
5712 // StringBuffer sb = new StringBuffer();
5713 String newres = jalview.analysis.AlignSeq.extractGaps(
5714 jalview.util.Comparison.GapChars, sq.getSequenceAsString());
5715 if (!newres.equalsIgnoreCase(dsq.getSequenceAsString())
5716 && newres.length() > dsq.getLength())
5718 // Update with the longer sequence.
5722 * if (pre) { sb.insert(0, newres .substring(0, dsq.getStart() -
5723 * sq.getStart())); dsq.setStart(sq.getStart()); } if (post) {
5724 * sb.append(newres.substring(newres.length() - sq.getEnd() -
5725 * dsq.getEnd())); dsq.setEnd(sq.getEnd()); }
5727 dsq.setSequence(newres);
5729 // TODO: merges will never happen if we 'know' we have the real dataset
5730 // sequence - this should be detected when id==dssid
5732 "DEBUG Notice: Merged dataset sequence (if you see this often, post at http://issues.jalview.org/browse/JAL-1474)"); // ("
5733 // + (pre ? "prepended" : "") + " "
5734 // + (post ? "appended" : ""));
5739 // sequence refs are identical. We may need to update the existing dataset
5740 // alignment with this one, though.
5741 if (ds != null && dseqs == null)
5743 int opos = ds.findIndex(dsq);
5744 SequenceI tseq = null;
5745 if (opos != -1 && vseqpos != opos)
5747 // remove from old position
5748 ds.deleteSequence(dsq);
5750 if (vseqpos < ds.getHeight())
5752 if (vseqpos != opos)
5754 // save sequence at destination position
5755 tseq = ds.getSequenceAt(vseqpos);
5756 ds.replaceSequenceAt(vseqpos, dsq);
5757 ds.addSequence(tseq);
5762 ds.addSequence(dsq);
5769 * TODO use AlignmentI here and in related methods - needs
5770 * AlignmentI.getDataset() changed to return AlignmentI instead of Alignment
5772 Hashtable<String, AlignmentI> datasetIds = null;
5774 IdentityHashMap<AlignmentI, String> dataset2Ids = null;
5776 private AlignmentI getDatasetFor(String datasetId)
5778 if (datasetIds == null)
5780 datasetIds = new Hashtable<>();
5783 if (datasetIds.containsKey(datasetId))
5785 return datasetIds.get(datasetId);
5790 private void addDatasetRef(String datasetId, AlignmentI dataset)
5792 if (datasetIds == null)
5794 datasetIds = new Hashtable<>();
5796 datasetIds.put(datasetId, dataset);
5800 * make a new dataset ID for this jalview dataset alignment
5805 private String getDatasetIdRef(AlignmentI dataset)
5807 if (dataset.getDataset() != null)
5809 warn("Serious issue! Dataset Object passed to getDatasetIdRef is not a Jalview DATASET alignment...");
5811 String datasetId = makeHashCode(dataset, null);
5812 if (datasetId == null)
5814 // make a new datasetId and record it
5815 if (dataset2Ids == null)
5817 dataset2Ids = new IdentityHashMap<>();
5821 datasetId = dataset2Ids.get(dataset);
5823 if (datasetId == null)
5825 datasetId = "ds" + dataset2Ids.size() + 1;
5826 dataset2Ids.put(dataset, datasetId);
5833 * Add any saved DBRefEntry's to the sequence. An entry flagged as 'locus' is
5834 * constructed as a special subclass GeneLocus.
5836 * @param datasetSequence
5839 private void addDBRefs(SequenceI datasetSequence, Sequence sequence)
5841 for (int d = 0; d < sequence.getDBRef().size(); d++)
5843 DBRef dr = sequence.getDBRef().get(d);
5847 entry = new GeneLocus(dr.getSource(), dr.getVersion(),
5848 dr.getAccessionId());
5852 entry = new DBRefEntry(dr.getSource(), dr.getVersion(),
5853 dr.getAccessionId());
5855 if (dr.getMapping() != null)
5857 entry.setMap(addMapping(dr.getMapping()));
5859 datasetSequence.addDBRef(entry);
5863 private jalview.datamodel.Mapping addMapping(Mapping m)
5865 SequenceI dsto = null;
5866 // Mapping m = dr.getMapping();
5867 int fr[] = new int[m.getMapListFrom().size() * 2];
5868 Iterator<MapListFrom> from = m.getMapListFrom().iterator();// enumerateMapListFrom();
5869 for (int _i = 0; from.hasNext(); _i += 2)
5871 MapListFrom mf = from.next();
5872 fr[_i] = mf.getStart();
5873 fr[_i + 1] = mf.getEnd();
5875 int fto[] = new int[m.getMapListTo().size() * 2];
5876 Iterator<MapListTo> to = m.getMapListTo().iterator();// enumerateMapListTo();
5877 for (int _i = 0; to.hasNext(); _i += 2)
5879 MapListTo mf = to.next();
5880 fto[_i] = mf.getStart();
5881 fto[_i + 1] = mf.getEnd();
5883 jalview.datamodel.Mapping jmap = new jalview.datamodel.Mapping(dsto, fr,
5884 fto, m.getMapFromUnit().intValue(),
5885 m.getMapToUnit().intValue());
5888 * (optional) choice of dseqFor or Sequence
5890 if (m.getDseqFor() != null)
5892 String dsfor = m.getDseqFor();
5893 if (seqRefIds.containsKey(dsfor))
5898 jmap.setTo(seqRefIds.get(dsfor));
5902 frefedSequence.add(newMappingRef(dsfor, jmap));
5905 else if (m.getSequence() != null)
5908 * local sequence definition
5910 Sequence ms = m.getSequence();
5911 SequenceI djs = null;
5912 String sqid = ms.getDsseqid();
5913 if (sqid != null && sqid.length() > 0)
5916 * recover dataset sequence
5918 djs = seqRefIds.get(sqid);
5923 "Warning - making up dataset sequence id for DbRef sequence map reference");
5924 sqid = ((Object) ms).toString(); // make up a new hascode for
5925 // undefined dataset sequence hash
5926 // (unlikely to happen)
5932 * make a new dataset sequence and add it to refIds hash
5934 djs = new jalview.datamodel.Sequence(ms.getName(),
5936 djs.setStart(jmap.getMap().getToLowest());
5937 djs.setEnd(jmap.getMap().getToHighest());
5938 djs.setVamsasId(uniqueSetSuffix + sqid);
5940 incompleteSeqs.put(sqid, djs);
5941 seqRefIds.put(sqid, djs);
5944 jalview.bin.Cache.log.debug("about to recurse on addDBRefs.");
5953 * Provides a 'copy' of an alignment view (on action New View) by 'saving' the
5954 * view as XML (but not to file), and then reloading it
5959 public AlignmentPanel copyAlignPanel(AlignmentPanel ap)
5962 JalviewModel jm = saveState(ap, null, null, null);
5965 jm.getVamsasModel().getSequenceSet().get(0).getDatasetId(),
5966 ap.getAlignment().getDataset());
5968 uniqueSetSuffix = "";
5969 // jm.getJalviewModelSequence().getViewport(0).setId(null);
5970 jm.getViewport().get(0).setId(null);
5971 // we don't overwrite the view we just copied
5973 if (this.frefedSequence == null)
5975 frefedSequence = new Vector<>();
5978 viewportsAdded.clear();
5980 AlignFrame af = loadFromObject(jm, null, false, null);
5981 af.getAlignPanels().clear();
5982 af.closeMenuItem_actionPerformed(true);
5985 * if(ap.av.getAlignment().getAlignmentAnnotation()!=null) { for(int i=0;
5986 * i<ap.av.getAlignment().getAlignmentAnnotation().length; i++) {
5987 * if(!ap.av.getAlignment().getAlignmentAnnotation()[i].autoCalculated) {
5988 * af.alignPanel.av.getAlignment().getAlignmentAnnotation()[i] =
5989 * ap.av.getAlignment().getAlignmentAnnotation()[i]; } } }
5992 return af.alignPanel;
5995 private Hashtable jvids2vobj;
5997 private void warn(String msg)
6002 private void warn(String msg, Exception e)
6004 if (Cache.log != null)
6008 Cache.log.warn(msg, e);
6012 Cache.log.warn(msg);
6017 System.err.println("Warning: " + msg);
6020 e.printStackTrace();
6025 private void debug(String string)
6027 debug(string, null);
6030 private void debug(String msg, Exception e)
6032 if (Cache.log != null)
6036 Cache.log.debug(msg, e);
6040 Cache.log.debug(msg);
6045 System.err.println("Warning: " + msg);
6048 e.printStackTrace();
6054 * set the object to ID mapping tables used to write/recover objects and XML
6055 * ID strings for the jalview project. If external tables are provided then
6056 * finalize and clearSeqRefs will not clear the tables when the Jalview2XML
6057 * object goes out of scope. - also populates the datasetIds hashtable with
6058 * alignment objects containing dataset sequences
6061 * Map from ID strings to jalview datamodel
6063 * Map from jalview datamodel to ID strings
6067 public void setObjectMappingTables(Hashtable vobj2jv,
6068 IdentityHashMap jv2vobj)
6070 this.jv2vobj = jv2vobj;
6071 this.vobj2jv = vobj2jv;
6072 Iterator ds = jv2vobj.keySet().iterator();
6074 while (ds.hasNext())
6076 Object jvobj = ds.next();
6077 id = jv2vobj.get(jvobj).toString();
6078 if (jvobj instanceof jalview.datamodel.Alignment)
6080 if (((jalview.datamodel.Alignment) jvobj).getDataset() == null)
6082 addDatasetRef(id, (jalview.datamodel.Alignment) jvobj);
6085 else if (jvobj instanceof jalview.datamodel.Sequence)
6087 // register sequence object so the XML parser can recover it.
6088 if (seqRefIds == null)
6090 seqRefIds = new HashMap<>();
6092 if (seqsToIds == null)
6094 seqsToIds = new IdentityHashMap<>();
6096 seqRefIds.put(jv2vobj.get(jvobj).toString(), (SequenceI) jvobj);
6097 seqsToIds.put((SequenceI) jvobj, id);
6099 else if (jvobj instanceof jalview.datamodel.AlignmentAnnotation)
6102 AlignmentAnnotation jvann = (AlignmentAnnotation) jvobj;
6103 annotationIds.put(anid = jv2vobj.get(jvobj).toString(), jvann);
6104 if (jvann.annotationId == null)
6106 jvann.annotationId = anid;
6108 if (!jvann.annotationId.equals(anid))
6110 // TODO verify that this is the correct behaviour
6111 this.warn("Overriding Annotation ID for " + anid
6112 + " from different id : " + jvann.annotationId);
6113 jvann.annotationId = anid;
6116 else if (jvobj instanceof String)
6118 if (jvids2vobj == null)
6120 jvids2vobj = new Hashtable();
6121 jvids2vobj.put(jvobj, jv2vobj.get(jvobj).toString());
6126 Cache.log.debug("Ignoring " + jvobj.getClass() + " (ID = " + id);
6132 * set the uniqueSetSuffix used to prefix/suffix object IDs for jalview
6133 * objects created from the project archive. If string is null (default for
6134 * construction) then suffix will be set automatically.
6138 public void setUniqueSetSuffix(String string)
6140 uniqueSetSuffix = string;
6145 * uses skipList2 as the skipList for skipping views on sequence sets
6146 * associated with keys in the skipList
6150 public void setSkipList(Hashtable skipList2)
6152 skipList = skipList2;
6156 * Reads the jar entry of given name and returns its contents, or null if the
6157 * entry is not found.
6160 * @param jarEntryName
6163 protected String readJarEntry(jarInputStreamProvider jprovider,
6164 String jarEntryName)
6166 String result = null;
6167 BufferedReader in = null;
6172 * Reopen the jar input stream and traverse its entries to find a matching
6175 JarInputStream jin = jprovider.getJarInputStream();
6176 JarEntry entry = null;
6179 entry = jin.getNextJarEntry();
6180 } while (entry != null && !entry.getName().equals(jarEntryName));
6184 StringBuilder out = new StringBuilder(256);
6185 in = new BufferedReader(new InputStreamReader(jin, UTF_8));
6188 while ((data = in.readLine()) != null)
6192 result = out.toString();
6196 warn("Couldn't find entry in Jalview Jar for " + jarEntryName);
6198 } catch (Exception ex)
6200 ex.printStackTrace();
6208 } catch (IOException e)
6219 * Returns an incrementing counter (0, 1, 2...)
6223 private synchronized int nextCounter()
6229 * Loads any saved PCA viewers
6234 protected void loadPCAViewers(JalviewModel model, AlignmentPanel ap)
6238 List<PcaViewer> pcaviewers = model.getPcaViewer();
6239 for (PcaViewer viewer : pcaviewers)
6241 String modelName = viewer.getScoreModelName();
6242 SimilarityParamsI params = new SimilarityParams(
6243 viewer.isIncludeGappedColumns(), viewer.isMatchGaps(),
6244 viewer.isIncludeGaps(),
6245 viewer.isDenominateByShortestLength());
6248 * create the panel (without computing the PCA)
6250 PCAPanel panel = new PCAPanel(ap, modelName, params);
6252 panel.setTitle(viewer.getTitle());
6253 panel.setBounds(new Rectangle(viewer.getXpos(), viewer.getYpos(),
6254 viewer.getWidth(), viewer.getHeight()));
6256 boolean showLabels = viewer.isShowLabels();
6257 panel.setShowLabels(showLabels);
6258 panel.getRotatableCanvas().setShowLabels(showLabels);
6259 panel.getRotatableCanvas()
6260 .setBgColour(new Color(viewer.getBgColour()));
6261 panel.getRotatableCanvas()
6262 .setApplyToAllViews(viewer.isLinkToAllViews());
6265 * load PCA output data
6267 ScoreModelI scoreModel = ScoreModels.getInstance()
6268 .getScoreModel(modelName, ap);
6269 PCA pca = new PCA(null, scoreModel, params);
6270 PcaDataType pcaData = viewer.getPcaData();
6272 MatrixI pairwise = loadDoubleMatrix(pcaData.getPairwiseMatrix());
6273 pca.setPairwiseScores(pairwise);
6275 MatrixI triDiag = loadDoubleMatrix(pcaData.getTridiagonalMatrix());
6276 pca.setTridiagonal(triDiag);
6278 MatrixI result = loadDoubleMatrix(pcaData.getEigenMatrix());
6279 pca.setEigenmatrix(result);
6281 panel.getPcaModel().setPCA(pca);
6284 * we haven't saved the input data! (JAL-2647 to do)
6286 panel.setInputData(null);
6289 * add the sequence points for the PCA display
6291 List<jalview.datamodel.SequencePoint> seqPoints = new ArrayList<>();
6292 for (SequencePoint sp : viewer.getSequencePoint())
6294 String seqId = sp.getSequenceRef();
6295 SequenceI seq = seqRefIds.get(seqId);
6298 throw new IllegalStateException(
6299 "Unmatched seqref for PCA: " + seqId);
6301 Point pt = new Point(sp.getXPos(), sp.getYPos(), sp.getZPos());
6302 jalview.datamodel.SequencePoint seqPoint = new jalview.datamodel.SequencePoint(
6304 seqPoints.add(seqPoint);
6306 panel.getRotatableCanvas().setPoints(seqPoints, seqPoints.size());
6309 * set min-max ranges and scale after setPoints (which recomputes them)
6311 panel.getRotatableCanvas().setScaleFactor(viewer.getScaleFactor());
6312 SeqPointMin spMin = viewer.getSeqPointMin();
6313 float[] min = new float[] { spMin.getXPos(), spMin.getYPos(),
6315 SeqPointMax spMax = viewer.getSeqPointMax();
6316 float[] max = new float[] { spMax.getXPos(), spMax.getYPos(),
6318 panel.getRotatableCanvas().setSeqMinMax(min, max);
6320 // todo: hold points list in PCAModel only
6321 panel.getPcaModel().setSequencePoints(seqPoints);
6323 panel.setSelectedDimensionIndex(viewer.getXDim(), X);
6324 panel.setSelectedDimensionIndex(viewer.getYDim(), Y);
6325 panel.setSelectedDimensionIndex(viewer.getZDim(), Z);
6327 // is this duplication needed?
6328 panel.setTop(seqPoints.size() - 1);
6329 panel.getPcaModel().setTop(seqPoints.size() - 1);
6332 * add the axes' end points for the display
6334 for (int i = 0; i < 3; i++)
6336 Axis axis = viewer.getAxis().get(i);
6337 panel.getRotatableCanvas().getAxisEndPoints()[i] = new Point(
6338 axis.getXPos(), axis.getYPos(), axis.getZPos());
6341 Desktop.addInternalFrame(panel, MessageManager.formatMessage(
6342 "label.calc_title", "PCA", modelName), 475, 450);
6344 } catch (Exception ex)
6346 Cache.log.error("Error loading PCA: " + ex.toString());
6351 * Create a new PyMol viewer
6357 protected void createPymolViewer(
6358 Entry<String, StructureViewerModel> viewerData, AlignFrame af,
6359 jarInputStreamProvider jprovider)
6361 StructureViewerModel data = viewerData.getValue();
6362 String pymolSessionFile = data.getStateData();
6365 * Copy PyMol session from jar entry "viewer_"+viewId to a temporary file
6367 * NB this is the 'saved' viewId as in the project file XML, _not_ the
6368 * 'uniquified' sviewid used to reconstruct the viewer here
6370 String viewerJarEntryName = getViewerJarEntryName(data.getViewId());
6371 pymolSessionFile = copyJarEntry(jprovider, viewerJarEntryName,
6374 Set<Entry<File, StructureData>> fileData = data.getFileData()
6376 List<PDBEntry> pdbs = new ArrayList<>();
6377 List<SequenceI[]> allseqs = new ArrayList<>();
6378 for (Entry<File, StructureData> pdb : fileData)
6380 String filePath = pdb.getValue().getFilePath();
6381 String pdbId = pdb.getValue().getPdbId();
6382 // pdbs.add(new PDBEntry(filePath, pdbId));
6383 pdbs.add(new PDBEntry(pdbId, null, PDBEntry.Type.PDB, filePath));
6384 final List<SequenceI> seqList = pdb.getValue().getSeqList();
6385 SequenceI[] seqs = seqList.toArray(new SequenceI[seqList.size()]);
6389 boolean colourByPymol = data.isColourByViewer();
6390 boolean colourBySequence = data.isColourWithAlignPanel();
6392 // TODO use StructureViewer as a factory here, see JAL-1761
6393 final PDBEntry[] pdbArray = pdbs.toArray(new PDBEntry[pdbs.size()]);
6394 final SequenceI[][] seqsArray = allseqs
6395 .toArray(new SequenceI[allseqs.size()][]);
6396 String newViewId = viewerData.getKey();
6398 PymolViewer pv = new PymolViewer(pymolSessionFile,
6399 af.alignPanel, pdbArray, seqsArray, colourByPymol,
6400 colourBySequence, newViewId);
6401 pv.setSize(data.getWidth(), data.getHeight());
6402 pv.setLocation(data.getX(), data.getY());
6406 * Populates an XML model of the feature colour scheme for one feature type
6408 * @param featureType
6412 public static Colour marshalColour(
6413 String featureType, FeatureColourI fcol)
6415 Colour col = new Colour();
6416 if (fcol.isSimpleColour())
6418 col.setRGB(Format.getHexString(fcol.getColour()));
6422 col.setRGB(Format.getHexString(fcol.getMaxColour()));
6423 col.setMin(fcol.getMin());
6424 col.setMax(fcol.getMax());
6425 col.setMinRGB(jalview.util.Format.getHexString(fcol.getMinColour()));
6426 col.setAutoScale(fcol.isAutoScaled());
6427 col.setThreshold(fcol.getThreshold());
6428 col.setColourByLabel(fcol.isColourByLabel());
6429 col.setThreshType(fcol.isAboveThreshold() ? ThresholdType.ABOVE
6430 : (fcol.isBelowThreshold() ? ThresholdType.BELOW
6431 : ThresholdType.NONE));
6432 if (fcol.isColourByAttribute())
6434 final String[] attName = fcol.getAttributeName();
6435 col.getAttributeName().add(attName[0]);
6436 if (attName.length > 1)
6438 col.getAttributeName().add(attName[1]);
6441 Color noColour = fcol.getNoColour();
6442 if (noColour == null)
6444 col.setNoValueColour(NoValueColour.NONE);
6446 else if (noColour == fcol.getMaxColour())
6448 col.setNoValueColour(NoValueColour.MAX);
6452 col.setNoValueColour(NoValueColour.MIN);
6455 col.setName(featureType);
6460 * Populates an XML model of the feature filter(s) for one feature type
6462 * @param firstMatcher
6463 * the first (or only) match condition)
6465 * remaining match conditions (if any)
6467 * if true, conditions are and-ed, else or-ed
6469 public static jalview.xml.binding.jalview.FeatureMatcherSet marshalFilter(
6470 FeatureMatcherI firstMatcher, Iterator<FeatureMatcherI> filters,
6473 jalview.xml.binding.jalview.FeatureMatcherSet result = new jalview.xml.binding.jalview.FeatureMatcherSet();
6475 if (filters.hasNext())
6480 CompoundMatcher compound = new CompoundMatcher();
6481 compound.setAnd(and);
6482 jalview.xml.binding.jalview.FeatureMatcherSet matcher1 = marshalFilter(
6483 firstMatcher, Collections.emptyIterator(), and);
6484 // compound.addMatcherSet(matcher1);
6485 compound.getMatcherSet().add(matcher1);
6486 FeatureMatcherI nextMatcher = filters.next();
6487 jalview.xml.binding.jalview.FeatureMatcherSet matcher2 = marshalFilter(
6488 nextMatcher, filters, and);
6489 // compound.addMatcherSet(matcher2);
6490 compound.getMatcherSet().add(matcher2);
6491 result.setCompoundMatcher(compound);
6496 * single condition matcher
6498 // MatchCondition matcherModel = new MatchCondition();
6499 jalview.xml.binding.jalview.FeatureMatcher matcherModel = new jalview.xml.binding.jalview.FeatureMatcher();
6500 matcherModel.setCondition(
6501 firstMatcher.getMatcher().getCondition().getStableName());
6502 matcherModel.setValue(firstMatcher.getMatcher().getPattern());
6503 if (firstMatcher.isByAttribute())
6505 matcherModel.setBy(FilterBy.BY_ATTRIBUTE);
6506 // matcherModel.setAttributeName(firstMatcher.getAttribute());
6507 String[] attName = firstMatcher.getAttribute();
6508 matcherModel.getAttributeName().add(attName[0]); // attribute
6509 if (attName.length > 1)
6511 matcherModel.getAttributeName().add(attName[1]); // sub-attribute
6514 else if (firstMatcher.isByLabel())
6516 matcherModel.setBy(FilterBy.BY_LABEL);
6518 else if (firstMatcher.isByScore())
6520 matcherModel.setBy(FilterBy.BY_SCORE);
6522 result.setMatchCondition(matcherModel);
6529 * Loads one XML model of a feature filter to a Jalview object
6531 * @param featureType
6532 * @param matcherSetModel
6535 public static FeatureMatcherSetI parseFilter(
6537 jalview.xml.binding.jalview.FeatureMatcherSet matcherSetModel)
6539 FeatureMatcherSetI result = new FeatureMatcherSet();
6542 parseFilterConditions(result, matcherSetModel, true);
6543 } catch (IllegalStateException e)
6545 // mixing AND and OR conditions perhaps
6547 String.format("Error reading filter conditions for '%s': %s",
6548 featureType, e.getMessage()));
6549 // return as much as was parsed up to the error
6556 * Adds feature match conditions to matcherSet as unmarshalled from XML
6557 * (possibly recursively for compound conditions)
6560 * @param matcherSetModel
6562 * if true, multiple conditions are AND-ed, else they are OR-ed
6563 * @throws IllegalStateException
6564 * if AND and OR conditions are mixed
6566 protected static void parseFilterConditions(
6567 FeatureMatcherSetI matcherSet,
6568 jalview.xml.binding.jalview.FeatureMatcherSet matcherSetModel,
6571 jalview.xml.binding.jalview.FeatureMatcher mc = matcherSetModel
6572 .getMatchCondition();
6578 FilterBy filterBy = mc.getBy();
6579 Condition cond = Condition.fromString(mc.getCondition());
6580 String pattern = mc.getValue();
6581 FeatureMatcherI matchCondition = null;
6582 if (filterBy == FilterBy.BY_LABEL)
6584 matchCondition = FeatureMatcher.byLabel(cond, pattern);
6586 else if (filterBy == FilterBy.BY_SCORE)
6588 matchCondition = FeatureMatcher.byScore(cond, pattern);
6591 else if (filterBy == FilterBy.BY_ATTRIBUTE)
6593 final List<String> attributeName = mc.getAttributeName();
6594 String[] attNames = attributeName
6595 .toArray(new String[attributeName.size()]);
6596 matchCondition = FeatureMatcher.byAttribute(cond, pattern,
6601 * note this throws IllegalStateException if AND-ing to a
6602 * previously OR-ed compound condition, or vice versa
6606 matcherSet.and(matchCondition);
6610 matcherSet.or(matchCondition);
6616 * compound condition
6618 List<jalview.xml.binding.jalview.FeatureMatcherSet> matchers = matcherSetModel
6619 .getCompoundMatcher().getMatcherSet();
6620 boolean anded = matcherSetModel.getCompoundMatcher().isAnd();
6621 if (matchers.size() == 2)
6623 parseFilterConditions(matcherSet, matchers.get(0), anded);
6624 parseFilterConditions(matcherSet, matchers.get(1), anded);
6628 System.err.println("Malformed compound filter condition");
6634 * Loads one XML model of a feature colour to a Jalview object
6636 * @param colourModel
6639 public static FeatureColourI parseColour(Colour colourModel)
6641 FeatureColourI colour = null;
6643 if (colourModel.getMax() != null)
6645 Color mincol = null;
6646 Color maxcol = null;
6647 Color noValueColour = null;
6651 mincol = new Color(Integer.parseInt(colourModel.getMinRGB(), 16));
6652 maxcol = new Color(Integer.parseInt(colourModel.getRGB(), 16));
6653 } catch (Exception e)
6655 Cache.log.warn("Couldn't parse out graduated feature color.", e);
6658 NoValueColour noCol = colourModel.getNoValueColour();
6659 if (noCol == NoValueColour.MIN)
6661 noValueColour = mincol;
6663 else if (noCol == NoValueColour.MAX)
6665 noValueColour = maxcol;
6668 colour = new FeatureColour(maxcol, mincol, maxcol, noValueColour,
6669 safeFloat(colourModel.getMin()),
6670 safeFloat(colourModel.getMax()));
6671 final List<String> attributeName = colourModel.getAttributeName();
6672 String[] attributes = attributeName
6673 .toArray(new String[attributeName.size()]);
6674 if (attributes != null && attributes.length > 0)
6676 colour.setAttributeName(attributes);
6678 if (colourModel.isAutoScale() != null)
6680 colour.setAutoScaled(colourModel.isAutoScale().booleanValue());
6682 if (colourModel.isColourByLabel() != null)
6684 colour.setColourByLabel(
6685 colourModel.isColourByLabel().booleanValue());
6687 if (colourModel.getThreshold() != null)
6689 colour.setThreshold(colourModel.getThreshold().floatValue());
6691 ThresholdType ttyp = colourModel.getThreshType();
6692 if (ttyp == ThresholdType.ABOVE)
6694 colour.setAboveThreshold(true);
6696 else if (ttyp == ThresholdType.BELOW)
6698 colour.setBelowThreshold(true);
6703 Color color = new Color(Integer.parseInt(colourModel.getRGB(), 16));
6704 colour = new FeatureColour(color);