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.GeneLocus;
43 import jalview.datamodel.GraphLine;
44 import jalview.datamodel.PDBEntry;
45 import jalview.datamodel.Point;
46 import jalview.datamodel.RnaViewerModel;
47 import jalview.datamodel.SequenceFeature;
48 import jalview.datamodel.SequenceGroup;
49 import jalview.datamodel.SequenceI;
50 import jalview.datamodel.StructureViewerModel;
51 import jalview.datamodel.StructureViewerModel.StructureData;
52 import jalview.datamodel.features.FeatureMatcher;
53 import jalview.datamodel.features.FeatureMatcherI;
54 import jalview.datamodel.features.FeatureMatcherSet;
55 import jalview.datamodel.features.FeatureMatcherSetI;
56 import jalview.ext.varna.RnaModel;
57 import jalview.gui.AlignFrame;
58 import jalview.gui.AlignViewport;
59 import jalview.gui.AlignmentPanel;
60 import jalview.gui.AppVarna;
61 import jalview.gui.ChimeraViewFrame;
62 import jalview.gui.Desktop;
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.structure.StructureSelectionManager;
86 import jalview.structures.models.AAStructureBindingModel;
87 import jalview.util.Format;
88 import jalview.util.MessageManager;
89 import jalview.util.Platform;
90 import jalview.util.StringUtils;
91 import jalview.util.jarInputStreamProvider;
92 import jalview.util.matcher.Condition;
93 import jalview.viewmodel.AlignmentViewport;
94 import jalview.viewmodel.PCAModel;
95 import jalview.viewmodel.ViewportRanges;
96 import jalview.viewmodel.seqfeatures.FeatureRendererModel;
97 import jalview.viewmodel.seqfeatures.FeatureRendererSettings;
98 import jalview.viewmodel.seqfeatures.FeaturesDisplayed;
99 import jalview.ws.jws2.Jws2Discoverer;
100 import jalview.ws.jws2.dm.AAConSettings;
101 import jalview.ws.jws2.jabaws2.Jws2Instance;
102 import jalview.ws.params.ArgumentI;
103 import jalview.ws.params.AutoCalcSetting;
104 import jalview.ws.params.WsParamSetI;
105 import jalview.xml.binding.jalview.AlcodonFrame;
106 import jalview.xml.binding.jalview.AlcodonFrame.AlcodMap;
107 import jalview.xml.binding.jalview.Annotation;
108 import jalview.xml.binding.jalview.Annotation.ThresholdLine;
109 import jalview.xml.binding.jalview.AnnotationColourScheme;
110 import jalview.xml.binding.jalview.AnnotationElement;
111 import jalview.xml.binding.jalview.DoubleMatrix;
112 import jalview.xml.binding.jalview.DoubleVector;
113 import jalview.xml.binding.jalview.Feature;
114 import jalview.xml.binding.jalview.Feature.OtherData;
115 import jalview.xml.binding.jalview.FeatureMatcherSet.CompoundMatcher;
116 import jalview.xml.binding.jalview.FilterBy;
117 import jalview.xml.binding.jalview.JalviewModel;
118 import jalview.xml.binding.jalview.JalviewModel.FeatureSettings;
119 import jalview.xml.binding.jalview.JalviewModel.FeatureSettings.Group;
120 import jalview.xml.binding.jalview.JalviewModel.FeatureSettings.Setting;
121 import jalview.xml.binding.jalview.JalviewModel.JGroup;
122 import jalview.xml.binding.jalview.JalviewModel.JSeq;
123 import jalview.xml.binding.jalview.JalviewModel.JSeq.Pdbids;
124 import jalview.xml.binding.jalview.JalviewModel.JSeq.Pdbids.StructureState;
125 import jalview.xml.binding.jalview.JalviewModel.JSeq.RnaViewer;
126 import jalview.xml.binding.jalview.JalviewModel.JSeq.RnaViewer.SecondaryStructure;
127 import jalview.xml.binding.jalview.JalviewModel.PcaViewer;
128 import jalview.xml.binding.jalview.JalviewModel.PcaViewer.Axis;
129 import jalview.xml.binding.jalview.JalviewModel.PcaViewer.SeqPointMax;
130 import jalview.xml.binding.jalview.JalviewModel.PcaViewer.SeqPointMin;
131 import jalview.xml.binding.jalview.JalviewModel.PcaViewer.SequencePoint;
132 import jalview.xml.binding.jalview.JalviewModel.Tree;
133 import jalview.xml.binding.jalview.JalviewModel.UserColours;
134 import jalview.xml.binding.jalview.JalviewModel.Viewport;
135 import jalview.xml.binding.jalview.JalviewModel.Viewport.CalcIdParam;
136 import jalview.xml.binding.jalview.JalviewModel.Viewport.HiddenColumns;
137 import jalview.xml.binding.jalview.JalviewUserColours;
138 import jalview.xml.binding.jalview.JalviewUserColours.Colour;
139 import jalview.xml.binding.jalview.MapListType.MapListFrom;
140 import jalview.xml.binding.jalview.MapListType.MapListTo;
141 import jalview.xml.binding.jalview.Mapping;
142 import jalview.xml.binding.jalview.NoValueColour;
143 import jalview.xml.binding.jalview.ObjectFactory;
144 import jalview.xml.binding.jalview.PcaDataType;
145 import jalview.xml.binding.jalview.Pdbentry.Property;
146 import jalview.xml.binding.jalview.Sequence;
147 import jalview.xml.binding.jalview.Sequence.DBRef;
148 import jalview.xml.binding.jalview.SequenceSet;
149 import jalview.xml.binding.jalview.SequenceSet.SequenceSetProperties;
150 import jalview.xml.binding.jalview.ThresholdType;
151 import jalview.xml.binding.jalview.VAMSAS;
153 import java.awt.Color;
154 import java.awt.Font;
155 import java.awt.Rectangle;
156 import java.io.BufferedReader;
157 import java.io.ByteArrayInputStream;
158 import java.io.DataInputStream;
159 import java.io.DataOutputStream;
161 import java.io.FileInputStream;
162 import java.io.FileOutputStream;
163 import java.io.IOException;
164 import java.io.InputStreamReader;
165 import java.io.OutputStreamWriter;
166 import java.io.PrintWriter;
167 import java.lang.reflect.InvocationTargetException;
168 import java.math.BigInteger;
169 import java.net.MalformedURLException;
171 import java.util.ArrayList;
172 import java.util.Arrays;
173 import java.util.Collections;
174 import java.util.Enumeration;
175 import java.util.GregorianCalendar;
176 import java.util.HashMap;
177 import java.util.HashSet;
178 import java.util.Hashtable;
179 import java.util.IdentityHashMap;
180 import java.util.Iterator;
181 import java.util.LinkedHashMap;
182 import java.util.List;
183 import java.util.Map;
184 import java.util.Map.Entry;
185 import java.util.Set;
186 import java.util.Vector;
187 import java.util.jar.JarEntry;
188 import java.util.jar.JarInputStream;
189 import java.util.jar.JarOutputStream;
191 import javax.swing.JInternalFrame;
192 import javax.swing.SwingUtilities;
193 import javax.xml.bind.JAXBContext;
194 import javax.xml.bind.JAXBElement;
195 import javax.xml.bind.Marshaller;
196 import javax.xml.datatype.DatatypeConfigurationException;
197 import javax.xml.datatype.DatatypeFactory;
198 import javax.xml.datatype.XMLGregorianCalendar;
199 import javax.xml.stream.XMLInputFactory;
200 import javax.xml.stream.XMLStreamReader;
203 * Write out the current jalview desktop state as a Jalview XML stream.
205 * Note: the vamsas objects referred to here are primitive versions of the
206 * VAMSAS project schema elements - they are not the same and most likely never
210 * @version $Revision: 1.134 $
212 public class Jalview2XML
215 // BH 2018 we add the .jvp binary extension to J2S so that
216 // it will declare that binary when we do the file save from the browser
220 Platform.addJ2SBinaryType(".jvp?");
223 private static final String VIEWER_PREFIX = "viewer_";
225 private static final String RNA_PREFIX = "rna_";
227 private static final String UTF_8 = "UTF-8";
230 * prefix for recovering datasets for alignments with multiple views where
231 * non-existent dataset IDs were written for some views
233 private static final String UNIQSEQSETID = "uniqueSeqSetId.";
235 // use this with nextCounter() to make unique names for entities
236 private int counter = 0;
239 * SequenceI reference -> XML ID string in jalview XML. Populated as XML reps
240 * of sequence objects are created.
242 IdentityHashMap<SequenceI, String> seqsToIds = null;
245 * jalview XML Sequence ID to jalview sequence object reference (both dataset
246 * and alignment sequences. Populated as XML reps of sequence objects are
249 Map<String, SequenceI> seqRefIds = null;
251 Map<String, SequenceI> incompleteSeqs = null;
253 List<SeqFref> frefedSequence = null;
255 boolean raiseGUI = true; // whether errors are raised in dialog boxes or not
258 * Map of reconstructed AlignFrame objects that appear to have come from
259 * SplitFrame objects (have a dna/protein complement view).
261 private Map<Viewport, AlignFrame> splitFrameCandidates = new HashMap<>();
264 * Map from displayed rna structure models to their saved session state jar
267 private Map<RnaModel, String> rnaSessions = new HashMap<>();
270 * A helper method for safely using the value of an optional attribute that
271 * may be null if not present in the XML. Answers the boolean value, or false
277 public static boolean safeBoolean(Boolean b)
279 return b == null ? false : b.booleanValue();
283 * A helper method for safely using the value of an optional attribute that
284 * may be null if not present in the XML. Answers the integer value, or zero
290 public static int safeInt(Integer i)
292 return i == null ? 0 : i.intValue();
296 * A helper method for safely using the value of an optional attribute that
297 * may be null if not present in the XML. Answers the float value, or zero if
303 public static float safeFloat(Float f)
305 return f == null ? 0f : f.floatValue();
309 * create/return unique hash string for sq
312 * @return new or existing unique string for sq
314 String seqHash(SequenceI sq)
316 if (seqsToIds == null)
320 if (seqsToIds.containsKey(sq))
322 return seqsToIds.get(sq);
326 // create sequential key
327 String key = "sq" + (seqsToIds.size() + 1);
328 key = makeHashCode(sq, key); // check we don't have an external reference
330 seqsToIds.put(sq, key);
337 if (seqsToIds == null)
339 seqsToIds = new IdentityHashMap<>();
341 if (seqRefIds == null)
343 seqRefIds = new HashMap<>();
345 if (incompleteSeqs == null)
347 incompleteSeqs = new HashMap<>();
349 if (frefedSequence == null)
351 frefedSequence = new ArrayList<>();
359 public Jalview2XML(boolean raiseGUI)
361 this.raiseGUI = raiseGUI;
365 * base class for resolving forward references to sequences by their ID
370 abstract class SeqFref
376 public SeqFref(String _sref, String type)
382 public String getSref()
387 public SequenceI getSrefSeq()
389 return seqRefIds.get(sref);
392 public boolean isResolvable()
394 return seqRefIds.get(sref) != null;
397 public SequenceI getSrefDatasetSeq()
399 SequenceI sq = seqRefIds.get(sref);
402 while (sq.getDatasetSequence() != null)
404 sq = sq.getDatasetSequence();
411 * @return true if the forward reference was fully resolved
413 abstract boolean resolve();
416 public String toString()
418 return type + " reference to " + sref;
423 * create forward reference for a mapping
429 public SeqFref newMappingRef(final String sref,
430 final jalview.datamodel.Mapping _jmap)
432 SeqFref fref = new SeqFref(sref, "Mapping")
434 public jalview.datamodel.Mapping jmap = _jmap;
439 SequenceI seq = getSrefDatasetSeq();
451 public SeqFref newAlcodMapRef(final String sref,
452 final AlignedCodonFrame _cf,
453 final jalview.datamodel.Mapping _jmap)
456 SeqFref fref = new SeqFref(sref, "Codon Frame")
458 AlignedCodonFrame cf = _cf;
460 public jalview.datamodel.Mapping mp = _jmap;
463 public boolean isResolvable()
465 return super.isResolvable() && mp.getTo() != null;
471 SequenceI seq = getSrefDatasetSeq();
476 cf.addMap(seq, mp.getTo(), mp.getMap());
483 public void resolveFrefedSequences()
485 Iterator<SeqFref> nextFref = frefedSequence.iterator();
486 int toresolve = frefedSequence.size();
487 int unresolved = 0, failedtoresolve = 0;
488 while (nextFref.hasNext())
490 SeqFref ref = nextFref.next();
491 if (ref.isResolvable())
503 } catch (Exception x)
506 "IMPLEMENTATION ERROR: Failed to resolve forward reference for sequence "
519 System.err.println("Jalview Project Import: There were " + unresolved
520 + " forward references left unresolved on the stack.");
522 if (failedtoresolve > 0)
524 System.err.println("SERIOUS! " + failedtoresolve
525 + " resolvable forward references failed to resolve.");
527 if (incompleteSeqs != null && incompleteSeqs.size() > 0)
530 "Jalview Project Import: There are " + incompleteSeqs.size()
531 + " sequences which may have incomplete metadata.");
532 if (incompleteSeqs.size() < 10)
534 for (SequenceI s : incompleteSeqs.values())
536 System.err.println(s.toString());
542 "Too many to report. Skipping output of incomplete sequences.");
548 * This maintains a map of viewports, the key being the seqSetId. Important to
549 * set historyItem and redoList for multiple views
551 Map<String, AlignViewport> viewportsAdded = new HashMap<>();
553 Map<String, AlignmentAnnotation> annotationIds = new HashMap<>();
555 String uniqueSetSuffix = "";
558 * List of pdbfiles added to Jar
560 List<String> pdbfiles = null;
562 // SAVES SEVERAL ALIGNMENT WINDOWS TO SAME JARFILE
563 public void saveState(File statefile)
565 FileOutputStream fos = null;
570 fos = new FileOutputStream(statefile);
572 JarOutputStream jout = new JarOutputStream(fos);
576 } catch (Exception e)
578 Cache.log.error("Couln't write Jalview state to " + statefile, e);
579 // TODO: inform user of the problem - they need to know if their data was
581 if (errorMessage == null)
583 errorMessage = "Did't write Jalview Archive to output file '"
584 + statefile + "' - See console error log for details";
588 errorMessage += "(Didn't write Jalview Archive to output file '"
599 } catch (IOException e)
609 * Writes a jalview project archive to the given Jar output stream.
613 public void saveState(JarOutputStream jout)
615 AlignFrame[] frames = Desktop.getAlignFrames();
621 saveAllFrames(Arrays.asList(frames), jout);
625 * core method for storing state for a set of AlignFrames.
628 * - frames involving all data to be exported (including containing
631 * - project output stream
633 private void saveAllFrames(List<AlignFrame> frames, JarOutputStream jout)
635 Hashtable<String, AlignFrame> dsses = new Hashtable<>();
638 * ensure cached data is clear before starting
640 // todo tidy up seqRefIds, seqsToIds initialisation / reset
642 splitFrameCandidates.clear();
647 // NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS
648 // //////////////////////////////////////////////////
650 List<String> shortNames = new ArrayList<>();
651 List<String> viewIds = new ArrayList<>();
654 for (int i = frames.size() - 1; i > -1; i--)
656 AlignFrame af = frames.get(i);
658 if (skipList != null && skipList
659 .containsKey(af.getViewport().getSequenceSetId()))
664 String shortName = makeFilename(af, shortNames);
666 int apSize = af.getAlignPanels().size();
668 for (int ap = 0; ap < apSize; ap++)
670 AlignmentPanel apanel = (AlignmentPanel) af.getAlignPanels()
672 String fileName = apSize == 1 ? shortName : ap + shortName;
673 if (!fileName.endsWith(".xml"))
675 fileName = fileName + ".xml";
678 saveState(apanel, fileName, jout, viewIds);
680 String dssid = getDatasetIdRef(
681 af.getViewport().getAlignment().getDataset());
682 if (!dsses.containsKey(dssid))
684 dsses.put(dssid, af);
689 writeDatasetFor(dsses, "" + jout.hashCode() + " " + uniqueSetSuffix,
695 } catch (Exception foo)
699 } catch (Exception ex)
701 // TODO: inform user of the problem - they need to know if their data was
703 if (errorMessage == null)
705 errorMessage = "Couldn't write Jalview Archive - see error output for details";
707 ex.printStackTrace();
712 * Generates a distinct file name, based on the title of the AlignFrame, by
713 * appending _n for increasing n until an unused name is generated. The new
714 * name (without its extension) is added to the list.
718 * @return the generated name, with .xml extension
720 protected String makeFilename(AlignFrame af, List<String> namesUsed)
722 String shortName = af.getTitle();
724 if (shortName.indexOf(File.separatorChar) > -1)
726 shortName = shortName
727 .substring(shortName.lastIndexOf(File.separatorChar) + 1);
732 while (namesUsed.contains(shortName))
734 if (shortName.endsWith("_" + (count - 1)))
736 shortName = shortName.substring(0, shortName.lastIndexOf("_"));
739 shortName = shortName.concat("_" + count);
743 namesUsed.add(shortName);
745 if (!shortName.endsWith(".xml"))
747 shortName = shortName + ".xml";
752 // USE THIS METHOD TO SAVE A SINGLE ALIGNMENT WINDOW
753 public boolean saveAlignment(AlignFrame af, String jarFile,
758 // create backupfiles object and get new temp filename destination
759 boolean doBackup = BackupFiles.getEnabled();
760 BackupFiles backupfiles = doBackup ? new BackupFiles(jarFile) : null;
761 FileOutputStream fos = new FileOutputStream(doBackup ?
762 backupfiles.getTempFilePath() : jarFile);
764 JarOutputStream jout = new JarOutputStream(fos);
765 List<AlignFrame> frames = new ArrayList<>();
767 // resolve splitframes
768 if (af.getViewport().getCodingComplement() != null)
770 frames = ((SplitFrame) af.getSplitViewContainer()).getAlignFrames();
776 saveAllFrames(frames, jout);
780 } catch (Exception foo)
784 boolean success = true;
788 backupfiles.setWriteSuccess(success);
789 success = backupfiles.rollBackupsAndRenameTempFile();
793 } catch (Exception ex)
795 errorMessage = "Couldn't Write alignment view to Jalview Archive - see error output for details";
796 ex.printStackTrace();
801 private void writeDatasetFor(Hashtable<String, AlignFrame> dsses,
802 String fileName, JarOutputStream jout)
805 for (String dssids : dsses.keySet())
807 AlignFrame _af = dsses.get(dssids);
808 String jfileName = fileName + " Dataset for " + _af.getTitle();
809 if (!jfileName.endsWith(".xml"))
811 jfileName = jfileName + ".xml";
813 saveState(_af.alignPanel, jfileName, true, jout, null);
818 * create a JalviewModel from an alignment view and marshall it to a
822 * panel to create jalview model for
824 * name of alignment panel written to output stream
831 public JalviewModel saveState(AlignmentPanel ap, String fileName,
832 JarOutputStream jout, List<String> viewIds)
834 return saveState(ap, fileName, false, jout, viewIds);
838 * create a JalviewModel from an alignment view and marshall it to a
842 * panel to create jalview model for
844 * name of alignment panel written to output stream
846 * when true, only write the dataset for the alignment, not the data
847 * associated with the view.
853 public JalviewModel saveState(AlignmentPanel ap, String fileName,
854 boolean storeDS, JarOutputStream jout, List<String> viewIds)
858 viewIds = new ArrayList<>();
863 List<UserColourScheme> userColours = new ArrayList<>();
865 AlignViewport av = ap.av;
866 ViewportRanges vpRanges = av.getRanges();
868 final ObjectFactory objectFactory = new ObjectFactory();
869 JalviewModel object = objectFactory.createJalviewModel();
870 object.setVamsasModel(new VAMSAS());
872 // object.setCreationDate(new java.util.Date(System.currentTimeMillis()));
875 GregorianCalendar c = new GregorianCalendar();
876 DatatypeFactory datatypeFactory = DatatypeFactory.newInstance();
877 XMLGregorianCalendar now = datatypeFactory.newXMLGregorianCalendar(c);// gregorianCalendar);
878 object.setCreationDate(now);
879 } catch (DatatypeConfigurationException e)
881 System.err.println("error writing date: " + e.toString());
884 jalview.bin.Cache.getDefault("VERSION", "Development Build"));
887 * rjal is full height alignment, jal is actual alignment with full metadata
888 * but excludes hidden sequences.
890 jalview.datamodel.AlignmentI rjal = av.getAlignment(), jal = rjal;
892 if (av.hasHiddenRows())
894 rjal = jal.getHiddenSequences().getFullAlignment();
897 SequenceSet vamsasSet = new SequenceSet();
899 // JalviewModelSequence jms = new JalviewModelSequence();
901 vamsasSet.setGapChar(jal.getGapCharacter() + "");
903 if (jal.getDataset() != null)
905 // dataset id is the dataset's hashcode
906 vamsasSet.setDatasetId(getDatasetIdRef(jal.getDataset()));
909 // switch jal and the dataset
910 jal = jal.getDataset();
914 if (jal.getProperties() != null)
916 Enumeration en = jal.getProperties().keys();
917 while (en.hasMoreElements())
919 String key = en.nextElement().toString();
920 SequenceSetProperties ssp = new SequenceSetProperties();
922 ssp.setValue(jal.getProperties().get(key).toString());
923 // vamsasSet.addSequenceSetProperties(ssp);
924 vamsasSet.getSequenceSetProperties().add(ssp);
929 Set<String> calcIdSet = new HashSet<>();
930 // record the set of vamsas sequence XML POJO we create.
931 HashMap<String, Sequence> vamsasSetIds = new HashMap<>();
933 for (final SequenceI jds : rjal.getSequences())
935 final SequenceI jdatasq = jds.getDatasetSequence() == null ? jds
936 : jds.getDatasetSequence();
937 String id = seqHash(jds);
938 if (vamsasSetIds.get(id) == null)
940 if (seqRefIds.get(id) != null && !storeDS)
942 // This happens for two reasons: 1. multiple views are being
944 // 2. the hashCode has collided with another sequence's code. This
946 // HAPPEN! (PF00072.15.stk does this)
947 // JBPNote: Uncomment to debug writing out of files that do not read
948 // back in due to ArrayOutOfBoundExceptions.
949 // System.err.println("vamsasSeq backref: "+id+"");
950 // System.err.println(jds.getName()+"
951 // "+jds.getStart()+"-"+jds.getEnd()+" "+jds.getSequenceAsString());
952 // System.err.println("Hashcode: "+seqHash(jds));
953 // SequenceI rsq = (SequenceI) seqRefIds.get(id + "");
954 // System.err.println(rsq.getName()+"
955 // "+rsq.getStart()+"-"+rsq.getEnd()+" "+rsq.getSequenceAsString());
956 // System.err.println("Hashcode: "+seqHash(rsq));
960 vamsasSeq = createVamsasSequence(id, jds);
961 // vamsasSet.addSequence(vamsasSeq);
962 vamsasSet.getSequence().add(vamsasSeq);
963 vamsasSetIds.put(id, vamsasSeq);
964 seqRefIds.put(id, jds);
968 jseq.setStart(jds.getStart());
969 jseq.setEnd(jds.getEnd());
970 jseq.setColour(av.getSequenceColour(jds).getRGB());
972 jseq.setId(id); // jseq id should be a string not a number
975 // Store any sequences this sequence represents
976 if (av.hasHiddenRows())
978 // use rjal, contains the full height alignment
980 av.getAlignment().getHiddenSequences().isHidden(jds));
982 if (av.isHiddenRepSequence(jds))
984 jalview.datamodel.SequenceI[] reps = av
985 .getRepresentedSequences(jds).getSequencesInOrder(rjal);
987 for (int h = 0; h < reps.length; h++)
991 // jseq.addHiddenSequences(rjal.findIndex(reps[h]));
992 jseq.getHiddenSequences().add(rjal.findIndex(reps[h]));
997 // mark sequence as reference - if it is the reference for this view
1000 jseq.setViewreference(jds == jal.getSeqrep());
1004 // TODO: omit sequence features from each alignment view's XML dump if we
1005 // are storing dataset
1006 List<SequenceFeature> sfs = jds.getSequenceFeatures();
1007 for (SequenceFeature sf : sfs)
1009 // Features features = new Features();
1010 Feature features = new Feature();
1012 features.setBegin(sf.getBegin());
1013 features.setEnd(sf.getEnd());
1014 features.setDescription(sf.getDescription());
1015 features.setType(sf.getType());
1016 features.setFeatureGroup(sf.getFeatureGroup());
1017 features.setScore(sf.getScore());
1018 if (sf.links != null)
1020 for (int l = 0; l < sf.links.size(); l++)
1022 OtherData keyValue = new OtherData();
1023 keyValue.setKey("LINK_" + l);
1024 keyValue.setValue(sf.links.elementAt(l).toString());
1025 // features.addOtherData(keyValue);
1026 features.getOtherData().add(keyValue);
1029 if (sf.otherDetails != null)
1032 * save feature attributes, which may be simple strings or
1033 * map valued (have sub-attributes)
1035 for (Entry<String, Object> entry : sf.otherDetails.entrySet())
1037 String key = entry.getKey();
1038 Object value = entry.getValue();
1039 if (value instanceof Map<?, ?>)
1041 for (Entry<String, Object> subAttribute : ((Map<String, Object>) value)
1044 OtherData otherData = new OtherData();
1045 otherData.setKey(key);
1046 otherData.setKey2(subAttribute.getKey());
1047 otherData.setValue(subAttribute.getValue().toString());
1048 // features.addOtherData(otherData);
1049 features.getOtherData().add(otherData);
1054 OtherData otherData = new OtherData();
1055 otherData.setKey(key);
1056 otherData.setValue(value.toString());
1057 // features.addOtherData(otherData);
1058 features.getOtherData().add(otherData);
1063 // jseq.addFeatures(features);
1064 jseq.getFeatures().add(features);
1067 if (jdatasq.getAllPDBEntries() != null)
1069 Enumeration<PDBEntry> en = jdatasq.getAllPDBEntries().elements();
1070 while (en.hasMoreElements())
1072 Pdbids pdb = new Pdbids();
1073 jalview.datamodel.PDBEntry entry = en.nextElement();
1075 String pdbId = entry.getId();
1077 pdb.setType(entry.getType());
1080 * Store any structure views associated with this sequence. This
1081 * section copes with duplicate entries in the project, so a dataset
1082 * only view *should* be coped with sensibly.
1084 // This must have been loaded, is it still visible?
1085 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1086 String matchedFile = null;
1087 for (int f = frames.length - 1; f > -1; f--)
1089 if (frames[f] instanceof StructureViewerBase)
1091 StructureViewerBase viewFrame = (StructureViewerBase) frames[f];
1092 matchedFile = saveStructureState(ap, jds, pdb, entry, viewIds,
1093 matchedFile, viewFrame);
1095 * Only store each structure viewer's state once in the project
1096 * jar. First time through only (storeDS==false)
1098 String viewId = viewFrame.getViewId();
1099 if (!storeDS && !viewIds.contains(viewId))
1101 viewIds.add(viewId);
1104 String viewerState = viewFrame.getStateInfo();
1105 writeJarEntry(jout, getViewerJarEntryName(viewId),
1106 viewerState.getBytes());
1107 } catch (IOException e)
1110 "Error saving viewer state: " + e.getMessage());
1116 if (matchedFile != null || entry.getFile() != null)
1118 if (entry.getFile() != null)
1121 matchedFile = entry.getFile();
1123 pdb.setFile(matchedFile); // entry.getFile());
1124 if (pdbfiles == null)
1126 pdbfiles = new ArrayList<>();
1129 if (!pdbfiles.contains(pdbId))
1131 pdbfiles.add(pdbId);
1132 copyFileToJar(jout, matchedFile, pdbId);
1136 Enumeration<String> props = entry.getProperties();
1137 if (props.hasMoreElements())
1139 // PdbentryItem item = new PdbentryItem();
1140 while (props.hasMoreElements())
1142 Property prop = new Property();
1143 String key = props.nextElement();
1145 prop.setValue(entry.getProperty(key).toString());
1146 // item.addProperty(prop);
1147 pdb.getProperty().add(prop);
1149 // pdb.addPdbentryItem(item);
1152 // jseq.addPdbids(pdb);
1153 jseq.getPdbids().add(pdb);
1157 saveRnaViewers(jout, jseq, jds, viewIds, ap, storeDS);
1159 // jms.addJSeq(jseq);
1160 object.getJSeq().add(jseq);
1163 if (!storeDS && av.hasHiddenRows())
1165 jal = av.getAlignment();
1169 if (storeDS && jal.getCodonFrames() != null)
1171 List<AlignedCodonFrame> jac = jal.getCodonFrames();
1172 for (AlignedCodonFrame acf : jac)
1174 AlcodonFrame alc = new AlcodonFrame();
1175 if (acf.getProtMappings() != null
1176 && acf.getProtMappings().length > 0)
1178 boolean hasMap = false;
1179 SequenceI[] dnas = acf.getdnaSeqs();
1180 jalview.datamodel.Mapping[] pmaps = acf.getProtMappings();
1181 for (int m = 0; m < pmaps.length; m++)
1183 AlcodMap alcmap = new AlcodMap();
1184 alcmap.setDnasq(seqHash(dnas[m]));
1186 createVamsasMapping(pmaps[m], dnas[m], null, false));
1187 // alc.addAlcodMap(alcmap);
1188 alc.getAlcodMap().add(alcmap);
1193 // vamsasSet.addAlcodonFrame(alc);
1194 vamsasSet.getAlcodonFrame().add(alc);
1197 // TODO: delete this ? dead code from 2.8.3->2.9 ?
1199 // AlcodonFrame alc = new AlcodonFrame();
1200 // vamsasSet.addAlcodonFrame(alc);
1201 // for (int p = 0; p < acf.aaWidth; p++)
1203 // Alcodon cmap = new Alcodon();
1204 // if (acf.codons[p] != null)
1206 // // Null codons indicate a gapped column in the translated peptide
1208 // cmap.setPos1(acf.codons[p][0]);
1209 // cmap.setPos2(acf.codons[p][1]);
1210 // cmap.setPos3(acf.codons[p][2]);
1212 // alc.addAlcodon(cmap);
1214 // if (acf.getProtMappings() != null
1215 // && acf.getProtMappings().length > 0)
1217 // SequenceI[] dnas = acf.getdnaSeqs();
1218 // jalview.datamodel.Mapping[] pmaps = acf.getProtMappings();
1219 // for (int m = 0; m < pmaps.length; m++)
1221 // AlcodMap alcmap = new AlcodMap();
1222 // alcmap.setDnasq(seqHash(dnas[m]));
1223 // alcmap.setMapping(createVamsasMapping(pmaps[m], dnas[m], null,
1225 // alc.addAlcodMap(alcmap);
1232 // /////////////////////////////////
1233 if (!storeDS && av.getCurrentTree() != null)
1235 // FIND ANY ASSOCIATED TREES
1236 // NOT IMPLEMENTED FOR HEADLESS STATE AT PRESENT
1237 if (Desktop.desktop != null)
1239 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1241 for (int t = 0; t < frames.length; t++)
1243 if (frames[t] instanceof TreePanel)
1245 TreePanel tp = (TreePanel) frames[t];
1247 if (tp.getTreeCanvas().getViewport().getAlignment() == jal)
1249 JalviewModel.Tree tree = new JalviewModel.Tree();
1250 tree.setTitle(tp.getTitle());
1251 tree.setCurrentTree((av.getCurrentTree() == tp.getTree()));
1252 tree.setNewick(tp.getTree().print());
1253 tree.setThreshold(tp.getTreeCanvas().getThreshold());
1255 tree.setFitToWindow(tp.fitToWindow.getState());
1256 tree.setFontName(tp.getTreeFont().getName());
1257 tree.setFontSize(tp.getTreeFont().getSize());
1258 tree.setFontStyle(tp.getTreeFont().getStyle());
1259 tree.setMarkUnlinked(tp.placeholdersMenu.getState());
1261 tree.setShowBootstrap(tp.bootstrapMenu.getState());
1262 tree.setShowDistances(tp.distanceMenu.getState());
1264 tree.setHeight(tp.getHeight());
1265 tree.setWidth(tp.getWidth());
1266 tree.setXpos(tp.getX());
1267 tree.setYpos(tp.getY());
1268 tree.setId(makeHashCode(tp, null));
1269 tree.setLinkToAllViews(
1270 tp.getTreeCanvas().isApplyToAllViews());
1272 // jms.addTree(tree);
1273 object.getTree().add(tree);
1283 if (!storeDS && Desktop.desktop != null)
1285 for (JInternalFrame frame : Desktop.desktop.getAllFrames())
1287 if (frame instanceof PCAPanel)
1289 PCAPanel panel = (PCAPanel) frame;
1290 if (panel.getAlignViewport().getAlignment() == jal)
1292 savePCA(panel, object);
1300 * store forward refs from an annotationRow to any groups
1302 IdentityHashMap<SequenceGroup, String> groupRefs = new IdentityHashMap<>();
1305 for (SequenceI sq : jal.getSequences())
1307 // Store annotation on dataset sequences only
1308 AlignmentAnnotation[] aa = sq.getAnnotation();
1309 if (aa != null && aa.length > 0)
1311 storeAlignmentAnnotation(aa, groupRefs, av, calcIdSet, storeDS,
1318 if (jal.getAlignmentAnnotation() != null)
1320 // Store the annotation shown on the alignment.
1321 AlignmentAnnotation[] aa = jal.getAlignmentAnnotation();
1322 storeAlignmentAnnotation(aa, groupRefs, av, calcIdSet, storeDS,
1327 if (jal.getGroups() != null)
1329 JGroup[] groups = new JGroup[jal.getGroups().size()];
1331 for (jalview.datamodel.SequenceGroup sg : jal.getGroups())
1333 JGroup jGroup = new JGroup();
1334 groups[++i] = jGroup;
1336 jGroup.setStart(sg.getStartRes());
1337 jGroup.setEnd(sg.getEndRes());
1338 jGroup.setName(sg.getName());
1339 if (groupRefs.containsKey(sg))
1341 // group has references so set its ID field
1342 jGroup.setId(groupRefs.get(sg));
1344 ColourSchemeI colourScheme = sg.getColourScheme();
1345 if (colourScheme != null)
1347 ResidueShaderI groupColourScheme = sg.getGroupColourScheme();
1348 if (groupColourScheme.conservationApplied())
1350 jGroup.setConsThreshold(groupColourScheme.getConservationInc());
1352 if (colourScheme instanceof jalview.schemes.UserColourScheme)
1355 setUserColourScheme(colourScheme, userColours,
1360 jGroup.setColour(colourScheme.getSchemeName());
1363 else if (colourScheme instanceof jalview.schemes.AnnotationColourGradient)
1365 jGroup.setColour("AnnotationColourGradient");
1366 jGroup.setAnnotationColours(constructAnnotationColours(
1367 (jalview.schemes.AnnotationColourGradient) colourScheme,
1368 userColours, object));
1370 else if (colourScheme instanceof jalview.schemes.UserColourScheme)
1373 setUserColourScheme(colourScheme, userColours, object));
1377 jGroup.setColour(colourScheme.getSchemeName());
1380 jGroup.setPidThreshold(groupColourScheme.getThreshold());
1383 jGroup.setOutlineColour(sg.getOutlineColour().getRGB());
1384 jGroup.setDisplayBoxes(sg.getDisplayBoxes());
1385 jGroup.setDisplayText(sg.getDisplayText());
1386 jGroup.setColourText(sg.getColourText());
1387 jGroup.setTextCol1(sg.textColour.getRGB());
1388 jGroup.setTextCol2(sg.textColour2.getRGB());
1389 jGroup.setTextColThreshold(sg.thresholdTextColour);
1390 jGroup.setShowUnconserved(sg.getShowNonconserved());
1391 jGroup.setIgnoreGapsinConsensus(sg.getIgnoreGapsConsensus());
1392 jGroup.setShowConsensusHistogram(sg.isShowConsensusHistogram());
1393 jGroup.setShowSequenceLogo(sg.isShowSequenceLogo());
1394 jGroup.setNormaliseSequenceLogo(sg.isNormaliseSequenceLogo());
1395 for (SequenceI seq : sg.getSequences())
1397 // jGroup.addSeq(seqHash(seq));
1398 jGroup.getSeq().add(seqHash(seq));
1402 //jms.setJGroup(groups);
1404 for (JGroup grp : groups)
1406 object.getJGroup().add(grp);
1411 // /////////SAVE VIEWPORT
1412 Viewport view = new Viewport();
1413 view.setTitle(ap.alignFrame.getTitle());
1414 view.setSequenceSetId(
1415 makeHashCode(av.getSequenceSetId(), av.getSequenceSetId()));
1416 view.setId(av.getViewId());
1417 if (av.getCodingComplement() != null)
1419 view.setComplementId(av.getCodingComplement().getViewId());
1421 view.setViewName(av.getViewName());
1422 view.setGatheredViews(av.isGatherViewsHere());
1424 Rectangle size = ap.av.getExplodedGeometry();
1425 Rectangle position = size;
1428 size = ap.alignFrame.getBounds();
1429 if (av.getCodingComplement() != null)
1431 position = ((SplitFrame) ap.alignFrame.getSplitViewContainer())
1439 view.setXpos(position.x);
1440 view.setYpos(position.y);
1442 view.setWidth(size.width);
1443 view.setHeight(size.height);
1445 view.setStartRes(vpRanges.getStartRes());
1446 view.setStartSeq(vpRanges.getStartSeq());
1448 if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme)
1450 view.setBgColour(setUserColourScheme(av.getGlobalColourScheme(),
1451 userColours, object));
1454 .getGlobalColourScheme() instanceof jalview.schemes.AnnotationColourGradient)
1456 AnnotationColourScheme ac = constructAnnotationColours(
1457 (jalview.schemes.AnnotationColourGradient) av
1458 .getGlobalColourScheme(),
1459 userColours, object);
1461 view.setAnnotationColours(ac);
1462 view.setBgColour("AnnotationColourGradient");
1466 view.setBgColour(ColourSchemeProperty
1467 .getColourName(av.getGlobalColourScheme()));
1470 ResidueShaderI vcs = av.getResidueShading();
1471 ColourSchemeI cs = av.getGlobalColourScheme();
1475 if (vcs.conservationApplied())
1477 view.setConsThreshold(vcs.getConservationInc());
1478 if (cs instanceof jalview.schemes.UserColourScheme)
1480 view.setBgColour(setUserColourScheme(cs, userColours, object));
1483 view.setPidThreshold(vcs.getThreshold());
1486 view.setConservationSelected(av.getConservationSelected());
1487 view.setPidSelected(av.getAbovePIDThreshold());
1488 final Font font = av.getFont();
1489 view.setFontName(font.getName());
1490 view.setFontSize(font.getSize());
1491 view.setFontStyle(font.getStyle());
1492 view.setScaleProteinAsCdna(av.getViewStyle().isScaleProteinAsCdna());
1493 view.setRenderGaps(av.isRenderGaps());
1494 view.setShowAnnotation(av.isShowAnnotation());
1495 view.setShowBoxes(av.getShowBoxes());
1496 view.setShowColourText(av.getColourText());
1497 view.setShowFullId(av.getShowJVSuffix());
1498 view.setRightAlignIds(av.isRightAlignIds());
1499 view.setShowSequenceFeatures(av.isShowSequenceFeatures());
1500 view.setShowText(av.getShowText());
1501 view.setShowUnconserved(av.getShowUnconserved());
1502 view.setWrapAlignment(av.getWrapAlignment());
1503 view.setTextCol1(av.getTextColour().getRGB());
1504 view.setTextCol2(av.getTextColour2().getRGB());
1505 view.setTextColThreshold(av.getThresholdTextColour());
1506 view.setShowConsensusHistogram(av.isShowConsensusHistogram());
1507 view.setShowSequenceLogo(av.isShowSequenceLogo());
1508 view.setNormaliseSequenceLogo(av.isNormaliseSequenceLogo());
1509 view.setShowGroupConsensus(av.isShowGroupConsensus());
1510 view.setShowGroupConservation(av.isShowGroupConservation());
1511 view.setShowNPfeatureTooltip(av.isShowNPFeats());
1512 view.setShowDbRefTooltip(av.isShowDBRefs());
1513 view.setFollowHighlight(av.isFollowHighlight());
1514 view.setFollowSelection(av.followSelection);
1515 view.setIgnoreGapsinConsensus(av.isIgnoreGapsConsensus());
1516 view.setShowComplementFeatures(av.isShowComplementFeatures());
1517 view.setShowComplementFeaturesOnTop(
1518 av.isShowComplementFeaturesOnTop());
1519 if (av.getFeaturesDisplayed() != null)
1521 FeatureSettings fs = new FeatureSettings();
1523 FeatureRendererModel fr = ap.getSeqPanel().seqCanvas
1524 .getFeatureRenderer();
1525 String[] renderOrder = fr.getRenderOrder().toArray(new String[0]);
1527 Vector<String> settingsAdded = new Vector<>();
1528 if (renderOrder != null)
1530 for (String featureType : renderOrder)
1532 FeatureSettings.Setting setting = new FeatureSettings.Setting();
1533 setting.setType(featureType);
1536 * save any filter for the feature type
1538 FeatureMatcherSetI filter = fr.getFeatureFilter(featureType);
1539 if (filter != null) {
1540 Iterator<FeatureMatcherI> filters = filter.getMatchers().iterator();
1541 FeatureMatcherI firstFilter = filters.next();
1542 setting.setMatcherSet(Jalview2XML.marshalFilter(
1543 firstFilter, filters, filter.isAnded()));
1547 * save colour scheme for the feature type
1549 FeatureColourI fcol = fr.getFeatureStyle(featureType);
1550 if (!fcol.isSimpleColour())
1552 setting.setColour(fcol.getMaxColour().getRGB());
1553 setting.setMincolour(fcol.getMinColour().getRGB());
1554 setting.setMin(fcol.getMin());
1555 setting.setMax(fcol.getMax());
1556 setting.setColourByLabel(fcol.isColourByLabel());
1557 if (fcol.isColourByAttribute())
1559 String[] attName = fcol.getAttributeName();
1560 setting.getAttributeName().add(attName[0]);
1561 if (attName.length > 1)
1563 setting.getAttributeName().add(attName[1]);
1566 setting.setAutoScale(fcol.isAutoScaled());
1567 setting.setThreshold(fcol.getThreshold());
1568 Color noColour = fcol.getNoColour();
1569 if (noColour == null)
1571 setting.setNoValueColour(NoValueColour.NONE);
1573 else if (noColour.equals(fcol.getMaxColour()))
1575 setting.setNoValueColour(NoValueColour.MAX);
1579 setting.setNoValueColour(NoValueColour.MIN);
1581 // -1 = No threshold, 0 = Below, 1 = Above
1582 setting.setThreshstate(fcol.isAboveThreshold() ? 1
1583 : (fcol.isBelowThreshold() ? 0 : -1));
1587 setting.setColour(fcol.getColour().getRGB());
1591 av.getFeaturesDisplayed().isVisible(featureType));
1593 .getOrder(featureType);
1596 setting.setOrder(rorder);
1598 /// fs.addSetting(setting);
1599 fs.getSetting().add(setting);
1600 settingsAdded.addElement(featureType);
1604 // is groups actually supposed to be a map here ?
1605 Iterator<String> en = fr.getFeatureGroups().iterator();
1606 Vector<String> groupsAdded = new Vector<>();
1607 while (en.hasNext())
1609 String grp = en.next();
1610 if (groupsAdded.contains(grp))
1614 Group g = new Group();
1616 g.setDisplay(((Boolean) fr.checkGroupVisibility(grp, false))
1619 fs.getGroup().add(g);
1620 groupsAdded.addElement(grp);
1622 // jms.setFeatureSettings(fs);
1623 object.setFeatureSettings(fs);
1626 if (av.hasHiddenColumns())
1628 jalview.datamodel.HiddenColumns hidden = av.getAlignment()
1629 .getHiddenColumns();
1632 warn("REPORT BUG: avoided null columnselection bug (DMAM reported). Please contact Jim about this.");
1636 Iterator<int[]> hiddenRegions = hidden.iterator();
1637 while (hiddenRegions.hasNext())
1639 int[] region = hiddenRegions.next();
1640 HiddenColumns hc = new HiddenColumns();
1641 hc.setStart(region[0]);
1642 hc.setEnd(region[1]);
1643 // view.addHiddenColumns(hc);
1644 view.getHiddenColumns().add(hc);
1648 if (calcIdSet.size() > 0)
1650 for (String calcId : calcIdSet)
1652 if (calcId.trim().length() > 0)
1654 CalcIdParam cidp = createCalcIdParam(calcId, av);
1655 // Some calcIds have no parameters.
1658 // view.addCalcIdParam(cidp);
1659 view.getCalcIdParam().add(cidp);
1665 // jms.addViewport(view);
1666 object.getViewport().add(view);
1668 // object.setJalviewModelSequence(jms);
1669 // object.getVamsasModel().addSequenceSet(vamsasSet);
1670 object.getVamsasModel().getSequenceSet().add(vamsasSet);
1672 if (jout != null && fileName != null)
1674 // We may not want to write the object to disk,
1675 // eg we can copy the alignViewport to a new view object
1676 // using save and then load
1679 fileName = fileName.replace('\\', '/');
1680 System.out.println("Writing jar entry " + fileName);
1681 JarEntry entry = new JarEntry(fileName);
1682 jout.putNextEntry(entry);
1683 PrintWriter pout = new PrintWriter(
1684 new OutputStreamWriter(jout, UTF_8));
1685 JAXBContext jaxbContext = JAXBContext
1686 .newInstance(JalviewModel.class);
1687 Marshaller jaxbMarshaller = jaxbContext.createMarshaller();
1689 // output pretty printed
1690 // jaxbMarshaller.setProperty(Marshaller.JAXB_FORMATTED_OUTPUT, true);
1691 jaxbMarshaller.marshal(
1692 new ObjectFactory().createJalviewModel(object), pout);
1694 // jaxbMarshaller.marshal(object, pout);
1695 // marshaller.marshal(object);
1698 } catch (Exception ex)
1700 // TODO: raise error in GUI if marshalling failed.
1701 System.err.println("Error writing Jalview project");
1702 ex.printStackTrace();
1709 * Writes PCA viewer attributes and computed values to an XML model object and
1710 * adds it to the JalviewModel. Any exceptions are reported by logging.
1712 protected void savePCA(PCAPanel panel, JalviewModel object)
1716 PcaViewer viewer = new PcaViewer();
1717 viewer.setHeight(panel.getHeight());
1718 viewer.setWidth(panel.getWidth());
1719 viewer.setXpos(panel.getX());
1720 viewer.setYpos(panel.getY());
1721 viewer.setTitle(panel.getTitle());
1722 PCAModel pcaModel = panel.getPcaModel();
1723 viewer.setScoreModelName(pcaModel.getScoreModelName());
1724 viewer.setXDim(panel.getSelectedDimensionIndex(X));
1725 viewer.setYDim(panel.getSelectedDimensionIndex(Y));
1726 viewer.setZDim(panel.getSelectedDimensionIndex(Z));
1728 panel.getRotatableCanvas().getBackgroundColour().getRGB());
1729 viewer.setScaleFactor(panel.getRotatableCanvas().getScaleFactor());
1730 float[] spMin = panel.getRotatableCanvas().getSeqMin();
1731 SeqPointMin spmin = new SeqPointMin();
1732 spmin.setXPos(spMin[0]);
1733 spmin.setYPos(spMin[1]);
1734 spmin.setZPos(spMin[2]);
1735 viewer.setSeqPointMin(spmin);
1736 float[] spMax = panel.getRotatableCanvas().getSeqMax();
1737 SeqPointMax spmax = new SeqPointMax();
1738 spmax.setXPos(spMax[0]);
1739 spmax.setYPos(spMax[1]);
1740 spmax.setZPos(spMax[2]);
1741 viewer.setSeqPointMax(spmax);
1742 viewer.setShowLabels(panel.getRotatableCanvas().isShowLabels());
1743 viewer.setLinkToAllViews(
1744 panel.getRotatableCanvas().isApplyToAllViews());
1745 SimilarityParamsI sp = pcaModel.getSimilarityParameters();
1746 viewer.setIncludeGaps(sp.includeGaps());
1747 viewer.setMatchGaps(sp.matchGaps());
1748 viewer.setIncludeGappedColumns(sp.includeGappedColumns());
1749 viewer.setDenominateByShortestLength(sp.denominateByShortestLength());
1752 * sequence points on display
1754 for (jalview.datamodel.SequencePoint spt : pcaModel
1755 .getSequencePoints())
1757 SequencePoint point = new SequencePoint();
1758 point.setSequenceRef(seqHash(spt.getSequence()));
1759 point.setXPos(spt.coord.x);
1760 point.setYPos(spt.coord.y);
1761 point.setZPos(spt.coord.z);
1762 viewer.getSequencePoint().add(point);
1766 * (end points of) axes on display
1768 for (Point p : panel.getRotatableCanvas().getAxisEndPoints())
1771 Axis axis = new Axis();
1775 viewer.getAxis().add(axis);
1779 * raw PCA data (note we are not restoring PCA inputs here -
1780 * alignment view, score model, similarity parameters)
1782 PcaDataType data = new PcaDataType();
1783 viewer.setPcaData(data);
1784 PCA pca = pcaModel.getPcaData();
1786 DoubleMatrix pm = new DoubleMatrix();
1787 saveDoubleMatrix(pca.getPairwiseScores(), pm);
1788 data.setPairwiseMatrix(pm);
1790 DoubleMatrix tm = new DoubleMatrix();
1791 saveDoubleMatrix(pca.getTridiagonal(), tm);
1792 data.setTridiagonalMatrix(tm);
1794 DoubleMatrix eigenMatrix = new DoubleMatrix();
1795 data.setEigenMatrix(eigenMatrix);
1796 saveDoubleMatrix(pca.getEigenmatrix(), eigenMatrix);
1798 object.getPcaViewer().add(viewer);
1799 } catch (Throwable t)
1801 Cache.log.error("Error saving PCA: " + t.getMessage());
1806 * Stores values from a matrix into an XML element, including (if present) the
1811 * @see #loadDoubleMatrix(DoubleMatrix)
1813 protected void saveDoubleMatrix(MatrixI m, DoubleMatrix xmlMatrix)
1815 xmlMatrix.setRows(m.height());
1816 xmlMatrix.setColumns(m.width());
1817 for (int i = 0; i < m.height(); i++)
1819 DoubleVector row = new DoubleVector();
1820 for (int j = 0; j < m.width(); j++)
1822 row.getV().add(m.getValue(i, j));
1824 xmlMatrix.getRow().add(row);
1826 if (m.getD() != null)
1828 DoubleVector dVector = new DoubleVector();
1829 for (double d : m.getD())
1831 dVector.getV().add(d);
1833 xmlMatrix.setD(dVector);
1835 if (m.getE() != null)
1837 DoubleVector eVector = new DoubleVector();
1838 for (double e : m.getE())
1840 eVector.getV().add(e);
1842 xmlMatrix.setE(eVector);
1847 * Loads XML matrix data into a new Matrix object, including the D and/or E
1848 * vectors (if present)
1852 * @see Jalview2XML#saveDoubleMatrix(MatrixI, DoubleMatrix)
1854 protected MatrixI loadDoubleMatrix(DoubleMatrix mData)
1856 int rows = mData.getRows();
1857 double[][] vals = new double[rows][];
1859 for (int i = 0; i < rows; i++)
1861 List<Double> dVector = mData.getRow().get(i).getV();
1862 vals[i] = new double[dVector.size()];
1864 for (Double d : dVector)
1870 MatrixI m = new Matrix(vals);
1872 if (mData.getD() != null)
1874 List<Double> dVector = mData.getD().getV();
1875 double[] vec = new double[dVector.size()];
1877 for (Double d : dVector)
1883 if (mData.getE() != null)
1885 List<Double> dVector = mData.getE().getV();
1886 double[] vec = new double[dVector.size()];
1888 for (Double d : dVector)
1899 * Save any Varna viewers linked to this sequence. Writes an rnaViewer element
1900 * for each viewer, with
1902 * <li>viewer geometry (position, size, split pane divider location)</li>
1903 * <li>index of the selected structure in the viewer (currently shows gapped
1905 * <li>the id of the annotation holding RNA secondary structure</li>
1906 * <li>(currently only one SS is shown per viewer, may be more in future)</li>
1908 * Varna viewer state is also written out (in native Varna XML) to separate
1909 * project jar entries. A separate entry is written for each RNA structure
1910 * displayed, with the naming convention
1912 * <li>rna_viewId_sequenceId_annotationId_[gapped|trimmed]</li>
1920 * @param storeDataset
1922 protected void saveRnaViewers(JarOutputStream jout, JSeq jseq,
1923 final SequenceI jds, List<String> viewIds, AlignmentPanel ap,
1924 boolean storeDataset)
1926 if (Desktop.desktop == null)
1930 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1931 for (int f = frames.length - 1; f > -1; f--)
1933 if (frames[f] instanceof AppVarna)
1935 AppVarna varna = (AppVarna) frames[f];
1937 * link the sequence to every viewer that is showing it and is linked to
1938 * its alignment panel
1940 if (varna.isListeningFor(jds) && ap == varna.getAlignmentPanel())
1942 String viewId = varna.getViewId();
1943 RnaViewer rna = new RnaViewer();
1944 rna.setViewId(viewId);
1945 rna.setTitle(varna.getTitle());
1946 rna.setXpos(varna.getX());
1947 rna.setYpos(varna.getY());
1948 rna.setWidth(varna.getWidth());
1949 rna.setHeight(varna.getHeight());
1950 rna.setDividerLocation(varna.getDividerLocation());
1951 rna.setSelectedRna(varna.getSelectedIndex());
1952 // jseq.addRnaViewer(rna);
1953 jseq.getRnaViewer().add(rna);
1956 * Store each Varna panel's state once in the project per sequence.
1957 * First time through only (storeDataset==false)
1959 // boolean storeSessions = false;
1960 // String sequenceViewId = viewId + seqsToIds.get(jds);
1961 // if (!storeDataset && !viewIds.contains(sequenceViewId))
1963 // viewIds.add(sequenceViewId);
1964 // storeSessions = true;
1966 for (RnaModel model : varna.getModels())
1968 if (model.seq == jds)
1971 * VARNA saves each view (sequence or alignment secondary
1972 * structure, gapped or trimmed) as a separate XML file
1974 String jarEntryName = rnaSessions.get(model);
1975 if (jarEntryName == null)
1978 String varnaStateFile = varna.getStateInfo(model.rna);
1979 jarEntryName = RNA_PREFIX + viewId + "_" + nextCounter();
1980 copyFileToJar(jout, varnaStateFile, jarEntryName);
1981 rnaSessions.put(model, jarEntryName);
1983 SecondaryStructure ss = new SecondaryStructure();
1984 String annotationId = varna.getAnnotation(jds).annotationId;
1985 ss.setAnnotationId(annotationId);
1986 ss.setViewerState(jarEntryName);
1987 ss.setGapped(model.gapped);
1988 ss.setTitle(model.title);
1989 // rna.addSecondaryStructure(ss);
1990 rna.getSecondaryStructure().add(ss);
1999 * Copy the contents of a file to a new entry added to the output jar
2003 * @param jarEntryName
2005 protected void copyFileToJar(JarOutputStream jout, String infilePath,
2006 String jarEntryName)
2008 DataInputStream dis = null;
2011 File file = new File(infilePath);
2012 if (file.exists() && jout != null)
2014 dis = new DataInputStream(new FileInputStream(file));
2015 byte[] data = new byte[(int) file.length()];
2016 dis.readFully(data);
2017 writeJarEntry(jout, jarEntryName, data);
2019 } catch (Exception ex)
2021 ex.printStackTrace();
2029 } catch (IOException e)
2038 * Write the data to a new entry of given name in the output jar file
2041 * @param jarEntryName
2043 * @throws IOException
2045 protected void writeJarEntry(JarOutputStream jout, String jarEntryName,
2046 byte[] data) throws IOException
2050 jarEntryName = jarEntryName.replace('\\','/');
2051 System.out.println("Writing jar entry " + jarEntryName);
2052 jout.putNextEntry(new JarEntry(jarEntryName));
2053 DataOutputStream dout = new DataOutputStream(jout);
2054 dout.write(data, 0, data.length);
2061 * Save the state of a structure viewer
2066 * the archive XML element under which to save the state
2069 * @param matchedFile
2073 protected String saveStructureState(AlignmentPanel ap, SequenceI jds,
2074 Pdbids pdb, PDBEntry entry, List<String> viewIds,
2075 String matchedFile, StructureViewerBase viewFrame)
2077 final AAStructureBindingModel bindingModel = viewFrame.getBinding();
2080 * Look for any bindings for this viewer to the PDB file of interest
2081 * (including part matches excluding chain id)
2083 for (int peid = 0; peid < bindingModel.getPdbCount(); peid++)
2085 final PDBEntry pdbentry = bindingModel.getPdbEntry(peid);
2086 final String pdbId = pdbentry.getId();
2087 if (!pdbId.equals(entry.getId())
2088 && !(entry.getId().length() > 4 && entry.getId().toLowerCase()
2089 .startsWith(pdbId.toLowerCase())))
2092 * not interested in a binding to a different PDB entry here
2096 if (matchedFile == null)
2098 matchedFile = pdbentry.getFile();
2100 else if (!matchedFile.equals(pdbentry.getFile()))
2103 "Probably lost some PDB-Sequence mappings for this structure file (which apparently has same PDB Entry code): "
2104 + pdbentry.getFile());
2108 // can get at it if the ID
2109 // match is ambiguous (e.g.
2112 for (int smap = 0; smap < viewFrame.getBinding()
2113 .getSequence()[peid].length; smap++)
2115 // if (jal.findIndex(jmol.jmb.sequence[peid][smap]) > -1)
2116 if (jds == viewFrame.getBinding().getSequence()[peid][smap])
2118 StructureState state = new StructureState();
2119 state.setVisible(true);
2120 state.setXpos(viewFrame.getX());
2121 state.setYpos(viewFrame.getY());
2122 state.setWidth(viewFrame.getWidth());
2123 state.setHeight(viewFrame.getHeight());
2124 final String viewId = viewFrame.getViewId();
2125 state.setViewId(viewId);
2126 state.setAlignwithAlignPanel(viewFrame.isUsedforaligment(ap));
2127 state.setColourwithAlignPanel(viewFrame.isUsedforcolourby(ap));
2128 state.setColourByJmol(viewFrame.isColouredByViewer());
2129 state.setType(viewFrame.getViewerType().toString());
2130 // pdb.addStructureState(state);
2131 pdb.getStructureState().add(state);
2139 * Populates the AnnotationColourScheme xml for save. This captures the
2140 * settings of the options in the 'Colour by Annotation' dialog.
2143 * @param userColours
2147 private AnnotationColourScheme constructAnnotationColours(
2148 AnnotationColourGradient acg, List<UserColourScheme> userColours,
2151 AnnotationColourScheme ac = new AnnotationColourScheme();
2152 ac.setAboveThreshold(acg.getAboveThreshold());
2153 ac.setThreshold(acg.getAnnotationThreshold());
2154 // 2.10.2 save annotationId (unique) not annotation label
2155 ac.setAnnotation(acg.getAnnotation().annotationId);
2156 if (acg.getBaseColour() instanceof UserColourScheme)
2159 setUserColourScheme(acg.getBaseColour(), userColours, jm));
2164 ColourSchemeProperty.getColourName(acg.getBaseColour()));
2167 ac.setMaxColour(acg.getMaxColour().getRGB());
2168 ac.setMinColour(acg.getMinColour().getRGB());
2169 ac.setPerSequence(acg.isSeqAssociated());
2170 ac.setPredefinedColours(acg.isPredefinedColours());
2174 private void storeAlignmentAnnotation(AlignmentAnnotation[] aa,
2175 IdentityHashMap<SequenceGroup, String> groupRefs,
2176 AlignmentViewport av, Set<String> calcIdSet, boolean storeDS,
2177 SequenceSet vamsasSet)
2180 for (int i = 0; i < aa.length; i++)
2182 Annotation an = new Annotation();
2184 AlignmentAnnotation annotation = aa[i];
2185 if (annotation.annotationId != null)
2187 annotationIds.put(annotation.annotationId, annotation);
2190 an.setId(annotation.annotationId);
2192 an.setVisible(annotation.visible);
2194 an.setDescription(annotation.description);
2196 if (annotation.sequenceRef != null)
2198 // 2.9 JAL-1781 xref on sequence id rather than name
2199 an.setSequenceRef(seqsToIds.get(annotation.sequenceRef));
2201 if (annotation.groupRef != null)
2203 String groupIdr = groupRefs.get(annotation.groupRef);
2204 if (groupIdr == null)
2206 // make a locally unique String
2207 groupRefs.put(annotation.groupRef,
2208 groupIdr = ("" + System.currentTimeMillis()
2209 + annotation.groupRef.getName()
2210 + groupRefs.size()));
2212 an.setGroupRef(groupIdr.toString());
2215 // store all visualization attributes for annotation
2216 an.setGraphHeight(annotation.graphHeight);
2217 an.setCentreColLabels(annotation.centreColLabels);
2218 an.setScaleColLabels(annotation.scaleColLabel);
2219 an.setShowAllColLabels(annotation.showAllColLabels);
2220 an.setBelowAlignment(annotation.belowAlignment);
2222 if (annotation.graph > 0)
2225 an.setGraphType(annotation.graph);
2226 an.setGraphGroup(annotation.graphGroup);
2227 if (annotation.getThreshold() != null)
2229 ThresholdLine line = new ThresholdLine();
2230 line.setLabel(annotation.getThreshold().label);
2231 line.setValue(annotation.getThreshold().value);
2232 line.setColour(annotation.getThreshold().colour.getRGB());
2233 an.setThresholdLine(line);
2241 an.setLabel(annotation.label);
2243 if (annotation == av.getAlignmentQualityAnnot()
2244 || annotation == av.getAlignmentConservationAnnotation()
2245 || annotation == av.getAlignmentConsensusAnnotation()
2246 || annotation.autoCalculated)
2248 // new way of indicating autocalculated annotation -
2249 an.setAutoCalculated(annotation.autoCalculated);
2251 if (annotation.hasScore())
2253 an.setScore(annotation.getScore());
2256 if (annotation.getCalcId() != null)
2258 calcIdSet.add(annotation.getCalcId());
2259 an.setCalcId(annotation.getCalcId());
2261 if (annotation.hasProperties())
2263 for (String pr : annotation.getProperties())
2265 jalview.xml.binding.jalview.Annotation.Property prop = new jalview.xml.binding.jalview.Annotation.Property();
2267 prop.setValue(annotation.getProperty(pr));
2268 // an.addProperty(prop);
2269 an.getProperty().add(prop);
2273 AnnotationElement ae;
2274 if (annotation.annotations != null)
2276 an.setScoreOnly(false);
2277 for (int a = 0; a < annotation.annotations.length; a++)
2279 if ((annotation == null) || (annotation.annotations[a] == null))
2284 ae = new AnnotationElement();
2285 if (annotation.annotations[a].description != null)
2287 ae.setDescription(annotation.annotations[a].description);
2289 if (annotation.annotations[a].displayCharacter != null)
2291 ae.setDisplayCharacter(
2292 annotation.annotations[a].displayCharacter);
2295 if (!Float.isNaN(annotation.annotations[a].value))
2297 ae.setValue(annotation.annotations[a].value);
2301 if (annotation.annotations[a].secondaryStructure > ' ')
2303 ae.setSecondaryStructure(
2304 annotation.annotations[a].secondaryStructure + "");
2307 if (annotation.annotations[a].colour != null
2308 && annotation.annotations[a].colour != java.awt.Color.black)
2310 ae.setColour(annotation.annotations[a].colour.getRGB());
2313 // an.addAnnotationElement(ae);
2314 an.getAnnotationElement().add(ae);
2315 if (annotation.autoCalculated)
2317 // only write one non-null entry into the annotation row -
2318 // sufficient to get the visualization attributes necessary to
2326 an.setScoreOnly(true);
2328 if (!storeDS || (storeDS && !annotation.autoCalculated))
2330 // skip autocalculated annotation - these are only provided for
2332 // vamsasSet.addAnnotation(an);
2333 vamsasSet.getAnnotation().add(an);
2339 private CalcIdParam createCalcIdParam(String calcId, AlignViewport av)
2341 AutoCalcSetting settings = av.getCalcIdSettingsFor(calcId);
2342 if (settings != null)
2344 CalcIdParam vCalcIdParam = new CalcIdParam();
2345 vCalcIdParam.setCalcId(calcId);
2346 // vCalcIdParam.addServiceURL(settings.getServiceURI());
2347 vCalcIdParam.getServiceURL().add(settings.getServiceURI());
2348 // generic URI allowing a third party to resolve another instance of the
2349 // service used for this calculation
2350 for (String url : settings.getServiceURLs())
2352 // vCalcIdParam.addServiceURL(urls);
2353 vCalcIdParam.getServiceURL().add(url);
2355 vCalcIdParam.setVersion("1.0");
2356 if (settings.getPreset() != null)
2358 WsParamSetI setting = settings.getPreset();
2359 vCalcIdParam.setName(setting.getName());
2360 vCalcIdParam.setDescription(setting.getDescription());
2364 vCalcIdParam.setName("");
2365 vCalcIdParam.setDescription("Last used parameters");
2367 // need to be able to recover 1) settings 2) user-defined presets or
2368 // recreate settings from preset 3) predefined settings provided by
2369 // service - or settings that can be transferred (or discarded)
2370 vCalcIdParam.setParameters(
2371 settings.getWsParamFile().replace("\n", "|\\n|"));
2372 vCalcIdParam.setAutoUpdate(settings.isAutoUpdate());
2373 // todo - decide if updateImmediately is needed for any projects.
2375 return vCalcIdParam;
2380 private boolean recoverCalcIdParam(CalcIdParam calcIdParam,
2383 if (calcIdParam.getVersion().equals("1.0"))
2385 final String[] calcIds = calcIdParam.getServiceURL().toArray(new String[0]);
2386 Jws2Instance service = Jws2Discoverer.getDiscoverer()
2387 .getPreferredServiceFor(calcIds);
2388 if (service != null)
2390 WsParamSetI parmSet = null;
2393 parmSet = service.getParamStore().parseServiceParameterFile(
2394 calcIdParam.getName(), calcIdParam.getDescription(),
2396 calcIdParam.getParameters().replace("|\\n|", "\n"));
2397 } catch (IOException x)
2399 warn("Couldn't parse parameter data for "
2400 + calcIdParam.getCalcId(), x);
2403 List<ArgumentI> argList = null;
2404 if (calcIdParam.getName().length() > 0)
2406 parmSet = service.getParamStore()
2407 .getPreset(calcIdParam.getName());
2408 if (parmSet != null)
2410 // TODO : check we have a good match with settings in AACon -
2411 // otherwise we'll need to create a new preset
2416 argList = parmSet.getArguments();
2419 AAConSettings settings = new AAConSettings(
2420 calcIdParam.isAutoUpdate(), service, parmSet, argList);
2421 av.setCalcIdSettingsFor(calcIdParam.getCalcId(), settings,
2422 calcIdParam.isNeedsUpdate());
2427 warn("Cannot resolve a service for the parameters used in this project. Try configuring a JABAWS server.");
2431 throw new Error(MessageManager.formatMessage(
2432 "error.unsupported_version_calcIdparam", new Object[]
2433 { calcIdParam.toString() }));
2437 * External mapping between jalview objects and objects yielding a valid and
2438 * unique object ID string. This is null for normal Jalview project IO, but
2439 * non-null when a jalview project is being read or written as part of a
2442 IdentityHashMap jv2vobj = null;
2445 * Construct a unique ID for jvobj using either existing bindings or if none
2446 * exist, the result of the hashcode call for the object.
2449 * jalview data object
2450 * @return unique ID for referring to jvobj
2452 private String makeHashCode(Object jvobj, String altCode)
2454 if (jv2vobj != null)
2456 Object id = jv2vobj.get(jvobj);
2459 return id.toString();
2461 // check string ID mappings
2462 if (jvids2vobj != null && jvobj instanceof String)
2464 id = jvids2vobj.get(jvobj);
2468 return id.toString();
2470 // give up and warn that something has gone wrong
2471 warn("Cannot find ID for object in external mapping : " + jvobj);
2477 * return local jalview object mapped to ID, if it exists
2481 * @return null or object bound to idcode
2483 private Object retrieveExistingObj(String idcode)
2485 if (idcode != null && vobj2jv != null)
2487 return vobj2jv.get(idcode);
2493 * binding from ID strings from external mapping table to jalview data model
2496 private Hashtable vobj2jv;
2498 private Sequence createVamsasSequence(String id, SequenceI jds)
2500 return createVamsasSequence(true, id, jds, null);
2503 private Sequence createVamsasSequence(boolean recurse, String id,
2504 SequenceI jds, SequenceI parentseq)
2506 Sequence vamsasSeq = new Sequence();
2507 vamsasSeq.setId(id);
2508 vamsasSeq.setName(jds.getName());
2509 vamsasSeq.setSequence(jds.getSequenceAsString());
2510 vamsasSeq.setDescription(jds.getDescription());
2511 List<DBRefEntry> dbrefs = null;
2512 if (jds.getDatasetSequence() != null)
2514 vamsasSeq.setDsseqid(seqHash(jds.getDatasetSequence()));
2518 // seqId==dsseqid so we can tell which sequences really are
2519 // dataset sequences only
2520 vamsasSeq.setDsseqid(id);
2521 dbrefs = jds.getDBRefs();
2522 if (parentseq == null)
2529 * save any dbrefs; special subclass GeneLocus is flagged as 'locus'
2533 for (int d = 0, nd = dbrefs.size(); d < nd; d++)
2535 DBRef dbref = new DBRef();
2536 DBRefEntry ref = dbrefs.get(d);
2537 dbref.setSource(ref.getSource());
2538 dbref.setVersion(ref.getVersion());
2539 dbref.setAccessionId(ref.getAccessionId());
2540 if (ref instanceof GeneLocus)
2542 dbref.setLocus(true);
2546 Mapping mp = createVamsasMapping(ref.getMap(), parentseq,
2548 dbref.setMapping(mp);
2550 vamsasSeq.getDBRef().add(dbref);
2556 private Mapping createVamsasMapping(jalview.datamodel.Mapping jmp,
2557 SequenceI parentseq, SequenceI jds, boolean recurse)
2560 if (jmp.getMap() != null)
2564 jalview.util.MapList mlst = jmp.getMap();
2565 List<int[]> r = mlst.getFromRanges();
2566 for (int[] range : r)
2568 MapListFrom mfrom = new MapListFrom();
2569 mfrom.setStart(range[0]);
2570 mfrom.setEnd(range[1]);
2571 // mp.addMapListFrom(mfrom);
2572 mp.getMapListFrom().add(mfrom);
2574 r = mlst.getToRanges();
2575 for (int[] range : r)
2577 MapListTo mto = new MapListTo();
2578 mto.setStart(range[0]);
2579 mto.setEnd(range[1]);
2580 // mp.addMapListTo(mto);
2581 mp.getMapListTo().add(mto);
2583 mp.setMapFromUnit(BigInteger.valueOf(mlst.getFromRatio()));
2584 mp.setMapToUnit(BigInteger.valueOf(mlst.getToRatio()));
2585 if (jmp.getTo() != null)
2587 // MappingChoice mpc = new MappingChoice();
2589 // check/create ID for the sequence referenced by getTo()
2592 SequenceI ps = null;
2593 if (parentseq != jmp.getTo()
2594 && parentseq.getDatasetSequence() != jmp.getTo())
2596 // chaining dbref rather than a handshaking one
2597 jmpid = seqHash(ps = jmp.getTo());
2601 jmpid = seqHash(ps = parentseq);
2603 // mpc.setDseqFor(jmpid);
2604 mp.setDseqFor(jmpid);
2605 if (!seqRefIds.containsKey(jmpid))
2607 jalview.bin.Cache.log.debug("creatign new DseqFor ID");
2608 seqRefIds.put(jmpid, ps);
2612 jalview.bin.Cache.log.debug("reusing DseqFor ID");
2615 // mp.setMappingChoice(mpc);
2621 String setUserColourScheme(jalview.schemes.ColourSchemeI cs,
2622 List<UserColourScheme> userColours, JalviewModel jm)
2625 jalview.schemes.UserColourScheme ucs = (jalview.schemes.UserColourScheme) cs;
2626 boolean newucs = false;
2627 if (!userColours.contains(ucs))
2629 userColours.add(ucs);
2632 id = "ucs" + userColours.indexOf(ucs);
2635 // actually create the scheme's entry in the XML model
2636 java.awt.Color[] colours = ucs.getColours();
2637 UserColours uc = new UserColours();
2638 // UserColourScheme jbucs = new UserColourScheme();
2639 JalviewUserColours jbucs = new JalviewUserColours();
2641 for (int i = 0; i < colours.length; i++)
2643 Colour col = new Colour();
2644 col.setName(ResidueProperties.aa[i]);
2645 col.setRGB(jalview.util.Format.getHexString(colours[i]));
2646 // jbucs.addColour(col);
2647 jbucs.getColour().add(col);
2649 if (ucs.getLowerCaseColours() != null)
2651 colours = ucs.getLowerCaseColours();
2652 for (int i = 0; i < colours.length; i++)
2654 Colour col = new Colour();
2655 col.setName(ResidueProperties.aa[i].toLowerCase());
2656 col.setRGB(jalview.util.Format.getHexString(colours[i]));
2657 // jbucs.addColour(col);
2658 jbucs.getColour().add(col);
2663 uc.setUserColourScheme(jbucs);
2664 // jm.addUserColours(uc);
2665 jm.getUserColours().add(uc);
2671 jalview.schemes.UserColourScheme getUserColourScheme(
2672 JalviewModel jm, String id)
2674 List<UserColours> uc = jm.getUserColours();
2675 UserColours colours = null;
2677 for (int i = 0; i < uc.length; i++)
2679 if (uc[i].getId().equals(id))
2686 for (UserColours c : uc)
2688 if (c.getId().equals(id))
2695 java.awt.Color[] newColours = new java.awt.Color[24];
2697 for (int i = 0; i < 24; i++)
2699 newColours[i] = new java.awt.Color(Integer.parseInt(
2700 // colours.getUserColourScheme().getColour(i).getRGB(), 16));
2701 colours.getUserColourScheme().getColour().get(i).getRGB(),
2705 jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(
2708 if (colours.getUserColourScheme().getColour().size()/*Count()*/ > 24)
2710 newColours = new java.awt.Color[23];
2711 for (int i = 0; i < 23; i++)
2713 newColours[i] = new java.awt.Color(Integer.parseInt(
2714 colours.getUserColourScheme().getColour().get(i + 24)
2718 ucs.setLowerCaseColours(newColours);
2725 * contains last error message (if any) encountered by XML loader.
2727 String errorMessage = null;
2730 * flag to control whether the Jalview2XML_V1 parser should be deferred to if
2731 * exceptions are raised during project XML parsing
2733 public boolean attemptversion1parse = false;
2736 * Load a jalview project archive from a jar file
2739 * - HTTP URL or filename
2741 public AlignFrame loadJalviewAlign(final Object file)
2744 jalview.gui.AlignFrame af = null;
2748 // create list to store references for any new Jmol viewers created
2749 newStructureViewers = new Vector<>();
2750 // UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
2751 // Workaround is to make sure caller implements the JarInputStreamProvider
2753 // so we can re-open the jar input stream for each entry.
2755 jarInputStreamProvider jprovider = createjarInputStreamProvider(file);
2756 af = loadJalviewAlign(jprovider);
2759 af.setMenusForViewport();
2761 } catch (MalformedURLException e)
2763 errorMessage = "Invalid URL format for '" + file + "'";
2769 SwingUtilities.invokeAndWait(new Runnable()
2774 setLoadingFinishedForNewStructureViewers();
2777 } catch (Exception x)
2779 System.err.println("Error loading alignment: " + x.getMessage());
2785 @SuppressWarnings("unused")
2786 private jarInputStreamProvider createjarInputStreamProvider(final Object ofile) throws MalformedURLException {
2788 // BH 2018 allow for bytes already attached to File object
2790 String file = (ofile instanceof File ? ((File) ofile).getCanonicalPath() : ofile.toString());
2791 byte[] bytes = Platform.isJS() ? Platform.getFileBytes((File) ofile)
2794 errorMessage = null;
2795 uniqueSetSuffix = null;
2797 viewportsAdded.clear();
2798 frefedSequence = null;
2800 if (file.startsWith("http://")) {
2801 url = new URL(file);
2803 final URL _url = url;
2804 return new jarInputStreamProvider() {
2807 public JarInputStream getJarInputStream() throws IOException {
2808 if (bytes != null) {
2809 // System.out.println("Jalview2XML: opening byte jarInputStream for bytes.length=" + bytes.length);
2810 return new JarInputStream(new ByteArrayInputStream(bytes));
2813 // System.out.println("Jalview2XML: opening url jarInputStream for " + _url);
2814 return new JarInputStream(_url.openStream());
2816 // System.out.println("Jalview2XML: opening file jarInputStream for " + file);
2817 return new JarInputStream(new FileInputStream(file));
2822 public String getFilename() {
2826 } catch (IOException e) {
2827 e.printStackTrace();
2833 * Recover jalview session from a jalview project archive. Caller may
2834 * initialise uniqueSetSuffix, seqRefIds, viewportsAdded and frefedSequence
2835 * themselves. Any null fields will be initialised with default values,
2836 * non-null fields are left alone.
2841 public AlignFrame loadJalviewAlign(final jarInputStreamProvider jprovider)
2843 errorMessage = null;
2844 if (uniqueSetSuffix == null)
2846 uniqueSetSuffix = System.currentTimeMillis() % 100000 + "";
2848 if (seqRefIds == null)
2852 AlignFrame af = null, _af = null;
2853 IdentityHashMap<AlignmentI, AlignmentI> importedDatasets = new IdentityHashMap<>();
2854 Map<String, AlignFrame> gatherToThisFrame = new HashMap<>();
2855 final String file = jprovider.getFilename();
2858 JarInputStream jin = null;
2859 JarEntry jarentry = null;
2864 jin = jprovider.getJarInputStream();
2865 for (int i = 0; i < entryCount; i++)
2867 jarentry = jin.getNextJarEntry();
2870 if (jarentry != null && jarentry.getName().endsWith(".xml"))
2872 JAXBContext jc = JAXBContext
2873 .newInstance("jalview.xml.binding.jalview");
2874 XMLStreamReader streamReader = XMLInputFactory.newInstance()
2875 .createXMLStreamReader(jin);
2876 javax.xml.bind.Unmarshaller um = jc.createUnmarshaller();
2877 JAXBElement<JalviewModel> jbe = um
2878 .unmarshal(streamReader, JalviewModel.class);
2879 JalviewModel object = jbe.getValue();
2881 if (true) // !skipViewport(object))
2883 _af = loadFromObject(object, file, true, jprovider);
2884 if (_af != null && object.getViewport().size() > 0)
2885 // getJalviewModelSequence().getViewportCount() > 0)
2889 // store a reference to the first view
2892 if (_af.getViewport().isGatherViewsHere())
2894 // if this is a gathered view, keep its reference since
2895 // after gathering views, only this frame will remain
2897 gatherToThisFrame.put(_af.getViewport().getSequenceSetId(),
2900 // Save dataset to register mappings once all resolved
2901 importedDatasets.put(
2902 af.getViewport().getAlignment().getDataset(),
2903 af.getViewport().getAlignment().getDataset());
2908 else if (jarentry != null)
2910 // Some other file here.
2913 } while (jarentry != null);
2914 resolveFrefedSequences();
2915 } catch (IOException ex)
2917 ex.printStackTrace();
2918 errorMessage = "Couldn't locate Jalview XML file : " + file;
2920 "Exception whilst loading jalview XML file : " + ex + "\n");
2921 } catch (Exception ex)
2923 System.err.println("Parsing as Jalview Version 2 file failed.");
2924 ex.printStackTrace(System.err);
2925 if (attemptversion1parse)
2927 // used to attempt to parse as V1 castor-generated xml
2929 if (Desktop.instance != null)
2931 Desktop.instance.stopLoading();
2935 System.out.println("Successfully loaded archive file");
2938 ex.printStackTrace();
2941 "Exception whilst loading jalview XML file : " + ex + "\n");
2942 } catch (OutOfMemoryError e)
2944 // Don't use the OOM Window here
2945 errorMessage = "Out of memory loading jalview XML file";
2946 System.err.println("Out of memory whilst loading jalview XML file");
2947 e.printStackTrace();
2951 * Regather multiple views (with the same sequence set id) to the frame (if
2952 * any) that is flagged as the one to gather to, i.e. convert them to tabbed
2953 * views instead of separate frames. Note this doesn't restore a state where
2954 * some expanded views in turn have tabbed views - the last "first tab" read
2955 * in will play the role of gatherer for all.
2957 for (AlignFrame fr : gatherToThisFrame.values())
2959 Desktop.instance.gatherViews(fr);
2962 restoreSplitFrames();
2963 for (AlignmentI ds : importedDatasets.keySet())
2965 if (ds.getCodonFrames() != null)
2967 StructureSelectionManager
2968 .getStructureSelectionManager(Desktop.instance)
2969 .registerMappings(ds.getCodonFrames());
2972 if (errorMessage != null)
2977 if (Desktop.instance != null)
2979 Desktop.instance.stopLoading();
2986 * Try to reconstruct and display SplitFrame windows, where each contains
2987 * complementary dna and protein alignments. Done by pairing up AlignFrame
2988 * objects (created earlier) which have complementary viewport ids associated.
2990 protected void restoreSplitFrames()
2992 List<SplitFrame> gatherTo = new ArrayList<>();
2993 List<AlignFrame> addedToSplitFrames = new ArrayList<>();
2994 Map<String, AlignFrame> dna = new HashMap<>();
2997 * Identify the DNA alignments
2999 for (Entry<Viewport, AlignFrame> candidate : splitFrameCandidates
3002 AlignFrame af = candidate.getValue();
3003 if (af.getViewport().getAlignment().isNucleotide())
3005 dna.put(candidate.getKey().getId(), af);
3010 * Try to match up the protein complements
3012 for (Entry<Viewport, AlignFrame> candidate : splitFrameCandidates
3015 AlignFrame af = candidate.getValue();
3016 if (!af.getViewport().getAlignment().isNucleotide())
3018 String complementId = candidate.getKey().getComplementId();
3019 // only non-null complements should be in the Map
3020 if (complementId != null && dna.containsKey(complementId))
3022 final AlignFrame dnaFrame = dna.get(complementId);
3023 SplitFrame sf = createSplitFrame(dnaFrame, af);
3024 addedToSplitFrames.add(dnaFrame);
3025 addedToSplitFrames.add(af);
3026 dnaFrame.setMenusForViewport();
3027 af.setMenusForViewport();
3028 if (af.getViewport().isGatherViewsHere())
3037 * Open any that we failed to pair up (which shouldn't happen!) as
3038 * standalone AlignFrame's.
3040 for (Entry<Viewport, AlignFrame> candidate : splitFrameCandidates
3043 AlignFrame af = candidate.getValue();
3044 if (!addedToSplitFrames.contains(af))
3046 Viewport view = candidate.getKey();
3047 Desktop.addInternalFrame(af, view.getTitle(),
3048 safeInt(view.getWidth()), safeInt(view.getHeight()));
3049 af.setMenusForViewport();
3050 System.err.println("Failed to restore view " + view.getTitle()
3051 + " to split frame");
3056 * Gather back into tabbed views as flagged.
3058 for (SplitFrame sf : gatherTo)
3060 Desktop.instance.gatherViews(sf);
3063 splitFrameCandidates.clear();
3067 * Construct and display one SplitFrame holding DNA and protein alignments.
3070 * @param proteinFrame
3073 protected SplitFrame createSplitFrame(AlignFrame dnaFrame,
3074 AlignFrame proteinFrame)
3076 SplitFrame splitFrame = new SplitFrame(dnaFrame, proteinFrame);
3077 String title = MessageManager.getString("label.linked_view_title");
3078 int width = (int) dnaFrame.getBounds().getWidth();
3079 int height = (int) (dnaFrame.getBounds().getHeight()
3080 + proteinFrame.getBounds().getHeight() + 50);
3083 * SplitFrame location is saved to both enclosed frames
3085 splitFrame.setLocation(dnaFrame.getX(), dnaFrame.getY());
3086 Desktop.addInternalFrame(splitFrame, title, width, height);
3089 * And compute cDNA consensus (couldn't do earlier with consensus as
3090 * mappings were not yet present)
3092 proteinFrame.getViewport().alignmentChanged(proteinFrame.alignPanel);
3098 * check errorMessage for a valid error message and raise an error box in the
3099 * GUI or write the current errorMessage to stderr and then clear the error
3102 protected void reportErrors()
3104 reportErrors(false);
3107 protected void reportErrors(final boolean saving)
3109 if (errorMessage != null)
3111 final String finalErrorMessage = errorMessage;
3114 javax.swing.SwingUtilities.invokeLater(new Runnable()
3119 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
3121 "Error " + (saving ? "saving" : "loading")
3123 JvOptionPane.WARNING_MESSAGE);
3129 System.err.println("Problem loading Jalview file: " + errorMessage);
3132 errorMessage = null;
3135 Map<String, String> alreadyLoadedPDB = new HashMap<>();
3138 * when set, local views will be updated from view stored in JalviewXML
3139 * Currently (28th Sep 2008) things will go horribly wrong in vamsas document
3140 * sync if this is set to true.
3142 private final boolean updateLocalViews = false;
3145 * Returns the path to a temporary file holding the PDB file for the given PDB
3146 * id. The first time of asking, searches for a file of that name in the
3147 * Jalview project jar, and copies it to a new temporary file. Any repeat
3148 * requests just return the path to the file previously created.
3154 String loadPDBFile(jarInputStreamProvider jprovider, String pdbId,
3157 if (alreadyLoadedPDB.containsKey(pdbId))
3159 return alreadyLoadedPDB.get(pdbId).toString();
3162 String tempFile = copyJarEntry(jprovider, pdbId, "jalview_pdb",
3164 if (tempFile != null)
3166 alreadyLoadedPDB.put(pdbId, tempFile);
3172 * Copies the jar entry of given name to a new temporary file and returns the
3173 * path to the file, or null if the entry is not found.
3176 * @param jarEntryName
3178 * a prefix for the temporary file name, must be at least three
3180 * @param suffixModel
3181 * null or original file - so new file can be given the same suffix
3185 protected String copyJarEntry(jarInputStreamProvider jprovider,
3186 String jarEntryName, String prefix, String suffixModel)
3188 BufferedReader in = null;
3189 PrintWriter out = null;
3190 String suffix = ".tmp";
3191 if (suffixModel == null)
3193 suffixModel = jarEntryName;
3195 int sfpos = suffixModel.lastIndexOf(".");
3196 if (sfpos > -1 && sfpos < (suffixModel.length() - 1))
3198 suffix = "." + suffixModel.substring(sfpos + 1);
3202 JarInputStream jin = jprovider.getJarInputStream();
3204 * if (jprovider.startsWith("http://")) { jin = new JarInputStream(new
3205 * URL(jprovider).openStream()); } else { jin = new JarInputStream(new
3206 * FileInputStream(jprovider)); }
3209 JarEntry entry = null;
3212 entry = jin.getNextJarEntry();
3213 } while (entry != null && !entry.getName().equals(jarEntryName));
3216 in = new BufferedReader(new InputStreamReader(jin, UTF_8));
3217 File outFile = File.createTempFile(prefix, suffix);
3218 outFile.deleteOnExit();
3219 out = new PrintWriter(new FileOutputStream(outFile));
3222 while ((data = in.readLine()) != null)
3227 String t = outFile.getAbsolutePath();
3232 warn("Couldn't find entry in Jalview Jar for " + jarEntryName);
3234 } catch (Exception ex)
3236 ex.printStackTrace();
3244 } catch (IOException e)
3258 private class JvAnnotRow
3260 public JvAnnotRow(int i, AlignmentAnnotation jaa)
3267 * persisted version of annotation row from which to take vis properties
3269 public jalview.datamodel.AlignmentAnnotation template;
3272 * original position of the annotation row in the alignment
3278 * Load alignment frame from jalview XML DOM object
3280 * @param jalviewModel
3283 * filename source string
3284 * @param loadTreesAndStructures
3285 * when false only create Viewport
3287 * data source provider
3288 * @return alignment frame created from view stored in DOM
3290 AlignFrame loadFromObject(JalviewModel jalviewModel, String file,
3291 boolean loadTreesAndStructures, jarInputStreamProvider jprovider)
3293 SequenceSet vamsasSet = jalviewModel.getVamsasModel().getSequenceSet().get(0);
3294 List<Sequence> vamsasSeqs = vamsasSet.getSequence();
3296 // JalviewModelSequence jms = object.getJalviewModelSequence();
3298 // Viewport view = (jms.getViewportCount() > 0) ? jms.getViewport(0)
3300 Viewport view = (jalviewModel.getViewport().size() > 0)
3301 ? jalviewModel.getViewport().get(0)
3304 // ////////////////////////////////
3305 // INITIALISE ALIGNMENT SEQUENCESETID AND VIEWID
3308 // If we just load in the same jar file again, the sequenceSetId
3309 // will be the same, and we end up with multiple references
3310 // to the same sequenceSet. We must modify this id on load
3311 // so that each load of the file gives a unique id
3314 * used to resolve correct alignment dataset for alignments with multiple
3317 String uniqueSeqSetId = null;
3318 String viewId = null;
3321 uniqueSeqSetId = view.getSequenceSetId() + uniqueSetSuffix;
3322 viewId = (view.getId() == null ? null
3323 : view.getId() + uniqueSetSuffix);
3326 // ////////////////////////////////
3329 List<SequenceI> hiddenSeqs = null;
3331 List<SequenceI> tmpseqs = new ArrayList<>();
3333 boolean multipleView = false;
3334 SequenceI referenceseqForView = null;
3335 // JSeq[] jseqs = object.getJalviewModelSequence().getJSeq();
3336 List<JSeq> jseqs = jalviewModel.getJSeq();
3337 int vi = 0; // counter in vamsasSeq array
3338 for (int i = 0; i < jseqs.size(); i++)
3340 JSeq jseq = jseqs.get(i);
3341 String seqId = jseq.getId();
3343 SequenceI tmpSeq = seqRefIds.get(seqId);
3346 if (!incompleteSeqs.containsKey(seqId))
3348 // may not need this check, but keep it for at least 2.9,1 release
3349 if (tmpSeq.getStart() != jseq.getStart()
3350 || tmpSeq.getEnd() != jseq.getEnd())
3353 "Warning JAL-2154 regression: updating start/end for sequence "
3354 + tmpSeq.toString() + " to " + jseq);
3359 incompleteSeqs.remove(seqId);
3361 if (vamsasSeqs.size() > vi
3362 && vamsasSeqs.get(vi).getId().equals(seqId))
3364 // most likely we are reading a dataset XML document so
3365 // update from vamsasSeq section of XML for this sequence
3366 tmpSeq.setName(vamsasSeqs.get(vi).getName());
3367 tmpSeq.setDescription(vamsasSeqs.get(vi).getDescription());
3368 tmpSeq.setSequence(vamsasSeqs.get(vi).getSequence());
3373 // reading multiple views, so vamsasSeq set is a subset of JSeq
3374 multipleView = true;
3376 tmpSeq.setStart(jseq.getStart());
3377 tmpSeq.setEnd(jseq.getEnd());
3378 tmpseqs.add(tmpSeq);
3382 Sequence vamsasSeq = vamsasSeqs.get(vi);
3383 tmpSeq = new jalview.datamodel.Sequence(vamsasSeq.getName(),
3384 vamsasSeq.getSequence());
3385 tmpSeq.setDescription(vamsasSeq.getDescription());
3386 tmpSeq.setStart(jseq.getStart());
3387 tmpSeq.setEnd(jseq.getEnd());
3388 tmpSeq.setVamsasId(uniqueSetSuffix + seqId);
3389 seqRefIds.put(vamsasSeq.getId(), tmpSeq);
3390 tmpseqs.add(tmpSeq);
3394 if (safeBoolean(jseq.isViewreference()))
3396 referenceseqForView = tmpseqs.get(tmpseqs.size() - 1);
3399 if (jseq.isHidden() != null && jseq.isHidden().booleanValue())
3401 if (hiddenSeqs == null)
3403 hiddenSeqs = new ArrayList<>();
3406 hiddenSeqs.add(tmpSeq);
3411 // Create the alignment object from the sequence set
3412 // ///////////////////////////////
3413 SequenceI[] orderedSeqs = tmpseqs
3414 .toArray(new SequenceI[tmpseqs.size()]);
3416 AlignmentI al = null;
3417 // so we must create or recover the dataset alignment before going further
3418 // ///////////////////////////////
3419 if (vamsasSet.getDatasetId() == null || vamsasSet.getDatasetId() == "")
3421 // older jalview projects do not have a dataset - so creat alignment and
3423 al = new Alignment(orderedSeqs);
3424 al.setDataset(null);
3428 boolean isdsal = jalviewModel.getViewport().isEmpty();
3431 // we are importing a dataset record, so
3432 // recover reference to an alignment already materialsed as dataset
3433 al = getDatasetFor(vamsasSet.getDatasetId());
3437 // materialse the alignment
3438 al = new Alignment(orderedSeqs);
3442 addDatasetRef(vamsasSet.getDatasetId(), al);
3445 // finally, verify all data in vamsasSet is actually present in al
3446 // passing on flag indicating if it is actually a stored dataset
3447 recoverDatasetFor(vamsasSet, al, isdsal, uniqueSeqSetId);
3450 if (referenceseqForView != null)
3452 al.setSeqrep(referenceseqForView);
3454 // / Add the alignment properties
3455 for (int i = 0; i < vamsasSet.getSequenceSetProperties().size(); i++)
3457 SequenceSetProperties ssp = vamsasSet.getSequenceSetProperties()
3459 al.setProperty(ssp.getKey(), ssp.getValue());
3462 // ///////////////////////////////
3464 Hashtable pdbloaded = new Hashtable(); // TODO nothing writes to this??
3467 // load sequence features, database references and any associated PDB
3468 // structures for the alignment
3470 // prior to 2.10, this part would only be executed the first time a
3471 // sequence was encountered, but not afterwards.
3472 // now, for 2.10 projects, this is also done if the xml doc includes
3473 // dataset sequences not actually present in any particular view.
3475 for (int i = 0; i < vamsasSeqs.size(); i++)
3477 JSeq jseq = jseqs.get(i);
3478 if (jseq.getFeatures().size() > 0)
3480 List<Feature> features = jseq.getFeatures();
3481 for (int f = 0; f < features.size(); f++)
3483 Feature feat = features.get(f);
3484 SequenceFeature sf = new SequenceFeature(feat.getType(),
3485 feat.getDescription(), feat.getBegin(), feat.getEnd(),
3486 safeFloat(feat.getScore()), feat.getFeatureGroup());
3487 sf.setStatus(feat.getStatus());
3490 * load any feature attributes - include map-valued attributes
3492 Map<String, Map<String, String>> mapAttributes = new HashMap<>();
3493 for (int od = 0; od < feat.getOtherData().size(); od++)
3495 OtherData keyValue = feat.getOtherData().get(od);
3496 String attributeName = keyValue.getKey();
3497 String attributeValue = keyValue.getValue();
3498 if (attributeName.startsWith("LINK"))
3500 sf.addLink(attributeValue);
3504 String subAttribute = keyValue.getKey2();
3505 if (subAttribute == null)
3507 // simple string-valued attribute
3508 sf.setValue(attributeName, attributeValue);
3512 // attribute 'key' has sub-attribute 'key2'
3513 if (!mapAttributes.containsKey(attributeName))
3515 mapAttributes.put(attributeName, new HashMap<>());
3517 mapAttributes.get(attributeName).put(subAttribute,
3522 for (Entry<String, Map<String, String>> mapAttribute : mapAttributes
3525 sf.setValue(mapAttribute.getKey(), mapAttribute.getValue());
3528 // adds feature to datasequence's feature set (since Jalview 2.10)
3529 al.getSequenceAt(i).addSequenceFeature(sf);
3532 if (vamsasSeqs.get(i).getDBRef().size() > 0)
3534 // adds dbrefs to datasequence's set (since Jalview 2.10)
3536 al.getSequenceAt(i).getDatasetSequence() == null
3537 ? al.getSequenceAt(i)
3538 : al.getSequenceAt(i).getDatasetSequence(),
3541 if (jseq.getPdbids().size() > 0)
3543 List<Pdbids> ids = jseq.getPdbids();
3544 for (int p = 0; p < ids.size(); p++)
3546 Pdbids pdbid = ids.get(p);
3547 jalview.datamodel.PDBEntry entry = new jalview.datamodel.PDBEntry();
3548 entry.setId(pdbid.getId());
3549 if (pdbid.getType() != null)
3551 if (PDBEntry.Type.getType(pdbid.getType()) != null)
3553 entry.setType(PDBEntry.Type.getType(pdbid.getType()));
3557 entry.setType(PDBEntry.Type.FILE);
3560 // jprovider is null when executing 'New View'
3561 if (pdbid.getFile() != null && jprovider != null)
3563 if (!pdbloaded.containsKey(pdbid.getFile()))
3565 entry.setFile(loadPDBFile(jprovider, pdbid.getId(),
3570 entry.setFile(pdbloaded.get(pdbid.getId()).toString());
3574 if (pdbid.getPdbentryItem() != null)
3576 for (PdbentryItem item : pdbid.getPdbentryItem())
3578 for (Property pr : item.getProperty())
3580 entry.setProperty(pr.getName(), pr.getValue());
3585 for (Property prop : pdbid.getProperty())
3587 entry.setProperty(prop.getName(), prop.getValue());
3589 StructureSelectionManager
3590 .getStructureSelectionManager(Desktop.instance)
3591 .registerPDBEntry(entry);
3592 // adds PDBEntry to datasequence's set (since Jalview 2.10)
3593 if (al.getSequenceAt(i).getDatasetSequence() != null)
3595 al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
3599 al.getSequenceAt(i).addPDBId(entry);
3604 } // end !multipleview
3606 // ///////////////////////////////
3607 // LOAD SEQUENCE MAPPINGS
3609 if (vamsasSet.getAlcodonFrame().size() > 0)
3611 // TODO Potentially this should only be done once for all views of an
3613 List<AlcodonFrame> alc = vamsasSet.getAlcodonFrame();
3614 for (int i = 0; i < alc.size(); i++)
3616 AlignedCodonFrame cf = new AlignedCodonFrame();
3617 if (alc.get(i).getAlcodMap().size() > 0)
3619 List<AlcodMap> maps = alc.get(i).getAlcodMap();
3620 for (int m = 0; m < maps.size(); m++)
3622 AlcodMap map = maps.get(m);
3623 SequenceI dnaseq = seqRefIds.get(map.getDnasq());
3625 jalview.datamodel.Mapping mapping = null;
3626 // attach to dna sequence reference.
3627 if (map.getMapping() != null)
3629 mapping = addMapping(map.getMapping());
3630 if (dnaseq != null && mapping.getTo() != null)
3632 cf.addMap(dnaseq, mapping.getTo(), mapping.getMap());
3638 newAlcodMapRef(map.getDnasq(), cf, mapping));
3642 al.addCodonFrame(cf);
3647 // ////////////////////////////////
3649 List<JvAnnotRow> autoAlan = new ArrayList<>();
3652 * store any annotations which forward reference a group's ID
3654 Map<String, List<AlignmentAnnotation>> groupAnnotRefs = new Hashtable<>();
3656 if (vamsasSet.getAnnotation().size()/*Count()*/ > 0)
3658 List<Annotation> an = vamsasSet.getAnnotation();
3660 for (int i = 0; i < an.size(); i++)
3662 Annotation annotation = an.get(i);
3665 * test if annotation is automatically calculated for this view only
3667 boolean autoForView = false;
3668 if (annotation.getLabel().equals("Quality")
3669 || annotation.getLabel().equals("Conservation")
3670 || annotation.getLabel().equals("Consensus"))
3672 // Kludge for pre 2.5 projects which lacked the autocalculated flag
3674 // JAXB has no has() test; schema defaults value to false
3675 // if (!annotation.hasAutoCalculated())
3677 // annotation.setAutoCalculated(true);
3680 if (autoForView || annotation.isAutoCalculated())
3682 // remove ID - we don't recover annotation from other views for
3683 // view-specific annotation
3684 annotation.setId(null);
3687 // set visibility for other annotation in this view
3688 String annotationId = annotation.getId();
3689 if (annotationId != null && annotationIds.containsKey(annotationId))
3691 AlignmentAnnotation jda = annotationIds.get(annotationId);
3692 // in principle Visible should always be true for annotation displayed
3693 // in multiple views
3694 if (annotation.isVisible() != null)
3696 jda.visible = annotation.isVisible();
3699 al.addAnnotation(jda);
3703 // Construct new annotation from model.
3704 List<AnnotationElement> ae = annotation.getAnnotationElement();
3705 jalview.datamodel.Annotation[] anot = null;
3706 java.awt.Color firstColour = null;
3708 if (!annotation.isScoreOnly())
3710 anot = new jalview.datamodel.Annotation[al.getWidth()];
3711 for (int aa = 0; aa < ae.size() && aa < anot.length; aa++)
3713 AnnotationElement annElement = ae.get(aa);
3714 anpos = annElement.getPosition();
3716 if (anpos >= anot.length)
3721 float value = safeFloat(annElement.getValue());
3722 anot[anpos] = new jalview.datamodel.Annotation(
3723 annElement.getDisplayCharacter(),
3724 annElement.getDescription(),
3725 (annElement.getSecondaryStructure() == null
3726 || annElement.getSecondaryStructure()
3730 .getSecondaryStructure()
3733 anot[anpos].colour = new Color(safeInt(annElement.getColour()));
3734 if (firstColour == null)
3736 firstColour = anot[anpos].colour;
3740 jalview.datamodel.AlignmentAnnotation jaa = null;
3742 if (annotation.isGraph())
3744 float llim = 0, hlim = 0;
3745 // if (autoForView || an[i].isAutoCalculated()) {
3748 jaa = new jalview.datamodel.AlignmentAnnotation(
3749 annotation.getLabel(), annotation.getDescription(), anot,
3750 llim, hlim, safeInt(annotation.getGraphType()));
3752 jaa.graphGroup = safeInt(annotation.getGraphGroup());
3753 jaa._linecolour = firstColour;
3754 if (annotation.getThresholdLine() != null)
3756 jaa.setThreshold(new jalview.datamodel.GraphLine(
3757 safeFloat(annotation.getThresholdLine().getValue()),
3758 annotation.getThresholdLine().getLabel(),
3759 new java.awt.Color(safeInt(
3760 annotation.getThresholdLine().getColour()))));
3762 if (autoForView || annotation.isAutoCalculated())
3764 // Hardwire the symbol display line to ensure that labels for
3765 // histograms are displayed
3771 jaa = new jalview.datamodel.AlignmentAnnotation(
3772 annotation.getLabel(), annotation.getDescription(), anot);
3773 jaa._linecolour = firstColour;
3775 // register new annotation
3776 if (annotation.getId() != null)
3778 annotationIds.put(annotation.getId(), jaa);
3779 jaa.annotationId = annotation.getId();
3781 // recover sequence association
3782 String sequenceRef = annotation.getSequenceRef();
3783 if (sequenceRef != null)
3785 // from 2.9 sequenceRef is to sequence id (JAL-1781)
3786 SequenceI sequence = seqRefIds.get(sequenceRef);
3787 if (sequence == null)
3789 // in pre-2.9 projects sequence ref is to sequence name
3790 sequence = al.findName(sequenceRef);
3792 if (sequence != null)
3794 jaa.createSequenceMapping(sequence, 1, true);
3795 sequence.addAlignmentAnnotation(jaa);
3798 // and make a note of any group association
3799 if (annotation.getGroupRef() != null
3800 && annotation.getGroupRef().length() > 0)
3802 List<jalview.datamodel.AlignmentAnnotation> aal = groupAnnotRefs
3803 .get(annotation.getGroupRef());
3806 aal = new ArrayList<>();
3807 groupAnnotRefs.put(annotation.getGroupRef(), aal);
3812 if (annotation.getScore() != null)
3814 jaa.setScore(annotation.getScore().doubleValue());
3816 if (annotation.isVisible() != null)
3818 jaa.visible = annotation.isVisible().booleanValue();
3821 if (annotation.isCentreColLabels() != null)
3823 jaa.centreColLabels = annotation.isCentreColLabels()
3827 if (annotation.isScaleColLabels() != null)
3829 jaa.scaleColLabel = annotation.isScaleColLabels().booleanValue();
3831 if (annotation.isAutoCalculated())
3833 // newer files have an 'autoCalculated' flag and store calculation
3834 // state in viewport properties
3835 jaa.autoCalculated = true; // means annotation will be marked for
3836 // update at end of load.
3838 if (annotation.getGraphHeight() != null)
3840 jaa.graphHeight = annotation.getGraphHeight().intValue();
3842 jaa.belowAlignment = annotation.isBelowAlignment();
3843 jaa.setCalcId(annotation.getCalcId());
3844 if (annotation.getProperty().size() > 0)
3846 for (Annotation.Property prop : annotation
3849 jaa.setProperty(prop.getName(), prop.getValue());
3852 if (jaa.autoCalculated)
3854 autoAlan.add(new JvAnnotRow(i, jaa));
3857 // if (!autoForView)
3859 // add autocalculated group annotation and any user created annotation
3861 al.addAnnotation(jaa);
3865 // ///////////////////////
3867 // Create alignment markup and styles for this view
3868 if (jalviewModel.getJGroup().size() > 0)
3870 List<JGroup> groups = jalviewModel.getJGroup();
3871 boolean addAnnotSchemeGroup = false;
3872 for (int i = 0; i < groups.size(); i++)
3874 JGroup jGroup = groups.get(i);
3875 ColourSchemeI cs = null;
3876 if (jGroup.getColour() != null)
3878 if (jGroup.getColour().startsWith("ucs"))
3880 cs = getUserColourScheme(jalviewModel, jGroup.getColour());
3882 else if (jGroup.getColour().equals("AnnotationColourGradient")
3883 && jGroup.getAnnotationColours() != null)
3885 addAnnotSchemeGroup = true;
3889 cs = ColourSchemeProperty.getColourScheme(null, al,
3890 jGroup.getColour());
3893 int pidThreshold = safeInt(jGroup.getPidThreshold());
3895 Vector<SequenceI> seqs = new Vector<>();
3897 for (int s = 0; s < jGroup.getSeq().size(); s++)
3899 String seqId = jGroup.getSeq().get(s);
3900 SequenceI ts = seqRefIds.get(seqId);
3904 seqs.addElement(ts);
3908 if (seqs.size() < 1)
3913 SequenceGroup sg = new SequenceGroup(seqs, jGroup.getName(), cs,
3914 safeBoolean(jGroup.isDisplayBoxes()),
3915 safeBoolean(jGroup.isDisplayText()),
3916 safeBoolean(jGroup.isColourText()),
3917 safeInt(jGroup.getStart()), safeInt(jGroup.getEnd()));
3918 sg.getGroupColourScheme().setThreshold(pidThreshold, true);
3919 sg.getGroupColourScheme()
3920 .setConservationInc(safeInt(jGroup.getConsThreshold()));
3921 sg.setOutlineColour(new Color(safeInt(jGroup.getOutlineColour())));
3923 sg.textColour = new Color(safeInt(jGroup.getTextCol1()));
3924 sg.textColour2 = new Color(safeInt(jGroup.getTextCol2()));
3925 sg.setShowNonconserved(safeBoolean(jGroup.isShowUnconserved()));
3926 sg.thresholdTextColour = safeInt(jGroup.getTextColThreshold());
3927 // attributes with a default in the schema are never null
3928 sg.setShowConsensusHistogram(jGroup.isShowConsensusHistogram());
3929 sg.setshowSequenceLogo(jGroup.isShowSequenceLogo());
3930 sg.setNormaliseSequenceLogo(jGroup.isNormaliseSequenceLogo());
3931 sg.setIgnoreGapsConsensus(jGroup.isIgnoreGapsinConsensus());
3932 if (jGroup.getConsThreshold() != null
3933 && jGroup.getConsThreshold().intValue() != 0)
3935 Conservation c = new Conservation("All", sg.getSequences(null), 0,
3938 c.verdict(false, 25);
3939 sg.cs.setConservation(c);
3942 if (jGroup.getId() != null && groupAnnotRefs.size() > 0)
3944 // re-instate unique group/annotation row reference
3945 List<AlignmentAnnotation> jaal = groupAnnotRefs
3946 .get(jGroup.getId());
3949 for (AlignmentAnnotation jaa : jaal)
3952 if (jaa.autoCalculated)
3954 // match up and try to set group autocalc alignment row for this
3956 if (jaa.label.startsWith("Consensus for "))
3958 sg.setConsensus(jaa);
3960 // match up and try to set group autocalc alignment row for this
3962 if (jaa.label.startsWith("Conservation for "))
3964 sg.setConservationRow(jaa);
3971 if (addAnnotSchemeGroup)
3973 // reconstruct the annotation colourscheme
3974 sg.setColourScheme(constructAnnotationColour(
3975 jGroup.getAnnotationColours(), null, al, jalviewModel, false));
3981 // only dataset in this model, so just return.
3984 // ///////////////////////////////
3987 AlignFrame af = null;
3988 AlignViewport av = null;
3989 // now check to see if we really need to create a new viewport.
3990 if (multipleView && viewportsAdded.size() == 0)
3992 // We recovered an alignment for which a viewport already exists.
3993 // TODO: fix up any settings necessary for overlaying stored state onto
3994 // state recovered from another document. (may not be necessary).
3995 // we may need a binding from a viewport in memory to one recovered from
3997 // and then recover its containing af to allow the settings to be applied.
3998 // TODO: fix for vamsas demo
4000 "About to recover a viewport for existing alignment: Sequence set ID is "
4002 Object seqsetobj = retrieveExistingObj(uniqueSeqSetId);
4003 if (seqsetobj != null)
4005 if (seqsetobj instanceof String)
4007 uniqueSeqSetId = (String) seqsetobj;
4009 "Recovered extant sequence set ID mapping for ID : New Sequence set ID is "
4015 "Warning : Collision between sequence set ID string and existing jalview object mapping.");
4021 * indicate that annotation colours are applied across all groups (pre
4022 * Jalview 2.8.1 behaviour)
4024 boolean doGroupAnnColour = Jalview2XML.isVersionStringLaterThan("2.8.1",
4025 jalviewModel.getVersion());
4027 AlignmentPanel ap = null;
4028 boolean isnewview = true;
4031 // Check to see if this alignment already has a view id == viewId
4032 jalview.gui.AlignmentPanel views[] = Desktop
4033 .getAlignmentPanels(uniqueSeqSetId);
4034 if (views != null && views.length > 0)
4036 for (int v = 0; v < views.length; v++)
4038 if (views[v].av.getViewId().equalsIgnoreCase(viewId))
4040 // recover the existing alignpanel, alignframe, viewport
4041 af = views[v].alignFrame;
4044 // TODO: could even skip resetting view settings if we don't want to
4045 // change the local settings from other jalview processes
4054 af = loadViewport(file, jseqs, hiddenSeqs, al, jalviewModel, view,
4055 uniqueSeqSetId, viewId, autoAlan);
4056 av = af.getViewport();
4061 * Load any trees, PDB structures and viewers
4063 * Not done if flag is false (when this method is used for New View)
4065 if (loadTreesAndStructures)
4067 loadTrees(jalviewModel, view, af, av, ap);
4068 loadPCAViewers(jalviewModel, ap);
4069 loadPDBStructures(jprovider, jseqs, af, ap);
4070 loadRnaViewers(jprovider, jseqs, ap);
4072 // and finally return.
4077 * Instantiate and link any saved RNA (Varna) viewers. The state of the Varna
4078 * panel is restored from separate jar entries, two (gapped and trimmed) per
4079 * sequence and secondary structure.
4081 * Currently each viewer shows just one sequence and structure (gapped and
4082 * trimmed), however this method is designed to support multiple sequences or
4083 * structures in viewers if wanted in future.
4089 private void loadRnaViewers(jarInputStreamProvider jprovider,
4090 List<JSeq> jseqs, AlignmentPanel ap)
4093 * scan the sequences for references to viewers; create each one the first
4094 * time it is referenced, add Rna models to existing viewers
4096 for (JSeq jseq : jseqs)
4098 for (int i = 0; i < jseq.getRnaViewer().size(); i++)
4100 RnaViewer viewer = jseq.getRnaViewer().get(i);
4101 AppVarna appVarna = findOrCreateVarnaViewer(viewer, uniqueSetSuffix,
4104 for (int j = 0; j < viewer.getSecondaryStructure().size(); j++)
4106 SecondaryStructure ss = viewer.getSecondaryStructure().get(j);
4107 SequenceI seq = seqRefIds.get(jseq.getId());
4108 AlignmentAnnotation ann = this.annotationIds
4109 .get(ss.getAnnotationId());
4112 * add the structure to the Varna display (with session state copied
4113 * from the jar to a temporary file)
4115 boolean gapped = safeBoolean(ss.isGapped());
4116 String rnaTitle = ss.getTitle();
4117 String sessionState = ss.getViewerState();
4118 String tempStateFile = copyJarEntry(jprovider, sessionState,
4120 RnaModel rna = new RnaModel(rnaTitle, ann, seq, null, gapped);
4121 appVarna.addModelSession(rna, rnaTitle, tempStateFile);
4123 appVarna.setInitialSelection(safeInt(viewer.getSelectedRna()));
4129 * Locate and return an already instantiated matching AppVarna, or create one
4133 * @param viewIdSuffix
4137 protected AppVarna findOrCreateVarnaViewer(RnaViewer viewer,
4138 String viewIdSuffix, AlignmentPanel ap)
4141 * on each load a suffix is appended to the saved viewId, to avoid conflicts
4142 * if load is repeated
4144 String postLoadId = viewer.getViewId() + viewIdSuffix;
4145 for (JInternalFrame frame : getAllFrames())
4147 if (frame instanceof AppVarna)
4149 AppVarna varna = (AppVarna) frame;
4150 if (postLoadId.equals(varna.getViewId()))
4152 // this viewer is already instantiated
4153 // could in future here add ap as another 'parent' of the
4154 // AppVarna window; currently just 1-to-many
4161 * viewer not found - make it
4163 RnaViewerModel model = new RnaViewerModel(postLoadId, viewer.getTitle(),
4164 safeInt(viewer.getXpos()), safeInt(viewer.getYpos()),
4165 safeInt(viewer.getWidth()), safeInt(viewer.getHeight()),
4166 safeInt(viewer.getDividerLocation()));
4167 AppVarna varna = new AppVarna(model, ap);
4173 * Load any saved trees
4181 protected void loadTrees(JalviewModel jm, Viewport view,
4182 AlignFrame af, AlignViewport av, AlignmentPanel ap)
4184 // TODO result of automated refactoring - are all these parameters needed?
4187 for (int t = 0; t < jm.getTree().size(); t++)
4190 Tree tree = jm.getTree().get(t);
4192 TreePanel tp = (TreePanel) retrieveExistingObj(tree.getId());
4195 tp = af.showNewickTree(new NewickFile(tree.getNewick()),
4196 tree.getTitle(), safeInt(tree.getWidth()),
4197 safeInt(tree.getHeight()), safeInt(tree.getXpos()),
4198 safeInt(tree.getYpos()));
4199 if (tree.getId() != null)
4201 // perhaps bind the tree id to something ?
4206 // update local tree attributes ?
4207 // TODO: should check if tp has been manipulated by user - if so its
4208 // settings shouldn't be modified
4209 tp.setTitle(tree.getTitle());
4210 tp.setBounds(new Rectangle(safeInt(tree.getXpos()),
4211 safeInt(tree.getYpos()), safeInt(tree.getWidth()),
4212 safeInt(tree.getHeight())));
4213 tp.setViewport(av); // af.viewport;
4214 // TODO: verify 'associate with all views' works still
4215 tp.getTreeCanvas().setViewport(av); // af.viewport;
4216 tp.getTreeCanvas().setAssociatedPanel(ap); // af.alignPanel;
4218 tp.getTreeCanvas().setApplyToAllViews(tree.isLinkToAllViews());
4221 warn("There was a problem recovering stored Newick tree: \n"
4222 + tree.getNewick());
4226 tp.fitToWindow.setState(safeBoolean(tree.isFitToWindow()));
4227 tp.fitToWindow_actionPerformed(null);
4229 if (tree.getFontName() != null)
4232 new Font(tree.getFontName(), safeInt(tree.getFontStyle()),
4233 safeInt(tree.getFontSize())));
4238 new Font(view.getFontName(), safeInt(view.getFontStyle()),
4239 safeInt(view.getFontSize())));
4242 tp.showPlaceholders(safeBoolean(tree.isMarkUnlinked()));
4243 tp.showBootstrap(safeBoolean(tree.isShowBootstrap()));
4244 tp.showDistances(safeBoolean(tree.isShowDistances()));
4246 tp.getTreeCanvas().setThreshold(safeFloat(tree.getThreshold()));
4248 if (safeBoolean(tree.isCurrentTree()))
4250 af.getViewport().setCurrentTree(tp.getTree());
4254 } catch (Exception ex)
4256 ex.printStackTrace();
4261 * Load and link any saved structure viewers.
4268 protected void loadPDBStructures(jarInputStreamProvider jprovider,
4269 List<JSeq> jseqs, AlignFrame af, AlignmentPanel ap)
4272 * Run through all PDB ids on the alignment, and collect mappings between
4273 * distinct view ids and all sequences referring to that view.
4275 Map<String, StructureViewerModel> structureViewers = new LinkedHashMap<>();
4277 for (int i = 0; i < jseqs.size(); i++)
4279 JSeq jseq = jseqs.get(i);
4280 if (jseq.getPdbids().size() > 0)
4282 List<Pdbids> ids = jseq.getPdbids();
4283 for (int p = 0; p < ids.size(); p++)
4285 Pdbids pdbid = ids.get(p);
4286 final int structureStateCount = pdbid.getStructureState().size();
4287 for (int s = 0; s < structureStateCount; s++)
4289 // check to see if we haven't already created this structure view
4290 final StructureState structureState = pdbid
4291 .getStructureState().get(s);
4292 String sviewid = (structureState.getViewId() == null) ? null
4293 : structureState.getViewId() + uniqueSetSuffix;
4294 jalview.datamodel.PDBEntry jpdb = new jalview.datamodel.PDBEntry();
4295 // Originally : pdbid.getFile()
4296 // : TODO: verify external PDB file recovery still works in normal
4297 // jalview project load
4299 loadPDBFile(jprovider, pdbid.getId(), pdbid.getFile()));
4300 jpdb.setId(pdbid.getId());
4302 int x = safeInt(structureState.getXpos());
4303 int y = safeInt(structureState.getYpos());
4304 int width = safeInt(structureState.getWidth());
4305 int height = safeInt(structureState.getHeight());
4307 // Probably don't need to do this anymore...
4308 // Desktop.desktop.getComponentAt(x, y);
4309 // TODO: NOW: check that this recovers the PDB file correctly.
4310 String pdbFile = loadPDBFile(jprovider, pdbid.getId(),
4312 jalview.datamodel.SequenceI seq = seqRefIds
4313 .get(jseq.getId() + "");
4314 if (sviewid == null)
4316 sviewid = "_jalview_pre2_4_" + x + "," + y + "," + width + ","
4319 if (!structureViewers.containsKey(sviewid))
4321 structureViewers.put(sviewid,
4322 new StructureViewerModel(x, y, width, height, false,
4323 false, true, structureState.getViewId(),
4324 structureState.getType()));
4325 // Legacy pre-2.7 conversion JAL-823 :
4326 // do not assume any view has to be linked for colour by
4330 // assemble String[] { pdb files }, String[] { id for each
4331 // file }, orig_fileloc, SequenceI[][] {{ seqs_file 1 }, {
4332 // seqs_file 2}, boolean[] {
4333 // linkAlignPanel,superposeWithAlignpanel}} from hash
4334 StructureViewerModel jmoldat = structureViewers.get(sviewid);
4335 jmoldat.setAlignWithPanel(jmoldat.isAlignWithPanel()
4336 || structureState.isAlignwithAlignPanel());
4339 * Default colour by linked panel to false if not specified (e.g.
4340 * for pre-2.7 projects)
4342 boolean colourWithAlignPanel = jmoldat.isColourWithAlignPanel();
4343 colourWithAlignPanel |= structureState.isColourwithAlignPanel();
4344 jmoldat.setColourWithAlignPanel(colourWithAlignPanel);
4347 * Default colour by viewer to true if not specified (e.g. for
4350 boolean colourByViewer = jmoldat.isColourByViewer();
4351 colourByViewer &= structureState.isColourByJmol();
4352 jmoldat.setColourByViewer(colourByViewer);
4354 if (jmoldat.getStateData().length() < structureState
4355 .getValue()/*Content()*/.length())
4357 jmoldat.setStateData(structureState.getValue());// Content());
4359 if (pdbid.getFile() != null)
4361 File mapkey = new File(pdbid.getFile());
4362 StructureData seqstrmaps = jmoldat.getFileData().get(mapkey);
4363 if (seqstrmaps == null)
4365 jmoldat.getFileData().put(mapkey,
4366 seqstrmaps = jmoldat.new StructureData(pdbFile,
4369 if (!seqstrmaps.getSeqList().contains(seq))
4371 seqstrmaps.getSeqList().add(seq);
4377 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");
4384 // Instantiate the associated structure views
4385 for (Entry<String, StructureViewerModel> entry : structureViewers
4390 createOrLinkStructureViewer(entry, af, ap, jprovider);
4391 } catch (Exception e)
4394 "Error loading structure viewer: " + e.getMessage());
4395 // failed - try the next one
4407 protected void createOrLinkStructureViewer(
4408 Entry<String, StructureViewerModel> viewerData, AlignFrame af,
4409 AlignmentPanel ap, jarInputStreamProvider jprovider)
4411 final StructureViewerModel stateData = viewerData.getValue();
4414 * Search for any viewer windows already open from other alignment views
4415 * that exactly match the stored structure state
4417 StructureViewerBase comp = findMatchingViewer(viewerData);
4421 linkStructureViewer(ap, comp, stateData);
4426 * From 2.9: stateData.type contains JMOL or CHIMERA, data is in jar entry
4427 * "viewer_"+stateData.viewId
4429 if (ViewerType.CHIMERA.toString().equals(stateData.getType()))
4431 createChimeraViewer(viewerData, af, jprovider);
4436 * else Jmol (if pre-2.9, stateData contains JMOL state string)
4438 createJmolViewer(viewerData, af, jprovider);
4443 * Create a new Chimera viewer.
4449 protected void createChimeraViewer(
4450 Entry<String, StructureViewerModel> viewerData, AlignFrame af,
4451 jarInputStreamProvider jprovider)
4453 StructureViewerModel data = viewerData.getValue();
4454 String chimeraSessionFile = data.getStateData();
4457 * Copy Chimera session from jar entry "viewer_"+viewId to a temporary file
4459 * NB this is the 'saved' viewId as in the project file XML, _not_ the
4460 * 'uniquified' sviewid used to reconstruct the viewer here
4462 String viewerJarEntryName = getViewerJarEntryName(data.getViewId());
4463 chimeraSessionFile = copyJarEntry(jprovider, viewerJarEntryName,
4466 Set<Entry<File, StructureData>> fileData = data.getFileData()
4468 List<PDBEntry> pdbs = new ArrayList<>();
4469 List<SequenceI[]> allseqs = new ArrayList<>();
4470 for (Entry<File, StructureData> pdb : fileData)
4472 String filePath = pdb.getValue().getFilePath();
4473 String pdbId = pdb.getValue().getPdbId();
4474 // pdbs.add(new PDBEntry(filePath, pdbId));
4475 pdbs.add(new PDBEntry(pdbId, null, PDBEntry.Type.PDB, filePath));
4476 final List<SequenceI> seqList = pdb.getValue().getSeqList();
4477 SequenceI[] seqs = seqList.toArray(new SequenceI[seqList.size()]);
4481 boolean colourByChimera = data.isColourByViewer();
4482 boolean colourBySequence = data.isColourWithAlignPanel();
4484 // TODO use StructureViewer as a factory here, see JAL-1761
4485 final PDBEntry[] pdbArray = pdbs.toArray(new PDBEntry[pdbs.size()]);
4486 final SequenceI[][] seqsArray = allseqs
4487 .toArray(new SequenceI[allseqs.size()][]);
4488 String newViewId = viewerData.getKey();
4490 ChimeraViewFrame cvf = new ChimeraViewFrame(chimeraSessionFile,
4491 af.alignPanel, pdbArray, seqsArray, colourByChimera,
4492 colourBySequence, newViewId);
4493 cvf.setSize(data.getWidth(), data.getHeight());
4494 cvf.setLocation(data.getX(), data.getY());
4498 * Create a new Jmol window. First parse the Jmol state to translate filenames
4499 * loaded into the view, and record the order in which files are shown in the
4500 * Jmol view, so we can add the sequence mappings in same order.
4506 protected void createJmolViewer(
4507 final Entry<String, StructureViewerModel> viewerData,
4508 AlignFrame af, jarInputStreamProvider jprovider)
4510 final StructureViewerModel svattrib = viewerData.getValue();
4511 String state = svattrib.getStateData();
4514 * Pre-2.9: state element value is the Jmol state string
4516 * 2.9+: @type is "JMOL", state data is in a Jar file member named "viewer_"
4519 if (ViewerType.JMOL.toString().equals(svattrib.getType()))
4521 state = readJarEntry(jprovider,
4522 getViewerJarEntryName(svattrib.getViewId()));
4525 List<String> pdbfilenames = new ArrayList<>();
4526 List<SequenceI[]> seqmaps = new ArrayList<>();
4527 List<String> pdbids = new ArrayList<>();
4528 StringBuilder newFileLoc = new StringBuilder(64);
4529 int cp = 0, ncp, ecp;
4530 Map<File, StructureData> oldFiles = svattrib.getFileData();
4531 while ((ncp = state.indexOf("load ", cp)) > -1)
4535 // look for next filename in load statement
4536 newFileLoc.append(state.substring(cp,
4537 ncp = (state.indexOf("\"", ncp + 1) + 1)));
4538 String oldfilenam = state.substring(ncp,
4539 ecp = state.indexOf("\"", ncp));
4540 // recover the new mapping data for this old filename
4541 // have to normalize filename - since Jmol and jalview do
4543 // translation differently.
4544 StructureData filedat = oldFiles.get(new File(oldfilenam));
4545 if (filedat == null)
4547 String reformatedOldFilename = oldfilenam.replaceAll("/", "\\\\");
4548 filedat = oldFiles.get(new File(reformatedOldFilename));
4550 newFileLoc.append(Platform.escapeBackslashes(filedat.getFilePath()));
4551 pdbfilenames.add(filedat.getFilePath());
4552 pdbids.add(filedat.getPdbId());
4553 seqmaps.add(filedat.getSeqList().toArray(new SequenceI[0]));
4554 newFileLoc.append("\"");
4555 cp = ecp + 1; // advance beyond last \" and set cursor so we can
4556 // look for next file statement.
4557 } while ((ncp = state.indexOf("/*file*/", cp)) > -1);
4561 // just append rest of state
4562 newFileLoc.append(state.substring(cp));
4566 System.err.print("Ignoring incomplete Jmol state for PDB ids: ");
4567 newFileLoc = new StringBuilder(state);
4568 newFileLoc.append("; load append ");
4569 for (File id : oldFiles.keySet())
4571 // add this and any other pdb files that should be present in
4573 StructureData filedat = oldFiles.get(id);
4574 newFileLoc.append(filedat.getFilePath());
4575 pdbfilenames.add(filedat.getFilePath());
4576 pdbids.add(filedat.getPdbId());
4577 seqmaps.add(filedat.getSeqList().toArray(new SequenceI[0]));
4578 newFileLoc.append(" \"");
4579 newFileLoc.append(filedat.getFilePath());
4580 newFileLoc.append("\"");
4583 newFileLoc.append(";");
4586 if (newFileLoc.length() == 0)
4590 int histbug = newFileLoc.indexOf("history = ");
4594 * change "history = [true|false];" to "history = [1|0];"
4597 int diff = histbug == -1 ? -1 : newFileLoc.indexOf(";", histbug);
4598 String val = (diff == -1) ? null
4599 : newFileLoc.substring(histbug, diff);
4600 if (val != null && val.length() >= 4)
4602 if (val.contains("e")) // eh? what can it be?
4604 if (val.trim().equals("true"))
4612 newFileLoc.replace(histbug, diff, val);
4617 final String[] pdbf = pdbfilenames
4618 .toArray(new String[pdbfilenames.size()]);
4619 final String[] id = pdbids.toArray(new String[pdbids.size()]);
4620 final SequenceI[][] sq = seqmaps
4621 .toArray(new SequenceI[seqmaps.size()][]);
4622 final String fileloc = newFileLoc.toString();
4623 final String sviewid = viewerData.getKey();
4624 final AlignFrame alf = af;
4625 final Rectangle rect = new Rectangle(svattrib.getX(), svattrib.getY(),
4626 svattrib.getWidth(), svattrib.getHeight());
4629 javax.swing.SwingUtilities.invokeAndWait(new Runnable()
4634 JalviewStructureDisplayI sview = null;
4637 sview = new StructureViewer(
4638 alf.alignPanel.getStructureSelectionManager())
4639 .createView(StructureViewer.ViewerType.JMOL,
4640 pdbf, id, sq, alf.alignPanel, svattrib,
4641 fileloc, rect, sviewid);
4642 addNewStructureViewer(sview);
4643 } catch (OutOfMemoryError ex)
4645 new OOMWarning("restoring structure view for PDB id " + id,
4646 (OutOfMemoryError) ex.getCause());
4647 if (sview != null && sview.isVisible())
4649 sview.closeViewer(false);
4650 sview.setVisible(false);
4656 } catch (InvocationTargetException ex)
4658 warn("Unexpected error when opening Jmol view.", ex);
4660 } catch (InterruptedException e)
4662 // e.printStackTrace();
4668 * Generates a name for the entry in the project jar file to hold state
4669 * information for a structure viewer
4674 protected String getViewerJarEntryName(String viewId)
4676 return VIEWER_PREFIX + viewId;
4680 * Returns any open frame that matches given structure viewer data. The match
4681 * is based on the unique viewId, or (for older project versions) the frame's
4687 protected StructureViewerBase findMatchingViewer(
4688 Entry<String, StructureViewerModel> viewerData)
4690 final String sviewid = viewerData.getKey();
4691 final StructureViewerModel svattrib = viewerData.getValue();
4692 StructureViewerBase comp = null;
4693 JInternalFrame[] frames = getAllFrames();
4694 for (JInternalFrame frame : frames)
4696 if (frame instanceof StructureViewerBase)
4699 * Post jalview 2.4 schema includes structure view id
4701 if (sviewid != null && ((StructureViewerBase) frame).getViewId()
4704 comp = (StructureViewerBase) frame;
4705 break; // break added in 2.9
4708 * Otherwise test for matching position and size of viewer frame
4710 else if (frame.getX() == svattrib.getX()
4711 && frame.getY() == svattrib.getY()
4712 && frame.getHeight() == svattrib.getHeight()
4713 && frame.getWidth() == svattrib.getWidth())
4715 comp = (StructureViewerBase) frame;
4716 // no break in faint hope of an exact match on viewId
4724 * Link an AlignmentPanel to an existing structure viewer.
4729 * @param useinViewerSuperpos
4730 * @param usetoColourbyseq
4731 * @param viewerColouring
4733 protected void linkStructureViewer(AlignmentPanel ap,
4734 StructureViewerBase viewer, StructureViewerModel stateData)
4736 // NOTE: if the jalview project is part of a shared session then
4737 // view synchronization should/could be done here.
4739 final boolean useinViewerSuperpos = stateData.isAlignWithPanel();
4740 final boolean usetoColourbyseq = stateData.isColourWithAlignPanel();
4741 final boolean viewerColouring = stateData.isColourByViewer();
4742 Map<File, StructureData> oldFiles = stateData.getFileData();
4745 * Add mapping for sequences in this view to an already open viewer
4747 final AAStructureBindingModel binding = viewer.getBinding();
4748 for (File id : oldFiles.keySet())
4750 // add this and any other pdb files that should be present in the
4752 StructureData filedat = oldFiles.get(id);
4753 String pdbFile = filedat.getFilePath();
4754 SequenceI[] seq = filedat.getSeqList().toArray(new SequenceI[0]);
4755 binding.getSsm().setMapping(seq, null, pdbFile, DataSourceType.FILE,
4757 binding.addSequenceForStructFile(pdbFile, seq);
4759 // and add the AlignmentPanel's reference to the view panel
4760 viewer.addAlignmentPanel(ap);
4761 if (useinViewerSuperpos)
4763 viewer.useAlignmentPanelForSuperposition(ap);
4767 viewer.excludeAlignmentPanelForSuperposition(ap);
4769 if (usetoColourbyseq)
4771 viewer.useAlignmentPanelForColourbyseq(ap, !viewerColouring);
4775 viewer.excludeAlignmentPanelForColourbyseq(ap);
4780 * Get all frames within the Desktop.
4784 protected JInternalFrame[] getAllFrames()
4786 JInternalFrame[] frames = null;
4787 // TODO is this necessary - is it safe - risk of hanging?
4792 frames = Desktop.desktop.getAllFrames();
4793 } catch (ArrayIndexOutOfBoundsException e)
4795 // occasional No such child exceptions are thrown here...
4799 } catch (InterruptedException f)
4803 } while (frames == null);
4808 * Answers true if 'version' is equal to or later than 'supported', where each
4809 * is formatted as major/minor versions like "2.8.3" or "2.3.4b1" for bugfix
4810 * changes. Development and test values for 'version' are leniently treated
4814 * - minimum version we are comparing against
4816 * - version of data being processsed
4819 public static boolean isVersionStringLaterThan(String supported,
4822 if (supported == null || version == null
4823 || version.equalsIgnoreCase("DEVELOPMENT BUILD")
4824 || version.equalsIgnoreCase("Test")
4825 || version.equalsIgnoreCase("AUTOMATED BUILD"))
4827 System.err.println("Assuming project file with "
4828 + (version == null ? "null" : version)
4829 + " is compatible with Jalview version " + supported);
4834 return StringUtils.compareVersions(version, supported, "b") >= 0;
4838 Vector<JalviewStructureDisplayI> newStructureViewers = null;
4840 protected void addNewStructureViewer(JalviewStructureDisplayI sview)
4842 if (newStructureViewers != null)
4844 sview.getBinding().setFinishedLoadingFromArchive(false);
4845 newStructureViewers.add(sview);
4849 protected void setLoadingFinishedForNewStructureViewers()
4851 if (newStructureViewers != null)
4853 for (JalviewStructureDisplayI sview : newStructureViewers)
4855 sview.getBinding().setFinishedLoadingFromArchive(true);
4857 newStructureViewers.clear();
4858 newStructureViewers = null;
4862 AlignFrame loadViewport(String file, List<JSeq> JSEQ,
4863 List<SequenceI> hiddenSeqs, AlignmentI al,
4864 JalviewModel jm, Viewport view, String uniqueSeqSetId,
4865 String viewId, List<JvAnnotRow> autoAlan)
4867 AlignFrame af = null;
4868 af = new AlignFrame(al, safeInt(view.getWidth()),
4869 safeInt(view.getHeight()), uniqueSeqSetId, viewId)
4873 // protected void processKeyEvent(java.awt.event.KeyEvent e) {
4874 // System.out.println("Jalview2XML AF " + e);
4875 // super.processKeyEvent(e);
4882 af.setFileName(file, FileFormat.Jalview);
4884 final AlignViewport viewport = af.getViewport();
4885 for (int i = 0; i < JSEQ.size(); i++)
4887 int colour = safeInt(JSEQ.get(i).getColour());
4888 viewport.setSequenceColour(viewport.getAlignment().getSequenceAt(i),
4894 viewport.setColourByReferenceSeq(true);
4895 viewport.setDisplayReferenceSeq(true);
4898 viewport.setGatherViewsHere(safeBoolean(view.isGatheredViews()));
4900 if (view.getSequenceSetId() != null)
4902 AlignmentViewport av = viewportsAdded.get(uniqueSeqSetId);
4904 viewport.setSequenceSetId(uniqueSeqSetId);
4907 // propagate shared settings to this new view
4908 viewport.setHistoryList(av.getHistoryList());
4909 viewport.setRedoList(av.getRedoList());
4913 viewportsAdded.put(uniqueSeqSetId, viewport);
4915 // TODO: check if this method can be called repeatedly without
4916 // side-effects if alignpanel already registered.
4917 PaintRefresher.Register(af.alignPanel, uniqueSeqSetId);
4919 // apply Hidden regions to view.
4920 if (hiddenSeqs != null)
4922 for (int s = 0; s < JSEQ.size(); s++)
4924 SequenceGroup hidden = new SequenceGroup();
4925 boolean isRepresentative = false;
4926 for (int r = 0; r < JSEQ.get(s).getHiddenSequences().size(); r++)
4928 isRepresentative = true;
4929 SequenceI sequenceToHide = al
4930 .getSequenceAt(JSEQ.get(s).getHiddenSequences().get(r));
4931 hidden.addSequence(sequenceToHide, false);
4932 // remove from hiddenSeqs list so we don't try to hide it twice
4933 hiddenSeqs.remove(sequenceToHide);
4935 if (isRepresentative)
4937 SequenceI representativeSequence = al.getSequenceAt(s);
4938 hidden.addSequence(representativeSequence, false);
4939 viewport.hideRepSequences(representativeSequence, hidden);
4943 SequenceI[] hseqs = hiddenSeqs
4944 .toArray(new SequenceI[hiddenSeqs.size()]);
4945 viewport.hideSequence(hseqs);
4948 // recover view properties and display parameters
4950 viewport.setShowAnnotation(safeBoolean(view.isShowAnnotation()));
4951 viewport.setAbovePIDThreshold(safeBoolean(view.isPidSelected()));
4952 final int pidThreshold = safeInt(view.getPidThreshold());
4953 viewport.setThreshold(pidThreshold);
4955 viewport.setColourText(safeBoolean(view.isShowColourText()));
4958 .setConservationSelected(
4959 safeBoolean(view.isConservationSelected()));
4960 viewport.setIncrement(safeInt(view.getConsThreshold()));
4961 viewport.setShowJVSuffix(safeBoolean(view.isShowFullId()));
4962 viewport.setRightAlignIds(safeBoolean(view.isRightAlignIds()));
4963 viewport.setFont(new Font(view.getFontName(),
4964 safeInt(view.getFontStyle()), safeInt(view.getFontSize())),
4966 ViewStyleI vs = viewport.getViewStyle();
4967 vs.setScaleProteinAsCdna(view.isScaleProteinAsCdna());
4968 viewport.setViewStyle(vs);
4969 // TODO: allow custom charWidth/Heights to be restored by updating them
4970 // after setting font - which means set above to false
4971 viewport.setRenderGaps(safeBoolean(view.isRenderGaps()));
4972 viewport.setWrapAlignment(safeBoolean(view.isWrapAlignment()));
4973 viewport.setShowAnnotation(safeBoolean(view.isShowAnnotation()));
4975 viewport.setShowBoxes(safeBoolean(view.isShowBoxes()));
4977 viewport.setShowText(safeBoolean(view.isShowText()));
4979 viewport.setTextColour(new Color(safeInt(view.getTextCol1())));
4980 viewport.setTextColour2(new Color(safeInt(view.getTextCol2())));
4981 viewport.setThresholdTextColour(safeInt(view.getTextColThreshold()));
4982 viewport.setShowUnconserved(view.isShowUnconserved());
4983 viewport.getRanges().setStartRes(safeInt(view.getStartRes()));
4985 if (view.getViewName() != null)
4987 viewport.setViewName(view.getViewName());
4988 af.setInitialTabVisible();
4990 af.setBounds(safeInt(view.getXpos()), safeInt(view.getYpos()),
4991 safeInt(view.getWidth()), safeInt(view.getHeight()));
4992 // startSeq set in af.alignPanel.updateLayout below
4993 af.alignPanel.updateLayout();
4994 ColourSchemeI cs = null;
4995 // apply colourschemes
4996 if (view.getBgColour() != null)
4998 if (view.getBgColour().startsWith("ucs"))
5000 cs = getUserColourScheme(jm, view.getBgColour());
5002 else if (view.getBgColour().startsWith("Annotation"))
5004 AnnotationColourScheme viewAnnColour = view.getAnnotationColours();
5005 cs = constructAnnotationColour(viewAnnColour, af, al, jm, true);
5012 cs = ColourSchemeProperty.getColourScheme(af.getViewport(), al,
5013 view.getBgColour());
5018 * turn off 'alignment colour applies to all groups'
5019 * while restoring global colour scheme
5021 viewport.setColourAppliesToAllGroups(false);
5022 viewport.setGlobalColourScheme(cs);
5023 viewport.getResidueShading().setThreshold(pidThreshold,
5024 view.isIgnoreGapsinConsensus());
5025 viewport.getResidueShading()
5026 .setConsensus(viewport.getSequenceConsensusHash());
5027 if (safeBoolean(view.isConservationSelected()) && cs != null)
5029 viewport.getResidueShading()
5030 .setConservationInc(safeInt(view.getConsThreshold()));
5032 af.changeColour(cs);
5033 viewport.setColourAppliesToAllGroups(true);
5036 .setShowSequenceFeatures(
5037 safeBoolean(view.isShowSequenceFeatures()));
5039 viewport.setCentreColumnLabels(view.isCentreColumnLabels());
5040 viewport.setIgnoreGapsConsensus(view.isIgnoreGapsinConsensus(), null);
5041 viewport.setFollowHighlight(view.isFollowHighlight());
5042 viewport.followSelection = view.isFollowSelection();
5043 viewport.setShowConsensusHistogram(view.isShowConsensusHistogram());
5044 viewport.setShowSequenceLogo(view.isShowSequenceLogo());
5045 viewport.setNormaliseSequenceLogo(view.isNormaliseSequenceLogo());
5046 viewport.setShowDBRefs(safeBoolean(view.isShowDbRefTooltip()));
5047 viewport.setShowNPFeats(safeBoolean(view.isShowNPfeatureTooltip()));
5048 viewport.setShowGroupConsensus(view.isShowGroupConsensus());
5049 viewport.setShowGroupConservation(view.isShowGroupConservation());
5050 viewport.setShowComplementFeatures(view.isShowComplementFeatures());
5051 viewport.setShowComplementFeaturesOnTop(
5052 view.isShowComplementFeaturesOnTop());
5054 // recover feature settings
5055 if (jm.getFeatureSettings() != null)
5057 FeatureRendererModel fr = af.alignPanel.getSeqPanel().seqCanvas
5058 .getFeatureRenderer();
5059 FeaturesDisplayed fdi;
5060 viewport.setFeaturesDisplayed(fdi = new FeaturesDisplayed());
5061 String[] renderOrder = new String[jm.getFeatureSettings()
5062 .getSetting().size()];
5063 Map<String, FeatureColourI> featureColours = new Hashtable<>();
5064 Map<String, Float> featureOrder = new Hashtable<>();
5066 for (int fs = 0; fs < jm.getFeatureSettings()
5067 .getSetting().size(); fs++)
5069 Setting setting = jm.getFeatureSettings().getSetting().get(fs);
5070 String featureType = setting.getType();
5073 * restore feature filters (if any)
5075 jalview.xml.binding.jalview.FeatureMatcherSet filters = setting
5077 if (filters != null)
5079 FeatureMatcherSetI filter = Jalview2XML
5080 .parseFilter(featureType, filters);
5081 if (!filter.isEmpty())
5083 fr.setFeatureFilter(featureType, filter);
5088 * restore feature colour scheme
5090 Color maxColour = new Color(setting.getColour());
5091 if (setting.getMincolour() != null)
5094 * minColour is always set unless a simple colour
5095 * (including for colour by label though it doesn't use it)
5097 Color minColour = new Color(setting.getMincolour().intValue());
5098 Color noValueColour = minColour;
5099 NoValueColour noColour = setting.getNoValueColour();
5100 if (noColour == NoValueColour.NONE)
5102 noValueColour = null;
5104 else if (noColour == NoValueColour.MAX)
5106 noValueColour = maxColour;
5108 float min = safeFloat(safeFloat(setting.getMin()));
5109 float max = setting.getMax() == null ? 1f
5110 : setting.getMax().floatValue();
5111 FeatureColourI gc = new FeatureColour(maxColour, minColour,
5113 noValueColour, min, max);
5114 if (setting.getAttributeName().size() > 0)
5116 gc.setAttributeName(setting.getAttributeName().toArray(
5117 new String[setting.getAttributeName().size()]));
5119 if (setting.getThreshold() != null)
5121 gc.setThreshold(setting.getThreshold().floatValue());
5122 int threshstate = safeInt(setting.getThreshstate());
5123 // -1 = None, 0 = Below, 1 = Above threshold
5124 if (threshstate == 0)
5126 gc.setBelowThreshold(true);
5128 else if (threshstate == 1)
5130 gc.setAboveThreshold(true);
5133 gc.setAutoScaled(true); // default
5134 if (setting.isAutoScale() != null)
5136 gc.setAutoScaled(setting.isAutoScale());
5138 if (setting.isColourByLabel() != null)
5140 gc.setColourByLabel(setting.isColourByLabel());
5142 // and put in the feature colour table.
5143 featureColours.put(featureType, gc);
5147 featureColours.put(featureType,
5148 new FeatureColour(maxColour));
5150 renderOrder[fs] = featureType;
5151 if (setting.getOrder() != null)
5153 featureOrder.put(featureType, setting.getOrder().floatValue());
5157 featureOrder.put(featureType, Float.valueOf(
5158 fs / jm.getFeatureSettings().getSetting().size()));
5160 if (safeBoolean(setting.isDisplay()))
5162 fdi.setVisible(featureType);
5165 Map<String, Boolean> fgtable = new Hashtable<>();
5166 for (int gs = 0; gs < jm.getFeatureSettings().getGroup().size(); gs++)
5168 Group grp = jm.getFeatureSettings().getGroup().get(gs);
5169 fgtable.put(grp.getName(), Boolean.valueOf(grp.isDisplay()));
5171 // FeatureRendererSettings frs = new FeatureRendererSettings(renderOrder,
5172 // fgtable, featureColours, jms.getFeatureSettings().hasTransparency() ?
5173 // jms.getFeatureSettings().getTransparency() : 0.0, featureOrder);
5174 FeatureRendererSettings frs = new FeatureRendererSettings(renderOrder,
5175 fgtable, featureColours, 1.0f, featureOrder);
5176 fr.transferSettings(frs);
5179 if (view.getHiddenColumns().size() > 0)
5181 for (int c = 0; c < view.getHiddenColumns().size(); c++)
5183 final HiddenColumns hc = view.getHiddenColumns().get(c);
5184 viewport.hideColumns(safeInt(hc.getStart()),
5185 safeInt(hc.getEnd()) /* +1 */);
5188 if (view.getCalcIdParam() != null)
5190 for (CalcIdParam calcIdParam : view.getCalcIdParam())
5192 if (calcIdParam != null)
5194 if (recoverCalcIdParam(calcIdParam, viewport))
5199 warn("Couldn't recover parameters for "
5200 + calcIdParam.getCalcId());
5205 af.setMenusFromViewport(viewport);
5206 af.setTitle(view.getTitle());
5207 // TODO: we don't need to do this if the viewport is aready visible.
5209 * Add the AlignFrame to the desktop (it may be 'gathered' later), unless it
5210 * has a 'cdna/protein complement' view, in which case save it in order to
5211 * populate a SplitFrame once all views have been read in.
5213 String complementaryViewId = view.getComplementId();
5214 if (complementaryViewId == null)
5216 Desktop.addInternalFrame(af, view.getTitle(),
5217 safeInt(view.getWidth()), safeInt(view.getHeight()));
5218 // recompute any autoannotation
5219 af.alignPanel.updateAnnotation(false, true);
5220 reorderAutoannotation(af, al, autoAlan);
5221 af.alignPanel.alignmentChanged();
5225 splitFrameCandidates.put(view, af);
5231 * Reads saved data to restore Colour by Annotation settings
5233 * @param viewAnnColour
5237 * @param checkGroupAnnColour
5240 private ColourSchemeI constructAnnotationColour(
5241 AnnotationColourScheme viewAnnColour, AlignFrame af,
5242 AlignmentI al, JalviewModel model, boolean checkGroupAnnColour)
5244 boolean propagateAnnColour = false;
5245 AlignmentI annAlignment = af != null ? af.getViewport().getAlignment()
5247 if (checkGroupAnnColour && al.getGroups() != null
5248 && al.getGroups().size() > 0)
5250 // pre 2.8.1 behaviour
5251 // check to see if we should transfer annotation colours
5252 propagateAnnColour = true;
5253 for (SequenceGroup sg : al.getGroups())
5255 if (sg.getColourScheme() instanceof AnnotationColourGradient)
5257 propagateAnnColour = false;
5263 * 2.10.2- : saved annotationId is AlignmentAnnotation.annotationId
5265 String annotationId = viewAnnColour.getAnnotation();
5266 AlignmentAnnotation matchedAnnotation = annotationIds.get(annotationId);
5269 * pre 2.10.2: saved annotationId is AlignmentAnnotation.label
5271 if (matchedAnnotation == null
5272 && annAlignment.getAlignmentAnnotation() != null)
5274 for (int i = 0; i < annAlignment.getAlignmentAnnotation().length; i++)
5277 .equals(annAlignment.getAlignmentAnnotation()[i].label))
5279 matchedAnnotation = annAlignment.getAlignmentAnnotation()[i];
5284 if (matchedAnnotation == null)
5286 System.err.println("Failed to match annotation colour scheme for "
5290 if (matchedAnnotation.getThreshold() == null)
5292 matchedAnnotation.setThreshold(
5293 new GraphLine(safeFloat(viewAnnColour.getThreshold()),
5294 "Threshold", Color.black));
5297 AnnotationColourGradient cs = null;
5298 if (viewAnnColour.getColourScheme().equals("None"))
5300 cs = new AnnotationColourGradient(matchedAnnotation,
5301 new Color(safeInt(viewAnnColour.getMinColour())),
5302 new Color(safeInt(viewAnnColour.getMaxColour())),
5303 safeInt(viewAnnColour.getAboveThreshold()));
5305 else if (viewAnnColour.getColourScheme().startsWith("ucs"))
5307 cs = new AnnotationColourGradient(matchedAnnotation,
5308 getUserColourScheme(model, viewAnnColour.getColourScheme()),
5309 safeInt(viewAnnColour.getAboveThreshold()));
5313 cs = new AnnotationColourGradient(matchedAnnotation,
5314 ColourSchemeProperty.getColourScheme(af.getViewport(), al,
5315 viewAnnColour.getColourScheme()),
5316 safeInt(viewAnnColour.getAboveThreshold()));
5319 boolean perSequenceOnly = safeBoolean(viewAnnColour.isPerSequence());
5320 boolean useOriginalColours = safeBoolean(
5321 viewAnnColour.isPredefinedColours());
5322 cs.setSeqAssociated(perSequenceOnly);
5323 cs.setPredefinedColours(useOriginalColours);
5325 if (propagateAnnColour && al.getGroups() != null)
5327 // Also use these settings for all the groups
5328 for (int g = 0; g < al.getGroups().size(); g++)
5330 SequenceGroup sg = al.getGroups().get(g);
5331 if (sg.getGroupColourScheme() == null)
5336 AnnotationColourGradient groupScheme = new AnnotationColourGradient(
5337 matchedAnnotation, sg.getColourScheme(),
5338 safeInt(viewAnnColour.getAboveThreshold()));
5339 sg.setColourScheme(groupScheme);
5340 groupScheme.setSeqAssociated(perSequenceOnly);
5341 groupScheme.setPredefinedColours(useOriginalColours);
5347 private void reorderAutoannotation(AlignFrame af, AlignmentI al,
5348 List<JvAnnotRow> autoAlan)
5350 // copy over visualization settings for autocalculated annotation in the
5352 if (al.getAlignmentAnnotation() != null)
5355 * Kludge for magic autoannotation names (see JAL-811)
5357 String[] magicNames = new String[] { "Consensus", "Quality",
5359 JvAnnotRow nullAnnot = new JvAnnotRow(-1, null);
5360 Hashtable<String, JvAnnotRow> visan = new Hashtable<>();
5361 for (String nm : magicNames)
5363 visan.put(nm, nullAnnot);
5365 for (JvAnnotRow auan : autoAlan)
5367 visan.put(auan.template.label
5368 + (auan.template.getCalcId() == null ? ""
5369 : "\t" + auan.template.getCalcId()),
5372 int hSize = al.getAlignmentAnnotation().length;
5373 List<JvAnnotRow> reorder = new ArrayList<>();
5374 // work through any autoCalculated annotation already on the view
5375 // removing it if it should be placed in a different location on the
5376 // annotation panel.
5377 List<String> remains = new ArrayList<>(visan.keySet());
5378 for (int h = 0; h < hSize; h++)
5380 jalview.datamodel.AlignmentAnnotation jalan = al
5381 .getAlignmentAnnotation()[h];
5382 if (jalan.autoCalculated)
5385 JvAnnotRow valan = visan.get(k = jalan.label);
5386 if (jalan.getCalcId() != null)
5388 valan = visan.get(k = jalan.label + "\t" + jalan.getCalcId());
5393 // delete the auto calculated row from the alignment
5394 al.deleteAnnotation(jalan, false);
5398 if (valan != nullAnnot)
5400 if (jalan != valan.template)
5402 // newly created autoannotation row instance
5403 // so keep a reference to the visible annotation row
5404 // and copy over all relevant attributes
5405 if (valan.template.graphHeight >= 0)
5408 jalan.graphHeight = valan.template.graphHeight;
5410 jalan.visible = valan.template.visible;
5412 reorder.add(new JvAnnotRow(valan.order, jalan));
5417 // Add any (possibly stale) autocalculated rows that were not appended to
5418 // the view during construction
5419 for (String other : remains)
5421 JvAnnotRow othera = visan.get(other);
5422 if (othera != nullAnnot && othera.template.getCalcId() != null
5423 && othera.template.getCalcId().length() > 0)
5425 reorder.add(othera);
5428 // now put the automatic annotation in its correct place
5429 int s = 0, srt[] = new int[reorder.size()];
5430 JvAnnotRow[] rws = new JvAnnotRow[reorder.size()];
5431 for (JvAnnotRow jvar : reorder)
5434 srt[s++] = jvar.order;
5437 jalview.util.QuickSort.sort(srt, rws);
5438 // and re-insert the annotation at its correct position
5439 for (JvAnnotRow jvar : rws)
5441 al.addAnnotation(jvar.template, jvar.order);
5443 af.alignPanel.adjustAnnotationHeight();
5447 Hashtable skipList = null;
5450 * TODO remove this method
5453 * @return AlignFrame bound to sequenceSetId from view, if one exists. private
5454 * AlignFrame getSkippedFrame(Viewport view) { if (skipList==null) {
5455 * throw new Error("Implementation Error. No skipList defined for this
5456 * Jalview2XML instance."); } return (AlignFrame)
5457 * skipList.get(view.getSequenceSetId()); }
5461 * Check if the Jalview view contained in object should be skipped or not.
5464 * @return true if view's sequenceSetId is a key in skipList
5466 private boolean skipViewport(JalviewModel object)
5468 if (skipList == null)
5472 String id = object.getViewport().get(0).getSequenceSetId();
5473 if (skipList.containsKey(id))
5475 if (Cache.log != null && Cache.log.isDebugEnabled())
5477 Cache.log.debug("Skipping seuqence set id " + id);
5484 public void addToSkipList(AlignFrame af)
5486 if (skipList == null)
5488 skipList = new Hashtable();
5490 skipList.put(af.getViewport().getSequenceSetId(), af);
5493 public void clearSkipList()
5495 if (skipList != null)
5502 private void recoverDatasetFor(SequenceSet vamsasSet, AlignmentI al,
5503 boolean ignoreUnrefed, String uniqueSeqSetId)
5505 jalview.datamodel.AlignmentI ds = getDatasetFor(
5506 vamsasSet.getDatasetId());
5507 AlignmentI xtant_ds = ds;
5508 if (xtant_ds == null)
5510 // good chance we are about to create a new dataset, but check if we've
5511 // seen some of the dataset sequence IDs before.
5512 // TODO: skip this check if we are working with project generated by
5513 // version 2.11 or later
5514 xtant_ds = checkIfHasDataset(vamsasSet.getSequence());
5515 if (xtant_ds != null)
5518 addDatasetRef(vamsasSet.getDatasetId(), ds);
5521 Vector dseqs = null;
5524 // recovering an alignment View
5525 AlignmentI seqSetDS = getDatasetFor(UNIQSEQSETID + uniqueSeqSetId);
5526 if (seqSetDS != null)
5528 if (ds != null && ds != seqSetDS)
5530 warn("JAL-3171 regression: Overwriting a dataset reference for an alignment"
5531 + " - CDS/Protein crossreference data may be lost");
5532 if (xtant_ds != null)
5534 // This can only happen if the unique sequence set ID was bound to a
5535 // dataset that did not contain any of the sequences in the view
5536 // currently being restored.
5537 warn("JAL-3171 SERIOUS! TOTAL CONFUSION - please consider contacting the Jalview Development team so they can investigate why your project caused this message to be displayed.");
5541 addDatasetRef(vamsasSet.getDatasetId(), ds);
5546 // try even harder to restore dataset
5547 AlignmentI xtantDS = checkIfHasDataset(vamsasSet.getSequence());
5548 // create a list of new dataset sequences
5549 dseqs = new Vector();
5551 for (int i = 0, iSize = vamsasSet.getSequence().size(); i < iSize; i++)
5553 Sequence vamsasSeq = vamsasSet.getSequence().get(i);
5554 ensureJalviewDatasetSequence(vamsasSeq, ds, dseqs, ignoreUnrefed, i);
5556 // create a new dataset
5559 SequenceI[] dsseqs = new SequenceI[dseqs.size()];
5560 dseqs.copyInto(dsseqs);
5561 ds = new jalview.datamodel.Alignment(dsseqs);
5562 debug("Created new dataset " + vamsasSet.getDatasetId()
5563 + " for alignment " + System.identityHashCode(al));
5564 addDatasetRef(vamsasSet.getDatasetId(), ds);
5566 // set the dataset for the newly imported alignment.
5567 if (al.getDataset() == null && !ignoreUnrefed)
5570 // register dataset for the alignment's uniqueSeqSetId for legacy projects
5571 addDatasetRef(UNIQSEQSETID + uniqueSeqSetId, ds);
5573 updateSeqDatasetBinding(vamsasSet.getSequence(), ds);
5577 * XML dataset sequence ID to materialised dataset reference
5579 HashMap<String, AlignmentI> seqToDataset = new HashMap<>();
5582 * @return the first materialised dataset reference containing a dataset
5583 * sequence referenced in the given view
5585 * - sequences from the view
5587 AlignmentI checkIfHasDataset(List<Sequence> list)
5589 for (Sequence restoredSeq : list)
5591 AlignmentI datasetFor = seqToDataset.get(restoredSeq.getDsseqid());
5592 if (datasetFor != null)
5601 * Register ds as the containing dataset for the dataset sequences referenced
5602 * by sequences in list
5605 * - sequences in a view
5608 void updateSeqDatasetBinding(List<Sequence> list, AlignmentI ds)
5610 for (Sequence restoredSeq : list)
5612 AlignmentI prevDS = seqToDataset.put(restoredSeq.getDsseqid(), ds);
5613 if (prevDS != null && prevDS != ds)
5615 warn("Dataset sequence appears in many datasets: "
5616 + restoredSeq.getDsseqid());
5617 // TODO: try to merge!
5624 * sequence definition to create/merge dataset sequence for
5628 * vector to add new dataset sequence to
5629 * @param ignoreUnrefed
5630 * - when true, don't create new sequences from vamsasSeq if it's id
5631 * doesn't already have an asssociated Jalview sequence.
5633 * - used to reorder the sequence in the alignment according to the
5634 * vamsasSeq array ordering, to preserve ordering of dataset
5636 private void ensureJalviewDatasetSequence(Sequence vamsasSeq,
5637 AlignmentI ds, Vector dseqs, boolean ignoreUnrefed, int vseqpos)
5639 // JBP TODO: Check this is called for AlCodonFrames to support recovery of
5641 SequenceI sq = seqRefIds.get(vamsasSeq.getId());
5642 boolean reorder = false;
5643 SequenceI dsq = null;
5644 if (sq != null && sq.getDatasetSequence() != null)
5646 dsq = sq.getDatasetSequence();
5652 if (sq == null && ignoreUnrefed)
5656 String sqid = vamsasSeq.getDsseqid();
5659 // need to create or add a new dataset sequence reference to this sequence
5662 dsq = seqRefIds.get(sqid);
5667 // make a new dataset sequence
5668 dsq = sq.createDatasetSequence();
5671 // make up a new dataset reference for this sequence
5672 sqid = seqHash(dsq);
5674 dsq.setVamsasId(uniqueSetSuffix + sqid);
5675 seqRefIds.put(sqid, dsq);
5680 dseqs.addElement(dsq);
5685 ds.addSequence(dsq);
5691 { // make this dataset sequence sq's dataset sequence
5692 sq.setDatasetSequence(dsq);
5693 // and update the current dataset alignment
5698 if (!dseqs.contains(dsq))
5705 if (ds.findIndex(dsq) < 0)
5707 ds.addSequence(dsq);
5714 // TODO: refactor this as a merge dataset sequence function
5715 // now check that sq (the dataset sequence) sequence really is the union of
5716 // all references to it
5717 // boolean pre = sq.getStart() < dsq.getStart();
5718 // boolean post = sq.getEnd() > dsq.getEnd();
5722 // StringBuffer sb = new StringBuffer();
5723 String newres = jalview.analysis.AlignSeq.extractGaps(
5724 jalview.util.Comparison.GapChars, sq.getSequenceAsString());
5725 if (!newres.equalsIgnoreCase(dsq.getSequenceAsString())
5726 && newres.length() > dsq.getLength())
5728 // Update with the longer sequence.
5732 * if (pre) { sb.insert(0, newres .substring(0, dsq.getStart() -
5733 * sq.getStart())); dsq.setStart(sq.getStart()); } if (post) {
5734 * sb.append(newres.substring(newres.length() - sq.getEnd() -
5735 * dsq.getEnd())); dsq.setEnd(sq.getEnd()); }
5737 dsq.setSequence(newres);
5739 // TODO: merges will never happen if we 'know' we have the real dataset
5740 // sequence - this should be detected when id==dssid
5742 "DEBUG Notice: Merged dataset sequence (if you see this often, post at http://issues.jalview.org/browse/JAL-1474)"); // ("
5743 // + (pre ? "prepended" : "") + " "
5744 // + (post ? "appended" : ""));
5749 // sequence refs are identical. We may need to update the existing dataset
5750 // alignment with this one, though.
5751 if (ds != null && dseqs == null)
5753 int opos = ds.findIndex(dsq);
5754 SequenceI tseq = null;
5755 if (opos != -1 && vseqpos != opos)
5757 // remove from old position
5758 ds.deleteSequence(dsq);
5760 if (vseqpos < ds.getHeight())
5762 if (vseqpos != opos)
5764 // save sequence at destination position
5765 tseq = ds.getSequenceAt(vseqpos);
5766 ds.replaceSequenceAt(vseqpos, dsq);
5767 ds.addSequence(tseq);
5772 ds.addSequence(dsq);
5779 * TODO use AlignmentI here and in related methods - needs
5780 * AlignmentI.getDataset() changed to return AlignmentI instead of Alignment
5782 Hashtable<String, AlignmentI> datasetIds = null;
5784 IdentityHashMap<AlignmentI, String> dataset2Ids = null;
5786 private AlignmentI getDatasetFor(String datasetId)
5788 if (datasetIds == null)
5790 datasetIds = new Hashtable<>();
5793 if (datasetIds.containsKey(datasetId))
5795 return datasetIds.get(datasetId);
5800 private void addDatasetRef(String datasetId, AlignmentI dataset)
5802 if (datasetIds == null)
5804 datasetIds = new Hashtable<>();
5806 datasetIds.put(datasetId, dataset);
5810 * make a new dataset ID for this jalview dataset alignment
5815 private String getDatasetIdRef(AlignmentI dataset)
5817 if (dataset.getDataset() != null)
5819 warn("Serious issue! Dataset Object passed to getDatasetIdRef is not a Jalview DATASET alignment...");
5821 String datasetId = makeHashCode(dataset, null);
5822 if (datasetId == null)
5824 // make a new datasetId and record it
5825 if (dataset2Ids == null)
5827 dataset2Ids = new IdentityHashMap<>();
5831 datasetId = dataset2Ids.get(dataset);
5833 if (datasetId == null)
5835 datasetId = "ds" + dataset2Ids.size() + 1;
5836 dataset2Ids.put(dataset, datasetId);
5843 * Add any saved DBRefEntry's to the sequence. An entry flagged as 'locus' is
5844 * constructed as a special subclass GeneLocus.
5846 * @param datasetSequence
5849 private void addDBRefs(SequenceI datasetSequence, Sequence sequence)
5851 for (int d = 0; d < sequence.getDBRef().size(); d++)
5853 DBRef dr = sequence.getDBRef().get(d);
5857 entry = new GeneLocus(dr.getSource(), dr.getVersion(),
5858 dr.getAccessionId());
5862 entry = new DBRefEntry(dr.getSource(), dr.getVersion(),
5863 dr.getAccessionId());
5865 if (dr.getMapping() != null)
5867 entry.setMap(addMapping(dr.getMapping()));
5869 datasetSequence.addDBRef(entry);
5873 private jalview.datamodel.Mapping addMapping(Mapping m)
5875 SequenceI dsto = null;
5876 // Mapping m = dr.getMapping();
5877 int fr[] = new int[m.getMapListFrom().size() * 2];
5878 Iterator<MapListFrom> from = m.getMapListFrom().iterator();// enumerateMapListFrom();
5879 for (int _i = 0; from.hasNext(); _i += 2)
5881 MapListFrom mf = from.next();
5882 fr[_i] = mf.getStart();
5883 fr[_i + 1] = mf.getEnd();
5885 int fto[] = new int[m.getMapListTo().size() * 2];
5886 Iterator<MapListTo> to = m.getMapListTo().iterator();// enumerateMapListTo();
5887 for (int _i = 0; to.hasNext(); _i += 2)
5889 MapListTo mf = to.next();
5890 fto[_i] = mf.getStart();
5891 fto[_i + 1] = mf.getEnd();
5893 jalview.datamodel.Mapping jmap = new jalview.datamodel.Mapping(dsto, fr,
5894 fto, m.getMapFromUnit().intValue(),
5895 m.getMapToUnit().intValue());
5898 * (optional) choice of dseqFor or Sequence
5900 if (m.getDseqFor() != null)
5902 String dsfor = m.getDseqFor();
5903 if (seqRefIds.containsKey(dsfor))
5908 jmap.setTo(seqRefIds.get(dsfor));
5912 frefedSequence.add(newMappingRef(dsfor, jmap));
5915 else if (m.getSequence() != null)
5918 * local sequence definition
5920 Sequence ms = m.getSequence();
5921 SequenceI djs = null;
5922 String sqid = ms.getDsseqid();
5923 if (sqid != null && sqid.length() > 0)
5926 * recover dataset sequence
5928 djs = seqRefIds.get(sqid);
5933 "Warning - making up dataset sequence id for DbRef sequence map reference");
5934 sqid = ((Object) ms).toString(); // make up a new hascode for
5935 // undefined dataset sequence hash
5936 // (unlikely to happen)
5942 * make a new dataset sequence and add it to refIds hash
5944 djs = new jalview.datamodel.Sequence(ms.getName(),
5946 djs.setStart(jmap.getMap().getToLowest());
5947 djs.setEnd(jmap.getMap().getToHighest());
5948 djs.setVamsasId(uniqueSetSuffix + sqid);
5950 incompleteSeqs.put(sqid, djs);
5951 seqRefIds.put(sqid, djs);
5954 jalview.bin.Cache.log.debug("about to recurse on addDBRefs.");
5963 * Provides a 'copy' of an alignment view (on action New View) by 'saving' the
5964 * view as XML (but not to file), and then reloading it
5969 public AlignmentPanel copyAlignPanel(AlignmentPanel ap)
5972 JalviewModel jm = saveState(ap, null, null, null);
5975 jm.getVamsasModel().getSequenceSet().get(0).getDatasetId(),
5976 ap.getAlignment().getDataset());
5978 uniqueSetSuffix = "";
5979 // jm.getJalviewModelSequence().getViewport(0).setId(null);
5980 jm.getViewport().get(0).setId(null);
5981 // we don't overwrite the view we just copied
5983 if (this.frefedSequence == null)
5985 frefedSequence = new Vector<>();
5988 viewportsAdded.clear();
5990 AlignFrame af = loadFromObject(jm, null, false, null);
5991 af.getAlignPanels().clear();
5992 af.closeMenuItem_actionPerformed(true);
5995 * if(ap.av.getAlignment().getAlignmentAnnotation()!=null) { for(int i=0;
5996 * i<ap.av.getAlignment().getAlignmentAnnotation().length; i++) {
5997 * if(!ap.av.getAlignment().getAlignmentAnnotation()[i].autoCalculated) {
5998 * af.alignPanel.av.getAlignment().getAlignmentAnnotation()[i] =
5999 * ap.av.getAlignment().getAlignmentAnnotation()[i]; } } }
6002 return af.alignPanel;
6005 private Hashtable jvids2vobj;
6007 private void warn(String msg)
6012 private void warn(String msg, Exception e)
6014 if (Cache.log != null)
6018 Cache.log.warn(msg, e);
6022 Cache.log.warn(msg);
6027 System.err.println("Warning: " + msg);
6030 e.printStackTrace();
6035 private void debug(String string)
6037 debug(string, null);
6040 private void debug(String msg, Exception e)
6042 if (Cache.log != null)
6046 Cache.log.debug(msg, e);
6050 Cache.log.debug(msg);
6055 System.err.println("Warning: " + msg);
6058 e.printStackTrace();
6064 * set the object to ID mapping tables used to write/recover objects and XML
6065 * ID strings for the jalview project. If external tables are provided then
6066 * finalize and clearSeqRefs will not clear the tables when the Jalview2XML
6067 * object goes out of scope. - also populates the datasetIds hashtable with
6068 * alignment objects containing dataset sequences
6071 * Map from ID strings to jalview datamodel
6073 * Map from jalview datamodel to ID strings
6077 public void setObjectMappingTables(Hashtable vobj2jv,
6078 IdentityHashMap jv2vobj)
6080 this.jv2vobj = jv2vobj;
6081 this.vobj2jv = vobj2jv;
6082 Iterator ds = jv2vobj.keySet().iterator();
6084 while (ds.hasNext())
6086 Object jvobj = ds.next();
6087 id = jv2vobj.get(jvobj).toString();
6088 if (jvobj instanceof jalview.datamodel.Alignment)
6090 if (((jalview.datamodel.Alignment) jvobj).getDataset() == null)
6092 addDatasetRef(id, (jalview.datamodel.Alignment) jvobj);
6095 else if (jvobj instanceof jalview.datamodel.Sequence)
6097 // register sequence object so the XML parser can recover it.
6098 if (seqRefIds == null)
6100 seqRefIds = new HashMap<>();
6102 if (seqsToIds == null)
6104 seqsToIds = new IdentityHashMap<>();
6106 seqRefIds.put(jv2vobj.get(jvobj).toString(), (SequenceI) jvobj);
6107 seqsToIds.put((SequenceI) jvobj, id);
6109 else if (jvobj instanceof jalview.datamodel.AlignmentAnnotation)
6112 AlignmentAnnotation jvann = (AlignmentAnnotation) jvobj;
6113 annotationIds.put(anid = jv2vobj.get(jvobj).toString(), jvann);
6114 if (jvann.annotationId == null)
6116 jvann.annotationId = anid;
6118 if (!jvann.annotationId.equals(anid))
6120 // TODO verify that this is the correct behaviour
6121 this.warn("Overriding Annotation ID for " + anid
6122 + " from different id : " + jvann.annotationId);
6123 jvann.annotationId = anid;
6126 else if (jvobj instanceof String)
6128 if (jvids2vobj == null)
6130 jvids2vobj = new Hashtable();
6131 jvids2vobj.put(jvobj, jv2vobj.get(jvobj).toString());
6136 Cache.log.debug("Ignoring " + jvobj.getClass() + " (ID = " + id);
6142 * set the uniqueSetSuffix used to prefix/suffix object IDs for jalview
6143 * objects created from the project archive. If string is null (default for
6144 * construction) then suffix will be set automatically.
6148 public void setUniqueSetSuffix(String string)
6150 uniqueSetSuffix = string;
6155 * uses skipList2 as the skipList for skipping views on sequence sets
6156 * associated with keys in the skipList
6160 public void setSkipList(Hashtable skipList2)
6162 skipList = skipList2;
6166 * Reads the jar entry of given name and returns its contents, or null if the
6167 * entry is not found.
6170 * @param jarEntryName
6173 protected String readJarEntry(jarInputStreamProvider jprovider,
6174 String jarEntryName)
6176 String result = null;
6177 BufferedReader in = null;
6182 * Reopen the jar input stream and traverse its entries to find a matching
6185 JarInputStream jin = jprovider.getJarInputStream();
6186 JarEntry entry = null;
6189 entry = jin.getNextJarEntry();
6190 } while (entry != null && !entry.getName().equals(jarEntryName));
6194 StringBuilder out = new StringBuilder(256);
6195 in = new BufferedReader(new InputStreamReader(jin, UTF_8));
6198 while ((data = in.readLine()) != null)
6202 result = out.toString();
6206 warn("Couldn't find entry in Jalview Jar for " + jarEntryName);
6208 } catch (Exception ex)
6210 ex.printStackTrace();
6218 } catch (IOException e)
6229 * Returns an incrementing counter (0, 1, 2...)
6233 private synchronized int nextCounter()
6239 * Loads any saved PCA viewers
6244 protected void loadPCAViewers(JalviewModel model, AlignmentPanel ap)
6248 List<PcaViewer> pcaviewers = model.getPcaViewer();
6249 for (PcaViewer viewer : pcaviewers)
6251 String modelName = viewer.getScoreModelName();
6252 SimilarityParamsI params = new SimilarityParams(
6253 viewer.isIncludeGappedColumns(), viewer.isMatchGaps(),
6254 viewer.isIncludeGaps(),
6255 viewer.isDenominateByShortestLength());
6258 * create the panel (without computing the PCA)
6260 PCAPanel panel = new PCAPanel(ap, modelName, params);
6262 panel.setTitle(viewer.getTitle());
6263 panel.setBounds(new Rectangle(viewer.getXpos(), viewer.getYpos(),
6264 viewer.getWidth(), viewer.getHeight()));
6266 boolean showLabels = viewer.isShowLabels();
6267 panel.setShowLabels(showLabels);
6268 panel.getRotatableCanvas().setShowLabels(showLabels);
6269 panel.getRotatableCanvas()
6270 .setBgColour(new Color(viewer.getBgColour()));
6271 panel.getRotatableCanvas()
6272 .setApplyToAllViews(viewer.isLinkToAllViews());
6275 * load PCA output data
6277 ScoreModelI scoreModel = ScoreModels.getInstance()
6278 .getScoreModel(modelName, ap);
6279 PCA pca = new PCA(null, scoreModel, params);
6280 PcaDataType pcaData = viewer.getPcaData();
6282 MatrixI pairwise = loadDoubleMatrix(pcaData.getPairwiseMatrix());
6283 pca.setPairwiseScores(pairwise);
6285 MatrixI triDiag = loadDoubleMatrix(pcaData.getTridiagonalMatrix());
6286 pca.setTridiagonal(triDiag);
6288 MatrixI result = loadDoubleMatrix(pcaData.getEigenMatrix());
6289 pca.setEigenmatrix(result);
6291 panel.getPcaModel().setPCA(pca);
6294 * we haven't saved the input data! (JAL-2647 to do)
6296 panel.setInputData(null);
6299 * add the sequence points for the PCA display
6301 List<jalview.datamodel.SequencePoint> seqPoints = new ArrayList<>();
6302 for (SequencePoint sp : viewer.getSequencePoint())
6304 String seqId = sp.getSequenceRef();
6305 SequenceI seq = seqRefIds.get(seqId);
6308 throw new IllegalStateException(
6309 "Unmatched seqref for PCA: " + seqId);
6311 Point pt = new Point(sp.getXPos(), sp.getYPos(), sp.getZPos());
6312 jalview.datamodel.SequencePoint seqPoint = new jalview.datamodel.SequencePoint(
6314 seqPoints.add(seqPoint);
6316 panel.getRotatableCanvas().setPoints(seqPoints, seqPoints.size());
6319 * set min-max ranges and scale after setPoints (which recomputes them)
6321 panel.getRotatableCanvas().setScaleFactor(viewer.getScaleFactor());
6322 SeqPointMin spMin = viewer.getSeqPointMin();
6323 float[] min = new float[] { spMin.getXPos(), spMin.getYPos(),
6325 SeqPointMax spMax = viewer.getSeqPointMax();
6326 float[] max = new float[] { spMax.getXPos(), spMax.getYPos(),
6328 panel.getRotatableCanvas().setSeqMinMax(min, max);
6330 // todo: hold points list in PCAModel only
6331 panel.getPcaModel().setSequencePoints(seqPoints);
6333 panel.setSelectedDimensionIndex(viewer.getXDim(), X);
6334 panel.setSelectedDimensionIndex(viewer.getYDim(), Y);
6335 panel.setSelectedDimensionIndex(viewer.getZDim(), Z);
6337 // is this duplication needed?
6338 panel.setTop(seqPoints.size() - 1);
6339 panel.getPcaModel().setTop(seqPoints.size() - 1);
6342 * add the axes' end points for the display
6344 for (int i = 0; i < 3; i++)
6346 Axis axis = viewer.getAxis().get(i);
6347 panel.getRotatableCanvas().getAxisEndPoints()[i] = new Point(
6348 axis.getXPos(), axis.getYPos(), axis.getZPos());
6351 Desktop.addInternalFrame(panel, MessageManager.formatMessage(
6352 "label.calc_title", "PCA", modelName), 475, 450);
6354 } catch (Exception ex)
6356 Cache.log.error("Error loading PCA: " + ex.toString());
6361 * Populates an XML model of the feature colour scheme for one feature type
6363 * @param featureType
6367 public static Colour marshalColour(
6368 String featureType, FeatureColourI fcol)
6370 Colour col = new Colour();
6371 if (fcol.isSimpleColour())
6373 col.setRGB(Format.getHexString(fcol.getColour()));
6377 col.setRGB(Format.getHexString(fcol.getMaxColour()));
6378 col.setMin(fcol.getMin());
6379 col.setMax(fcol.getMax());
6380 col.setMinRGB(jalview.util.Format.getHexString(fcol.getMinColour()));
6381 col.setAutoScale(fcol.isAutoScaled());
6382 col.setThreshold(fcol.getThreshold());
6383 col.setColourByLabel(fcol.isColourByLabel());
6384 col.setThreshType(fcol.isAboveThreshold() ? ThresholdType.ABOVE
6385 : (fcol.isBelowThreshold() ? ThresholdType.BELOW
6386 : ThresholdType.NONE));
6387 if (fcol.isColourByAttribute())
6389 final String[] attName = fcol.getAttributeName();
6390 col.getAttributeName().add(attName[0]);
6391 if (attName.length > 1)
6393 col.getAttributeName().add(attName[1]);
6396 Color noColour = fcol.getNoColour();
6397 if (noColour == null)
6399 col.setNoValueColour(NoValueColour.NONE);
6401 else if (noColour == fcol.getMaxColour())
6403 col.setNoValueColour(NoValueColour.MAX);
6407 col.setNoValueColour(NoValueColour.MIN);
6410 col.setName(featureType);
6415 * Populates an XML model of the feature filter(s) for one feature type
6417 * @param firstMatcher
6418 * the first (or only) match condition)
6420 * remaining match conditions (if any)
6422 * if true, conditions are and-ed, else or-ed
6424 public static jalview.xml.binding.jalview.FeatureMatcherSet marshalFilter(
6425 FeatureMatcherI firstMatcher, Iterator<FeatureMatcherI> filters,
6428 jalview.xml.binding.jalview.FeatureMatcherSet result = new jalview.xml.binding.jalview.FeatureMatcherSet();
6430 if (filters.hasNext())
6435 CompoundMatcher compound = new CompoundMatcher();
6436 compound.setAnd(and);
6437 jalview.xml.binding.jalview.FeatureMatcherSet matcher1 = marshalFilter(
6438 firstMatcher, Collections.emptyIterator(), and);
6439 // compound.addMatcherSet(matcher1);
6440 compound.getMatcherSet().add(matcher1);
6441 FeatureMatcherI nextMatcher = filters.next();
6442 jalview.xml.binding.jalview.FeatureMatcherSet matcher2 = marshalFilter(
6443 nextMatcher, filters, and);
6444 // compound.addMatcherSet(matcher2);
6445 compound.getMatcherSet().add(matcher2);
6446 result.setCompoundMatcher(compound);
6451 * single condition matcher
6453 // MatchCondition matcherModel = new MatchCondition();
6454 jalview.xml.binding.jalview.FeatureMatcher matcherModel = new jalview.xml.binding.jalview.FeatureMatcher();
6455 matcherModel.setCondition(
6456 firstMatcher.getMatcher().getCondition().getStableName());
6457 matcherModel.setValue(firstMatcher.getMatcher().getPattern());
6458 if (firstMatcher.isByAttribute())
6460 matcherModel.setBy(FilterBy.BY_ATTRIBUTE);
6461 // matcherModel.setAttributeName(firstMatcher.getAttribute());
6462 String[] attName = firstMatcher.getAttribute();
6463 matcherModel.getAttributeName().add(attName[0]); // attribute
6464 if (attName.length > 1)
6466 matcherModel.getAttributeName().add(attName[1]); // sub-attribute
6469 else if (firstMatcher.isByLabel())
6471 matcherModel.setBy(FilterBy.BY_LABEL);
6473 else if (firstMatcher.isByScore())
6475 matcherModel.setBy(FilterBy.BY_SCORE);
6477 result.setMatchCondition(matcherModel);
6484 * Loads one XML model of a feature filter to a Jalview object
6486 * @param featureType
6487 * @param matcherSetModel
6490 public static FeatureMatcherSetI parseFilter(
6492 jalview.xml.binding.jalview.FeatureMatcherSet matcherSetModel)
6494 FeatureMatcherSetI result = new FeatureMatcherSet();
6497 parseFilterConditions(result, matcherSetModel, true);
6498 } catch (IllegalStateException e)
6500 // mixing AND and OR conditions perhaps
6502 String.format("Error reading filter conditions for '%s': %s",
6503 featureType, e.getMessage()));
6504 // return as much as was parsed up to the error
6511 * Adds feature match conditions to matcherSet as unmarshalled from XML
6512 * (possibly recursively for compound conditions)
6515 * @param matcherSetModel
6517 * if true, multiple conditions are AND-ed, else they are OR-ed
6518 * @throws IllegalStateException
6519 * if AND and OR conditions are mixed
6521 protected static void parseFilterConditions(
6522 FeatureMatcherSetI matcherSet,
6523 jalview.xml.binding.jalview.FeatureMatcherSet matcherSetModel,
6526 jalview.xml.binding.jalview.FeatureMatcher mc = matcherSetModel
6527 .getMatchCondition();
6533 FilterBy filterBy = mc.getBy();
6534 Condition cond = Condition.fromString(mc.getCondition());
6535 String pattern = mc.getValue();
6536 FeatureMatcherI matchCondition = null;
6537 if (filterBy == FilterBy.BY_LABEL)
6539 matchCondition = FeatureMatcher.byLabel(cond, pattern);
6541 else if (filterBy == FilterBy.BY_SCORE)
6543 matchCondition = FeatureMatcher.byScore(cond, pattern);
6546 else if (filterBy == FilterBy.BY_ATTRIBUTE)
6548 final List<String> attributeName = mc.getAttributeName();
6549 String[] attNames = attributeName
6550 .toArray(new String[attributeName.size()]);
6551 matchCondition = FeatureMatcher.byAttribute(cond, pattern,
6556 * note this throws IllegalStateException if AND-ing to a
6557 * previously OR-ed compound condition, or vice versa
6561 matcherSet.and(matchCondition);
6565 matcherSet.or(matchCondition);
6571 * compound condition
6573 List<jalview.xml.binding.jalview.FeatureMatcherSet> matchers = matcherSetModel
6574 .getCompoundMatcher().getMatcherSet();
6575 boolean anded = matcherSetModel.getCompoundMatcher().isAnd();
6576 if (matchers.size() == 2)
6578 parseFilterConditions(matcherSet, matchers.get(0), anded);
6579 parseFilterConditions(matcherSet, matchers.get(1), anded);
6583 System.err.println("Malformed compound filter condition");
6589 * Loads one XML model of a feature colour to a Jalview object
6591 * @param colourModel
6594 public static FeatureColourI parseColour(Colour colourModel)
6596 FeatureColourI colour = null;
6598 if (colourModel.getMax() != null)
6600 Color mincol = null;
6601 Color maxcol = null;
6602 Color noValueColour = null;
6606 mincol = new Color(Integer.parseInt(colourModel.getMinRGB(), 16));
6607 maxcol = new Color(Integer.parseInt(colourModel.getRGB(), 16));
6608 } catch (Exception e)
6610 Cache.log.warn("Couldn't parse out graduated feature color.", e);
6613 NoValueColour noCol = colourModel.getNoValueColour();
6614 if (noCol == NoValueColour.MIN)
6616 noValueColour = mincol;
6618 else if (noCol == NoValueColour.MAX)
6620 noValueColour = maxcol;
6623 colour = new FeatureColour(maxcol, mincol, maxcol, noValueColour,
6624 safeFloat(colourModel.getMin()),
6625 safeFloat(colourModel.getMax()));
6626 final List<String> attributeName = colourModel.getAttributeName();
6627 String[] attributes = attributeName
6628 .toArray(new String[attributeName.size()]);
6629 if (attributes != null && attributes.length > 0)
6631 colour.setAttributeName(attributes);
6633 if (colourModel.isAutoScale() != null)
6635 colour.setAutoScaled(colourModel.isAutoScale().booleanValue());
6637 if (colourModel.isColourByLabel() != null)
6639 colour.setColourByLabel(
6640 colourModel.isColourByLabel().booleanValue());
6642 if (colourModel.getThreshold() != null)
6644 colour.setThreshold(colourModel.getThreshold().floatValue());
6646 ThresholdType ttyp = colourModel.getThreshType();
6647 if (ttyp == ThresholdType.ABOVE)
6649 colour.setAboveThreshold(true);
6651 else if (ttyp == ThresholdType.BELOW)
6653 colour.setBelowThreshold(true);
6658 Color color = new Color(Integer.parseInt(colourModel.getRGB(), 16));
6659 colour = new FeatureColour(color);