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.FeatureRenderer;
64 import jalview.gui.JvOptionPane;
65 import jalview.gui.OOMWarning;
66 import jalview.gui.PCAPanel;
67 import jalview.gui.PaintRefresher;
68 import jalview.gui.SplitFrame;
69 import jalview.gui.StructureViewer;
70 import jalview.gui.StructureViewer.ViewerType;
71 import jalview.gui.StructureViewerBase;
72 import jalview.gui.TreePanel;
73 import jalview.io.BackupFiles;
74 import jalview.io.DataSourceType;
75 import jalview.io.FileFormat;
76 import jalview.io.NewickFile;
77 import jalview.math.Matrix;
78 import jalview.math.MatrixI;
79 import jalview.renderer.ResidueShaderI;
80 import jalview.schemes.AnnotationColourGradient;
81 import jalview.schemes.ColourSchemeI;
82 import jalview.schemes.ColourSchemeProperty;
83 import jalview.schemes.FeatureColour;
84 import jalview.schemes.ResidueProperties;
85 import jalview.schemes.UserColourScheme;
86 import jalview.structure.StructureSelectionManager;
87 import jalview.structures.models.AAStructureBindingModel;
88 import jalview.util.Format;
89 import jalview.util.MessageManager;
90 import jalview.util.Platform;
91 import jalview.util.StringUtils;
92 import jalview.util.jarInputStreamProvider;
93 import jalview.util.matcher.Condition;
94 import jalview.viewmodel.AlignmentViewport;
95 import jalview.viewmodel.PCAModel;
96 import jalview.viewmodel.ViewportRanges;
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 if (av.getFeaturesDisplayed() != null)
1518 FeatureSettings fs = new FeatureSettings();
1520 FeatureRenderer fr = ap.getSeqPanel().seqCanvas
1521 .getFeatureRenderer();
1522 String[] renderOrder = fr.getRenderOrder().toArray(new String[0]);
1524 Vector<String> settingsAdded = new Vector<>();
1525 if (renderOrder != null)
1527 for (String featureType : renderOrder)
1529 FeatureSettings.Setting setting = new FeatureSettings.Setting();
1530 setting.setType(featureType);
1533 * save any filter for the feature type
1535 FeatureMatcherSetI filter = fr.getFeatureFilter(featureType);
1536 if (filter != null) {
1537 Iterator<FeatureMatcherI> filters = filter.getMatchers().iterator();
1538 FeatureMatcherI firstFilter = filters.next();
1539 setting.setMatcherSet(Jalview2XML.marshalFilter(
1540 firstFilter, filters, filter.isAnded()));
1544 * save colour scheme for the feature type
1546 FeatureColourI fcol = fr.getFeatureStyle(featureType);
1547 if (!fcol.isSimpleColour())
1549 setting.setColour(fcol.getMaxColour().getRGB());
1550 setting.setMincolour(fcol.getMinColour().getRGB());
1551 setting.setMin(fcol.getMin());
1552 setting.setMax(fcol.getMax());
1553 setting.setColourByLabel(fcol.isColourByLabel());
1554 if (fcol.isColourByAttribute())
1556 String[] attName = fcol.getAttributeName();
1557 setting.getAttributeName().add(attName[0]);
1558 if (attName.length > 1)
1560 setting.getAttributeName().add(attName[1]);
1563 setting.setAutoScale(fcol.isAutoScaled());
1564 setting.setThreshold(fcol.getThreshold());
1565 Color noColour = fcol.getNoColour();
1566 if (noColour == null)
1568 setting.setNoValueColour(NoValueColour.NONE);
1570 else if (noColour.equals(fcol.getMaxColour()))
1572 setting.setNoValueColour(NoValueColour.MAX);
1576 setting.setNoValueColour(NoValueColour.MIN);
1578 // -1 = No threshold, 0 = Below, 1 = Above
1579 setting.setThreshstate(fcol.isAboveThreshold() ? 1
1580 : (fcol.isBelowThreshold() ? 0 : -1));
1584 setting.setColour(fcol.getColour().getRGB());
1588 av.getFeaturesDisplayed().isVisible(featureType));
1590 .getOrder(featureType);
1593 setting.setOrder(rorder);
1595 /// fs.addSetting(setting);
1596 fs.getSetting().add(setting);
1597 settingsAdded.addElement(featureType);
1601 // is groups actually supposed to be a map here ?
1602 Iterator<String> en = fr.getFeatureGroups().iterator();
1603 Vector<String> groupsAdded = new Vector<>();
1604 while (en.hasNext())
1606 String grp = en.next();
1607 if (groupsAdded.contains(grp))
1611 Group g = new Group();
1613 g.setDisplay(((Boolean) fr.checkGroupVisibility(grp, false))
1616 fs.getGroup().add(g);
1617 groupsAdded.addElement(grp);
1619 // jms.setFeatureSettings(fs);
1620 object.setFeatureSettings(fs);
1623 if (av.hasHiddenColumns())
1625 jalview.datamodel.HiddenColumns hidden = av.getAlignment()
1626 .getHiddenColumns();
1629 warn("REPORT BUG: avoided null columnselection bug (DMAM reported). Please contact Jim about this.");
1633 Iterator<int[]> hiddenRegions = hidden.iterator();
1634 while (hiddenRegions.hasNext())
1636 int[] region = hiddenRegions.next();
1637 HiddenColumns hc = new HiddenColumns();
1638 hc.setStart(region[0]);
1639 hc.setEnd(region[1]);
1640 // view.addHiddenColumns(hc);
1641 view.getHiddenColumns().add(hc);
1645 if (calcIdSet.size() > 0)
1647 for (String calcId : calcIdSet)
1649 if (calcId.trim().length() > 0)
1651 CalcIdParam cidp = createCalcIdParam(calcId, av);
1652 // Some calcIds have no parameters.
1655 // view.addCalcIdParam(cidp);
1656 view.getCalcIdParam().add(cidp);
1662 // jms.addViewport(view);
1663 object.getViewport().add(view);
1665 // object.setJalviewModelSequence(jms);
1666 // object.getVamsasModel().addSequenceSet(vamsasSet);
1667 object.getVamsasModel().getSequenceSet().add(vamsasSet);
1669 if (jout != null && fileName != null)
1671 // We may not want to write the object to disk,
1672 // eg we can copy the alignViewport to a new view object
1673 // using save and then load
1676 fileName = fileName.replace('\\', '/');
1677 System.out.println("Writing jar entry " + fileName);
1678 JarEntry entry = new JarEntry(fileName);
1679 jout.putNextEntry(entry);
1680 PrintWriter pout = new PrintWriter(
1681 new OutputStreamWriter(jout, UTF_8));
1682 JAXBContext jaxbContext = JAXBContext
1683 .newInstance(JalviewModel.class);
1684 Marshaller jaxbMarshaller = jaxbContext.createMarshaller();
1686 // output pretty printed
1687 // jaxbMarshaller.setProperty(Marshaller.JAXB_FORMATTED_OUTPUT, true);
1688 jaxbMarshaller.marshal(
1689 new ObjectFactory().createJalviewModel(object), pout);
1691 // jaxbMarshaller.marshal(object, pout);
1692 // marshaller.marshal(object);
1695 } catch (Exception ex)
1697 // TODO: raise error in GUI if marshalling failed.
1698 System.err.println("Error writing Jalview project");
1699 ex.printStackTrace();
1706 * Writes PCA viewer attributes and computed values to an XML model object and
1707 * adds it to the JalviewModel. Any exceptions are reported by logging.
1709 protected void savePCA(PCAPanel panel, JalviewModel object)
1713 PcaViewer viewer = new PcaViewer();
1714 viewer.setHeight(panel.getHeight());
1715 viewer.setWidth(panel.getWidth());
1716 viewer.setXpos(panel.getX());
1717 viewer.setYpos(panel.getY());
1718 viewer.setTitle(panel.getTitle());
1719 PCAModel pcaModel = panel.getPcaModel();
1720 viewer.setScoreModelName(pcaModel.getScoreModelName());
1721 viewer.setXDim(panel.getSelectedDimensionIndex(X));
1722 viewer.setYDim(panel.getSelectedDimensionIndex(Y));
1723 viewer.setZDim(panel.getSelectedDimensionIndex(Z));
1725 panel.getRotatableCanvas().getBackgroundColour().getRGB());
1726 viewer.setScaleFactor(panel.getRotatableCanvas().getScaleFactor());
1727 float[] spMin = panel.getRotatableCanvas().getSeqMin();
1728 SeqPointMin spmin = new SeqPointMin();
1729 spmin.setXPos(spMin[0]);
1730 spmin.setYPos(spMin[1]);
1731 spmin.setZPos(spMin[2]);
1732 viewer.setSeqPointMin(spmin);
1733 float[] spMax = panel.getRotatableCanvas().getSeqMax();
1734 SeqPointMax spmax = new SeqPointMax();
1735 spmax.setXPos(spMax[0]);
1736 spmax.setYPos(spMax[1]);
1737 spmax.setZPos(spMax[2]);
1738 viewer.setSeqPointMax(spmax);
1739 viewer.setShowLabels(panel.getRotatableCanvas().isShowLabels());
1740 viewer.setLinkToAllViews(
1741 panel.getRotatableCanvas().isApplyToAllViews());
1742 SimilarityParamsI sp = pcaModel.getSimilarityParameters();
1743 viewer.setIncludeGaps(sp.includeGaps());
1744 viewer.setMatchGaps(sp.matchGaps());
1745 viewer.setIncludeGappedColumns(sp.includeGappedColumns());
1746 viewer.setDenominateByShortestLength(sp.denominateByShortestLength());
1749 * sequence points on display
1751 for (jalview.datamodel.SequencePoint spt : pcaModel
1752 .getSequencePoints())
1754 SequencePoint point = new SequencePoint();
1755 point.setSequenceRef(seqHash(spt.getSequence()));
1756 point.setXPos(spt.coord.x);
1757 point.setYPos(spt.coord.y);
1758 point.setZPos(spt.coord.z);
1759 viewer.getSequencePoint().add(point);
1763 * (end points of) axes on display
1765 for (Point p : panel.getRotatableCanvas().getAxisEndPoints())
1768 Axis axis = new Axis();
1772 viewer.getAxis().add(axis);
1776 * raw PCA data (note we are not restoring PCA inputs here -
1777 * alignment view, score model, similarity parameters)
1779 PcaDataType data = new PcaDataType();
1780 viewer.setPcaData(data);
1781 PCA pca = pcaModel.getPcaData();
1783 DoubleMatrix pm = new DoubleMatrix();
1784 saveDoubleMatrix(pca.getPairwiseScores(), pm);
1785 data.setPairwiseMatrix(pm);
1787 DoubleMatrix tm = new DoubleMatrix();
1788 saveDoubleMatrix(pca.getTridiagonal(), tm);
1789 data.setTridiagonalMatrix(tm);
1791 DoubleMatrix eigenMatrix = new DoubleMatrix();
1792 data.setEigenMatrix(eigenMatrix);
1793 saveDoubleMatrix(pca.getEigenmatrix(), eigenMatrix);
1795 object.getPcaViewer().add(viewer);
1796 } catch (Throwable t)
1798 Cache.log.error("Error saving PCA: " + t.getMessage());
1803 * Stores values from a matrix into an XML element, including (if present) the
1808 * @see #loadDoubleMatrix(DoubleMatrix)
1810 protected void saveDoubleMatrix(MatrixI m, DoubleMatrix xmlMatrix)
1812 xmlMatrix.setRows(m.height());
1813 xmlMatrix.setColumns(m.width());
1814 for (int i = 0; i < m.height(); i++)
1816 DoubleVector row = new DoubleVector();
1817 for (int j = 0; j < m.width(); j++)
1819 row.getV().add(m.getValue(i, j));
1821 xmlMatrix.getRow().add(row);
1823 if (m.getD() != null)
1825 DoubleVector dVector = new DoubleVector();
1826 for (double d : m.getD())
1828 dVector.getV().add(d);
1830 xmlMatrix.setD(dVector);
1832 if (m.getE() != null)
1834 DoubleVector eVector = new DoubleVector();
1835 for (double e : m.getE())
1837 eVector.getV().add(e);
1839 xmlMatrix.setE(eVector);
1844 * Loads XML matrix data into a new Matrix object, including the D and/or E
1845 * vectors (if present)
1849 * @see Jalview2XML#saveDoubleMatrix(MatrixI, DoubleMatrix)
1851 protected MatrixI loadDoubleMatrix(DoubleMatrix mData)
1853 int rows = mData.getRows();
1854 double[][] vals = new double[rows][];
1856 for (int i = 0; i < rows; i++)
1858 List<Double> dVector = mData.getRow().get(i).getV();
1859 vals[i] = new double[dVector.size()];
1861 for (Double d : dVector)
1867 MatrixI m = new Matrix(vals);
1869 if (mData.getD() != null)
1871 List<Double> dVector = mData.getD().getV();
1872 double[] vec = new double[dVector.size()];
1874 for (Double d : dVector)
1880 if (mData.getE() != null)
1882 List<Double> dVector = mData.getE().getV();
1883 double[] vec = new double[dVector.size()];
1885 for (Double d : dVector)
1896 * Save any Varna viewers linked to this sequence. Writes an rnaViewer element
1897 * for each viewer, with
1899 * <li>viewer geometry (position, size, split pane divider location)</li>
1900 * <li>index of the selected structure in the viewer (currently shows gapped
1902 * <li>the id of the annotation holding RNA secondary structure</li>
1903 * <li>(currently only one SS is shown per viewer, may be more in future)</li>
1905 * Varna viewer state is also written out (in native Varna XML) to separate
1906 * project jar entries. A separate entry is written for each RNA structure
1907 * displayed, with the naming convention
1909 * <li>rna_viewId_sequenceId_annotationId_[gapped|trimmed]</li>
1917 * @param storeDataset
1919 protected void saveRnaViewers(JarOutputStream jout, JSeq jseq,
1920 final SequenceI jds, List<String> viewIds, AlignmentPanel ap,
1921 boolean storeDataset)
1923 if (Desktop.desktop == null)
1927 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1928 for (int f = frames.length - 1; f > -1; f--)
1930 if (frames[f] instanceof AppVarna)
1932 AppVarna varna = (AppVarna) frames[f];
1934 * link the sequence to every viewer that is showing it and is linked to
1935 * its alignment panel
1937 if (varna.isListeningFor(jds) && ap == varna.getAlignmentPanel())
1939 String viewId = varna.getViewId();
1940 RnaViewer rna = new RnaViewer();
1941 rna.setViewId(viewId);
1942 rna.setTitle(varna.getTitle());
1943 rna.setXpos(varna.getX());
1944 rna.setYpos(varna.getY());
1945 rna.setWidth(varna.getWidth());
1946 rna.setHeight(varna.getHeight());
1947 rna.setDividerLocation(varna.getDividerLocation());
1948 rna.setSelectedRna(varna.getSelectedIndex());
1949 // jseq.addRnaViewer(rna);
1950 jseq.getRnaViewer().add(rna);
1953 * Store each Varna panel's state once in the project per sequence.
1954 * First time through only (storeDataset==false)
1956 // boolean storeSessions = false;
1957 // String sequenceViewId = viewId + seqsToIds.get(jds);
1958 // if (!storeDataset && !viewIds.contains(sequenceViewId))
1960 // viewIds.add(sequenceViewId);
1961 // storeSessions = true;
1963 for (RnaModel model : varna.getModels())
1965 if (model.seq == jds)
1968 * VARNA saves each view (sequence or alignment secondary
1969 * structure, gapped or trimmed) as a separate XML file
1971 String jarEntryName = rnaSessions.get(model);
1972 if (jarEntryName == null)
1975 String varnaStateFile = varna.getStateInfo(model.rna);
1976 jarEntryName = RNA_PREFIX + viewId + "_" + nextCounter();
1977 copyFileToJar(jout, varnaStateFile, jarEntryName);
1978 rnaSessions.put(model, jarEntryName);
1980 SecondaryStructure ss = new SecondaryStructure();
1981 String annotationId = varna.getAnnotation(jds).annotationId;
1982 ss.setAnnotationId(annotationId);
1983 ss.setViewerState(jarEntryName);
1984 ss.setGapped(model.gapped);
1985 ss.setTitle(model.title);
1986 // rna.addSecondaryStructure(ss);
1987 rna.getSecondaryStructure().add(ss);
1996 * Copy the contents of a file to a new entry added to the output jar
2000 * @param jarEntryName
2002 protected void copyFileToJar(JarOutputStream jout, String infilePath,
2003 String jarEntryName)
2005 DataInputStream dis = null;
2008 File file = new File(infilePath);
2009 if (file.exists() && jout != null)
2011 dis = new DataInputStream(new FileInputStream(file));
2012 byte[] data = new byte[(int) file.length()];
2013 dis.readFully(data);
2014 writeJarEntry(jout, jarEntryName, data);
2016 } catch (Exception ex)
2018 ex.printStackTrace();
2026 } catch (IOException e)
2035 * Write the data to a new entry of given name in the output jar file
2038 * @param jarEntryName
2040 * @throws IOException
2042 protected void writeJarEntry(JarOutputStream jout, String jarEntryName,
2043 byte[] data) throws IOException
2047 jarEntryName = jarEntryName.replace('\\','/');
2048 System.out.println("Writing jar entry " + jarEntryName);
2049 jout.putNextEntry(new JarEntry(jarEntryName));
2050 DataOutputStream dout = new DataOutputStream(jout);
2051 dout.write(data, 0, data.length);
2058 * Save the state of a structure viewer
2063 * the archive XML element under which to save the state
2066 * @param matchedFile
2070 protected String saveStructureState(AlignmentPanel ap, SequenceI jds,
2071 Pdbids pdb, PDBEntry entry, List<String> viewIds,
2072 String matchedFile, StructureViewerBase viewFrame)
2074 final AAStructureBindingModel bindingModel = viewFrame.getBinding();
2077 * Look for any bindings for this viewer to the PDB file of interest
2078 * (including part matches excluding chain id)
2080 for (int peid = 0; peid < bindingModel.getPdbCount(); peid++)
2082 final PDBEntry pdbentry = bindingModel.getPdbEntry(peid);
2083 final String pdbId = pdbentry.getId();
2084 if (!pdbId.equals(entry.getId())
2085 && !(entry.getId().length() > 4 && entry.getId().toLowerCase()
2086 .startsWith(pdbId.toLowerCase())))
2089 * not interested in a binding to a different PDB entry here
2093 if (matchedFile == null)
2095 matchedFile = pdbentry.getFile();
2097 else if (!matchedFile.equals(pdbentry.getFile()))
2100 "Probably lost some PDB-Sequence mappings for this structure file (which apparently has same PDB Entry code): "
2101 + pdbentry.getFile());
2105 // can get at it if the ID
2106 // match is ambiguous (e.g.
2109 for (int smap = 0; smap < viewFrame.getBinding()
2110 .getSequence()[peid].length; smap++)
2112 // if (jal.findIndex(jmol.jmb.sequence[peid][smap]) > -1)
2113 if (jds == viewFrame.getBinding().getSequence()[peid][smap])
2115 StructureState state = new StructureState();
2116 state.setVisible(true);
2117 state.setXpos(viewFrame.getX());
2118 state.setYpos(viewFrame.getY());
2119 state.setWidth(viewFrame.getWidth());
2120 state.setHeight(viewFrame.getHeight());
2121 final String viewId = viewFrame.getViewId();
2122 state.setViewId(viewId);
2123 state.setAlignwithAlignPanel(viewFrame.isUsedforaligment(ap));
2124 state.setColourwithAlignPanel(viewFrame.isUsedforcolourby(ap));
2125 state.setColourByJmol(viewFrame.isColouredByViewer());
2126 state.setType(viewFrame.getViewerType().toString());
2127 // pdb.addStructureState(state);
2128 pdb.getStructureState().add(state);
2136 * Populates the AnnotationColourScheme xml for save. This captures the
2137 * settings of the options in the 'Colour by Annotation' dialog.
2140 * @param userColours
2144 private AnnotationColourScheme constructAnnotationColours(
2145 AnnotationColourGradient acg, List<UserColourScheme> userColours,
2148 AnnotationColourScheme ac = new AnnotationColourScheme();
2149 ac.setAboveThreshold(acg.getAboveThreshold());
2150 ac.setThreshold(acg.getAnnotationThreshold());
2151 // 2.10.2 save annotationId (unique) not annotation label
2152 ac.setAnnotation(acg.getAnnotation().annotationId);
2153 if (acg.getBaseColour() instanceof UserColourScheme)
2156 setUserColourScheme(acg.getBaseColour(), userColours, jm));
2161 ColourSchemeProperty.getColourName(acg.getBaseColour()));
2164 ac.setMaxColour(acg.getMaxColour().getRGB());
2165 ac.setMinColour(acg.getMinColour().getRGB());
2166 ac.setPerSequence(acg.isSeqAssociated());
2167 ac.setPredefinedColours(acg.isPredefinedColours());
2171 private void storeAlignmentAnnotation(AlignmentAnnotation[] aa,
2172 IdentityHashMap<SequenceGroup, String> groupRefs,
2173 AlignmentViewport av, Set<String> calcIdSet, boolean storeDS,
2174 SequenceSet vamsasSet)
2177 for (int i = 0; i < aa.length; i++)
2179 Annotation an = new Annotation();
2181 AlignmentAnnotation annotation = aa[i];
2182 if (annotation.annotationId != null)
2184 annotationIds.put(annotation.annotationId, annotation);
2187 an.setId(annotation.annotationId);
2189 an.setVisible(annotation.visible);
2191 an.setDescription(annotation.description);
2193 if (annotation.sequenceRef != null)
2195 // 2.9 JAL-1781 xref on sequence id rather than name
2196 an.setSequenceRef(seqsToIds.get(annotation.sequenceRef));
2198 if (annotation.groupRef != null)
2200 String groupIdr = groupRefs.get(annotation.groupRef);
2201 if (groupIdr == null)
2203 // make a locally unique String
2204 groupRefs.put(annotation.groupRef,
2205 groupIdr = ("" + System.currentTimeMillis()
2206 + annotation.groupRef.getName()
2207 + groupRefs.size()));
2209 an.setGroupRef(groupIdr.toString());
2212 // store all visualization attributes for annotation
2213 an.setGraphHeight(annotation.graphHeight);
2214 an.setCentreColLabels(annotation.centreColLabels);
2215 an.setScaleColLabels(annotation.scaleColLabel);
2216 an.setShowAllColLabels(annotation.showAllColLabels);
2217 an.setBelowAlignment(annotation.belowAlignment);
2219 if (annotation.graph > 0)
2222 an.setGraphType(annotation.graph);
2223 an.setGraphGroup(annotation.graphGroup);
2224 if (annotation.getThreshold() != null)
2226 ThresholdLine line = new ThresholdLine();
2227 line.setLabel(annotation.getThreshold().label);
2228 line.setValue(annotation.getThreshold().value);
2229 line.setColour(annotation.getThreshold().colour.getRGB());
2230 an.setThresholdLine(line);
2238 an.setLabel(annotation.label);
2240 if (annotation == av.getAlignmentQualityAnnot()
2241 || annotation == av.getAlignmentConservationAnnotation()
2242 || annotation == av.getAlignmentConsensusAnnotation()
2243 || annotation.autoCalculated)
2245 // new way of indicating autocalculated annotation -
2246 an.setAutoCalculated(annotation.autoCalculated);
2248 if (annotation.hasScore())
2250 an.setScore(annotation.getScore());
2253 if (annotation.getCalcId() != null)
2255 calcIdSet.add(annotation.getCalcId());
2256 an.setCalcId(annotation.getCalcId());
2258 if (annotation.hasProperties())
2260 for (String pr : annotation.getProperties())
2262 jalview.xml.binding.jalview.Annotation.Property prop = new jalview.xml.binding.jalview.Annotation.Property();
2264 prop.setValue(annotation.getProperty(pr));
2265 // an.addProperty(prop);
2266 an.getProperty().add(prop);
2270 AnnotationElement ae;
2271 if (annotation.annotations != null)
2273 an.setScoreOnly(false);
2274 for (int a = 0; a < annotation.annotations.length; a++)
2276 if ((annotation == null) || (annotation.annotations[a] == null))
2281 ae = new AnnotationElement();
2282 if (annotation.annotations[a].description != null)
2284 ae.setDescription(annotation.annotations[a].description);
2286 if (annotation.annotations[a].displayCharacter != null)
2288 ae.setDisplayCharacter(
2289 annotation.annotations[a].displayCharacter);
2292 if (!Float.isNaN(annotation.annotations[a].value))
2294 ae.setValue(annotation.annotations[a].value);
2298 if (annotation.annotations[a].secondaryStructure > ' ')
2300 ae.setSecondaryStructure(
2301 annotation.annotations[a].secondaryStructure + "");
2304 if (annotation.annotations[a].colour != null
2305 && annotation.annotations[a].colour != java.awt.Color.black)
2307 ae.setColour(annotation.annotations[a].colour.getRGB());
2310 // an.addAnnotationElement(ae);
2311 an.getAnnotationElement().add(ae);
2312 if (annotation.autoCalculated)
2314 // only write one non-null entry into the annotation row -
2315 // sufficient to get the visualization attributes necessary to
2323 an.setScoreOnly(true);
2325 if (!storeDS || (storeDS && !annotation.autoCalculated))
2327 // skip autocalculated annotation - these are only provided for
2329 // vamsasSet.addAnnotation(an);
2330 vamsasSet.getAnnotation().add(an);
2336 private CalcIdParam createCalcIdParam(String calcId, AlignViewport av)
2338 AutoCalcSetting settings = av.getCalcIdSettingsFor(calcId);
2339 if (settings != null)
2341 CalcIdParam vCalcIdParam = new CalcIdParam();
2342 vCalcIdParam.setCalcId(calcId);
2343 // vCalcIdParam.addServiceURL(settings.getServiceURI());
2344 vCalcIdParam.getServiceURL().add(settings.getServiceURI());
2345 // generic URI allowing a third party to resolve another instance of the
2346 // service used for this calculation
2347 for (String url : settings.getServiceURLs())
2349 // vCalcIdParam.addServiceURL(urls);
2350 vCalcIdParam.getServiceURL().add(url);
2352 vCalcIdParam.setVersion("1.0");
2353 if (settings.getPreset() != null)
2355 WsParamSetI setting = settings.getPreset();
2356 vCalcIdParam.setName(setting.getName());
2357 vCalcIdParam.setDescription(setting.getDescription());
2361 vCalcIdParam.setName("");
2362 vCalcIdParam.setDescription("Last used parameters");
2364 // need to be able to recover 1) settings 2) user-defined presets or
2365 // recreate settings from preset 3) predefined settings provided by
2366 // service - or settings that can be transferred (or discarded)
2367 vCalcIdParam.setParameters(
2368 settings.getWsParamFile().replace("\n", "|\\n|"));
2369 vCalcIdParam.setAutoUpdate(settings.isAutoUpdate());
2370 // todo - decide if updateImmediately is needed for any projects.
2372 return vCalcIdParam;
2377 private boolean recoverCalcIdParam(CalcIdParam calcIdParam,
2380 if (calcIdParam.getVersion().equals("1.0"))
2382 final String[] calcIds = calcIdParam.getServiceURL().toArray(new String[0]);
2383 Jws2Instance service = Jws2Discoverer.getDiscoverer()
2384 .getPreferredServiceFor(calcIds);
2385 if (service != null)
2387 WsParamSetI parmSet = null;
2390 parmSet = service.getParamStore().parseServiceParameterFile(
2391 calcIdParam.getName(), calcIdParam.getDescription(),
2393 calcIdParam.getParameters().replace("|\\n|", "\n"));
2394 } catch (IOException x)
2396 warn("Couldn't parse parameter data for "
2397 + calcIdParam.getCalcId(), x);
2400 List<ArgumentI> argList = null;
2401 if (calcIdParam.getName().length() > 0)
2403 parmSet = service.getParamStore()
2404 .getPreset(calcIdParam.getName());
2405 if (parmSet != null)
2407 // TODO : check we have a good match with settings in AACon -
2408 // otherwise we'll need to create a new preset
2413 argList = parmSet.getArguments();
2416 AAConSettings settings = new AAConSettings(
2417 calcIdParam.isAutoUpdate(), service, parmSet, argList);
2418 av.setCalcIdSettingsFor(calcIdParam.getCalcId(), settings,
2419 calcIdParam.isNeedsUpdate());
2424 warn("Cannot resolve a service for the parameters used in this project. Try configuring a JABAWS server.");
2428 throw new Error(MessageManager.formatMessage(
2429 "error.unsupported_version_calcIdparam", new Object[]
2430 { calcIdParam.toString() }));
2434 * External mapping between jalview objects and objects yielding a valid and
2435 * unique object ID string. This is null for normal Jalview project IO, but
2436 * non-null when a jalview project is being read or written as part of a
2439 IdentityHashMap jv2vobj = null;
2442 * Construct a unique ID for jvobj using either existing bindings or if none
2443 * exist, the result of the hashcode call for the object.
2446 * jalview data object
2447 * @return unique ID for referring to jvobj
2449 private String makeHashCode(Object jvobj, String altCode)
2451 if (jv2vobj != null)
2453 Object id = jv2vobj.get(jvobj);
2456 return id.toString();
2458 // check string ID mappings
2459 if (jvids2vobj != null && jvobj instanceof String)
2461 id = jvids2vobj.get(jvobj);
2465 return id.toString();
2467 // give up and warn that something has gone wrong
2468 warn("Cannot find ID for object in external mapping : " + jvobj);
2474 * return local jalview object mapped to ID, if it exists
2478 * @return null or object bound to idcode
2480 private Object retrieveExistingObj(String idcode)
2482 if (idcode != null && vobj2jv != null)
2484 return vobj2jv.get(idcode);
2490 * binding from ID strings from external mapping table to jalview data model
2493 private Hashtable vobj2jv;
2495 private Sequence createVamsasSequence(String id, SequenceI jds)
2497 return createVamsasSequence(true, id, jds, null);
2500 private Sequence createVamsasSequence(boolean recurse, String id,
2501 SequenceI jds, SequenceI parentseq)
2503 Sequence vamsasSeq = new Sequence();
2504 vamsasSeq.setId(id);
2505 vamsasSeq.setName(jds.getName());
2506 vamsasSeq.setSequence(jds.getSequenceAsString());
2507 vamsasSeq.setDescription(jds.getDescription());
2508 List<DBRefEntry> dbrefs = null;
2509 if (jds.getDatasetSequence() != null)
2511 vamsasSeq.setDsseqid(seqHash(jds.getDatasetSequence()));
2515 // seqId==dsseqid so we can tell which sequences really are
2516 // dataset sequences only
2517 vamsasSeq.setDsseqid(id);
2518 dbrefs = jds.getDBRefs();
2519 if (parentseq == null)
2526 * save any dbrefs; special subclass GeneLocus is flagged as 'locus'
2530 for (int d = 0, nd = dbrefs.size(); d < nd; d++)
2532 DBRef dbref = new DBRef();
2533 DBRefEntry ref = dbrefs.get(d);
2534 dbref.setSource(ref.getSource());
2535 dbref.setVersion(ref.getVersion());
2536 dbref.setAccessionId(ref.getAccessionId());
2537 if (ref instanceof GeneLocus)
2539 dbref.setLocus(true);
2543 Mapping mp = createVamsasMapping(ref.getMap(), parentseq,
2545 dbref.setMapping(mp);
2547 vamsasSeq.getDBRef().add(dbref);
2553 private Mapping createVamsasMapping(jalview.datamodel.Mapping jmp,
2554 SequenceI parentseq, SequenceI jds, boolean recurse)
2557 if (jmp.getMap() != null)
2561 jalview.util.MapList mlst = jmp.getMap();
2562 List<int[]> r = mlst.getFromRanges();
2563 for (int[] range : r)
2565 MapListFrom mfrom = new MapListFrom();
2566 mfrom.setStart(range[0]);
2567 mfrom.setEnd(range[1]);
2568 // mp.addMapListFrom(mfrom);
2569 mp.getMapListFrom().add(mfrom);
2571 r = mlst.getToRanges();
2572 for (int[] range : r)
2574 MapListTo mto = new MapListTo();
2575 mto.setStart(range[0]);
2576 mto.setEnd(range[1]);
2577 // mp.addMapListTo(mto);
2578 mp.getMapListTo().add(mto);
2580 mp.setMapFromUnit(BigInteger.valueOf(mlst.getFromRatio()));
2581 mp.setMapToUnit(BigInteger.valueOf(mlst.getToRatio()));
2582 if (jmp.getTo() != null)
2584 // MappingChoice mpc = new MappingChoice();
2586 // check/create ID for the sequence referenced by getTo()
2589 SequenceI ps = null;
2590 if (parentseq != jmp.getTo()
2591 && parentseq.getDatasetSequence() != jmp.getTo())
2593 // chaining dbref rather than a handshaking one
2594 jmpid = seqHash(ps = jmp.getTo());
2598 jmpid = seqHash(ps = parentseq);
2600 // mpc.setDseqFor(jmpid);
2601 mp.setDseqFor(jmpid);
2602 if (!seqRefIds.containsKey(jmpid))
2604 jalview.bin.Cache.log.debug("creatign new DseqFor ID");
2605 seqRefIds.put(jmpid, ps);
2609 jalview.bin.Cache.log.debug("reusing DseqFor ID");
2612 // mp.setMappingChoice(mpc);
2618 String setUserColourScheme(jalview.schemes.ColourSchemeI cs,
2619 List<UserColourScheme> userColours, JalviewModel jm)
2622 jalview.schemes.UserColourScheme ucs = (jalview.schemes.UserColourScheme) cs;
2623 boolean newucs = false;
2624 if (!userColours.contains(ucs))
2626 userColours.add(ucs);
2629 id = "ucs" + userColours.indexOf(ucs);
2632 // actually create the scheme's entry in the XML model
2633 java.awt.Color[] colours = ucs.getColours();
2634 UserColours uc = new UserColours();
2635 // UserColourScheme jbucs = new UserColourScheme();
2636 JalviewUserColours jbucs = new JalviewUserColours();
2638 for (int i = 0; i < colours.length; i++)
2640 Colour col = new Colour();
2641 col.setName(ResidueProperties.aa[i]);
2642 col.setRGB(jalview.util.Format.getHexString(colours[i]));
2643 // jbucs.addColour(col);
2644 jbucs.getColour().add(col);
2646 if (ucs.getLowerCaseColours() != null)
2648 colours = ucs.getLowerCaseColours();
2649 for (int i = 0; i < colours.length; i++)
2651 Colour col = new Colour();
2652 col.setName(ResidueProperties.aa[i].toLowerCase());
2653 col.setRGB(jalview.util.Format.getHexString(colours[i]));
2654 // jbucs.addColour(col);
2655 jbucs.getColour().add(col);
2660 uc.setUserColourScheme(jbucs);
2661 // jm.addUserColours(uc);
2662 jm.getUserColours().add(uc);
2668 jalview.schemes.UserColourScheme getUserColourScheme(
2669 JalviewModel jm, String id)
2671 List<UserColours> uc = jm.getUserColours();
2672 UserColours colours = null;
2674 for (int i = 0; i < uc.length; i++)
2676 if (uc[i].getId().equals(id))
2683 for (UserColours c : uc)
2685 if (c.getId().equals(id))
2692 java.awt.Color[] newColours = new java.awt.Color[24];
2694 for (int i = 0; i < 24; i++)
2696 newColours[i] = new java.awt.Color(Integer.parseInt(
2697 // colours.getUserColourScheme().getColour(i).getRGB(), 16));
2698 colours.getUserColourScheme().getColour().get(i).getRGB(),
2702 jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(
2705 if (colours.getUserColourScheme().getColour().size()/*Count()*/ > 24)
2707 newColours = new java.awt.Color[23];
2708 for (int i = 0; i < 23; i++)
2710 newColours[i] = new java.awt.Color(Integer.parseInt(
2711 colours.getUserColourScheme().getColour().get(i + 24)
2715 ucs.setLowerCaseColours(newColours);
2722 * contains last error message (if any) encountered by XML loader.
2724 String errorMessage = null;
2727 * flag to control whether the Jalview2XML_V1 parser should be deferred to if
2728 * exceptions are raised during project XML parsing
2730 public boolean attemptversion1parse = false;
2733 * Load a jalview project archive from a jar file
2736 * - HTTP URL or filename
2738 public AlignFrame loadJalviewAlign(final Object file)
2741 jalview.gui.AlignFrame af = null;
2745 // create list to store references for any new Jmol viewers created
2746 newStructureViewers = new Vector<>();
2747 // UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
2748 // Workaround is to make sure caller implements the JarInputStreamProvider
2750 // so we can re-open the jar input stream for each entry.
2752 jarInputStreamProvider jprovider = createjarInputStreamProvider(file);
2753 af = loadJalviewAlign(jprovider);
2756 af.setMenusForViewport();
2758 } catch (MalformedURLException e)
2760 errorMessage = "Invalid URL format for '" + file + "'";
2766 SwingUtilities.invokeAndWait(new Runnable()
2771 setLoadingFinishedForNewStructureViewers();
2774 } catch (Exception x)
2776 System.err.println("Error loading alignment: " + x.getMessage());
2782 @SuppressWarnings("unused")
2783 private jarInputStreamProvider createjarInputStreamProvider(final Object ofile) throws MalformedURLException {
2785 // BH 2018 allow for bytes already attached to File object
2787 String file = (ofile instanceof File ? ((File) ofile).getCanonicalPath() : ofile.toString());
2788 byte[] bytes = Platform.isJS() ? Platform.getFileBytes((File) ofile)
2791 errorMessage = null;
2792 uniqueSetSuffix = null;
2794 viewportsAdded.clear();
2795 frefedSequence = null;
2797 if (file.startsWith("http://")) {
2798 url = new URL(file);
2800 final URL _url = url;
2801 return new jarInputStreamProvider() {
2804 public JarInputStream getJarInputStream() throws IOException {
2805 if (bytes != null) {
2806 // System.out.println("Jalview2XML: opening byte jarInputStream for bytes.length=" + bytes.length);
2807 return new JarInputStream(new ByteArrayInputStream(bytes));
2810 // System.out.println("Jalview2XML: opening url jarInputStream for " + _url);
2811 return new JarInputStream(_url.openStream());
2813 // System.out.println("Jalview2XML: opening file jarInputStream for " + file);
2814 return new JarInputStream(new FileInputStream(file));
2819 public String getFilename() {
2823 } catch (IOException e) {
2824 e.printStackTrace();
2830 * Recover jalview session from a jalview project archive. Caller may
2831 * initialise uniqueSetSuffix, seqRefIds, viewportsAdded and frefedSequence
2832 * themselves. Any null fields will be initialised with default values,
2833 * non-null fields are left alone.
2838 public AlignFrame loadJalviewAlign(final jarInputStreamProvider jprovider)
2840 errorMessage = null;
2841 if (uniqueSetSuffix == null)
2843 uniqueSetSuffix = System.currentTimeMillis() % 100000 + "";
2845 if (seqRefIds == null)
2849 AlignFrame af = null, _af = null;
2850 IdentityHashMap<AlignmentI, AlignmentI> importedDatasets = new IdentityHashMap<>();
2851 Map<String, AlignFrame> gatherToThisFrame = new HashMap<>();
2852 final String file = jprovider.getFilename();
2855 JarInputStream jin = null;
2856 JarEntry jarentry = null;
2861 jin = jprovider.getJarInputStream();
2862 for (int i = 0; i < entryCount; i++)
2864 jarentry = jin.getNextJarEntry();
2867 if (jarentry != null && jarentry.getName().endsWith(".xml"))
2869 JAXBContext jc = JAXBContext
2870 .newInstance("jalview.xml.binding.jalview");
2871 XMLStreamReader streamReader = XMLInputFactory.newInstance()
2872 .createXMLStreamReader(jin);
2873 javax.xml.bind.Unmarshaller um = jc.createUnmarshaller();
2874 JAXBElement<JalviewModel> jbe = um
2875 .unmarshal(streamReader, JalviewModel.class);
2876 JalviewModel object = jbe.getValue();
2878 if (true) // !skipViewport(object))
2880 _af = loadFromObject(object, file, true, jprovider);
2881 if (_af != null && object.getViewport().size() > 0)
2882 // getJalviewModelSequence().getViewportCount() > 0)
2886 // store a reference to the first view
2889 if (_af.getViewport().isGatherViewsHere())
2891 // if this is a gathered view, keep its reference since
2892 // after gathering views, only this frame will remain
2894 gatherToThisFrame.put(_af.getViewport().getSequenceSetId(),
2897 // Save dataset to register mappings once all resolved
2898 importedDatasets.put(
2899 af.getViewport().getAlignment().getDataset(),
2900 af.getViewport().getAlignment().getDataset());
2905 else if (jarentry != null)
2907 // Some other file here.
2910 } while (jarentry != null);
2911 resolveFrefedSequences();
2912 } catch (IOException ex)
2914 ex.printStackTrace();
2915 errorMessage = "Couldn't locate Jalview XML file : " + file;
2917 "Exception whilst loading jalview XML file : " + ex + "\n");
2918 } catch (Exception ex)
2920 System.err.println("Parsing as Jalview Version 2 file failed.");
2921 ex.printStackTrace(System.err);
2922 if (attemptversion1parse)
2924 // used to attempt to parse as V1 castor-generated xml
2926 if (Desktop.instance != null)
2928 Desktop.instance.stopLoading();
2932 System.out.println("Successfully loaded archive file");
2935 ex.printStackTrace();
2938 "Exception whilst loading jalview XML file : " + ex + "\n");
2939 } catch (OutOfMemoryError e)
2941 // Don't use the OOM Window here
2942 errorMessage = "Out of memory loading jalview XML file";
2943 System.err.println("Out of memory whilst loading jalview XML file");
2944 e.printStackTrace();
2948 * Regather multiple views (with the same sequence set id) to the frame (if
2949 * any) that is flagged as the one to gather to, i.e. convert them to tabbed
2950 * views instead of separate frames. Note this doesn't restore a state where
2951 * some expanded views in turn have tabbed views - the last "first tab" read
2952 * in will play the role of gatherer for all.
2954 for (AlignFrame fr : gatherToThisFrame.values())
2956 Desktop.instance.gatherViews(fr);
2959 restoreSplitFrames();
2960 for (AlignmentI ds : importedDatasets.keySet())
2962 if (ds.getCodonFrames() != null)
2964 StructureSelectionManager
2965 .getStructureSelectionManager(Desktop.instance)
2966 .registerMappings(ds.getCodonFrames());
2969 if (errorMessage != null)
2974 if (Desktop.instance != null)
2976 Desktop.instance.stopLoading();
2983 * Try to reconstruct and display SplitFrame windows, where each contains
2984 * complementary dna and protein alignments. Done by pairing up AlignFrame
2985 * objects (created earlier) which have complementary viewport ids associated.
2987 protected void restoreSplitFrames()
2989 List<SplitFrame> gatherTo = new ArrayList<>();
2990 List<AlignFrame> addedToSplitFrames = new ArrayList<>();
2991 Map<String, AlignFrame> dna = new HashMap<>();
2994 * Identify the DNA alignments
2996 for (Entry<Viewport, AlignFrame> candidate : splitFrameCandidates
2999 AlignFrame af = candidate.getValue();
3000 if (af.getViewport().getAlignment().isNucleotide())
3002 dna.put(candidate.getKey().getId(), af);
3007 * Try to match up the protein complements
3009 for (Entry<Viewport, AlignFrame> candidate : splitFrameCandidates
3012 AlignFrame af = candidate.getValue();
3013 if (!af.getViewport().getAlignment().isNucleotide())
3015 String complementId = candidate.getKey().getComplementId();
3016 // only non-null complements should be in the Map
3017 if (complementId != null && dna.containsKey(complementId))
3019 final AlignFrame dnaFrame = dna.get(complementId);
3020 SplitFrame sf = createSplitFrame(dnaFrame, af);
3021 addedToSplitFrames.add(dnaFrame);
3022 addedToSplitFrames.add(af);
3023 dnaFrame.setMenusForViewport();
3024 af.setMenusForViewport();
3025 if (af.getViewport().isGatherViewsHere())
3034 * Open any that we failed to pair up (which shouldn't happen!) as
3035 * standalone AlignFrame's.
3037 for (Entry<Viewport, AlignFrame> candidate : splitFrameCandidates
3040 AlignFrame af = candidate.getValue();
3041 if (!addedToSplitFrames.contains(af))
3043 Viewport view = candidate.getKey();
3044 Desktop.addInternalFrame(af, view.getTitle(),
3045 safeInt(view.getWidth()), safeInt(view.getHeight()));
3046 af.setMenusForViewport();
3047 System.err.println("Failed to restore view " + view.getTitle()
3048 + " to split frame");
3053 * Gather back into tabbed views as flagged.
3055 for (SplitFrame sf : gatherTo)
3057 Desktop.instance.gatherViews(sf);
3060 splitFrameCandidates.clear();
3064 * Construct and display one SplitFrame holding DNA and protein alignments.
3067 * @param proteinFrame
3070 protected SplitFrame createSplitFrame(AlignFrame dnaFrame,
3071 AlignFrame proteinFrame)
3073 SplitFrame splitFrame = new SplitFrame(dnaFrame, proteinFrame);
3074 String title = MessageManager.getString("label.linked_view_title");
3075 int width = (int) dnaFrame.getBounds().getWidth();
3076 int height = (int) (dnaFrame.getBounds().getHeight()
3077 + proteinFrame.getBounds().getHeight() + 50);
3080 * SplitFrame location is saved to both enclosed frames
3082 splitFrame.setLocation(dnaFrame.getX(), dnaFrame.getY());
3083 Desktop.addInternalFrame(splitFrame, title, width, height);
3086 * And compute cDNA consensus (couldn't do earlier with consensus as
3087 * mappings were not yet present)
3089 proteinFrame.getViewport().alignmentChanged(proteinFrame.alignPanel);
3095 * check errorMessage for a valid error message and raise an error box in the
3096 * GUI or write the current errorMessage to stderr and then clear the error
3099 protected void reportErrors()
3101 reportErrors(false);
3104 protected void reportErrors(final boolean saving)
3106 if (errorMessage != null)
3108 final String finalErrorMessage = errorMessage;
3111 javax.swing.SwingUtilities.invokeLater(new Runnable()
3116 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
3118 "Error " + (saving ? "saving" : "loading")
3120 JvOptionPane.WARNING_MESSAGE);
3126 System.err.println("Problem loading Jalview file: " + errorMessage);
3129 errorMessage = null;
3132 Map<String, String> alreadyLoadedPDB = new HashMap<>();
3135 * when set, local views will be updated from view stored in JalviewXML
3136 * Currently (28th Sep 2008) things will go horribly wrong in vamsas document
3137 * sync if this is set to true.
3139 private final boolean updateLocalViews = false;
3142 * Returns the path to a temporary file holding the PDB file for the given PDB
3143 * id. The first time of asking, searches for a file of that name in the
3144 * Jalview project jar, and copies it to a new temporary file. Any repeat
3145 * requests just return the path to the file previously created.
3151 String loadPDBFile(jarInputStreamProvider jprovider, String pdbId,
3154 if (alreadyLoadedPDB.containsKey(pdbId))
3156 return alreadyLoadedPDB.get(pdbId).toString();
3159 String tempFile = copyJarEntry(jprovider, pdbId, "jalview_pdb",
3161 if (tempFile != null)
3163 alreadyLoadedPDB.put(pdbId, tempFile);
3169 * Copies the jar entry of given name to a new temporary file and returns the
3170 * path to the file, or null if the entry is not found.
3173 * @param jarEntryName
3175 * a prefix for the temporary file name, must be at least three
3178 * null or original file - so new file can be given the same suffix
3182 protected String copyJarEntry(jarInputStreamProvider jprovider,
3183 String jarEntryName, String prefix, String origFile)
3185 BufferedReader in = null;
3186 PrintWriter out = null;
3187 String suffix = ".tmp";
3188 if (origFile == null)
3190 origFile = jarEntryName;
3192 int sfpos = origFile.lastIndexOf(".");
3193 if (sfpos > -1 && sfpos < (origFile.length() - 3))
3195 suffix = "." + origFile.substring(sfpos + 1);
3199 JarInputStream jin = jprovider.getJarInputStream();
3201 * if (jprovider.startsWith("http://")) { jin = new JarInputStream(new
3202 * URL(jprovider).openStream()); } else { jin = new JarInputStream(new
3203 * FileInputStream(jprovider)); }
3206 JarEntry entry = null;
3209 entry = jin.getNextJarEntry();
3210 } while (entry != null && !entry.getName().equals(jarEntryName));
3213 in = new BufferedReader(new InputStreamReader(jin, UTF_8));
3214 File outFile = File.createTempFile(prefix, suffix);
3215 outFile.deleteOnExit();
3216 out = new PrintWriter(new FileOutputStream(outFile));
3219 while ((data = in.readLine()) != null)
3224 String t = outFile.getAbsolutePath();
3229 warn("Couldn't find entry in Jalview Jar for " + jarEntryName);
3231 } catch (Exception ex)
3233 ex.printStackTrace();
3241 } catch (IOException e)
3255 private class JvAnnotRow
3257 public JvAnnotRow(int i, AlignmentAnnotation jaa)
3264 * persisted version of annotation row from which to take vis properties
3266 public jalview.datamodel.AlignmentAnnotation template;
3269 * original position of the annotation row in the alignment
3275 * Load alignment frame from jalview XML DOM object
3277 * @param jalviewModel
3280 * filename source string
3281 * @param loadTreesAndStructures
3282 * when false only create Viewport
3284 * data source provider
3285 * @return alignment frame created from view stored in DOM
3287 AlignFrame loadFromObject(JalviewModel jalviewModel, String file,
3288 boolean loadTreesAndStructures, jarInputStreamProvider jprovider)
3290 SequenceSet vamsasSet = jalviewModel.getVamsasModel().getSequenceSet().get(0);
3291 List<Sequence> vamsasSeqs = vamsasSet.getSequence();
3293 // JalviewModelSequence jms = object.getJalviewModelSequence();
3295 // Viewport view = (jms.getViewportCount() > 0) ? jms.getViewport(0)
3297 Viewport view = (jalviewModel.getViewport().size() > 0)
3298 ? jalviewModel.getViewport().get(0)
3301 // ////////////////////////////////
3302 // INITIALISE ALIGNMENT SEQUENCESETID AND VIEWID
3305 // If we just load in the same jar file again, the sequenceSetId
3306 // will be the same, and we end up with multiple references
3307 // to the same sequenceSet. We must modify this id on load
3308 // so that each load of the file gives a unique id
3311 * used to resolve correct alignment dataset for alignments with multiple
3314 String uniqueSeqSetId = null;
3315 String viewId = null;
3318 uniqueSeqSetId = view.getSequenceSetId() + uniqueSetSuffix;
3319 viewId = (view.getId() == null ? null
3320 : view.getId() + uniqueSetSuffix);
3323 // ////////////////////////////////
3326 List<SequenceI> hiddenSeqs = null;
3328 List<SequenceI> tmpseqs = new ArrayList<>();
3330 boolean multipleView = false;
3331 SequenceI referenceseqForView = null;
3332 // JSeq[] jseqs = object.getJalviewModelSequence().getJSeq();
3333 List<JSeq> jseqs = jalviewModel.getJSeq();
3334 int vi = 0; // counter in vamsasSeq array
3335 for (int i = 0; i < jseqs.size(); i++)
3337 JSeq jseq = jseqs.get(i);
3338 String seqId = jseq.getId();
3340 SequenceI tmpSeq = seqRefIds.get(seqId);
3343 if (!incompleteSeqs.containsKey(seqId))
3345 // may not need this check, but keep it for at least 2.9,1 release
3346 if (tmpSeq.getStart() != jseq.getStart()
3347 || tmpSeq.getEnd() != jseq.getEnd())
3350 "Warning JAL-2154 regression: updating start/end for sequence "
3351 + tmpSeq.toString() + " to " + jseq);
3356 incompleteSeqs.remove(seqId);
3358 if (vamsasSeqs.size() > vi
3359 && vamsasSeqs.get(vi).getId().equals(seqId))
3361 // most likely we are reading a dataset XML document so
3362 // update from vamsasSeq section of XML for this sequence
3363 tmpSeq.setName(vamsasSeqs.get(vi).getName());
3364 tmpSeq.setDescription(vamsasSeqs.get(vi).getDescription());
3365 tmpSeq.setSequence(vamsasSeqs.get(vi).getSequence());
3370 // reading multiple views, so vamsasSeq set is a subset of JSeq
3371 multipleView = true;
3373 tmpSeq.setStart(jseq.getStart());
3374 tmpSeq.setEnd(jseq.getEnd());
3375 tmpseqs.add(tmpSeq);
3379 Sequence vamsasSeq = vamsasSeqs.get(vi);
3380 tmpSeq = new jalview.datamodel.Sequence(vamsasSeq.getName(),
3381 vamsasSeq.getSequence());
3382 tmpSeq.setDescription(vamsasSeq.getDescription());
3383 tmpSeq.setStart(jseq.getStart());
3384 tmpSeq.setEnd(jseq.getEnd());
3385 tmpSeq.setVamsasId(uniqueSetSuffix + seqId);
3386 seqRefIds.put(vamsasSeq.getId(), tmpSeq);
3387 tmpseqs.add(tmpSeq);
3391 if (safeBoolean(jseq.isViewreference()))
3393 referenceseqForView = tmpseqs.get(tmpseqs.size() - 1);
3396 if (jseq.isHidden() != null && jseq.isHidden().booleanValue())
3398 if (hiddenSeqs == null)
3400 hiddenSeqs = new ArrayList<>();
3403 hiddenSeqs.add(tmpSeq);
3408 // Create the alignment object from the sequence set
3409 // ///////////////////////////////
3410 SequenceI[] orderedSeqs = tmpseqs
3411 .toArray(new SequenceI[tmpseqs.size()]);
3413 AlignmentI al = null;
3414 // so we must create or recover the dataset alignment before going further
3415 // ///////////////////////////////
3416 if (vamsasSet.getDatasetId() == null || vamsasSet.getDatasetId() == "")
3418 // older jalview projects do not have a dataset - so creat alignment and
3420 al = new Alignment(orderedSeqs);
3421 al.setDataset(null);
3425 boolean isdsal = jalviewModel.getViewport().isEmpty();
3428 // we are importing a dataset record, so
3429 // recover reference to an alignment already materialsed as dataset
3430 al = getDatasetFor(vamsasSet.getDatasetId());
3434 // materialse the alignment
3435 al = new Alignment(orderedSeqs);
3439 addDatasetRef(vamsasSet.getDatasetId(), al);
3442 // finally, verify all data in vamsasSet is actually present in al
3443 // passing on flag indicating if it is actually a stored dataset
3444 recoverDatasetFor(vamsasSet, al, isdsal, uniqueSeqSetId);
3447 if (referenceseqForView != null)
3449 al.setSeqrep(referenceseqForView);
3451 // / Add the alignment properties
3452 for (int i = 0; i < vamsasSet.getSequenceSetProperties().size(); i++)
3454 SequenceSetProperties ssp = vamsasSet.getSequenceSetProperties()
3456 al.setProperty(ssp.getKey(), ssp.getValue());
3459 // ///////////////////////////////
3461 Hashtable pdbloaded = new Hashtable(); // TODO nothing writes to this??
3464 // load sequence features, database references and any associated PDB
3465 // structures for the alignment
3467 // prior to 2.10, this part would only be executed the first time a
3468 // sequence was encountered, but not afterwards.
3469 // now, for 2.10 projects, this is also done if the xml doc includes
3470 // dataset sequences not actually present in any particular view.
3472 for (int i = 0; i < vamsasSeqs.size(); i++)
3474 JSeq jseq = jseqs.get(i);
3475 if (jseq.getFeatures().size() > 0)
3477 List<Feature> features = jseq.getFeatures();
3478 for (int f = 0; f < features.size(); f++)
3480 Feature feat = features.get(f);
3481 SequenceFeature sf = new SequenceFeature(feat.getType(),
3482 feat.getDescription(), feat.getBegin(), feat.getEnd(),
3483 safeFloat(feat.getScore()), feat.getFeatureGroup());
3484 sf.setStatus(feat.getStatus());
3487 * load any feature attributes - include map-valued attributes
3489 Map<String, Map<String, String>> mapAttributes = new HashMap<>();
3490 for (int od = 0; od < feat.getOtherData().size(); od++)
3492 OtherData keyValue = feat.getOtherData().get(od);
3493 String attributeName = keyValue.getKey();
3494 String attributeValue = keyValue.getValue();
3495 if (attributeName.startsWith("LINK"))
3497 sf.addLink(attributeValue);
3501 String subAttribute = keyValue.getKey2();
3502 if (subAttribute == null)
3504 // simple string-valued attribute
3505 sf.setValue(attributeName, attributeValue);
3509 // attribute 'key' has sub-attribute 'key2'
3510 if (!mapAttributes.containsKey(attributeName))
3512 mapAttributes.put(attributeName, new HashMap<>());
3514 mapAttributes.get(attributeName).put(subAttribute,
3519 for (Entry<String, Map<String, String>> mapAttribute : mapAttributes
3522 sf.setValue(mapAttribute.getKey(), mapAttribute.getValue());
3525 // adds feature to datasequence's feature set (since Jalview 2.10)
3526 al.getSequenceAt(i).addSequenceFeature(sf);
3529 if (vamsasSeqs.get(i).getDBRef().size() > 0)
3531 // adds dbrefs to datasequence's set (since Jalview 2.10)
3533 al.getSequenceAt(i).getDatasetSequence() == null
3534 ? al.getSequenceAt(i)
3535 : al.getSequenceAt(i).getDatasetSequence(),
3538 if (jseq.getPdbids().size() > 0)
3540 List<Pdbids> ids = jseq.getPdbids();
3541 for (int p = 0; p < ids.size(); p++)
3543 Pdbids pdbid = ids.get(p);
3544 jalview.datamodel.PDBEntry entry = new jalview.datamodel.PDBEntry();
3545 entry.setId(pdbid.getId());
3546 if (pdbid.getType() != null)
3548 if (PDBEntry.Type.getType(pdbid.getType()) != null)
3550 entry.setType(PDBEntry.Type.getType(pdbid.getType()));
3554 entry.setType(PDBEntry.Type.FILE);
3557 // jprovider is null when executing 'New View'
3558 if (pdbid.getFile() != null && jprovider != null)
3560 if (!pdbloaded.containsKey(pdbid.getFile()))
3562 entry.setFile(loadPDBFile(jprovider, pdbid.getId(),
3567 entry.setFile(pdbloaded.get(pdbid.getId()).toString());
3571 if (pdbid.getPdbentryItem() != null)
3573 for (PdbentryItem item : pdbid.getPdbentryItem())
3575 for (Property pr : item.getProperty())
3577 entry.setProperty(pr.getName(), pr.getValue());
3582 for (Property prop : pdbid.getProperty())
3584 entry.setProperty(prop.getName(), prop.getValue());
3586 StructureSelectionManager
3587 .getStructureSelectionManager(Desktop.instance)
3588 .registerPDBEntry(entry);
3589 // adds PDBEntry to datasequence's set (since Jalview 2.10)
3590 if (al.getSequenceAt(i).getDatasetSequence() != null)
3592 al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
3596 al.getSequenceAt(i).addPDBId(entry);
3601 } // end !multipleview
3603 // ///////////////////////////////
3604 // LOAD SEQUENCE MAPPINGS
3606 if (vamsasSet.getAlcodonFrame().size() > 0)
3608 // TODO Potentially this should only be done once for all views of an
3610 List<AlcodonFrame> alc = vamsasSet.getAlcodonFrame();
3611 for (int i = 0; i < alc.size(); i++)
3613 AlignedCodonFrame cf = new AlignedCodonFrame();
3614 if (alc.get(i).getAlcodMap().size() > 0)
3616 List<AlcodMap> maps = alc.get(i).getAlcodMap();
3617 for (int m = 0; m < maps.size(); m++)
3619 AlcodMap map = maps.get(m);
3620 SequenceI dnaseq = seqRefIds.get(map.getDnasq());
3622 jalview.datamodel.Mapping mapping = null;
3623 // attach to dna sequence reference.
3624 if (map.getMapping() != null)
3626 mapping = addMapping(map.getMapping());
3627 if (dnaseq != null && mapping.getTo() != null)
3629 cf.addMap(dnaseq, mapping.getTo(), mapping.getMap());
3635 newAlcodMapRef(map.getDnasq(), cf, mapping));
3639 al.addCodonFrame(cf);
3644 // ////////////////////////////////
3646 List<JvAnnotRow> autoAlan = new ArrayList<>();
3649 * store any annotations which forward reference a group's ID
3651 Map<String, List<AlignmentAnnotation>> groupAnnotRefs = new Hashtable<>();
3653 if (vamsasSet.getAnnotation().size()/*Count()*/ > 0)
3655 List<Annotation> an = vamsasSet.getAnnotation();
3657 for (int i = 0; i < an.size(); i++)
3659 Annotation annotation = an.get(i);
3662 * test if annotation is automatically calculated for this view only
3664 boolean autoForView = false;
3665 if (annotation.getLabel().equals("Quality")
3666 || annotation.getLabel().equals("Conservation")
3667 || annotation.getLabel().equals("Consensus"))
3669 // Kludge for pre 2.5 projects which lacked the autocalculated flag
3671 // JAXB has no has() test; schema defaults value to false
3672 // if (!annotation.hasAutoCalculated())
3674 // annotation.setAutoCalculated(true);
3677 if (autoForView || annotation.isAutoCalculated())
3679 // remove ID - we don't recover annotation from other views for
3680 // view-specific annotation
3681 annotation.setId(null);
3684 // set visibility for other annotation in this view
3685 String annotationId = annotation.getId();
3686 if (annotationId != null && annotationIds.containsKey(annotationId))
3688 AlignmentAnnotation jda = annotationIds.get(annotationId);
3689 // in principle Visible should always be true for annotation displayed
3690 // in multiple views
3691 if (annotation.isVisible() != null)
3693 jda.visible = annotation.isVisible();
3696 al.addAnnotation(jda);
3700 // Construct new annotation from model.
3701 List<AnnotationElement> ae = annotation.getAnnotationElement();
3702 jalview.datamodel.Annotation[] anot = null;
3703 java.awt.Color firstColour = null;
3705 if (!annotation.isScoreOnly())
3707 anot = new jalview.datamodel.Annotation[al.getWidth()];
3708 for (int aa = 0; aa < ae.size() && aa < anot.length; aa++)
3710 AnnotationElement annElement = ae.get(aa);
3711 anpos = annElement.getPosition();
3713 if (anpos >= anot.length)
3718 float value = safeFloat(annElement.getValue());
3719 anot[anpos] = new jalview.datamodel.Annotation(
3720 annElement.getDisplayCharacter(),
3721 annElement.getDescription(),
3722 (annElement.getSecondaryStructure() == null
3723 || annElement.getSecondaryStructure()
3727 .getSecondaryStructure()
3730 anot[anpos].colour = new Color(safeInt(annElement.getColour()));
3731 if (firstColour == null)
3733 firstColour = anot[anpos].colour;
3737 jalview.datamodel.AlignmentAnnotation jaa = null;
3739 if (annotation.isGraph())
3741 float llim = 0, hlim = 0;
3742 // if (autoForView || an[i].isAutoCalculated()) {
3745 jaa = new jalview.datamodel.AlignmentAnnotation(
3746 annotation.getLabel(), annotation.getDescription(), anot,
3747 llim, hlim, safeInt(annotation.getGraphType()));
3749 jaa.graphGroup = safeInt(annotation.getGraphGroup());
3750 jaa._linecolour = firstColour;
3751 if (annotation.getThresholdLine() != null)
3753 jaa.setThreshold(new jalview.datamodel.GraphLine(
3754 safeFloat(annotation.getThresholdLine().getValue()),
3755 annotation.getThresholdLine().getLabel(),
3756 new java.awt.Color(safeInt(
3757 annotation.getThresholdLine().getColour()))));
3759 if (autoForView || annotation.isAutoCalculated())
3761 // Hardwire the symbol display line to ensure that labels for
3762 // histograms are displayed
3768 jaa = new jalview.datamodel.AlignmentAnnotation(
3769 annotation.getLabel(), annotation.getDescription(), anot);
3770 jaa._linecolour = firstColour;
3772 // register new annotation
3773 if (annotation.getId() != null)
3775 annotationIds.put(annotation.getId(), jaa);
3776 jaa.annotationId = annotation.getId();
3778 // recover sequence association
3779 String sequenceRef = annotation.getSequenceRef();
3780 if (sequenceRef != null)
3782 // from 2.9 sequenceRef is to sequence id (JAL-1781)
3783 SequenceI sequence = seqRefIds.get(sequenceRef);
3784 if (sequence == null)
3786 // in pre-2.9 projects sequence ref is to sequence name
3787 sequence = al.findName(sequenceRef);
3789 if (sequence != null)
3791 jaa.createSequenceMapping(sequence, 1, true);
3792 sequence.addAlignmentAnnotation(jaa);
3795 // and make a note of any group association
3796 if (annotation.getGroupRef() != null
3797 && annotation.getGroupRef().length() > 0)
3799 List<jalview.datamodel.AlignmentAnnotation> aal = groupAnnotRefs
3800 .get(annotation.getGroupRef());
3803 aal = new ArrayList<>();
3804 groupAnnotRefs.put(annotation.getGroupRef(), aal);
3809 if (annotation.getScore() != null)
3811 jaa.setScore(annotation.getScore().doubleValue());
3813 if (annotation.isVisible() != null)
3815 jaa.visible = annotation.isVisible().booleanValue();
3818 if (annotation.isCentreColLabels() != null)
3820 jaa.centreColLabels = annotation.isCentreColLabels()
3824 if (annotation.isScaleColLabels() != null)
3826 jaa.scaleColLabel = annotation.isScaleColLabels().booleanValue();
3828 if (annotation.isAutoCalculated())
3830 // newer files have an 'autoCalculated' flag and store calculation
3831 // state in viewport properties
3832 jaa.autoCalculated = true; // means annotation will be marked for
3833 // update at end of load.
3835 if (annotation.getGraphHeight() != null)
3837 jaa.graphHeight = annotation.getGraphHeight().intValue();
3839 jaa.belowAlignment = annotation.isBelowAlignment();
3840 jaa.setCalcId(annotation.getCalcId());
3841 if (annotation.getProperty().size() > 0)
3843 for (Annotation.Property prop : annotation
3846 jaa.setProperty(prop.getName(), prop.getValue());
3849 if (jaa.autoCalculated)
3851 autoAlan.add(new JvAnnotRow(i, jaa));
3854 // if (!autoForView)
3856 // add autocalculated group annotation and any user created annotation
3858 al.addAnnotation(jaa);
3862 // ///////////////////////
3864 // Create alignment markup and styles for this view
3865 if (jalviewModel.getJGroup().size() > 0)
3867 List<JGroup> groups = jalviewModel.getJGroup();
3868 boolean addAnnotSchemeGroup = false;
3869 for (int i = 0; i < groups.size(); i++)
3871 JGroup jGroup = groups.get(i);
3872 ColourSchemeI cs = null;
3873 if (jGroup.getColour() != null)
3875 if (jGroup.getColour().startsWith("ucs"))
3877 cs = getUserColourScheme(jalviewModel, jGroup.getColour());
3879 else if (jGroup.getColour().equals("AnnotationColourGradient")
3880 && jGroup.getAnnotationColours() != null)
3882 addAnnotSchemeGroup = true;
3886 cs = ColourSchemeProperty.getColourScheme(null, al,
3887 jGroup.getColour());
3890 int pidThreshold = safeInt(jGroup.getPidThreshold());
3892 Vector<SequenceI> seqs = new Vector<>();
3894 for (int s = 0; s < jGroup.getSeq().size(); s++)
3896 String seqId = jGroup.getSeq().get(s);
3897 SequenceI ts = seqRefIds.get(seqId);
3901 seqs.addElement(ts);
3905 if (seqs.size() < 1)
3910 SequenceGroup sg = new SequenceGroup(seqs, jGroup.getName(), cs,
3911 safeBoolean(jGroup.isDisplayBoxes()),
3912 safeBoolean(jGroup.isDisplayText()),
3913 safeBoolean(jGroup.isColourText()),
3914 safeInt(jGroup.getStart()), safeInt(jGroup.getEnd()));
3915 sg.getGroupColourScheme().setThreshold(pidThreshold, true);
3916 sg.getGroupColourScheme()
3917 .setConservationInc(safeInt(jGroup.getConsThreshold()));
3918 sg.setOutlineColour(new Color(safeInt(jGroup.getOutlineColour())));
3920 sg.textColour = new Color(safeInt(jGroup.getTextCol1()));
3921 sg.textColour2 = new Color(safeInt(jGroup.getTextCol2()));
3922 sg.setShowNonconserved(safeBoolean(jGroup.isShowUnconserved()));
3923 sg.thresholdTextColour = safeInt(jGroup.getTextColThreshold());
3924 // attributes with a default in the schema are never null
3925 sg.setShowConsensusHistogram(jGroup.isShowConsensusHistogram());
3926 sg.setshowSequenceLogo(jGroup.isShowSequenceLogo());
3927 sg.setNormaliseSequenceLogo(jGroup.isNormaliseSequenceLogo());
3928 sg.setIgnoreGapsConsensus(jGroup.isIgnoreGapsinConsensus());
3929 if (jGroup.getConsThreshold() != null
3930 && jGroup.getConsThreshold().intValue() != 0)
3932 Conservation c = new Conservation("All", sg.getSequences(null), 0,
3935 c.verdict(false, 25);
3936 sg.cs.setConservation(c);
3939 if (jGroup.getId() != null && groupAnnotRefs.size() > 0)
3941 // re-instate unique group/annotation row reference
3942 List<AlignmentAnnotation> jaal = groupAnnotRefs
3943 .get(jGroup.getId());
3946 for (AlignmentAnnotation jaa : jaal)
3949 if (jaa.autoCalculated)
3951 // match up and try to set group autocalc alignment row for this
3953 if (jaa.label.startsWith("Consensus for "))
3955 sg.setConsensus(jaa);
3957 // match up and try to set group autocalc alignment row for this
3959 if (jaa.label.startsWith("Conservation for "))
3961 sg.setConservationRow(jaa);
3968 if (addAnnotSchemeGroup)
3970 // reconstruct the annotation colourscheme
3971 sg.setColourScheme(constructAnnotationColour(
3972 jGroup.getAnnotationColours(), null, al, jalviewModel, false));
3978 // only dataset in this model, so just return.
3981 // ///////////////////////////////
3984 AlignFrame af = null;
3985 AlignViewport av = null;
3986 // now check to see if we really need to create a new viewport.
3987 if (multipleView && viewportsAdded.size() == 0)
3989 // We recovered an alignment for which a viewport already exists.
3990 // TODO: fix up any settings necessary for overlaying stored state onto
3991 // state recovered from another document. (may not be necessary).
3992 // we may need a binding from a viewport in memory to one recovered from
3994 // and then recover its containing af to allow the settings to be applied.
3995 // TODO: fix for vamsas demo
3997 "About to recover a viewport for existing alignment: Sequence set ID is "
3999 Object seqsetobj = retrieveExistingObj(uniqueSeqSetId);
4000 if (seqsetobj != null)
4002 if (seqsetobj instanceof String)
4004 uniqueSeqSetId = (String) seqsetobj;
4006 "Recovered extant sequence set ID mapping for ID : New Sequence set ID is "
4012 "Warning : Collision between sequence set ID string and existing jalview object mapping.");
4018 * indicate that annotation colours are applied across all groups (pre
4019 * Jalview 2.8.1 behaviour)
4021 boolean doGroupAnnColour = Jalview2XML.isVersionStringLaterThan("2.8.1",
4022 jalviewModel.getVersion());
4024 AlignmentPanel ap = null;
4025 boolean isnewview = true;
4028 // Check to see if this alignment already has a view id == viewId
4029 jalview.gui.AlignmentPanel views[] = Desktop
4030 .getAlignmentPanels(uniqueSeqSetId);
4031 if (views != null && views.length > 0)
4033 for (int v = 0; v < views.length; v++)
4035 if (views[v].av.getViewId().equalsIgnoreCase(viewId))
4037 // recover the existing alignpanel, alignframe, viewport
4038 af = views[v].alignFrame;
4041 // TODO: could even skip resetting view settings if we don't want to
4042 // change the local settings from other jalview processes
4051 af = loadViewport(file, jseqs, hiddenSeqs, al, jalviewModel, view,
4052 uniqueSeqSetId, viewId, autoAlan);
4053 av = af.getViewport();
4058 * Load any trees, PDB structures and viewers
4060 * Not done if flag is false (when this method is used for New View)
4062 if (loadTreesAndStructures)
4064 loadTrees(jalviewModel, view, af, av, ap);
4065 loadPCAViewers(jalviewModel, ap);
4066 loadPDBStructures(jprovider, jseqs, af, ap);
4067 loadRnaViewers(jprovider, jseqs, ap);
4069 // and finally return.
4074 * Instantiate and link any saved RNA (Varna) viewers. The state of the Varna
4075 * panel is restored from separate jar entries, two (gapped and trimmed) per
4076 * sequence and secondary structure.
4078 * Currently each viewer shows just one sequence and structure (gapped and
4079 * trimmed), however this method is designed to support multiple sequences or
4080 * structures in viewers if wanted in future.
4086 private void loadRnaViewers(jarInputStreamProvider jprovider,
4087 List<JSeq> jseqs, AlignmentPanel ap)
4090 * scan the sequences for references to viewers; create each one the first
4091 * time it is referenced, add Rna models to existing viewers
4093 for (JSeq jseq : jseqs)
4095 for (int i = 0; i < jseq.getRnaViewer().size(); i++)
4097 RnaViewer viewer = jseq.getRnaViewer().get(i);
4098 AppVarna appVarna = findOrCreateVarnaViewer(viewer, uniqueSetSuffix,
4101 for (int j = 0; j < viewer.getSecondaryStructure().size(); j++)
4103 SecondaryStructure ss = viewer.getSecondaryStructure().get(j);
4104 SequenceI seq = seqRefIds.get(jseq.getId());
4105 AlignmentAnnotation ann = this.annotationIds
4106 .get(ss.getAnnotationId());
4109 * add the structure to the Varna display (with session state copied
4110 * from the jar to a temporary file)
4112 boolean gapped = safeBoolean(ss.isGapped());
4113 String rnaTitle = ss.getTitle();
4114 String sessionState = ss.getViewerState();
4115 String tempStateFile = copyJarEntry(jprovider, sessionState,
4117 RnaModel rna = new RnaModel(rnaTitle, ann, seq, null, gapped);
4118 appVarna.addModelSession(rna, rnaTitle, tempStateFile);
4120 appVarna.setInitialSelection(safeInt(viewer.getSelectedRna()));
4126 * Locate and return an already instantiated matching AppVarna, or create one
4130 * @param viewIdSuffix
4134 protected AppVarna findOrCreateVarnaViewer(RnaViewer viewer,
4135 String viewIdSuffix, AlignmentPanel ap)
4138 * on each load a suffix is appended to the saved viewId, to avoid conflicts
4139 * if load is repeated
4141 String postLoadId = viewer.getViewId() + viewIdSuffix;
4142 for (JInternalFrame frame : getAllFrames())
4144 if (frame instanceof AppVarna)
4146 AppVarna varna = (AppVarna) frame;
4147 if (postLoadId.equals(varna.getViewId()))
4149 // this viewer is already instantiated
4150 // could in future here add ap as another 'parent' of the
4151 // AppVarna window; currently just 1-to-many
4158 * viewer not found - make it
4160 RnaViewerModel model = new RnaViewerModel(postLoadId, viewer.getTitle(),
4161 safeInt(viewer.getXpos()), safeInt(viewer.getYpos()),
4162 safeInt(viewer.getWidth()), safeInt(viewer.getHeight()),
4163 safeInt(viewer.getDividerLocation()));
4164 AppVarna varna = new AppVarna(model, ap);
4170 * Load any saved trees
4178 protected void loadTrees(JalviewModel jm, Viewport view,
4179 AlignFrame af, AlignViewport av, AlignmentPanel ap)
4181 // TODO result of automated refactoring - are all these parameters needed?
4184 for (int t = 0; t < jm.getTree().size(); t++)
4187 Tree tree = jm.getTree().get(t);
4189 TreePanel tp = (TreePanel) retrieveExistingObj(tree.getId());
4192 tp = af.showNewickTree(new NewickFile(tree.getNewick()),
4193 tree.getTitle(), safeInt(tree.getWidth()),
4194 safeInt(tree.getHeight()), safeInt(tree.getXpos()),
4195 safeInt(tree.getYpos()));
4196 if (tree.getId() != null)
4198 // perhaps bind the tree id to something ?
4203 // update local tree attributes ?
4204 // TODO: should check if tp has been manipulated by user - if so its
4205 // settings shouldn't be modified
4206 tp.setTitle(tree.getTitle());
4207 tp.setBounds(new Rectangle(safeInt(tree.getXpos()),
4208 safeInt(tree.getYpos()), safeInt(tree.getWidth()),
4209 safeInt(tree.getHeight())));
4210 tp.setViewport(av); // af.viewport;
4211 // TODO: verify 'associate with all views' works still
4212 tp.getTreeCanvas().setViewport(av); // af.viewport;
4213 tp.getTreeCanvas().setAssociatedPanel(ap); // af.alignPanel;
4215 tp.getTreeCanvas().setApplyToAllViews(tree.isLinkToAllViews());
4218 warn("There was a problem recovering stored Newick tree: \n"
4219 + tree.getNewick());
4223 tp.fitToWindow.setState(safeBoolean(tree.isFitToWindow()));
4224 tp.fitToWindow_actionPerformed(null);
4226 if (tree.getFontName() != null)
4229 new Font(tree.getFontName(), safeInt(tree.getFontStyle()),
4230 safeInt(tree.getFontSize())));
4235 new Font(view.getFontName(), safeInt(view.getFontStyle()),
4236 safeInt(view.getFontSize())));
4239 tp.showPlaceholders(safeBoolean(tree.isMarkUnlinked()));
4240 tp.showBootstrap(safeBoolean(tree.isShowBootstrap()));
4241 tp.showDistances(safeBoolean(tree.isShowDistances()));
4243 tp.getTreeCanvas().setThreshold(safeFloat(tree.getThreshold()));
4245 if (safeBoolean(tree.isCurrentTree()))
4247 af.getViewport().setCurrentTree(tp.getTree());
4251 } catch (Exception ex)
4253 ex.printStackTrace();
4258 * Load and link any saved structure viewers.
4265 protected void loadPDBStructures(jarInputStreamProvider jprovider,
4266 List<JSeq> jseqs, AlignFrame af, AlignmentPanel ap)
4269 * Run through all PDB ids on the alignment, and collect mappings between
4270 * distinct view ids and all sequences referring to that view.
4272 Map<String, StructureViewerModel> structureViewers = new LinkedHashMap<>();
4274 for (int i = 0; i < jseqs.size(); i++)
4276 JSeq jseq = jseqs.get(i);
4277 if (jseq.getPdbids().size() > 0)
4279 List<Pdbids> ids = jseq.getPdbids();
4280 for (int p = 0; p < ids.size(); p++)
4282 Pdbids pdbid = ids.get(p);
4283 final int structureStateCount = pdbid.getStructureState().size();
4284 for (int s = 0; s < structureStateCount; s++)
4286 // check to see if we haven't already created this structure view
4287 final StructureState structureState = pdbid
4288 .getStructureState().get(s);
4289 String sviewid = (structureState.getViewId() == null) ? null
4290 : structureState.getViewId() + uniqueSetSuffix;
4291 jalview.datamodel.PDBEntry jpdb = new jalview.datamodel.PDBEntry();
4292 // Originally : pdbid.getFile()
4293 // : TODO: verify external PDB file recovery still works in normal
4294 // jalview project load
4296 loadPDBFile(jprovider, pdbid.getId(), pdbid.getFile()));
4297 jpdb.setId(pdbid.getId());
4299 int x = safeInt(structureState.getXpos());
4300 int y = safeInt(structureState.getYpos());
4301 int width = safeInt(structureState.getWidth());
4302 int height = safeInt(structureState.getHeight());
4304 // Probably don't need to do this anymore...
4305 // Desktop.desktop.getComponentAt(x, y);
4306 // TODO: NOW: check that this recovers the PDB file correctly.
4307 String pdbFile = loadPDBFile(jprovider, pdbid.getId(),
4309 jalview.datamodel.SequenceI seq = seqRefIds
4310 .get(jseq.getId() + "");
4311 if (sviewid == null)
4313 sviewid = "_jalview_pre2_4_" + x + "," + y + "," + width + ","
4316 if (!structureViewers.containsKey(sviewid))
4318 structureViewers.put(sviewid,
4319 new StructureViewerModel(x, y, width, height, false,
4320 false, true, structureState.getViewId(),
4321 structureState.getType()));
4322 // Legacy pre-2.7 conversion JAL-823 :
4323 // do not assume any view has to be linked for colour by
4327 // assemble String[] { pdb files }, String[] { id for each
4328 // file }, orig_fileloc, SequenceI[][] {{ seqs_file 1 }, {
4329 // seqs_file 2}, boolean[] {
4330 // linkAlignPanel,superposeWithAlignpanel}} from hash
4331 StructureViewerModel jmoldat = structureViewers.get(sviewid);
4332 jmoldat.setAlignWithPanel(jmoldat.isAlignWithPanel()
4333 || structureState.isAlignwithAlignPanel());
4336 * Default colour by linked panel to false if not specified (e.g.
4337 * for pre-2.7 projects)
4339 boolean colourWithAlignPanel = jmoldat.isColourWithAlignPanel();
4340 colourWithAlignPanel |= structureState.isColourwithAlignPanel();
4341 jmoldat.setColourWithAlignPanel(colourWithAlignPanel);
4344 * Default colour by viewer to true if not specified (e.g. for
4347 boolean colourByViewer = jmoldat.isColourByViewer();
4348 colourByViewer &= structureState.isColourByJmol();
4349 jmoldat.setColourByViewer(colourByViewer);
4351 if (jmoldat.getStateData().length() < structureState
4352 .getValue()/*Content()*/.length())
4354 jmoldat.setStateData(structureState.getValue());// Content());
4356 if (pdbid.getFile() != null)
4358 File mapkey = new File(pdbid.getFile());
4359 StructureData seqstrmaps = jmoldat.getFileData().get(mapkey);
4360 if (seqstrmaps == null)
4362 jmoldat.getFileData().put(mapkey,
4363 seqstrmaps = jmoldat.new StructureData(pdbFile,
4366 if (!seqstrmaps.getSeqList().contains(seq))
4368 seqstrmaps.getSeqList().add(seq);
4374 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");
4381 // Instantiate the associated structure views
4382 for (Entry<String, StructureViewerModel> entry : structureViewers
4387 createOrLinkStructureViewer(entry, af, ap, jprovider);
4388 } catch (Exception e)
4391 "Error loading structure viewer: " + e.getMessage());
4392 // failed - try the next one
4404 protected void createOrLinkStructureViewer(
4405 Entry<String, StructureViewerModel> viewerData, AlignFrame af,
4406 AlignmentPanel ap, jarInputStreamProvider jprovider)
4408 final StructureViewerModel stateData = viewerData.getValue();
4411 * Search for any viewer windows already open from other alignment views
4412 * that exactly match the stored structure state
4414 StructureViewerBase comp = findMatchingViewer(viewerData);
4418 linkStructureViewer(ap, comp, stateData);
4423 * From 2.9: stateData.type contains JMOL or CHIMERA, data is in jar entry
4424 * "viewer_"+stateData.viewId
4426 if (ViewerType.CHIMERA.toString().equals(stateData.getType()))
4428 createChimeraViewer(viewerData, af, jprovider);
4433 * else Jmol (if pre-2.9, stateData contains JMOL state string)
4435 createJmolViewer(viewerData, af, jprovider);
4440 * Create a new Chimera viewer.
4446 protected void createChimeraViewer(
4447 Entry<String, StructureViewerModel> viewerData, AlignFrame af,
4448 jarInputStreamProvider jprovider)
4450 StructureViewerModel data = viewerData.getValue();
4451 String chimeraSessionFile = data.getStateData();
4454 * Copy Chimera session from jar entry "viewer_"+viewId to a temporary file
4456 * NB this is the 'saved' viewId as in the project file XML, _not_ the
4457 * 'uniquified' sviewid used to reconstruct the viewer here
4459 String viewerJarEntryName = getViewerJarEntryName(data.getViewId());
4460 chimeraSessionFile = copyJarEntry(jprovider, viewerJarEntryName,
4463 Set<Entry<File, StructureData>> fileData = data.getFileData()
4465 List<PDBEntry> pdbs = new ArrayList<>();
4466 List<SequenceI[]> allseqs = new ArrayList<>();
4467 for (Entry<File, StructureData> pdb : fileData)
4469 String filePath = pdb.getValue().getFilePath();
4470 String pdbId = pdb.getValue().getPdbId();
4471 // pdbs.add(new PDBEntry(filePath, pdbId));
4472 pdbs.add(new PDBEntry(pdbId, null, PDBEntry.Type.PDB, filePath));
4473 final List<SequenceI> seqList = pdb.getValue().getSeqList();
4474 SequenceI[] seqs = seqList.toArray(new SequenceI[seqList.size()]);
4478 boolean colourByChimera = data.isColourByViewer();
4479 boolean colourBySequence = data.isColourWithAlignPanel();
4481 // TODO use StructureViewer as a factory here, see JAL-1761
4482 final PDBEntry[] pdbArray = pdbs.toArray(new PDBEntry[pdbs.size()]);
4483 final SequenceI[][] seqsArray = allseqs
4484 .toArray(new SequenceI[allseqs.size()][]);
4485 String newViewId = viewerData.getKey();
4487 ChimeraViewFrame cvf = new ChimeraViewFrame(chimeraSessionFile,
4488 af.alignPanel, pdbArray, seqsArray, colourByChimera,
4489 colourBySequence, newViewId);
4490 cvf.setSize(data.getWidth(), data.getHeight());
4491 cvf.setLocation(data.getX(), data.getY());
4495 * Create a new Jmol window. First parse the Jmol state to translate filenames
4496 * loaded into the view, and record the order in which files are shown in the
4497 * Jmol view, so we can add the sequence mappings in same order.
4503 protected void createJmolViewer(
4504 final Entry<String, StructureViewerModel> viewerData,
4505 AlignFrame af, jarInputStreamProvider jprovider)
4507 final StructureViewerModel svattrib = viewerData.getValue();
4508 String state = svattrib.getStateData();
4511 * Pre-2.9: state element value is the Jmol state string
4513 * 2.9+: @type is "JMOL", state data is in a Jar file member named "viewer_"
4516 if (ViewerType.JMOL.toString().equals(svattrib.getType()))
4518 state = readJarEntry(jprovider,
4519 getViewerJarEntryName(svattrib.getViewId()));
4522 List<String> pdbfilenames = new ArrayList<>();
4523 List<SequenceI[]> seqmaps = new ArrayList<>();
4524 List<String> pdbids = new ArrayList<>();
4525 StringBuilder newFileLoc = new StringBuilder(64);
4526 int cp = 0, ncp, ecp;
4527 Map<File, StructureData> oldFiles = svattrib.getFileData();
4528 while ((ncp = state.indexOf("load ", cp)) > -1)
4532 // look for next filename in load statement
4533 newFileLoc.append(state.substring(cp,
4534 ncp = (state.indexOf("\"", ncp + 1) + 1)));
4535 String oldfilenam = state.substring(ncp,
4536 ecp = state.indexOf("\"", ncp));
4537 // recover the new mapping data for this old filename
4538 // have to normalize filename - since Jmol and jalview do
4540 // translation differently.
4541 StructureData filedat = oldFiles.get(new File(oldfilenam));
4542 if (filedat == null)
4544 String reformatedOldFilename = oldfilenam.replaceAll("/", "\\\\");
4545 filedat = oldFiles.get(new File(reformatedOldFilename));
4547 newFileLoc.append(Platform.escapeBackslashes(filedat.getFilePath()));
4548 pdbfilenames.add(filedat.getFilePath());
4549 pdbids.add(filedat.getPdbId());
4550 seqmaps.add(filedat.getSeqList().toArray(new SequenceI[0]));
4551 newFileLoc.append("\"");
4552 cp = ecp + 1; // advance beyond last \" and set cursor so we can
4553 // look for next file statement.
4554 } while ((ncp = state.indexOf("/*file*/", cp)) > -1);
4558 // just append rest of state
4559 newFileLoc.append(state.substring(cp));
4563 System.err.print("Ignoring incomplete Jmol state for PDB ids: ");
4564 newFileLoc = new StringBuilder(state);
4565 newFileLoc.append("; load append ");
4566 for (File id : oldFiles.keySet())
4568 // add this and any other pdb files that should be present in
4570 StructureData filedat = oldFiles.get(id);
4571 newFileLoc.append(filedat.getFilePath());
4572 pdbfilenames.add(filedat.getFilePath());
4573 pdbids.add(filedat.getPdbId());
4574 seqmaps.add(filedat.getSeqList().toArray(new SequenceI[0]));
4575 newFileLoc.append(" \"");
4576 newFileLoc.append(filedat.getFilePath());
4577 newFileLoc.append("\"");
4580 newFileLoc.append(";");
4583 if (newFileLoc.length() == 0)
4587 int histbug = newFileLoc.indexOf("history = ");
4591 * change "history = [true|false];" to "history = [1|0];"
4594 int diff = histbug == -1 ? -1 : newFileLoc.indexOf(";", histbug);
4595 String val = (diff == -1) ? null
4596 : newFileLoc.substring(histbug, diff);
4597 if (val != null && val.length() >= 4)
4599 if (val.contains("e")) // eh? what can it be?
4601 if (val.trim().equals("true"))
4609 newFileLoc.replace(histbug, diff, val);
4614 final String[] pdbf = pdbfilenames
4615 .toArray(new String[pdbfilenames.size()]);
4616 final String[] id = pdbids.toArray(new String[pdbids.size()]);
4617 final SequenceI[][] sq = seqmaps
4618 .toArray(new SequenceI[seqmaps.size()][]);
4619 final String fileloc = newFileLoc.toString();
4620 final String sviewid = viewerData.getKey();
4621 final AlignFrame alf = af;
4622 final Rectangle rect = new Rectangle(svattrib.getX(), svattrib.getY(),
4623 svattrib.getWidth(), svattrib.getHeight());
4626 javax.swing.SwingUtilities.invokeAndWait(new Runnable()
4631 JalviewStructureDisplayI sview = null;
4634 sview = new StructureViewer(
4635 alf.alignPanel.getStructureSelectionManager())
4636 .createView(StructureViewer.ViewerType.JMOL,
4637 pdbf, id, sq, alf.alignPanel, svattrib,
4638 fileloc, rect, sviewid);
4639 addNewStructureViewer(sview);
4640 } catch (OutOfMemoryError ex)
4642 new OOMWarning("restoring structure view for PDB id " + id,
4643 (OutOfMemoryError) ex.getCause());
4644 if (sview != null && sview.isVisible())
4646 sview.closeViewer(false);
4647 sview.setVisible(false);
4653 } catch (InvocationTargetException ex)
4655 warn("Unexpected error when opening Jmol view.", ex);
4657 } catch (InterruptedException e)
4659 // e.printStackTrace();
4665 * Generates a name for the entry in the project jar file to hold state
4666 * information for a structure viewer
4671 protected String getViewerJarEntryName(String viewId)
4673 return VIEWER_PREFIX + viewId;
4677 * Returns any open frame that matches given structure viewer data. The match
4678 * is based on the unique viewId, or (for older project versions) the frame's
4684 protected StructureViewerBase findMatchingViewer(
4685 Entry<String, StructureViewerModel> viewerData)
4687 final String sviewid = viewerData.getKey();
4688 final StructureViewerModel svattrib = viewerData.getValue();
4689 StructureViewerBase comp = null;
4690 JInternalFrame[] frames = getAllFrames();
4691 for (JInternalFrame frame : frames)
4693 if (frame instanceof StructureViewerBase)
4696 * Post jalview 2.4 schema includes structure view id
4698 if (sviewid != null && ((StructureViewerBase) frame).getViewId()
4701 comp = (StructureViewerBase) frame;
4702 break; // break added in 2.9
4705 * Otherwise test for matching position and size of viewer frame
4707 else if (frame.getX() == svattrib.getX()
4708 && frame.getY() == svattrib.getY()
4709 && frame.getHeight() == svattrib.getHeight()
4710 && frame.getWidth() == svattrib.getWidth())
4712 comp = (StructureViewerBase) frame;
4713 // no break in faint hope of an exact match on viewId
4721 * Link an AlignmentPanel to an existing structure viewer.
4726 * @param useinViewerSuperpos
4727 * @param usetoColourbyseq
4728 * @param viewerColouring
4730 protected void linkStructureViewer(AlignmentPanel ap,
4731 StructureViewerBase viewer, StructureViewerModel stateData)
4733 // NOTE: if the jalview project is part of a shared session then
4734 // view synchronization should/could be done here.
4736 final boolean useinViewerSuperpos = stateData.isAlignWithPanel();
4737 final boolean usetoColourbyseq = stateData.isColourWithAlignPanel();
4738 final boolean viewerColouring = stateData.isColourByViewer();
4739 Map<File, StructureData> oldFiles = stateData.getFileData();
4742 * Add mapping for sequences in this view to an already open viewer
4744 final AAStructureBindingModel binding = viewer.getBinding();
4745 for (File id : oldFiles.keySet())
4747 // add this and any other pdb files that should be present in the
4749 StructureData filedat = oldFiles.get(id);
4750 String pdbFile = filedat.getFilePath();
4751 SequenceI[] seq = filedat.getSeqList().toArray(new SequenceI[0]);
4752 binding.getSsm().setMapping(seq, null, pdbFile, DataSourceType.FILE,
4754 binding.addSequenceForStructFile(pdbFile, seq);
4756 // and add the AlignmentPanel's reference to the view panel
4757 viewer.addAlignmentPanel(ap);
4758 if (useinViewerSuperpos)
4760 viewer.useAlignmentPanelForSuperposition(ap);
4764 viewer.excludeAlignmentPanelForSuperposition(ap);
4766 if (usetoColourbyseq)
4768 viewer.useAlignmentPanelForColourbyseq(ap, !viewerColouring);
4772 viewer.excludeAlignmentPanelForColourbyseq(ap);
4777 * Get all frames within the Desktop.
4781 protected JInternalFrame[] getAllFrames()
4783 JInternalFrame[] frames = null;
4784 // TODO is this necessary - is it safe - risk of hanging?
4789 frames = Desktop.desktop.getAllFrames();
4790 } catch (ArrayIndexOutOfBoundsException e)
4792 // occasional No such child exceptions are thrown here...
4796 } catch (InterruptedException f)
4800 } while (frames == null);
4805 * Answers true if 'version' is equal to or later than 'supported', where each
4806 * is formatted as major/minor versions like "2.8.3" or "2.3.4b1" for bugfix
4807 * changes. Development and test values for 'version' are leniently treated
4811 * - minimum version we are comparing against
4813 * - version of data being processsed
4816 public static boolean isVersionStringLaterThan(String supported,
4819 if (supported == null || version == null
4820 || version.equalsIgnoreCase("DEVELOPMENT BUILD")
4821 || version.equalsIgnoreCase("Test")
4822 || version.equalsIgnoreCase("AUTOMATED BUILD"))
4824 System.err.println("Assuming project file with "
4825 + (version == null ? "null" : version)
4826 + " is compatible with Jalview version " + supported);
4831 return StringUtils.compareVersions(version, supported, "b") >= 0;
4835 Vector<JalviewStructureDisplayI> newStructureViewers = null;
4837 protected void addNewStructureViewer(JalviewStructureDisplayI sview)
4839 if (newStructureViewers != null)
4841 sview.getBinding().setFinishedLoadingFromArchive(false);
4842 newStructureViewers.add(sview);
4846 protected void setLoadingFinishedForNewStructureViewers()
4848 if (newStructureViewers != null)
4850 for (JalviewStructureDisplayI sview : newStructureViewers)
4852 sview.getBinding().setFinishedLoadingFromArchive(true);
4854 newStructureViewers.clear();
4855 newStructureViewers = null;
4859 AlignFrame loadViewport(String file, List<JSeq> JSEQ,
4860 List<SequenceI> hiddenSeqs, AlignmentI al,
4861 JalviewModel jm, Viewport view, String uniqueSeqSetId,
4862 String viewId, List<JvAnnotRow> autoAlan)
4864 AlignFrame af = null;
4865 af = new AlignFrame(al, safeInt(view.getWidth()),
4866 safeInt(view.getHeight()), uniqueSeqSetId, viewId)
4870 // protected void processKeyEvent(java.awt.event.KeyEvent e) {
4871 // System.out.println("Jalview2XML AF " + e);
4872 // super.processKeyEvent(e);
4879 af.setFileName(file, FileFormat.Jalview);
4881 final AlignViewport viewport = af.getViewport();
4882 for (int i = 0; i < JSEQ.size(); i++)
4884 int colour = safeInt(JSEQ.get(i).getColour());
4885 viewport.setSequenceColour(viewport.getAlignment().getSequenceAt(i),
4891 viewport.setColourByReferenceSeq(true);
4892 viewport.setDisplayReferenceSeq(true);
4895 viewport.setGatherViewsHere(safeBoolean(view.isGatheredViews()));
4897 if (view.getSequenceSetId() != null)
4899 AlignmentViewport av = viewportsAdded.get(uniqueSeqSetId);
4901 viewport.setSequenceSetId(uniqueSeqSetId);
4904 // propagate shared settings to this new view
4905 viewport.setHistoryList(av.getHistoryList());
4906 viewport.setRedoList(av.getRedoList());
4910 viewportsAdded.put(uniqueSeqSetId, viewport);
4912 // TODO: check if this method can be called repeatedly without
4913 // side-effects if alignpanel already registered.
4914 PaintRefresher.Register(af.alignPanel, uniqueSeqSetId);
4916 // apply Hidden regions to view.
4917 if (hiddenSeqs != null)
4919 for (int s = 0; s < JSEQ.size(); s++)
4921 SequenceGroup hidden = new SequenceGroup();
4922 boolean isRepresentative = false;
4923 for (int r = 0; r < JSEQ.get(s).getHiddenSequences().size(); r++)
4925 isRepresentative = true;
4926 SequenceI sequenceToHide = al
4927 .getSequenceAt(JSEQ.get(s).getHiddenSequences().get(r));
4928 hidden.addSequence(sequenceToHide, false);
4929 // remove from hiddenSeqs list so we don't try to hide it twice
4930 hiddenSeqs.remove(sequenceToHide);
4932 if (isRepresentative)
4934 SequenceI representativeSequence = al.getSequenceAt(s);
4935 hidden.addSequence(representativeSequence, false);
4936 viewport.hideRepSequences(representativeSequence, hidden);
4940 SequenceI[] hseqs = hiddenSeqs
4941 .toArray(new SequenceI[hiddenSeqs.size()]);
4942 viewport.hideSequence(hseqs);
4945 // recover view properties and display parameters
4947 viewport.setShowAnnotation(safeBoolean(view.isShowAnnotation()));
4948 viewport.setAbovePIDThreshold(safeBoolean(view.isPidSelected()));
4949 final int pidThreshold = safeInt(view.getPidThreshold());
4950 viewport.setThreshold(pidThreshold);
4952 viewport.setColourText(safeBoolean(view.isShowColourText()));
4955 .setConservationSelected(
4956 safeBoolean(view.isConservationSelected()));
4957 viewport.setIncrement(safeInt(view.getConsThreshold()));
4958 viewport.setShowJVSuffix(safeBoolean(view.isShowFullId()));
4959 viewport.setRightAlignIds(safeBoolean(view.isRightAlignIds()));
4960 viewport.setFont(new Font(view.getFontName(),
4961 safeInt(view.getFontStyle()), safeInt(view.getFontSize())),
4963 ViewStyleI vs = viewport.getViewStyle();
4964 vs.setScaleProteinAsCdna(view.isScaleProteinAsCdna());
4965 viewport.setViewStyle(vs);
4966 // TODO: allow custom charWidth/Heights to be restored by updating them
4967 // after setting font - which means set above to false
4968 viewport.setRenderGaps(safeBoolean(view.isRenderGaps()));
4969 viewport.setWrapAlignment(safeBoolean(view.isWrapAlignment()));
4970 viewport.setShowAnnotation(safeBoolean(view.isShowAnnotation()));
4972 viewport.setShowBoxes(safeBoolean(view.isShowBoxes()));
4974 viewport.setShowText(safeBoolean(view.isShowText()));
4976 viewport.setTextColour(new Color(safeInt(view.getTextCol1())));
4977 viewport.setTextColour2(new Color(safeInt(view.getTextCol2())));
4978 viewport.setThresholdTextColour(safeInt(view.getTextColThreshold()));
4979 viewport.setShowUnconserved(view.isShowUnconserved());
4980 viewport.getRanges().setStartRes(safeInt(view.getStartRes()));
4982 if (view.getViewName() != null)
4984 viewport.setViewName(view.getViewName());
4985 af.setInitialTabVisible();
4987 af.setBounds(safeInt(view.getXpos()), safeInt(view.getYpos()),
4988 safeInt(view.getWidth()), safeInt(view.getHeight()));
4989 // startSeq set in af.alignPanel.updateLayout below
4990 af.alignPanel.updateLayout();
4991 ColourSchemeI cs = null;
4992 // apply colourschemes
4993 if (view.getBgColour() != null)
4995 if (view.getBgColour().startsWith("ucs"))
4997 cs = getUserColourScheme(jm, view.getBgColour());
4999 else if (view.getBgColour().startsWith("Annotation"))
5001 AnnotationColourScheme viewAnnColour = view.getAnnotationColours();
5002 cs = constructAnnotationColour(viewAnnColour, af, al, jm, true);
5009 cs = ColourSchemeProperty.getColourScheme(af.getViewport(), al,
5010 view.getBgColour());
5015 * turn off 'alignment colour applies to all groups'
5016 * while restoring global colour scheme
5018 viewport.setColourAppliesToAllGroups(false);
5019 viewport.setGlobalColourScheme(cs);
5020 viewport.getResidueShading().setThreshold(pidThreshold,
5021 view.isIgnoreGapsinConsensus());
5022 viewport.getResidueShading()
5023 .setConsensus(viewport.getSequenceConsensusHash());
5024 if (safeBoolean(view.isConservationSelected()) && cs != null)
5026 viewport.getResidueShading()
5027 .setConservationInc(safeInt(view.getConsThreshold()));
5029 af.changeColour(cs);
5030 viewport.setColourAppliesToAllGroups(true);
5033 .setShowSequenceFeatures(
5034 safeBoolean(view.isShowSequenceFeatures()));
5036 viewport.setCentreColumnLabels(view.isCentreColumnLabels());
5037 viewport.setIgnoreGapsConsensus(view.isIgnoreGapsinConsensus(), null);
5038 viewport.setFollowHighlight(view.isFollowHighlight());
5039 viewport.followSelection = view.isFollowSelection();
5040 viewport.setShowConsensusHistogram(view.isShowConsensusHistogram());
5041 viewport.setShowSequenceLogo(view.isShowSequenceLogo());
5042 viewport.setNormaliseSequenceLogo(view.isNormaliseSequenceLogo());
5043 viewport.setShowDBRefs(safeBoolean(view.isShowDbRefTooltip()));
5044 viewport.setShowNPFeats(safeBoolean(view.isShowNPfeatureTooltip()));
5045 viewport.setShowGroupConsensus(view.isShowGroupConsensus());
5046 viewport.setShowGroupConservation(view.isShowGroupConservation());
5048 // recover feature settings
5049 if (jm.getFeatureSettings() != null)
5051 FeatureRenderer fr = af.alignPanel.getSeqPanel().seqCanvas
5052 .getFeatureRenderer();
5053 FeaturesDisplayed fdi;
5054 viewport.setFeaturesDisplayed(fdi = new FeaturesDisplayed());
5055 String[] renderOrder = new String[jm.getFeatureSettings()
5056 .getSetting().size()];
5057 Map<String, FeatureColourI> featureColours = new Hashtable<>();
5058 Map<String, Float> featureOrder = new Hashtable<>();
5060 for (int fs = 0; fs < jm.getFeatureSettings()
5061 .getSetting().size(); fs++)
5063 Setting setting = jm.getFeatureSettings().getSetting().get(fs);
5064 String featureType = setting.getType();
5067 * restore feature filters (if any)
5069 jalview.xml.binding.jalview.FeatureMatcherSet filters = setting
5071 if (filters != null)
5073 FeatureMatcherSetI filter = Jalview2XML
5074 .parseFilter(featureType, filters);
5075 if (!filter.isEmpty())
5077 fr.setFeatureFilter(featureType, filter);
5082 * restore feature colour scheme
5084 Color maxColour = new Color(setting.getColour());
5085 if (setting.getMincolour() != null)
5088 * minColour is always set unless a simple colour
5089 * (including for colour by label though it doesn't use it)
5091 Color minColour = new Color(setting.getMincolour().intValue());
5092 Color noValueColour = minColour;
5093 NoValueColour noColour = setting.getNoValueColour();
5094 if (noColour == NoValueColour.NONE)
5096 noValueColour = null;
5098 else if (noColour == NoValueColour.MAX)
5100 noValueColour = maxColour;
5102 float min = safeFloat(safeFloat(setting.getMin()));
5103 float max = setting.getMax() == null ? 1f
5104 : setting.getMax().floatValue();
5105 FeatureColourI gc = new FeatureColour(maxColour, minColour,
5107 noValueColour, min, max);
5108 if (setting.getAttributeName().size() > 0)
5110 gc.setAttributeName(setting.getAttributeName().toArray(
5111 new String[setting.getAttributeName().size()]));
5113 if (setting.getThreshold() != null)
5115 gc.setThreshold(setting.getThreshold().floatValue());
5116 int threshstate = safeInt(setting.getThreshstate());
5117 // -1 = None, 0 = Below, 1 = Above threshold
5118 if (threshstate == 0)
5120 gc.setBelowThreshold(true);
5122 else if (threshstate == 1)
5124 gc.setAboveThreshold(true);
5127 gc.setAutoScaled(true); // default
5128 if (setting.isAutoScale() != null)
5130 gc.setAutoScaled(setting.isAutoScale());
5132 if (setting.isColourByLabel() != null)
5134 gc.setColourByLabel(setting.isColourByLabel());
5136 // and put in the feature colour table.
5137 featureColours.put(featureType, gc);
5141 featureColours.put(featureType,
5142 new FeatureColour(maxColour));
5144 renderOrder[fs] = featureType;
5145 if (setting.getOrder() != null)
5147 featureOrder.put(featureType, setting.getOrder().floatValue());
5151 featureOrder.put(featureType, Float.valueOf(
5152 fs / jm.getFeatureSettings().getSetting().size()));
5154 if (safeBoolean(setting.isDisplay()))
5156 fdi.setVisible(featureType);
5159 Map<String, Boolean> fgtable = new Hashtable<>();
5160 for (int gs = 0; gs < jm.getFeatureSettings().getGroup().size(); gs++)
5162 Group grp = jm.getFeatureSettings().getGroup().get(gs);
5163 fgtable.put(grp.getName(), Boolean.valueOf(grp.isDisplay()));
5165 // FeatureRendererSettings frs = new FeatureRendererSettings(renderOrder,
5166 // fgtable, featureColours, jms.getFeatureSettings().hasTransparency() ?
5167 // jms.getFeatureSettings().getTransparency() : 0.0, featureOrder);
5168 FeatureRendererSettings frs = new FeatureRendererSettings(renderOrder,
5169 fgtable, featureColours, 1.0f, featureOrder);
5170 fr.transferSettings(frs);
5173 if (view.getHiddenColumns().size() > 0)
5175 for (int c = 0; c < view.getHiddenColumns().size(); c++)
5177 final HiddenColumns hc = view.getHiddenColumns().get(c);
5178 viewport.hideColumns(safeInt(hc.getStart()),
5179 safeInt(hc.getEnd()) /* +1 */);
5182 if (view.getCalcIdParam() != null)
5184 for (CalcIdParam calcIdParam : view.getCalcIdParam())
5186 if (calcIdParam != null)
5188 if (recoverCalcIdParam(calcIdParam, viewport))
5193 warn("Couldn't recover parameters for "
5194 + calcIdParam.getCalcId());
5199 af.setMenusFromViewport(viewport);
5200 af.setTitle(view.getTitle());
5201 // TODO: we don't need to do this if the viewport is aready visible.
5203 * Add the AlignFrame to the desktop (it may be 'gathered' later), unless it
5204 * has a 'cdna/protein complement' view, in which case save it in order to
5205 * populate a SplitFrame once all views have been read in.
5207 String complementaryViewId = view.getComplementId();
5208 if (complementaryViewId == null)
5210 Desktop.addInternalFrame(af, view.getTitle(),
5211 safeInt(view.getWidth()), safeInt(view.getHeight()));
5212 // recompute any autoannotation
5213 af.alignPanel.updateAnnotation(false, true);
5214 reorderAutoannotation(af, al, autoAlan);
5215 af.alignPanel.alignmentChanged();
5219 splitFrameCandidates.put(view, af);
5225 * Reads saved data to restore Colour by Annotation settings
5227 * @param viewAnnColour
5231 * @param checkGroupAnnColour
5234 private ColourSchemeI constructAnnotationColour(
5235 AnnotationColourScheme viewAnnColour, AlignFrame af,
5236 AlignmentI al, JalviewModel model, boolean checkGroupAnnColour)
5238 boolean propagateAnnColour = false;
5239 AlignmentI annAlignment = af != null ? af.getViewport().getAlignment()
5241 if (checkGroupAnnColour && al.getGroups() != null
5242 && al.getGroups().size() > 0)
5244 // pre 2.8.1 behaviour
5245 // check to see if we should transfer annotation colours
5246 propagateAnnColour = true;
5247 for (SequenceGroup sg : al.getGroups())
5249 if (sg.getColourScheme() instanceof AnnotationColourGradient)
5251 propagateAnnColour = false;
5257 * 2.10.2- : saved annotationId is AlignmentAnnotation.annotationId
5259 String annotationId = viewAnnColour.getAnnotation();
5260 AlignmentAnnotation matchedAnnotation = annotationIds.get(annotationId);
5263 * pre 2.10.2: saved annotationId is AlignmentAnnotation.label
5265 if (matchedAnnotation == null
5266 && annAlignment.getAlignmentAnnotation() != null)
5268 for (int i = 0; i < annAlignment.getAlignmentAnnotation().length; i++)
5271 .equals(annAlignment.getAlignmentAnnotation()[i].label))
5273 matchedAnnotation = annAlignment.getAlignmentAnnotation()[i];
5278 if (matchedAnnotation == null)
5280 System.err.println("Failed to match annotation colour scheme for "
5284 if (matchedAnnotation.getThreshold() == null)
5286 matchedAnnotation.setThreshold(
5287 new GraphLine(safeFloat(viewAnnColour.getThreshold()),
5288 "Threshold", Color.black));
5291 AnnotationColourGradient cs = null;
5292 if (viewAnnColour.getColourScheme().equals("None"))
5294 cs = new AnnotationColourGradient(matchedAnnotation,
5295 new Color(safeInt(viewAnnColour.getMinColour())),
5296 new Color(safeInt(viewAnnColour.getMaxColour())),
5297 safeInt(viewAnnColour.getAboveThreshold()));
5299 else if (viewAnnColour.getColourScheme().startsWith("ucs"))
5301 cs = new AnnotationColourGradient(matchedAnnotation,
5302 getUserColourScheme(model, viewAnnColour.getColourScheme()),
5303 safeInt(viewAnnColour.getAboveThreshold()));
5307 cs = new AnnotationColourGradient(matchedAnnotation,
5308 ColourSchemeProperty.getColourScheme(af.getViewport(), al,
5309 viewAnnColour.getColourScheme()),
5310 safeInt(viewAnnColour.getAboveThreshold()));
5313 boolean perSequenceOnly = safeBoolean(viewAnnColour.isPerSequence());
5314 boolean useOriginalColours = safeBoolean(
5315 viewAnnColour.isPredefinedColours());
5316 cs.setSeqAssociated(perSequenceOnly);
5317 cs.setPredefinedColours(useOriginalColours);
5319 if (propagateAnnColour && al.getGroups() != null)
5321 // Also use these settings for all the groups
5322 for (int g = 0; g < al.getGroups().size(); g++)
5324 SequenceGroup sg = al.getGroups().get(g);
5325 if (sg.getGroupColourScheme() == null)
5330 AnnotationColourGradient groupScheme = new AnnotationColourGradient(
5331 matchedAnnotation, sg.getColourScheme(),
5332 safeInt(viewAnnColour.getAboveThreshold()));
5333 sg.setColourScheme(groupScheme);
5334 groupScheme.setSeqAssociated(perSequenceOnly);
5335 groupScheme.setPredefinedColours(useOriginalColours);
5341 private void reorderAutoannotation(AlignFrame af, AlignmentI al,
5342 List<JvAnnotRow> autoAlan)
5344 // copy over visualization settings for autocalculated annotation in the
5346 if (al.getAlignmentAnnotation() != null)
5349 * Kludge for magic autoannotation names (see JAL-811)
5351 String[] magicNames = new String[] { "Consensus", "Quality",
5353 JvAnnotRow nullAnnot = new JvAnnotRow(-1, null);
5354 Hashtable<String, JvAnnotRow> visan = new Hashtable<>();
5355 for (String nm : magicNames)
5357 visan.put(nm, nullAnnot);
5359 for (JvAnnotRow auan : autoAlan)
5361 visan.put(auan.template.label
5362 + (auan.template.getCalcId() == null ? ""
5363 : "\t" + auan.template.getCalcId()),
5366 int hSize = al.getAlignmentAnnotation().length;
5367 List<JvAnnotRow> reorder = new ArrayList<>();
5368 // work through any autoCalculated annotation already on the view
5369 // removing it if it should be placed in a different location on the
5370 // annotation panel.
5371 List<String> remains = new ArrayList<>(visan.keySet());
5372 for (int h = 0; h < hSize; h++)
5374 jalview.datamodel.AlignmentAnnotation jalan = al
5375 .getAlignmentAnnotation()[h];
5376 if (jalan.autoCalculated)
5379 JvAnnotRow valan = visan.get(k = jalan.label);
5380 if (jalan.getCalcId() != null)
5382 valan = visan.get(k = jalan.label + "\t" + jalan.getCalcId());
5387 // delete the auto calculated row from the alignment
5388 al.deleteAnnotation(jalan, false);
5392 if (valan != nullAnnot)
5394 if (jalan != valan.template)
5396 // newly created autoannotation row instance
5397 // so keep a reference to the visible annotation row
5398 // and copy over all relevant attributes
5399 if (valan.template.graphHeight >= 0)
5402 jalan.graphHeight = valan.template.graphHeight;
5404 jalan.visible = valan.template.visible;
5406 reorder.add(new JvAnnotRow(valan.order, jalan));
5411 // Add any (possibly stale) autocalculated rows that were not appended to
5412 // the view during construction
5413 for (String other : remains)
5415 JvAnnotRow othera = visan.get(other);
5416 if (othera != nullAnnot && othera.template.getCalcId() != null
5417 && othera.template.getCalcId().length() > 0)
5419 reorder.add(othera);
5422 // now put the automatic annotation in its correct place
5423 int s = 0, srt[] = new int[reorder.size()];
5424 JvAnnotRow[] rws = new JvAnnotRow[reorder.size()];
5425 for (JvAnnotRow jvar : reorder)
5428 srt[s++] = jvar.order;
5431 jalview.util.QuickSort.sort(srt, rws);
5432 // and re-insert the annotation at its correct position
5433 for (JvAnnotRow jvar : rws)
5435 al.addAnnotation(jvar.template, jvar.order);
5437 af.alignPanel.adjustAnnotationHeight();
5441 Hashtable skipList = null;
5444 * TODO remove this method
5447 * @return AlignFrame bound to sequenceSetId from view, if one exists. private
5448 * AlignFrame getSkippedFrame(Viewport view) { if (skipList==null) {
5449 * throw new Error("Implementation Error. No skipList defined for this
5450 * Jalview2XML instance."); } return (AlignFrame)
5451 * skipList.get(view.getSequenceSetId()); }
5455 * Check if the Jalview view contained in object should be skipped or not.
5458 * @return true if view's sequenceSetId is a key in skipList
5460 private boolean skipViewport(JalviewModel object)
5462 if (skipList == null)
5466 String id = object.getViewport().get(0).getSequenceSetId();
5467 if (skipList.containsKey(id))
5469 if (Cache.log != null && Cache.log.isDebugEnabled())
5471 Cache.log.debug("Skipping seuqence set id " + id);
5478 public void addToSkipList(AlignFrame af)
5480 if (skipList == null)
5482 skipList = new Hashtable();
5484 skipList.put(af.getViewport().getSequenceSetId(), af);
5487 public void clearSkipList()
5489 if (skipList != null)
5496 private void recoverDatasetFor(SequenceSet vamsasSet, AlignmentI al,
5497 boolean ignoreUnrefed, String uniqueSeqSetId)
5499 jalview.datamodel.AlignmentI ds = getDatasetFor(
5500 vamsasSet.getDatasetId());
5501 AlignmentI xtant_ds = ds;
5502 if (xtant_ds == null)
5504 // good chance we are about to create a new dataset, but check if we've
5505 // seen some of the dataset sequence IDs before.
5506 // TODO: skip this check if we are working with project generated by
5507 // version 2.11 or later
5508 xtant_ds = checkIfHasDataset(vamsasSet.getSequence());
5509 if (xtant_ds != null)
5512 addDatasetRef(vamsasSet.getDatasetId(), ds);
5515 Vector dseqs = null;
5518 // recovering an alignment View
5519 AlignmentI seqSetDS = getDatasetFor(UNIQSEQSETID + uniqueSeqSetId);
5520 if (seqSetDS != null)
5522 if (ds != null && ds != seqSetDS)
5524 warn("JAL-3171 regression: Overwriting a dataset reference for an alignment"
5525 + " - CDS/Protein crossreference data may be lost");
5526 if (xtant_ds != null)
5528 // This can only happen if the unique sequence set ID was bound to a
5529 // dataset that did not contain any of the sequences in the view
5530 // currently being restored.
5531 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.");
5535 addDatasetRef(vamsasSet.getDatasetId(), ds);
5540 // try even harder to restore dataset
5541 AlignmentI xtantDS = checkIfHasDataset(vamsasSet.getSequence());
5542 // create a list of new dataset sequences
5543 dseqs = new Vector();
5545 for (int i = 0, iSize = vamsasSet.getSequence().size(); i < iSize; i++)
5547 Sequence vamsasSeq = vamsasSet.getSequence().get(i);
5548 ensureJalviewDatasetSequence(vamsasSeq, ds, dseqs, ignoreUnrefed, i);
5550 // create a new dataset
5553 SequenceI[] dsseqs = new SequenceI[dseqs.size()];
5554 dseqs.copyInto(dsseqs);
5555 ds = new jalview.datamodel.Alignment(dsseqs);
5556 debug("Created new dataset " + vamsasSet.getDatasetId()
5557 + " for alignment " + System.identityHashCode(al));
5558 addDatasetRef(vamsasSet.getDatasetId(), ds);
5560 // set the dataset for the newly imported alignment.
5561 if (al.getDataset() == null && !ignoreUnrefed)
5564 // register dataset for the alignment's uniqueSeqSetId for legacy projects
5565 addDatasetRef(UNIQSEQSETID + uniqueSeqSetId, ds);
5567 updateSeqDatasetBinding(vamsasSet.getSequence(), ds);
5571 * XML dataset sequence ID to materialised dataset reference
5573 HashMap<String, AlignmentI> seqToDataset = new HashMap<>();
5576 * @return the first materialised dataset reference containing a dataset
5577 * sequence referenced in the given view
5579 * - sequences from the view
5581 AlignmentI checkIfHasDataset(List<Sequence> list)
5583 for (Sequence restoredSeq : list)
5585 AlignmentI datasetFor = seqToDataset.get(restoredSeq.getDsseqid());
5586 if (datasetFor != null)
5595 * Register ds as the containing dataset for the dataset sequences referenced
5596 * by sequences in list
5599 * - sequences in a view
5602 void updateSeqDatasetBinding(List<Sequence> list, AlignmentI ds)
5604 for (Sequence restoredSeq : list)
5606 AlignmentI prevDS = seqToDataset.put(restoredSeq.getDsseqid(), ds);
5607 if (prevDS != null && prevDS != ds)
5609 warn("Dataset sequence appears in many datasets: "
5610 + restoredSeq.getDsseqid());
5611 // TODO: try to merge!
5618 * sequence definition to create/merge dataset sequence for
5622 * vector to add new dataset sequence to
5623 * @param ignoreUnrefed
5624 * - when true, don't create new sequences from vamsasSeq if it's id
5625 * doesn't already have an asssociated Jalview sequence.
5627 * - used to reorder the sequence in the alignment according to the
5628 * vamsasSeq array ordering, to preserve ordering of dataset
5630 private void ensureJalviewDatasetSequence(Sequence vamsasSeq,
5631 AlignmentI ds, Vector dseqs, boolean ignoreUnrefed, int vseqpos)
5633 // JBP TODO: Check this is called for AlCodonFrames to support recovery of
5635 SequenceI sq = seqRefIds.get(vamsasSeq.getId());
5636 boolean reorder = false;
5637 SequenceI dsq = null;
5638 if (sq != null && sq.getDatasetSequence() != null)
5640 dsq = sq.getDatasetSequence();
5646 if (sq == null && ignoreUnrefed)
5650 String sqid = vamsasSeq.getDsseqid();
5653 // need to create or add a new dataset sequence reference to this sequence
5656 dsq = seqRefIds.get(sqid);
5661 // make a new dataset sequence
5662 dsq = sq.createDatasetSequence();
5665 // make up a new dataset reference for this sequence
5666 sqid = seqHash(dsq);
5668 dsq.setVamsasId(uniqueSetSuffix + sqid);
5669 seqRefIds.put(sqid, dsq);
5674 dseqs.addElement(dsq);
5679 ds.addSequence(dsq);
5685 { // make this dataset sequence sq's dataset sequence
5686 sq.setDatasetSequence(dsq);
5687 // and update the current dataset alignment
5692 if (!dseqs.contains(dsq))
5699 if (ds.findIndex(dsq) < 0)
5701 ds.addSequence(dsq);
5708 // TODO: refactor this as a merge dataset sequence function
5709 // now check that sq (the dataset sequence) sequence really is the union of
5710 // all references to it
5711 // boolean pre = sq.getStart() < dsq.getStart();
5712 // boolean post = sq.getEnd() > dsq.getEnd();
5716 // StringBuffer sb = new StringBuffer();
5717 String newres = jalview.analysis.AlignSeq.extractGaps(
5718 jalview.util.Comparison.GapChars, sq.getSequenceAsString());
5719 if (!newres.equalsIgnoreCase(dsq.getSequenceAsString())
5720 && newres.length() > dsq.getLength())
5722 // Update with the longer sequence.
5726 * if (pre) { sb.insert(0, newres .substring(0, dsq.getStart() -
5727 * sq.getStart())); dsq.setStart(sq.getStart()); } if (post) {
5728 * sb.append(newres.substring(newres.length() - sq.getEnd() -
5729 * dsq.getEnd())); dsq.setEnd(sq.getEnd()); }
5731 dsq.setSequence(newres);
5733 // TODO: merges will never happen if we 'know' we have the real dataset
5734 // sequence - this should be detected when id==dssid
5736 "DEBUG Notice: Merged dataset sequence (if you see this often, post at http://issues.jalview.org/browse/JAL-1474)"); // ("
5737 // + (pre ? "prepended" : "") + " "
5738 // + (post ? "appended" : ""));
5743 // sequence refs are identical. We may need to update the existing dataset
5744 // alignment with this one, though.
5745 if (ds != null && dseqs == null)
5747 int opos = ds.findIndex(dsq);
5748 SequenceI tseq = null;
5749 if (opos != -1 && vseqpos != opos)
5751 // remove from old position
5752 ds.deleteSequence(dsq);
5754 if (vseqpos < ds.getHeight())
5756 if (vseqpos != opos)
5758 // save sequence at destination position
5759 tseq = ds.getSequenceAt(vseqpos);
5760 ds.replaceSequenceAt(vseqpos, dsq);
5761 ds.addSequence(tseq);
5766 ds.addSequence(dsq);
5773 * TODO use AlignmentI here and in related methods - needs
5774 * AlignmentI.getDataset() changed to return AlignmentI instead of Alignment
5776 Hashtable<String, AlignmentI> datasetIds = null;
5778 IdentityHashMap<AlignmentI, String> dataset2Ids = null;
5780 private AlignmentI getDatasetFor(String datasetId)
5782 if (datasetIds == null)
5784 datasetIds = new Hashtable<>();
5787 if (datasetIds.containsKey(datasetId))
5789 return datasetIds.get(datasetId);
5794 private void addDatasetRef(String datasetId, AlignmentI dataset)
5796 if (datasetIds == null)
5798 datasetIds = new Hashtable<>();
5800 datasetIds.put(datasetId, dataset);
5804 * make a new dataset ID for this jalview dataset alignment
5809 private String getDatasetIdRef(AlignmentI dataset)
5811 if (dataset.getDataset() != null)
5813 warn("Serious issue! Dataset Object passed to getDatasetIdRef is not a Jalview DATASET alignment...");
5815 String datasetId = makeHashCode(dataset, null);
5816 if (datasetId == null)
5818 // make a new datasetId and record it
5819 if (dataset2Ids == null)
5821 dataset2Ids = new IdentityHashMap<>();
5825 datasetId = dataset2Ids.get(dataset);
5827 if (datasetId == null)
5829 datasetId = "ds" + dataset2Ids.size() + 1;
5830 dataset2Ids.put(dataset, datasetId);
5837 * Add any saved DBRefEntry's to the sequence. An entry flagged as 'locus' is
5838 * constructed as a special subclass GeneLocus.
5840 * @param datasetSequence
5843 private void addDBRefs(SequenceI datasetSequence, Sequence sequence)
5845 for (int d = 0; d < sequence.getDBRef().size(); d++)
5847 DBRef dr = sequence.getDBRef().get(d);
5851 entry = new GeneLocus(dr.getSource(), dr.getVersion(),
5852 dr.getAccessionId());
5856 entry = new DBRefEntry(dr.getSource(), dr.getVersion(),
5857 dr.getAccessionId());
5859 if (dr.getMapping() != null)
5861 entry.setMap(addMapping(dr.getMapping()));
5863 datasetSequence.addDBRef(entry);
5867 private jalview.datamodel.Mapping addMapping(Mapping m)
5869 SequenceI dsto = null;
5870 // Mapping m = dr.getMapping();
5871 int fr[] = new int[m.getMapListFrom().size() * 2];
5872 Iterator<MapListFrom> from = m.getMapListFrom().iterator();// enumerateMapListFrom();
5873 for (int _i = 0; from.hasNext(); _i += 2)
5875 MapListFrom mf = from.next();
5876 fr[_i] = mf.getStart();
5877 fr[_i + 1] = mf.getEnd();
5879 int fto[] = new int[m.getMapListTo().size() * 2];
5880 Iterator<MapListTo> to = m.getMapListTo().iterator();// enumerateMapListTo();
5881 for (int _i = 0; to.hasNext(); _i += 2)
5883 MapListTo mf = to.next();
5884 fto[_i] = mf.getStart();
5885 fto[_i + 1] = mf.getEnd();
5887 jalview.datamodel.Mapping jmap = new jalview.datamodel.Mapping(dsto, fr,
5888 fto, m.getMapFromUnit().intValue(),
5889 m.getMapToUnit().intValue());
5892 * (optional) choice of dseqFor or Sequence
5894 if (m.getDseqFor() != null)
5896 String dsfor = m.getDseqFor();
5897 if (seqRefIds.containsKey(dsfor))
5902 jmap.setTo(seqRefIds.get(dsfor));
5906 frefedSequence.add(newMappingRef(dsfor, jmap));
5909 else if (m.getSequence() != null)
5912 * local sequence definition
5914 Sequence ms = m.getSequence();
5915 SequenceI djs = null;
5916 String sqid = ms.getDsseqid();
5917 if (sqid != null && sqid.length() > 0)
5920 * recover dataset sequence
5922 djs = seqRefIds.get(sqid);
5927 "Warning - making up dataset sequence id for DbRef sequence map reference");
5928 sqid = ((Object) ms).toString(); // make up a new hascode for
5929 // undefined dataset sequence hash
5930 // (unlikely to happen)
5936 * make a new dataset sequence and add it to refIds hash
5938 djs = new jalview.datamodel.Sequence(ms.getName(),
5940 djs.setStart(jmap.getMap().getToLowest());
5941 djs.setEnd(jmap.getMap().getToHighest());
5942 djs.setVamsasId(uniqueSetSuffix + sqid);
5944 incompleteSeqs.put(sqid, djs);
5945 seqRefIds.put(sqid, djs);
5948 jalview.bin.Cache.log.debug("about to recurse on addDBRefs.");
5957 * Provides a 'copy' of an alignment view (on action New View) by 'saving' the
5958 * view as XML (but not to file), and then reloading it
5963 public AlignmentPanel copyAlignPanel(AlignmentPanel ap)
5966 JalviewModel jm = saveState(ap, null, null, null);
5969 jm.getVamsasModel().getSequenceSet().get(0).getDatasetId(),
5970 ap.getAlignment().getDataset());
5972 uniqueSetSuffix = "";
5973 // jm.getJalviewModelSequence().getViewport(0).setId(null);
5974 jm.getViewport().get(0).setId(null);
5975 // we don't overwrite the view we just copied
5977 if (this.frefedSequence == null)
5979 frefedSequence = new Vector<>();
5982 viewportsAdded.clear();
5984 AlignFrame af = loadFromObject(jm, null, false, null);
5985 af.getAlignPanels().clear();
5986 af.closeMenuItem_actionPerformed(true);
5989 * if(ap.av.getAlignment().getAlignmentAnnotation()!=null) { for(int i=0;
5990 * i<ap.av.getAlignment().getAlignmentAnnotation().length; i++) {
5991 * if(!ap.av.getAlignment().getAlignmentAnnotation()[i].autoCalculated) {
5992 * af.alignPanel.av.getAlignment().getAlignmentAnnotation()[i] =
5993 * ap.av.getAlignment().getAlignmentAnnotation()[i]; } } }
5996 return af.alignPanel;
5999 private Hashtable jvids2vobj;
6001 private void warn(String msg)
6006 private void warn(String msg, Exception e)
6008 if (Cache.log != null)
6012 Cache.log.warn(msg, e);
6016 Cache.log.warn(msg);
6021 System.err.println("Warning: " + msg);
6024 e.printStackTrace();
6029 private void debug(String string)
6031 debug(string, null);
6034 private void debug(String msg, Exception e)
6036 if (Cache.log != null)
6040 Cache.log.debug(msg, e);
6044 Cache.log.debug(msg);
6049 System.err.println("Warning: " + msg);
6052 e.printStackTrace();
6058 * set the object to ID mapping tables used to write/recover objects and XML
6059 * ID strings for the jalview project. If external tables are provided then
6060 * finalize and clearSeqRefs will not clear the tables when the Jalview2XML
6061 * object goes out of scope. - also populates the datasetIds hashtable with
6062 * alignment objects containing dataset sequences
6065 * Map from ID strings to jalview datamodel
6067 * Map from jalview datamodel to ID strings
6071 public void setObjectMappingTables(Hashtable vobj2jv,
6072 IdentityHashMap jv2vobj)
6074 this.jv2vobj = jv2vobj;
6075 this.vobj2jv = vobj2jv;
6076 Iterator ds = jv2vobj.keySet().iterator();
6078 while (ds.hasNext())
6080 Object jvobj = ds.next();
6081 id = jv2vobj.get(jvobj).toString();
6082 if (jvobj instanceof jalview.datamodel.Alignment)
6084 if (((jalview.datamodel.Alignment) jvobj).getDataset() == null)
6086 addDatasetRef(id, (jalview.datamodel.Alignment) jvobj);
6089 else if (jvobj instanceof jalview.datamodel.Sequence)
6091 // register sequence object so the XML parser can recover it.
6092 if (seqRefIds == null)
6094 seqRefIds = new HashMap<>();
6096 if (seqsToIds == null)
6098 seqsToIds = new IdentityHashMap<>();
6100 seqRefIds.put(jv2vobj.get(jvobj).toString(), (SequenceI) jvobj);
6101 seqsToIds.put((SequenceI) jvobj, id);
6103 else if (jvobj instanceof jalview.datamodel.AlignmentAnnotation)
6106 AlignmentAnnotation jvann = (AlignmentAnnotation) jvobj;
6107 annotationIds.put(anid = jv2vobj.get(jvobj).toString(), jvann);
6108 if (jvann.annotationId == null)
6110 jvann.annotationId = anid;
6112 if (!jvann.annotationId.equals(anid))
6114 // TODO verify that this is the correct behaviour
6115 this.warn("Overriding Annotation ID for " + anid
6116 + " from different id : " + jvann.annotationId);
6117 jvann.annotationId = anid;
6120 else if (jvobj instanceof String)
6122 if (jvids2vobj == null)
6124 jvids2vobj = new Hashtable();
6125 jvids2vobj.put(jvobj, jv2vobj.get(jvobj).toString());
6130 Cache.log.debug("Ignoring " + jvobj.getClass() + " (ID = " + id);
6136 * set the uniqueSetSuffix used to prefix/suffix object IDs for jalview
6137 * objects created from the project archive. If string is null (default for
6138 * construction) then suffix will be set automatically.
6142 public void setUniqueSetSuffix(String string)
6144 uniqueSetSuffix = string;
6149 * uses skipList2 as the skipList for skipping views on sequence sets
6150 * associated with keys in the skipList
6154 public void setSkipList(Hashtable skipList2)
6156 skipList = skipList2;
6160 * Reads the jar entry of given name and returns its contents, or null if the
6161 * entry is not found.
6164 * @param jarEntryName
6167 protected String readJarEntry(jarInputStreamProvider jprovider,
6168 String jarEntryName)
6170 String result = null;
6171 BufferedReader in = null;
6176 * Reopen the jar input stream and traverse its entries to find a matching
6179 JarInputStream jin = jprovider.getJarInputStream();
6180 JarEntry entry = null;
6183 entry = jin.getNextJarEntry();
6184 } while (entry != null && !entry.getName().equals(jarEntryName));
6188 StringBuilder out = new StringBuilder(256);
6189 in = new BufferedReader(new InputStreamReader(jin, UTF_8));
6192 while ((data = in.readLine()) != null)
6196 result = out.toString();
6200 warn("Couldn't find entry in Jalview Jar for " + jarEntryName);
6202 } catch (Exception ex)
6204 ex.printStackTrace();
6212 } catch (IOException e)
6223 * Returns an incrementing counter (0, 1, 2...)
6227 private synchronized int nextCounter()
6233 * Loads any saved PCA viewers
6238 protected void loadPCAViewers(JalviewModel model, AlignmentPanel ap)
6242 List<PcaViewer> pcaviewers = model.getPcaViewer();
6243 for (PcaViewer viewer : pcaviewers)
6245 String modelName = viewer.getScoreModelName();
6246 SimilarityParamsI params = new SimilarityParams(
6247 viewer.isIncludeGappedColumns(), viewer.isMatchGaps(),
6248 viewer.isIncludeGaps(),
6249 viewer.isDenominateByShortestLength());
6252 * create the panel (without computing the PCA)
6254 PCAPanel panel = new PCAPanel(ap, modelName, params);
6256 panel.setTitle(viewer.getTitle());
6257 panel.setBounds(new Rectangle(viewer.getXpos(), viewer.getYpos(),
6258 viewer.getWidth(), viewer.getHeight()));
6260 boolean showLabels = viewer.isShowLabels();
6261 panel.setShowLabels(showLabels);
6262 panel.getRotatableCanvas().setShowLabels(showLabels);
6263 panel.getRotatableCanvas()
6264 .setBgColour(new Color(viewer.getBgColour()));
6265 panel.getRotatableCanvas()
6266 .setApplyToAllViews(viewer.isLinkToAllViews());
6269 * load PCA output data
6271 ScoreModelI scoreModel = ScoreModels.getInstance()
6272 .getScoreModel(modelName, ap);
6273 PCA pca = new PCA(null, scoreModel, params);
6274 PcaDataType pcaData = viewer.getPcaData();
6276 MatrixI pairwise = loadDoubleMatrix(pcaData.getPairwiseMatrix());
6277 pca.setPairwiseScores(pairwise);
6279 MatrixI triDiag = loadDoubleMatrix(pcaData.getTridiagonalMatrix());
6280 pca.setTridiagonal(triDiag);
6282 MatrixI result = loadDoubleMatrix(pcaData.getEigenMatrix());
6283 pca.setEigenmatrix(result);
6285 panel.getPcaModel().setPCA(pca);
6288 * we haven't saved the input data! (JAL-2647 to do)
6290 panel.setInputData(null);
6293 * add the sequence points for the PCA display
6295 List<jalview.datamodel.SequencePoint> seqPoints = new ArrayList<>();
6296 for (SequencePoint sp : viewer.getSequencePoint())
6298 String seqId = sp.getSequenceRef();
6299 SequenceI seq = seqRefIds.get(seqId);
6302 throw new IllegalStateException(
6303 "Unmatched seqref for PCA: " + seqId);
6305 Point pt = new Point(sp.getXPos(), sp.getYPos(), sp.getZPos());
6306 jalview.datamodel.SequencePoint seqPoint = new jalview.datamodel.SequencePoint(
6308 seqPoints.add(seqPoint);
6310 panel.getRotatableCanvas().setPoints(seqPoints, seqPoints.size());
6313 * set min-max ranges and scale after setPoints (which recomputes them)
6315 panel.getRotatableCanvas().setScaleFactor(viewer.getScaleFactor());
6316 SeqPointMin spMin = viewer.getSeqPointMin();
6317 float[] min = new float[] { spMin.getXPos(), spMin.getYPos(),
6319 SeqPointMax spMax = viewer.getSeqPointMax();
6320 float[] max = new float[] { spMax.getXPos(), spMax.getYPos(),
6322 panel.getRotatableCanvas().setSeqMinMax(min, max);
6324 // todo: hold points list in PCAModel only
6325 panel.getPcaModel().setSequencePoints(seqPoints);
6327 panel.setSelectedDimensionIndex(viewer.getXDim(), X);
6328 panel.setSelectedDimensionIndex(viewer.getYDim(), Y);
6329 panel.setSelectedDimensionIndex(viewer.getZDim(), Z);
6331 // is this duplication needed?
6332 panel.setTop(seqPoints.size() - 1);
6333 panel.getPcaModel().setTop(seqPoints.size() - 1);
6336 * add the axes' end points for the display
6338 for (int i = 0; i < 3; i++)
6340 Axis axis = viewer.getAxis().get(i);
6341 panel.getRotatableCanvas().getAxisEndPoints()[i] = new Point(
6342 axis.getXPos(), axis.getYPos(), axis.getZPos());
6345 Desktop.addInternalFrame(panel, MessageManager.formatMessage(
6346 "label.calc_title", "PCA", modelName), 475, 450);
6348 } catch (Exception ex)
6350 Cache.log.error("Error loading PCA: " + ex.toString());
6355 * Populates an XML model of the feature colour scheme for one feature type
6357 * @param featureType
6361 public static Colour marshalColour(
6362 String featureType, FeatureColourI fcol)
6364 Colour col = new Colour();
6365 if (fcol.isSimpleColour())
6367 col.setRGB(Format.getHexString(fcol.getColour()));
6371 col.setRGB(Format.getHexString(fcol.getMaxColour()));
6372 col.setMin(fcol.getMin());
6373 col.setMax(fcol.getMax());
6374 col.setMinRGB(jalview.util.Format.getHexString(fcol.getMinColour()));
6375 col.setAutoScale(fcol.isAutoScaled());
6376 col.setThreshold(fcol.getThreshold());
6377 col.setColourByLabel(fcol.isColourByLabel());
6378 col.setThreshType(fcol.isAboveThreshold() ? ThresholdType.ABOVE
6379 : (fcol.isBelowThreshold() ? ThresholdType.BELOW
6380 : ThresholdType.NONE));
6381 if (fcol.isColourByAttribute())
6383 final String[] attName = fcol.getAttributeName();
6384 col.getAttributeName().add(attName[0]);
6385 if (attName.length > 1)
6387 col.getAttributeName().add(attName[1]);
6390 Color noColour = fcol.getNoColour();
6391 if (noColour == null)
6393 col.setNoValueColour(NoValueColour.NONE);
6395 else if (noColour == fcol.getMaxColour())
6397 col.setNoValueColour(NoValueColour.MAX);
6401 col.setNoValueColour(NoValueColour.MIN);
6404 col.setName(featureType);
6409 * Populates an XML model of the feature filter(s) for one feature type
6411 * @param firstMatcher
6412 * the first (or only) match condition)
6414 * remaining match conditions (if any)
6416 * if true, conditions are and-ed, else or-ed
6418 public static jalview.xml.binding.jalview.FeatureMatcherSet marshalFilter(
6419 FeatureMatcherI firstMatcher, Iterator<FeatureMatcherI> filters,
6422 jalview.xml.binding.jalview.FeatureMatcherSet result = new jalview.xml.binding.jalview.FeatureMatcherSet();
6424 if (filters.hasNext())
6429 CompoundMatcher compound = new CompoundMatcher();
6430 compound.setAnd(and);
6431 jalview.xml.binding.jalview.FeatureMatcherSet matcher1 = marshalFilter(
6432 firstMatcher, Collections.emptyIterator(), and);
6433 // compound.addMatcherSet(matcher1);
6434 compound.getMatcherSet().add(matcher1);
6435 FeatureMatcherI nextMatcher = filters.next();
6436 jalview.xml.binding.jalview.FeatureMatcherSet matcher2 = marshalFilter(
6437 nextMatcher, filters, and);
6438 // compound.addMatcherSet(matcher2);
6439 compound.getMatcherSet().add(matcher2);
6440 result.setCompoundMatcher(compound);
6445 * single condition matcher
6447 // MatchCondition matcherModel = new MatchCondition();
6448 jalview.xml.binding.jalview.FeatureMatcher matcherModel = new jalview.xml.binding.jalview.FeatureMatcher();
6449 matcherModel.setCondition(
6450 firstMatcher.getMatcher().getCondition().getStableName());
6451 matcherModel.setValue(firstMatcher.getMatcher().getPattern());
6452 if (firstMatcher.isByAttribute())
6454 matcherModel.setBy(FilterBy.BY_ATTRIBUTE);
6455 // matcherModel.setAttributeName(firstMatcher.getAttribute());
6456 String[] attName = firstMatcher.getAttribute();
6457 matcherModel.getAttributeName().add(attName[0]); // attribute
6458 if (attName.length > 1)
6460 matcherModel.getAttributeName().add(attName[1]); // sub-attribute
6463 else if (firstMatcher.isByLabel())
6465 matcherModel.setBy(FilterBy.BY_LABEL);
6467 else if (firstMatcher.isByScore())
6469 matcherModel.setBy(FilterBy.BY_SCORE);
6471 result.setMatchCondition(matcherModel);
6478 * Loads one XML model of a feature filter to a Jalview object
6480 * @param featureType
6481 * @param matcherSetModel
6484 public static FeatureMatcherSetI parseFilter(
6486 jalview.xml.binding.jalview.FeatureMatcherSet matcherSetModel)
6488 FeatureMatcherSetI result = new FeatureMatcherSet();
6491 parseFilterConditions(result, matcherSetModel, true);
6492 } catch (IllegalStateException e)
6494 // mixing AND and OR conditions perhaps
6496 String.format("Error reading filter conditions for '%s': %s",
6497 featureType, e.getMessage()));
6498 // return as much as was parsed up to the error
6505 * Adds feature match conditions to matcherSet as unmarshalled from XML
6506 * (possibly recursively for compound conditions)
6509 * @param matcherSetModel
6511 * if true, multiple conditions are AND-ed, else they are OR-ed
6512 * @throws IllegalStateException
6513 * if AND and OR conditions are mixed
6515 protected static void parseFilterConditions(
6516 FeatureMatcherSetI matcherSet,
6517 jalview.xml.binding.jalview.FeatureMatcherSet matcherSetModel,
6520 jalview.xml.binding.jalview.FeatureMatcher mc = matcherSetModel
6521 .getMatchCondition();
6527 FilterBy filterBy = mc.getBy();
6528 Condition cond = Condition.fromString(mc.getCondition());
6529 String pattern = mc.getValue();
6530 FeatureMatcherI matchCondition = null;
6531 if (filterBy == FilterBy.BY_LABEL)
6533 matchCondition = FeatureMatcher.byLabel(cond, pattern);
6535 else if (filterBy == FilterBy.BY_SCORE)
6537 matchCondition = FeatureMatcher.byScore(cond, pattern);
6540 else if (filterBy == FilterBy.BY_ATTRIBUTE)
6542 final List<String> attributeName = mc.getAttributeName();
6543 String[] attNames = attributeName
6544 .toArray(new String[attributeName.size()]);
6545 matchCondition = FeatureMatcher.byAttribute(cond, pattern,
6550 * note this throws IllegalStateException if AND-ing to a
6551 * previously OR-ed compound condition, or vice versa
6555 matcherSet.and(matchCondition);
6559 matcherSet.or(matchCondition);
6565 * compound condition
6567 List<jalview.xml.binding.jalview.FeatureMatcherSet> matchers = matcherSetModel
6568 .getCompoundMatcher().getMatcherSet();
6569 boolean anded = matcherSetModel.getCompoundMatcher().isAnd();
6570 if (matchers.size() == 2)
6572 parseFilterConditions(matcherSet, matchers.get(0), anded);
6573 parseFilterConditions(matcherSet, matchers.get(1), anded);
6577 System.err.println("Malformed compound filter condition");
6583 * Loads one XML model of a feature colour to a Jalview object
6585 * @param colourModel
6588 public static FeatureColourI parseColour(Colour colourModel)
6590 FeatureColourI colour = null;
6592 if (colourModel.getMax() != null)
6594 Color mincol = null;
6595 Color maxcol = null;
6596 Color noValueColour = null;
6600 mincol = new Color(Integer.parseInt(colourModel.getMinRGB(), 16));
6601 maxcol = new Color(Integer.parseInt(colourModel.getRGB(), 16));
6602 } catch (Exception e)
6604 Cache.log.warn("Couldn't parse out graduated feature color.", e);
6607 NoValueColour noCol = colourModel.getNoValueColour();
6608 if (noCol == NoValueColour.MIN)
6610 noValueColour = mincol;
6612 else if (noCol == NoValueColour.MAX)
6614 noValueColour = maxcol;
6617 colour = new FeatureColour(maxcol, mincol, maxcol, noValueColour,
6618 safeFloat(colourModel.getMin()),
6619 safeFloat(colourModel.getMax()));
6620 final List<String> attributeName = colourModel.getAttributeName();
6621 String[] attributes = attributeName
6622 .toArray(new String[attributeName.size()]);
6623 if (attributes != null && attributes.length > 0)
6625 colour.setAttributeName(attributes);
6627 if (colourModel.isAutoScale() != null)
6629 colour.setAutoScaled(colourModel.isAutoScale().booleanValue());
6631 if (colourModel.isColourByLabel() != null)
6633 colour.setColourByLabel(
6634 colourModel.isColourByLabel().booleanValue());
6636 if (colourModel.getThreshold() != null)
6638 colour.setThreshold(colourModel.getThreshold().floatValue());
6640 ThresholdType ttyp = colourModel.getThreshType();
6641 if (ttyp == ThresholdType.ABOVE)
6643 colour.setAboveThreshold(true);
6645 else if (ttyp == ThresholdType.BELOW)
6647 colour.setBelowThreshold(true);
6652 Color color = new Color(Integer.parseInt(colourModel.getRGB(), 16));
6653 colour = new FeatureColour(color);