2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 package jalview.project;
23 import static jalview.math.RotatableMatrix.Axis.X;
24 import static jalview.math.RotatableMatrix.Axis.Y;
25 import static jalview.math.RotatableMatrix.Axis.Z;
27 import jalview.analysis.Conservation;
28 import jalview.analysis.PCA;
29 import jalview.analysis.scoremodels.ScoreModels;
30 import jalview.analysis.scoremodels.SimilarityParams;
31 import jalview.api.FeatureColourI;
32 import jalview.api.ViewStyleI;
33 import jalview.api.analysis.ScoreModelI;
34 import jalview.api.analysis.SimilarityParamsI;
35 import jalview.api.structures.JalviewStructureDisplayI;
36 import jalview.bin.Cache;
37 import jalview.datamodel.AlignedCodonFrame;
38 import jalview.datamodel.Alignment;
39 import jalview.datamodel.AlignmentAnnotation;
40 import jalview.datamodel.AlignmentI;
41 import jalview.datamodel.DBRefEntry;
42 import jalview.datamodel.GraphLine;
43 import jalview.datamodel.PDBEntry;
44 import jalview.datamodel.Point;
45 import jalview.datamodel.RnaViewerModel;
46 import jalview.datamodel.SequenceFeature;
47 import jalview.datamodel.SequenceGroup;
48 import jalview.datamodel.SequenceI;
49 import jalview.datamodel.StructureViewerModel;
50 import jalview.datamodel.StructureViewerModel.StructureData;
51 import jalview.datamodel.features.FeatureMatcher;
52 import jalview.datamodel.features.FeatureMatcherI;
53 import jalview.datamodel.features.FeatureMatcherSet;
54 import jalview.datamodel.features.FeatureMatcherSetI;
55 import jalview.ext.varna.RnaModel;
56 import jalview.gui.AlignFrame;
57 import jalview.gui.AlignViewport;
58 import jalview.gui.AlignmentPanel;
59 import jalview.gui.AppVarna;
60 import jalview.gui.ChimeraViewFrame;
61 import jalview.gui.Desktop;
62 import jalview.gui.FeatureRenderer;
63 import jalview.gui.JvOptionPane;
64 import jalview.gui.OOMWarning;
65 import jalview.gui.PCAPanel;
66 import jalview.gui.PaintRefresher;
67 import jalview.gui.SplitFrame;
68 import jalview.gui.StructureViewer;
69 import jalview.gui.StructureViewer.ViewerType;
70 import jalview.gui.StructureViewerBase;
71 import jalview.gui.TreePanel;
72 import jalview.io.BackupFiles;
73 import jalview.io.DataSourceType;
74 import jalview.io.FileFormat;
75 import jalview.io.NewickFile;
76 import jalview.math.Matrix;
77 import jalview.math.MatrixI;
78 import jalview.renderer.ResidueShaderI;
79 import jalview.schemes.AnnotationColourGradient;
80 import jalview.schemes.ColourSchemeI;
81 import jalview.schemes.ColourSchemeProperty;
82 import jalview.schemes.FeatureColour;
83 import jalview.schemes.ResidueProperties;
84 import jalview.schemes.UserColourScheme;
85 import jalview.structures.models.AAStructureBindingModel;
86 import jalview.util.Format;
87 import jalview.util.MessageManager;
88 import jalview.util.Platform;
89 import jalview.util.StringUtils;
90 import jalview.util.jarInputStreamProvider;
91 import jalview.util.matcher.Condition;
92 import jalview.viewmodel.AlignmentViewport;
93 import jalview.viewmodel.PCAModel;
94 import jalview.viewmodel.ViewportRanges;
95 import jalview.viewmodel.seqfeatures.FeatureRendererSettings;
96 import jalview.viewmodel.seqfeatures.FeaturesDisplayed;
97 import jalview.ws.jws2.Jws2Discoverer;
98 import jalview.ws.jws2.dm.AAConSettings;
99 import jalview.ws.jws2.jabaws2.Jws2Instance;
100 import jalview.ws.params.ArgumentI;
101 import jalview.ws.params.AutoCalcSetting;
102 import jalview.ws.params.WsParamSetI;
103 import jalview.xml.binding.jalview.AlcodonFrame;
104 import jalview.xml.binding.jalview.AlcodonFrame.AlcodMap;
105 import jalview.xml.binding.jalview.Annotation;
106 import jalview.xml.binding.jalview.Annotation.ThresholdLine;
107 import jalview.xml.binding.jalview.AnnotationColourScheme;
108 import jalview.xml.binding.jalview.AnnotationElement;
109 import jalview.xml.binding.jalview.DoubleMatrix;
110 import jalview.xml.binding.jalview.DoubleVector;
111 import jalview.xml.binding.jalview.Feature;
112 import jalview.xml.binding.jalview.Feature.OtherData;
113 import jalview.xml.binding.jalview.FeatureMatcherSet.CompoundMatcher;
114 import jalview.xml.binding.jalview.FilterBy;
115 import jalview.xml.binding.jalview.JalviewModel;
116 import jalview.xml.binding.jalview.JalviewModel.FeatureSettings;
117 import jalview.xml.binding.jalview.JalviewModel.FeatureSettings.Group;
118 import jalview.xml.binding.jalview.JalviewModel.FeatureSettings.Setting;
119 import jalview.xml.binding.jalview.JalviewModel.JGroup;
120 import jalview.xml.binding.jalview.JalviewModel.JSeq;
121 import jalview.xml.binding.jalview.JalviewModel.JSeq.Pdbids;
122 import jalview.xml.binding.jalview.JalviewModel.JSeq.Pdbids.StructureState;
123 import jalview.xml.binding.jalview.JalviewModel.JSeq.RnaViewer;
124 import jalview.xml.binding.jalview.JalviewModel.JSeq.RnaViewer.SecondaryStructure;
125 import jalview.xml.binding.jalview.JalviewModel.PcaViewer;
126 import jalview.xml.binding.jalview.JalviewModel.PcaViewer.Axis;
127 import jalview.xml.binding.jalview.JalviewModel.PcaViewer.SeqPointMax;
128 import jalview.xml.binding.jalview.JalviewModel.PcaViewer.SeqPointMin;
129 import jalview.xml.binding.jalview.JalviewModel.PcaViewer.SequencePoint;
130 import jalview.xml.binding.jalview.JalviewModel.Tree;
131 import jalview.xml.binding.jalview.JalviewModel.UserColours;
132 import jalview.xml.binding.jalview.JalviewModel.Viewport;
133 import jalview.xml.binding.jalview.JalviewModel.Viewport.CalcIdParam;
134 import jalview.xml.binding.jalview.JalviewModel.Viewport.HiddenColumns;
135 import jalview.xml.binding.jalview.JalviewUserColours;
136 import jalview.xml.binding.jalview.JalviewUserColours.Colour;
137 import jalview.xml.binding.jalview.MapListType.MapListFrom;
138 import jalview.xml.binding.jalview.MapListType.MapListTo;
139 import jalview.xml.binding.jalview.Mapping;
140 import jalview.xml.binding.jalview.NoValueColour;
141 import jalview.xml.binding.jalview.ObjectFactory;
142 import jalview.xml.binding.jalview.PcaDataType;
143 import jalview.xml.binding.jalview.Pdbentry.Property;
144 import jalview.xml.binding.jalview.Sequence;
145 import jalview.xml.binding.jalview.Sequence.DBRef;
146 import jalview.xml.binding.jalview.SequenceSet;
147 import jalview.xml.binding.jalview.SequenceSet.SequenceSetProperties;
148 import jalview.xml.binding.jalview.ThresholdType;
149 import jalview.xml.binding.jalview.VAMSAS;
151 import java.awt.Color;
152 import java.awt.Font;
153 import java.awt.Rectangle;
154 import java.io.BufferedReader;
155 import java.io.ByteArrayInputStream;
156 import java.io.DataInputStream;
157 import java.io.DataOutputStream;
159 import java.io.FileInputStream;
160 import java.io.FileOutputStream;
161 import java.io.IOException;
162 import java.io.InputStreamReader;
163 import java.io.OutputStreamWriter;
164 import java.io.PrintWriter;
165 import java.lang.reflect.InvocationTargetException;
166 import java.math.BigInteger;
167 import java.net.MalformedURLException;
169 import java.util.ArrayList;
170 import java.util.Arrays;
171 import java.util.Collections;
172 import java.util.Enumeration;
173 import java.util.GregorianCalendar;
174 import java.util.HashMap;
175 import java.util.HashSet;
176 import java.util.Hashtable;
177 import java.util.IdentityHashMap;
178 import java.util.Iterator;
179 import java.util.LinkedHashMap;
180 import java.util.List;
181 import java.util.Map;
182 import java.util.Map.Entry;
183 import java.util.Set;
184 import java.util.Vector;
185 import java.util.jar.JarEntry;
186 import java.util.jar.JarInputStream;
187 import java.util.jar.JarOutputStream;
189 import javax.swing.JInternalFrame;
190 import javax.swing.SwingUtilities;
191 import javax.xml.bind.JAXBContext;
192 import javax.xml.bind.JAXBElement;
193 import javax.xml.bind.Marshaller;
194 import javax.xml.datatype.DatatypeConfigurationException;
195 import javax.xml.datatype.DatatypeFactory;
196 import javax.xml.datatype.XMLGregorianCalendar;
197 import javax.xml.stream.XMLInputFactory;
198 import javax.xml.stream.XMLStreamReader;
201 * Write out the current jalview desktop state as a Jalview XML stream.
203 * Note: the vamsas objects referred to here are primitive versions of the
204 * VAMSAS project schema elements - they are not the same and most likely never
208 * @version $Revision: 1.134 $
210 public class Jalview2XML
213 // BH 2018 we add the .jvp binary extension to J2S so that
214 // it will declare that binary when we do the file save from the browser
218 Platform.addJ2SBinaryType(".jvp?");
221 private static final String VIEWER_PREFIX = "viewer_";
223 private static final String RNA_PREFIX = "rna_";
225 private static final String UTF_8 = "UTF-8";
228 * prefix for recovering datasets for alignments with multiple views where
229 * non-existent dataset IDs were written for some views
231 private static final String UNIQSEQSETID = "uniqueSeqSetId.";
233 // use this with nextCounter() to make unique names for entities
234 private int counter = 0;
237 * SequenceI reference -> XML ID string in jalview XML. Populated as XML reps
238 * of sequence objects are created.
240 IdentityHashMap<SequenceI, String> seqsToIds = null;
243 * jalview XML Sequence ID to jalview sequence object reference (both dataset
244 * and alignment sequences. Populated as XML reps of sequence objects are
247 Map<String, SequenceI> seqRefIds = null;
249 Map<String, SequenceI> incompleteSeqs = null;
251 List<SeqFref> frefedSequence = null;
253 boolean raiseGUI = true; // whether errors are raised in dialog boxes or not
256 * Map of reconstructed AlignFrame objects that appear to have come from
257 * SplitFrame objects (have a dna/protein complement view).
259 private Map<Viewport, AlignFrame> splitFrameCandidates = new HashMap<>();
262 * Map from displayed rna structure models to their saved session state jar
265 private Map<RnaModel, String> rnaSessions = new HashMap<>();
268 * A helper method for safely using the value of an optional attribute that
269 * may be null if not present in the XML. Answers the boolean value, or false
275 public static boolean safeBoolean(Boolean b)
277 return b == null ? false : b.booleanValue();
281 * A helper method for safely using the value of an optional attribute that
282 * may be null if not present in the XML. Answers the integer value, or zero
288 public static int safeInt(Integer i)
290 return i == null ? 0 : i.intValue();
294 * A helper method for safely using the value of an optional attribute that
295 * may be null if not present in the XML. Answers the float value, or zero if
301 public static float safeFloat(Float f)
303 return f == null ? 0f : f.floatValue();
307 * create/return unique hash string for sq
310 * @return new or existing unique string for sq
312 String seqHash(SequenceI sq)
314 if (seqsToIds == null)
318 if (seqsToIds.containsKey(sq))
320 return seqsToIds.get(sq);
324 // create sequential key
325 String key = "sq" + (seqsToIds.size() + 1);
326 key = makeHashCode(sq, key); // check we don't have an external reference
328 seqsToIds.put(sq, key);
335 if (seqsToIds == null)
337 seqsToIds = new IdentityHashMap<>();
339 if (seqRefIds == null)
341 seqRefIds = new HashMap<>();
343 if (incompleteSeqs == null)
345 incompleteSeqs = new HashMap<>();
347 if (frefedSequence == null)
349 frefedSequence = new ArrayList<>();
357 public Jalview2XML(boolean raiseGUI)
359 this.raiseGUI = raiseGUI;
363 * base class for resolving forward references to sequences by their ID
368 abstract class SeqFref
374 public SeqFref(String _sref, String type)
380 public String getSref()
385 public SequenceI getSrefSeq()
387 return seqRefIds.get(sref);
390 public boolean isResolvable()
392 return seqRefIds.get(sref) != null;
395 public SequenceI getSrefDatasetSeq()
397 SequenceI sq = seqRefIds.get(sref);
400 while (sq.getDatasetSequence() != null)
402 sq = sq.getDatasetSequence();
409 * @return true if the forward reference was fully resolved
411 abstract boolean resolve();
414 public String toString()
416 return type + " reference to " + sref;
421 * create forward reference for a mapping
427 public SeqFref newMappingRef(final String sref,
428 final jalview.datamodel.Mapping _jmap)
430 SeqFref fref = new SeqFref(sref, "Mapping")
432 public jalview.datamodel.Mapping jmap = _jmap;
437 SequenceI seq = getSrefDatasetSeq();
449 public SeqFref newAlcodMapRef(final String sref,
450 final AlignedCodonFrame _cf,
451 final jalview.datamodel.Mapping _jmap)
454 SeqFref fref = new SeqFref(sref, "Codon Frame")
456 AlignedCodonFrame cf = _cf;
458 public jalview.datamodel.Mapping mp = _jmap;
461 public boolean isResolvable()
463 return super.isResolvable() && mp.getTo() != null;
469 SequenceI seq = getSrefDatasetSeq();
474 cf.addMap(seq, mp.getTo(), mp.getMap());
481 public void resolveFrefedSequences()
483 Iterator<SeqFref> nextFref = frefedSequence.iterator();
484 int toresolve = frefedSequence.size();
485 int unresolved = 0, failedtoresolve = 0;
486 while (nextFref.hasNext())
488 SeqFref ref = nextFref.next();
489 if (ref.isResolvable())
501 } catch (Exception x)
504 "IMPLEMENTATION ERROR: Failed to resolve forward reference for sequence "
517 System.err.println("Jalview Project Import: There were " + unresolved
518 + " forward references left unresolved on the stack.");
520 if (failedtoresolve > 0)
522 System.err.println("SERIOUS! " + failedtoresolve
523 + " resolvable forward references failed to resolve.");
525 if (incompleteSeqs != null && incompleteSeqs.size() > 0)
528 "Jalview Project Import: There are " + incompleteSeqs.size()
529 + " sequences which may have incomplete metadata.");
530 if (incompleteSeqs.size() < 10)
532 for (SequenceI s : incompleteSeqs.values())
534 System.err.println(s.toString());
540 "Too many to report. Skipping output of incomplete sequences.");
546 * This maintains a map of viewports, the key being the seqSetId. Important to
547 * set historyItem and redoList for multiple views
549 Map<String, AlignViewport> viewportsAdded = new HashMap<>();
551 Map<String, AlignmentAnnotation> annotationIds = new HashMap<>();
553 String uniqueSetSuffix = "";
556 * List of pdbfiles added to Jar
558 List<String> pdbfiles = null;
560 // SAVES SEVERAL ALIGNMENT WINDOWS TO SAME JARFILE
561 public void saveState(File statefile)
563 FileOutputStream fos = null;
568 fos = new FileOutputStream(statefile);
570 JarOutputStream jout = new JarOutputStream(fos);
574 } catch (Exception e)
576 Cache.log.error("Couln't write Jalview state to " + statefile, e);
577 // TODO: inform user of the problem - they need to know if their data was
579 if (errorMessage == null)
581 errorMessage = "Did't write Jalview Archive to output file '"
582 + statefile + "' - See console error log for details";
586 errorMessage += "(Didn't write Jalview Archive to output file '"
597 } catch (IOException e)
607 * Writes a jalview project archive to the given Jar output stream.
611 public void saveState(JarOutputStream jout)
613 AlignFrame[] frames = Desktop.getAlignFrames();
619 saveAllFrames(Arrays.asList(frames), jout);
623 * core method for storing state for a set of AlignFrames.
626 * - frames involving all data to be exported (including containing
629 * - project output stream
631 private void saveAllFrames(List<AlignFrame> frames, JarOutputStream jout)
633 Hashtable<String, AlignFrame> dsses = new Hashtable<>();
636 * ensure cached data is clear before starting
638 // todo tidy up seqRefIds, seqsToIds initialisation / reset
640 splitFrameCandidates.clear();
645 // NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS
646 // //////////////////////////////////////////////////
648 List<String> shortNames = new ArrayList<>();
649 List<String> viewIds = new ArrayList<>();
652 for (int i = frames.size() - 1; i > -1; i--)
654 AlignFrame af = frames.get(i);
656 if (skipList != null && skipList
657 .containsKey(af.getViewport().getSequenceSetId()))
662 String shortName = makeFilename(af, shortNames);
664 int apSize = af.getAlignPanels().size();
666 for (int ap = 0; ap < apSize; ap++)
668 AlignmentPanel apanel = (AlignmentPanel) af.getAlignPanels()
670 String fileName = apSize == 1 ? shortName : ap + shortName;
671 if (!fileName.endsWith(".xml"))
673 fileName = fileName + ".xml";
676 saveState(apanel, fileName, jout, viewIds);
678 String dssid = getDatasetIdRef(
679 af.getViewport().getAlignment().getDataset());
680 if (!dsses.containsKey(dssid))
682 dsses.put(dssid, af);
687 writeDatasetFor(dsses, "" + jout.hashCode() + " " + uniqueSetSuffix,
693 } catch (Exception foo)
697 } catch (Exception ex)
699 // TODO: inform user of the problem - they need to know if their data was
701 if (errorMessage == null)
703 errorMessage = "Couldn't write Jalview Archive - see error output for details";
705 ex.printStackTrace();
710 * Generates a distinct file name, based on the title of the AlignFrame, by
711 * appending _n for increasing n until an unused name is generated. The new
712 * name (without its extension) is added to the list.
716 * @return the generated name, with .xml extension
718 protected String makeFilename(AlignFrame af, List<String> namesUsed)
720 String shortName = af.getTitle();
722 if (shortName.indexOf(File.separatorChar) > -1)
724 shortName = shortName
725 .substring(shortName.lastIndexOf(File.separatorChar) + 1);
730 while (namesUsed.contains(shortName))
732 if (shortName.endsWith("_" + (count - 1)))
734 shortName = shortName.substring(0, shortName.lastIndexOf("_"));
737 shortName = shortName.concat("_" + count);
741 namesUsed.add(shortName);
743 if (!shortName.endsWith(".xml"))
745 shortName = shortName + ".xml";
750 // USE THIS METHOD TO SAVE A SINGLE ALIGNMENT WINDOW
751 public boolean saveAlignment(AlignFrame af, String jarFile,
756 // create backupfiles object and get new temp filename destination
757 boolean doBackup = BackupFiles.getEnabled();
758 BackupFiles backupfiles = doBackup ? new BackupFiles(jarFile) : null;
759 FileOutputStream fos = new FileOutputStream(doBackup ?
760 backupfiles.getTempFilePath() : jarFile);
762 JarOutputStream jout = new JarOutputStream(fos);
763 List<AlignFrame> frames = new ArrayList<>();
765 // resolve splitframes
766 if (af.getViewport().getCodingComplement() != null)
768 frames = ((SplitFrame) af.getSplitViewContainer()).getAlignFrames();
774 saveAllFrames(frames, jout);
778 } catch (Exception foo)
782 boolean success = true;
786 backupfiles.setWriteSuccess(success);
787 success = backupfiles.rollBackupsAndRenameTempFile();
791 } catch (Exception ex)
793 errorMessage = "Couldn't Write alignment view to Jalview Archive - see error output for details";
794 ex.printStackTrace();
799 private void writeDatasetFor(Hashtable<String, AlignFrame> dsses,
800 String fileName, JarOutputStream jout)
803 for (String dssids : dsses.keySet())
805 AlignFrame _af = dsses.get(dssids);
806 String jfileName = fileName + " Dataset for " + _af.getTitle();
807 if (!jfileName.endsWith(".xml"))
809 jfileName = jfileName + ".xml";
811 saveState(_af.alignPanel, jfileName, true, jout, null);
816 * create a JalviewModel from an alignment view and marshall it to a
820 * panel to create jalview model for
822 * name of alignment panel written to output stream
829 public JalviewModel saveState(AlignmentPanel ap, String fileName,
830 JarOutputStream jout, List<String> viewIds)
832 return saveState(ap, fileName, false, jout, viewIds);
836 * create a JalviewModel from an alignment view and marshall it to a
840 * panel to create jalview model for
842 * name of alignment panel written to output stream
844 * when true, only write the dataset for the alignment, not the data
845 * associated with the view.
851 public JalviewModel saveState(AlignmentPanel ap, String fileName,
852 boolean storeDS, JarOutputStream jout, List<String> viewIds)
856 viewIds = new ArrayList<>();
861 List<UserColourScheme> userColours = new ArrayList<>();
863 AlignViewport av = ap.av;
864 ViewportRanges vpRanges = av.getRanges();
866 final ObjectFactory objectFactory = new ObjectFactory();
867 JalviewModel object = objectFactory.createJalviewModel();
868 object.setVamsasModel(new VAMSAS());
870 // object.setCreationDate(new java.util.Date(System.currentTimeMillis()));
873 GregorianCalendar c = new GregorianCalendar();
874 DatatypeFactory datatypeFactory = DatatypeFactory.newInstance();
875 XMLGregorianCalendar now = datatypeFactory.newXMLGregorianCalendar(c);// gregorianCalendar);
876 object.setCreationDate(now);
877 } catch (DatatypeConfigurationException e)
879 System.err.println("error writing date: " + e.toString());
882 jalview.bin.Cache.getDefault("VERSION", "Development Build"));
885 * rjal is full height alignment, jal is actual alignment with full metadata
886 * but excludes hidden sequences.
888 jalview.datamodel.AlignmentI rjal = av.getAlignment(), jal = rjal;
890 if (av.hasHiddenRows())
892 rjal = jal.getHiddenSequences().getFullAlignment();
895 SequenceSet vamsasSet = new SequenceSet();
897 // JalviewModelSequence jms = new JalviewModelSequence();
899 vamsasSet.setGapChar(jal.getGapCharacter() + "");
901 if (jal.getDataset() != null)
903 // dataset id is the dataset's hashcode
904 vamsasSet.setDatasetId(getDatasetIdRef(jal.getDataset()));
907 // switch jal and the dataset
908 jal = jal.getDataset();
912 if (jal.getProperties() != null)
914 Enumeration en = jal.getProperties().keys();
915 while (en.hasMoreElements())
917 String key = en.nextElement().toString();
918 SequenceSetProperties ssp = new SequenceSetProperties();
920 ssp.setValue(jal.getProperties().get(key).toString());
921 // vamsasSet.addSequenceSetProperties(ssp);
922 vamsasSet.getSequenceSetProperties().add(ssp);
927 Set<String> calcIdSet = new HashSet<>();
928 // record the set of vamsas sequence XML POJO we create.
929 HashMap<String, Sequence> vamsasSetIds = new HashMap<>();
931 for (final SequenceI jds : rjal.getSequences())
933 final SequenceI jdatasq = jds.getDatasetSequence() == null ? jds
934 : jds.getDatasetSequence();
935 String id = seqHash(jds);
936 if (vamsasSetIds.get(id) == null)
938 if (seqRefIds.get(id) != null && !storeDS)
940 // This happens for two reasons: 1. multiple views are being
942 // 2. the hashCode has collided with another sequence's code. This
944 // HAPPEN! (PF00072.15.stk does this)
945 // JBPNote: Uncomment to debug writing out of files that do not read
946 // back in due to ArrayOutOfBoundExceptions.
947 // System.err.println("vamsasSeq backref: "+id+"");
948 // System.err.println(jds.getName()+"
949 // "+jds.getStart()+"-"+jds.getEnd()+" "+jds.getSequenceAsString());
950 // System.err.println("Hashcode: "+seqHash(jds));
951 // SequenceI rsq = (SequenceI) seqRefIds.get(id + "");
952 // System.err.println(rsq.getName()+"
953 // "+rsq.getStart()+"-"+rsq.getEnd()+" "+rsq.getSequenceAsString());
954 // System.err.println("Hashcode: "+seqHash(rsq));
958 vamsasSeq = createVamsasSequence(id, jds);
959 // vamsasSet.addSequence(vamsasSeq);
960 vamsasSet.getSequence().add(vamsasSeq);
961 vamsasSetIds.put(id, vamsasSeq);
962 seqRefIds.put(id, jds);
966 jseq.setStart(jds.getStart());
967 jseq.setEnd(jds.getEnd());
968 jseq.setColour(av.getSequenceColour(jds).getRGB());
970 jseq.setId(id); // jseq id should be a string not a number
973 // Store any sequences this sequence represents
974 if (av.hasHiddenRows())
976 // use rjal, contains the full height alignment
978 av.getAlignment().getHiddenSequences().isHidden(jds));
980 if (av.isHiddenRepSequence(jds))
982 jalview.datamodel.SequenceI[] reps = av
983 .getRepresentedSequences(jds).getSequencesInOrder(rjal);
985 for (int h = 0; h < reps.length; h++)
989 // jseq.addHiddenSequences(rjal.findIndex(reps[h]));
990 jseq.getHiddenSequences().add(rjal.findIndex(reps[h]));
995 // mark sequence as reference - if it is the reference for this view
998 jseq.setViewreference(jds == jal.getSeqrep());
1002 // TODO: omit sequence features from each alignment view's XML dump if we
1003 // are storing dataset
1004 List<SequenceFeature> sfs = jds.getSequenceFeatures();
1005 for (SequenceFeature sf : sfs)
1007 // Features features = new Features();
1008 Feature features = new Feature();
1010 features.setBegin(sf.getBegin());
1011 features.setEnd(sf.getEnd());
1012 features.setDescription(sf.getDescription());
1013 features.setType(sf.getType());
1014 features.setFeatureGroup(sf.getFeatureGroup());
1015 features.setScore(sf.getScore());
1016 if (sf.links != null)
1018 for (int l = 0; l < sf.links.size(); l++)
1020 OtherData keyValue = new OtherData();
1021 keyValue.setKey("LINK_" + l);
1022 keyValue.setValue(sf.links.elementAt(l).toString());
1023 // features.addOtherData(keyValue);
1024 features.getOtherData().add(keyValue);
1027 if (sf.otherDetails != null)
1030 * save feature attributes, which may be simple strings or
1031 * map valued (have sub-attributes)
1033 for (Entry<String, Object> entry : sf.otherDetails.entrySet())
1035 String key = entry.getKey();
1036 Object value = entry.getValue();
1037 if (value instanceof Map<?, ?>)
1039 for (Entry<String, Object> subAttribute : ((Map<String, Object>) value)
1042 OtherData otherData = new OtherData();
1043 otherData.setKey(key);
1044 otherData.setKey2(subAttribute.getKey());
1045 otherData.setValue(subAttribute.getValue().toString());
1046 // features.addOtherData(otherData);
1047 features.getOtherData().add(otherData);
1052 OtherData otherData = new OtherData();
1053 otherData.setKey(key);
1054 otherData.setValue(value.toString());
1055 // features.addOtherData(otherData);
1056 features.getOtherData().add(otherData);
1061 // jseq.addFeatures(features);
1062 jseq.getFeatures().add(features);
1065 if (jdatasq.getAllPDBEntries() != null)
1067 Enumeration<PDBEntry> en = jdatasq.getAllPDBEntries().elements();
1068 while (en.hasMoreElements())
1070 Pdbids pdb = new Pdbids();
1071 jalview.datamodel.PDBEntry entry = en.nextElement();
1073 String pdbId = entry.getId();
1075 pdb.setType(entry.getType());
1078 * Store any structure views associated with this sequence. This
1079 * section copes with duplicate entries in the project, so a dataset
1080 * only view *should* be coped with sensibly.
1082 // This must have been loaded, is it still visible?
1083 JInternalFrame[] frames = Desktop.getDesktopPane().getAllFrames();
1084 String matchedFile = null;
1085 for (int f = frames.length - 1; f > -1; f--)
1087 if (frames[f] instanceof StructureViewerBase)
1089 StructureViewerBase viewFrame = (StructureViewerBase) frames[f];
1090 matchedFile = saveStructureState(ap, jds, pdb, entry, viewIds,
1091 matchedFile, viewFrame);
1093 * Only store each structure viewer's state once in the project
1094 * jar. First time through only (storeDS==false)
1096 String viewId = viewFrame.getViewId();
1097 if (!storeDS && !viewIds.contains(viewId))
1099 viewIds.add(viewId);
1102 String viewerState = viewFrame.getStateInfo();
1103 writeJarEntry(jout, getViewerJarEntryName(viewId),
1104 viewerState.getBytes());
1105 } catch (IOException e)
1108 "Error saving viewer state: " + e.getMessage());
1114 if (matchedFile != null || entry.getFile() != null)
1116 if (entry.getFile() != null)
1119 matchedFile = entry.getFile();
1121 pdb.setFile(matchedFile); // entry.getFile());
1122 if (pdbfiles == null)
1124 pdbfiles = new ArrayList<>();
1127 if (!pdbfiles.contains(pdbId))
1129 pdbfiles.add(pdbId);
1130 copyFileToJar(jout, matchedFile, pdbId);
1134 Enumeration<String> props = entry.getProperties();
1135 if (props.hasMoreElements())
1137 // PdbentryItem item = new PdbentryItem();
1138 while (props.hasMoreElements())
1140 Property prop = new Property();
1141 String key = props.nextElement();
1143 prop.setValue(entry.getProperty(key).toString());
1144 // item.addProperty(prop);
1145 pdb.getProperty().add(prop);
1147 // pdb.addPdbentryItem(item);
1150 // jseq.addPdbids(pdb);
1151 jseq.getPdbids().add(pdb);
1155 saveRnaViewers(jout, jseq, jds, viewIds, ap, storeDS);
1157 // jms.addJSeq(jseq);
1158 object.getJSeq().add(jseq);
1161 if (!storeDS && av.hasHiddenRows())
1163 jal = av.getAlignment();
1167 if (storeDS && jal.getCodonFrames() != null)
1169 List<AlignedCodonFrame> jac = jal.getCodonFrames();
1170 for (AlignedCodonFrame acf : jac)
1172 AlcodonFrame alc = new AlcodonFrame();
1173 if (acf.getProtMappings() != null
1174 && acf.getProtMappings().length > 0)
1176 boolean hasMap = false;
1177 SequenceI[] dnas = acf.getdnaSeqs();
1178 jalview.datamodel.Mapping[] pmaps = acf.getProtMappings();
1179 for (int m = 0; m < pmaps.length; m++)
1181 AlcodMap alcmap = new AlcodMap();
1182 alcmap.setDnasq(seqHash(dnas[m]));
1184 createVamsasMapping(pmaps[m], dnas[m], null, false));
1185 // alc.addAlcodMap(alcmap);
1186 alc.getAlcodMap().add(alcmap);
1191 // vamsasSet.addAlcodonFrame(alc);
1192 vamsasSet.getAlcodonFrame().add(alc);
1195 // TODO: delete this ? dead code from 2.8.3->2.9 ?
1197 // AlcodonFrame alc = new AlcodonFrame();
1198 // vamsasSet.addAlcodonFrame(alc);
1199 // for (int p = 0; p < acf.aaWidth; p++)
1201 // Alcodon cmap = new Alcodon();
1202 // if (acf.codons[p] != null)
1204 // // Null codons indicate a gapped column in the translated peptide
1206 // cmap.setPos1(acf.codons[p][0]);
1207 // cmap.setPos2(acf.codons[p][1]);
1208 // cmap.setPos3(acf.codons[p][2]);
1210 // alc.addAlcodon(cmap);
1212 // if (acf.getProtMappings() != null
1213 // && acf.getProtMappings().length > 0)
1215 // SequenceI[] dnas = acf.getdnaSeqs();
1216 // jalview.datamodel.Mapping[] pmaps = acf.getProtMappings();
1217 // for (int m = 0; m < pmaps.length; m++)
1219 // AlcodMap alcmap = new AlcodMap();
1220 // alcmap.setDnasq(seqHash(dnas[m]));
1221 // alcmap.setMapping(createVamsasMapping(pmaps[m], dnas[m], null,
1223 // alc.addAlcodMap(alcmap);
1230 // /////////////////////////////////
1231 if (!storeDS && av.getCurrentTree() != null)
1233 // FIND ANY ASSOCIATED TREES
1234 // NOT IMPLEMENTED FOR HEADLESS STATE AT PRESENT
1235 if (Desktop.getDesktopPane() != null)
1237 JInternalFrame[] frames = Desktop.getDesktopPane().getAllFrames();
1239 for (int t = 0; t < frames.length; t++)
1241 if (frames[t] instanceof TreePanel)
1243 TreePanel tp = (TreePanel) frames[t];
1245 if (tp.getTreeCanvas().getViewport().getAlignment() == jal)
1247 JalviewModel.Tree tree = new JalviewModel.Tree();
1248 tree.setTitle(tp.getTitle());
1249 tree.setCurrentTree((av.getCurrentTree() == tp.getTree()));
1250 tree.setNewick(tp.getTree().print());
1251 tree.setThreshold(tp.getTreeCanvas().getThreshold());
1253 tree.setFitToWindow(tp.fitToWindow.getState());
1254 tree.setFontName(tp.getTreeFont().getName());
1255 tree.setFontSize(tp.getTreeFont().getSize());
1256 tree.setFontStyle(tp.getTreeFont().getStyle());
1257 tree.setMarkUnlinked(tp.placeholdersMenu.getState());
1259 tree.setShowBootstrap(tp.bootstrapMenu.getState());
1260 tree.setShowDistances(tp.distanceMenu.getState());
1262 tree.setHeight(tp.getHeight());
1263 tree.setWidth(tp.getWidth());
1264 tree.setXpos(tp.getX());
1265 tree.setYpos(tp.getY());
1266 tree.setId(makeHashCode(tp, null));
1267 tree.setLinkToAllViews(
1268 tp.getTreeCanvas().isApplyToAllViews());
1270 // jms.addTree(tree);
1271 object.getTree().add(tree);
1281 if (!storeDS && Desktop.getDesktopPane() != null)
1283 for (JInternalFrame frame : Desktop.getDesktopPane().getAllFrames())
1285 if (frame instanceof PCAPanel)
1287 PCAPanel panel = (PCAPanel) frame;
1288 if (panel.getAlignViewport().getAlignment() == jal)
1290 savePCA(panel, object);
1298 * store forward refs from an annotationRow to any groups
1300 IdentityHashMap<SequenceGroup, String> groupRefs = new IdentityHashMap<>();
1303 for (SequenceI sq : jal.getSequences())
1305 // Store annotation on dataset sequences only
1306 AlignmentAnnotation[] aa = sq.getAnnotation();
1307 if (aa != null && aa.length > 0)
1309 storeAlignmentAnnotation(aa, groupRefs, av, calcIdSet, storeDS,
1316 if (jal.getAlignmentAnnotation() != null)
1318 // Store the annotation shown on the alignment.
1319 AlignmentAnnotation[] aa = jal.getAlignmentAnnotation();
1320 storeAlignmentAnnotation(aa, groupRefs, av, calcIdSet, storeDS,
1325 if (jal.getGroups() != null)
1327 JGroup[] groups = new JGroup[jal.getGroups().size()];
1329 for (jalview.datamodel.SequenceGroup sg : jal.getGroups())
1331 JGroup jGroup = new JGroup();
1332 groups[++i] = jGroup;
1334 jGroup.setStart(sg.getStartRes());
1335 jGroup.setEnd(sg.getEndRes());
1336 jGroup.setName(sg.getName());
1337 if (groupRefs.containsKey(sg))
1339 // group has references so set its ID field
1340 jGroup.setId(groupRefs.get(sg));
1342 ColourSchemeI colourScheme = sg.getColourScheme();
1343 if (colourScheme != null)
1345 ResidueShaderI groupColourScheme = sg.getGroupColourScheme();
1346 if (groupColourScheme.conservationApplied())
1348 jGroup.setConsThreshold(groupColourScheme.getConservationInc());
1350 if (colourScheme instanceof jalview.schemes.UserColourScheme)
1353 setUserColourScheme(colourScheme, userColours,
1358 jGroup.setColour(colourScheme.getSchemeName());
1361 else if (colourScheme instanceof jalview.schemes.AnnotationColourGradient)
1363 jGroup.setColour("AnnotationColourGradient");
1364 jGroup.setAnnotationColours(constructAnnotationColours(
1365 (jalview.schemes.AnnotationColourGradient) colourScheme,
1366 userColours, object));
1368 else if (colourScheme instanceof jalview.schemes.UserColourScheme)
1371 setUserColourScheme(colourScheme, userColours, object));
1375 jGroup.setColour(colourScheme.getSchemeName());
1378 jGroup.setPidThreshold(groupColourScheme.getThreshold());
1381 jGroup.setOutlineColour(sg.getOutlineColour().getRGB());
1382 jGroup.setDisplayBoxes(sg.getDisplayBoxes());
1383 jGroup.setDisplayText(sg.getDisplayText());
1384 jGroup.setColourText(sg.getColourText());
1385 jGroup.setTextCol1(sg.textColour.getRGB());
1386 jGroup.setTextCol2(sg.textColour2.getRGB());
1387 jGroup.setTextColThreshold(sg.thresholdTextColour);
1388 jGroup.setShowUnconserved(sg.getShowNonconserved());
1389 jGroup.setIgnoreGapsinConsensus(sg.getIgnoreGapsConsensus());
1390 jGroup.setShowConsensusHistogram(sg.isShowConsensusHistogram());
1391 jGroup.setShowSequenceLogo(sg.isShowSequenceLogo());
1392 jGroup.setNormaliseSequenceLogo(sg.isNormaliseSequenceLogo());
1393 for (SequenceI seq : sg.getSequences())
1395 // jGroup.addSeq(seqHash(seq));
1396 jGroup.getSeq().add(seqHash(seq));
1400 //jms.setJGroup(groups);
1402 for (JGroup grp : groups)
1404 object.getJGroup().add(grp);
1409 // /////////SAVE VIEWPORT
1410 Viewport view = new Viewport();
1411 view.setTitle(ap.alignFrame.getTitle());
1412 view.setSequenceSetId(
1413 makeHashCode(av.getSequenceSetId(), av.getSequenceSetId()));
1414 view.setId(av.getViewId());
1415 if (av.getCodingComplement() != null)
1417 view.setComplementId(av.getCodingComplement().getViewId());
1419 view.setViewName(av.getViewName());
1420 view.setGatheredViews(av.isGatherViewsHere());
1422 Rectangle size = ap.av.getExplodedGeometry();
1423 Rectangle position = size;
1426 size = ap.alignFrame.getBounds();
1427 if (av.getCodingComplement() != null)
1429 position = ((SplitFrame) ap.alignFrame.getSplitViewContainer())
1437 view.setXpos(position.x);
1438 view.setYpos(position.y);
1440 view.setWidth(size.width);
1441 view.setHeight(size.height);
1443 view.setStartRes(vpRanges.getStartRes());
1444 view.setStartSeq(vpRanges.getStartSeq());
1446 if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme)
1448 view.setBgColour(setUserColourScheme(av.getGlobalColourScheme(),
1449 userColours, object));
1452 .getGlobalColourScheme() instanceof jalview.schemes.AnnotationColourGradient)
1454 AnnotationColourScheme ac = constructAnnotationColours(
1455 (jalview.schemes.AnnotationColourGradient) av
1456 .getGlobalColourScheme(),
1457 userColours, object);
1459 view.setAnnotationColours(ac);
1460 view.setBgColour("AnnotationColourGradient");
1464 view.setBgColour(ColourSchemeProperty
1465 .getColourName(av.getGlobalColourScheme()));
1468 ResidueShaderI vcs = av.getResidueShading();
1469 ColourSchemeI cs = av.getGlobalColourScheme();
1473 if (vcs.conservationApplied())
1475 view.setConsThreshold(vcs.getConservationInc());
1476 if (cs instanceof jalview.schemes.UserColourScheme)
1478 view.setBgColour(setUserColourScheme(cs, userColours, object));
1481 view.setPidThreshold(vcs.getThreshold());
1484 view.setConservationSelected(av.getConservationSelected());
1485 view.setPidSelected(av.getAbovePIDThreshold());
1486 final Font font = av.getFont();
1487 view.setFontName(font.getName());
1488 view.setFontSize(font.getSize());
1489 view.setFontStyle(font.getStyle());
1490 view.setScaleProteinAsCdna(av.getViewStyle().isScaleProteinAsCdna());
1491 view.setRenderGaps(av.isRenderGaps());
1492 view.setShowAnnotation(av.isShowAnnotation());
1493 view.setShowBoxes(av.getShowBoxes());
1494 view.setShowColourText(av.getColourText());
1495 view.setShowFullId(av.getShowJVSuffix());
1496 view.setRightAlignIds(av.isRightAlignIds());
1497 view.setShowSequenceFeatures(av.isShowSequenceFeatures());
1498 view.setShowText(av.getShowText());
1499 view.setShowUnconserved(av.getShowUnconserved());
1500 view.setWrapAlignment(av.getWrapAlignment());
1501 view.setTextCol1(av.getTextColour().getRGB());
1502 view.setTextCol2(av.getTextColour2().getRGB());
1503 view.setTextColThreshold(av.getThresholdTextColour());
1504 view.setShowConsensusHistogram(av.isShowConsensusHistogram());
1505 view.setShowSequenceLogo(av.isShowSequenceLogo());
1506 view.setNormaliseSequenceLogo(av.isNormaliseSequenceLogo());
1507 view.setShowGroupConsensus(av.isShowGroupConsensus());
1508 view.setShowGroupConservation(av.isShowGroupConservation());
1509 view.setShowNPfeatureTooltip(av.isShowNPFeats());
1510 view.setShowDbRefTooltip(av.isShowDBRefs());
1511 view.setFollowHighlight(av.isFollowHighlight());
1512 view.setFollowSelection(av.followSelection);
1513 view.setIgnoreGapsinConsensus(av.isIgnoreGapsConsensus());
1514 if (av.getFeaturesDisplayed() != null)
1516 FeatureSettings fs = new FeatureSettings();
1518 FeatureRenderer 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 fileName = fileName.replace('\\', '/');
1675 System.out.println("Writing jar entry " + fileName);
1676 JarEntry entry = new JarEntry(fileName);
1677 jout.putNextEntry(entry);
1678 PrintWriter pout = new PrintWriter(
1679 new OutputStreamWriter(jout, UTF_8));
1680 JAXBContext jaxbContext = JAXBContext
1681 .newInstance(JalviewModel.class);
1682 Marshaller jaxbMarshaller = jaxbContext.createMarshaller();
1684 // output pretty printed
1685 // jaxbMarshaller.setProperty(Marshaller.JAXB_FORMATTED_OUTPUT, true);
1686 jaxbMarshaller.marshal(
1687 new ObjectFactory().createJalviewModel(object), pout);
1689 // jaxbMarshaller.marshal(object, pout);
1690 // marshaller.marshal(object);
1693 } catch (Exception ex)
1695 // TODO: raise error in GUI if marshalling failed.
1696 System.err.println("Error writing Jalview project");
1697 ex.printStackTrace();
1704 * Writes PCA viewer attributes and computed values to an XML model object and
1705 * adds it to the JalviewModel. Any exceptions are reported by logging.
1707 protected void savePCA(PCAPanel panel, JalviewModel object)
1711 PcaViewer viewer = new PcaViewer();
1712 viewer.setHeight(panel.getHeight());
1713 viewer.setWidth(panel.getWidth());
1714 viewer.setXpos(panel.getX());
1715 viewer.setYpos(panel.getY());
1716 viewer.setTitle(panel.getTitle());
1717 PCAModel pcaModel = panel.getPcaModel();
1718 viewer.setScoreModelName(pcaModel.getScoreModelName());
1719 viewer.setXDim(panel.getSelectedDimensionIndex(X));
1720 viewer.setYDim(panel.getSelectedDimensionIndex(Y));
1721 viewer.setZDim(panel.getSelectedDimensionIndex(Z));
1723 panel.getRotatableCanvas().getBackgroundColour().getRGB());
1724 viewer.setScaleFactor(panel.getRotatableCanvas().getScaleFactor());
1725 float[] spMin = panel.getRotatableCanvas().getSeqMin();
1726 SeqPointMin spmin = new SeqPointMin();
1727 spmin.setXPos(spMin[0]);
1728 spmin.setYPos(spMin[1]);
1729 spmin.setZPos(spMin[2]);
1730 viewer.setSeqPointMin(spmin);
1731 float[] spMax = panel.getRotatableCanvas().getSeqMax();
1732 SeqPointMax spmax = new SeqPointMax();
1733 spmax.setXPos(spMax[0]);
1734 spmax.setYPos(spMax[1]);
1735 spmax.setZPos(spMax[2]);
1736 viewer.setSeqPointMax(spmax);
1737 viewer.setShowLabels(panel.getRotatableCanvas().isShowLabels());
1738 viewer.setLinkToAllViews(
1739 panel.getRotatableCanvas().isApplyToAllViews());
1740 SimilarityParamsI sp = pcaModel.getSimilarityParameters();
1741 viewer.setIncludeGaps(sp.includeGaps());
1742 viewer.setMatchGaps(sp.matchGaps());
1743 viewer.setIncludeGappedColumns(sp.includeGappedColumns());
1744 viewer.setDenominateByShortestLength(sp.denominateByShortestLength());
1747 * sequence points on display
1749 for (jalview.datamodel.SequencePoint spt : pcaModel
1750 .getSequencePoints())
1752 SequencePoint point = new SequencePoint();
1753 point.setSequenceRef(seqHash(spt.getSequence()));
1754 point.setXPos(spt.coord.x);
1755 point.setYPos(spt.coord.y);
1756 point.setZPos(spt.coord.z);
1757 viewer.getSequencePoint().add(point);
1761 * (end points of) axes on display
1763 for (Point p : panel.getRotatableCanvas().getAxisEndPoints())
1766 Axis axis = new Axis();
1770 viewer.getAxis().add(axis);
1774 * raw PCA data (note we are not restoring PCA inputs here -
1775 * alignment view, score model, similarity parameters)
1777 PcaDataType data = new PcaDataType();
1778 viewer.setPcaData(data);
1779 PCA pca = pcaModel.getPcaData();
1781 DoubleMatrix pm = new DoubleMatrix();
1782 saveDoubleMatrix(pca.getPairwiseScores(), pm);
1783 data.setPairwiseMatrix(pm);
1785 DoubleMatrix tm = new DoubleMatrix();
1786 saveDoubleMatrix(pca.getTridiagonal(), tm);
1787 data.setTridiagonalMatrix(tm);
1789 DoubleMatrix eigenMatrix = new DoubleMatrix();
1790 data.setEigenMatrix(eigenMatrix);
1791 saveDoubleMatrix(pca.getEigenmatrix(), eigenMatrix);
1793 object.getPcaViewer().add(viewer);
1794 } catch (Throwable t)
1796 Cache.log.error("Error saving PCA: " + t.getMessage());
1801 * Stores values from a matrix into an XML element, including (if present) the
1806 * @see #loadDoubleMatrix(DoubleMatrix)
1808 protected void saveDoubleMatrix(MatrixI m, DoubleMatrix xmlMatrix)
1810 xmlMatrix.setRows(m.height());
1811 xmlMatrix.setColumns(m.width());
1812 for (int i = 0; i < m.height(); i++)
1814 DoubleVector row = new DoubleVector();
1815 for (int j = 0; j < m.width(); j++)
1817 row.getV().add(m.getValue(i, j));
1819 xmlMatrix.getRow().add(row);
1821 if (m.getD() != null)
1823 DoubleVector dVector = new DoubleVector();
1824 for (double d : m.getD())
1826 dVector.getV().add(d);
1828 xmlMatrix.setD(dVector);
1830 if (m.getE() != null)
1832 DoubleVector eVector = new DoubleVector();
1833 for (double e : m.getE())
1835 eVector.getV().add(e);
1837 xmlMatrix.setE(eVector);
1842 * Loads XML matrix data into a new Matrix object, including the D and/or E
1843 * vectors (if present)
1847 * @see Jalview2XML#saveDoubleMatrix(MatrixI, DoubleMatrix)
1849 protected MatrixI loadDoubleMatrix(DoubleMatrix mData)
1851 int rows = mData.getRows();
1852 double[][] vals = new double[rows][];
1854 for (int i = 0; i < rows; i++)
1856 List<Double> dVector = mData.getRow().get(i).getV();
1857 vals[i] = new double[dVector.size()];
1859 for (Double d : dVector)
1865 MatrixI m = new Matrix(vals);
1867 if (mData.getD() != null)
1869 List<Double> dVector = mData.getD().getV();
1870 double[] vec = new double[dVector.size()];
1872 for (Double d : dVector)
1878 if (mData.getE() != null)
1880 List<Double> dVector = mData.getE().getV();
1881 double[] vec = new double[dVector.size()];
1883 for (Double d : dVector)
1894 * Save any Varna viewers linked to this sequence. Writes an rnaViewer element
1895 * for each viewer, with
1897 * <li>viewer geometry (position, size, split pane divider location)</li>
1898 * <li>index of the selected structure in the viewer (currently shows gapped
1900 * <li>the id of the annotation holding RNA secondary structure</li>
1901 * <li>(currently only one SS is shown per viewer, may be more in future)</li>
1903 * Varna viewer state is also written out (in native Varna XML) to separate
1904 * project jar entries. A separate entry is written for each RNA structure
1905 * displayed, with the naming convention
1907 * <li>rna_viewId_sequenceId_annotationId_[gapped|trimmed]</li>
1915 * @param storeDataset
1917 protected void saveRnaViewers(JarOutputStream jout, JSeq jseq,
1918 final SequenceI jds, List<String> viewIds, AlignmentPanel ap,
1919 boolean storeDataset)
1921 if (Desktop.getDesktopPane() == null)
1925 JInternalFrame[] frames = Desktop.getDesktopPane().getAllFrames();
1926 for (int f = frames.length - 1; f > -1; f--)
1928 if (frames[f] instanceof AppVarna)
1930 AppVarna varna = (AppVarna) frames[f];
1932 * link the sequence to every viewer that is showing it and is linked to
1933 * its alignment panel
1935 if (varna.isListeningFor(jds) && ap == varna.getAlignmentPanel())
1937 String viewId = varna.getViewId();
1938 RnaViewer rna = new RnaViewer();
1939 rna.setViewId(viewId);
1940 rna.setTitle(varna.getTitle());
1941 rna.setXpos(varna.getX());
1942 rna.setYpos(varna.getY());
1943 rna.setWidth(varna.getWidth());
1944 rna.setHeight(varna.getHeight());
1945 rna.setDividerLocation(varna.getDividerLocation());
1946 rna.setSelectedRna(varna.getSelectedIndex());
1947 // jseq.addRnaViewer(rna);
1948 jseq.getRnaViewer().add(rna);
1951 * Store each Varna panel's state once in the project per sequence.
1952 * First time through only (storeDataset==false)
1954 // boolean storeSessions = false;
1955 // String sequenceViewId = viewId + seqsToIds.get(jds);
1956 // if (!storeDataset && !viewIds.contains(sequenceViewId))
1958 // viewIds.add(sequenceViewId);
1959 // storeSessions = true;
1961 for (RnaModel model : varna.getModels())
1963 if (model.seq == jds)
1966 * VARNA saves each view (sequence or alignment secondary
1967 * structure, gapped or trimmed) as a separate XML file
1969 String jarEntryName = rnaSessions.get(model);
1970 if (jarEntryName == null)
1973 String varnaStateFile = varna.getStateInfo(model.rna);
1974 jarEntryName = RNA_PREFIX + viewId + "_" + nextCounter();
1975 copyFileToJar(jout, varnaStateFile, jarEntryName);
1976 rnaSessions.put(model, jarEntryName);
1978 SecondaryStructure ss = new SecondaryStructure();
1979 String annotationId = varna.getAnnotation(jds).annotationId;
1980 ss.setAnnotationId(annotationId);
1981 ss.setViewerState(jarEntryName);
1982 ss.setGapped(model.gapped);
1983 ss.setTitle(model.title);
1984 // rna.addSecondaryStructure(ss);
1985 rna.getSecondaryStructure().add(ss);
1994 * Copy the contents of a file to a new entry added to the output jar
1998 * @param jarEntryName
2000 protected void copyFileToJar(JarOutputStream jout, String infilePath,
2001 String jarEntryName)
2003 DataInputStream dis = null;
2006 File file = new File(infilePath);
2007 if (file.exists() && jout != null)
2009 dis = new DataInputStream(new FileInputStream(file));
2010 byte[] data = new byte[(int) file.length()];
2011 dis.readFully(data);
2012 writeJarEntry(jout, jarEntryName, data);
2014 } catch (Exception ex)
2016 ex.printStackTrace();
2024 } catch (IOException e)
2033 * Write the data to a new entry of given name in the output jar file
2036 * @param jarEntryName
2038 * @throws IOException
2040 protected void writeJarEntry(JarOutputStream jout, String jarEntryName,
2041 byte[] data) throws IOException
2045 jarEntryName = jarEntryName.replace('\\','/');
2046 System.out.println("Writing jar entry " + jarEntryName);
2047 jout.putNextEntry(new JarEntry(jarEntryName));
2048 DataOutputStream dout = new DataOutputStream(jout);
2049 dout.write(data, 0, data.length);
2056 * Save the state of a structure viewer
2061 * the archive XML element under which to save the state
2064 * @param matchedFile
2068 protected String saveStructureState(AlignmentPanel ap, SequenceI jds,
2069 Pdbids pdb, PDBEntry entry, List<String> viewIds,
2070 String matchedFile, StructureViewerBase viewFrame)
2072 final AAStructureBindingModel bindingModel = viewFrame.getBinding();
2075 * Look for any bindings for this viewer to the PDB file of interest
2076 * (including part matches excluding chain id)
2078 for (int peid = 0; peid < bindingModel.getPdbCount(); peid++)
2080 final PDBEntry pdbentry = bindingModel.getPdbEntry(peid);
2081 final String pdbId = pdbentry.getId();
2082 if (!pdbId.equals(entry.getId())
2083 && !(entry.getId().length() > 4 && entry.getId().toLowerCase()
2084 .startsWith(pdbId.toLowerCase())))
2087 * not interested in a binding to a different PDB entry here
2091 if (matchedFile == null)
2093 matchedFile = pdbentry.getFile();
2095 else if (!matchedFile.equals(pdbentry.getFile()))
2098 "Probably lost some PDB-Sequence mappings for this structure file (which apparently has same PDB Entry code): "
2099 + pdbentry.getFile());
2103 // can get at it if the ID
2104 // match is ambiguous (e.g.
2107 for (int smap = 0; smap < viewFrame.getBinding()
2108 .getSequence()[peid].length; smap++)
2110 // if (jal.findIndex(jmol.jmb.sequence[peid][smap]) > -1)
2111 if (jds == viewFrame.getBinding().getSequence()[peid][smap])
2113 StructureState state = new StructureState();
2114 state.setVisible(true);
2115 state.setXpos(viewFrame.getX());
2116 state.setYpos(viewFrame.getY());
2117 state.setWidth(viewFrame.getWidth());
2118 state.setHeight(viewFrame.getHeight());
2119 final String viewId = viewFrame.getViewId();
2120 state.setViewId(viewId);
2121 state.setAlignwithAlignPanel(viewFrame.isUsedforaligment(ap));
2122 state.setColourwithAlignPanel(viewFrame.isUsedforcolourby(ap));
2123 state.setColourByJmol(viewFrame.isColouredByViewer());
2124 state.setType(viewFrame.getViewerType().toString());
2125 // pdb.addStructureState(state);
2126 pdb.getStructureState().add(state);
2134 * Populates the AnnotationColourScheme xml for save. This captures the
2135 * settings of the options in the 'Colour by Annotation' dialog.
2138 * @param userColours
2142 private AnnotationColourScheme constructAnnotationColours(
2143 AnnotationColourGradient acg, List<UserColourScheme> userColours,
2146 AnnotationColourScheme ac = new AnnotationColourScheme();
2147 ac.setAboveThreshold(acg.getAboveThreshold());
2148 ac.setThreshold(acg.getAnnotationThreshold());
2149 // 2.10.2 save annotationId (unique) not annotation label
2150 ac.setAnnotation(acg.getAnnotation().annotationId);
2151 if (acg.getBaseColour() instanceof UserColourScheme)
2154 setUserColourScheme(acg.getBaseColour(), userColours, jm));
2159 ColourSchemeProperty.getColourName(acg.getBaseColour()));
2162 ac.setMaxColour(acg.getMaxColour().getRGB());
2163 ac.setMinColour(acg.getMinColour().getRGB());
2164 ac.setPerSequence(acg.isSeqAssociated());
2165 ac.setPredefinedColours(acg.isPredefinedColours());
2169 private void storeAlignmentAnnotation(AlignmentAnnotation[] aa,
2170 IdentityHashMap<SequenceGroup, String> groupRefs,
2171 AlignmentViewport av, Set<String> calcIdSet, boolean storeDS,
2172 SequenceSet vamsasSet)
2175 for (int i = 0; i < aa.length; i++)
2177 Annotation an = new Annotation();
2179 AlignmentAnnotation annotation = aa[i];
2180 if (annotation.annotationId != null)
2182 annotationIds.put(annotation.annotationId, annotation);
2185 an.setId(annotation.annotationId);
2187 an.setVisible(annotation.visible);
2189 an.setDescription(annotation.description);
2191 if (annotation.sequenceRef != null)
2193 // 2.9 JAL-1781 xref on sequence id rather than name
2194 an.setSequenceRef(seqsToIds.get(annotation.sequenceRef));
2196 if (annotation.groupRef != null)
2198 String groupIdr = groupRefs.get(annotation.groupRef);
2199 if (groupIdr == null)
2201 // make a locally unique String
2202 groupRefs.put(annotation.groupRef,
2203 groupIdr = ("" + System.currentTimeMillis()
2204 + annotation.groupRef.getName()
2205 + groupRefs.size()));
2207 an.setGroupRef(groupIdr.toString());
2210 // store all visualization attributes for annotation
2211 an.setGraphHeight(annotation.graphHeight);
2212 an.setCentreColLabels(annotation.centreColLabels);
2213 an.setScaleColLabels(annotation.scaleColLabel);
2214 an.setShowAllColLabels(annotation.showAllColLabels);
2215 an.setBelowAlignment(annotation.belowAlignment);
2217 if (annotation.graph > 0)
2220 an.setGraphType(annotation.graph);
2221 an.setGraphGroup(annotation.graphGroup);
2222 if (annotation.getThreshold() != null)
2224 ThresholdLine line = new ThresholdLine();
2225 line.setLabel(annotation.getThreshold().label);
2226 line.setValue(annotation.getThreshold().value);
2227 line.setColour(annotation.getThreshold().colour.getRGB());
2228 an.setThresholdLine(line);
2236 an.setLabel(annotation.label);
2238 if (annotation == av.getAlignmentQualityAnnot()
2239 || annotation == av.getAlignmentConservationAnnotation()
2240 || annotation == av.getAlignmentConsensusAnnotation()
2241 || annotation.autoCalculated)
2243 // new way of indicating autocalculated annotation -
2244 an.setAutoCalculated(annotation.autoCalculated);
2246 if (annotation.hasScore())
2248 an.setScore(annotation.getScore());
2251 if (annotation.getCalcId() != null)
2253 calcIdSet.add(annotation.getCalcId());
2254 an.setCalcId(annotation.getCalcId());
2256 if (annotation.hasProperties())
2258 for (String pr : annotation.getProperties())
2260 jalview.xml.binding.jalview.Annotation.Property prop = new jalview.xml.binding.jalview.Annotation.Property();
2262 prop.setValue(annotation.getProperty(pr));
2263 // an.addProperty(prop);
2264 an.getProperty().add(prop);
2268 AnnotationElement ae;
2269 if (annotation.annotations != null)
2271 an.setScoreOnly(false);
2272 for (int a = 0; a < annotation.annotations.length; a++)
2274 if ((annotation == null) || (annotation.annotations[a] == null))
2279 ae = new AnnotationElement();
2280 if (annotation.annotations[a].description != null)
2282 ae.setDescription(annotation.annotations[a].description);
2284 if (annotation.annotations[a].displayCharacter != null)
2286 ae.setDisplayCharacter(
2287 annotation.annotations[a].displayCharacter);
2290 if (!Float.isNaN(annotation.annotations[a].value))
2292 ae.setValue(annotation.annotations[a].value);
2296 if (annotation.annotations[a].secondaryStructure > ' ')
2298 ae.setSecondaryStructure(
2299 annotation.annotations[a].secondaryStructure + "");
2302 if (annotation.annotations[a].colour != null
2303 && annotation.annotations[a].colour != java.awt.Color.black)
2305 ae.setColour(annotation.annotations[a].colour.getRGB());
2308 // an.addAnnotationElement(ae);
2309 an.getAnnotationElement().add(ae);
2310 if (annotation.autoCalculated)
2312 // only write one non-null entry into the annotation row -
2313 // sufficient to get the visualization attributes necessary to
2321 an.setScoreOnly(true);
2323 if (!storeDS || (storeDS && !annotation.autoCalculated))
2325 // skip autocalculated annotation - these are only provided for
2327 // vamsasSet.addAnnotation(an);
2328 vamsasSet.getAnnotation().add(an);
2334 private CalcIdParam createCalcIdParam(String calcId, AlignViewport av)
2336 AutoCalcSetting settings = av.getCalcIdSettingsFor(calcId);
2337 if (settings != null)
2339 CalcIdParam vCalcIdParam = new CalcIdParam();
2340 vCalcIdParam.setCalcId(calcId);
2341 // vCalcIdParam.addServiceURL(settings.getServiceURI());
2342 vCalcIdParam.getServiceURL().add(settings.getServiceURI());
2343 // generic URI allowing a third party to resolve another instance of the
2344 // service used for this calculation
2345 for (String url : settings.getServiceURLs())
2347 // vCalcIdParam.addServiceURL(urls);
2348 vCalcIdParam.getServiceURL().add(url);
2350 vCalcIdParam.setVersion("1.0");
2351 if (settings.getPreset() != null)
2353 WsParamSetI setting = settings.getPreset();
2354 vCalcIdParam.setName(setting.getName());
2355 vCalcIdParam.setDescription(setting.getDescription());
2359 vCalcIdParam.setName("");
2360 vCalcIdParam.setDescription("Last used parameters");
2362 // need to be able to recover 1) settings 2) user-defined presets or
2363 // recreate settings from preset 3) predefined settings provided by
2364 // service - or settings that can be transferred (or discarded)
2365 vCalcIdParam.setParameters(
2366 settings.getWsParamFile().replace("\n", "|\\n|"));
2367 vCalcIdParam.setAutoUpdate(settings.isAutoUpdate());
2368 // todo - decide if updateImmediately is needed for any projects.
2370 return vCalcIdParam;
2375 private boolean recoverCalcIdParam(CalcIdParam calcIdParam,
2378 if (calcIdParam.getVersion().equals("1.0"))
2380 final String[] calcIds = calcIdParam.getServiceURL().toArray(new String[0]);
2381 Jws2Instance service = Jws2Discoverer.getInstance()
2382 .getPreferredServiceFor(calcIds);
2383 if (service != null)
2385 WsParamSetI parmSet = null;
2388 parmSet = service.getParamStore().parseServiceParameterFile(
2389 calcIdParam.getName(), calcIdParam.getDescription(),
2391 calcIdParam.getParameters().replace("|\\n|", "\n"));
2392 } catch (IOException x)
2394 warn("Couldn't parse parameter data for "
2395 + calcIdParam.getCalcId(), x);
2398 List<ArgumentI> argList = null;
2399 if (calcIdParam.getName().length() > 0)
2401 parmSet = service.getParamStore()
2402 .getPreset(calcIdParam.getName());
2403 if (parmSet != null)
2405 // TODO : check we have a good match with settings in AACon -
2406 // otherwise we'll need to create a new preset
2411 argList = parmSet.getArguments();
2414 AAConSettings settings = new AAConSettings(
2415 calcIdParam.isAutoUpdate(), service, parmSet, argList);
2416 av.setCalcIdSettingsFor(calcIdParam.getCalcId(), settings,
2417 calcIdParam.isNeedsUpdate());
2422 warn("Cannot resolve a service for the parameters used in this project. Try configuring a JABAWS server.");
2426 throw new Error(MessageManager.formatMessage(
2427 "error.unsupported_version_calcIdparam", new Object[]
2428 { calcIdParam.toString() }));
2432 * External mapping between jalview objects and objects yielding a valid and
2433 * unique object ID string. This is null for normal Jalview project IO, but
2434 * non-null when a jalview project is being read or written as part of a
2437 IdentityHashMap jv2vobj = null;
2440 * Construct a unique ID for jvobj using either existing bindings or if none
2441 * exist, the result of the hashcode call for the object.
2444 * jalview data object
2445 * @return unique ID for referring to jvobj
2447 private String makeHashCode(Object jvobj, String altCode)
2449 if (jv2vobj != null)
2451 Object id = jv2vobj.get(jvobj);
2454 return id.toString();
2456 // check string ID mappings
2457 if (jvids2vobj != null && jvobj instanceof String)
2459 id = jvids2vobj.get(jvobj);
2463 return id.toString();
2465 // give up and warn that something has gone wrong
2466 warn("Cannot find ID for object in external mapping : " + jvobj);
2472 * return local jalview object mapped to ID, if it exists
2476 * @return null or object bound to idcode
2478 private Object retrieveExistingObj(String idcode)
2480 if (idcode != null && vobj2jv != null)
2482 return vobj2jv.get(idcode);
2488 * binding from ID strings from external mapping table to jalview data model
2491 private Hashtable vobj2jv;
2493 private Sequence createVamsasSequence(String id, SequenceI jds)
2495 return createVamsasSequence(true, id, jds, null);
2498 private Sequence createVamsasSequence(boolean recurse, String id,
2499 SequenceI jds, SequenceI parentseq)
2501 Sequence vamsasSeq = new Sequence();
2502 vamsasSeq.setId(id);
2503 vamsasSeq.setName(jds.getName());
2504 vamsasSeq.setSequence(jds.getSequenceAsString());
2505 vamsasSeq.setDescription(jds.getDescription());
2506 List<DBRefEntry> dbrefs = null;
2507 if (jds.getDatasetSequence() != null)
2509 vamsasSeq.setDsseqid(seqHash(jds.getDatasetSequence()));
2513 // seqId==dsseqid so we can tell which sequences really are
2514 // dataset sequences only
2515 vamsasSeq.setDsseqid(id);
2516 dbrefs = jds.getDBRefs();
2517 if (parentseq == null)
2524 for (int d = 0, nd = dbrefs.size(); d < nd; d++)
2526 DBRef dbref = new DBRef();
2527 DBRefEntry ref = dbrefs.get(d);
2528 dbref.setSource(ref.getSource());
2529 dbref.setVersion(ref.getVersion());
2530 dbref.setAccessionId(ref.getAccessionId());
2533 Mapping mp = createVamsasMapping(ref.getMap(), parentseq,
2535 dbref.setMapping(mp);
2537 // vamsasSeq.addDBRef(dbref);
2538 vamsasSeq.getDBRef().add(dbref);
2544 private Mapping createVamsasMapping(jalview.datamodel.Mapping jmp,
2545 SequenceI parentseq, SequenceI jds, boolean recurse)
2548 if (jmp.getMap() != null)
2552 jalview.util.MapList mlst = jmp.getMap();
2553 List<int[]> r = mlst.getFromRanges();
2554 for (int[] range : r)
2556 MapListFrom mfrom = new MapListFrom();
2557 mfrom.setStart(range[0]);
2558 mfrom.setEnd(range[1]);
2559 // mp.addMapListFrom(mfrom);
2560 mp.getMapListFrom().add(mfrom);
2562 r = mlst.getToRanges();
2563 for (int[] range : r)
2565 MapListTo mto = new MapListTo();
2566 mto.setStart(range[0]);
2567 mto.setEnd(range[1]);
2568 // mp.addMapListTo(mto);
2569 mp.getMapListTo().add(mto);
2571 mp.setMapFromUnit(BigInteger.valueOf(mlst.getFromRatio()));
2572 mp.setMapToUnit(BigInteger.valueOf(mlst.getToRatio()));
2573 if (jmp.getTo() != null)
2575 // MappingChoice mpc = new MappingChoice();
2577 // check/create ID for the sequence referenced by getTo()
2580 SequenceI ps = null;
2581 if (parentseq != jmp.getTo()
2582 && parentseq.getDatasetSequence() != jmp.getTo())
2584 // chaining dbref rather than a handshaking one
2585 jmpid = seqHash(ps = jmp.getTo());
2589 jmpid = seqHash(ps = parentseq);
2591 // mpc.setDseqFor(jmpid);
2592 mp.setDseqFor(jmpid);
2593 if (!seqRefIds.containsKey(jmpid))
2595 jalview.bin.Cache.log.debug("creatign new DseqFor ID");
2596 seqRefIds.put(jmpid, ps);
2600 jalview.bin.Cache.log.debug("reusing DseqFor ID");
2603 // mp.setMappingChoice(mpc);
2609 String setUserColourScheme(jalview.schemes.ColourSchemeI cs,
2610 List<UserColourScheme> userColours, JalviewModel jm)
2613 jalview.schemes.UserColourScheme ucs = (jalview.schemes.UserColourScheme) cs;
2614 boolean newucs = false;
2615 if (!userColours.contains(ucs))
2617 userColours.add(ucs);
2620 id = "ucs" + userColours.indexOf(ucs);
2623 // actually create the scheme's entry in the XML model
2624 java.awt.Color[] colours = ucs.getColours();
2625 UserColours uc = new UserColours();
2626 // UserColourScheme jbucs = new UserColourScheme();
2627 JalviewUserColours jbucs = new JalviewUserColours();
2629 for (int i = 0; i < colours.length; i++)
2631 Colour col = new Colour();
2632 col.setName(ResidueProperties.aa[i]);
2633 col.setRGB(jalview.util.Format.getHexString(colours[i]));
2634 // jbucs.addColour(col);
2635 jbucs.getColour().add(col);
2637 if (ucs.getLowerCaseColours() != null)
2639 colours = ucs.getLowerCaseColours();
2640 for (int i = 0; i < colours.length; i++)
2642 Colour col = new Colour();
2643 col.setName(ResidueProperties.aa[i].toLowerCase());
2644 col.setRGB(jalview.util.Format.getHexString(colours[i]));
2645 // jbucs.addColour(col);
2646 jbucs.getColour().add(col);
2651 uc.setUserColourScheme(jbucs);
2652 // jm.addUserColours(uc);
2653 jm.getUserColours().add(uc);
2659 jalview.schemes.UserColourScheme getUserColourScheme(
2660 JalviewModel jm, String id)
2662 List<UserColours> uc = jm.getUserColours();
2663 UserColours colours = null;
2665 for (int i = 0; i < uc.length; i++)
2667 if (uc[i].getId().equals(id))
2674 for (UserColours c : uc)
2676 if (c.getId().equals(id))
2683 java.awt.Color[] newColours = new java.awt.Color[24];
2685 for (int i = 0; i < 24; i++)
2687 newColours[i] = new java.awt.Color(Integer.parseInt(
2688 // colours.getUserColourScheme().getColour(i).getRGB(), 16));
2689 colours.getUserColourScheme().getColour().get(i).getRGB(),
2693 jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(
2696 if (colours.getUserColourScheme().getColour().size()/*Count()*/ > 24)
2698 newColours = new java.awt.Color[23];
2699 for (int i = 0; i < 23; i++)
2701 newColours[i] = new java.awt.Color(Integer.parseInt(
2702 colours.getUserColourScheme().getColour().get(i + 24)
2706 ucs.setLowerCaseColours(newColours);
2713 * contains last error message (if any) encountered by XML loader.
2715 String errorMessage = null;
2718 * flag to control whether the Jalview2XML_V1 parser should be deferred to if
2719 * exceptions are raised during project XML parsing
2721 public boolean attemptversion1parse = false;
2724 * Load a jalview project archive from a jar file
2727 * - HTTP URL or filename
2729 public AlignFrame loadJalviewAlign(final Object file)
2732 jalview.gui.AlignFrame af = null;
2736 // create list to store references for any new Jmol viewers created
2737 newStructureViewers = new Vector<>();
2738 // UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
2739 // Workaround is to make sure caller implements the JarInputStreamProvider
2741 // so we can re-open the jar input stream for each entry.
2743 jarInputStreamProvider jprovider = createjarInputStreamProvider(file);
2744 af = loadJalviewAlign(jprovider);
2747 af.setMenusForViewport();
2749 } catch (MalformedURLException e)
2751 errorMessage = "Invalid URL format for '" + file + "'";
2757 SwingUtilities.invokeAndWait(new Runnable()
2762 setLoadingFinishedForNewStructureViewers();
2765 } catch (Exception x)
2767 System.err.println("Error loading alignment: " + x.getMessage());
2773 @SuppressWarnings("unused")
2774 private jarInputStreamProvider createjarInputStreamProvider(final Object ofile) throws MalformedURLException {
2776 // BH 2018 allow for bytes already attached to File object
2778 String file = (ofile instanceof File ? ((File) ofile).getCanonicalPath() : ofile.toString());
2779 byte[] bytes = Platform.isJS() ? Platform.getFileBytes((File) ofile)
2782 errorMessage = null;
2783 uniqueSetSuffix = null;
2785 viewportsAdded.clear();
2786 frefedSequence = null;
2788 if (file.startsWith("http://")) {
2789 url = new URL(file);
2791 final URL _url = url;
2792 return new jarInputStreamProvider() {
2795 public JarInputStream getJarInputStream() throws IOException {
2796 if (bytes != null) {
2797 // System.out.println("Jalview2XML: opening byte jarInputStream for bytes.length=" + bytes.length);
2798 return new JarInputStream(new ByteArrayInputStream(bytes));
2801 // System.out.println("Jalview2XML: opening url jarInputStream for " + _url);
2802 return new JarInputStream(_url.openStream());
2804 // System.out.println("Jalview2XML: opening file jarInputStream for " + file);
2805 return new JarInputStream(new FileInputStream(file));
2810 public String getFilename() {
2814 } catch (IOException e) {
2815 e.printStackTrace();
2821 * Recover jalview session from a jalview project archive. Caller may
2822 * initialise uniqueSetSuffix, seqRefIds, viewportsAdded and frefedSequence
2823 * themselves. Any null fields will be initialised with default values,
2824 * non-null fields are left alone.
2829 public AlignFrame loadJalviewAlign(final jarInputStreamProvider jprovider)
2831 errorMessage = null;
2832 if (uniqueSetSuffix == null)
2834 uniqueSetSuffix = System.currentTimeMillis() % 100000 + "";
2836 if (seqRefIds == null)
2840 AlignFrame af = null, _af = null;
2841 IdentityHashMap<AlignmentI, AlignmentI> importedDatasets = new IdentityHashMap<>();
2842 Map<String, AlignFrame> gatherToThisFrame = new HashMap<>();
2843 final String file = jprovider.getFilename();
2846 JarInputStream jin = null;
2847 JarEntry jarentry = null;
2852 jin = jprovider.getJarInputStream();
2853 for (int i = 0; i < entryCount; i++)
2855 jarentry = jin.getNextJarEntry();
2858 if (jarentry != null && jarentry.getName().endsWith(".xml"))
2860 JAXBContext jc = JAXBContext
2861 .newInstance("jalview.xml.binding.jalview");
2862 XMLStreamReader streamReader = XMLInputFactory.newInstance()
2863 .createXMLStreamReader(jin);
2864 javax.xml.bind.Unmarshaller um = jc.createUnmarshaller();
2865 JAXBElement<JalviewModel> jbe = um
2866 .unmarshal(streamReader, JalviewModel.class);
2867 JalviewModel object = jbe.getValue();
2869 if (true) // !skipViewport(object))
2871 _af = loadFromObject(object, file, true, jprovider);
2872 if (_af != null && object.getViewport().size() > 0)
2873 // getJalviewModelSequence().getViewportCount() > 0)
2877 // store a reference to the first view
2880 if (_af.getViewport().isGatherViewsHere())
2882 // if this is a gathered view, keep its reference since
2883 // after gathering views, only this frame will remain
2885 gatherToThisFrame.put(_af.getViewport().getSequenceSetId(),
2888 // Save dataset to register mappings once all resolved
2889 importedDatasets.put(
2890 af.getViewport().getAlignment().getDataset(),
2891 af.getViewport().getAlignment().getDataset());
2896 else if (jarentry != null)
2898 // Some other file here.
2901 } while (jarentry != null);
2902 resolveFrefedSequences();
2903 } catch (IOException ex)
2905 ex.printStackTrace();
2906 errorMessage = "Couldn't locate Jalview XML file : " + file;
2908 "Exception whilst loading jalview XML file : " + ex + "\n");
2909 } catch (Exception ex)
2911 System.err.println("Parsing as Jalview Version 2 file failed.");
2912 ex.printStackTrace(System.err);
2913 if (attemptversion1parse)
2915 // used to attempt to parse as V1 castor-generated xml
2917 if (Desktop.getInstance() != null)
2919 Desktop.getInstance().stopLoading();
2923 System.out.println("Successfully loaded archive file");
2926 ex.printStackTrace();
2929 "Exception whilst loading jalview XML file : " + ex + "\n");
2930 } catch (OutOfMemoryError e)
2932 // Don't use the OOM Window here
2933 errorMessage = "Out of memory loading jalview XML file";
2934 System.err.println("Out of memory whilst loading jalview XML file");
2935 e.printStackTrace();
2939 * Regather multiple views (with the same sequence set id) to the frame (if
2940 * any) that is flagged as the one to gather to, i.e. convert them to tabbed
2941 * views instead of separate frames. Note this doesn't restore a state where
2942 * some expanded views in turn have tabbed views - the last "first tab" read
2943 * in will play the role of gatherer for all.
2945 for (AlignFrame fr : gatherToThisFrame.values())
2947 Desktop.getInstance().gatherViews(fr);
2950 restoreSplitFrames();
2951 for (AlignmentI ds : importedDatasets.keySet())
2953 if (ds.getCodonFrames() != null)
2955 Desktop.getStructureSelectionManager()
2956 .registerMappings(ds.getCodonFrames());
2959 if (errorMessage != null)
2964 if (Desktop.getInstance() != null)
2966 Desktop.getInstance().stopLoading();
2973 * Try to reconstruct and display SplitFrame windows, where each contains
2974 * complementary dna and protein alignments. Done by pairing up AlignFrame
2975 * objects (created earlier) which have complementary viewport ids associated.
2977 protected void restoreSplitFrames()
2979 List<SplitFrame> gatherTo = new ArrayList<>();
2980 List<AlignFrame> addedToSplitFrames = new ArrayList<>();
2981 Map<String, AlignFrame> dna = new HashMap<>();
2984 * Identify the DNA alignments
2986 for (Entry<Viewport, AlignFrame> candidate : splitFrameCandidates
2989 AlignFrame af = candidate.getValue();
2990 if (af.getViewport().getAlignment().isNucleotide())
2992 dna.put(candidate.getKey().getId(), af);
2997 * Try to match up the protein complements
2999 for (Entry<Viewport, AlignFrame> candidate : splitFrameCandidates
3002 AlignFrame af = candidate.getValue();
3003 if (!af.getViewport().getAlignment().isNucleotide())
3005 String complementId = candidate.getKey().getComplementId();
3006 // only non-null complements should be in the Map
3007 if (complementId != null && dna.containsKey(complementId))
3009 final AlignFrame dnaFrame = dna.get(complementId);
3010 SplitFrame sf = createSplitFrame(dnaFrame, af);
3011 addedToSplitFrames.add(dnaFrame);
3012 addedToSplitFrames.add(af);
3013 dnaFrame.setMenusForViewport();
3014 af.setMenusForViewport();
3015 if (af.getViewport().isGatherViewsHere())
3024 * Open any that we failed to pair up (which shouldn't happen!) as
3025 * standalone AlignFrame's.
3027 for (Entry<Viewport, AlignFrame> candidate : splitFrameCandidates
3030 AlignFrame af = candidate.getValue();
3031 if (!addedToSplitFrames.contains(af))
3033 Viewport view = candidate.getKey();
3034 Desktop.addInternalFrame(af, view.getTitle(),
3035 safeInt(view.getWidth()), safeInt(view.getHeight()));
3036 af.setMenusForViewport();
3037 System.err.println("Failed to restore view " + view.getTitle()
3038 + " to split frame");
3043 * Gather back into tabbed views as flagged.
3045 for (SplitFrame sf : gatherTo)
3047 Desktop.getInstance().gatherViews(sf);
3050 splitFrameCandidates.clear();
3054 * Construct and display one SplitFrame holding DNA and protein alignments.
3057 * @param proteinFrame
3060 protected SplitFrame createSplitFrame(AlignFrame dnaFrame,
3061 AlignFrame proteinFrame)
3063 SplitFrame splitFrame = new SplitFrame(dnaFrame, proteinFrame);
3064 String title = MessageManager.getString("label.linked_view_title");
3065 int width = (int) dnaFrame.getBounds().getWidth();
3066 int height = (int) (dnaFrame.getBounds().getHeight()
3067 + proteinFrame.getBounds().getHeight() + 50);
3070 * SplitFrame location is saved to both enclosed frames
3072 splitFrame.setLocation(dnaFrame.getX(), dnaFrame.getY());
3073 Desktop.addInternalFrame(splitFrame, title, width, height);
3076 * And compute cDNA consensus (couldn't do earlier with consensus as
3077 * mappings were not yet present)
3079 proteinFrame.getViewport().alignmentChanged(proteinFrame.alignPanel);
3085 * check errorMessage for a valid error message and raise an error box in the
3086 * GUI or write the current errorMessage to stderr and then clear the error
3089 protected void reportErrors()
3091 reportErrors(false);
3094 protected void reportErrors(final boolean saving)
3096 if (errorMessage != null)
3098 final String finalErrorMessage = errorMessage;
3101 javax.swing.SwingUtilities.invokeLater(new Runnable()
3106 JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(),
3108 "Error " + (saving ? "saving" : "loading")
3110 JvOptionPane.WARNING_MESSAGE);
3116 System.err.println("Problem loading Jalview file: " + errorMessage);
3119 errorMessage = null;
3122 Map<String, String> alreadyLoadedPDB = new HashMap<>();
3125 * when set, local views will be updated from view stored in JalviewXML
3126 * Currently (28th Sep 2008) things will go horribly wrong in vamsas document
3127 * sync if this is set to true.
3129 private final boolean updateLocalViews = false;
3132 * Returns the path to a temporary file holding the PDB file for the given PDB
3133 * id. The first time of asking, searches for a file of that name in the
3134 * Jalview project jar, and copies it to a new temporary file. Any repeat
3135 * requests just return the path to the file previously created.
3141 String loadPDBFile(jarInputStreamProvider jprovider, String pdbId,
3144 if (alreadyLoadedPDB.containsKey(pdbId))
3146 return alreadyLoadedPDB.get(pdbId).toString();
3149 String tempFile = copyJarEntry(jprovider, pdbId, "jalview_pdb",
3151 if (tempFile != null)
3153 alreadyLoadedPDB.put(pdbId, tempFile);
3159 * Copies the jar entry of given name to a new temporary file and returns the
3160 * path to the file, or null if the entry is not found.
3163 * @param jarEntryName
3165 * a prefix for the temporary file name, must be at least three
3168 * null or original file - so new file can be given the same suffix
3172 protected String copyJarEntry(jarInputStreamProvider jprovider,
3173 String jarEntryName, String prefix, String origFile)
3175 BufferedReader in = null;
3176 PrintWriter out = null;
3177 String suffix = ".tmp";
3178 if (origFile == null)
3180 origFile = jarEntryName;
3182 int sfpos = origFile.lastIndexOf(".");
3183 if (sfpos > -1 && sfpos < (origFile.length() - 3))
3185 suffix = "." + origFile.substring(sfpos + 1);
3189 JarInputStream jin = jprovider.getJarInputStream();
3191 * if (jprovider.startsWith("http://")) { jin = new JarInputStream(new
3192 * URL(jprovider).openStream()); } else { jin = new JarInputStream(new
3193 * FileInputStream(jprovider)); }
3196 JarEntry entry = null;
3199 entry = jin.getNextJarEntry();
3200 } while (entry != null && !entry.getName().equals(jarEntryName));
3203 in = new BufferedReader(new InputStreamReader(jin, UTF_8));
3204 File outFile = File.createTempFile(prefix, suffix);
3205 outFile.deleteOnExit();
3206 out = new PrintWriter(new FileOutputStream(outFile));
3209 while ((data = in.readLine()) != null)
3214 String t = outFile.getAbsolutePath();
3219 warn("Couldn't find entry in Jalview Jar for " + jarEntryName);
3221 } catch (Exception ex)
3223 ex.printStackTrace();
3231 } catch (IOException e)
3245 private class JvAnnotRow
3247 public JvAnnotRow(int i, AlignmentAnnotation jaa)
3254 * persisted version of annotation row from which to take vis properties
3256 public jalview.datamodel.AlignmentAnnotation template;
3259 * original position of the annotation row in the alignment
3265 * Load alignment frame from jalview XML DOM object
3267 * @param jalviewModel
3270 * filename source string
3271 * @param loadTreesAndStructures
3272 * when false only create Viewport
3274 * data source provider
3275 * @return alignment frame created from view stored in DOM
3277 AlignFrame loadFromObject(JalviewModel jalviewModel, String file,
3278 boolean loadTreesAndStructures, jarInputStreamProvider jprovider)
3280 SequenceSet vamsasSet = jalviewModel.getVamsasModel().getSequenceSet().get(0);
3281 List<Sequence> vamsasSeqs = vamsasSet.getSequence();
3283 // JalviewModelSequence jms = object.getJalviewModelSequence();
3285 // Viewport view = (jms.getViewportCount() > 0) ? jms.getViewport(0)
3287 Viewport view = (jalviewModel.getViewport().size() > 0)
3288 ? jalviewModel.getViewport().get(0)
3291 // ////////////////////////////////
3292 // INITIALISE ALIGNMENT SEQUENCESETID AND VIEWID
3295 // If we just load in the same jar file again, the sequenceSetId
3296 // will be the same, and we end up with multiple references
3297 // to the same sequenceSet. We must modify this id on load
3298 // so that each load of the file gives a unique id
3301 * used to resolve correct alignment dataset for alignments with multiple
3304 String uniqueSeqSetId = null;
3305 String viewId = null;
3308 uniqueSeqSetId = view.getSequenceSetId() + uniqueSetSuffix;
3309 viewId = (view.getId() == null ? null
3310 : view.getId() + uniqueSetSuffix);
3313 // ////////////////////////////////
3316 List<SequenceI> hiddenSeqs = null;
3318 List<SequenceI> tmpseqs = new ArrayList<>();
3320 boolean multipleView = false;
3321 SequenceI referenceseqForView = null;
3322 // JSeq[] jseqs = object.getJalviewModelSequence().getJSeq();
3323 List<JSeq> jseqs = jalviewModel.getJSeq();
3324 int vi = 0; // counter in vamsasSeq array
3325 for (int i = 0; i < jseqs.size(); i++)
3327 JSeq jseq = jseqs.get(i);
3328 String seqId = jseq.getId();
3330 SequenceI tmpSeq = seqRefIds.get(seqId);
3333 if (!incompleteSeqs.containsKey(seqId))
3335 // may not need this check, but keep it for at least 2.9,1 release
3336 if (tmpSeq.getStart() != jseq.getStart()
3337 || tmpSeq.getEnd() != jseq.getEnd())
3340 "Warning JAL-2154 regression: updating start/end for sequence "
3341 + tmpSeq.toString() + " to " + jseq);
3346 incompleteSeqs.remove(seqId);
3348 if (vamsasSeqs.size() > vi
3349 && vamsasSeqs.get(vi).getId().equals(seqId))
3351 // most likely we are reading a dataset XML document so
3352 // update from vamsasSeq section of XML for this sequence
3353 tmpSeq.setName(vamsasSeqs.get(vi).getName());
3354 tmpSeq.setDescription(vamsasSeqs.get(vi).getDescription());
3355 tmpSeq.setSequence(vamsasSeqs.get(vi).getSequence());
3360 // reading multiple views, so vamsasSeq set is a subset of JSeq
3361 multipleView = true;
3363 tmpSeq.setStart(jseq.getStart());
3364 tmpSeq.setEnd(jseq.getEnd());
3365 tmpseqs.add(tmpSeq);
3369 Sequence vamsasSeq = vamsasSeqs.get(vi);
3370 tmpSeq = new jalview.datamodel.Sequence(vamsasSeq.getName(),
3371 vamsasSeq.getSequence());
3372 tmpSeq.setDescription(vamsasSeq.getDescription());
3373 tmpSeq.setStart(jseq.getStart());
3374 tmpSeq.setEnd(jseq.getEnd());
3375 tmpSeq.setVamsasId(uniqueSetSuffix + seqId);
3376 seqRefIds.put(vamsasSeq.getId(), tmpSeq);
3377 tmpseqs.add(tmpSeq);
3381 if (safeBoolean(jseq.isViewreference()))
3383 referenceseqForView = tmpseqs.get(tmpseqs.size() - 1);
3386 if (jseq.isHidden() != null && jseq.isHidden().booleanValue())
3388 if (hiddenSeqs == null)
3390 hiddenSeqs = new ArrayList<>();
3393 hiddenSeqs.add(tmpSeq);
3398 // Create the alignment object from the sequence set
3399 // ///////////////////////////////
3400 SequenceI[] orderedSeqs = tmpseqs
3401 .toArray(new SequenceI[tmpseqs.size()]);
3403 AlignmentI al = null;
3404 // so we must create or recover the dataset alignment before going further
3405 // ///////////////////////////////
3406 if (vamsasSet.getDatasetId() == null || vamsasSet.getDatasetId() == "")
3408 // older jalview projects do not have a dataset - so creat alignment and
3410 al = new Alignment(orderedSeqs);
3411 al.setDataset(null);
3415 boolean isdsal = jalviewModel.getViewport().isEmpty();
3418 // we are importing a dataset record, so
3419 // recover reference to an alignment already materialsed as dataset
3420 al = getDatasetFor(vamsasSet.getDatasetId());
3424 // materialse the alignment
3425 al = new Alignment(orderedSeqs);
3429 addDatasetRef(vamsasSet.getDatasetId(), al);
3432 // finally, verify all data in vamsasSet is actually present in al
3433 // passing on flag indicating if it is actually a stored dataset
3434 recoverDatasetFor(vamsasSet, al, isdsal, uniqueSeqSetId);
3437 if (referenceseqForView != null)
3439 al.setSeqrep(referenceseqForView);
3441 // / Add the alignment properties
3442 for (int i = 0; i < vamsasSet.getSequenceSetProperties().size(); i++)
3444 SequenceSetProperties ssp = vamsasSet.getSequenceSetProperties()
3446 al.setProperty(ssp.getKey(), ssp.getValue());
3449 // ///////////////////////////////
3451 Hashtable pdbloaded = new Hashtable(); // TODO nothing writes to this??
3454 // load sequence features, database references and any associated PDB
3455 // structures for the alignment
3457 // prior to 2.10, this part would only be executed the first time a
3458 // sequence was encountered, but not afterwards.
3459 // now, for 2.10 projects, this is also done if the xml doc includes
3460 // dataset sequences not actually present in any particular view.
3462 for (int i = 0; i < vamsasSeqs.size(); i++)
3464 JSeq jseq = jseqs.get(i);
3465 if (jseq.getFeatures().size() > 0)
3467 List<Feature> features = jseq.getFeatures();
3468 for (int f = 0; f < features.size(); f++)
3470 Feature feat = features.get(f);
3471 SequenceFeature sf = new SequenceFeature(feat.getType(),
3472 feat.getDescription(), feat.getBegin(), feat.getEnd(),
3473 safeFloat(feat.getScore()), feat.getFeatureGroup());
3474 sf.setStatus(feat.getStatus());
3477 * load any feature attributes - include map-valued attributes
3479 Map<String, Map<String, String>> mapAttributes = new HashMap<>();
3480 for (int od = 0; od < feat.getOtherData().size(); od++)
3482 OtherData keyValue = feat.getOtherData().get(od);
3483 String attributeName = keyValue.getKey();
3484 String attributeValue = keyValue.getValue();
3485 if (attributeName.startsWith("LINK"))
3487 sf.addLink(attributeValue);
3491 String subAttribute = keyValue.getKey2();
3492 if (subAttribute == null)
3494 // simple string-valued attribute
3495 sf.setValue(attributeName, attributeValue);
3499 // attribute 'key' has sub-attribute 'key2'
3500 if (!mapAttributes.containsKey(attributeName))
3502 mapAttributes.put(attributeName, new HashMap<>());
3504 mapAttributes.get(attributeName).put(subAttribute,
3509 for (Entry<String, Map<String, String>> mapAttribute : mapAttributes
3512 sf.setValue(mapAttribute.getKey(), mapAttribute.getValue());
3515 // adds feature to datasequence's feature set (since Jalview 2.10)
3516 al.getSequenceAt(i).addSequenceFeature(sf);
3519 if (vamsasSeqs.get(i).getDBRef().size() > 0)
3521 // adds dbrefs to datasequence's set (since Jalview 2.10)
3523 al.getSequenceAt(i).getDatasetSequence() == null
3524 ? al.getSequenceAt(i)
3525 : al.getSequenceAt(i).getDatasetSequence(),
3528 if (jseq.getPdbids().size() > 0)
3530 List<Pdbids> ids = jseq.getPdbids();
3531 for (int p = 0; p < ids.size(); p++)
3533 Pdbids pdbid = ids.get(p);
3534 jalview.datamodel.PDBEntry entry = new jalview.datamodel.PDBEntry();
3535 entry.setId(pdbid.getId());
3536 if (pdbid.getType() != null)
3538 if (PDBEntry.Type.getType(pdbid.getType()) != null)
3540 entry.setType(PDBEntry.Type.getType(pdbid.getType()));
3544 entry.setType(PDBEntry.Type.FILE);
3547 // jprovider is null when executing 'New View'
3548 if (pdbid.getFile() != null && jprovider != null)
3550 if (!pdbloaded.containsKey(pdbid.getFile()))
3552 entry.setFile(loadPDBFile(jprovider, pdbid.getId(),
3557 entry.setFile(pdbloaded.get(pdbid.getId()).toString());
3561 if (pdbid.getPdbentryItem() != null)
3563 for (PdbentryItem item : pdbid.getPdbentryItem())
3565 for (Property pr : item.getProperty())
3567 entry.setProperty(pr.getName(), pr.getValue());
3572 for (Property prop : pdbid.getProperty())
3574 entry.setProperty(prop.getName(), prop.getValue());
3576 Desktop.getStructureSelectionManager().registerPDBEntry(entry);
3577 // adds PDBEntry to datasequence's set (since Jalview 2.10)
3578 if (al.getSequenceAt(i).getDatasetSequence() != null)
3580 al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
3584 al.getSequenceAt(i).addPDBId(entry);
3589 } // end !multipleview
3591 // ///////////////////////////////
3592 // LOAD SEQUENCE MAPPINGS
3594 if (vamsasSet.getAlcodonFrame().size() > 0)
3596 // TODO Potentially this should only be done once for all views of an
3598 List<AlcodonFrame> alc = vamsasSet.getAlcodonFrame();
3599 for (int i = 0; i < alc.size(); i++)
3601 AlignedCodonFrame cf = new AlignedCodonFrame();
3602 if (alc.get(i).getAlcodMap().size() > 0)
3604 List<AlcodMap> maps = alc.get(i).getAlcodMap();
3605 for (int m = 0; m < maps.size(); m++)
3607 AlcodMap map = maps.get(m);
3608 SequenceI dnaseq = seqRefIds.get(map.getDnasq());
3610 jalview.datamodel.Mapping mapping = null;
3611 // attach to dna sequence reference.
3612 if (map.getMapping() != null)
3614 mapping = addMapping(map.getMapping());
3615 if (dnaseq != null && mapping.getTo() != null)
3617 cf.addMap(dnaseq, mapping.getTo(), mapping.getMap());
3623 newAlcodMapRef(map.getDnasq(), cf, mapping));
3627 al.addCodonFrame(cf);
3632 // ////////////////////////////////
3634 List<JvAnnotRow> autoAlan = new ArrayList<>();
3637 * store any annotations which forward reference a group's ID
3639 Map<String, List<AlignmentAnnotation>> groupAnnotRefs = new Hashtable<>();
3641 if (vamsasSet.getAnnotation().size()/*Count()*/ > 0)
3643 List<Annotation> an = vamsasSet.getAnnotation();
3645 for (int i = 0; i < an.size(); i++)
3647 Annotation annotation = an.get(i);
3650 * test if annotation is automatically calculated for this view only
3652 boolean autoForView = false;
3653 if (annotation.getLabel().equals("Quality")
3654 || annotation.getLabel().equals("Conservation")
3655 || annotation.getLabel().equals("Consensus"))
3657 // Kludge for pre 2.5 projects which lacked the autocalculated flag
3659 // JAXB has no has() test; schema defaults value to false
3660 // if (!annotation.hasAutoCalculated())
3662 // annotation.setAutoCalculated(true);
3665 if (autoForView || annotation.isAutoCalculated())
3667 // remove ID - we don't recover annotation from other views for
3668 // view-specific annotation
3669 annotation.setId(null);
3672 // set visibility for other annotation in this view
3673 String annotationId = annotation.getId();
3674 if (annotationId != null && annotationIds.containsKey(annotationId))
3676 AlignmentAnnotation jda = annotationIds.get(annotationId);
3677 // in principle Visible should always be true for annotation displayed
3678 // in multiple views
3679 if (annotation.isVisible() != null)
3681 jda.visible = annotation.isVisible();
3684 al.addAnnotation(jda);
3688 // Construct new annotation from model.
3689 List<AnnotationElement> ae = annotation.getAnnotationElement();
3690 jalview.datamodel.Annotation[] anot = null;
3691 java.awt.Color firstColour = null;
3693 if (!annotation.isScoreOnly())
3695 anot = new jalview.datamodel.Annotation[al.getWidth()];
3696 for (int aa = 0; aa < ae.size() && aa < anot.length; aa++)
3698 AnnotationElement annElement = ae.get(aa);
3699 anpos = annElement.getPosition();
3701 if (anpos >= anot.length)
3706 float value = safeFloat(annElement.getValue());
3707 anot[anpos] = new jalview.datamodel.Annotation(
3708 annElement.getDisplayCharacter(),
3709 annElement.getDescription(),
3710 (annElement.getSecondaryStructure() == null
3711 || annElement.getSecondaryStructure()
3715 .getSecondaryStructure()
3718 anot[anpos].colour = new Color(safeInt(annElement.getColour()));
3719 if (firstColour == null)
3721 firstColour = anot[anpos].colour;
3725 jalview.datamodel.AlignmentAnnotation jaa = null;
3727 if (annotation.isGraph())
3729 float llim = 0, hlim = 0;
3730 // if (autoForView || an[i].isAutoCalculated()) {
3733 jaa = new jalview.datamodel.AlignmentAnnotation(
3734 annotation.getLabel(), annotation.getDescription(), anot,
3735 llim, hlim, safeInt(annotation.getGraphType()));
3737 jaa.graphGroup = safeInt(annotation.getGraphGroup());
3738 jaa._linecolour = firstColour;
3739 if (annotation.getThresholdLine() != null)
3741 jaa.setThreshold(new jalview.datamodel.GraphLine(
3742 safeFloat(annotation.getThresholdLine().getValue()),
3743 annotation.getThresholdLine().getLabel(),
3744 new java.awt.Color(safeInt(
3745 annotation.getThresholdLine().getColour()))));
3747 if (autoForView || annotation.isAutoCalculated())
3749 // Hardwire the symbol display line to ensure that labels for
3750 // histograms are displayed
3756 jaa = new jalview.datamodel.AlignmentAnnotation(
3757 annotation.getLabel(), annotation.getDescription(), anot);
3758 jaa._linecolour = firstColour;
3760 // register new annotation
3761 if (annotation.getId() != null)
3763 annotationIds.put(annotation.getId(), jaa);
3764 jaa.annotationId = annotation.getId();
3766 // recover sequence association
3767 String sequenceRef = annotation.getSequenceRef();
3768 if (sequenceRef != null)
3770 // from 2.9 sequenceRef is to sequence id (JAL-1781)
3771 SequenceI sequence = seqRefIds.get(sequenceRef);
3772 if (sequence == null)
3774 // in pre-2.9 projects sequence ref is to sequence name
3775 sequence = al.findName(sequenceRef);
3777 if (sequence != null)
3779 jaa.createSequenceMapping(sequence, 1, true);
3780 sequence.addAlignmentAnnotation(jaa);
3783 // and make a note of any group association
3784 if (annotation.getGroupRef() != null
3785 && annotation.getGroupRef().length() > 0)
3787 List<jalview.datamodel.AlignmentAnnotation> aal = groupAnnotRefs
3788 .get(annotation.getGroupRef());
3791 aal = new ArrayList<>();
3792 groupAnnotRefs.put(annotation.getGroupRef(), aal);
3797 if (annotation.getScore() != null)
3799 jaa.setScore(annotation.getScore().doubleValue());
3801 if (annotation.isVisible() != null)
3803 jaa.visible = annotation.isVisible().booleanValue();
3806 if (annotation.isCentreColLabels() != null)
3808 jaa.centreColLabels = annotation.isCentreColLabels()
3812 if (annotation.isScaleColLabels() != null)
3814 jaa.scaleColLabel = annotation.isScaleColLabels().booleanValue();
3816 if (annotation.isAutoCalculated())
3818 // newer files have an 'autoCalculated' flag and store calculation
3819 // state in viewport properties
3820 jaa.autoCalculated = true; // means annotation will be marked for
3821 // update at end of load.
3823 if (annotation.getGraphHeight() != null)
3825 jaa.graphHeight = annotation.getGraphHeight().intValue();
3827 jaa.belowAlignment = annotation.isBelowAlignment();
3828 jaa.setCalcId(annotation.getCalcId());
3829 if (annotation.getProperty().size() > 0)
3831 for (Annotation.Property prop : annotation
3834 jaa.setProperty(prop.getName(), prop.getValue());
3837 if (jaa.autoCalculated)
3839 autoAlan.add(new JvAnnotRow(i, jaa));
3842 // if (!autoForView)
3844 // add autocalculated group annotation and any user created annotation
3846 al.addAnnotation(jaa);
3850 // ///////////////////////
3852 // Create alignment markup and styles for this view
3853 if (jalviewModel.getJGroup().size() > 0)
3855 List<JGroup> groups = jalviewModel.getJGroup();
3856 boolean addAnnotSchemeGroup = false;
3857 for (int i = 0; i < groups.size(); i++)
3859 JGroup jGroup = groups.get(i);
3860 ColourSchemeI cs = null;
3861 if (jGroup.getColour() != null)
3863 if (jGroup.getColour().startsWith("ucs"))
3865 cs = getUserColourScheme(jalviewModel, jGroup.getColour());
3867 else if (jGroup.getColour().equals("AnnotationColourGradient")
3868 && jGroup.getAnnotationColours() != null)
3870 addAnnotSchemeGroup = true;
3874 cs = ColourSchemeProperty.getColourScheme(null, al,
3875 jGroup.getColour());
3878 int pidThreshold = safeInt(jGroup.getPidThreshold());
3880 Vector<SequenceI> seqs = new Vector<>();
3882 for (int s = 0; s < jGroup.getSeq().size(); s++)
3884 String seqId = jGroup.getSeq().get(s);
3885 SequenceI ts = seqRefIds.get(seqId);
3889 seqs.addElement(ts);
3893 if (seqs.size() < 1)
3898 SequenceGroup sg = new SequenceGroup(seqs, jGroup.getName(), cs,
3899 safeBoolean(jGroup.isDisplayBoxes()),
3900 safeBoolean(jGroup.isDisplayText()),
3901 safeBoolean(jGroup.isColourText()),
3902 safeInt(jGroup.getStart()), safeInt(jGroup.getEnd()));
3903 sg.getGroupColourScheme().setThreshold(pidThreshold, true);
3904 sg.getGroupColourScheme()
3905 .setConservationInc(safeInt(jGroup.getConsThreshold()));
3906 sg.setOutlineColour(new Color(safeInt(jGroup.getOutlineColour())));
3908 sg.textColour = new Color(safeInt(jGroup.getTextCol1()));
3909 sg.textColour2 = new Color(safeInt(jGroup.getTextCol2()));
3910 sg.setShowNonconserved(safeBoolean(jGroup.isShowUnconserved()));
3911 sg.thresholdTextColour = safeInt(jGroup.getTextColThreshold());
3912 // attributes with a default in the schema are never null
3913 sg.setShowConsensusHistogram(jGroup.isShowConsensusHistogram());
3914 sg.setshowSequenceLogo(jGroup.isShowSequenceLogo());
3915 sg.setNormaliseSequenceLogo(jGroup.isNormaliseSequenceLogo());
3916 sg.setIgnoreGapsConsensus(jGroup.isIgnoreGapsinConsensus());
3917 if (jGroup.getConsThreshold() != null
3918 && jGroup.getConsThreshold().intValue() != 0)
3920 Conservation c = new Conservation("All", sg.getSequences(null), 0,
3923 c.verdict(false, 25);
3924 sg.cs.setConservation(c);
3927 if (jGroup.getId() != null && groupAnnotRefs.size() > 0)
3929 // re-instate unique group/annotation row reference
3930 List<AlignmentAnnotation> jaal = groupAnnotRefs
3931 .get(jGroup.getId());
3934 for (AlignmentAnnotation jaa : jaal)
3937 if (jaa.autoCalculated)
3939 // match up and try to set group autocalc alignment row for this
3941 if (jaa.label.startsWith("Consensus for "))
3943 sg.setConsensus(jaa);
3945 // match up and try to set group autocalc alignment row for this
3947 if (jaa.label.startsWith("Conservation for "))
3949 sg.setConservationRow(jaa);
3956 if (addAnnotSchemeGroup)
3958 // reconstruct the annotation colourscheme
3959 sg.setColourScheme(constructAnnotationColour(
3960 jGroup.getAnnotationColours(), null, al, jalviewModel, false));
3966 // only dataset in this model, so just return.
3969 // ///////////////////////////////
3972 AlignFrame af = null;
3973 AlignViewport av = null;
3974 // now check to see if we really need to create a new viewport.
3975 if (multipleView && viewportsAdded.size() == 0)
3977 // We recovered an alignment for which a viewport already exists.
3978 // TODO: fix up any settings necessary for overlaying stored state onto
3979 // state recovered from another document. (may not be necessary).
3980 // we may need a binding from a viewport in memory to one recovered from
3982 // and then recover its containing af to allow the settings to be applied.
3983 // TODO: fix for vamsas demo
3985 "About to recover a viewport for existing alignment: Sequence set ID is "
3987 Object seqsetobj = retrieveExistingObj(uniqueSeqSetId);
3988 if (seqsetobj != null)
3990 if (seqsetobj instanceof String)
3992 uniqueSeqSetId = (String) seqsetobj;
3994 "Recovered extant sequence set ID mapping for ID : New Sequence set ID is "
4000 "Warning : Collision between sequence set ID string and existing jalview object mapping.");
4006 * indicate that annotation colours are applied across all groups (pre
4007 * Jalview 2.8.1 behaviour)
4009 boolean doGroupAnnColour = Jalview2XML.isVersionStringLaterThan("2.8.1",
4010 jalviewModel.getVersion());
4012 AlignmentPanel ap = null;
4013 boolean isnewview = true;
4016 // Check to see if this alignment already has a view id == viewId
4017 jalview.gui.AlignmentPanel views[] = Desktop
4018 .getAlignmentPanels(uniqueSeqSetId);
4019 if (views != null && views.length > 0)
4021 for (int v = 0; v < views.length; v++)
4023 if (views[v].av.getViewId().equalsIgnoreCase(viewId))
4025 // recover the existing alignpanel, alignframe, viewport
4026 af = views[v].alignFrame;
4029 // TODO: could even skip resetting view settings if we don't want to
4030 // change the local settings from other jalview processes
4039 af = loadViewport(file, jseqs, hiddenSeqs, al, jalviewModel, view,
4040 uniqueSeqSetId, viewId, autoAlan);
4041 av = af.getViewport();
4046 * Load any trees, PDB structures and viewers
4048 * Not done if flag is false (when this method is used for New View)
4050 if (loadTreesAndStructures)
4052 loadTrees(jalviewModel, view, af, av, ap);
4053 loadPCAViewers(jalviewModel, ap);
4054 loadPDBStructures(jprovider, jseqs, af, ap);
4055 loadRnaViewers(jprovider, jseqs, ap);
4057 // and finally return.
4062 * Instantiate and link any saved RNA (Varna) viewers. The state of the Varna
4063 * panel is restored from separate jar entries, two (gapped and trimmed) per
4064 * sequence and secondary structure.
4066 * Currently each viewer shows just one sequence and structure (gapped and
4067 * trimmed), however this method is designed to support multiple sequences or
4068 * structures in viewers if wanted in future.
4074 private void loadRnaViewers(jarInputStreamProvider jprovider,
4075 List<JSeq> jseqs, AlignmentPanel ap)
4078 * scan the sequences for references to viewers; create each one the first
4079 * time it is referenced, add Rna models to existing viewers
4081 for (JSeq jseq : jseqs)
4083 for (int i = 0; i < jseq.getRnaViewer().size(); i++)
4085 RnaViewer viewer = jseq.getRnaViewer().get(i);
4086 AppVarna appVarna = findOrCreateVarnaViewer(viewer, uniqueSetSuffix,
4089 for (int j = 0; j < viewer.getSecondaryStructure().size(); j++)
4091 SecondaryStructure ss = viewer.getSecondaryStructure().get(j);
4092 SequenceI seq = seqRefIds.get(jseq.getId());
4093 AlignmentAnnotation ann = this.annotationIds
4094 .get(ss.getAnnotationId());
4097 * add the structure to the Varna display (with session state copied
4098 * from the jar to a temporary file)
4100 boolean gapped = safeBoolean(ss.isGapped());
4101 String rnaTitle = ss.getTitle();
4102 String sessionState = ss.getViewerState();
4103 String tempStateFile = copyJarEntry(jprovider, sessionState,
4105 RnaModel rna = new RnaModel(rnaTitle, ann, seq, null, gapped);
4106 appVarna.addModelSession(rna, rnaTitle, tempStateFile);
4108 appVarna.setInitialSelection(safeInt(viewer.getSelectedRna()));
4114 * Locate and return an already instantiated matching AppVarna, or create one
4118 * @param viewIdSuffix
4122 protected AppVarna findOrCreateVarnaViewer(RnaViewer viewer,
4123 String viewIdSuffix, AlignmentPanel ap)
4126 * on each load a suffix is appended to the saved viewId, to avoid conflicts
4127 * if load is repeated
4129 String postLoadId = viewer.getViewId() + viewIdSuffix;
4130 for (JInternalFrame frame : getAllFrames())
4132 if (frame instanceof AppVarna)
4134 AppVarna varna = (AppVarna) frame;
4135 if (postLoadId.equals(varna.getViewId()))
4137 // this viewer is already instantiated
4138 // could in future here add ap as another 'parent' of the
4139 // AppVarna window; currently just 1-to-many
4146 * viewer not found - make it
4148 RnaViewerModel model = new RnaViewerModel(postLoadId, viewer.getTitle(),
4149 safeInt(viewer.getXpos()), safeInt(viewer.getYpos()),
4150 safeInt(viewer.getWidth()), safeInt(viewer.getHeight()),
4151 safeInt(viewer.getDividerLocation()));
4152 AppVarna varna = new AppVarna(model, ap);
4158 * Load any saved trees
4166 protected void loadTrees(JalviewModel jm, Viewport view,
4167 AlignFrame af, AlignViewport av, AlignmentPanel ap)
4169 // TODO result of automated refactoring - are all these parameters needed?
4172 for (int t = 0; t < jm.getTree().size(); t++)
4175 Tree tree = jm.getTree().get(t);
4177 TreePanel tp = (TreePanel) retrieveExistingObj(tree.getId());
4180 tp = af.showNewickTree(new NewickFile(tree.getNewick()),
4181 tree.getTitle(), safeInt(tree.getWidth()),
4182 safeInt(tree.getHeight()), safeInt(tree.getXpos()),
4183 safeInt(tree.getYpos()));
4184 if (tree.getId() != null)
4186 // perhaps bind the tree id to something ?
4191 // update local tree attributes ?
4192 // TODO: should check if tp has been manipulated by user - if so its
4193 // settings shouldn't be modified
4194 tp.setTitle(tree.getTitle());
4195 tp.setBounds(new Rectangle(safeInt(tree.getXpos()),
4196 safeInt(tree.getYpos()), safeInt(tree.getWidth()),
4197 safeInt(tree.getHeight())));
4198 tp.setViewport(av); // af.viewport;
4199 // TODO: verify 'associate with all views' works still
4200 tp.getTreeCanvas().setViewport(av); // af.viewport;
4201 tp.getTreeCanvas().setAssociatedPanel(ap); // af.alignPanel;
4203 tp.getTreeCanvas().setApplyToAllViews(tree.isLinkToAllViews());
4206 warn("There was a problem recovering stored Newick tree: \n"
4207 + tree.getNewick());
4211 tp.fitToWindow.setState(safeBoolean(tree.isFitToWindow()));
4212 tp.fitToWindow_actionPerformed(null);
4214 if (tree.getFontName() != null)
4217 new Font(tree.getFontName(), safeInt(tree.getFontStyle()),
4218 safeInt(tree.getFontSize())));
4223 new Font(view.getFontName(), safeInt(view.getFontStyle()),
4224 safeInt(view.getFontSize())));
4227 tp.showPlaceholders(safeBoolean(tree.isMarkUnlinked()));
4228 tp.showBootstrap(safeBoolean(tree.isShowBootstrap()));
4229 tp.showDistances(safeBoolean(tree.isShowDistances()));
4231 tp.getTreeCanvas().setThreshold(safeFloat(tree.getThreshold()));
4233 if (safeBoolean(tree.isCurrentTree()))
4235 af.getViewport().setCurrentTree(tp.getTree());
4239 } catch (Exception ex)
4241 ex.printStackTrace();
4246 * Load and link any saved structure viewers.
4253 protected void loadPDBStructures(jarInputStreamProvider jprovider,
4254 List<JSeq> jseqs, AlignFrame af, AlignmentPanel ap)
4257 * Run through all PDB ids on the alignment, and collect mappings between
4258 * distinct view ids and all sequences referring to that view.
4260 Map<String, StructureViewerModel> structureViewers = new LinkedHashMap<>();
4262 for (int i = 0; i < jseqs.size(); i++)
4264 JSeq jseq = jseqs.get(i);
4265 if (jseq.getPdbids().size() > 0)
4267 List<Pdbids> ids = jseq.getPdbids();
4268 for (int p = 0; p < ids.size(); p++)
4270 Pdbids pdbid = ids.get(p);
4271 final int structureStateCount = pdbid.getStructureState().size();
4272 for (int s = 0; s < structureStateCount; s++)
4274 // check to see if we haven't already created this structure view
4275 final StructureState structureState = pdbid
4276 .getStructureState().get(s);
4277 String sviewid = (structureState.getViewId() == null) ? null
4278 : structureState.getViewId() + uniqueSetSuffix;
4279 jalview.datamodel.PDBEntry jpdb = new jalview.datamodel.PDBEntry();
4280 // Originally : pdbid.getFile()
4281 // : TODO: verify external PDB file recovery still works in normal
4282 // jalview project load
4284 loadPDBFile(jprovider, pdbid.getId(), pdbid.getFile()));
4285 jpdb.setId(pdbid.getId());
4287 int x = safeInt(structureState.getXpos());
4288 int y = safeInt(structureState.getYpos());
4289 int width = safeInt(structureState.getWidth());
4290 int height = safeInt(structureState.getHeight());
4292 // Probably don't need to do this anymore...
4293 // Desktop.getDesktop().getComponentAt(x, y);
4294 // TODO: NOW: check that this recovers the PDB file correctly.
4295 String pdbFile = loadPDBFile(jprovider, pdbid.getId(),
4297 jalview.datamodel.SequenceI seq = seqRefIds
4298 .get(jseq.getId() + "");
4299 if (sviewid == null)
4301 sviewid = "_jalview_pre2_4_" + x + "," + y + "," + width + ","
4304 if (!structureViewers.containsKey(sviewid))
4306 structureViewers.put(sviewid,
4307 new StructureViewerModel(x, y, width, height, false,
4308 false, true, structureState.getViewId(),
4309 structureState.getType()));
4310 // Legacy pre-2.7 conversion JAL-823 :
4311 // do not assume any view has to be linked for colour by
4315 // assemble String[] { pdb files }, String[] { id for each
4316 // file }, orig_fileloc, SequenceI[][] {{ seqs_file 1 }, {
4317 // seqs_file 2}, boolean[] {
4318 // linkAlignPanel,superposeWithAlignpanel}} from hash
4319 StructureViewerModel jmoldat = structureViewers.get(sviewid);
4320 jmoldat.setAlignWithPanel(jmoldat.isAlignWithPanel()
4321 || structureState.isAlignwithAlignPanel());
4324 * Default colour by linked panel to false if not specified (e.g.
4325 * for pre-2.7 projects)
4327 boolean colourWithAlignPanel = jmoldat.isColourWithAlignPanel();
4328 colourWithAlignPanel |= structureState.isColourwithAlignPanel();
4329 jmoldat.setColourWithAlignPanel(colourWithAlignPanel);
4332 * Default colour by viewer to true if not specified (e.g. for
4335 boolean colourByViewer = jmoldat.isColourByViewer();
4336 colourByViewer &= structureState.isColourByJmol();
4337 jmoldat.setColourByViewer(colourByViewer);
4339 if (jmoldat.getStateData().length() < structureState
4340 .getValue()/*Content()*/.length())
4342 jmoldat.setStateData(structureState.getValue());// Content());
4344 if (pdbid.getFile() != null)
4346 File mapkey = new File(pdbid.getFile());
4347 StructureData seqstrmaps = jmoldat.getFileData().get(mapkey);
4348 if (seqstrmaps == null)
4350 jmoldat.getFileData().put(mapkey,
4351 seqstrmaps = jmoldat.new StructureData(pdbFile,
4354 if (!seqstrmaps.getSeqList().contains(seq))
4356 seqstrmaps.getSeqList().add(seq);
4362 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");
4369 // Instantiate the associated structure views
4370 for (Entry<String, StructureViewerModel> entry : structureViewers
4375 createOrLinkStructureViewer(entry, af, ap, jprovider);
4376 } catch (Exception e)
4379 "Error loading structure viewer: " + e.getMessage());
4380 // failed - try the next one
4392 protected void createOrLinkStructureViewer(
4393 Entry<String, StructureViewerModel> viewerData, AlignFrame af,
4394 AlignmentPanel ap, jarInputStreamProvider jprovider)
4396 final StructureViewerModel stateData = viewerData.getValue();
4399 * Search for any viewer windows already open from other alignment views
4400 * that exactly match the stored structure state
4402 StructureViewerBase comp = findMatchingViewer(viewerData);
4406 linkStructureViewer(ap, comp, stateData);
4411 * From 2.9: stateData.type contains JMOL or CHIMERA, data is in jar entry
4412 * "viewer_"+stateData.viewId
4414 if (ViewerType.CHIMERA.toString().equals(stateData.getType()))
4416 createChimeraViewer(viewerData, af, jprovider);
4421 * else Jmol (if pre-2.9, stateData contains JMOL state string)
4423 createJmolViewer(viewerData, af, jprovider);
4428 * Create a new Chimera viewer.
4434 protected void createChimeraViewer(
4435 Entry<String, StructureViewerModel> viewerData, AlignFrame af,
4436 jarInputStreamProvider jprovider)
4438 StructureViewerModel data = viewerData.getValue();
4439 String chimeraSessionFile = data.getStateData();
4442 * Copy Chimera session from jar entry "viewer_"+viewId to a temporary file
4444 * NB this is the 'saved' viewId as in the project file XML, _not_ the
4445 * 'uniquified' sviewid used to reconstruct the viewer here
4447 String viewerJarEntryName = getViewerJarEntryName(data.getViewId());
4448 chimeraSessionFile = copyJarEntry(jprovider, viewerJarEntryName,
4451 Set<Entry<File, StructureData>> fileData = data.getFileData()
4453 List<PDBEntry> pdbs = new ArrayList<>();
4454 List<SequenceI[]> allseqs = new ArrayList<>();
4455 for (Entry<File, StructureData> pdb : fileData)
4457 String filePath = pdb.getValue().getFilePath();
4458 String pdbId = pdb.getValue().getPdbId();
4459 // pdbs.add(new PDBEntry(filePath, pdbId));
4460 pdbs.add(new PDBEntry(pdbId, null, PDBEntry.Type.PDB, filePath));
4461 final List<SequenceI> seqList = pdb.getValue().getSeqList();
4462 SequenceI[] seqs = seqList.toArray(new SequenceI[seqList.size()]);
4466 boolean colourByChimera = data.isColourByViewer();
4467 boolean colourBySequence = data.isColourWithAlignPanel();
4469 // TODO use StructureViewer as a factory here, see JAL-1761
4470 final PDBEntry[] pdbArray = pdbs.toArray(new PDBEntry[pdbs.size()]);
4471 final SequenceI[][] seqsArray = allseqs
4472 .toArray(new SequenceI[allseqs.size()][]);
4473 String newViewId = viewerData.getKey();
4475 ChimeraViewFrame cvf = new ChimeraViewFrame(chimeraSessionFile,
4476 af.alignPanel, pdbArray, seqsArray, colourByChimera,
4477 colourBySequence, newViewId);
4478 cvf.setSize(data.getWidth(), data.getHeight());
4479 cvf.setLocation(data.getX(), data.getY());
4483 * Create a new Jmol window. First parse the Jmol state to translate filenames
4484 * loaded into the view, and record the order in which files are shown in the
4485 * Jmol view, so we can add the sequence mappings in same order.
4491 protected void createJmolViewer(
4492 final Entry<String, StructureViewerModel> viewerData,
4493 AlignFrame af, jarInputStreamProvider jprovider)
4495 final StructureViewerModel svattrib = viewerData.getValue();
4496 String state = svattrib.getStateData();
4499 * Pre-2.9: state element value is the Jmol state string
4501 * 2.9+: @type is "JMOL", state data is in a Jar file member named "viewer_"
4504 if (ViewerType.JMOL.toString().equals(svattrib.getType()))
4506 state = readJarEntry(jprovider,
4507 getViewerJarEntryName(svattrib.getViewId()));
4510 List<String> pdbfilenames = new ArrayList<>();
4511 List<SequenceI[]> seqmaps = new ArrayList<>();
4512 List<String> pdbids = new ArrayList<>();
4513 StringBuilder newFileLoc = new StringBuilder(64);
4514 int cp = 0, ncp, ecp;
4515 Map<File, StructureData> oldFiles = svattrib.getFileData();
4516 while ((ncp = state.indexOf("load ", cp)) > -1)
4520 // look for next filename in load statement
4521 newFileLoc.append(state.substring(cp,
4522 ncp = (state.indexOf("\"", ncp + 1) + 1)));
4523 String oldfilenam = state.substring(ncp,
4524 ecp = state.indexOf("\"", ncp));
4525 // recover the new mapping data for this old filename
4526 // have to normalize filename - since Jmol and jalview do
4528 // translation differently.
4529 StructureData filedat = oldFiles.get(new File(oldfilenam));
4530 if (filedat == null)
4532 String reformatedOldFilename = oldfilenam.replaceAll("/", "\\\\");
4533 filedat = oldFiles.get(new File(reformatedOldFilename));
4535 newFileLoc.append(Platform.escapeString(filedat.getFilePath()));
4536 pdbfilenames.add(filedat.getFilePath());
4537 pdbids.add(filedat.getPdbId());
4538 seqmaps.add(filedat.getSeqList().toArray(new SequenceI[0]));
4539 newFileLoc.append("\"");
4540 cp = ecp + 1; // advance beyond last \" and set cursor so we can
4541 // look for next file statement.
4542 } while ((ncp = state.indexOf("/*file*/", cp)) > -1);
4546 // just append rest of state
4547 newFileLoc.append(state.substring(cp));
4551 System.err.print("Ignoring incomplete Jmol state for PDB ids: ");
4552 newFileLoc = new StringBuilder(state);
4553 newFileLoc.append("; load append ");
4554 for (File id : oldFiles.keySet())
4556 // add this and any other pdb files that should be present in
4558 StructureData filedat = oldFiles.get(id);
4559 newFileLoc.append(filedat.getFilePath());
4560 pdbfilenames.add(filedat.getFilePath());
4561 pdbids.add(filedat.getPdbId());
4562 seqmaps.add(filedat.getSeqList().toArray(new SequenceI[0]));
4563 newFileLoc.append(" \"");
4564 newFileLoc.append(filedat.getFilePath());
4565 newFileLoc.append("\"");
4568 newFileLoc.append(";");
4571 if (newFileLoc.length() == 0)
4575 int histbug = newFileLoc.indexOf("history = ");
4579 * change "history = [true|false];" to "history = [1|0];"
4582 int diff = histbug == -1 ? -1 : newFileLoc.indexOf(";", histbug);
4583 String val = (diff == -1) ? null
4584 : newFileLoc.substring(histbug, diff);
4585 if (val != null && val.length() >= 4)
4587 if (val.contains("e")) // eh? what can it be?
4589 if (val.trim().equals("true"))
4597 newFileLoc.replace(histbug, diff, val);
4602 final String[] pdbf = pdbfilenames
4603 .toArray(new String[pdbfilenames.size()]);
4604 final String[] id = pdbids.toArray(new String[pdbids.size()]);
4605 final SequenceI[][] sq = seqmaps
4606 .toArray(new SequenceI[seqmaps.size()][]);
4607 final String fileloc = newFileLoc.toString();
4608 final String sviewid = viewerData.getKey();
4609 final AlignFrame alf = af;
4610 final Rectangle rect = new Rectangle(svattrib.getX(), svattrib.getY(),
4611 svattrib.getWidth(), svattrib.getHeight());
4614 javax.swing.SwingUtilities.invokeAndWait(new Runnable()
4619 JalviewStructureDisplayI sview = null;
4622 sview = new StructureViewer(
4623 alf.alignPanel.getStructureSelectionManager())
4624 .createView(StructureViewer.ViewerType.JMOL,
4625 pdbf, id, sq, alf.alignPanel, svattrib,
4626 fileloc, rect, sviewid);
4627 addNewStructureViewer(sview);
4628 } catch (OutOfMemoryError ex)
4630 new OOMWarning("restoring structure view for PDB id " + id,
4631 (OutOfMemoryError) ex.getCause());
4632 if (sview != null && sview.isVisible())
4634 sview.closeViewer(false);
4635 sview.setVisible(false);
4641 } catch (InvocationTargetException ex)
4643 warn("Unexpected error when opening Jmol view.", ex);
4645 } catch (InterruptedException e)
4647 // e.printStackTrace();
4653 * Generates a name for the entry in the project jar file to hold state
4654 * information for a structure viewer
4659 protected String getViewerJarEntryName(String viewId)
4661 return VIEWER_PREFIX + viewId;
4665 * Returns any open frame that matches given structure viewer data. The match
4666 * is based on the unique viewId, or (for older project versions) the frame's
4672 protected StructureViewerBase findMatchingViewer(
4673 Entry<String, StructureViewerModel> viewerData)
4675 final String sviewid = viewerData.getKey();
4676 final StructureViewerModel svattrib = viewerData.getValue();
4677 StructureViewerBase comp = null;
4678 JInternalFrame[] frames = getAllFrames();
4679 for (JInternalFrame frame : frames)
4681 if (frame instanceof StructureViewerBase)
4684 * Post jalview 2.4 schema includes structure view id
4686 if (sviewid != null && ((StructureViewerBase) frame).getViewId()
4689 comp = (StructureViewerBase) frame;
4690 break; // break added in 2.9
4693 * Otherwise test for matching position and size of viewer frame
4695 else if (frame.getX() == svattrib.getX()
4696 && frame.getY() == svattrib.getY()
4697 && frame.getHeight() == svattrib.getHeight()
4698 && frame.getWidth() == svattrib.getWidth())
4700 comp = (StructureViewerBase) frame;
4701 // no break in faint hope of an exact match on viewId
4709 * Link an AlignmentPanel to an existing structure viewer.
4714 * @param useinViewerSuperpos
4715 * @param usetoColourbyseq
4716 * @param viewerColouring
4718 protected void linkStructureViewer(AlignmentPanel ap,
4719 StructureViewerBase viewer, StructureViewerModel stateData)
4721 // NOTE: if the jalview project is part of a shared session then
4722 // view synchronization should/could be done here.
4724 final boolean useinViewerSuperpos = stateData.isAlignWithPanel();
4725 final boolean usetoColourbyseq = stateData.isColourWithAlignPanel();
4726 final boolean viewerColouring = stateData.isColourByViewer();
4727 Map<File, StructureData> oldFiles = stateData.getFileData();
4730 * Add mapping for sequences in this view to an already open viewer
4732 final AAStructureBindingModel binding = viewer.getBinding();
4733 for (File id : oldFiles.keySet())
4735 // add this and any other pdb files that should be present in the
4737 StructureData filedat = oldFiles.get(id);
4738 String pdbFile = filedat.getFilePath();
4739 SequenceI[] seq = filedat.getSeqList().toArray(new SequenceI[0]);
4740 binding.getSsm().setMapping(seq, null, pdbFile, DataSourceType.FILE,
4742 binding.addSequenceForStructFile(pdbFile, seq);
4744 // and add the AlignmentPanel's reference to the view panel
4745 viewer.addAlignmentPanel(ap);
4746 if (useinViewerSuperpos)
4748 viewer.useAlignmentPanelForSuperposition(ap);
4752 viewer.excludeAlignmentPanelForSuperposition(ap);
4754 if (usetoColourbyseq)
4756 viewer.useAlignmentPanelForColourbyseq(ap, !viewerColouring);
4760 viewer.excludeAlignmentPanelForColourbyseq(ap);
4765 * Get all frames within the Desktop.
4769 protected JInternalFrame[] getAllFrames()
4771 JInternalFrame[] frames = null;
4772 // TODO is this necessary - is it safe - risk of hanging?
4777 frames = Desktop.getDesktopPane().getAllFrames();
4778 } catch (ArrayIndexOutOfBoundsException e)
4780 // occasional No such child exceptions are thrown here...
4784 } catch (InterruptedException f)
4788 } while (frames == null);
4793 * Answers true if 'version' is equal to or later than 'supported', where each
4794 * is formatted as major/minor versions like "2.8.3" or "2.3.4b1" for bugfix
4795 * changes. Development and test values for 'version' are leniently treated
4799 * - minimum version we are comparing against
4801 * - version of data being processsed
4804 public static boolean isVersionStringLaterThan(String supported,
4807 if (supported == null || version == null
4808 || version.equalsIgnoreCase("DEVELOPMENT BUILD")
4809 || version.equalsIgnoreCase("Test")
4810 || version.equalsIgnoreCase("AUTOMATED BUILD"))
4812 System.err.println("Assuming project file with "
4813 + (version == null ? "null" : version)
4814 + " is compatible with Jalview version " + supported);
4819 return StringUtils.compareVersions(version, supported, "b") >= 0;
4823 Vector<JalviewStructureDisplayI> newStructureViewers = null;
4825 protected void addNewStructureViewer(JalviewStructureDisplayI sview)
4827 if (newStructureViewers != null)
4829 sview.getBinding().setFinishedLoadingFromArchive(false);
4830 newStructureViewers.add(sview);
4834 protected void setLoadingFinishedForNewStructureViewers()
4836 if (newStructureViewers != null)
4838 for (JalviewStructureDisplayI sview : newStructureViewers)
4840 sview.getBinding().setFinishedLoadingFromArchive(true);
4842 newStructureViewers.clear();
4843 newStructureViewers = null;
4847 AlignFrame loadViewport(String file, List<JSeq> JSEQ,
4848 List<SequenceI> hiddenSeqs, AlignmentI al,
4849 JalviewModel jm, Viewport view, String uniqueSeqSetId,
4850 String viewId, List<JvAnnotRow> autoAlan)
4852 AlignFrame af = null;
4853 af = new AlignFrame(al, safeInt(view.getWidth()),
4854 safeInt(view.getHeight()), uniqueSeqSetId, viewId)
4858 // protected void processKeyEvent(java.awt.event.KeyEvent e) {
4859 // System.out.println("Jalview2XML AF " + e);
4860 // super.processKeyEvent(e);
4867 af.setFileName(file, FileFormat.Jalview);
4869 final AlignViewport viewport = af.getViewport();
4870 for (int i = 0; i < JSEQ.size(); i++)
4872 int colour = safeInt(JSEQ.get(i).getColour());
4873 viewport.setSequenceColour(viewport.getAlignment().getSequenceAt(i),
4879 viewport.setColourByReferenceSeq(true);
4880 viewport.setDisplayReferenceSeq(true);
4883 viewport.setGatherViewsHere(safeBoolean(view.isGatheredViews()));
4885 if (view.getSequenceSetId() != null)
4887 AlignmentViewport av = viewportsAdded.get(uniqueSeqSetId);
4889 viewport.setSequenceSetId(uniqueSeqSetId);
4892 // propagate shared settings to this new view
4893 viewport.setHistoryList(av.getHistoryList());
4894 viewport.setRedoList(av.getRedoList());
4898 viewportsAdded.put(uniqueSeqSetId, viewport);
4900 // TODO: check if this method can be called repeatedly without
4901 // side-effects if alignpanel already registered.
4902 PaintRefresher.Register(af.alignPanel, uniqueSeqSetId);
4904 // apply Hidden regions to view.
4905 if (hiddenSeqs != null)
4907 for (int s = 0; s < JSEQ.size(); s++)
4909 SequenceGroup hidden = new SequenceGroup();
4910 boolean isRepresentative = false;
4911 for (int r = 0; r < JSEQ.get(s).getHiddenSequences().size(); r++)
4913 isRepresentative = true;
4914 SequenceI sequenceToHide = al
4915 .getSequenceAt(JSEQ.get(s).getHiddenSequences().get(r));
4916 hidden.addSequence(sequenceToHide, false);
4917 // remove from hiddenSeqs list so we don't try to hide it twice
4918 hiddenSeqs.remove(sequenceToHide);
4920 if (isRepresentative)
4922 SequenceI representativeSequence = al.getSequenceAt(s);
4923 hidden.addSequence(representativeSequence, false);
4924 viewport.hideRepSequences(representativeSequence, hidden);
4928 SequenceI[] hseqs = hiddenSeqs
4929 .toArray(new SequenceI[hiddenSeqs.size()]);
4930 viewport.hideSequence(hseqs);
4933 // recover view properties and display parameters
4935 viewport.setShowAnnotation(safeBoolean(view.isShowAnnotation()));
4936 viewport.setAbovePIDThreshold(safeBoolean(view.isPidSelected()));
4937 final int pidThreshold = safeInt(view.getPidThreshold());
4938 viewport.setThreshold(pidThreshold);
4940 viewport.setColourText(safeBoolean(view.isShowColourText()));
4943 .setConservationSelected(
4944 safeBoolean(view.isConservationSelected()));
4945 viewport.setIncrement(safeInt(view.getConsThreshold()));
4946 viewport.setShowJVSuffix(safeBoolean(view.isShowFullId()));
4947 viewport.setRightAlignIds(safeBoolean(view.isRightAlignIds()));
4948 viewport.setFont(new Font(view.getFontName(),
4949 safeInt(view.getFontStyle()), safeInt(view.getFontSize())),
4951 ViewStyleI vs = viewport.getViewStyle();
4952 vs.setScaleProteinAsCdna(view.isScaleProteinAsCdna());
4953 viewport.setViewStyle(vs);
4954 // TODO: allow custom charWidth/Heights to be restored by updating them
4955 // after setting font - which means set above to false
4956 viewport.setRenderGaps(safeBoolean(view.isRenderGaps()));
4957 viewport.setWrapAlignment(safeBoolean(view.isWrapAlignment()));
4958 viewport.setShowAnnotation(safeBoolean(view.isShowAnnotation()));
4960 viewport.setShowBoxes(safeBoolean(view.isShowBoxes()));
4962 viewport.setShowText(safeBoolean(view.isShowText()));
4964 viewport.setTextColour(new Color(safeInt(view.getTextCol1())));
4965 viewport.setTextColour2(new Color(safeInt(view.getTextCol2())));
4966 viewport.setThresholdTextColour(safeInt(view.getTextColThreshold()));
4967 viewport.setShowUnconserved(view.isShowUnconserved());
4968 viewport.getRanges().setStartRes(safeInt(view.getStartRes()));
4970 if (view.getViewName() != null)
4972 viewport.setViewName(view.getViewName());
4973 af.setInitialTabVisible();
4975 af.setBounds(safeInt(view.getXpos()), safeInt(view.getYpos()),
4976 safeInt(view.getWidth()), safeInt(view.getHeight()));
4977 // startSeq set in af.alignPanel.updateLayout below
4978 af.alignPanel.updateLayout();
4979 ColourSchemeI cs = null;
4980 // apply colourschemes
4981 if (view.getBgColour() != null)
4983 if (view.getBgColour().startsWith("ucs"))
4985 cs = getUserColourScheme(jm, view.getBgColour());
4987 else if (view.getBgColour().startsWith("Annotation"))
4989 AnnotationColourScheme viewAnnColour = view.getAnnotationColours();
4990 cs = constructAnnotationColour(viewAnnColour, af, al, jm, true);
4997 cs = ColourSchemeProperty.getColourScheme(af.getViewport(), al,
4998 view.getBgColour());
5003 * turn off 'alignment colour applies to all groups'
5004 * while restoring global colour scheme
5006 viewport.setColourAppliesToAllGroups(false);
5007 viewport.setGlobalColourScheme(cs);
5008 viewport.getResidueShading().setThreshold(pidThreshold,
5009 view.isIgnoreGapsinConsensus());
5010 viewport.getResidueShading()
5011 .setConsensus(viewport.getSequenceConsensusHash());
5012 if (safeBoolean(view.isConservationSelected()) && cs != null)
5014 viewport.getResidueShading()
5015 .setConservationInc(safeInt(view.getConsThreshold()));
5017 af.changeColour(cs);
5018 viewport.setColourAppliesToAllGroups(true);
5021 .setShowSequenceFeatures(
5022 safeBoolean(view.isShowSequenceFeatures()));
5024 viewport.setCentreColumnLabels(view.isCentreColumnLabels());
5025 viewport.setIgnoreGapsConsensus(view.isIgnoreGapsinConsensus(), null);
5026 viewport.setFollowHighlight(view.isFollowHighlight());
5027 viewport.followSelection = view.isFollowSelection();
5028 viewport.setShowConsensusHistogram(view.isShowConsensusHistogram());
5029 viewport.setShowSequenceLogo(view.isShowSequenceLogo());
5030 viewport.setNormaliseSequenceLogo(view.isNormaliseSequenceLogo());
5031 viewport.setShowDBRefs(safeBoolean(view.isShowDbRefTooltip()));
5032 viewport.setShowNPFeats(safeBoolean(view.isShowNPfeatureTooltip()));
5033 viewport.setShowGroupConsensus(view.isShowGroupConsensus());
5034 viewport.setShowGroupConservation(view.isShowGroupConservation());
5036 // recover feature settings
5037 if (jm.getFeatureSettings() != null)
5039 FeatureRenderer fr = af.alignPanel.getSeqPanel().seqCanvas
5040 .getFeatureRenderer();
5041 FeaturesDisplayed fdi;
5042 viewport.setFeaturesDisplayed(fdi = new FeaturesDisplayed());
5043 String[] renderOrder = new String[jm.getFeatureSettings()
5044 .getSetting().size()];
5045 Map<String, FeatureColourI> featureColours = new Hashtable<>();
5046 Map<String, Float> featureOrder = new Hashtable<>();
5048 for (int fs = 0; fs < jm.getFeatureSettings()
5049 .getSetting().size(); fs++)
5051 Setting setting = jm.getFeatureSettings().getSetting().get(fs);
5052 String featureType = setting.getType();
5055 * restore feature filters (if any)
5057 jalview.xml.binding.jalview.FeatureMatcherSet filters = setting
5059 if (filters != null)
5061 FeatureMatcherSetI filter = Jalview2XML
5062 .parseFilter(featureType, filters);
5063 if (!filter.isEmpty())
5065 fr.setFeatureFilter(featureType, filter);
5070 * restore feature colour scheme
5072 Color maxColour = new Color(setting.getColour());
5073 if (setting.getMincolour() != null)
5076 * minColour is always set unless a simple colour
5077 * (including for colour by label though it doesn't use it)
5079 Color minColour = new Color(setting.getMincolour().intValue());
5080 Color noValueColour = minColour;
5081 NoValueColour noColour = setting.getNoValueColour();
5082 if (noColour == NoValueColour.NONE)
5084 noValueColour = null;
5086 else if (noColour == NoValueColour.MAX)
5088 noValueColour = maxColour;
5090 float min = safeFloat(safeFloat(setting.getMin()));
5091 float max = setting.getMax() == null ? 1f
5092 : setting.getMax().floatValue();
5093 FeatureColourI gc = new FeatureColour(maxColour, minColour,
5095 noValueColour, min, max);
5096 if (setting.getAttributeName().size() > 0)
5098 gc.setAttributeName(setting.getAttributeName().toArray(
5099 new String[setting.getAttributeName().size()]));
5101 if (setting.getThreshold() != null)
5103 gc.setThreshold(setting.getThreshold().floatValue());
5104 int threshstate = safeInt(setting.getThreshstate());
5105 // -1 = None, 0 = Below, 1 = Above threshold
5106 if (threshstate == 0)
5108 gc.setBelowThreshold(true);
5110 else if (threshstate == 1)
5112 gc.setAboveThreshold(true);
5115 gc.setAutoScaled(true); // default
5116 if (setting.isAutoScale() != null)
5118 gc.setAutoScaled(setting.isAutoScale());
5120 if (setting.isColourByLabel() != null)
5122 gc.setColourByLabel(setting.isColourByLabel());
5124 // and put in the feature colour table.
5125 featureColours.put(featureType, gc);
5129 featureColours.put(featureType,
5130 new FeatureColour(maxColour));
5132 renderOrder[fs] = featureType;
5133 if (setting.getOrder() != null)
5135 featureOrder.put(featureType, setting.getOrder().floatValue());
5139 featureOrder.put(featureType, new Float(
5140 fs / jm.getFeatureSettings().getSetting().size()));
5142 if (safeBoolean(setting.isDisplay()))
5144 fdi.setVisible(featureType);
5147 Map<String, Boolean> fgtable = new Hashtable<>();
5148 for (int gs = 0; gs < jm.getFeatureSettings().getGroup().size(); gs++)
5150 Group grp = jm.getFeatureSettings().getGroup().get(gs);
5151 fgtable.put(grp.getName(), new Boolean(grp.isDisplay()));
5153 // FeatureRendererSettings frs = new FeatureRendererSettings(renderOrder,
5154 // fgtable, featureColours, jms.getFeatureSettings().hasTransparency() ?
5155 // jms.getFeatureSettings().getTransparency() : 0.0, featureOrder);
5156 FeatureRendererSettings frs = new FeatureRendererSettings(renderOrder,
5157 fgtable, featureColours, 1.0f, featureOrder);
5158 fr.transferSettings(frs);
5161 if (view.getHiddenColumns().size() > 0)
5163 for (int c = 0; c < view.getHiddenColumns().size(); c++)
5165 final HiddenColumns hc = view.getHiddenColumns().get(c);
5166 viewport.hideColumns(safeInt(hc.getStart()),
5167 safeInt(hc.getEnd()) /* +1 */);
5170 if (view.getCalcIdParam() != null)
5172 for (CalcIdParam calcIdParam : view.getCalcIdParam())
5174 if (calcIdParam != null)
5176 if (recoverCalcIdParam(calcIdParam, viewport))
5181 warn("Couldn't recover parameters for "
5182 + calcIdParam.getCalcId());
5187 af.setMenusFromViewport(viewport);
5188 af.setTitle(view.getTitle());
5189 // TODO: we don't need to do this if the viewport is aready visible.
5191 * Add the AlignFrame to the desktop (it may be 'gathered' later), unless it
5192 * has a 'cdna/protein complement' view, in which case save it in order to
5193 * populate a SplitFrame once all views have been read in.
5195 String complementaryViewId = view.getComplementId();
5196 if (complementaryViewId == null)
5198 Desktop.addInternalFrame(af, view.getTitle(),
5199 safeInt(view.getWidth()), safeInt(view.getHeight()));
5200 // recompute any autoannotation
5201 af.alignPanel.updateAnnotation(false, true);
5202 reorderAutoannotation(af, al, autoAlan);
5203 af.alignPanel.alignmentChanged();
5207 splitFrameCandidates.put(view, af);
5213 * Reads saved data to restore Colour by Annotation settings
5215 * @param viewAnnColour
5219 * @param checkGroupAnnColour
5222 private ColourSchemeI constructAnnotationColour(
5223 AnnotationColourScheme viewAnnColour, AlignFrame af,
5224 AlignmentI al, JalviewModel model, boolean checkGroupAnnColour)
5226 boolean propagateAnnColour = false;
5227 AlignmentI annAlignment = af != null ? af.getViewport().getAlignment()
5229 if (checkGroupAnnColour && al.getGroups() != null
5230 && al.getGroups().size() > 0)
5232 // pre 2.8.1 behaviour
5233 // check to see if we should transfer annotation colours
5234 propagateAnnColour = true;
5235 for (SequenceGroup sg : al.getGroups())
5237 if (sg.getColourScheme() instanceof AnnotationColourGradient)
5239 propagateAnnColour = false;
5245 * 2.10.2- : saved annotationId is AlignmentAnnotation.annotationId
5247 String annotationId = viewAnnColour.getAnnotation();
5248 AlignmentAnnotation matchedAnnotation = annotationIds.get(annotationId);
5251 * pre 2.10.2: saved annotationId is AlignmentAnnotation.label
5253 if (matchedAnnotation == null
5254 && annAlignment.getAlignmentAnnotation() != null)
5256 for (int i = 0; i < annAlignment.getAlignmentAnnotation().length; i++)
5259 .equals(annAlignment.getAlignmentAnnotation()[i].label))
5261 matchedAnnotation = annAlignment.getAlignmentAnnotation()[i];
5266 if (matchedAnnotation == null)
5268 System.err.println("Failed to match annotation colour scheme for "
5272 if (matchedAnnotation.getThreshold() == null)
5274 matchedAnnotation.setThreshold(
5275 new GraphLine(safeFloat(viewAnnColour.getThreshold()),
5276 "Threshold", Color.black));
5279 AnnotationColourGradient cs = null;
5280 if (viewAnnColour.getColourScheme().equals("None"))
5282 cs = new AnnotationColourGradient(matchedAnnotation,
5283 new Color(safeInt(viewAnnColour.getMinColour())),
5284 new Color(safeInt(viewAnnColour.getMaxColour())),
5285 safeInt(viewAnnColour.getAboveThreshold()));
5287 else if (viewAnnColour.getColourScheme().startsWith("ucs"))
5289 cs = new AnnotationColourGradient(matchedAnnotation,
5290 getUserColourScheme(model, viewAnnColour.getColourScheme()),
5291 safeInt(viewAnnColour.getAboveThreshold()));
5295 cs = new AnnotationColourGradient(matchedAnnotation,
5296 ColourSchemeProperty.getColourScheme(af.getViewport(), al,
5297 viewAnnColour.getColourScheme()),
5298 safeInt(viewAnnColour.getAboveThreshold()));
5301 boolean perSequenceOnly = safeBoolean(viewAnnColour.isPerSequence());
5302 boolean useOriginalColours = safeBoolean(
5303 viewAnnColour.isPredefinedColours());
5304 cs.setSeqAssociated(perSequenceOnly);
5305 cs.setPredefinedColours(useOriginalColours);
5307 if (propagateAnnColour && al.getGroups() != null)
5309 // Also use these settings for all the groups
5310 for (int g = 0; g < al.getGroups().size(); g++)
5312 SequenceGroup sg = al.getGroups().get(g);
5313 if (sg.getGroupColourScheme() == null)
5318 AnnotationColourGradient groupScheme = new AnnotationColourGradient(
5319 matchedAnnotation, sg.getColourScheme(),
5320 safeInt(viewAnnColour.getAboveThreshold()));
5321 sg.setColourScheme(groupScheme);
5322 groupScheme.setSeqAssociated(perSequenceOnly);
5323 groupScheme.setPredefinedColours(useOriginalColours);
5329 private void reorderAutoannotation(AlignFrame af, AlignmentI al,
5330 List<JvAnnotRow> autoAlan)
5332 // copy over visualization settings for autocalculated annotation in the
5334 if (al.getAlignmentAnnotation() != null)
5337 * Kludge for magic autoannotation names (see JAL-811)
5339 String[] magicNames = new String[] { "Consensus", "Quality",
5341 JvAnnotRow nullAnnot = new JvAnnotRow(-1, null);
5342 Hashtable<String, JvAnnotRow> visan = new Hashtable<>();
5343 for (String nm : magicNames)
5345 visan.put(nm, nullAnnot);
5347 for (JvAnnotRow auan : autoAlan)
5349 visan.put(auan.template.label
5350 + (auan.template.getCalcId() == null ? ""
5351 : "\t" + auan.template.getCalcId()),
5354 int hSize = al.getAlignmentAnnotation().length;
5355 List<JvAnnotRow> reorder = new ArrayList<>();
5356 // work through any autoCalculated annotation already on the view
5357 // removing it if it should be placed in a different location on the
5358 // annotation panel.
5359 List<String> remains = new ArrayList<>(visan.keySet());
5360 for (int h = 0; h < hSize; h++)
5362 jalview.datamodel.AlignmentAnnotation jalan = al
5363 .getAlignmentAnnotation()[h];
5364 if (jalan.autoCalculated)
5367 JvAnnotRow valan = visan.get(k = jalan.label);
5368 if (jalan.getCalcId() != null)
5370 valan = visan.get(k = jalan.label + "\t" + jalan.getCalcId());
5375 // delete the auto calculated row from the alignment
5376 al.deleteAnnotation(jalan, false);
5380 if (valan != nullAnnot)
5382 if (jalan != valan.template)
5384 // newly created autoannotation row instance
5385 // so keep a reference to the visible annotation row
5386 // and copy over all relevant attributes
5387 if (valan.template.graphHeight >= 0)
5390 jalan.graphHeight = valan.template.graphHeight;
5392 jalan.visible = valan.template.visible;
5394 reorder.add(new JvAnnotRow(valan.order, jalan));
5399 // Add any (possibly stale) autocalculated rows that were not appended to
5400 // the view during construction
5401 for (String other : remains)
5403 JvAnnotRow othera = visan.get(other);
5404 if (othera != nullAnnot && othera.template.getCalcId() != null
5405 && othera.template.getCalcId().length() > 0)
5407 reorder.add(othera);
5410 // now put the automatic annotation in its correct place
5411 int s = 0, srt[] = new int[reorder.size()];
5412 JvAnnotRow[] rws = new JvAnnotRow[reorder.size()];
5413 for (JvAnnotRow jvar : reorder)
5416 srt[s++] = jvar.order;
5419 jalview.util.QuickSort.sort(srt, rws);
5420 // and re-insert the annotation at its correct position
5421 for (JvAnnotRow jvar : rws)
5423 al.addAnnotation(jvar.template, jvar.order);
5425 af.alignPanel.adjustAnnotationHeight();
5429 Hashtable skipList = null;
5432 * TODO remove this method
5435 * @return AlignFrame bound to sequenceSetId from view, if one exists. private
5436 * AlignFrame getSkippedFrame(Viewport view) { if (skipList==null) {
5437 * throw new Error("Implementation Error. No skipList defined for this
5438 * Jalview2XML instance."); } return (AlignFrame)
5439 * skipList.get(view.getSequenceSetId()); }
5443 * Check if the Jalview view contained in object should be skipped or not.
5446 * @return true if view's sequenceSetId is a key in skipList
5448 private boolean skipViewport(JalviewModel object)
5450 if (skipList == null)
5454 String id = object.getViewport().get(0).getSequenceSetId();
5455 if (skipList.containsKey(id))
5457 if (Cache.log != null && Cache.log.isDebugEnabled())
5459 Cache.log.debug("Skipping seuqence set id " + id);
5466 public void addToSkipList(AlignFrame af)
5468 if (skipList == null)
5470 skipList = new Hashtable();
5472 skipList.put(af.getViewport().getSequenceSetId(), af);
5475 public void clearSkipList()
5477 if (skipList != null)
5484 private void recoverDatasetFor(SequenceSet vamsasSet, AlignmentI al,
5485 boolean ignoreUnrefed, String uniqueSeqSetId)
5487 jalview.datamodel.AlignmentI ds = getDatasetFor(
5488 vamsasSet.getDatasetId());
5489 AlignmentI xtant_ds = ds;
5490 if (xtant_ds == null)
5492 // good chance we are about to create a new dataset, but check if we've
5493 // seen some of the dataset sequence IDs before.
5494 // TODO: skip this check if we are working with project generated by
5495 // version 2.11 or later
5496 xtant_ds = checkIfHasDataset(vamsasSet.getSequence());
5497 if (xtant_ds != null)
5500 addDatasetRef(vamsasSet.getDatasetId(), ds);
5503 Vector dseqs = null;
5506 // recovering an alignment View
5507 AlignmentI seqSetDS = getDatasetFor(UNIQSEQSETID + uniqueSeqSetId);
5508 if (seqSetDS != null)
5510 if (ds != null && ds != seqSetDS)
5512 warn("JAL-3171 regression: Overwriting a dataset reference for an alignment"
5513 + " - CDS/Protein crossreference data may be lost");
5514 if (xtant_ds != null)
5516 // This can only happen if the unique sequence set ID was bound to a
5517 // dataset that did not contain any of the sequences in the view
5518 // currently being restored.
5519 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.");
5523 addDatasetRef(vamsasSet.getDatasetId(), ds);
5528 // try even harder to restore dataset
5529 AlignmentI xtantDS = checkIfHasDataset(vamsasSet.getSequence());
5530 // create a list of new dataset sequences
5531 dseqs = new Vector();
5533 for (int i = 0, iSize = vamsasSet.getSequence().size(); i < iSize; i++)
5535 Sequence vamsasSeq = vamsasSet.getSequence().get(i);
5536 ensureJalviewDatasetSequence(vamsasSeq, ds, dseqs, ignoreUnrefed, i);
5538 // create a new dataset
5541 SequenceI[] dsseqs = new SequenceI[dseqs.size()];
5542 dseqs.copyInto(dsseqs);
5543 ds = new jalview.datamodel.Alignment(dsseqs);
5544 debug("Created new dataset " + vamsasSet.getDatasetId()
5545 + " for alignment " + System.identityHashCode(al));
5546 addDatasetRef(vamsasSet.getDatasetId(), ds);
5548 // set the dataset for the newly imported alignment.
5549 if (al.getDataset() == null && !ignoreUnrefed)
5552 // register dataset for the alignment's uniqueSeqSetId for legacy projects
5553 addDatasetRef(UNIQSEQSETID + uniqueSeqSetId, ds);
5555 updateSeqDatasetBinding(vamsasSet.getSequence(), ds);
5559 * XML dataset sequence ID to materialised dataset reference
5561 HashMap<String, AlignmentI> seqToDataset = new HashMap<>();
5564 * @return the first materialised dataset reference containing a dataset
5565 * sequence referenced in the given view
5567 * - sequences from the view
5569 AlignmentI checkIfHasDataset(List<Sequence> list)
5571 for (Sequence restoredSeq : list)
5573 AlignmentI datasetFor = seqToDataset.get(restoredSeq.getDsseqid());
5574 if (datasetFor != null)
5583 * Register ds as the containing dataset for the dataset sequences referenced
5584 * by sequences in list
5587 * - sequences in a view
5590 void updateSeqDatasetBinding(List<Sequence> list, AlignmentI ds)
5592 for (Sequence restoredSeq : list)
5594 AlignmentI prevDS = seqToDataset.put(restoredSeq.getDsseqid(), ds);
5595 if (prevDS != null && prevDS != ds)
5597 warn("Dataset sequence appears in many datasets: "
5598 + restoredSeq.getDsseqid());
5599 // TODO: try to merge!
5606 * sequence definition to create/merge dataset sequence for
5610 * vector to add new dataset sequence to
5611 * @param ignoreUnrefed
5612 * - when true, don't create new sequences from vamsasSeq if it's id
5613 * doesn't already have an asssociated Jalview sequence.
5615 * - used to reorder the sequence in the alignment according to the
5616 * vamsasSeq array ordering, to preserve ordering of dataset
5618 private void ensureJalviewDatasetSequence(Sequence vamsasSeq,
5619 AlignmentI ds, Vector dseqs, boolean ignoreUnrefed, int vseqpos)
5621 // JBP TODO: Check this is called for AlCodonFrames to support recovery of
5623 SequenceI sq = seqRefIds.get(vamsasSeq.getId());
5624 boolean reorder = false;
5625 SequenceI dsq = null;
5626 if (sq != null && sq.getDatasetSequence() != null)
5628 dsq = sq.getDatasetSequence();
5634 if (sq == null && ignoreUnrefed)
5638 String sqid = vamsasSeq.getDsseqid();
5641 // need to create or add a new dataset sequence reference to this sequence
5644 dsq = seqRefIds.get(sqid);
5649 // make a new dataset sequence
5650 dsq = sq.createDatasetSequence();
5653 // make up a new dataset reference for this sequence
5654 sqid = seqHash(dsq);
5656 dsq.setVamsasId(uniqueSetSuffix + sqid);
5657 seqRefIds.put(sqid, dsq);
5662 dseqs.addElement(dsq);
5667 ds.addSequence(dsq);
5673 { // make this dataset sequence sq's dataset sequence
5674 sq.setDatasetSequence(dsq);
5675 // and update the current dataset alignment
5680 if (!dseqs.contains(dsq))
5687 if (ds.findIndex(dsq) < 0)
5689 ds.addSequence(dsq);
5696 // TODO: refactor this as a merge dataset sequence function
5697 // now check that sq (the dataset sequence) sequence really is the union of
5698 // all references to it
5699 // boolean pre = sq.getStart() < dsq.getStart();
5700 // boolean post = sq.getEnd() > dsq.getEnd();
5704 // StringBuffer sb = new StringBuffer();
5705 String newres = jalview.analysis.AlignSeq.extractGaps(
5706 jalview.util.Comparison.GapChars, sq.getSequenceAsString());
5707 if (!newres.equalsIgnoreCase(dsq.getSequenceAsString())
5708 && newres.length() > dsq.getLength())
5710 // Update with the longer sequence.
5714 * if (pre) { sb.insert(0, newres .substring(0, dsq.getStart() -
5715 * sq.getStart())); dsq.setStart(sq.getStart()); } if (post) {
5716 * sb.append(newres.substring(newres.length() - sq.getEnd() -
5717 * dsq.getEnd())); dsq.setEnd(sq.getEnd()); }
5719 dsq.setSequence(newres);
5721 // TODO: merges will never happen if we 'know' we have the real dataset
5722 // sequence - this should be detected when id==dssid
5724 "DEBUG Notice: Merged dataset sequence (if you see this often, post at http://issues.jalview.org/browse/JAL-1474)"); // ("
5725 // + (pre ? "prepended" : "") + " "
5726 // + (post ? "appended" : ""));
5731 // sequence refs are identical. We may need to update the existing dataset
5732 // alignment with this one, though.
5733 if (ds != null && dseqs == null)
5735 int opos = ds.findIndex(dsq);
5736 SequenceI tseq = null;
5737 if (opos != -1 && vseqpos != opos)
5739 // remove from old position
5740 ds.deleteSequence(dsq);
5742 if (vseqpos < ds.getHeight())
5744 if (vseqpos != opos)
5746 // save sequence at destination position
5747 tseq = ds.getSequenceAt(vseqpos);
5748 ds.replaceSequenceAt(vseqpos, dsq);
5749 ds.addSequence(tseq);
5754 ds.addSequence(dsq);
5761 * TODO use AlignmentI here and in related methods - needs
5762 * AlignmentI.getDataset() changed to return AlignmentI instead of Alignment
5764 Hashtable<String, AlignmentI> datasetIds = null;
5766 IdentityHashMap<AlignmentI, String> dataset2Ids = null;
5768 private AlignmentI getDatasetFor(String datasetId)
5770 if (datasetIds == null)
5772 datasetIds = new Hashtable<>();
5775 if (datasetIds.containsKey(datasetId))
5777 return datasetIds.get(datasetId);
5782 private void addDatasetRef(String datasetId, AlignmentI dataset)
5784 if (datasetIds == null)
5786 datasetIds = new Hashtable<>();
5788 datasetIds.put(datasetId, dataset);
5792 * make a new dataset ID for this jalview dataset alignment
5797 private String getDatasetIdRef(AlignmentI dataset)
5799 if (dataset.getDataset() != null)
5801 warn("Serious issue! Dataset Object passed to getDatasetIdRef is not a Jalview DATASET alignment...");
5803 String datasetId = makeHashCode(dataset, null);
5804 if (datasetId == null)
5806 // make a new datasetId and record it
5807 if (dataset2Ids == null)
5809 dataset2Ids = new IdentityHashMap<>();
5813 datasetId = dataset2Ids.get(dataset);
5815 if (datasetId == null)
5817 datasetId = "ds" + dataset2Ids.size() + 1;
5818 dataset2Ids.put(dataset, datasetId);
5824 private void addDBRefs(SequenceI datasetSequence, Sequence sequence)
5826 for (int d = 0; d < sequence.getDBRef().size(); d++)
5828 DBRef dr = sequence.getDBRef().get(d);
5829 jalview.datamodel.DBRefEntry entry = new jalview.datamodel.DBRefEntry(
5830 dr.getSource(), dr.getVersion(), dr.getAccessionId());
5831 if (dr.getMapping() != null)
5833 entry.setMap(addMapping(dr.getMapping()));
5835 datasetSequence.addDBRef(entry);
5839 private jalview.datamodel.Mapping addMapping(Mapping m)
5841 SequenceI dsto = null;
5842 // Mapping m = dr.getMapping();
5843 int fr[] = new int[m.getMapListFrom().size() * 2];
5844 Iterator<MapListFrom> from = m.getMapListFrom().iterator();// enumerateMapListFrom();
5845 for (int _i = 0; from.hasNext(); _i += 2)
5847 MapListFrom mf = from.next();
5848 fr[_i] = mf.getStart();
5849 fr[_i + 1] = mf.getEnd();
5851 int fto[] = new int[m.getMapListTo().size() * 2];
5852 Iterator<MapListTo> to = m.getMapListTo().iterator();// enumerateMapListTo();
5853 for (int _i = 0; to.hasNext(); _i += 2)
5855 MapListTo mf = to.next();
5856 fto[_i] = mf.getStart();
5857 fto[_i + 1] = mf.getEnd();
5859 jalview.datamodel.Mapping jmap = new jalview.datamodel.Mapping(dsto, fr,
5860 fto, m.getMapFromUnit().intValue(),
5861 m.getMapToUnit().intValue());
5864 * (optional) choice of dseqFor or Sequence
5866 if (m.getDseqFor() != null)
5868 String dsfor = m.getDseqFor();
5869 if (seqRefIds.containsKey(dsfor))
5874 jmap.setTo(seqRefIds.get(dsfor));
5878 frefedSequence.add(newMappingRef(dsfor, jmap));
5881 else if (m.getSequence() != null)
5884 * local sequence definition
5886 Sequence ms = m.getSequence();
5887 SequenceI djs = null;
5888 String sqid = ms.getDsseqid();
5889 if (sqid != null && sqid.length() > 0)
5892 * recover dataset sequence
5894 djs = seqRefIds.get(sqid);
5899 "Warning - making up dataset sequence id for DbRef sequence map reference");
5900 sqid = ((Object) ms).toString(); // make up a new hascode for
5901 // undefined dataset sequence hash
5902 // (unlikely to happen)
5908 * make a new dataset sequence and add it to refIds hash
5910 djs = new jalview.datamodel.Sequence(ms.getName(),
5912 djs.setStart(jmap.getMap().getToLowest());
5913 djs.setEnd(jmap.getMap().getToHighest());
5914 djs.setVamsasId(uniqueSetSuffix + sqid);
5916 incompleteSeqs.put(sqid, djs);
5917 seqRefIds.put(sqid, djs);
5920 jalview.bin.Cache.log.debug("about to recurse on addDBRefs.");
5929 * Provides a 'copy' of an alignment view (on action New View) by 'saving' the
5930 * view as XML (but not to file), and then reloading it
5935 public AlignmentPanel copyAlignPanel(AlignmentPanel ap)
5938 JalviewModel jm = saveState(ap, null, null, null);
5941 jm.getVamsasModel().getSequenceSet().get(0).getDatasetId(),
5942 ap.getAlignment().getDataset());
5944 uniqueSetSuffix = "";
5945 // jm.getJalviewModelSequence().getViewport(0).setId(null);
5946 jm.getViewport().get(0).setId(null);
5947 // we don't overwrite the view we just copied
5949 if (this.frefedSequence == null)
5951 frefedSequence = new Vector<>();
5954 viewportsAdded.clear();
5956 AlignFrame af = loadFromObject(jm, null, false, null);
5957 af.getAlignPanels().clear();
5958 af.closeMenuItem_actionPerformed(true);
5961 * if(ap.av.getAlignment().getAlignmentAnnotation()!=null) { for(int i=0;
5962 * i<ap.av.getAlignment().getAlignmentAnnotation().length; i++) {
5963 * if(!ap.av.getAlignment().getAlignmentAnnotation()[i].autoCalculated) {
5964 * af.alignPanel.av.getAlignment().getAlignmentAnnotation()[i] =
5965 * ap.av.getAlignment().getAlignmentAnnotation()[i]; } } }
5968 return af.alignPanel;
5971 private Hashtable jvids2vobj;
5973 private void warn(String msg)
5978 private void warn(String msg, Exception e)
5980 if (Cache.log != null)
5984 Cache.log.warn(msg, e);
5988 Cache.log.warn(msg);
5993 System.err.println("Warning: " + msg);
5996 e.printStackTrace();
6001 private void debug(String string)
6003 debug(string, null);
6006 private void debug(String msg, Exception e)
6008 if (Cache.log != null)
6012 Cache.log.debug(msg, e);
6016 Cache.log.debug(msg);
6021 System.err.println("Warning: " + msg);
6024 e.printStackTrace();
6030 * set the object to ID mapping tables used to write/recover objects and XML
6031 * ID strings for the jalview project. If external tables are provided then
6032 * finalize and clearSeqRefs will not clear the tables when the Jalview2XML
6033 * object goes out of scope. - also populates the datasetIds hashtable with
6034 * alignment objects containing dataset sequences
6037 * Map from ID strings to jalview datamodel
6039 * Map from jalview datamodel to ID strings
6043 public void setObjectMappingTables(Hashtable vobj2jv,
6044 IdentityHashMap jv2vobj)
6046 this.jv2vobj = jv2vobj;
6047 this.vobj2jv = vobj2jv;
6048 Iterator ds = jv2vobj.keySet().iterator();
6050 while (ds.hasNext())
6052 Object jvobj = ds.next();
6053 id = jv2vobj.get(jvobj).toString();
6054 if (jvobj instanceof jalview.datamodel.Alignment)
6056 if (((jalview.datamodel.Alignment) jvobj).getDataset() == null)
6058 addDatasetRef(id, (jalview.datamodel.Alignment) jvobj);
6061 else if (jvobj instanceof jalview.datamodel.Sequence)
6063 // register sequence object so the XML parser can recover it.
6064 if (seqRefIds == null)
6066 seqRefIds = new HashMap<>();
6068 if (seqsToIds == null)
6070 seqsToIds = new IdentityHashMap<>();
6072 seqRefIds.put(jv2vobj.get(jvobj).toString(), (SequenceI) jvobj);
6073 seqsToIds.put((SequenceI) jvobj, id);
6075 else if (jvobj instanceof jalview.datamodel.AlignmentAnnotation)
6078 AlignmentAnnotation jvann = (AlignmentAnnotation) jvobj;
6079 annotationIds.put(anid = jv2vobj.get(jvobj).toString(), jvann);
6080 if (jvann.annotationId == null)
6082 jvann.annotationId = anid;
6084 if (!jvann.annotationId.equals(anid))
6086 // TODO verify that this is the correct behaviour
6087 this.warn("Overriding Annotation ID for " + anid
6088 + " from different id : " + jvann.annotationId);
6089 jvann.annotationId = anid;
6092 else if (jvobj instanceof String)
6094 if (jvids2vobj == null)
6096 jvids2vobj = new Hashtable();
6097 jvids2vobj.put(jvobj, jv2vobj.get(jvobj).toString());
6102 Cache.log.debug("Ignoring " + jvobj.getClass() + " (ID = " + id);
6108 * set the uniqueSetSuffix used to prefix/suffix object IDs for jalview
6109 * objects created from the project archive. If string is null (default for
6110 * construction) then suffix will be set automatically.
6114 public void setUniqueSetSuffix(String string)
6116 uniqueSetSuffix = string;
6121 * uses skipList2 as the skipList for skipping views on sequence sets
6122 * associated with keys in the skipList
6126 public void setSkipList(Hashtable skipList2)
6128 skipList = skipList2;
6132 * Reads the jar entry of given name and returns its contents, or null if the
6133 * entry is not found.
6136 * @param jarEntryName
6139 protected String readJarEntry(jarInputStreamProvider jprovider,
6140 String jarEntryName)
6142 String result = null;
6143 BufferedReader in = null;
6148 * Reopen the jar input stream and traverse its entries to find a matching
6151 JarInputStream jin = jprovider.getJarInputStream();
6152 JarEntry entry = null;
6155 entry = jin.getNextJarEntry();
6156 } while (entry != null && !entry.getName().equals(jarEntryName));
6160 StringBuilder out = new StringBuilder(256);
6161 in = new BufferedReader(new InputStreamReader(jin, UTF_8));
6164 while ((data = in.readLine()) != null)
6168 result = out.toString();
6172 warn("Couldn't find entry in Jalview Jar for " + jarEntryName);
6174 } catch (Exception ex)
6176 ex.printStackTrace();
6184 } catch (IOException e)
6195 * Returns an incrementing counter (0, 1, 2...)
6199 private synchronized int nextCounter()
6205 * Loads any saved PCA viewers
6210 protected void loadPCAViewers(JalviewModel model, AlignmentPanel ap)
6214 List<PcaViewer> pcaviewers = model.getPcaViewer();
6215 for (PcaViewer viewer : pcaviewers)
6217 String modelName = viewer.getScoreModelName();
6218 SimilarityParamsI params = new SimilarityParams(
6219 viewer.isIncludeGappedColumns(), viewer.isMatchGaps(),
6220 viewer.isIncludeGaps(),
6221 viewer.isDenominateByShortestLength());
6224 * create the panel (without computing the PCA)
6226 PCAPanel panel = new PCAPanel(ap, modelName, params);
6228 panel.setTitle(viewer.getTitle());
6229 panel.setBounds(new Rectangle(viewer.getXpos(), viewer.getYpos(),
6230 viewer.getWidth(), viewer.getHeight()));
6232 boolean showLabels = viewer.isShowLabels();
6233 panel.setShowLabels(showLabels);
6234 panel.getRotatableCanvas().setShowLabels(showLabels);
6235 panel.getRotatableCanvas()
6236 .setBgColour(new Color(viewer.getBgColour()));
6237 panel.getRotatableCanvas()
6238 .setApplyToAllViews(viewer.isLinkToAllViews());
6241 * load PCA output data
6243 ScoreModelI scoreModel = ScoreModels.getInstance()
6244 .getScoreModel(modelName, ap);
6245 PCA pca = new PCA(null, scoreModel, params);
6246 PcaDataType pcaData = viewer.getPcaData();
6248 MatrixI pairwise = loadDoubleMatrix(pcaData.getPairwiseMatrix());
6249 pca.setPairwiseScores(pairwise);
6251 MatrixI triDiag = loadDoubleMatrix(pcaData.getTridiagonalMatrix());
6252 pca.setTridiagonal(triDiag);
6254 MatrixI result = loadDoubleMatrix(pcaData.getEigenMatrix());
6255 pca.setEigenmatrix(result);
6257 panel.getPcaModel().setPCA(pca);
6260 * we haven't saved the input data! (JAL-2647 to do)
6262 panel.setInputData(null);
6265 * add the sequence points for the PCA display
6267 List<jalview.datamodel.SequencePoint> seqPoints = new ArrayList<>();
6268 for (SequencePoint sp : viewer.getSequencePoint())
6270 String seqId = sp.getSequenceRef();
6271 SequenceI seq = seqRefIds.get(seqId);
6274 throw new IllegalStateException(
6275 "Unmatched seqref for PCA: " + seqId);
6277 Point pt = new Point(sp.getXPos(), sp.getYPos(), sp.getZPos());
6278 jalview.datamodel.SequencePoint seqPoint = new jalview.datamodel.SequencePoint(
6280 seqPoints.add(seqPoint);
6282 panel.getRotatableCanvas().setPoints(seqPoints, seqPoints.size());
6285 * set min-max ranges and scale after setPoints (which recomputes them)
6287 panel.getRotatableCanvas().setScaleFactor(viewer.getScaleFactor());
6288 SeqPointMin spMin = viewer.getSeqPointMin();
6289 float[] min = new float[] { spMin.getXPos(), spMin.getYPos(),
6291 SeqPointMax spMax = viewer.getSeqPointMax();
6292 float[] max = new float[] { spMax.getXPos(), spMax.getYPos(),
6294 panel.getRotatableCanvas().setSeqMinMax(min, max);
6296 // todo: hold points list in PCAModel only
6297 panel.getPcaModel().setSequencePoints(seqPoints);
6299 panel.setSelectedDimensionIndex(viewer.getXDim(), X);
6300 panel.setSelectedDimensionIndex(viewer.getYDim(), Y);
6301 panel.setSelectedDimensionIndex(viewer.getZDim(), Z);
6303 // is this duplication needed?
6304 panel.setTop(seqPoints.size() - 1);
6305 panel.getPcaModel().setTop(seqPoints.size() - 1);
6308 * add the axes' end points for the display
6310 for (int i = 0; i < 3; i++)
6312 Axis axis = viewer.getAxis().get(i);
6313 panel.getRotatableCanvas().getAxisEndPoints()[i] = new Point(
6314 axis.getXPos(), axis.getYPos(), axis.getZPos());
6317 Desktop.addInternalFrame(panel, MessageManager.formatMessage(
6318 "label.calc_title", "PCA", modelName), 475, 450);
6320 } catch (Exception ex)
6322 Cache.log.error("Error loading PCA: " + ex.toString());
6327 * Populates an XML model of the feature colour scheme for one feature type
6329 * @param featureType
6333 public static Colour marshalColour(
6334 String featureType, FeatureColourI fcol)
6336 Colour col = new Colour();
6337 if (fcol.isSimpleColour())
6339 col.setRGB(Format.getHexString(fcol.getColour()));
6343 col.setRGB(Format.getHexString(fcol.getMaxColour()));
6344 col.setMin(fcol.getMin());
6345 col.setMax(fcol.getMax());
6346 col.setMinRGB(jalview.util.Format.getHexString(fcol.getMinColour()));
6347 col.setAutoScale(fcol.isAutoScaled());
6348 col.setThreshold(fcol.getThreshold());
6349 col.setColourByLabel(fcol.isColourByLabel());
6350 col.setThreshType(fcol.isAboveThreshold() ? ThresholdType.ABOVE
6351 : (fcol.isBelowThreshold() ? ThresholdType.BELOW
6352 : ThresholdType.NONE));
6353 if (fcol.isColourByAttribute())
6355 final String[] attName = fcol.getAttributeName();
6356 col.getAttributeName().add(attName[0]);
6357 if (attName.length > 1)
6359 col.getAttributeName().add(attName[1]);
6362 Color noColour = fcol.getNoColour();
6363 if (noColour == null)
6365 col.setNoValueColour(NoValueColour.NONE);
6367 else if (noColour == fcol.getMaxColour())
6369 col.setNoValueColour(NoValueColour.MAX);
6373 col.setNoValueColour(NoValueColour.MIN);
6376 col.setName(featureType);
6381 * Populates an XML model of the feature filter(s) for one feature type
6383 * @param firstMatcher
6384 * the first (or only) match condition)
6386 * remaining match conditions (if any)
6388 * if true, conditions are and-ed, else or-ed
6390 public static jalview.xml.binding.jalview.FeatureMatcherSet marshalFilter(
6391 FeatureMatcherI firstMatcher, Iterator<FeatureMatcherI> filters,
6394 jalview.xml.binding.jalview.FeatureMatcherSet result = new jalview.xml.binding.jalview.FeatureMatcherSet();
6396 if (filters.hasNext())
6401 CompoundMatcher compound = new CompoundMatcher();
6402 compound.setAnd(and);
6403 jalview.xml.binding.jalview.FeatureMatcherSet matcher1 = marshalFilter(
6404 firstMatcher, Collections.emptyIterator(), and);
6405 // compound.addMatcherSet(matcher1);
6406 compound.getMatcherSet().add(matcher1);
6407 FeatureMatcherI nextMatcher = filters.next();
6408 jalview.xml.binding.jalview.FeatureMatcherSet matcher2 = marshalFilter(
6409 nextMatcher, filters, and);
6410 // compound.addMatcherSet(matcher2);
6411 compound.getMatcherSet().add(matcher2);
6412 result.setCompoundMatcher(compound);
6417 * single condition matcher
6419 // MatchCondition matcherModel = new MatchCondition();
6420 jalview.xml.binding.jalview.FeatureMatcher matcherModel = new jalview.xml.binding.jalview.FeatureMatcher();
6421 matcherModel.setCondition(
6422 firstMatcher.getMatcher().getCondition().getStableName());
6423 matcherModel.setValue(firstMatcher.getMatcher().getPattern());
6424 if (firstMatcher.isByAttribute())
6426 matcherModel.setBy(FilterBy.BY_ATTRIBUTE);
6427 // matcherModel.setAttributeName(firstMatcher.getAttribute());
6428 String[] attName = firstMatcher.getAttribute();
6429 matcherModel.getAttributeName().add(attName[0]); // attribute
6430 if (attName.length > 1)
6432 matcherModel.getAttributeName().add(attName[1]); // sub-attribute
6435 else if (firstMatcher.isByLabel())
6437 matcherModel.setBy(FilterBy.BY_LABEL);
6439 else if (firstMatcher.isByScore())
6441 matcherModel.setBy(FilterBy.BY_SCORE);
6443 result.setMatchCondition(matcherModel);
6450 * Loads one XML model of a feature filter to a Jalview object
6452 * @param featureType
6453 * @param matcherSetModel
6456 public static FeatureMatcherSetI parseFilter(
6458 jalview.xml.binding.jalview.FeatureMatcherSet matcherSetModel)
6460 FeatureMatcherSetI result = new FeatureMatcherSet();
6463 parseFilterConditions(result, matcherSetModel, true);
6464 } catch (IllegalStateException e)
6466 // mixing AND and OR conditions perhaps
6468 String.format("Error reading filter conditions for '%s': %s",
6469 featureType, e.getMessage()));
6470 // return as much as was parsed up to the error
6477 * Adds feature match conditions to matcherSet as unmarshalled from XML
6478 * (possibly recursively for compound conditions)
6481 * @param matcherSetModel
6483 * if true, multiple conditions are AND-ed, else they are OR-ed
6484 * @throws IllegalStateException
6485 * if AND and OR conditions are mixed
6487 protected static void parseFilterConditions(
6488 FeatureMatcherSetI matcherSet,
6489 jalview.xml.binding.jalview.FeatureMatcherSet matcherSetModel,
6492 jalview.xml.binding.jalview.FeatureMatcher mc = matcherSetModel
6493 .getMatchCondition();
6499 FilterBy filterBy = mc.getBy();
6500 Condition cond = Condition.fromString(mc.getCondition());
6501 String pattern = mc.getValue();
6502 FeatureMatcherI matchCondition = null;
6503 if (filterBy == FilterBy.BY_LABEL)
6505 matchCondition = FeatureMatcher.byLabel(cond, pattern);
6507 else if (filterBy == FilterBy.BY_SCORE)
6509 matchCondition = FeatureMatcher.byScore(cond, pattern);
6512 else if (filterBy == FilterBy.BY_ATTRIBUTE)
6514 final List<String> attributeName = mc.getAttributeName();
6515 String[] attNames = attributeName
6516 .toArray(new String[attributeName.size()]);
6517 matchCondition = FeatureMatcher.byAttribute(cond, pattern,
6522 * note this throws IllegalStateException if AND-ing to a
6523 * previously OR-ed compound condition, or vice versa
6527 matcherSet.and(matchCondition);
6531 matcherSet.or(matchCondition);
6537 * compound condition
6539 List<jalview.xml.binding.jalview.FeatureMatcherSet> matchers = matcherSetModel
6540 .getCompoundMatcher().getMatcherSet();
6541 boolean anded = matcherSetModel.getCompoundMatcher().isAnd();
6542 if (matchers.size() == 2)
6544 parseFilterConditions(matcherSet, matchers.get(0), anded);
6545 parseFilterConditions(matcherSet, matchers.get(1), anded);
6549 System.err.println("Malformed compound filter condition");
6555 * Loads one XML model of a feature colour to a Jalview object
6557 * @param colourModel
6560 public static FeatureColourI parseColour(Colour colourModel)
6562 FeatureColourI colour = null;
6564 if (colourModel.getMax() != null)
6566 Color mincol = null;
6567 Color maxcol = null;
6568 Color noValueColour = null;
6572 mincol = new Color(Integer.parseInt(colourModel.getMinRGB(), 16));
6573 maxcol = new Color(Integer.parseInt(colourModel.getRGB(), 16));
6574 } catch (Exception e)
6576 Cache.log.warn("Couldn't parse out graduated feature color.", e);
6579 NoValueColour noCol = colourModel.getNoValueColour();
6580 if (noCol == NoValueColour.MIN)
6582 noValueColour = mincol;
6584 else if (noCol == NoValueColour.MAX)
6586 noValueColour = maxcol;
6589 colour = new FeatureColour(maxcol, mincol, maxcol, noValueColour,
6590 safeFloat(colourModel.getMin()),
6591 safeFloat(colourModel.getMax()));
6592 final List<String> attributeName = colourModel.getAttributeName();
6593 String[] attributes = attributeName
6594 .toArray(new String[attributeName.size()]);
6595 if (attributes != null && attributes.length > 0)
6597 colour.setAttributeName(attributes);
6599 if (colourModel.isAutoScale() != null)
6601 colour.setAutoScaled(colourModel.isAutoScale().booleanValue());
6603 if (colourModel.isColourByLabel() != null)
6605 colour.setColourByLabel(
6606 colourModel.isColourByLabel().booleanValue());
6608 if (colourModel.getThreshold() != null)
6610 colour.setThreshold(colourModel.getThreshold().floatValue());
6612 ThresholdType ttyp = colourModel.getThreshType();
6613 if (ttyp == ThresholdType.ABOVE)
6615 colour.setAboveThreshold(true);
6617 else if (ttyp == ThresholdType.BELOW)
6619 colour.setBelowThreshold(true);
6624 Color color = new Color(Integer.parseInt(colourModel.getRGB(), 16));
6625 colour = new FeatureColour(color);