2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 package jalview.project;
23 import static jalview.math.RotatableMatrix.Axis.X;
24 import static jalview.math.RotatableMatrix.Axis.Y;
25 import static jalview.math.RotatableMatrix.Axis.Z;
27 import jalview.analysis.Conservation;
28 import jalview.analysis.PCA;
29 import jalview.analysis.scoremodels.ScoreModels;
30 import jalview.analysis.scoremodels.SimilarityParams;
31 import jalview.api.FeatureColourI;
32 import jalview.api.ViewStyleI;
33 import jalview.api.analysis.ScoreModelI;
34 import jalview.api.analysis.SimilarityParamsI;
35 import jalview.api.structures.JalviewStructureDisplayI;
36 import jalview.bin.Cache;
37 import jalview.datamodel.AlignedCodonFrame;
38 import jalview.datamodel.Alignment;
39 import jalview.datamodel.AlignmentAnnotation;
40 import jalview.datamodel.AlignmentI;
41 import jalview.datamodel.DBRefEntry;
42 import jalview.datamodel.GeneLocus;
43 import jalview.datamodel.GraphLine;
44 import jalview.datamodel.PDBEntry;
45 import jalview.datamodel.Point;
46 import jalview.datamodel.RnaViewerModel;
47 import jalview.datamodel.SequenceFeature;
48 import jalview.datamodel.SequenceGroup;
49 import jalview.datamodel.SequenceI;
50 import jalview.datamodel.StructureViewerModel;
51 import jalview.datamodel.StructureViewerModel.StructureData;
52 import jalview.datamodel.features.FeatureMatcher;
53 import jalview.datamodel.features.FeatureMatcherI;
54 import jalview.datamodel.features.FeatureMatcherSet;
55 import jalview.datamodel.features.FeatureMatcherSetI;
56 import jalview.ext.varna.RnaModel;
57 import jalview.gui.AlignFrame;
58 import jalview.gui.AlignViewport;
59 import jalview.gui.AlignmentPanel;
60 import jalview.gui.AppVarna;
61 import jalview.gui.ChimeraViewFrame;
62 import jalview.gui.Desktop;
63 import jalview.gui.JvOptionPane;
64 import jalview.gui.OOMWarning;
65 import jalview.gui.PCAPanel;
66 import jalview.gui.PaintRefresher;
67 import jalview.gui.SplitFrame;
68 import jalview.gui.StructureViewer;
69 import jalview.gui.StructureViewer.ViewerType;
70 import jalview.gui.StructureViewerBase;
71 import jalview.gui.TreePanel;
72 import jalview.io.BackupFiles;
73 import jalview.io.DataSourceType;
74 import jalview.io.FileFormat;
75 import jalview.io.NewickFile;
76 import jalview.math.Matrix;
77 import jalview.math.MatrixI;
78 import jalview.renderer.ResidueShaderI;
79 import jalview.schemes.AnnotationColourGradient;
80 import jalview.schemes.ColourSchemeI;
81 import jalview.schemes.ColourSchemeProperty;
82 import jalview.schemes.FeatureColour;
83 import jalview.schemes.ResidueProperties;
84 import jalview.schemes.UserColourScheme;
85 import jalview.structure.StructureSelectionManager;
86 import jalview.structures.models.AAStructureBindingModel;
87 import jalview.util.Format;
88 import jalview.util.MessageManager;
89 import jalview.util.Platform;
90 import jalview.util.StringUtils;
91 import jalview.util.jarInputStreamProvider;
92 import jalview.util.matcher.Condition;
93 import jalview.viewmodel.AlignmentViewport;
94 import jalview.viewmodel.PCAModel;
95 import jalview.viewmodel.ViewportRanges;
96 import jalview.viewmodel.seqfeatures.FeatureRendererModel;
97 import jalview.viewmodel.seqfeatures.FeatureRendererSettings;
98 import jalview.viewmodel.seqfeatures.FeaturesDisplayed;
99 import jalview.ws.jws2.Jws2Discoverer;
100 import jalview.ws.jws2.dm.AAConSettings;
101 import jalview.ws.jws2.jabaws2.Jws2Instance;
102 import jalview.ws.params.ArgumentI;
103 import jalview.ws.params.AutoCalcSetting;
104 import jalview.ws.params.WsParamSetI;
105 import jalview.xml.binding.jalview.AlcodonFrame;
106 import jalview.xml.binding.jalview.AlcodonFrame.AlcodMap;
107 import jalview.xml.binding.jalview.Annotation;
108 import jalview.xml.binding.jalview.Annotation.ThresholdLine;
109 import jalview.xml.binding.jalview.AnnotationColourScheme;
110 import jalview.xml.binding.jalview.AnnotationElement;
111 import jalview.xml.binding.jalview.DoubleMatrix;
112 import jalview.xml.binding.jalview.DoubleVector;
113 import jalview.xml.binding.jalview.Feature;
114 import jalview.xml.binding.jalview.Feature.OtherData;
115 import jalview.xml.binding.jalview.FeatureMatcherSet.CompoundMatcher;
116 import jalview.xml.binding.jalview.FilterBy;
117 import jalview.xml.binding.jalview.JalviewModel;
118 import jalview.xml.binding.jalview.JalviewModel.FeatureSettings;
119 import jalview.xml.binding.jalview.JalviewModel.FeatureSettings.Group;
120 import jalview.xml.binding.jalview.JalviewModel.FeatureSettings.Setting;
121 import jalview.xml.binding.jalview.JalviewModel.JGroup;
122 import jalview.xml.binding.jalview.JalviewModel.JSeq;
123 import jalview.xml.binding.jalview.JalviewModel.JSeq.Pdbids;
124 import jalview.xml.binding.jalview.JalviewModel.JSeq.Pdbids.StructureState;
125 import jalview.xml.binding.jalview.JalviewModel.JSeq.RnaViewer;
126 import jalview.xml.binding.jalview.JalviewModel.JSeq.RnaViewer.SecondaryStructure;
127 import jalview.xml.binding.jalview.JalviewModel.PcaViewer;
128 import jalview.xml.binding.jalview.JalviewModel.PcaViewer.Axis;
129 import jalview.xml.binding.jalview.JalviewModel.PcaViewer.SeqPointMax;
130 import jalview.xml.binding.jalview.JalviewModel.PcaViewer.SeqPointMin;
131 import jalview.xml.binding.jalview.JalviewModel.PcaViewer.SequencePoint;
132 import jalview.xml.binding.jalview.JalviewModel.Tree;
133 import jalview.xml.binding.jalview.JalviewModel.UserColours;
134 import jalview.xml.binding.jalview.JalviewModel.Viewport;
135 import jalview.xml.binding.jalview.JalviewModel.Viewport.CalcIdParam;
136 import jalview.xml.binding.jalview.JalviewModel.Viewport.HiddenColumns;
137 import jalview.xml.binding.jalview.JalviewUserColours;
138 import jalview.xml.binding.jalview.JalviewUserColours.Colour;
139 import jalview.xml.binding.jalview.MapListType.MapListFrom;
140 import jalview.xml.binding.jalview.MapListType.MapListTo;
141 import jalview.xml.binding.jalview.Mapping;
142 import jalview.xml.binding.jalview.NoValueColour;
143 import jalview.xml.binding.jalview.ObjectFactory;
144 import jalview.xml.binding.jalview.PcaDataType;
145 import jalview.xml.binding.jalview.Pdbentry.Property;
146 import jalview.xml.binding.jalview.Sequence;
147 import jalview.xml.binding.jalview.Sequence.DBRef;
148 import jalview.xml.binding.jalview.SequenceSet;
149 import jalview.xml.binding.jalview.SequenceSet.SequenceSetProperties;
150 import jalview.xml.binding.jalview.ThresholdType;
151 import jalview.xml.binding.jalview.VAMSAS;
153 import java.awt.Color;
154 import java.awt.Font;
155 import java.awt.Rectangle;
156 import java.io.BufferedReader;
157 import java.io.ByteArrayInputStream;
158 import java.io.DataInputStream;
159 import java.io.DataOutputStream;
161 import java.io.FileInputStream;
162 import java.io.FileOutputStream;
163 import java.io.IOException;
164 import java.io.InputStreamReader;
165 import java.io.OutputStreamWriter;
166 import java.io.PrintWriter;
167 import java.lang.reflect.InvocationTargetException;
168 import java.math.BigInteger;
169 import java.net.MalformedURLException;
171 import java.util.ArrayList;
172 import java.util.Arrays;
173 import java.util.Collections;
174 import java.util.Enumeration;
175 import java.util.GregorianCalendar;
176 import java.util.HashMap;
177 import java.util.HashSet;
178 import java.util.Hashtable;
179 import java.util.IdentityHashMap;
180 import java.util.Iterator;
181 import java.util.LinkedHashMap;
182 import java.util.List;
183 import java.util.Map;
184 import java.util.Map.Entry;
185 import java.util.Set;
186 import java.util.Vector;
187 import java.util.jar.JarEntry;
188 import java.util.jar.JarInputStream;
189 import java.util.jar.JarOutputStream;
191 import javax.swing.JInternalFrame;
192 import javax.swing.SwingUtilities;
193 import javax.xml.bind.JAXBContext;
194 import javax.xml.bind.JAXBElement;
195 import javax.xml.bind.Marshaller;
196 import javax.xml.datatype.DatatypeConfigurationException;
197 import javax.xml.datatype.DatatypeFactory;
198 import javax.xml.datatype.XMLGregorianCalendar;
199 import javax.xml.stream.XMLInputFactory;
200 import javax.xml.stream.XMLStreamReader;
203 * Write out the current jalview desktop state as a Jalview XML stream.
205 * Note: the vamsas objects referred to here are primitive versions of the
206 * VAMSAS project schema elements - they are not the same and most likely never
210 * @version $Revision: 1.134 $
212 public class Jalview2XML
215 // BH 2018 we add the .jvp binary extension to J2S so that
216 // it will declare that binary when we do the file save from the browser
220 Platform.addJ2SBinaryType(".jvp?");
223 private static final String VIEWER_PREFIX = "viewer_";
225 private static final String RNA_PREFIX = "rna_";
227 private static final String UTF_8 = "UTF-8";
230 * prefix for recovering datasets for alignments with multiple views where
231 * non-existent dataset IDs were written for some views
233 private static final String UNIQSEQSETID = "uniqueSeqSetId.";
235 // use this with nextCounter() to make unique names for entities
236 private int counter = 0;
239 * SequenceI reference -> XML ID string in jalview XML. Populated as XML reps
240 * of sequence objects are created.
242 IdentityHashMap<SequenceI, String> seqsToIds = null;
245 * jalview XML Sequence ID to jalview sequence object reference (both dataset
246 * and alignment sequences. Populated as XML reps of sequence objects are
249 Map<String, SequenceI> seqRefIds = null;
251 Map<String, SequenceI> incompleteSeqs = null;
253 List<SeqFref> frefedSequence = null;
255 boolean raiseGUI = true; // whether errors are raised in dialog boxes or not
258 * Map of reconstructed AlignFrame objects that appear to have come from
259 * SplitFrame objects (have a dna/protein complement view).
261 private Map<Viewport, AlignFrame> splitFrameCandidates = new HashMap<>();
264 * Map from displayed rna structure models to their saved session state jar
267 private Map<RnaModel, String> rnaSessions = new HashMap<>();
270 * A helper method for safely using the value of an optional attribute that
271 * may be null if not present in the XML. Answers the boolean value, or false
277 public static boolean safeBoolean(Boolean b)
279 return b == null ? false : b.booleanValue();
283 * A helper method for safely using the value of an optional attribute that
284 * may be null if not present in the XML. Answers the integer value, or zero
290 public static int safeInt(Integer i)
292 return i == null ? 0 : i.intValue();
296 * A helper method for safely using the value of an optional attribute that
297 * may be null if not present in the XML. Answers the float value, or zero if
303 public static float safeFloat(Float f)
305 return f == null ? 0f : f.floatValue();
309 * create/return unique hash string for sq
312 * @return new or existing unique string for sq
314 String seqHash(SequenceI sq)
316 if (seqsToIds == null)
320 if (seqsToIds.containsKey(sq))
322 return seqsToIds.get(sq);
326 // create sequential key
327 String key = "sq" + (seqsToIds.size() + 1);
328 key = makeHashCode(sq, key); // check we don't have an external reference
330 seqsToIds.put(sq, key);
337 if (seqsToIds == null)
339 seqsToIds = new IdentityHashMap<>();
341 if (seqRefIds == null)
343 seqRefIds = new HashMap<>();
345 if (incompleteSeqs == null)
347 incompleteSeqs = new HashMap<>();
349 if (frefedSequence == null)
351 frefedSequence = new ArrayList<>();
359 public Jalview2XML(boolean raiseGUI)
361 this.raiseGUI = raiseGUI;
365 * base class for resolving forward references to sequences by their ID
370 abstract class SeqFref
376 public SeqFref(String _sref, String type)
382 public String getSref()
387 public SequenceI getSrefSeq()
389 return seqRefIds.get(sref);
392 public boolean isResolvable()
394 return seqRefIds.get(sref) != null;
397 public SequenceI getSrefDatasetSeq()
399 SequenceI sq = seqRefIds.get(sref);
402 while (sq.getDatasetSequence() != null)
404 sq = sq.getDatasetSequence();
411 * @return true if the forward reference was fully resolved
413 abstract boolean resolve();
416 public String toString()
418 return type + " reference to " + sref;
423 * create forward reference for a mapping
429 public SeqFref newMappingRef(final String sref,
430 final jalview.datamodel.Mapping _jmap)
432 SeqFref fref = new SeqFref(sref, "Mapping")
434 public jalview.datamodel.Mapping jmap = _jmap;
439 SequenceI seq = getSrefDatasetSeq();
451 public SeqFref newAlcodMapRef(final String sref,
452 final AlignedCodonFrame _cf,
453 final jalview.datamodel.Mapping _jmap)
456 SeqFref fref = new SeqFref(sref, "Codon Frame")
458 AlignedCodonFrame cf = _cf;
460 public jalview.datamodel.Mapping mp = _jmap;
463 public boolean isResolvable()
465 return super.isResolvable() && mp.getTo() != null;
471 SequenceI seq = getSrefDatasetSeq();
476 cf.addMap(seq, mp.getTo(), mp.getMap());
483 public void resolveFrefedSequences()
485 Iterator<SeqFref> nextFref = frefedSequence.iterator();
486 int toresolve = frefedSequence.size();
487 int unresolved = 0, failedtoresolve = 0;
488 while (nextFref.hasNext())
490 SeqFref ref = nextFref.next();
491 if (ref.isResolvable())
503 } catch (Exception x)
506 "IMPLEMENTATION ERROR: Failed to resolve forward reference for sequence "
519 System.err.println("Jalview Project Import: There were " + unresolved
520 + " forward references left unresolved on the stack.");
522 if (failedtoresolve > 0)
524 System.err.println("SERIOUS! " + failedtoresolve
525 + " resolvable forward references failed to resolve.");
527 if (incompleteSeqs != null && incompleteSeqs.size() > 0)
530 "Jalview Project Import: There are " + incompleteSeqs.size()
531 + " sequences which may have incomplete metadata.");
532 if (incompleteSeqs.size() < 10)
534 for (SequenceI s : incompleteSeqs.values())
536 System.err.println(s.toString());
542 "Too many to report. Skipping output of incomplete sequences.");
548 * This maintains a map of viewports, the key being the seqSetId. Important to
549 * set historyItem and redoList for multiple views
551 Map<String, AlignViewport> viewportsAdded = new HashMap<>();
553 Map<String, AlignmentAnnotation> annotationIds = new HashMap<>();
555 String uniqueSetSuffix = "";
558 * List of pdbfiles added to Jar
560 List<String> pdbfiles = null;
562 // SAVES SEVERAL ALIGNMENT WINDOWS TO SAME JARFILE
563 public void saveState(File statefile)
565 FileOutputStream fos = null;
570 fos = new FileOutputStream(statefile);
572 JarOutputStream jout = new JarOutputStream(fos);
576 } catch (Exception e)
578 Cache.log.error("Couln't write Jalview state to " + statefile, e);
579 // TODO: inform user of the problem - they need to know if their data was
581 if (errorMessage == null)
583 errorMessage = "Did't write Jalview Archive to output file '"
584 + statefile + "' - See console error log for details";
588 errorMessage += "(Didn't write Jalview Archive to output file '"
599 } catch (IOException e)
609 * Writes a jalview project archive to the given Jar output stream.
613 public void saveState(JarOutputStream jout)
615 AlignFrame[] frames = Desktop.getAlignFrames();
621 saveAllFrames(Arrays.asList(frames), jout);
625 * core method for storing state for a set of AlignFrames.
628 * - frames involving all data to be exported (including containing
631 * - project output stream
633 private void saveAllFrames(List<AlignFrame> frames, JarOutputStream jout)
635 Hashtable<String, AlignFrame> dsses = new Hashtable<>();
638 * ensure cached data is clear before starting
640 // todo tidy up seqRefIds, seqsToIds initialisation / reset
642 splitFrameCandidates.clear();
647 // NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS
648 // //////////////////////////////////////////////////
650 List<String> shortNames = new ArrayList<>();
651 List<String> viewIds = new ArrayList<>();
654 for (int i = frames.size() - 1; i > -1; i--)
656 AlignFrame af = frames.get(i);
658 if (skipList != null && skipList
659 .containsKey(af.getViewport().getSequenceSetId()))
664 String shortName = makeFilename(af, shortNames);
666 int apSize = af.getAlignPanels().size();
668 for (int ap = 0; ap < apSize; ap++)
670 AlignmentPanel apanel = (AlignmentPanel) af.getAlignPanels()
672 String fileName = apSize == 1 ? shortName : ap + shortName;
673 if (!fileName.endsWith(".xml"))
675 fileName = fileName + ".xml";
678 saveState(apanel, fileName, jout, viewIds);
680 String dssid = getDatasetIdRef(
681 af.getViewport().getAlignment().getDataset());
682 if (!dsses.containsKey(dssid))
684 dsses.put(dssid, af);
689 writeDatasetFor(dsses, "" + jout.hashCode() + " " + uniqueSetSuffix,
695 } catch (Exception foo)
699 } catch (Exception ex)
701 // TODO: inform user of the problem - they need to know if their data was
703 if (errorMessage == null)
705 errorMessage = "Couldn't write Jalview Archive - see error output for details";
707 ex.printStackTrace();
712 * Generates a distinct file name, based on the title of the AlignFrame, by
713 * appending _n for increasing n until an unused name is generated. The new
714 * name (without its extension) is added to the list.
718 * @return the generated name, with .xml extension
720 protected String makeFilename(AlignFrame af, List<String> namesUsed)
722 String shortName = af.getTitle();
724 if (shortName.indexOf(File.separatorChar) > -1)
726 shortName = shortName
727 .substring(shortName.lastIndexOf(File.separatorChar) + 1);
732 while (namesUsed.contains(shortName))
734 if (shortName.endsWith("_" + (count - 1)))
736 shortName = shortName.substring(0, shortName.lastIndexOf("_"));
739 shortName = shortName.concat("_" + count);
743 namesUsed.add(shortName);
745 if (!shortName.endsWith(".xml"))
747 shortName = shortName + ".xml";
752 // USE THIS METHOD TO SAVE A SINGLE ALIGNMENT WINDOW
753 public boolean saveAlignment(AlignFrame af, String jarFile,
758 // create backupfiles object and get new temp filename destination
759 boolean doBackup = BackupFiles.getEnabled();
760 BackupFiles backupfiles = doBackup ? new BackupFiles(jarFile) : null;
761 FileOutputStream fos = new FileOutputStream(doBackup ?
762 backupfiles.getTempFilePath() : jarFile);
764 JarOutputStream jout = new JarOutputStream(fos);
765 List<AlignFrame> frames = new ArrayList<>();
767 // resolve splitframes
768 if (af.getViewport().getCodingComplement() != null)
770 frames = ((SplitFrame) af.getSplitViewContainer()).getAlignFrames();
776 saveAllFrames(frames, jout);
780 } catch (Exception foo)
784 boolean success = true;
788 backupfiles.setWriteSuccess(success);
789 success = backupfiles.rollBackupsAndRenameTempFile();
793 } catch (Exception ex)
795 errorMessage = "Couldn't Write alignment view to Jalview Archive - see error output for details";
796 ex.printStackTrace();
801 private void writeDatasetFor(Hashtable<String, AlignFrame> dsses,
802 String fileName, JarOutputStream jout)
805 for (String dssids : dsses.keySet())
807 AlignFrame _af = dsses.get(dssids);
808 String jfileName = fileName + " Dataset for " + _af.getTitle();
809 if (!jfileName.endsWith(".xml"))
811 jfileName = jfileName + ".xml";
813 saveState(_af.alignPanel, jfileName, true, jout, null);
818 * create a JalviewModel from an alignment view and marshall it to a
822 * panel to create jalview model for
824 * name of alignment panel written to output stream
831 public JalviewModel saveState(AlignmentPanel ap, String fileName,
832 JarOutputStream jout, List<String> viewIds)
834 return saveState(ap, fileName, false, jout, viewIds);
838 * create a JalviewModel from an alignment view and marshall it to a
842 * panel to create jalview model for
844 * name of alignment panel written to output stream
846 * when true, only write the dataset for the alignment, not the data
847 * associated with the view.
853 public JalviewModel saveState(AlignmentPanel ap, String fileName,
854 boolean storeDS, JarOutputStream jout, List<String> viewIds)
858 viewIds = new ArrayList<>();
863 List<UserColourScheme> userColours = new ArrayList<>();
865 AlignViewport av = ap.av;
866 ViewportRanges vpRanges = av.getRanges();
868 final ObjectFactory objectFactory = new ObjectFactory();
869 JalviewModel object = objectFactory.createJalviewModel();
870 object.setVamsasModel(new VAMSAS());
872 // object.setCreationDate(new java.util.Date(System.currentTimeMillis()));
875 GregorianCalendar c = new GregorianCalendar();
876 DatatypeFactory datatypeFactory = DatatypeFactory.newInstance();
877 XMLGregorianCalendar now = datatypeFactory.newXMLGregorianCalendar(c);// gregorianCalendar);
878 object.setCreationDate(now);
879 } catch (DatatypeConfigurationException e)
881 System.err.println("error writing date: " + e.toString());
884 jalview.bin.Cache.getDefault("VERSION", "Development Build"));
887 * rjal is full height alignment, jal is actual alignment with full metadata
888 * but excludes hidden sequences.
890 jalview.datamodel.AlignmentI rjal = av.getAlignment(), jal = rjal;
892 if (av.hasHiddenRows())
894 rjal = jal.getHiddenSequences().getFullAlignment();
897 SequenceSet vamsasSet = new SequenceSet();
899 // JalviewModelSequence jms = new JalviewModelSequence();
901 vamsasSet.setGapChar(jal.getGapCharacter() + "");
903 if (jal.getDataset() != null)
905 // dataset id is the dataset's hashcode
906 vamsasSet.setDatasetId(getDatasetIdRef(jal.getDataset()));
909 // switch jal and the dataset
910 jal = jal.getDataset();
914 if (jal.getProperties() != null)
916 Enumeration en = jal.getProperties().keys();
917 while (en.hasMoreElements())
919 String key = en.nextElement().toString();
920 SequenceSetProperties ssp = new SequenceSetProperties();
922 ssp.setValue(jal.getProperties().get(key).toString());
923 // vamsasSet.addSequenceSetProperties(ssp);
924 vamsasSet.getSequenceSetProperties().add(ssp);
929 Set<String> calcIdSet = new HashSet<>();
930 // record the set of vamsas sequence XML POJO we create.
931 HashMap<String, Sequence> vamsasSetIds = new HashMap<>();
933 for (final SequenceI jds : rjal.getSequences())
935 final SequenceI jdatasq = jds.getDatasetSequence() == null ? jds
936 : jds.getDatasetSequence();
937 String id = seqHash(jds);
938 if (vamsasSetIds.get(id) == null)
940 if (seqRefIds.get(id) != null && !storeDS)
942 // This happens for two reasons: 1. multiple views are being
944 // 2. the hashCode has collided with another sequence's code. This
946 // HAPPEN! (PF00072.15.stk does this)
947 // JBPNote: Uncomment to debug writing out of files that do not read
948 // back in due to ArrayOutOfBoundExceptions.
949 // System.err.println("vamsasSeq backref: "+id+"");
950 // System.err.println(jds.getName()+"
951 // "+jds.getStart()+"-"+jds.getEnd()+" "+jds.getSequenceAsString());
952 // System.err.println("Hashcode: "+seqHash(jds));
953 // SequenceI rsq = (SequenceI) seqRefIds.get(id + "");
954 // System.err.println(rsq.getName()+"
955 // "+rsq.getStart()+"-"+rsq.getEnd()+" "+rsq.getSequenceAsString());
956 // System.err.println("Hashcode: "+seqHash(rsq));
960 vamsasSeq = createVamsasSequence(id, jds);
961 // vamsasSet.addSequence(vamsasSeq);
962 vamsasSet.getSequence().add(vamsasSeq);
963 vamsasSetIds.put(id, vamsasSeq);
964 seqRefIds.put(id, jds);
968 jseq.setStart(jds.getStart());
969 jseq.setEnd(jds.getEnd());
970 jseq.setColour(av.getSequenceColour(jds).getRGB());
972 jseq.setId(id); // jseq id should be a string not a number
975 // Store any sequences this sequence represents
976 if (av.hasHiddenRows())
978 // use rjal, contains the full height alignment
980 av.getAlignment().getHiddenSequences().isHidden(jds));
982 if (av.isHiddenRepSequence(jds))
984 jalview.datamodel.SequenceI[] reps = av
985 .getRepresentedSequences(jds).getSequencesInOrder(rjal);
987 for (int h = 0; h < reps.length; h++)
991 // jseq.addHiddenSequences(rjal.findIndex(reps[h]));
992 jseq.getHiddenSequences().add(rjal.findIndex(reps[h]));
997 // mark sequence as reference - if it is the reference for this view
1000 jseq.setViewreference(jds == jal.getSeqrep());
1004 // TODO: omit sequence features from each alignment view's XML dump if we
1005 // are storing dataset
1006 List<SequenceFeature> sfs = jds.getSequenceFeatures();
1007 for (SequenceFeature sf : sfs)
1009 // Features features = new Features();
1010 Feature features = new Feature();
1012 features.setBegin(sf.getBegin());
1013 features.setEnd(sf.getEnd());
1014 features.setDescription(sf.getDescription());
1015 features.setType(sf.getType());
1016 features.setFeatureGroup(sf.getFeatureGroup());
1017 features.setScore(sf.getScore());
1018 if (sf.links != null)
1020 for (int l = 0; l < sf.links.size(); l++)
1022 OtherData keyValue = new OtherData();
1023 keyValue.setKey("LINK_" + l);
1024 keyValue.setValue(sf.links.elementAt(l).toString());
1025 // features.addOtherData(keyValue);
1026 features.getOtherData().add(keyValue);
1029 if (sf.otherDetails != null)
1032 * save feature attributes, which may be simple strings or
1033 * map valued (have sub-attributes)
1035 for (Entry<String, Object> entry : sf.otherDetails.entrySet())
1037 String key = entry.getKey();
1038 Object value = entry.getValue();
1039 if (value instanceof Map<?, ?>)
1041 for (Entry<String, Object> subAttribute : ((Map<String, Object>) value)
1044 OtherData otherData = new OtherData();
1045 otherData.setKey(key);
1046 otherData.setKey2(subAttribute.getKey());
1047 otherData.setValue(subAttribute.getValue().toString());
1048 // features.addOtherData(otherData);
1049 features.getOtherData().add(otherData);
1054 OtherData otherData = new OtherData();
1055 otherData.setKey(key);
1056 otherData.setValue(value.toString());
1057 // features.addOtherData(otherData);
1058 features.getOtherData().add(otherData);
1063 // jseq.addFeatures(features);
1064 jseq.getFeatures().add(features);
1067 if (jdatasq.getAllPDBEntries() != null)
1069 Enumeration<PDBEntry> en = jdatasq.getAllPDBEntries().elements();
1070 while (en.hasMoreElements())
1072 Pdbids pdb = new Pdbids();
1073 jalview.datamodel.PDBEntry entry = en.nextElement();
1075 String pdbId = entry.getId();
1077 pdb.setType(entry.getType());
1080 * Store any structure views associated with this sequence. This
1081 * section copes with duplicate entries in the project, so a dataset
1082 * only view *should* be coped with sensibly.
1084 // This must have been loaded, is it still visible?
1085 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1086 String matchedFile = null;
1087 for (int f = frames.length - 1; f > -1; f--)
1089 if (frames[f] instanceof StructureViewerBase)
1091 StructureViewerBase viewFrame = (StructureViewerBase) frames[f];
1092 matchedFile = saveStructureState(ap, jds, pdb, entry, viewIds,
1093 matchedFile, viewFrame);
1095 * Only store each structure viewer's state once in the project
1096 * jar. First time through only (storeDS==false)
1098 String viewId = viewFrame.getViewId();
1099 if (!storeDS && !viewIds.contains(viewId))
1101 viewIds.add(viewId);
1104 String viewerState = viewFrame.getStateInfo();
1105 writeJarEntry(jout, getViewerJarEntryName(viewId),
1106 viewerState.getBytes());
1107 } catch (IOException e)
1110 "Error saving viewer state: " + e.getMessage());
1116 if (matchedFile != null || entry.getFile() != null)
1118 if (entry.getFile() != null)
1121 matchedFile = entry.getFile();
1123 pdb.setFile(matchedFile); // entry.getFile());
1124 if (pdbfiles == null)
1126 pdbfiles = new ArrayList<>();
1129 if (!pdbfiles.contains(pdbId))
1131 pdbfiles.add(pdbId);
1132 copyFileToJar(jout, matchedFile, pdbId);
1136 Enumeration<String> props = entry.getProperties();
1137 if (props.hasMoreElements())
1139 // PdbentryItem item = new PdbentryItem();
1140 while (props.hasMoreElements())
1142 Property prop = new Property();
1143 String key = props.nextElement();
1145 prop.setValue(entry.getProperty(key).toString());
1146 // item.addProperty(prop);
1147 pdb.getProperty().add(prop);
1149 // pdb.addPdbentryItem(item);
1152 // jseq.addPdbids(pdb);
1153 jseq.getPdbids().add(pdb);
1157 saveRnaViewers(jout, jseq, jds, viewIds, ap, storeDS);
1159 // jms.addJSeq(jseq);
1160 object.getJSeq().add(jseq);
1163 if (!storeDS && av.hasHiddenRows())
1165 jal = av.getAlignment();
1169 if (storeDS && jal.getCodonFrames() != null)
1171 List<AlignedCodonFrame> jac = jal.getCodonFrames();
1172 for (AlignedCodonFrame acf : jac)
1174 AlcodonFrame alc = new AlcodonFrame();
1175 if (acf.getProtMappings() != null
1176 && acf.getProtMappings().length > 0)
1178 boolean hasMap = false;
1179 SequenceI[] dnas = acf.getdnaSeqs();
1180 jalview.datamodel.Mapping[] pmaps = acf.getProtMappings();
1181 for (int m = 0; m < pmaps.length; m++)
1183 AlcodMap alcmap = new AlcodMap();
1184 alcmap.setDnasq(seqHash(dnas[m]));
1186 createVamsasMapping(pmaps[m], dnas[m], null, false));
1187 // alc.addAlcodMap(alcmap);
1188 alc.getAlcodMap().add(alcmap);
1193 // vamsasSet.addAlcodonFrame(alc);
1194 vamsasSet.getAlcodonFrame().add(alc);
1197 // TODO: delete this ? dead code from 2.8.3->2.9 ?
1199 // AlcodonFrame alc = new AlcodonFrame();
1200 // vamsasSet.addAlcodonFrame(alc);
1201 // for (int p = 0; p < acf.aaWidth; p++)
1203 // Alcodon cmap = new Alcodon();
1204 // if (acf.codons[p] != null)
1206 // // Null codons indicate a gapped column in the translated peptide
1208 // cmap.setPos1(acf.codons[p][0]);
1209 // cmap.setPos2(acf.codons[p][1]);
1210 // cmap.setPos3(acf.codons[p][2]);
1212 // alc.addAlcodon(cmap);
1214 // if (acf.getProtMappings() != null
1215 // && acf.getProtMappings().length > 0)
1217 // SequenceI[] dnas = acf.getdnaSeqs();
1218 // jalview.datamodel.Mapping[] pmaps = acf.getProtMappings();
1219 // for (int m = 0; m < pmaps.length; m++)
1221 // AlcodMap alcmap = new AlcodMap();
1222 // alcmap.setDnasq(seqHash(dnas[m]));
1223 // alcmap.setMapping(createVamsasMapping(pmaps[m], dnas[m], null,
1225 // alc.addAlcodMap(alcmap);
1232 // /////////////////////////////////
1233 if (!storeDS && av.getCurrentTree() != null)
1235 // FIND ANY ASSOCIATED TREES
1236 // NOT IMPLEMENTED FOR HEADLESS STATE AT PRESENT
1237 if (Desktop.desktop != null)
1239 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1241 for (int t = 0; t < frames.length; t++)
1243 if (frames[t] instanceof TreePanel)
1245 TreePanel tp = (TreePanel) frames[t];
1247 if (tp.getTreeCanvas().getViewport().getAlignment() == jal)
1249 JalviewModel.Tree tree = new JalviewModel.Tree();
1250 tree.setTitle(tp.getTitle());
1251 tree.setCurrentTree((av.getCurrentTree() == tp.getTree()));
1252 tree.setNewick(tp.getTree().print());
1253 tree.setThreshold(tp.getTreeCanvas().getThreshold());
1255 tree.setFitToWindow(tp.fitToWindow.getState());
1256 tree.setFontName(tp.getTreeFont().getName());
1257 tree.setFontSize(tp.getTreeFont().getSize());
1258 tree.setFontStyle(tp.getTreeFont().getStyle());
1259 tree.setMarkUnlinked(tp.placeholdersMenu.getState());
1261 tree.setShowBootstrap(tp.bootstrapMenu.getState());
1262 tree.setShowDistances(tp.distanceMenu.getState());
1264 tree.setHeight(tp.getHeight());
1265 tree.setWidth(tp.getWidth());
1266 tree.setXpos(tp.getX());
1267 tree.setYpos(tp.getY());
1268 tree.setId(makeHashCode(tp, null));
1269 tree.setLinkToAllViews(
1270 tp.getTreeCanvas().isApplyToAllViews());
1272 // jms.addTree(tree);
1273 object.getTree().add(tree);
1283 if (!storeDS && Desktop.desktop != null)
1285 for (JInternalFrame frame : Desktop.desktop.getAllFrames())
1287 if (frame instanceof PCAPanel)
1289 PCAPanel panel = (PCAPanel) frame;
1290 if (panel.getAlignViewport().getAlignment() == jal)
1292 savePCA(panel, object);
1300 * store forward refs from an annotationRow to any groups
1302 IdentityHashMap<SequenceGroup, String> groupRefs = new IdentityHashMap<>();
1305 for (SequenceI sq : jal.getSequences())
1307 // Store annotation on dataset sequences only
1308 AlignmentAnnotation[] aa = sq.getAnnotation();
1309 if (aa != null && aa.length > 0)
1311 storeAlignmentAnnotation(aa, groupRefs, av, calcIdSet, storeDS,
1318 if (jal.getAlignmentAnnotation() != null)
1320 // Store the annotation shown on the alignment.
1321 AlignmentAnnotation[] aa = jal.getAlignmentAnnotation();
1322 storeAlignmentAnnotation(aa, groupRefs, av, calcIdSet, storeDS,
1327 if (jal.getGroups() != null)
1329 JGroup[] groups = new JGroup[jal.getGroups().size()];
1331 for (jalview.datamodel.SequenceGroup sg : jal.getGroups())
1333 JGroup jGroup = new JGroup();
1334 groups[++i] = jGroup;
1336 jGroup.setStart(sg.getStartRes());
1337 jGroup.setEnd(sg.getEndRes());
1338 jGroup.setName(sg.getName());
1339 if (groupRefs.containsKey(sg))
1341 // group has references so set its ID field
1342 jGroup.setId(groupRefs.get(sg));
1344 ColourSchemeI colourScheme = sg.getColourScheme();
1345 if (colourScheme != null)
1347 ResidueShaderI groupColourScheme = sg.getGroupColourScheme();
1348 if (groupColourScheme.conservationApplied())
1350 jGroup.setConsThreshold(groupColourScheme.getConservationInc());
1352 if (colourScheme instanceof jalview.schemes.UserColourScheme)
1355 setUserColourScheme(colourScheme, userColours,
1360 jGroup.setColour(colourScheme.getSchemeName());
1363 else if (colourScheme instanceof jalview.schemes.AnnotationColourGradient)
1365 jGroup.setColour("AnnotationColourGradient");
1366 jGroup.setAnnotationColours(constructAnnotationColours(
1367 (jalview.schemes.AnnotationColourGradient) colourScheme,
1368 userColours, object));
1370 else if (colourScheme instanceof jalview.schemes.UserColourScheme)
1373 setUserColourScheme(colourScheme, userColours, object));
1377 jGroup.setColour(colourScheme.getSchemeName());
1380 jGroup.setPidThreshold(groupColourScheme.getThreshold());
1383 jGroup.setOutlineColour(sg.getOutlineColour().getRGB());
1384 jGroup.setDisplayBoxes(sg.getDisplayBoxes());
1385 jGroup.setDisplayText(sg.getDisplayText());
1386 jGroup.setColourText(sg.getColourText());
1387 jGroup.setTextCol1(sg.textColour.getRGB());
1388 jGroup.setTextCol2(sg.textColour2.getRGB());
1389 jGroup.setTextColThreshold(sg.thresholdTextColour);
1390 jGroup.setShowUnconserved(sg.getShowNonconserved());
1391 jGroup.setIgnoreGapsinConsensus(sg.getIgnoreGapsConsensus());
1392 jGroup.setShowConsensusHistogram(sg.isShowConsensusHistogram());
1393 jGroup.setShowSequenceLogo(sg.isShowSequenceLogo());
1394 jGroup.setNormaliseSequenceLogo(sg.isNormaliseSequenceLogo());
1395 for (SequenceI seq : sg.getSequences())
1397 // jGroup.addSeq(seqHash(seq));
1398 jGroup.getSeq().add(seqHash(seq));
1402 //jms.setJGroup(groups);
1404 for (JGroup grp : groups)
1406 object.getJGroup().add(grp);
1411 // /////////SAVE VIEWPORT
1412 Viewport view = new Viewport();
1413 view.setTitle(ap.alignFrame.getTitle());
1414 view.setSequenceSetId(
1415 makeHashCode(av.getSequenceSetId(), av.getSequenceSetId()));
1416 view.setId(av.getViewId());
1417 if (av.getCodingComplement() != null)
1419 view.setComplementId(av.getCodingComplement().getViewId());
1421 view.setViewName(av.getViewName());
1422 view.setGatheredViews(av.isGatherViewsHere());
1424 Rectangle size = ap.av.getExplodedGeometry();
1425 Rectangle position = size;
1428 size = ap.alignFrame.getBounds();
1429 if (av.getCodingComplement() != null)
1431 position = ((SplitFrame) ap.alignFrame.getSplitViewContainer())
1439 view.setXpos(position.x);
1440 view.setYpos(position.y);
1442 view.setWidth(size.width);
1443 view.setHeight(size.height);
1445 view.setStartRes(vpRanges.getStartRes());
1446 view.setStartSeq(vpRanges.getStartSeq());
1448 if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme)
1450 view.setBgColour(setUserColourScheme(av.getGlobalColourScheme(),
1451 userColours, object));
1454 .getGlobalColourScheme() instanceof jalview.schemes.AnnotationColourGradient)
1456 AnnotationColourScheme ac = constructAnnotationColours(
1457 (jalview.schemes.AnnotationColourGradient) av
1458 .getGlobalColourScheme(),
1459 userColours, object);
1461 view.setAnnotationColours(ac);
1462 view.setBgColour("AnnotationColourGradient");
1466 view.setBgColour(ColourSchemeProperty
1467 .getColourName(av.getGlobalColourScheme()));
1470 ResidueShaderI vcs = av.getResidueShading();
1471 ColourSchemeI cs = av.getGlobalColourScheme();
1475 if (vcs.conservationApplied())
1477 view.setConsThreshold(vcs.getConservationInc());
1478 if (cs instanceof jalview.schemes.UserColourScheme)
1480 view.setBgColour(setUserColourScheme(cs, userColours, object));
1483 view.setPidThreshold(vcs.getThreshold());
1486 view.setConservationSelected(av.getConservationSelected());
1487 view.setPidSelected(av.getAbovePIDThreshold());
1488 final Font font = av.getFont();
1489 view.setFontName(font.getName());
1490 view.setFontSize(font.getSize());
1491 view.setFontStyle(font.getStyle());
1492 view.setScaleProteinAsCdna(av.getViewStyle().isScaleProteinAsCdna());
1493 view.setRenderGaps(av.isRenderGaps());
1494 view.setShowAnnotation(av.isShowAnnotation());
1495 view.setShowBoxes(av.getShowBoxes());
1496 view.setShowColourText(av.getColourText());
1497 view.setShowFullId(av.getShowJVSuffix());
1498 view.setRightAlignIds(av.isRightAlignIds());
1499 view.setShowSequenceFeatures(av.isShowSequenceFeatures());
1500 view.setShowText(av.getShowText());
1501 view.setShowUnconserved(av.getShowUnconserved());
1502 view.setWrapAlignment(av.getWrapAlignment());
1503 view.setTextCol1(av.getTextColour().getRGB());
1504 view.setTextCol2(av.getTextColour2().getRGB());
1505 view.setTextColThreshold(av.getThresholdTextColour());
1506 view.setShowConsensusHistogram(av.isShowConsensusHistogram());
1507 view.setShowSequenceLogo(av.isShowSequenceLogo());
1508 view.setNormaliseSequenceLogo(av.isNormaliseSequenceLogo());
1509 view.setShowGroupConsensus(av.isShowGroupConsensus());
1510 view.setShowGroupConservation(av.isShowGroupConservation());
1511 view.setShowNPfeatureTooltip(av.isShowNPFeats());
1512 view.setShowDbRefTooltip(av.isShowDBRefs());
1513 view.setFollowHighlight(av.isFollowHighlight());
1514 view.setFollowSelection(av.followSelection);
1515 view.setIgnoreGapsinConsensus(av.isIgnoreGapsConsensus());
1516 view.setShowComplementFeatures(av.isShowComplementFeatures());
1517 view.setShowComplementFeaturesOnTop(
1518 av.isShowComplementFeaturesOnTop());
1519 if (av.getFeaturesDisplayed() != null)
1521 FeatureSettings fs = new FeatureSettings();
1523 FeatureRendererModel fr = ap.getSeqPanel().seqCanvas
1524 .getFeatureRenderer();
1525 String[] renderOrder = fr.getRenderOrder().toArray(new String[0]);
1527 Vector<String> settingsAdded = new Vector<>();
1528 if (renderOrder != null)
1530 for (String featureType : renderOrder)
1532 FeatureSettings.Setting setting = new FeatureSettings.Setting();
1533 setting.setType(featureType);
1536 * save any filter for the feature type
1538 FeatureMatcherSetI filter = fr.getFeatureFilter(featureType);
1539 if (filter != null) {
1540 Iterator<FeatureMatcherI> filters = filter.getMatchers().iterator();
1541 FeatureMatcherI firstFilter = filters.next();
1542 setting.setMatcherSet(Jalview2XML.marshalFilter(
1543 firstFilter, filters, filter.isAnded()));
1547 * save colour scheme for the feature type
1549 FeatureColourI fcol = fr.getFeatureStyle(featureType);
1550 if (!fcol.isSimpleColour())
1552 setting.setColour(fcol.getMaxColour().getRGB());
1553 setting.setMincolour(fcol.getMinColour().getRGB());
1554 setting.setMin(fcol.getMin());
1555 setting.setMax(fcol.getMax());
1556 setting.setColourByLabel(fcol.isColourByLabel());
1557 if (fcol.isColourByAttribute())
1559 String[] attName = fcol.getAttributeName();
1560 setting.getAttributeName().add(attName[0]);
1561 if (attName.length > 1)
1563 setting.getAttributeName().add(attName[1]);
1566 setting.setAutoScale(fcol.isAutoScaled());
1567 setting.setThreshold(fcol.getThreshold());
1568 Color noColour = fcol.getNoColour();
1569 if (noColour == null)
1571 setting.setNoValueColour(NoValueColour.NONE);
1573 else if (noColour.equals(fcol.getMaxColour()))
1575 setting.setNoValueColour(NoValueColour.MAX);
1579 setting.setNoValueColour(NoValueColour.MIN);
1581 // -1 = No threshold, 0 = Below, 1 = Above
1582 setting.setThreshstate(fcol.isAboveThreshold() ? 1
1583 : (fcol.isBelowThreshold() ? 0 : -1));
1587 setting.setColour(fcol.getColour().getRGB());
1591 av.getFeaturesDisplayed().isVisible(featureType));
1593 .getOrder(featureType);
1596 setting.setOrder(rorder);
1598 /// fs.addSetting(setting);
1599 fs.getSetting().add(setting);
1600 settingsAdded.addElement(featureType);
1604 // is groups actually supposed to be a map here ?
1605 Iterator<String> en = fr.getFeatureGroups().iterator();
1606 Vector<String> groupsAdded = new Vector<>();
1607 while (en.hasNext())
1609 String grp = en.next();
1610 if (groupsAdded.contains(grp))
1614 Group g = new Group();
1616 g.setDisplay(((Boolean) fr.checkGroupVisibility(grp, false))
1619 fs.getGroup().add(g);
1620 groupsAdded.addElement(grp);
1622 // jms.setFeatureSettings(fs);
1623 object.setFeatureSettings(fs);
1626 if (av.hasHiddenColumns())
1628 jalview.datamodel.HiddenColumns hidden = av.getAlignment()
1629 .getHiddenColumns();
1632 warn("REPORT BUG: avoided null columnselection bug (DMAM reported). Please contact Jim about this.");
1636 Iterator<int[]> hiddenRegions = hidden.iterator();
1637 while (hiddenRegions.hasNext())
1639 int[] region = hiddenRegions.next();
1640 HiddenColumns hc = new HiddenColumns();
1641 hc.setStart(region[0]);
1642 hc.setEnd(region[1]);
1643 // view.addHiddenColumns(hc);
1644 view.getHiddenColumns().add(hc);
1648 if (calcIdSet.size() > 0)
1650 for (String calcId : calcIdSet)
1652 if (calcId.trim().length() > 0)
1654 CalcIdParam cidp = createCalcIdParam(calcId, av);
1655 // Some calcIds have no parameters.
1658 // view.addCalcIdParam(cidp);
1659 view.getCalcIdParam().add(cidp);
1665 // jms.addViewport(view);
1666 object.getViewport().add(view);
1668 // object.setJalviewModelSequence(jms);
1669 // object.getVamsasModel().addSequenceSet(vamsasSet);
1670 object.getVamsasModel().getSequenceSet().add(vamsasSet);
1672 if (jout != null && fileName != null)
1674 // We may not want to write the object to disk,
1675 // eg we can copy the alignViewport to a new view object
1676 // using save and then load
1679 fileName = fileName.replace('\\', '/');
1680 System.out.println("Writing jar entry " + fileName);
1681 JarEntry entry = new JarEntry(fileName);
1682 jout.putNextEntry(entry);
1683 PrintWriter pout = new PrintWriter(
1684 new OutputStreamWriter(jout, UTF_8));
1685 JAXBContext jaxbContext = JAXBContext
1686 .newInstance(JalviewModel.class);
1687 Marshaller jaxbMarshaller = jaxbContext.createMarshaller();
1689 // output pretty printed
1690 // jaxbMarshaller.setProperty(Marshaller.JAXB_FORMATTED_OUTPUT, true);
1691 jaxbMarshaller.marshal(
1692 new ObjectFactory().createJalviewModel(object), pout);
1694 // jaxbMarshaller.marshal(object, pout);
1695 // marshaller.marshal(object);
1698 } catch (Exception ex)
1700 // TODO: raise error in GUI if marshalling failed.
1701 System.err.println("Error writing Jalview project");
1702 ex.printStackTrace();
1709 * Writes PCA viewer attributes and computed values to an XML model object and
1710 * adds it to the JalviewModel. Any exceptions are reported by logging.
1712 protected void savePCA(PCAPanel panel, JalviewModel object)
1716 PcaViewer viewer = new PcaViewer();
1717 viewer.setHeight(panel.getHeight());
1718 viewer.setWidth(panel.getWidth());
1719 viewer.setXpos(panel.getX());
1720 viewer.setYpos(panel.getY());
1721 viewer.setTitle(panel.getTitle());
1722 PCAModel pcaModel = panel.getPcaModel();
1723 viewer.setScoreModelName(pcaModel.getScoreModelName());
1724 viewer.setXDim(panel.getSelectedDimensionIndex(X));
1725 viewer.setYDim(panel.getSelectedDimensionIndex(Y));
1726 viewer.setZDim(panel.getSelectedDimensionIndex(Z));
1728 panel.getRotatableCanvas().getBackgroundColour().getRGB());
1729 viewer.setScaleFactor(panel.getRotatableCanvas().getScaleFactor());
1730 float[] spMin = panel.getRotatableCanvas().getSeqMin();
1731 SeqPointMin spmin = new SeqPointMin();
1732 spmin.setXPos(spMin[0]);
1733 spmin.setYPos(spMin[1]);
1734 spmin.setZPos(spMin[2]);
1735 viewer.setSeqPointMin(spmin);
1736 float[] spMax = panel.getRotatableCanvas().getSeqMax();
1737 SeqPointMax spmax = new SeqPointMax();
1738 spmax.setXPos(spMax[0]);
1739 spmax.setYPos(spMax[1]);
1740 spmax.setZPos(spMax[2]);
1741 viewer.setSeqPointMax(spmax);
1742 viewer.setShowLabels(panel.getRotatableCanvas().isShowLabels());
1743 viewer.setLinkToAllViews(
1744 panel.getRotatableCanvas().isApplyToAllViews());
1745 SimilarityParamsI sp = pcaModel.getSimilarityParameters();
1746 viewer.setIncludeGaps(sp.includeGaps());
1747 viewer.setMatchGaps(sp.matchGaps());
1748 viewer.setIncludeGappedColumns(sp.includeGappedColumns());
1749 viewer.setDenominateByShortestLength(sp.denominateByShortestLength());
1752 * sequence points on display
1754 for (jalview.datamodel.SequencePoint spt : pcaModel
1755 .getSequencePoints())
1757 SequencePoint point = new SequencePoint();
1758 point.setSequenceRef(seqHash(spt.getSequence()));
1759 point.setXPos(spt.coord.x);
1760 point.setYPos(spt.coord.y);
1761 point.setZPos(spt.coord.z);
1762 viewer.getSequencePoint().add(point);
1766 * (end points of) axes on display
1768 for (Point p : panel.getRotatableCanvas().getAxisEndPoints())
1771 Axis axis = new Axis();
1775 viewer.getAxis().add(axis);
1779 * raw PCA data (note we are not restoring PCA inputs here -
1780 * alignment view, score model, similarity parameters)
1782 PcaDataType data = new PcaDataType();
1783 viewer.setPcaData(data);
1784 PCA pca = pcaModel.getPcaData();
1786 DoubleMatrix pm = new DoubleMatrix();
1787 saveDoubleMatrix(pca.getPairwiseScores(), pm);
1788 data.setPairwiseMatrix(pm);
1790 DoubleMatrix tm = new DoubleMatrix();
1791 saveDoubleMatrix(pca.getTridiagonal(), tm);
1792 data.setTridiagonalMatrix(tm);
1794 DoubleMatrix eigenMatrix = new DoubleMatrix();
1795 data.setEigenMatrix(eigenMatrix);
1796 saveDoubleMatrix(pca.getEigenmatrix(), eigenMatrix);
1798 object.getPcaViewer().add(viewer);
1799 } catch (Throwable t)
1801 Cache.log.error("Error saving PCA: " + t.getMessage());
1806 * Stores values from a matrix into an XML element, including (if present) the
1811 * @see #loadDoubleMatrix(DoubleMatrix)
1813 protected void saveDoubleMatrix(MatrixI m, DoubleMatrix xmlMatrix)
1815 xmlMatrix.setRows(m.height());
1816 xmlMatrix.setColumns(m.width());
1817 for (int i = 0; i < m.height(); i++)
1819 DoubleVector row = new DoubleVector();
1820 for (int j = 0; j < m.width(); j++)
1822 row.getV().add(m.getValue(i, j));
1824 xmlMatrix.getRow().add(row);
1826 if (m.getD() != null)
1828 DoubleVector dVector = new DoubleVector();
1829 for (double d : m.getD())
1831 dVector.getV().add(d);
1833 xmlMatrix.setD(dVector);
1835 if (m.getE() != null)
1837 DoubleVector eVector = new DoubleVector();
1838 for (double e : m.getE())
1840 eVector.getV().add(e);
1842 xmlMatrix.setE(eVector);
1847 * Loads XML matrix data into a new Matrix object, including the D and/or E
1848 * vectors (if present)
1852 * @see Jalview2XML#saveDoubleMatrix(MatrixI, DoubleMatrix)
1854 protected MatrixI loadDoubleMatrix(DoubleMatrix mData)
1856 int rows = mData.getRows();
1857 double[][] vals = new double[rows][];
1859 for (int i = 0; i < rows; i++)
1861 List<Double> dVector = mData.getRow().get(i).getV();
1862 vals[i] = new double[dVector.size()];
1864 for (Double d : dVector)
1870 MatrixI m = new Matrix(vals);
1872 if (mData.getD() != null)
1874 List<Double> dVector = mData.getD().getV();
1875 double[] vec = new double[dVector.size()];
1877 for (Double d : dVector)
1883 if (mData.getE() != null)
1885 List<Double> dVector = mData.getE().getV();
1886 double[] vec = new double[dVector.size()];
1888 for (Double d : dVector)
1899 * Save any Varna viewers linked to this sequence. Writes an rnaViewer element
1900 * for each viewer, with
1902 * <li>viewer geometry (position, size, split pane divider location)</li>
1903 * <li>index of the selected structure in the viewer (currently shows gapped
1905 * <li>the id of the annotation holding RNA secondary structure</li>
1906 * <li>(currently only one SS is shown per viewer, may be more in future)</li>
1908 * Varna viewer state is also written out (in native Varna XML) to separate
1909 * project jar entries. A separate entry is written for each RNA structure
1910 * displayed, with the naming convention
1912 * <li>rna_viewId_sequenceId_annotationId_[gapped|trimmed]</li>
1920 * @param storeDataset
1922 protected void saveRnaViewers(JarOutputStream jout, JSeq jseq,
1923 final SequenceI jds, List<String> viewIds, AlignmentPanel ap,
1924 boolean storeDataset)
1926 if (Desktop.desktop == null)
1930 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1931 for (int f = frames.length - 1; f > -1; f--)
1933 if (frames[f] instanceof AppVarna)
1935 AppVarna varna = (AppVarna) frames[f];
1937 * link the sequence to every viewer that is showing it and is linked to
1938 * its alignment panel
1940 if (varna.isListeningFor(jds) && ap == varna.getAlignmentPanel())
1942 String viewId = varna.getViewId();
1943 RnaViewer rna = new RnaViewer();
1944 rna.setViewId(viewId);
1945 rna.setTitle(varna.getTitle());
1946 rna.setXpos(varna.getX());
1947 rna.setYpos(varna.getY());
1948 rna.setWidth(varna.getWidth());
1949 rna.setHeight(varna.getHeight());
1950 rna.setDividerLocation(varna.getDividerLocation());
1951 rna.setSelectedRna(varna.getSelectedIndex());
1952 // jseq.addRnaViewer(rna);
1953 jseq.getRnaViewer().add(rna);
1956 * Store each Varna panel's state once in the project per sequence.
1957 * First time through only (storeDataset==false)
1959 // boolean storeSessions = false;
1960 // String sequenceViewId = viewId + seqsToIds.get(jds);
1961 // if (!storeDataset && !viewIds.contains(sequenceViewId))
1963 // viewIds.add(sequenceViewId);
1964 // storeSessions = true;
1966 for (RnaModel model : varna.getModels())
1968 if (model.seq == jds)
1971 * VARNA saves each view (sequence or alignment secondary
1972 * structure, gapped or trimmed) as a separate XML file
1974 String jarEntryName = rnaSessions.get(model);
1975 if (jarEntryName == null)
1978 String varnaStateFile = varna.getStateInfo(model.rna);
1979 jarEntryName = RNA_PREFIX + viewId + "_" + nextCounter();
1980 copyFileToJar(jout, varnaStateFile, jarEntryName);
1981 rnaSessions.put(model, jarEntryName);
1983 SecondaryStructure ss = new SecondaryStructure();
1984 String annotationId = varna.getAnnotation(jds).annotationId;
1985 ss.setAnnotationId(annotationId);
1986 ss.setViewerState(jarEntryName);
1987 ss.setGapped(model.gapped);
1988 ss.setTitle(model.title);
1989 // rna.addSecondaryStructure(ss);
1990 rna.getSecondaryStructure().add(ss);
1999 * Copy the contents of a file to a new entry added to the output jar
2003 * @param jarEntryName
2005 protected void copyFileToJar(JarOutputStream jout, String infilePath,
2006 String jarEntryName)
2008 DataInputStream dis = null;
2011 File file = new File(infilePath);
2012 if (file.exists() && jout != null)
2014 dis = new DataInputStream(new FileInputStream(file));
2015 byte[] data = new byte[(int) file.length()];
2016 dis.readFully(data);
2017 writeJarEntry(jout, jarEntryName, data);
2019 } catch (Exception ex)
2021 ex.printStackTrace();
2029 } catch (IOException e)
2038 * Write the data to a new entry of given name in the output jar file
2041 * @param jarEntryName
2043 * @throws IOException
2045 protected void writeJarEntry(JarOutputStream jout, String jarEntryName,
2046 byte[] data) throws IOException
2050 jarEntryName = jarEntryName.replace('\\','/');
2051 System.out.println("Writing jar entry " + jarEntryName);
2052 jout.putNextEntry(new JarEntry(jarEntryName));
2053 DataOutputStream dout = new DataOutputStream(jout);
2054 dout.write(data, 0, data.length);
2061 * Save the state of a structure viewer
2066 * the archive XML element under which to save the state
2069 * @param matchedFile
2073 protected String saveStructureState(AlignmentPanel ap, SequenceI jds,
2074 Pdbids pdb, PDBEntry entry, List<String> viewIds,
2075 String matchedFile, StructureViewerBase viewFrame)
2077 final AAStructureBindingModel bindingModel = viewFrame.getBinding();
2080 * Look for any bindings for this viewer to the PDB file of interest
2081 * (including part matches excluding chain id)
2083 for (int peid = 0; peid < bindingModel.getPdbCount(); peid++)
2085 final PDBEntry pdbentry = bindingModel.getPdbEntry(peid);
2086 final String pdbId = pdbentry.getId();
2087 if (!pdbId.equals(entry.getId())
2088 && !(entry.getId().length() > 4 && entry.getId().toLowerCase()
2089 .startsWith(pdbId.toLowerCase())))
2092 * not interested in a binding to a different PDB entry here
2096 if (matchedFile == null)
2098 matchedFile = pdbentry.getFile();
2100 else if (!matchedFile.equals(pdbentry.getFile()))
2103 "Probably lost some PDB-Sequence mappings for this structure file (which apparently has same PDB Entry code): "
2104 + pdbentry.getFile());
2108 // can get at it if the ID
2109 // match is ambiguous (e.g.
2112 for (int smap = 0; smap < viewFrame.getBinding()
2113 .getSequence()[peid].length; smap++)
2115 // if (jal.findIndex(jmol.jmb.sequence[peid][smap]) > -1)
2116 if (jds == viewFrame.getBinding().getSequence()[peid][smap])
2118 StructureState state = new StructureState();
2119 state.setVisible(true);
2120 state.setXpos(viewFrame.getX());
2121 state.setYpos(viewFrame.getY());
2122 state.setWidth(viewFrame.getWidth());
2123 state.setHeight(viewFrame.getHeight());
2124 final String viewId = viewFrame.getViewId();
2125 state.setViewId(viewId);
2126 state.setAlignwithAlignPanel(viewFrame.isUsedforaligment(ap));
2127 state.setColourwithAlignPanel(viewFrame.isUsedforcolourby(ap));
2128 state.setColourByJmol(viewFrame.isColouredByViewer());
2129 state.setType(viewFrame.getViewerType().toString());
2130 // pdb.addStructureState(state);
2131 pdb.getStructureState().add(state);
2139 * Populates the AnnotationColourScheme xml for save. This captures the
2140 * settings of the options in the 'Colour by Annotation' dialog.
2143 * @param userColours
2147 private AnnotationColourScheme constructAnnotationColours(
2148 AnnotationColourGradient acg, List<UserColourScheme> userColours,
2151 AnnotationColourScheme ac = new AnnotationColourScheme();
2152 ac.setAboveThreshold(acg.getAboveThreshold());
2153 ac.setThreshold(acg.getAnnotationThreshold());
2154 // 2.10.2 save annotationId (unique) not annotation label
2155 ac.setAnnotation(acg.getAnnotation().annotationId);
2156 if (acg.getBaseColour() instanceof UserColourScheme)
2159 setUserColourScheme(acg.getBaseColour(), userColours, jm));
2164 ColourSchemeProperty.getColourName(acg.getBaseColour()));
2167 ac.setMaxColour(acg.getMaxColour().getRGB());
2168 ac.setMinColour(acg.getMinColour().getRGB());
2169 ac.setPerSequence(acg.isSeqAssociated());
2170 ac.setPredefinedColours(acg.isPredefinedColours());
2174 private void storeAlignmentAnnotation(AlignmentAnnotation[] aa,
2175 IdentityHashMap<SequenceGroup, String> groupRefs,
2176 AlignmentViewport av, Set<String> calcIdSet, boolean storeDS,
2177 SequenceSet vamsasSet)
2180 for (int i = 0; i < aa.length; i++)
2182 Annotation an = new Annotation();
2184 AlignmentAnnotation annotation = aa[i];
2185 if (annotation.annotationId != null)
2187 annotationIds.put(annotation.annotationId, annotation);
2190 an.setId(annotation.annotationId);
2192 an.setVisible(annotation.visible);
2194 an.setDescription(annotation.description);
2196 if (annotation.sequenceRef != null)
2198 // 2.9 JAL-1781 xref on sequence id rather than name
2199 an.setSequenceRef(seqsToIds.get(annotation.sequenceRef));
2201 if (annotation.groupRef != null)
2203 String groupIdr = groupRefs.get(annotation.groupRef);
2204 if (groupIdr == null)
2206 // make a locally unique String
2207 groupRefs.put(annotation.groupRef,
2208 groupIdr = ("" + System.currentTimeMillis()
2209 + annotation.groupRef.getName()
2210 + groupRefs.size()));
2212 an.setGroupRef(groupIdr.toString());
2215 // store all visualization attributes for annotation
2216 an.setGraphHeight(annotation.graphHeight);
2217 an.setCentreColLabels(annotation.centreColLabels);
2218 an.setScaleColLabels(annotation.scaleColLabel);
2219 an.setShowAllColLabels(annotation.showAllColLabels);
2220 an.setBelowAlignment(annotation.belowAlignment);
2222 if (annotation.graph > 0)
2225 an.setGraphType(annotation.graph);
2226 an.setGraphGroup(annotation.graphGroup);
2227 if (annotation.getThreshold() != null)
2229 ThresholdLine line = new ThresholdLine();
2230 line.setLabel(annotation.getThreshold().label);
2231 line.setValue(annotation.getThreshold().value);
2232 line.setColour(annotation.getThreshold().colour.getRGB());
2233 an.setThresholdLine(line);
2241 an.setLabel(annotation.label);
2243 if (annotation == av.getAlignmentQualityAnnot()
2244 || annotation == av.getAlignmentConservationAnnotation()
2245 || annotation == av.getAlignmentConsensusAnnotation()
2246 || annotation.autoCalculated)
2248 // new way of indicating autocalculated annotation -
2249 an.setAutoCalculated(annotation.autoCalculated);
2251 if (annotation.hasScore())
2253 an.setScore(annotation.getScore());
2256 if (annotation.getCalcId() != null)
2258 calcIdSet.add(annotation.getCalcId());
2259 an.setCalcId(annotation.getCalcId());
2261 if (annotation.hasProperties())
2263 for (String pr : annotation.getProperties())
2265 jalview.xml.binding.jalview.Annotation.Property prop = new jalview.xml.binding.jalview.Annotation.Property();
2267 prop.setValue(annotation.getProperty(pr));
2268 // an.addProperty(prop);
2269 an.getProperty().add(prop);
2273 AnnotationElement ae;
2274 if (annotation.annotations != null)
2276 an.setScoreOnly(false);
2277 for (int a = 0; a < annotation.annotations.length; a++)
2279 if ((annotation == null) || (annotation.annotations[a] == null))
2284 ae = new AnnotationElement();
2285 if (annotation.annotations[a].description != null)
2287 ae.setDescription(annotation.annotations[a].description);
2289 if (annotation.annotations[a].displayCharacter != null)
2291 ae.setDisplayCharacter(
2292 annotation.annotations[a].displayCharacter);
2295 if (!Float.isNaN(annotation.annotations[a].value))
2297 ae.setValue(annotation.annotations[a].value);
2301 if (annotation.annotations[a].secondaryStructure > ' ')
2303 ae.setSecondaryStructure(
2304 annotation.annotations[a].secondaryStructure + "");
2307 if (annotation.annotations[a].colour != null
2308 && annotation.annotations[a].colour != java.awt.Color.black)
2310 ae.setColour(annotation.annotations[a].colour.getRGB());
2313 // an.addAnnotationElement(ae);
2314 an.getAnnotationElement().add(ae);
2315 if (annotation.autoCalculated)
2317 // only write one non-null entry into the annotation row -
2318 // sufficient to get the visualization attributes necessary to
2326 an.setScoreOnly(true);
2328 if (!storeDS || (storeDS && !annotation.autoCalculated))
2330 // skip autocalculated annotation - these are only provided for
2332 // vamsasSet.addAnnotation(an);
2333 vamsasSet.getAnnotation().add(an);
2339 private CalcIdParam createCalcIdParam(String calcId, AlignViewport av)
2341 AutoCalcSetting settings = av.getCalcIdSettingsFor(calcId);
2342 if (settings != null)
2344 CalcIdParam vCalcIdParam = new CalcIdParam();
2345 vCalcIdParam.setCalcId(calcId);
2346 // vCalcIdParam.addServiceURL(settings.getServiceURI());
2347 vCalcIdParam.getServiceURL().add(settings.getServiceURI());
2348 // generic URI allowing a third party to resolve another instance of the
2349 // service used for this calculation
2350 for (String url : settings.getServiceURLs())
2352 // vCalcIdParam.addServiceURL(urls);
2353 vCalcIdParam.getServiceURL().add(url);
2355 vCalcIdParam.setVersion("1.0");
2356 if (settings.getPreset() != null)
2358 WsParamSetI setting = settings.getPreset();
2359 vCalcIdParam.setName(setting.getName());
2360 vCalcIdParam.setDescription(setting.getDescription());
2364 vCalcIdParam.setName("");
2365 vCalcIdParam.setDescription("Last used parameters");
2367 // need to be able to recover 1) settings 2) user-defined presets or
2368 // recreate settings from preset 3) predefined settings provided by
2369 // service - or settings that can be transferred (or discarded)
2370 vCalcIdParam.setParameters(
2371 settings.getWsParamFile().replace("\n", "|\\n|"));
2372 vCalcIdParam.setAutoUpdate(settings.isAutoUpdate());
2373 // todo - decide if updateImmediately is needed for any projects.
2375 return vCalcIdParam;
2380 private boolean recoverCalcIdParam(CalcIdParam calcIdParam,
2383 if (calcIdParam.getVersion().equals("1.0"))
2385 final String[] calcIds = calcIdParam.getServiceURL().toArray(new String[0]);
2386 Jws2Instance service = Jws2Discoverer.getDiscoverer()
2387 .getPreferredServiceFor(calcIds);
2388 if (service != null)
2390 WsParamSetI parmSet = null;
2393 parmSet = service.getParamStore().parseServiceParameterFile(
2394 calcIdParam.getName(), calcIdParam.getDescription(),
2396 calcIdParam.getParameters().replace("|\\n|", "\n"));
2397 } catch (IOException x)
2399 warn("Couldn't parse parameter data for "
2400 + calcIdParam.getCalcId(), x);
2403 List<ArgumentI> argList = null;
2404 if (calcIdParam.getName().length() > 0)
2406 parmSet = service.getParamStore()
2407 .getPreset(calcIdParam.getName());
2408 if (parmSet != null)
2410 // TODO : check we have a good match with settings in AACon -
2411 // otherwise we'll need to create a new preset
2416 argList = parmSet.getArguments();
2419 AAConSettings settings = new AAConSettings(
2420 calcIdParam.isAutoUpdate(), service, parmSet, argList);
2421 av.setCalcIdSettingsFor(calcIdParam.getCalcId(), settings,
2422 calcIdParam.isNeedsUpdate());
2427 warn("Cannot resolve a service for the parameters used in this project. Try configuring a JABAWS server.");
2431 throw new Error(MessageManager.formatMessage(
2432 "error.unsupported_version_calcIdparam", new Object[]
2433 { calcIdParam.toString() }));
2437 * External mapping between jalview objects and objects yielding a valid and
2438 * unique object ID string. This is null for normal Jalview project IO, but
2439 * non-null when a jalview project is being read or written as part of a
2442 IdentityHashMap jv2vobj = null;
2445 * Construct a unique ID for jvobj using either existing bindings or if none
2446 * exist, the result of the hashcode call for the object.
2449 * jalview data object
2450 * @return unique ID for referring to jvobj
2452 private String makeHashCode(Object jvobj, String altCode)
2454 if (jv2vobj != null)
2456 Object id = jv2vobj.get(jvobj);
2459 return id.toString();
2461 // check string ID mappings
2462 if (jvids2vobj != null && jvobj instanceof String)
2464 id = jvids2vobj.get(jvobj);
2468 return id.toString();
2470 // give up and warn that something has gone wrong
2471 warn("Cannot find ID for object in external mapping : " + jvobj);
2477 * return local jalview object mapped to ID, if it exists
2481 * @return null or object bound to idcode
2483 private Object retrieveExistingObj(String idcode)
2485 if (idcode != null && vobj2jv != null)
2487 return vobj2jv.get(idcode);
2493 * binding from ID strings from external mapping table to jalview data model
2496 private Hashtable vobj2jv;
2498 private Sequence createVamsasSequence(String id, SequenceI jds)
2500 return createVamsasSequence(true, id, jds, null);
2503 private Sequence createVamsasSequence(boolean recurse, String id,
2504 SequenceI jds, SequenceI parentseq)
2506 Sequence vamsasSeq = new Sequence();
2507 vamsasSeq.setId(id);
2508 vamsasSeq.setName(jds.getName());
2509 vamsasSeq.setSequence(jds.getSequenceAsString());
2510 vamsasSeq.setDescription(jds.getDescription());
2511 List<DBRefEntry> dbrefs = null;
2512 if (jds.getDatasetSequence() != null)
2514 vamsasSeq.setDsseqid(seqHash(jds.getDatasetSequence()));
2518 // seqId==dsseqid so we can tell which sequences really are
2519 // dataset sequences only
2520 vamsasSeq.setDsseqid(id);
2521 dbrefs = jds.getDBRefs();
2522 if (parentseq == null)
2529 * save any dbrefs; special subclass GeneLocus is flagged as 'locus'
2533 for (int d = 0, nd = dbrefs.size(); d < nd; d++)
2535 DBRef dbref = new DBRef();
2536 DBRefEntry ref = dbrefs.get(d);
2537 dbref.setSource(ref.getSource());
2538 dbref.setVersion(ref.getVersion());
2539 dbref.setAccessionId(ref.getAccessionId());
2540 if (ref instanceof GeneLocus)
2542 dbref.setLocus(true);
2546 Mapping mp = createVamsasMapping(ref.getMap(), parentseq,
2548 dbref.setMapping(mp);
2550 vamsasSeq.getDBRef().add(dbref);
2556 private Mapping createVamsasMapping(jalview.datamodel.Mapping jmp,
2557 SequenceI parentseq, SequenceI jds, boolean recurse)
2560 if (jmp.getMap() != null)
2564 jalview.util.MapList mlst = jmp.getMap();
2565 List<int[]> r = mlst.getFromRanges();
2566 for (int[] range : r)
2568 MapListFrom mfrom = new MapListFrom();
2569 mfrom.setStart(range[0]);
2570 mfrom.setEnd(range[1]);
2571 // mp.addMapListFrom(mfrom);
2572 mp.getMapListFrom().add(mfrom);
2574 r = mlst.getToRanges();
2575 for (int[] range : r)
2577 MapListTo mto = new MapListTo();
2578 mto.setStart(range[0]);
2579 mto.setEnd(range[1]);
2580 // mp.addMapListTo(mto);
2581 mp.getMapListTo().add(mto);
2583 mp.setMapFromUnit(BigInteger.valueOf(mlst.getFromRatio()));
2584 mp.setMapToUnit(BigInteger.valueOf(mlst.getToRatio()));
2585 if (jmp.getTo() != null)
2587 // MappingChoice mpc = new MappingChoice();
2589 // check/create ID for the sequence referenced by getTo()
2592 SequenceI ps = null;
2593 if (parentseq != jmp.getTo()
2594 && parentseq.getDatasetSequence() != jmp.getTo())
2596 // chaining dbref rather than a handshaking one
2597 jmpid = seqHash(ps = jmp.getTo());
2601 jmpid = seqHash(ps = parentseq);
2603 // mpc.setDseqFor(jmpid);
2604 mp.setDseqFor(jmpid);
2605 if (!seqRefIds.containsKey(jmpid))
2607 jalview.bin.Cache.log.debug("creatign new DseqFor ID");
2608 seqRefIds.put(jmpid, ps);
2612 jalview.bin.Cache.log.debug("reusing DseqFor ID");
2615 // mp.setMappingChoice(mpc);
2621 String setUserColourScheme(jalview.schemes.ColourSchemeI cs,
2622 List<UserColourScheme> userColours, JalviewModel jm)
2625 jalview.schemes.UserColourScheme ucs = (jalview.schemes.UserColourScheme) cs;
2626 boolean newucs = false;
2627 if (!userColours.contains(ucs))
2629 userColours.add(ucs);
2632 id = "ucs" + userColours.indexOf(ucs);
2635 // actually create the scheme's entry in the XML model
2636 java.awt.Color[] colours = ucs.getColours();
2637 UserColours uc = new UserColours();
2638 // UserColourScheme jbucs = new UserColourScheme();
2639 JalviewUserColours jbucs = new JalviewUserColours();
2641 for (int i = 0; i < colours.length; i++)
2643 Colour col = new Colour();
2644 col.setName(ResidueProperties.aa[i]);
2645 col.setRGB(jalview.util.Format.getHexString(colours[i]));
2646 // jbucs.addColour(col);
2647 jbucs.getColour().add(col);
2649 if (ucs.getLowerCaseColours() != null)
2651 colours = ucs.getLowerCaseColours();
2652 for (int i = 0; i < colours.length; i++)
2654 Colour col = new Colour();
2655 col.setName(ResidueProperties.aa[i].toLowerCase());
2656 col.setRGB(jalview.util.Format.getHexString(colours[i]));
2657 // jbucs.addColour(col);
2658 jbucs.getColour().add(col);
2663 uc.setUserColourScheme(jbucs);
2664 // jm.addUserColours(uc);
2665 jm.getUserColours().add(uc);
2671 jalview.schemes.UserColourScheme getUserColourScheme(
2672 JalviewModel jm, String id)
2674 List<UserColours> uc = jm.getUserColours();
2675 UserColours colours = null;
2677 for (int i = 0; i < uc.length; i++)
2679 if (uc[i].getId().equals(id))
2686 for (UserColours c : uc)
2688 if (c.getId().equals(id))
2695 java.awt.Color[] newColours = new java.awt.Color[24];
2697 for (int i = 0; i < 24; i++)
2699 newColours[i] = new java.awt.Color(Integer.parseInt(
2700 // colours.getUserColourScheme().getColour(i).getRGB(), 16));
2701 colours.getUserColourScheme().getColour().get(i).getRGB(),
2705 jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(
2708 if (colours.getUserColourScheme().getColour().size()/*Count()*/ > 24)
2710 newColours = new java.awt.Color[23];
2711 for (int i = 0; i < 23; i++)
2713 newColours[i] = new java.awt.Color(Integer.parseInt(
2714 colours.getUserColourScheme().getColour().get(i + 24)
2718 ucs.setLowerCaseColours(newColours);
2725 * contains last error message (if any) encountered by XML loader.
2727 String errorMessage = null;
2730 * flag to control whether the Jalview2XML_V1 parser should be deferred to if
2731 * exceptions are raised during project XML parsing
2733 public boolean attemptversion1parse = false;
2736 * Load a jalview project archive from a jar file
2739 * - HTTP URL or filename
2741 public AlignFrame loadJalviewAlign(final Object file)
2744 jalview.gui.AlignFrame af = null;
2748 // create list to store references for any new Jmol viewers created
2749 newStructureViewers = new Vector<>();
2750 // UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
2751 // Workaround is to make sure caller implements the JarInputStreamProvider
2753 // so we can re-open the jar input stream for each entry.
2755 jarInputStreamProvider jprovider = createjarInputStreamProvider(file);
2756 af = loadJalviewAlign(jprovider);
2759 af.setMenusForViewport();
2761 } catch (MalformedURLException e)
2763 errorMessage = "Invalid URL format for '" + file + "'";
2769 SwingUtilities.invokeAndWait(new Runnable()
2774 setLoadingFinishedForNewStructureViewers();
2777 } catch (Exception x)
2779 System.err.println("Error loading alignment: " + x.getMessage());
2785 @SuppressWarnings("unused")
2786 private jarInputStreamProvider createjarInputStreamProvider(final Object ofile) throws MalformedURLException {
2788 // BH 2018 allow for bytes already attached to File object
2790 String file = (ofile instanceof File ? ((File) ofile).getCanonicalPath() : ofile.toString());
2791 byte[] bytes = Platform.isJS() ? Platform.getFileBytes((File) ofile)
2794 errorMessage = null;
2795 uniqueSetSuffix = null;
2797 viewportsAdded.clear();
2798 frefedSequence = null;
2800 if (file.startsWith("http://")) {
2801 url = new URL(file);
2803 final URL _url = url;
2804 return new jarInputStreamProvider() {
2807 public JarInputStream getJarInputStream() throws IOException {
2808 if (bytes != null) {
2809 // System.out.println("Jalview2XML: opening byte jarInputStream for bytes.length=" + bytes.length);
2810 return new JarInputStream(new ByteArrayInputStream(bytes));
2813 // System.out.println("Jalview2XML: opening url jarInputStream for " + _url);
2814 return new JarInputStream(_url.openStream());
2816 // System.out.println("Jalview2XML: opening file jarInputStream for " + file);
2817 return new JarInputStream(new FileInputStream(file));
2822 public String getFilename() {
2826 } catch (IOException e) {
2827 e.printStackTrace();
2833 * Recover jalview session from a jalview project archive. Caller may
2834 * initialise uniqueSetSuffix, seqRefIds, viewportsAdded and frefedSequence
2835 * themselves. Any null fields will be initialised with default values,
2836 * non-null fields are left alone.
2841 public AlignFrame loadJalviewAlign(final jarInputStreamProvider jprovider)
2843 errorMessage = null;
2844 if (uniqueSetSuffix == null)
2846 uniqueSetSuffix = System.currentTimeMillis() % 100000 + "";
2848 if (seqRefIds == null)
2852 AlignFrame af = null, _af = null;
2853 IdentityHashMap<AlignmentI, AlignmentI> importedDatasets = new IdentityHashMap<>();
2854 Map<String, AlignFrame> gatherToThisFrame = new HashMap<>();
2855 final String file = jprovider.getFilename();
2858 JarInputStream jin = null;
2859 JarEntry jarentry = null;
2864 jin = jprovider.getJarInputStream();
2865 for (int i = 0; i < entryCount; i++)
2867 jarentry = jin.getNextJarEntry();
2870 if (jarentry != null && jarentry.getName().endsWith(".xml"))
2872 JAXBContext jc = JAXBContext
2873 .newInstance("jalview.xml.binding.jalview");
2874 XMLStreamReader streamReader = XMLInputFactory.newInstance()
2875 .createXMLStreamReader(jin);
2876 javax.xml.bind.Unmarshaller um = jc.createUnmarshaller();
2877 JAXBElement<JalviewModel> jbe = um
2878 .unmarshal(streamReader, JalviewModel.class);
2879 JalviewModel object = jbe.getValue();
2881 if (true) // !skipViewport(object))
2883 _af = loadFromObject(object, file, true, jprovider);
2884 if (_af != null && object.getViewport().size() > 0)
2885 // getJalviewModelSequence().getViewportCount() > 0)
2889 // store a reference to the first view
2892 if (_af.getViewport().isGatherViewsHere())
2894 // if this is a gathered view, keep its reference since
2895 // after gathering views, only this frame will remain
2897 gatherToThisFrame.put(_af.getViewport().getSequenceSetId(),
2900 // Save dataset to register mappings once all resolved
2901 importedDatasets.put(
2902 af.getViewport().getAlignment().getDataset(),
2903 af.getViewport().getAlignment().getDataset());
2908 else if (jarentry != null)
2910 // Some other file here.
2913 } while (jarentry != null);
2914 resolveFrefedSequences();
2915 } catch (IOException ex)
2917 ex.printStackTrace();
2918 errorMessage = "Couldn't locate Jalview XML file : " + file;
2920 "Exception whilst loading jalview XML file : " + ex + "\n");
2921 } catch (Exception ex)
2923 System.err.println("Parsing as Jalview Version 2 file failed.");
2924 ex.printStackTrace(System.err);
2925 if (attemptversion1parse)
2927 // used to attempt to parse as V1 castor-generated xml
2929 if (Desktop.instance != null)
2931 Desktop.instance.stopLoading();
2935 System.out.println("Successfully loaded archive file");
2938 ex.printStackTrace();
2941 "Exception whilst loading jalview XML file : " + ex + "\n");
2942 } catch (OutOfMemoryError e)
2944 // Don't use the OOM Window here
2945 errorMessage = "Out of memory loading jalview XML file";
2946 System.err.println("Out of memory whilst loading jalview XML file");
2947 e.printStackTrace();
2951 * Regather multiple views (with the same sequence set id) to the frame (if
2952 * any) that is flagged as the one to gather to, i.e. convert them to tabbed
2953 * views instead of separate frames. Note this doesn't restore a state where
2954 * some expanded views in turn have tabbed views - the last "first tab" read
2955 * in will play the role of gatherer for all.
2957 for (AlignFrame fr : gatherToThisFrame.values())
2959 Desktop.instance.gatherViews(fr);
2962 restoreSplitFrames();
2963 for (AlignmentI ds : importedDatasets.keySet())
2965 if (ds.getCodonFrames() != null)
2967 StructureSelectionManager
2968 .getStructureSelectionManager(Desktop.instance)
2969 .registerMappings(ds.getCodonFrames());
2972 if (errorMessage != null)
2977 if (Desktop.instance != null)
2979 Desktop.instance.stopLoading();
2986 * Try to reconstruct and display SplitFrame windows, where each contains
2987 * complementary dna and protein alignments. Done by pairing up AlignFrame
2988 * objects (created earlier) which have complementary viewport ids associated.
2990 protected void restoreSplitFrames()
2992 List<SplitFrame> gatherTo = new ArrayList<>();
2993 List<AlignFrame> addedToSplitFrames = new ArrayList<>();
2994 Map<String, AlignFrame> dna = new HashMap<>();
2997 * Identify the DNA alignments
2999 for (Entry<Viewport, AlignFrame> candidate : splitFrameCandidates
3002 AlignFrame af = candidate.getValue();
3003 if (af.getViewport().getAlignment().isNucleotide())
3005 dna.put(candidate.getKey().getId(), af);
3010 * Try to match up the protein complements
3012 for (Entry<Viewport, AlignFrame> candidate : splitFrameCandidates
3015 AlignFrame af = candidate.getValue();
3016 if (!af.getViewport().getAlignment().isNucleotide())
3018 String complementId = candidate.getKey().getComplementId();
3019 // only non-null complements should be in the Map
3020 if (complementId != null && dna.containsKey(complementId))
3022 final AlignFrame dnaFrame = dna.get(complementId);
3023 SplitFrame sf = createSplitFrame(dnaFrame, af);
3024 addedToSplitFrames.add(dnaFrame);
3025 addedToSplitFrames.add(af);
3026 dnaFrame.setMenusForViewport();
3027 af.setMenusForViewport();
3028 if (af.getViewport().isGatherViewsHere())
3037 * Open any that we failed to pair up (which shouldn't happen!) as
3038 * standalone AlignFrame's.
3040 for (Entry<Viewport, AlignFrame> candidate : splitFrameCandidates
3043 AlignFrame af = candidate.getValue();
3044 if (!addedToSplitFrames.contains(af))
3046 Viewport view = candidate.getKey();
3047 Desktop.addInternalFrame(af, view.getTitle(),
3048 safeInt(view.getWidth()), safeInt(view.getHeight()));
3049 af.setMenusForViewport();
3050 System.err.println("Failed to restore view " + view.getTitle()
3051 + " to split frame");
3056 * Gather back into tabbed views as flagged.
3058 for (SplitFrame sf : gatherTo)
3060 Desktop.instance.gatherViews(sf);
3063 splitFrameCandidates.clear();
3067 * Construct and display one SplitFrame holding DNA and protein alignments.
3070 * @param proteinFrame
3073 protected SplitFrame createSplitFrame(AlignFrame dnaFrame,
3074 AlignFrame proteinFrame)
3076 SplitFrame splitFrame = new SplitFrame(dnaFrame, proteinFrame);
3077 String title = MessageManager.getString("label.linked_view_title");
3078 int width = (int) dnaFrame.getBounds().getWidth();
3079 int height = (int) (dnaFrame.getBounds().getHeight()
3080 + proteinFrame.getBounds().getHeight() + 50);
3083 * SplitFrame location is saved to both enclosed frames
3085 splitFrame.setLocation(dnaFrame.getX(), dnaFrame.getY());
3086 Desktop.addInternalFrame(splitFrame, title, width, height);
3089 * And compute cDNA consensus (couldn't do earlier with consensus as
3090 * mappings were not yet present)
3092 proteinFrame.getViewport().alignmentChanged(proteinFrame.alignPanel);
3098 * check errorMessage for a valid error message and raise an error box in the
3099 * GUI or write the current errorMessage to stderr and then clear the error
3102 protected void reportErrors()
3104 reportErrors(false);
3107 protected void reportErrors(final boolean saving)
3109 if (errorMessage != null)
3111 final String finalErrorMessage = errorMessage;
3114 javax.swing.SwingUtilities.invokeLater(new Runnable()
3119 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
3121 "Error " + (saving ? "saving" : "loading")
3123 JvOptionPane.WARNING_MESSAGE);
3129 System.err.println("Problem loading Jalview file: " + errorMessage);
3132 errorMessage = null;
3135 Map<String, String> alreadyLoadedPDB = new HashMap<>();
3138 * when set, local views will be updated from view stored in JalviewXML
3139 * Currently (28th Sep 2008) things will go horribly wrong in vamsas document
3140 * sync if this is set to true.
3142 private final boolean updateLocalViews = false;
3145 * Returns the path to a temporary file holding the PDB file for the given PDB
3146 * id. The first time of asking, searches for a file of that name in the
3147 * Jalview project jar, and copies it to a new temporary file. Any repeat
3148 * requests just return the path to the file previously created.
3154 String loadPDBFile(jarInputStreamProvider jprovider, String pdbId,
3157 if (alreadyLoadedPDB.containsKey(pdbId))
3159 return alreadyLoadedPDB.get(pdbId).toString();
3162 String tempFile = copyJarEntry(jprovider, pdbId, "jalview_pdb",
3164 if (tempFile != null)
3166 alreadyLoadedPDB.put(pdbId, tempFile);
3172 * Copies the jar entry of given name to a new temporary file and returns the
3173 * path to the file, or null if the entry is not found.
3176 * @param jarEntryName
3178 * a prefix for the temporary file name, must be at least three
3180 * @param suffixModel
3181 * null or original file - so new file can be given the same suffix
3185 protected String copyJarEntry(jarInputStreamProvider jprovider,
3186 String jarEntryName, String prefix, String suffixModel)
3188 BufferedReader in = null;
3189 PrintWriter out = null;
3190 String suffix = ".tmp";
3191 if (suffixModel == null)
3193 suffixModel = jarEntryName;
3195 int sfpos = suffixModel.lastIndexOf(".");
3196 if (sfpos > -1 && sfpos < (suffixModel.length() - 1))
3198 suffix = "." + suffixModel.substring(sfpos + 1);
3202 JarInputStream jin = jprovider.getJarInputStream();
3204 * if (jprovider.startsWith("http://")) { jin = new JarInputStream(new
3205 * URL(jprovider).openStream()); } else { jin = new JarInputStream(new
3206 * FileInputStream(jprovider)); }
3209 JarEntry entry = null;
3212 entry = jin.getNextJarEntry();
3213 } while (entry != null && !entry.getName().equals(jarEntryName));
3216 in = new BufferedReader(new InputStreamReader(jin, UTF_8));
3217 File outFile = File.createTempFile(prefix, suffix);
3218 outFile.deleteOnExit();
3219 out = new PrintWriter(new FileOutputStream(outFile));
3222 while ((data = in.readLine()) != null)
3227 String t = outFile.getAbsolutePath();
3232 warn("Couldn't find entry in Jalview Jar for " + jarEntryName);
3234 } catch (Exception ex)
3236 ex.printStackTrace();
3244 } catch (IOException e)
3258 private class JvAnnotRow
3260 public JvAnnotRow(int i, AlignmentAnnotation jaa)
3267 * persisted version of annotation row from which to take vis properties
3269 public jalview.datamodel.AlignmentAnnotation template;
3272 * original position of the annotation row in the alignment
3278 * Load alignment frame from jalview XML DOM object
3280 * @param jalviewModel
3283 * filename source string
3284 * @param loadTreesAndStructures
3285 * when false only create Viewport
3287 * data source provider
3288 * @return alignment frame created from view stored in DOM
3290 AlignFrame loadFromObject(JalviewModel jalviewModel, String file,
3291 boolean loadTreesAndStructures, jarInputStreamProvider jprovider)
3293 SequenceSet vamsasSet = jalviewModel.getVamsasModel().getSequenceSet().get(0);
3294 List<Sequence> vamsasSeqs = vamsasSet.getSequence();
3296 // JalviewModelSequence jms = object.getJalviewModelSequence();
3298 // Viewport view = (jms.getViewportCount() > 0) ? jms.getViewport(0)
3300 Viewport view = (jalviewModel.getViewport().size() > 0)
3301 ? jalviewModel.getViewport().get(0)
3304 // ////////////////////////////////
3305 // INITIALISE ALIGNMENT SEQUENCESETID AND VIEWID
3308 // If we just load in the same jar file again, the sequenceSetId
3309 // will be the same, and we end up with multiple references
3310 // to the same sequenceSet. We must modify this id on load
3311 // so that each load of the file gives a unique id
3314 * used to resolve correct alignment dataset for alignments with multiple
3317 String uniqueSeqSetId = null;
3318 String viewId = null;
3321 uniqueSeqSetId = view.getSequenceSetId() + uniqueSetSuffix;
3322 viewId = (view.getId() == null ? null
3323 : view.getId() + uniqueSetSuffix);
3326 // ////////////////////////////////
3329 List<SequenceI> hiddenSeqs = null;
3331 List<SequenceI> tmpseqs = new ArrayList<>();
3333 boolean multipleView = false;
3334 SequenceI referenceseqForView = null;
3335 // JSeq[] jseqs = object.getJalviewModelSequence().getJSeq();
3336 List<JSeq> jseqs = jalviewModel.getJSeq();
3337 int vi = 0; // counter in vamsasSeq array
3338 for (int i = 0; i < jseqs.size(); i++)
3340 JSeq jseq = jseqs.get(i);
3341 String seqId = jseq.getId();
3343 SequenceI tmpSeq = seqRefIds.get(seqId);
3346 if (!incompleteSeqs.containsKey(seqId))
3348 // may not need this check, but keep it for at least 2.9,1 release
3349 if (tmpSeq.getStart() != jseq.getStart()
3350 || tmpSeq.getEnd() != jseq.getEnd())
3353 String.format("Warning JAL-2154 regression: updating start/end for sequence %s from %d/%d to %d/%d",
3354 tmpSeq.getName(), tmpSeq.getStart(),
3355 tmpSeq.getEnd(), jseq.getStart(),
3361 incompleteSeqs.remove(seqId);
3363 if (vamsasSeqs.size() > vi
3364 && vamsasSeqs.get(vi).getId().equals(seqId))
3366 // most likely we are reading a dataset XML document so
3367 // update from vamsasSeq section of XML for this sequence
3368 tmpSeq.setName(vamsasSeqs.get(vi).getName());
3369 tmpSeq.setDescription(vamsasSeqs.get(vi).getDescription());
3370 tmpSeq.setSequence(vamsasSeqs.get(vi).getSequence());
3375 // reading multiple views, so vamsasSeq set is a subset of JSeq
3376 multipleView = true;
3378 tmpSeq.setStart(jseq.getStart());
3379 tmpSeq.setEnd(jseq.getEnd());
3380 tmpseqs.add(tmpSeq);
3384 Sequence vamsasSeq = vamsasSeqs.get(vi);
3385 tmpSeq = new jalview.datamodel.Sequence(vamsasSeq.getName(),
3386 vamsasSeq.getSequence());
3387 tmpSeq.setDescription(vamsasSeq.getDescription());
3388 tmpSeq.setStart(jseq.getStart());
3389 tmpSeq.setEnd(jseq.getEnd());
3390 tmpSeq.setVamsasId(uniqueSetSuffix + seqId);
3391 seqRefIds.put(vamsasSeq.getId(), tmpSeq);
3392 tmpseqs.add(tmpSeq);
3396 if (safeBoolean(jseq.isViewreference()))
3398 referenceseqForView = tmpseqs.get(tmpseqs.size() - 1);
3401 if (jseq.isHidden() != null && jseq.isHidden().booleanValue())
3403 if (hiddenSeqs == null)
3405 hiddenSeqs = new ArrayList<>();
3408 hiddenSeqs.add(tmpSeq);
3413 // Create the alignment object from the sequence set
3414 // ///////////////////////////////
3415 SequenceI[] orderedSeqs = tmpseqs
3416 .toArray(new SequenceI[tmpseqs.size()]);
3418 AlignmentI al = null;
3419 // so we must create or recover the dataset alignment before going further
3420 // ///////////////////////////////
3421 if (vamsasSet.getDatasetId() == null || vamsasSet.getDatasetId() == "")
3423 // older jalview projects do not have a dataset - so creat alignment and
3425 al = new Alignment(orderedSeqs);
3426 al.setDataset(null);
3430 boolean isdsal = jalviewModel.getViewport().isEmpty();
3433 // we are importing a dataset record, so
3434 // recover reference to an alignment already materialsed as dataset
3435 al = getDatasetFor(vamsasSet.getDatasetId());
3439 // materialse the alignment
3440 al = new Alignment(orderedSeqs);
3444 addDatasetRef(vamsasSet.getDatasetId(), al);
3447 // finally, verify all data in vamsasSet is actually present in al
3448 // passing on flag indicating if it is actually a stored dataset
3449 recoverDatasetFor(vamsasSet, al, isdsal, uniqueSeqSetId);
3452 if (referenceseqForView != null)
3454 al.setSeqrep(referenceseqForView);
3456 // / Add the alignment properties
3457 for (int i = 0; i < vamsasSet.getSequenceSetProperties().size(); i++)
3459 SequenceSetProperties ssp = vamsasSet.getSequenceSetProperties()
3461 al.setProperty(ssp.getKey(), ssp.getValue());
3464 // ///////////////////////////////
3466 Hashtable pdbloaded = new Hashtable(); // TODO nothing writes to this??
3469 // load sequence features, database references and any associated PDB
3470 // structures for the alignment
3472 // prior to 2.10, this part would only be executed the first time a
3473 // sequence was encountered, but not afterwards.
3474 // now, for 2.10 projects, this is also done if the xml doc includes
3475 // dataset sequences not actually present in any particular view.
3477 for (int i = 0; i < vamsasSeqs.size(); i++)
3479 JSeq jseq = jseqs.get(i);
3480 if (jseq.getFeatures().size() > 0)
3482 List<Feature> features = jseq.getFeatures();
3483 for (int f = 0; f < features.size(); f++)
3485 Feature feat = features.get(f);
3486 SequenceFeature sf = new SequenceFeature(feat.getType(),
3487 feat.getDescription(), feat.getBegin(), feat.getEnd(),
3488 safeFloat(feat.getScore()), feat.getFeatureGroup());
3489 sf.setStatus(feat.getStatus());
3492 * load any feature attributes - include map-valued attributes
3494 Map<String, Map<String, String>> mapAttributes = new HashMap<>();
3495 for (int od = 0; od < feat.getOtherData().size(); od++)
3497 OtherData keyValue = feat.getOtherData().get(od);
3498 String attributeName = keyValue.getKey();
3499 String attributeValue = keyValue.getValue();
3500 if (attributeName.startsWith("LINK"))
3502 sf.addLink(attributeValue);
3506 String subAttribute = keyValue.getKey2();
3507 if (subAttribute == null)
3509 // simple string-valued attribute
3510 sf.setValue(attributeName, attributeValue);
3514 // attribute 'key' has sub-attribute 'key2'
3515 if (!mapAttributes.containsKey(attributeName))
3517 mapAttributes.put(attributeName, new HashMap<>());
3519 mapAttributes.get(attributeName).put(subAttribute,
3524 for (Entry<String, Map<String, String>> mapAttribute : mapAttributes
3527 sf.setValue(mapAttribute.getKey(), mapAttribute.getValue());
3530 // adds feature to datasequence's feature set (since Jalview 2.10)
3531 al.getSequenceAt(i).addSequenceFeature(sf);
3534 if (vamsasSeqs.get(i).getDBRef().size() > 0)
3536 // adds dbrefs to datasequence's set (since Jalview 2.10)
3538 al.getSequenceAt(i).getDatasetSequence() == null
3539 ? al.getSequenceAt(i)
3540 : al.getSequenceAt(i).getDatasetSequence(),
3543 if (jseq.getPdbids().size() > 0)
3545 List<Pdbids> ids = jseq.getPdbids();
3546 for (int p = 0; p < ids.size(); p++)
3548 Pdbids pdbid = ids.get(p);
3549 jalview.datamodel.PDBEntry entry = new jalview.datamodel.PDBEntry();
3550 entry.setId(pdbid.getId());
3551 if (pdbid.getType() != null)
3553 if (PDBEntry.Type.getType(pdbid.getType()) != null)
3555 entry.setType(PDBEntry.Type.getType(pdbid.getType()));
3559 entry.setType(PDBEntry.Type.FILE);
3562 // jprovider is null when executing 'New View'
3563 if (pdbid.getFile() != null && jprovider != null)
3565 if (!pdbloaded.containsKey(pdbid.getFile()))
3567 entry.setFile(loadPDBFile(jprovider, pdbid.getId(),
3572 entry.setFile(pdbloaded.get(pdbid.getId()).toString());
3576 if (pdbid.getPdbentryItem() != null)
3578 for (PdbentryItem item : pdbid.getPdbentryItem())
3580 for (Property pr : item.getProperty())
3582 entry.setProperty(pr.getName(), pr.getValue());
3587 for (Property prop : pdbid.getProperty())
3589 entry.setProperty(prop.getName(), prop.getValue());
3591 StructureSelectionManager
3592 .getStructureSelectionManager(Desktop.instance)
3593 .registerPDBEntry(entry);
3594 // adds PDBEntry to datasequence's set (since Jalview 2.10)
3595 if (al.getSequenceAt(i).getDatasetSequence() != null)
3597 al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
3601 al.getSequenceAt(i).addPDBId(entry);
3606 } // end !multipleview
3608 // ///////////////////////////////
3609 // LOAD SEQUENCE MAPPINGS
3611 if (vamsasSet.getAlcodonFrame().size() > 0)
3613 // TODO Potentially this should only be done once for all views of an
3615 List<AlcodonFrame> alc = vamsasSet.getAlcodonFrame();
3616 for (int i = 0; i < alc.size(); i++)
3618 AlignedCodonFrame cf = new AlignedCodonFrame();
3619 if (alc.get(i).getAlcodMap().size() > 0)
3621 List<AlcodMap> maps = alc.get(i).getAlcodMap();
3622 for (int m = 0; m < maps.size(); m++)
3624 AlcodMap map = maps.get(m);
3625 SequenceI dnaseq = seqRefIds.get(map.getDnasq());
3627 jalview.datamodel.Mapping mapping = null;
3628 // attach to dna sequence reference.
3629 if (map.getMapping() != null)
3631 mapping = addMapping(map.getMapping());
3632 if (dnaseq != null && mapping.getTo() != null)
3634 cf.addMap(dnaseq, mapping.getTo(), mapping.getMap());
3640 newAlcodMapRef(map.getDnasq(), cf, mapping));
3644 al.addCodonFrame(cf);
3649 // ////////////////////////////////
3651 List<JvAnnotRow> autoAlan = new ArrayList<>();
3654 * store any annotations which forward reference a group's ID
3656 Map<String, List<AlignmentAnnotation>> groupAnnotRefs = new Hashtable<>();
3658 if (vamsasSet.getAnnotation().size()/*Count()*/ > 0)
3660 List<Annotation> an = vamsasSet.getAnnotation();
3662 for (int i = 0; i < an.size(); i++)
3664 Annotation annotation = an.get(i);
3667 * test if annotation is automatically calculated for this view only
3669 boolean autoForView = false;
3670 if (annotation.getLabel().equals("Quality")
3671 || annotation.getLabel().equals("Conservation")
3672 || annotation.getLabel().equals("Consensus"))
3674 // Kludge for pre 2.5 projects which lacked the autocalculated flag
3676 // JAXB has no has() test; schema defaults value to false
3677 // if (!annotation.hasAutoCalculated())
3679 // annotation.setAutoCalculated(true);
3682 if (autoForView || annotation.isAutoCalculated())
3684 // remove ID - we don't recover annotation from other views for
3685 // view-specific annotation
3686 annotation.setId(null);
3689 // set visibility for other annotation in this view
3690 String annotationId = annotation.getId();
3691 if (annotationId != null && annotationIds.containsKey(annotationId))
3693 AlignmentAnnotation jda = annotationIds.get(annotationId);
3694 // in principle Visible should always be true for annotation displayed
3695 // in multiple views
3696 if (annotation.isVisible() != null)
3698 jda.visible = annotation.isVisible();
3701 al.addAnnotation(jda);
3705 // Construct new annotation from model.
3706 List<AnnotationElement> ae = annotation.getAnnotationElement();
3707 jalview.datamodel.Annotation[] anot = null;
3708 java.awt.Color firstColour = null;
3710 if (!annotation.isScoreOnly())
3712 anot = new jalview.datamodel.Annotation[al.getWidth()];
3713 for (int aa = 0; aa < ae.size() && aa < anot.length; aa++)
3715 AnnotationElement annElement = ae.get(aa);
3716 anpos = annElement.getPosition();
3718 if (anpos >= anot.length)
3723 float value = safeFloat(annElement.getValue());
3724 anot[anpos] = new jalview.datamodel.Annotation(
3725 annElement.getDisplayCharacter(),
3726 annElement.getDescription(),
3727 (annElement.getSecondaryStructure() == null
3728 || annElement.getSecondaryStructure()
3732 .getSecondaryStructure()
3735 anot[anpos].colour = new Color(safeInt(annElement.getColour()));
3736 if (firstColour == null)
3738 firstColour = anot[anpos].colour;
3742 jalview.datamodel.AlignmentAnnotation jaa = null;
3744 if (annotation.isGraph())
3746 float llim = 0, hlim = 0;
3747 // if (autoForView || an[i].isAutoCalculated()) {
3750 jaa = new jalview.datamodel.AlignmentAnnotation(
3751 annotation.getLabel(), annotation.getDescription(), anot,
3752 llim, hlim, safeInt(annotation.getGraphType()));
3754 jaa.graphGroup = safeInt(annotation.getGraphGroup());
3755 jaa._linecolour = firstColour;
3756 if (annotation.getThresholdLine() != null)
3758 jaa.setThreshold(new jalview.datamodel.GraphLine(
3759 safeFloat(annotation.getThresholdLine().getValue()),
3760 annotation.getThresholdLine().getLabel(),
3761 new java.awt.Color(safeInt(
3762 annotation.getThresholdLine().getColour()))));
3764 if (autoForView || annotation.isAutoCalculated())
3766 // Hardwire the symbol display line to ensure that labels for
3767 // histograms are displayed
3773 jaa = new jalview.datamodel.AlignmentAnnotation(
3774 annotation.getLabel(), annotation.getDescription(), anot);
3775 jaa._linecolour = firstColour;
3777 // register new annotation
3778 if (annotation.getId() != null)
3780 annotationIds.put(annotation.getId(), jaa);
3781 jaa.annotationId = annotation.getId();
3783 // recover sequence association
3784 String sequenceRef = annotation.getSequenceRef();
3785 if (sequenceRef != null)
3787 // from 2.9 sequenceRef is to sequence id (JAL-1781)
3788 SequenceI sequence = seqRefIds.get(sequenceRef);
3789 if (sequence == null)
3791 // in pre-2.9 projects sequence ref is to sequence name
3792 sequence = al.findName(sequenceRef);
3794 if (sequence != null)
3796 jaa.createSequenceMapping(sequence, 1, true);
3797 sequence.addAlignmentAnnotation(jaa);
3800 // and make a note of any group association
3801 if (annotation.getGroupRef() != null
3802 && annotation.getGroupRef().length() > 0)
3804 List<jalview.datamodel.AlignmentAnnotation> aal = groupAnnotRefs
3805 .get(annotation.getGroupRef());
3808 aal = new ArrayList<>();
3809 groupAnnotRefs.put(annotation.getGroupRef(), aal);
3814 if (annotation.getScore() != null)
3816 jaa.setScore(annotation.getScore().doubleValue());
3818 if (annotation.isVisible() != null)
3820 jaa.visible = annotation.isVisible().booleanValue();
3823 if (annotation.isCentreColLabels() != null)
3825 jaa.centreColLabels = annotation.isCentreColLabels()
3829 if (annotation.isScaleColLabels() != null)
3831 jaa.scaleColLabel = annotation.isScaleColLabels().booleanValue();
3833 if (annotation.isAutoCalculated())
3835 // newer files have an 'autoCalculated' flag and store calculation
3836 // state in viewport properties
3837 jaa.autoCalculated = true; // means annotation will be marked for
3838 // update at end of load.
3840 if (annotation.getGraphHeight() != null)
3842 jaa.graphHeight = annotation.getGraphHeight().intValue();
3844 jaa.belowAlignment = annotation.isBelowAlignment();
3845 jaa.setCalcId(annotation.getCalcId());
3846 if (annotation.getProperty().size() > 0)
3848 for (Annotation.Property prop : annotation
3851 jaa.setProperty(prop.getName(), prop.getValue());
3854 if (jaa.autoCalculated)
3856 autoAlan.add(new JvAnnotRow(i, jaa));
3859 // if (!autoForView)
3861 // add autocalculated group annotation and any user created annotation
3863 al.addAnnotation(jaa);
3867 // ///////////////////////
3869 // Create alignment markup and styles for this view
3870 if (jalviewModel.getJGroup().size() > 0)
3872 List<JGroup> groups = jalviewModel.getJGroup();
3873 boolean addAnnotSchemeGroup = false;
3874 for (int i = 0; i < groups.size(); i++)
3876 JGroup jGroup = groups.get(i);
3877 ColourSchemeI cs = null;
3878 if (jGroup.getColour() != null)
3880 if (jGroup.getColour().startsWith("ucs"))
3882 cs = getUserColourScheme(jalviewModel, jGroup.getColour());
3884 else if (jGroup.getColour().equals("AnnotationColourGradient")
3885 && jGroup.getAnnotationColours() != null)
3887 addAnnotSchemeGroup = true;
3891 cs = ColourSchemeProperty.getColourScheme(null, al,
3892 jGroup.getColour());
3895 int pidThreshold = safeInt(jGroup.getPidThreshold());
3897 Vector<SequenceI> seqs = new Vector<>();
3899 for (int s = 0; s < jGroup.getSeq().size(); s++)
3901 String seqId = jGroup.getSeq().get(s);
3902 SequenceI ts = seqRefIds.get(seqId);
3906 seqs.addElement(ts);
3910 if (seqs.size() < 1)
3915 SequenceGroup sg = new SequenceGroup(seqs, jGroup.getName(), cs,
3916 safeBoolean(jGroup.isDisplayBoxes()),
3917 safeBoolean(jGroup.isDisplayText()),
3918 safeBoolean(jGroup.isColourText()),
3919 safeInt(jGroup.getStart()), safeInt(jGroup.getEnd()));
3920 sg.getGroupColourScheme().setThreshold(pidThreshold, true);
3921 sg.getGroupColourScheme()
3922 .setConservationInc(safeInt(jGroup.getConsThreshold()));
3923 sg.setOutlineColour(new Color(safeInt(jGroup.getOutlineColour())));
3925 sg.textColour = new Color(safeInt(jGroup.getTextCol1()));
3926 sg.textColour2 = new Color(safeInt(jGroup.getTextCol2()));
3927 sg.setShowNonconserved(safeBoolean(jGroup.isShowUnconserved()));
3928 sg.thresholdTextColour = safeInt(jGroup.getTextColThreshold());
3929 // attributes with a default in the schema are never null
3930 sg.setShowConsensusHistogram(jGroup.isShowConsensusHistogram());
3931 sg.setshowSequenceLogo(jGroup.isShowSequenceLogo());
3932 sg.setNormaliseSequenceLogo(jGroup.isNormaliseSequenceLogo());
3933 sg.setIgnoreGapsConsensus(jGroup.isIgnoreGapsinConsensus());
3934 if (jGroup.getConsThreshold() != null
3935 && jGroup.getConsThreshold().intValue() != 0)
3937 Conservation c = new Conservation("All", sg.getSequences(null), 0,
3940 c.verdict(false, 25);
3941 sg.cs.setConservation(c);
3944 if (jGroup.getId() != null && groupAnnotRefs.size() > 0)
3946 // re-instate unique group/annotation row reference
3947 List<AlignmentAnnotation> jaal = groupAnnotRefs
3948 .get(jGroup.getId());
3951 for (AlignmentAnnotation jaa : jaal)
3954 if (jaa.autoCalculated)
3956 // match up and try to set group autocalc alignment row for this
3958 if (jaa.label.startsWith("Consensus for "))
3960 sg.setConsensus(jaa);
3962 // match up and try to set group autocalc alignment row for this
3964 if (jaa.label.startsWith("Conservation for "))
3966 sg.setConservationRow(jaa);
3973 if (addAnnotSchemeGroup)
3975 // reconstruct the annotation colourscheme
3976 sg.setColourScheme(constructAnnotationColour(
3977 jGroup.getAnnotationColours(), null, al, jalviewModel, false));
3983 // only dataset in this model, so just return.
3986 // ///////////////////////////////
3989 AlignFrame af = null;
3990 AlignViewport av = null;
3991 // now check to see if we really need to create a new viewport.
3992 if (multipleView && viewportsAdded.size() == 0)
3994 // We recovered an alignment for which a viewport already exists.
3995 // TODO: fix up any settings necessary for overlaying stored state onto
3996 // state recovered from another document. (may not be necessary).
3997 // we may need a binding from a viewport in memory to one recovered from
3999 // and then recover its containing af to allow the settings to be applied.
4000 // TODO: fix for vamsas demo
4002 "About to recover a viewport for existing alignment: Sequence set ID is "
4004 Object seqsetobj = retrieveExistingObj(uniqueSeqSetId);
4005 if (seqsetobj != null)
4007 if (seqsetobj instanceof String)
4009 uniqueSeqSetId = (String) seqsetobj;
4011 "Recovered extant sequence set ID mapping for ID : New Sequence set ID is "
4017 "Warning : Collision between sequence set ID string and existing jalview object mapping.");
4023 * indicate that annotation colours are applied across all groups (pre
4024 * Jalview 2.8.1 behaviour)
4026 boolean doGroupAnnColour = Jalview2XML.isVersionStringLaterThan("2.8.1",
4027 jalviewModel.getVersion());
4029 AlignmentPanel ap = null;
4030 boolean isnewview = true;
4033 // Check to see if this alignment already has a view id == viewId
4034 jalview.gui.AlignmentPanel views[] = Desktop
4035 .getAlignmentPanels(uniqueSeqSetId);
4036 if (views != null && views.length > 0)
4038 for (int v = 0; v < views.length; v++)
4040 if (views[v].av.getViewId().equalsIgnoreCase(viewId))
4042 // recover the existing alignpanel, alignframe, viewport
4043 af = views[v].alignFrame;
4046 // TODO: could even skip resetting view settings if we don't want to
4047 // change the local settings from other jalview processes
4056 af = loadViewport(file, jseqs, hiddenSeqs, al, jalviewModel, view,
4057 uniqueSeqSetId, viewId, autoAlan);
4058 av = af.getViewport();
4063 * Load any trees, PDB structures and viewers
4065 * Not done if flag is false (when this method is used for New View)
4067 if (loadTreesAndStructures)
4069 loadTrees(jalviewModel, view, af, av, ap);
4070 loadPCAViewers(jalviewModel, ap);
4071 loadPDBStructures(jprovider, jseqs, af, ap);
4072 loadRnaViewers(jprovider, jseqs, ap);
4074 // and finally return.
4079 * Instantiate and link any saved RNA (Varna) viewers. The state of the Varna
4080 * panel is restored from separate jar entries, two (gapped and trimmed) per
4081 * sequence and secondary structure.
4083 * Currently each viewer shows just one sequence and structure (gapped and
4084 * trimmed), however this method is designed to support multiple sequences or
4085 * structures in viewers if wanted in future.
4091 private void loadRnaViewers(jarInputStreamProvider jprovider,
4092 List<JSeq> jseqs, AlignmentPanel ap)
4095 * scan the sequences for references to viewers; create each one the first
4096 * time it is referenced, add Rna models to existing viewers
4098 for (JSeq jseq : jseqs)
4100 for (int i = 0; i < jseq.getRnaViewer().size(); i++)
4102 RnaViewer viewer = jseq.getRnaViewer().get(i);
4103 AppVarna appVarna = findOrCreateVarnaViewer(viewer, uniqueSetSuffix,
4106 for (int j = 0; j < viewer.getSecondaryStructure().size(); j++)
4108 SecondaryStructure ss = viewer.getSecondaryStructure().get(j);
4109 SequenceI seq = seqRefIds.get(jseq.getId());
4110 AlignmentAnnotation ann = this.annotationIds
4111 .get(ss.getAnnotationId());
4114 * add the structure to the Varna display (with session state copied
4115 * from the jar to a temporary file)
4117 boolean gapped = safeBoolean(ss.isGapped());
4118 String rnaTitle = ss.getTitle();
4119 String sessionState = ss.getViewerState();
4120 String tempStateFile = copyJarEntry(jprovider, sessionState,
4122 RnaModel rna = new RnaModel(rnaTitle, ann, seq, null, gapped);
4123 appVarna.addModelSession(rna, rnaTitle, tempStateFile);
4125 appVarna.setInitialSelection(safeInt(viewer.getSelectedRna()));
4131 * Locate and return an already instantiated matching AppVarna, or create one
4135 * @param viewIdSuffix
4139 protected AppVarna findOrCreateVarnaViewer(RnaViewer viewer,
4140 String viewIdSuffix, AlignmentPanel ap)
4143 * on each load a suffix is appended to the saved viewId, to avoid conflicts
4144 * if load is repeated
4146 String postLoadId = viewer.getViewId() + viewIdSuffix;
4147 for (JInternalFrame frame : getAllFrames())
4149 if (frame instanceof AppVarna)
4151 AppVarna varna = (AppVarna) frame;
4152 if (postLoadId.equals(varna.getViewId()))
4154 // this viewer is already instantiated
4155 // could in future here add ap as another 'parent' of the
4156 // AppVarna window; currently just 1-to-many
4163 * viewer not found - make it
4165 RnaViewerModel model = new RnaViewerModel(postLoadId, viewer.getTitle(),
4166 safeInt(viewer.getXpos()), safeInt(viewer.getYpos()),
4167 safeInt(viewer.getWidth()), safeInt(viewer.getHeight()),
4168 safeInt(viewer.getDividerLocation()));
4169 AppVarna varna = new AppVarna(model, ap);
4175 * Load any saved trees
4183 protected void loadTrees(JalviewModel jm, Viewport view,
4184 AlignFrame af, AlignViewport av, AlignmentPanel ap)
4186 // TODO result of automated refactoring - are all these parameters needed?
4189 for (int t = 0; t < jm.getTree().size(); t++)
4192 Tree tree = jm.getTree().get(t);
4194 TreePanel tp = (TreePanel) retrieveExistingObj(tree.getId());
4197 tp = af.showNewickTree(new NewickFile(tree.getNewick()),
4198 tree.getTitle(), safeInt(tree.getWidth()),
4199 safeInt(tree.getHeight()), safeInt(tree.getXpos()),
4200 safeInt(tree.getYpos()));
4201 if (tree.getId() != null)
4203 // perhaps bind the tree id to something ?
4208 // update local tree attributes ?
4209 // TODO: should check if tp has been manipulated by user - if so its
4210 // settings shouldn't be modified
4211 tp.setTitle(tree.getTitle());
4212 tp.setBounds(new Rectangle(safeInt(tree.getXpos()),
4213 safeInt(tree.getYpos()), safeInt(tree.getWidth()),
4214 safeInt(tree.getHeight())));
4215 tp.setViewport(av); // af.viewport;
4216 // TODO: verify 'associate with all views' works still
4217 tp.getTreeCanvas().setViewport(av); // af.viewport;
4218 tp.getTreeCanvas().setAssociatedPanel(ap); // af.alignPanel;
4220 tp.getTreeCanvas().setApplyToAllViews(tree.isLinkToAllViews());
4223 warn("There was a problem recovering stored Newick tree: \n"
4224 + tree.getNewick());
4228 tp.fitToWindow.setState(safeBoolean(tree.isFitToWindow()));
4229 tp.fitToWindow_actionPerformed(null);
4231 if (tree.getFontName() != null)
4234 new Font(tree.getFontName(), safeInt(tree.getFontStyle()),
4235 safeInt(tree.getFontSize())));
4240 new Font(view.getFontName(), safeInt(view.getFontStyle()),
4241 safeInt(view.getFontSize())));
4244 tp.showPlaceholders(safeBoolean(tree.isMarkUnlinked()));
4245 tp.showBootstrap(safeBoolean(tree.isShowBootstrap()));
4246 tp.showDistances(safeBoolean(tree.isShowDistances()));
4248 tp.getTreeCanvas().setThreshold(safeFloat(tree.getThreshold()));
4250 if (safeBoolean(tree.isCurrentTree()))
4252 af.getViewport().setCurrentTree(tp.getTree());
4256 } catch (Exception ex)
4258 ex.printStackTrace();
4263 * Load and link any saved structure viewers.
4270 protected void loadPDBStructures(jarInputStreamProvider jprovider,
4271 List<JSeq> jseqs, AlignFrame af, AlignmentPanel ap)
4274 * Run through all PDB ids on the alignment, and collect mappings between
4275 * distinct view ids and all sequences referring to that view.
4277 Map<String, StructureViewerModel> structureViewers = new LinkedHashMap<>();
4279 for (int i = 0; i < jseqs.size(); i++)
4281 JSeq jseq = jseqs.get(i);
4282 if (jseq.getPdbids().size() > 0)
4284 List<Pdbids> ids = jseq.getPdbids();
4285 for (int p = 0; p < ids.size(); p++)
4287 Pdbids pdbid = ids.get(p);
4288 final int structureStateCount = pdbid.getStructureState().size();
4289 for (int s = 0; s < structureStateCount; s++)
4291 // check to see if we haven't already created this structure view
4292 final StructureState structureState = pdbid
4293 .getStructureState().get(s);
4294 String sviewid = (structureState.getViewId() == null) ? null
4295 : structureState.getViewId() + uniqueSetSuffix;
4296 jalview.datamodel.PDBEntry jpdb = new jalview.datamodel.PDBEntry();
4297 // Originally : pdbid.getFile()
4298 // : TODO: verify external PDB file recovery still works in normal
4299 // jalview project load
4301 loadPDBFile(jprovider, pdbid.getId(), pdbid.getFile()));
4302 jpdb.setId(pdbid.getId());
4304 int x = safeInt(structureState.getXpos());
4305 int y = safeInt(structureState.getYpos());
4306 int width = safeInt(structureState.getWidth());
4307 int height = safeInt(structureState.getHeight());
4309 // Probably don't need to do this anymore...
4310 // Desktop.desktop.getComponentAt(x, y);
4311 // TODO: NOW: check that this recovers the PDB file correctly.
4312 String pdbFile = loadPDBFile(jprovider, pdbid.getId(),
4314 jalview.datamodel.SequenceI seq = seqRefIds
4315 .get(jseq.getId() + "");
4316 if (sviewid == null)
4318 sviewid = "_jalview_pre2_4_" + x + "," + y + "," + width + ","
4321 if (!structureViewers.containsKey(sviewid))
4323 structureViewers.put(sviewid,
4324 new StructureViewerModel(x, y, width, height, false,
4325 false, true, structureState.getViewId(),
4326 structureState.getType()));
4327 // Legacy pre-2.7 conversion JAL-823 :
4328 // do not assume any view has to be linked for colour by
4332 // assemble String[] { pdb files }, String[] { id for each
4333 // file }, orig_fileloc, SequenceI[][] {{ seqs_file 1 }, {
4334 // seqs_file 2}, boolean[] {
4335 // linkAlignPanel,superposeWithAlignpanel}} from hash
4336 StructureViewerModel jmoldat = structureViewers.get(sviewid);
4337 jmoldat.setAlignWithPanel(jmoldat.isAlignWithPanel()
4338 || structureState.isAlignwithAlignPanel());
4341 * Default colour by linked panel to false if not specified (e.g.
4342 * for pre-2.7 projects)
4344 boolean colourWithAlignPanel = jmoldat.isColourWithAlignPanel();
4345 colourWithAlignPanel |= structureState.isColourwithAlignPanel();
4346 jmoldat.setColourWithAlignPanel(colourWithAlignPanel);
4349 * Default colour by viewer to true if not specified (e.g. for
4352 boolean colourByViewer = jmoldat.isColourByViewer();
4353 colourByViewer &= structureState.isColourByJmol();
4354 jmoldat.setColourByViewer(colourByViewer);
4356 if (jmoldat.getStateData().length() < structureState
4357 .getValue()/*Content()*/.length())
4359 jmoldat.setStateData(structureState.getValue());// Content());
4361 if (pdbid.getFile() != null)
4363 File mapkey = new File(pdbid.getFile());
4364 StructureData seqstrmaps = jmoldat.getFileData().get(mapkey);
4365 if (seqstrmaps == null)
4367 jmoldat.getFileData().put(mapkey,
4368 seqstrmaps = jmoldat.new StructureData(pdbFile,
4371 if (!seqstrmaps.getSeqList().contains(seq))
4373 seqstrmaps.getSeqList().add(seq);
4379 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");
4386 // Instantiate the associated structure views
4387 for (Entry<String, StructureViewerModel> entry : structureViewers
4392 createOrLinkStructureViewer(entry, af, ap, jprovider);
4393 } catch (Exception e)
4396 "Error loading structure viewer: " + e.getMessage());
4397 // failed - try the next one
4409 protected void createOrLinkStructureViewer(
4410 Entry<String, StructureViewerModel> viewerData, AlignFrame af,
4411 AlignmentPanel ap, jarInputStreamProvider jprovider)
4413 final StructureViewerModel stateData = viewerData.getValue();
4416 * Search for any viewer windows already open from other alignment views
4417 * that exactly match the stored structure state
4419 StructureViewerBase comp = findMatchingViewer(viewerData);
4423 linkStructureViewer(ap, comp, stateData);
4428 * From 2.9: stateData.type contains JMOL or CHIMERA, data is in jar entry
4429 * "viewer_"+stateData.viewId
4431 if (ViewerType.CHIMERA.toString().equals(stateData.getType()))
4433 createChimeraViewer(viewerData, af, jprovider);
4438 * else Jmol (if pre-2.9, stateData contains JMOL state string)
4440 createJmolViewer(viewerData, af, jprovider);
4445 * Create a new Chimera viewer.
4451 protected void createChimeraViewer(
4452 Entry<String, StructureViewerModel> viewerData, AlignFrame af,
4453 jarInputStreamProvider jprovider)
4455 StructureViewerModel data = viewerData.getValue();
4456 String chimeraSessionFile = data.getStateData();
4459 * Copy Chimera session from jar entry "viewer_"+viewId to a temporary file
4461 * NB this is the 'saved' viewId as in the project file XML, _not_ the
4462 * 'uniquified' sviewid used to reconstruct the viewer here
4464 String viewerJarEntryName = getViewerJarEntryName(data.getViewId());
4465 chimeraSessionFile = copyJarEntry(jprovider, viewerJarEntryName,
4468 Set<Entry<File, StructureData>> fileData = data.getFileData()
4470 List<PDBEntry> pdbs = new ArrayList<>();
4471 List<SequenceI[]> allseqs = new ArrayList<>();
4472 for (Entry<File, StructureData> pdb : fileData)
4474 String filePath = pdb.getValue().getFilePath();
4475 String pdbId = pdb.getValue().getPdbId();
4476 // pdbs.add(new PDBEntry(filePath, pdbId));
4477 pdbs.add(new PDBEntry(pdbId, null, PDBEntry.Type.PDB, filePath));
4478 final List<SequenceI> seqList = pdb.getValue().getSeqList();
4479 SequenceI[] seqs = seqList.toArray(new SequenceI[seqList.size()]);
4483 boolean colourByChimera = data.isColourByViewer();
4484 boolean colourBySequence = data.isColourWithAlignPanel();
4486 // TODO use StructureViewer as a factory here, see JAL-1761
4487 final PDBEntry[] pdbArray = pdbs.toArray(new PDBEntry[pdbs.size()]);
4488 final SequenceI[][] seqsArray = allseqs
4489 .toArray(new SequenceI[allseqs.size()][]);
4490 String newViewId = viewerData.getKey();
4492 ChimeraViewFrame cvf = new ChimeraViewFrame(chimeraSessionFile,
4493 af.alignPanel, pdbArray, seqsArray, colourByChimera,
4494 colourBySequence, newViewId);
4495 cvf.setSize(data.getWidth(), data.getHeight());
4496 cvf.setLocation(data.getX(), data.getY());
4500 * Create a new Jmol window. First parse the Jmol state to translate filenames
4501 * loaded into the view, and record the order in which files are shown in the
4502 * Jmol view, so we can add the sequence mappings in same order.
4508 protected void createJmolViewer(
4509 final Entry<String, StructureViewerModel> viewerData,
4510 AlignFrame af, jarInputStreamProvider jprovider)
4512 final StructureViewerModel svattrib = viewerData.getValue();
4513 String state = svattrib.getStateData();
4516 * Pre-2.9: state element value is the Jmol state string
4518 * 2.9+: @type is "JMOL", state data is in a Jar file member named "viewer_"
4521 if (ViewerType.JMOL.toString().equals(svattrib.getType()))
4523 state = readJarEntry(jprovider,
4524 getViewerJarEntryName(svattrib.getViewId()));
4527 List<String> pdbfilenames = new ArrayList<>();
4528 List<SequenceI[]> seqmaps = new ArrayList<>();
4529 List<String> pdbids = new ArrayList<>();
4530 StringBuilder newFileLoc = new StringBuilder(64);
4531 int cp = 0, ncp, ecp;
4532 Map<File, StructureData> oldFiles = svattrib.getFileData();
4533 while ((ncp = state.indexOf("load ", cp)) > -1)
4537 // look for next filename in load statement
4538 newFileLoc.append(state.substring(cp,
4539 ncp = (state.indexOf("\"", ncp + 1) + 1)));
4540 String oldfilenam = state.substring(ncp,
4541 ecp = state.indexOf("\"", ncp));
4542 // recover the new mapping data for this old filename
4543 // have to normalize filename - since Jmol and jalview do
4545 // translation differently.
4546 StructureData filedat = oldFiles.get(new File(oldfilenam));
4547 if (filedat == null)
4549 String reformatedOldFilename = oldfilenam.replaceAll("/", "\\\\");
4550 filedat = oldFiles.get(new File(reformatedOldFilename));
4552 newFileLoc.append(Platform.escapeBackslashes(filedat.getFilePath()));
4553 pdbfilenames.add(filedat.getFilePath());
4554 pdbids.add(filedat.getPdbId());
4555 seqmaps.add(filedat.getSeqList().toArray(new SequenceI[0]));
4556 newFileLoc.append("\"");
4557 cp = ecp + 1; // advance beyond last \" and set cursor so we can
4558 // look for next file statement.
4559 } while ((ncp = state.indexOf("/*file*/", cp)) > -1);
4563 // just append rest of state
4564 newFileLoc.append(state.substring(cp));
4568 System.err.print("Ignoring incomplete Jmol state for PDB ids: ");
4569 newFileLoc = new StringBuilder(state);
4570 newFileLoc.append("; load append ");
4571 for (File id : oldFiles.keySet())
4573 // add this and any other pdb files that should be present in
4575 StructureData filedat = oldFiles.get(id);
4576 newFileLoc.append(filedat.getFilePath());
4577 pdbfilenames.add(filedat.getFilePath());
4578 pdbids.add(filedat.getPdbId());
4579 seqmaps.add(filedat.getSeqList().toArray(new SequenceI[0]));
4580 newFileLoc.append(" \"");
4581 newFileLoc.append(filedat.getFilePath());
4582 newFileLoc.append("\"");
4585 newFileLoc.append(";");
4588 if (newFileLoc.length() == 0)
4592 int histbug = newFileLoc.indexOf("history = ");
4596 * change "history = [true|false];" to "history = [1|0];"
4599 int diff = histbug == -1 ? -1 : newFileLoc.indexOf(";", histbug);
4600 String val = (diff == -1) ? null
4601 : newFileLoc.substring(histbug, diff);
4602 if (val != null && val.length() >= 4)
4604 if (val.contains("e")) // eh? what can it be?
4606 if (val.trim().equals("true"))
4614 newFileLoc.replace(histbug, diff, val);
4619 final String[] pdbf = pdbfilenames
4620 .toArray(new String[pdbfilenames.size()]);
4621 final String[] id = pdbids.toArray(new String[pdbids.size()]);
4622 final SequenceI[][] sq = seqmaps
4623 .toArray(new SequenceI[seqmaps.size()][]);
4624 final String fileloc = newFileLoc.toString();
4625 final String sviewid = viewerData.getKey();
4626 final AlignFrame alf = af;
4627 final Rectangle rect = new Rectangle(svattrib.getX(), svattrib.getY(),
4628 svattrib.getWidth(), svattrib.getHeight());
4631 javax.swing.SwingUtilities.invokeAndWait(new Runnable()
4636 JalviewStructureDisplayI sview = null;
4639 sview = new StructureViewer(
4640 alf.alignPanel.getStructureSelectionManager())
4641 .createView(StructureViewer.ViewerType.JMOL,
4642 pdbf, id, sq, alf.alignPanel, svattrib,
4643 fileloc, rect, sviewid);
4644 addNewStructureViewer(sview);
4645 } catch (OutOfMemoryError ex)
4647 new OOMWarning("restoring structure view for PDB id " + id,
4648 (OutOfMemoryError) ex.getCause());
4649 if (sview != null && sview.isVisible())
4651 sview.closeViewer(false);
4652 sview.setVisible(false);
4658 } catch (InvocationTargetException ex)
4660 warn("Unexpected error when opening Jmol view.", ex);
4662 } catch (InterruptedException e)
4664 // e.printStackTrace();
4670 * Generates a name for the entry in the project jar file to hold state
4671 * information for a structure viewer
4676 protected String getViewerJarEntryName(String viewId)
4678 return VIEWER_PREFIX + viewId;
4682 * Returns any open frame that matches given structure viewer data. The match
4683 * is based on the unique viewId, or (for older project versions) the frame's
4689 protected StructureViewerBase findMatchingViewer(
4690 Entry<String, StructureViewerModel> viewerData)
4692 final String sviewid = viewerData.getKey();
4693 final StructureViewerModel svattrib = viewerData.getValue();
4694 StructureViewerBase comp = null;
4695 JInternalFrame[] frames = getAllFrames();
4696 for (JInternalFrame frame : frames)
4698 if (frame instanceof StructureViewerBase)
4701 * Post jalview 2.4 schema includes structure view id
4703 if (sviewid != null && ((StructureViewerBase) frame).getViewId()
4706 comp = (StructureViewerBase) frame;
4707 break; // break added in 2.9
4710 * Otherwise test for matching position and size of viewer frame
4712 else if (frame.getX() == svattrib.getX()
4713 && frame.getY() == svattrib.getY()
4714 && frame.getHeight() == svattrib.getHeight()
4715 && frame.getWidth() == svattrib.getWidth())
4717 comp = (StructureViewerBase) frame;
4718 // no break in faint hope of an exact match on viewId
4726 * Link an AlignmentPanel to an existing structure viewer.
4731 * @param useinViewerSuperpos
4732 * @param usetoColourbyseq
4733 * @param viewerColouring
4735 protected void linkStructureViewer(AlignmentPanel ap,
4736 StructureViewerBase viewer, StructureViewerModel stateData)
4738 // NOTE: if the jalview project is part of a shared session then
4739 // view synchronization should/could be done here.
4741 final boolean useinViewerSuperpos = stateData.isAlignWithPanel();
4742 final boolean usetoColourbyseq = stateData.isColourWithAlignPanel();
4743 final boolean viewerColouring = stateData.isColourByViewer();
4744 Map<File, StructureData> oldFiles = stateData.getFileData();
4747 * Add mapping for sequences in this view to an already open viewer
4749 final AAStructureBindingModel binding = viewer.getBinding();
4750 for (File id : oldFiles.keySet())
4752 // add this and any other pdb files that should be present in the
4754 StructureData filedat = oldFiles.get(id);
4755 String pdbFile = filedat.getFilePath();
4756 SequenceI[] seq = filedat.getSeqList().toArray(new SequenceI[0]);
4757 binding.getSsm().setMapping(seq, null, pdbFile, DataSourceType.FILE,
4759 binding.addSequenceForStructFile(pdbFile, seq);
4761 // and add the AlignmentPanel's reference to the view panel
4762 viewer.addAlignmentPanel(ap);
4763 if (useinViewerSuperpos)
4765 viewer.useAlignmentPanelForSuperposition(ap);
4769 viewer.excludeAlignmentPanelForSuperposition(ap);
4771 if (usetoColourbyseq)
4773 viewer.useAlignmentPanelForColourbyseq(ap, !viewerColouring);
4777 viewer.excludeAlignmentPanelForColourbyseq(ap);
4782 * Get all frames within the Desktop.
4786 protected JInternalFrame[] getAllFrames()
4788 JInternalFrame[] frames = null;
4789 // TODO is this necessary - is it safe - risk of hanging?
4794 frames = Desktop.desktop.getAllFrames();
4795 } catch (ArrayIndexOutOfBoundsException e)
4797 // occasional No such child exceptions are thrown here...
4801 } catch (InterruptedException f)
4805 } while (frames == null);
4810 * Answers true if 'version' is equal to or later than 'supported', where each
4811 * is formatted as major/minor versions like "2.8.3" or "2.3.4b1" for bugfix
4812 * changes. Development and test values for 'version' are leniently treated
4816 * - minimum version we are comparing against
4818 * - version of data being processsed
4821 public static boolean isVersionStringLaterThan(String supported,
4824 if (supported == null || version == null
4825 || version.equalsIgnoreCase("DEVELOPMENT BUILD")
4826 || version.equalsIgnoreCase("Test")
4827 || version.equalsIgnoreCase("AUTOMATED BUILD"))
4829 System.err.println("Assuming project file with "
4830 + (version == null ? "null" : version)
4831 + " is compatible with Jalview version " + supported);
4836 return StringUtils.compareVersions(version, supported, "b") >= 0;
4840 Vector<JalviewStructureDisplayI> newStructureViewers = null;
4842 protected void addNewStructureViewer(JalviewStructureDisplayI sview)
4844 if (newStructureViewers != null)
4846 sview.getBinding().setFinishedLoadingFromArchive(false);
4847 newStructureViewers.add(sview);
4851 protected void setLoadingFinishedForNewStructureViewers()
4853 if (newStructureViewers != null)
4855 for (JalviewStructureDisplayI sview : newStructureViewers)
4857 sview.getBinding().setFinishedLoadingFromArchive(true);
4859 newStructureViewers.clear();
4860 newStructureViewers = null;
4864 AlignFrame loadViewport(String file, List<JSeq> JSEQ,
4865 List<SequenceI> hiddenSeqs, AlignmentI al,
4866 JalviewModel jm, Viewport view, String uniqueSeqSetId,
4867 String viewId, List<JvAnnotRow> autoAlan)
4869 AlignFrame af = null;
4870 af = new AlignFrame(al, safeInt(view.getWidth()),
4871 safeInt(view.getHeight()), uniqueSeqSetId, viewId)
4875 // protected void processKeyEvent(java.awt.event.KeyEvent e) {
4876 // System.out.println("Jalview2XML AF " + e);
4877 // super.processKeyEvent(e);
4884 af.setFileName(file, FileFormat.Jalview);
4886 final AlignViewport viewport = af.getViewport();
4887 for (int i = 0; i < JSEQ.size(); i++)
4889 int colour = safeInt(JSEQ.get(i).getColour());
4890 viewport.setSequenceColour(viewport.getAlignment().getSequenceAt(i),
4896 viewport.setColourByReferenceSeq(true);
4897 viewport.setDisplayReferenceSeq(true);
4900 viewport.setGatherViewsHere(safeBoolean(view.isGatheredViews()));
4902 if (view.getSequenceSetId() != null)
4904 AlignmentViewport av = viewportsAdded.get(uniqueSeqSetId);
4906 viewport.setSequenceSetId(uniqueSeqSetId);
4909 // propagate shared settings to this new view
4910 viewport.setHistoryList(av.getHistoryList());
4911 viewport.setRedoList(av.getRedoList());
4915 viewportsAdded.put(uniqueSeqSetId, viewport);
4917 // TODO: check if this method can be called repeatedly without
4918 // side-effects if alignpanel already registered.
4919 PaintRefresher.Register(af.alignPanel, uniqueSeqSetId);
4921 // apply Hidden regions to view.
4922 if (hiddenSeqs != null)
4924 for (int s = 0; s < JSEQ.size(); s++)
4926 SequenceGroup hidden = new SequenceGroup();
4927 boolean isRepresentative = false;
4928 for (int r = 0; r < JSEQ.get(s).getHiddenSequences().size(); r++)
4930 isRepresentative = true;
4931 SequenceI sequenceToHide = al
4932 .getSequenceAt(JSEQ.get(s).getHiddenSequences().get(r));
4933 hidden.addSequence(sequenceToHide, false);
4934 // remove from hiddenSeqs list so we don't try to hide it twice
4935 hiddenSeqs.remove(sequenceToHide);
4937 if (isRepresentative)
4939 SequenceI representativeSequence = al.getSequenceAt(s);
4940 hidden.addSequence(representativeSequence, false);
4941 viewport.hideRepSequences(representativeSequence, hidden);
4945 SequenceI[] hseqs = hiddenSeqs
4946 .toArray(new SequenceI[hiddenSeqs.size()]);
4947 viewport.hideSequence(hseqs);
4950 // recover view properties and display parameters
4952 viewport.setShowAnnotation(safeBoolean(view.isShowAnnotation()));
4953 viewport.setAbovePIDThreshold(safeBoolean(view.isPidSelected()));
4954 final int pidThreshold = safeInt(view.getPidThreshold());
4955 viewport.setThreshold(pidThreshold);
4957 viewport.setColourText(safeBoolean(view.isShowColourText()));
4960 .setConservationSelected(
4961 safeBoolean(view.isConservationSelected()));
4962 viewport.setIncrement(safeInt(view.getConsThreshold()));
4963 viewport.setShowJVSuffix(safeBoolean(view.isShowFullId()));
4964 viewport.setRightAlignIds(safeBoolean(view.isRightAlignIds()));
4965 viewport.setFont(new Font(view.getFontName(),
4966 safeInt(view.getFontStyle()), safeInt(view.getFontSize())),
4968 ViewStyleI vs = viewport.getViewStyle();
4969 vs.setScaleProteinAsCdna(view.isScaleProteinAsCdna());
4970 viewport.setViewStyle(vs);
4971 // TODO: allow custom charWidth/Heights to be restored by updating them
4972 // after setting font - which means set above to false
4973 viewport.setRenderGaps(safeBoolean(view.isRenderGaps()));
4974 viewport.setWrapAlignment(safeBoolean(view.isWrapAlignment()));
4975 viewport.setShowAnnotation(safeBoolean(view.isShowAnnotation()));
4977 viewport.setShowBoxes(safeBoolean(view.isShowBoxes()));
4979 viewport.setShowText(safeBoolean(view.isShowText()));
4981 viewport.setTextColour(new Color(safeInt(view.getTextCol1())));
4982 viewport.setTextColour2(new Color(safeInt(view.getTextCol2())));
4983 viewport.setThresholdTextColour(safeInt(view.getTextColThreshold()));
4984 viewport.setShowUnconserved(view.isShowUnconserved());
4985 viewport.getRanges().setStartRes(safeInt(view.getStartRes()));
4987 if (view.getViewName() != null)
4989 viewport.setViewName(view.getViewName());
4990 af.setInitialTabVisible();
4992 af.setBounds(safeInt(view.getXpos()), safeInt(view.getYpos()),
4993 safeInt(view.getWidth()), safeInt(view.getHeight()));
4994 // startSeq set in af.alignPanel.updateLayout below
4995 af.alignPanel.updateLayout();
4996 ColourSchemeI cs = null;
4997 // apply colourschemes
4998 if (view.getBgColour() != null)
5000 if (view.getBgColour().startsWith("ucs"))
5002 cs = getUserColourScheme(jm, view.getBgColour());
5004 else if (view.getBgColour().startsWith("Annotation"))
5006 AnnotationColourScheme viewAnnColour = view.getAnnotationColours();
5007 cs = constructAnnotationColour(viewAnnColour, af, al, jm, true);
5014 cs = ColourSchemeProperty.getColourScheme(af.getViewport(), al,
5015 view.getBgColour());
5020 * turn off 'alignment colour applies to all groups'
5021 * while restoring global colour scheme
5023 viewport.setColourAppliesToAllGroups(false);
5024 viewport.setGlobalColourScheme(cs);
5025 viewport.getResidueShading().setThreshold(pidThreshold,
5026 view.isIgnoreGapsinConsensus());
5027 viewport.getResidueShading()
5028 .setConsensus(viewport.getSequenceConsensusHash());
5029 if (safeBoolean(view.isConservationSelected()) && cs != null)
5031 viewport.getResidueShading()
5032 .setConservationInc(safeInt(view.getConsThreshold()));
5034 af.changeColour(cs);
5035 viewport.setColourAppliesToAllGroups(true);
5038 .setShowSequenceFeatures(
5039 safeBoolean(view.isShowSequenceFeatures()));
5041 viewport.setCentreColumnLabels(view.isCentreColumnLabels());
5042 viewport.setIgnoreGapsConsensus(view.isIgnoreGapsinConsensus(), null);
5043 viewport.setFollowHighlight(view.isFollowHighlight());
5044 viewport.followSelection = view.isFollowSelection();
5045 viewport.setShowConsensusHistogram(view.isShowConsensusHistogram());
5046 viewport.setShowSequenceLogo(view.isShowSequenceLogo());
5047 viewport.setNormaliseSequenceLogo(view.isNormaliseSequenceLogo());
5048 viewport.setShowDBRefs(safeBoolean(view.isShowDbRefTooltip()));
5049 viewport.setShowNPFeats(safeBoolean(view.isShowNPfeatureTooltip()));
5050 viewport.setShowGroupConsensus(view.isShowGroupConsensus());
5051 viewport.setShowGroupConservation(view.isShowGroupConservation());
5052 viewport.setShowComplementFeatures(view.isShowComplementFeatures());
5053 viewport.setShowComplementFeaturesOnTop(
5054 view.isShowComplementFeaturesOnTop());
5056 // recover feature settings
5057 if (jm.getFeatureSettings() != null)
5059 FeatureRendererModel fr = af.alignPanel.getSeqPanel().seqCanvas
5060 .getFeatureRenderer();
5061 FeaturesDisplayed fdi;
5062 viewport.setFeaturesDisplayed(fdi = new FeaturesDisplayed());
5063 String[] renderOrder = new String[jm.getFeatureSettings()
5064 .getSetting().size()];
5065 Map<String, FeatureColourI> featureColours = new Hashtable<>();
5066 Map<String, Float> featureOrder = new Hashtable<>();
5068 for (int fs = 0; fs < jm.getFeatureSettings()
5069 .getSetting().size(); fs++)
5071 Setting setting = jm.getFeatureSettings().getSetting().get(fs);
5072 String featureType = setting.getType();
5075 * restore feature filters (if any)
5077 jalview.xml.binding.jalview.FeatureMatcherSet filters = setting
5079 if (filters != null)
5081 FeatureMatcherSetI filter = Jalview2XML
5082 .parseFilter(featureType, filters);
5083 if (!filter.isEmpty())
5085 fr.setFeatureFilter(featureType, filter);
5090 * restore feature colour scheme
5092 Color maxColour = new Color(setting.getColour());
5093 if (setting.getMincolour() != null)
5096 * minColour is always set unless a simple colour
5097 * (including for colour by label though it doesn't use it)
5099 Color minColour = new Color(setting.getMincolour().intValue());
5100 Color noValueColour = minColour;
5101 NoValueColour noColour = setting.getNoValueColour();
5102 if (noColour == NoValueColour.NONE)
5104 noValueColour = null;
5106 else if (noColour == NoValueColour.MAX)
5108 noValueColour = maxColour;
5110 float min = safeFloat(safeFloat(setting.getMin()));
5111 float max = setting.getMax() == null ? 1f
5112 : setting.getMax().floatValue();
5113 FeatureColourI gc = new FeatureColour(maxColour, minColour,
5115 noValueColour, min, max);
5116 if (setting.getAttributeName().size() > 0)
5118 gc.setAttributeName(setting.getAttributeName().toArray(
5119 new String[setting.getAttributeName().size()]));
5121 if (setting.getThreshold() != null)
5123 gc.setThreshold(setting.getThreshold().floatValue());
5124 int threshstate = safeInt(setting.getThreshstate());
5125 // -1 = None, 0 = Below, 1 = Above threshold
5126 if (threshstate == 0)
5128 gc.setBelowThreshold(true);
5130 else if (threshstate == 1)
5132 gc.setAboveThreshold(true);
5135 gc.setAutoScaled(true); // default
5136 if (setting.isAutoScale() != null)
5138 gc.setAutoScaled(setting.isAutoScale());
5140 if (setting.isColourByLabel() != null)
5142 gc.setColourByLabel(setting.isColourByLabel());
5144 // and put in the feature colour table.
5145 featureColours.put(featureType, gc);
5149 featureColours.put(featureType,
5150 new FeatureColour(maxColour));
5152 renderOrder[fs] = featureType;
5153 if (setting.getOrder() != null)
5155 featureOrder.put(featureType, setting.getOrder().floatValue());
5159 featureOrder.put(featureType, Float.valueOf(
5160 fs / jm.getFeatureSettings().getSetting().size()));
5162 if (safeBoolean(setting.isDisplay()))
5164 fdi.setVisible(featureType);
5167 Map<String, Boolean> fgtable = new Hashtable<>();
5168 for (int gs = 0; gs < jm.getFeatureSettings().getGroup().size(); gs++)
5170 Group grp = jm.getFeatureSettings().getGroup().get(gs);
5171 fgtable.put(grp.getName(), Boolean.valueOf(grp.isDisplay()));
5173 // FeatureRendererSettings frs = new FeatureRendererSettings(renderOrder,
5174 // fgtable, featureColours, jms.getFeatureSettings().hasTransparency() ?
5175 // jms.getFeatureSettings().getTransparency() : 0.0, featureOrder);
5176 FeatureRendererSettings frs = new FeatureRendererSettings(renderOrder,
5177 fgtable, featureColours, 1.0f, featureOrder);
5178 fr.transferSettings(frs);
5181 if (view.getHiddenColumns().size() > 0)
5183 for (int c = 0; c < view.getHiddenColumns().size(); c++)
5185 final HiddenColumns hc = view.getHiddenColumns().get(c);
5186 viewport.hideColumns(safeInt(hc.getStart()),
5187 safeInt(hc.getEnd()) /* +1 */);
5190 if (view.getCalcIdParam() != null)
5192 for (CalcIdParam calcIdParam : view.getCalcIdParam())
5194 if (calcIdParam != null)
5196 if (recoverCalcIdParam(calcIdParam, viewport))
5201 warn("Couldn't recover parameters for "
5202 + calcIdParam.getCalcId());
5207 af.setMenusFromViewport(viewport);
5208 af.setTitle(view.getTitle());
5209 // TODO: we don't need to do this if the viewport is aready visible.
5211 * Add the AlignFrame to the desktop (it may be 'gathered' later), unless it
5212 * has a 'cdna/protein complement' view, in which case save it in order to
5213 * populate a SplitFrame once all views have been read in.
5215 String complementaryViewId = view.getComplementId();
5216 if (complementaryViewId == null)
5218 Desktop.addInternalFrame(af, view.getTitle(),
5219 safeInt(view.getWidth()), safeInt(view.getHeight()));
5220 // recompute any autoannotation
5221 af.alignPanel.updateAnnotation(false, true);
5222 reorderAutoannotation(af, al, autoAlan);
5223 af.alignPanel.alignmentChanged();
5227 splitFrameCandidates.put(view, af);
5233 * Reads saved data to restore Colour by Annotation settings
5235 * @param viewAnnColour
5239 * @param checkGroupAnnColour
5242 private ColourSchemeI constructAnnotationColour(
5243 AnnotationColourScheme viewAnnColour, AlignFrame af,
5244 AlignmentI al, JalviewModel model, boolean checkGroupAnnColour)
5246 boolean propagateAnnColour = false;
5247 AlignmentI annAlignment = af != null ? af.getViewport().getAlignment()
5249 if (checkGroupAnnColour && al.getGroups() != null
5250 && al.getGroups().size() > 0)
5252 // pre 2.8.1 behaviour
5253 // check to see if we should transfer annotation colours
5254 propagateAnnColour = true;
5255 for (SequenceGroup sg : al.getGroups())
5257 if (sg.getColourScheme() instanceof AnnotationColourGradient)
5259 propagateAnnColour = false;
5265 * 2.10.2- : saved annotationId is AlignmentAnnotation.annotationId
5267 String annotationId = viewAnnColour.getAnnotation();
5268 AlignmentAnnotation matchedAnnotation = annotationIds.get(annotationId);
5271 * pre 2.10.2: saved annotationId is AlignmentAnnotation.label
5273 if (matchedAnnotation == null
5274 && annAlignment.getAlignmentAnnotation() != null)
5276 for (int i = 0; i < annAlignment.getAlignmentAnnotation().length; i++)
5279 .equals(annAlignment.getAlignmentAnnotation()[i].label))
5281 matchedAnnotation = annAlignment.getAlignmentAnnotation()[i];
5286 if (matchedAnnotation == null)
5288 System.err.println("Failed to match annotation colour scheme for "
5292 if (matchedAnnotation.getThreshold() == null)
5294 matchedAnnotation.setThreshold(
5295 new GraphLine(safeFloat(viewAnnColour.getThreshold()),
5296 "Threshold", Color.black));
5299 AnnotationColourGradient cs = null;
5300 if (viewAnnColour.getColourScheme().equals("None"))
5302 cs = new AnnotationColourGradient(matchedAnnotation,
5303 new Color(safeInt(viewAnnColour.getMinColour())),
5304 new Color(safeInt(viewAnnColour.getMaxColour())),
5305 safeInt(viewAnnColour.getAboveThreshold()));
5307 else if (viewAnnColour.getColourScheme().startsWith("ucs"))
5309 cs = new AnnotationColourGradient(matchedAnnotation,
5310 getUserColourScheme(model, viewAnnColour.getColourScheme()),
5311 safeInt(viewAnnColour.getAboveThreshold()));
5315 cs = new AnnotationColourGradient(matchedAnnotation,
5316 ColourSchemeProperty.getColourScheme(af.getViewport(), al,
5317 viewAnnColour.getColourScheme()),
5318 safeInt(viewAnnColour.getAboveThreshold()));
5321 boolean perSequenceOnly = safeBoolean(viewAnnColour.isPerSequence());
5322 boolean useOriginalColours = safeBoolean(
5323 viewAnnColour.isPredefinedColours());
5324 cs.setSeqAssociated(perSequenceOnly);
5325 cs.setPredefinedColours(useOriginalColours);
5327 if (propagateAnnColour && al.getGroups() != null)
5329 // Also use these settings for all the groups
5330 for (int g = 0; g < al.getGroups().size(); g++)
5332 SequenceGroup sg = al.getGroups().get(g);
5333 if (sg.getGroupColourScheme() == null)
5338 AnnotationColourGradient groupScheme = new AnnotationColourGradient(
5339 matchedAnnotation, sg.getColourScheme(),
5340 safeInt(viewAnnColour.getAboveThreshold()));
5341 sg.setColourScheme(groupScheme);
5342 groupScheme.setSeqAssociated(perSequenceOnly);
5343 groupScheme.setPredefinedColours(useOriginalColours);
5349 private void reorderAutoannotation(AlignFrame af, AlignmentI al,
5350 List<JvAnnotRow> autoAlan)
5352 // copy over visualization settings for autocalculated annotation in the
5354 if (al.getAlignmentAnnotation() != null)
5357 * Kludge for magic autoannotation names (see JAL-811)
5359 String[] magicNames = new String[] { "Consensus", "Quality",
5361 JvAnnotRow nullAnnot = new JvAnnotRow(-1, null);
5362 Hashtable<String, JvAnnotRow> visan = new Hashtable<>();
5363 for (String nm : magicNames)
5365 visan.put(nm, nullAnnot);
5367 for (JvAnnotRow auan : autoAlan)
5369 visan.put(auan.template.label
5370 + (auan.template.getCalcId() == null ? ""
5371 : "\t" + auan.template.getCalcId()),
5374 int hSize = al.getAlignmentAnnotation().length;
5375 List<JvAnnotRow> reorder = new ArrayList<>();
5376 // work through any autoCalculated annotation already on the view
5377 // removing it if it should be placed in a different location on the
5378 // annotation panel.
5379 List<String> remains = new ArrayList<>(visan.keySet());
5380 for (int h = 0; h < hSize; h++)
5382 jalview.datamodel.AlignmentAnnotation jalan = al
5383 .getAlignmentAnnotation()[h];
5384 if (jalan.autoCalculated)
5387 JvAnnotRow valan = visan.get(k = jalan.label);
5388 if (jalan.getCalcId() != null)
5390 valan = visan.get(k = jalan.label + "\t" + jalan.getCalcId());
5395 // delete the auto calculated row from the alignment
5396 al.deleteAnnotation(jalan, false);
5400 if (valan != nullAnnot)
5402 if (jalan != valan.template)
5404 // newly created autoannotation row instance
5405 // so keep a reference to the visible annotation row
5406 // and copy over all relevant attributes
5407 if (valan.template.graphHeight >= 0)
5410 jalan.graphHeight = valan.template.graphHeight;
5412 jalan.visible = valan.template.visible;
5414 reorder.add(new JvAnnotRow(valan.order, jalan));
5419 // Add any (possibly stale) autocalculated rows that were not appended to
5420 // the view during construction
5421 for (String other : remains)
5423 JvAnnotRow othera = visan.get(other);
5424 if (othera != nullAnnot && othera.template.getCalcId() != null
5425 && othera.template.getCalcId().length() > 0)
5427 reorder.add(othera);
5430 // now put the automatic annotation in its correct place
5431 int s = 0, srt[] = new int[reorder.size()];
5432 JvAnnotRow[] rws = new JvAnnotRow[reorder.size()];
5433 for (JvAnnotRow jvar : reorder)
5436 srt[s++] = jvar.order;
5439 jalview.util.QuickSort.sort(srt, rws);
5440 // and re-insert the annotation at its correct position
5441 for (JvAnnotRow jvar : rws)
5443 al.addAnnotation(jvar.template, jvar.order);
5445 af.alignPanel.adjustAnnotationHeight();
5449 Hashtable skipList = null;
5452 * TODO remove this method
5455 * @return AlignFrame bound to sequenceSetId from view, if one exists. private
5456 * AlignFrame getSkippedFrame(Viewport view) { if (skipList==null) {
5457 * throw new Error("Implementation Error. No skipList defined for this
5458 * Jalview2XML instance."); } return (AlignFrame)
5459 * skipList.get(view.getSequenceSetId()); }
5463 * Check if the Jalview view contained in object should be skipped or not.
5466 * @return true if view's sequenceSetId is a key in skipList
5468 private boolean skipViewport(JalviewModel object)
5470 if (skipList == null)
5474 String id = object.getViewport().get(0).getSequenceSetId();
5475 if (skipList.containsKey(id))
5477 if (Cache.log != null && Cache.log.isDebugEnabled())
5479 Cache.log.debug("Skipping seuqence set id " + id);
5486 public void addToSkipList(AlignFrame af)
5488 if (skipList == null)
5490 skipList = new Hashtable();
5492 skipList.put(af.getViewport().getSequenceSetId(), af);
5495 public void clearSkipList()
5497 if (skipList != null)
5504 private void recoverDatasetFor(SequenceSet vamsasSet, AlignmentI al,
5505 boolean ignoreUnrefed, String uniqueSeqSetId)
5507 jalview.datamodel.AlignmentI ds = getDatasetFor(
5508 vamsasSet.getDatasetId());
5509 AlignmentI xtant_ds = ds;
5510 if (xtant_ds == null)
5512 // good chance we are about to create a new dataset, but check if we've
5513 // seen some of the dataset sequence IDs before.
5514 // TODO: skip this check if we are working with project generated by
5515 // version 2.11 or later
5516 xtant_ds = checkIfHasDataset(vamsasSet.getSequence());
5517 if (xtant_ds != null)
5520 addDatasetRef(vamsasSet.getDatasetId(), ds);
5523 Vector dseqs = null;
5526 // recovering an alignment View
5527 AlignmentI seqSetDS = getDatasetFor(UNIQSEQSETID + uniqueSeqSetId);
5528 if (seqSetDS != null)
5530 if (ds != null && ds != seqSetDS)
5532 warn("JAL-3171 regression: Overwriting a dataset reference for an alignment"
5533 + " - CDS/Protein crossreference data may be lost");
5534 if (xtant_ds != null)
5536 // This can only happen if the unique sequence set ID was bound to a
5537 // dataset that did not contain any of the sequences in the view
5538 // currently being restored.
5539 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.");
5543 addDatasetRef(vamsasSet.getDatasetId(), ds);
5548 // try even harder to restore dataset
5549 AlignmentI xtantDS = checkIfHasDataset(vamsasSet.getSequence());
5550 // create a list of new dataset sequences
5551 dseqs = new Vector();
5553 for (int i = 0, iSize = vamsasSet.getSequence().size(); i < iSize; i++)
5555 Sequence vamsasSeq = vamsasSet.getSequence().get(i);
5556 ensureJalviewDatasetSequence(vamsasSeq, ds, dseqs, ignoreUnrefed, i);
5558 // create a new dataset
5561 SequenceI[] dsseqs = new SequenceI[dseqs.size()];
5562 dseqs.copyInto(dsseqs);
5563 ds = new jalview.datamodel.Alignment(dsseqs);
5564 debug("Created new dataset " + vamsasSet.getDatasetId()
5565 + " for alignment " + System.identityHashCode(al));
5566 addDatasetRef(vamsasSet.getDatasetId(), ds);
5568 // set the dataset for the newly imported alignment.
5569 if (al.getDataset() == null && !ignoreUnrefed)
5572 // register dataset for the alignment's uniqueSeqSetId for legacy projects
5573 addDatasetRef(UNIQSEQSETID + uniqueSeqSetId, ds);
5575 updateSeqDatasetBinding(vamsasSet.getSequence(), ds);
5579 * XML dataset sequence ID to materialised dataset reference
5581 HashMap<String, AlignmentI> seqToDataset = new HashMap<>();
5584 * @return the first materialised dataset reference containing a dataset
5585 * sequence referenced in the given view
5587 * - sequences from the view
5589 AlignmentI checkIfHasDataset(List<Sequence> list)
5591 for (Sequence restoredSeq : list)
5593 AlignmentI datasetFor = seqToDataset.get(restoredSeq.getDsseqid());
5594 if (datasetFor != null)
5603 * Register ds as the containing dataset for the dataset sequences referenced
5604 * by sequences in list
5607 * - sequences in a view
5610 void updateSeqDatasetBinding(List<Sequence> list, AlignmentI ds)
5612 for (Sequence restoredSeq : list)
5614 AlignmentI prevDS = seqToDataset.put(restoredSeq.getDsseqid(), ds);
5615 if (prevDS != null && prevDS != ds)
5617 warn("Dataset sequence appears in many datasets: "
5618 + restoredSeq.getDsseqid());
5619 // TODO: try to merge!
5626 * sequence definition to create/merge dataset sequence for
5630 * vector to add new dataset sequence to
5631 * @param ignoreUnrefed
5632 * - when true, don't create new sequences from vamsasSeq if it's id
5633 * doesn't already have an asssociated Jalview sequence.
5635 * - used to reorder the sequence in the alignment according to the
5636 * vamsasSeq array ordering, to preserve ordering of dataset
5638 private void ensureJalviewDatasetSequence(Sequence vamsasSeq,
5639 AlignmentI ds, Vector dseqs, boolean ignoreUnrefed, int vseqpos)
5641 // JBP TODO: Check this is called for AlCodonFrames to support recovery of
5643 SequenceI sq = seqRefIds.get(vamsasSeq.getId());
5644 boolean reorder = false;
5645 SequenceI dsq = null;
5646 if (sq != null && sq.getDatasetSequence() != null)
5648 dsq = sq.getDatasetSequence();
5654 if (sq == null && ignoreUnrefed)
5658 String sqid = vamsasSeq.getDsseqid();
5661 // need to create or add a new dataset sequence reference to this sequence
5664 dsq = seqRefIds.get(sqid);
5669 // make a new dataset sequence
5670 dsq = sq.createDatasetSequence();
5673 // make up a new dataset reference for this sequence
5674 sqid = seqHash(dsq);
5676 dsq.setVamsasId(uniqueSetSuffix + sqid);
5677 seqRefIds.put(sqid, dsq);
5682 dseqs.addElement(dsq);
5687 ds.addSequence(dsq);
5693 { // make this dataset sequence sq's dataset sequence
5694 sq.setDatasetSequence(dsq);
5695 // and update the current dataset alignment
5700 if (!dseqs.contains(dsq))
5707 if (ds.findIndex(dsq) < 0)
5709 ds.addSequence(dsq);
5716 // TODO: refactor this as a merge dataset sequence function
5717 // now check that sq (the dataset sequence) sequence really is the union of
5718 // all references to it
5719 // boolean pre = sq.getStart() < dsq.getStart();
5720 // boolean post = sq.getEnd() > dsq.getEnd();
5724 // StringBuffer sb = new StringBuffer();
5725 String newres = jalview.analysis.AlignSeq.extractGaps(
5726 jalview.util.Comparison.GapChars, sq.getSequenceAsString());
5727 if (!newres.equalsIgnoreCase(dsq.getSequenceAsString())
5728 && newres.length() > dsq.getLength())
5730 // Update with the longer sequence.
5734 * if (pre) { sb.insert(0, newres .substring(0, dsq.getStart() -
5735 * sq.getStart())); dsq.setStart(sq.getStart()); } if (post) {
5736 * sb.append(newres.substring(newres.length() - sq.getEnd() -
5737 * dsq.getEnd())); dsq.setEnd(sq.getEnd()); }
5739 dsq.setSequence(newres);
5741 // TODO: merges will never happen if we 'know' we have the real dataset
5742 // sequence - this should be detected when id==dssid
5744 "DEBUG Notice: Merged dataset sequence (if you see this often, post at http://issues.jalview.org/browse/JAL-1474)"); // ("
5745 // + (pre ? "prepended" : "") + " "
5746 // + (post ? "appended" : ""));
5751 // sequence refs are identical. We may need to update the existing dataset
5752 // alignment with this one, though.
5753 if (ds != null && dseqs == null)
5755 int opos = ds.findIndex(dsq);
5756 SequenceI tseq = null;
5757 if (opos != -1 && vseqpos != opos)
5759 // remove from old position
5760 ds.deleteSequence(dsq);
5762 if (vseqpos < ds.getHeight())
5764 if (vseqpos != opos)
5766 // save sequence at destination position
5767 tseq = ds.getSequenceAt(vseqpos);
5768 ds.replaceSequenceAt(vseqpos, dsq);
5769 ds.addSequence(tseq);
5774 ds.addSequence(dsq);
5781 * TODO use AlignmentI here and in related methods - needs
5782 * AlignmentI.getDataset() changed to return AlignmentI instead of Alignment
5784 Hashtable<String, AlignmentI> datasetIds = null;
5786 IdentityHashMap<AlignmentI, String> dataset2Ids = null;
5788 private AlignmentI getDatasetFor(String datasetId)
5790 if (datasetIds == null)
5792 datasetIds = new Hashtable<>();
5795 if (datasetIds.containsKey(datasetId))
5797 return datasetIds.get(datasetId);
5802 private void addDatasetRef(String datasetId, AlignmentI dataset)
5804 if (datasetIds == null)
5806 datasetIds = new Hashtable<>();
5808 datasetIds.put(datasetId, dataset);
5812 * make a new dataset ID for this jalview dataset alignment
5817 private String getDatasetIdRef(AlignmentI dataset)
5819 if (dataset.getDataset() != null)
5821 warn("Serious issue! Dataset Object passed to getDatasetIdRef is not a Jalview DATASET alignment...");
5823 String datasetId = makeHashCode(dataset, null);
5824 if (datasetId == null)
5826 // make a new datasetId and record it
5827 if (dataset2Ids == null)
5829 dataset2Ids = new IdentityHashMap<>();
5833 datasetId = dataset2Ids.get(dataset);
5835 if (datasetId == null)
5837 datasetId = "ds" + dataset2Ids.size() + 1;
5838 dataset2Ids.put(dataset, datasetId);
5845 * Add any saved DBRefEntry's to the sequence. An entry flagged as 'locus' is
5846 * constructed as a special subclass GeneLocus.
5848 * @param datasetSequence
5851 private void addDBRefs(SequenceI datasetSequence, Sequence sequence)
5853 for (int d = 0; d < sequence.getDBRef().size(); d++)
5855 DBRef dr = sequence.getDBRef().get(d);
5859 entry = new GeneLocus(dr.getSource(), dr.getVersion(),
5860 dr.getAccessionId());
5864 entry = new DBRefEntry(dr.getSource(), dr.getVersion(),
5865 dr.getAccessionId());
5867 if (dr.getMapping() != null)
5869 entry.setMap(addMapping(dr.getMapping()));
5871 datasetSequence.addDBRef(entry);
5875 private jalview.datamodel.Mapping addMapping(Mapping m)
5877 SequenceI dsto = null;
5878 // Mapping m = dr.getMapping();
5879 int fr[] = new int[m.getMapListFrom().size() * 2];
5880 Iterator<MapListFrom> from = m.getMapListFrom().iterator();// enumerateMapListFrom();
5881 for (int _i = 0; from.hasNext(); _i += 2)
5883 MapListFrom mf = from.next();
5884 fr[_i] = mf.getStart();
5885 fr[_i + 1] = mf.getEnd();
5887 int fto[] = new int[m.getMapListTo().size() * 2];
5888 Iterator<MapListTo> to = m.getMapListTo().iterator();// enumerateMapListTo();
5889 for (int _i = 0; to.hasNext(); _i += 2)
5891 MapListTo mf = to.next();
5892 fto[_i] = mf.getStart();
5893 fto[_i + 1] = mf.getEnd();
5895 jalview.datamodel.Mapping jmap = new jalview.datamodel.Mapping(dsto, fr,
5896 fto, m.getMapFromUnit().intValue(),
5897 m.getMapToUnit().intValue());
5900 * (optional) choice of dseqFor or Sequence
5902 if (m.getDseqFor() != null)
5904 String dsfor = m.getDseqFor();
5905 if (seqRefIds.containsKey(dsfor))
5910 jmap.setTo(seqRefIds.get(dsfor));
5914 frefedSequence.add(newMappingRef(dsfor, jmap));
5917 else if (m.getSequence() != null)
5920 * local sequence definition
5922 Sequence ms = m.getSequence();
5923 SequenceI djs = null;
5924 String sqid = ms.getDsseqid();
5925 if (sqid != null && sqid.length() > 0)
5928 * recover dataset sequence
5930 djs = seqRefIds.get(sqid);
5935 "Warning - making up dataset sequence id for DbRef sequence map reference");
5936 sqid = ((Object) ms).toString(); // make up a new hascode for
5937 // undefined dataset sequence hash
5938 // (unlikely to happen)
5944 * make a new dataset sequence and add it to refIds hash
5946 djs = new jalview.datamodel.Sequence(ms.getName(),
5948 djs.setStart(jmap.getMap().getToLowest());
5949 djs.setEnd(jmap.getMap().getToHighest());
5950 djs.setVamsasId(uniqueSetSuffix + sqid);
5952 incompleteSeqs.put(sqid, djs);
5953 seqRefIds.put(sqid, djs);
5956 jalview.bin.Cache.log.debug("about to recurse on addDBRefs.");
5965 * Provides a 'copy' of an alignment view (on action New View) by 'saving' the
5966 * view as XML (but not to file), and then reloading it
5971 public AlignmentPanel copyAlignPanel(AlignmentPanel ap)
5974 JalviewModel jm = saveState(ap, null, null, null);
5977 jm.getVamsasModel().getSequenceSet().get(0).getDatasetId(),
5978 ap.getAlignment().getDataset());
5980 uniqueSetSuffix = "";
5981 // jm.getJalviewModelSequence().getViewport(0).setId(null);
5982 jm.getViewport().get(0).setId(null);
5983 // we don't overwrite the view we just copied
5985 if (this.frefedSequence == null)
5987 frefedSequence = new Vector<>();
5990 viewportsAdded.clear();
5992 AlignFrame af = loadFromObject(jm, null, false, null);
5993 af.getAlignPanels().clear();
5994 af.closeMenuItem_actionPerformed(true);
5997 * if(ap.av.getAlignment().getAlignmentAnnotation()!=null) { for(int i=0;
5998 * i<ap.av.getAlignment().getAlignmentAnnotation().length; i++) {
5999 * if(!ap.av.getAlignment().getAlignmentAnnotation()[i].autoCalculated) {
6000 * af.alignPanel.av.getAlignment().getAlignmentAnnotation()[i] =
6001 * ap.av.getAlignment().getAlignmentAnnotation()[i]; } } }
6004 return af.alignPanel;
6007 private Hashtable jvids2vobj;
6009 private void warn(String msg)
6014 private void warn(String msg, Exception e)
6016 if (Cache.log != null)
6020 Cache.log.warn(msg, e);
6024 Cache.log.warn(msg);
6029 System.err.println("Warning: " + msg);
6032 e.printStackTrace();
6037 private void debug(String string)
6039 debug(string, null);
6042 private void debug(String msg, Exception e)
6044 if (Cache.log != null)
6048 Cache.log.debug(msg, e);
6052 Cache.log.debug(msg);
6057 System.err.println("Warning: " + msg);
6060 e.printStackTrace();
6066 * set the object to ID mapping tables used to write/recover objects and XML
6067 * ID strings for the jalview project. If external tables are provided then
6068 * finalize and clearSeqRefs will not clear the tables when the Jalview2XML
6069 * object goes out of scope. - also populates the datasetIds hashtable with
6070 * alignment objects containing dataset sequences
6073 * Map from ID strings to jalview datamodel
6075 * Map from jalview datamodel to ID strings
6079 public void setObjectMappingTables(Hashtable vobj2jv,
6080 IdentityHashMap jv2vobj)
6082 this.jv2vobj = jv2vobj;
6083 this.vobj2jv = vobj2jv;
6084 Iterator ds = jv2vobj.keySet().iterator();
6086 while (ds.hasNext())
6088 Object jvobj = ds.next();
6089 id = jv2vobj.get(jvobj).toString();
6090 if (jvobj instanceof jalview.datamodel.Alignment)
6092 if (((jalview.datamodel.Alignment) jvobj).getDataset() == null)
6094 addDatasetRef(id, (jalview.datamodel.Alignment) jvobj);
6097 else if (jvobj instanceof jalview.datamodel.Sequence)
6099 // register sequence object so the XML parser can recover it.
6100 if (seqRefIds == null)
6102 seqRefIds = new HashMap<>();
6104 if (seqsToIds == null)
6106 seqsToIds = new IdentityHashMap<>();
6108 seqRefIds.put(jv2vobj.get(jvobj).toString(), (SequenceI) jvobj);
6109 seqsToIds.put((SequenceI) jvobj, id);
6111 else if (jvobj instanceof jalview.datamodel.AlignmentAnnotation)
6114 AlignmentAnnotation jvann = (AlignmentAnnotation) jvobj;
6115 annotationIds.put(anid = jv2vobj.get(jvobj).toString(), jvann);
6116 if (jvann.annotationId == null)
6118 jvann.annotationId = anid;
6120 if (!jvann.annotationId.equals(anid))
6122 // TODO verify that this is the correct behaviour
6123 this.warn("Overriding Annotation ID for " + anid
6124 + " from different id : " + jvann.annotationId);
6125 jvann.annotationId = anid;
6128 else if (jvobj instanceof String)
6130 if (jvids2vobj == null)
6132 jvids2vobj = new Hashtable();
6133 jvids2vobj.put(jvobj, jv2vobj.get(jvobj).toString());
6138 Cache.log.debug("Ignoring " + jvobj.getClass() + " (ID = " + id);
6144 * set the uniqueSetSuffix used to prefix/suffix object IDs for jalview
6145 * objects created from the project archive. If string is null (default for
6146 * construction) then suffix will be set automatically.
6150 public void setUniqueSetSuffix(String string)
6152 uniqueSetSuffix = string;
6157 * uses skipList2 as the skipList for skipping views on sequence sets
6158 * associated with keys in the skipList
6162 public void setSkipList(Hashtable skipList2)
6164 skipList = skipList2;
6168 * Reads the jar entry of given name and returns its contents, or null if the
6169 * entry is not found.
6172 * @param jarEntryName
6175 protected String readJarEntry(jarInputStreamProvider jprovider,
6176 String jarEntryName)
6178 String result = null;
6179 BufferedReader in = null;
6184 * Reopen the jar input stream and traverse its entries to find a matching
6187 JarInputStream jin = jprovider.getJarInputStream();
6188 JarEntry entry = null;
6191 entry = jin.getNextJarEntry();
6192 } while (entry != null && !entry.getName().equals(jarEntryName));
6196 StringBuilder out = new StringBuilder(256);
6197 in = new BufferedReader(new InputStreamReader(jin, UTF_8));
6200 while ((data = in.readLine()) != null)
6204 result = out.toString();
6208 warn("Couldn't find entry in Jalview Jar for " + jarEntryName);
6210 } catch (Exception ex)
6212 ex.printStackTrace();
6220 } catch (IOException e)
6231 * Returns an incrementing counter (0, 1, 2...)
6235 private synchronized int nextCounter()
6241 * Loads any saved PCA viewers
6246 protected void loadPCAViewers(JalviewModel model, AlignmentPanel ap)
6250 List<PcaViewer> pcaviewers = model.getPcaViewer();
6251 for (PcaViewer viewer : pcaviewers)
6253 String modelName = viewer.getScoreModelName();
6254 SimilarityParamsI params = new SimilarityParams(
6255 viewer.isIncludeGappedColumns(), viewer.isMatchGaps(),
6256 viewer.isIncludeGaps(),
6257 viewer.isDenominateByShortestLength());
6260 * create the panel (without computing the PCA)
6262 PCAPanel panel = new PCAPanel(ap, modelName, params);
6264 panel.setTitle(viewer.getTitle());
6265 panel.setBounds(new Rectangle(viewer.getXpos(), viewer.getYpos(),
6266 viewer.getWidth(), viewer.getHeight()));
6268 boolean showLabels = viewer.isShowLabels();
6269 panel.setShowLabels(showLabels);
6270 panel.getRotatableCanvas().setShowLabels(showLabels);
6271 panel.getRotatableCanvas()
6272 .setBgColour(new Color(viewer.getBgColour()));
6273 panel.getRotatableCanvas()
6274 .setApplyToAllViews(viewer.isLinkToAllViews());
6277 * load PCA output data
6279 ScoreModelI scoreModel = ScoreModels.getInstance()
6280 .getScoreModel(modelName, ap);
6281 PCA pca = new PCA(null, scoreModel, params);
6282 PcaDataType pcaData = viewer.getPcaData();
6284 MatrixI pairwise = loadDoubleMatrix(pcaData.getPairwiseMatrix());
6285 pca.setPairwiseScores(pairwise);
6287 MatrixI triDiag = loadDoubleMatrix(pcaData.getTridiagonalMatrix());
6288 pca.setTridiagonal(triDiag);
6290 MatrixI result = loadDoubleMatrix(pcaData.getEigenMatrix());
6291 pca.setEigenmatrix(result);
6293 panel.getPcaModel().setPCA(pca);
6296 * we haven't saved the input data! (JAL-2647 to do)
6298 panel.setInputData(null);
6301 * add the sequence points for the PCA display
6303 List<jalview.datamodel.SequencePoint> seqPoints = new ArrayList<>();
6304 for (SequencePoint sp : viewer.getSequencePoint())
6306 String seqId = sp.getSequenceRef();
6307 SequenceI seq = seqRefIds.get(seqId);
6310 throw new IllegalStateException(
6311 "Unmatched seqref for PCA: " + seqId);
6313 Point pt = new Point(sp.getXPos(), sp.getYPos(), sp.getZPos());
6314 jalview.datamodel.SequencePoint seqPoint = new jalview.datamodel.SequencePoint(
6316 seqPoints.add(seqPoint);
6318 panel.getRotatableCanvas().setPoints(seqPoints, seqPoints.size());
6321 * set min-max ranges and scale after setPoints (which recomputes them)
6323 panel.getRotatableCanvas().setScaleFactor(viewer.getScaleFactor());
6324 SeqPointMin spMin = viewer.getSeqPointMin();
6325 float[] min = new float[] { spMin.getXPos(), spMin.getYPos(),
6327 SeqPointMax spMax = viewer.getSeqPointMax();
6328 float[] max = new float[] { spMax.getXPos(), spMax.getYPos(),
6330 panel.getRotatableCanvas().setSeqMinMax(min, max);
6332 // todo: hold points list in PCAModel only
6333 panel.getPcaModel().setSequencePoints(seqPoints);
6335 panel.setSelectedDimensionIndex(viewer.getXDim(), X);
6336 panel.setSelectedDimensionIndex(viewer.getYDim(), Y);
6337 panel.setSelectedDimensionIndex(viewer.getZDim(), Z);
6339 // is this duplication needed?
6340 panel.setTop(seqPoints.size() - 1);
6341 panel.getPcaModel().setTop(seqPoints.size() - 1);
6344 * add the axes' end points for the display
6346 for (int i = 0; i < 3; i++)
6348 Axis axis = viewer.getAxis().get(i);
6349 panel.getRotatableCanvas().getAxisEndPoints()[i] = new Point(
6350 axis.getXPos(), axis.getYPos(), axis.getZPos());
6353 Desktop.addInternalFrame(panel, MessageManager.formatMessage(
6354 "label.calc_title", "PCA", modelName), 475, 450);
6356 } catch (Exception ex)
6358 Cache.log.error("Error loading PCA: " + ex.toString());
6363 * Populates an XML model of the feature colour scheme for one feature type
6365 * @param featureType
6369 public static Colour marshalColour(
6370 String featureType, FeatureColourI fcol)
6372 Colour col = new Colour();
6373 if (fcol.isSimpleColour())
6375 col.setRGB(Format.getHexString(fcol.getColour()));
6379 col.setRGB(Format.getHexString(fcol.getMaxColour()));
6380 col.setMin(fcol.getMin());
6381 col.setMax(fcol.getMax());
6382 col.setMinRGB(jalview.util.Format.getHexString(fcol.getMinColour()));
6383 col.setAutoScale(fcol.isAutoScaled());
6384 col.setThreshold(fcol.getThreshold());
6385 col.setColourByLabel(fcol.isColourByLabel());
6386 col.setThreshType(fcol.isAboveThreshold() ? ThresholdType.ABOVE
6387 : (fcol.isBelowThreshold() ? ThresholdType.BELOW
6388 : ThresholdType.NONE));
6389 if (fcol.isColourByAttribute())
6391 final String[] attName = fcol.getAttributeName();
6392 col.getAttributeName().add(attName[0]);
6393 if (attName.length > 1)
6395 col.getAttributeName().add(attName[1]);
6398 Color noColour = fcol.getNoColour();
6399 if (noColour == null)
6401 col.setNoValueColour(NoValueColour.NONE);
6403 else if (noColour == fcol.getMaxColour())
6405 col.setNoValueColour(NoValueColour.MAX);
6409 col.setNoValueColour(NoValueColour.MIN);
6412 col.setName(featureType);
6417 * Populates an XML model of the feature filter(s) for one feature type
6419 * @param firstMatcher
6420 * the first (or only) match condition)
6422 * remaining match conditions (if any)
6424 * if true, conditions are and-ed, else or-ed
6426 public static jalview.xml.binding.jalview.FeatureMatcherSet marshalFilter(
6427 FeatureMatcherI firstMatcher, Iterator<FeatureMatcherI> filters,
6430 jalview.xml.binding.jalview.FeatureMatcherSet result = new jalview.xml.binding.jalview.FeatureMatcherSet();
6432 if (filters.hasNext())
6437 CompoundMatcher compound = new CompoundMatcher();
6438 compound.setAnd(and);
6439 jalview.xml.binding.jalview.FeatureMatcherSet matcher1 = marshalFilter(
6440 firstMatcher, Collections.emptyIterator(), and);
6441 // compound.addMatcherSet(matcher1);
6442 compound.getMatcherSet().add(matcher1);
6443 FeatureMatcherI nextMatcher = filters.next();
6444 jalview.xml.binding.jalview.FeatureMatcherSet matcher2 = marshalFilter(
6445 nextMatcher, filters, and);
6446 // compound.addMatcherSet(matcher2);
6447 compound.getMatcherSet().add(matcher2);
6448 result.setCompoundMatcher(compound);
6453 * single condition matcher
6455 // MatchCondition matcherModel = new MatchCondition();
6456 jalview.xml.binding.jalview.FeatureMatcher matcherModel = new jalview.xml.binding.jalview.FeatureMatcher();
6457 matcherModel.setCondition(
6458 firstMatcher.getMatcher().getCondition().getStableName());
6459 matcherModel.setValue(firstMatcher.getMatcher().getPattern());
6460 if (firstMatcher.isByAttribute())
6462 matcherModel.setBy(FilterBy.BY_ATTRIBUTE);
6463 // matcherModel.setAttributeName(firstMatcher.getAttribute());
6464 String[] attName = firstMatcher.getAttribute();
6465 matcherModel.getAttributeName().add(attName[0]); // attribute
6466 if (attName.length > 1)
6468 matcherModel.getAttributeName().add(attName[1]); // sub-attribute
6471 else if (firstMatcher.isByLabel())
6473 matcherModel.setBy(FilterBy.BY_LABEL);
6475 else if (firstMatcher.isByScore())
6477 matcherModel.setBy(FilterBy.BY_SCORE);
6479 result.setMatchCondition(matcherModel);
6486 * Loads one XML model of a feature filter to a Jalview object
6488 * @param featureType
6489 * @param matcherSetModel
6492 public static FeatureMatcherSetI parseFilter(
6494 jalview.xml.binding.jalview.FeatureMatcherSet matcherSetModel)
6496 FeatureMatcherSetI result = new FeatureMatcherSet();
6499 parseFilterConditions(result, matcherSetModel, true);
6500 } catch (IllegalStateException e)
6502 // mixing AND and OR conditions perhaps
6504 String.format("Error reading filter conditions for '%s': %s",
6505 featureType, e.getMessage()));
6506 // return as much as was parsed up to the error
6513 * Adds feature match conditions to matcherSet as unmarshalled from XML
6514 * (possibly recursively for compound conditions)
6517 * @param matcherSetModel
6519 * if true, multiple conditions are AND-ed, else they are OR-ed
6520 * @throws IllegalStateException
6521 * if AND and OR conditions are mixed
6523 protected static void parseFilterConditions(
6524 FeatureMatcherSetI matcherSet,
6525 jalview.xml.binding.jalview.FeatureMatcherSet matcherSetModel,
6528 jalview.xml.binding.jalview.FeatureMatcher mc = matcherSetModel
6529 .getMatchCondition();
6535 FilterBy filterBy = mc.getBy();
6536 Condition cond = Condition.fromString(mc.getCondition());
6537 String pattern = mc.getValue();
6538 FeatureMatcherI matchCondition = null;
6539 if (filterBy == FilterBy.BY_LABEL)
6541 matchCondition = FeatureMatcher.byLabel(cond, pattern);
6543 else if (filterBy == FilterBy.BY_SCORE)
6545 matchCondition = FeatureMatcher.byScore(cond, pattern);
6548 else if (filterBy == FilterBy.BY_ATTRIBUTE)
6550 final List<String> attributeName = mc.getAttributeName();
6551 String[] attNames = attributeName
6552 .toArray(new String[attributeName.size()]);
6553 matchCondition = FeatureMatcher.byAttribute(cond, pattern,
6558 * note this throws IllegalStateException if AND-ing to a
6559 * previously OR-ed compound condition, or vice versa
6563 matcherSet.and(matchCondition);
6567 matcherSet.or(matchCondition);
6573 * compound condition
6575 List<jalview.xml.binding.jalview.FeatureMatcherSet> matchers = matcherSetModel
6576 .getCompoundMatcher().getMatcherSet();
6577 boolean anded = matcherSetModel.getCompoundMatcher().isAnd();
6578 if (matchers.size() == 2)
6580 parseFilterConditions(matcherSet, matchers.get(0), anded);
6581 parseFilterConditions(matcherSet, matchers.get(1), anded);
6585 System.err.println("Malformed compound filter condition");
6591 * Loads one XML model of a feature colour to a Jalview object
6593 * @param colourModel
6596 public static FeatureColourI parseColour(Colour colourModel)
6598 FeatureColourI colour = null;
6600 if (colourModel.getMax() != null)
6602 Color mincol = null;
6603 Color maxcol = null;
6604 Color noValueColour = null;
6608 mincol = new Color(Integer.parseInt(colourModel.getMinRGB(), 16));
6609 maxcol = new Color(Integer.parseInt(colourModel.getRGB(), 16));
6610 } catch (Exception e)
6612 Cache.log.warn("Couldn't parse out graduated feature color.", e);
6615 NoValueColour noCol = colourModel.getNoValueColour();
6616 if (noCol == NoValueColour.MIN)
6618 noValueColour = mincol;
6620 else if (noCol == NoValueColour.MAX)
6622 noValueColour = maxcol;
6625 colour = new FeatureColour(maxcol, mincol, maxcol, noValueColour,
6626 safeFloat(colourModel.getMin()),
6627 safeFloat(colourModel.getMax()));
6628 final List<String> attributeName = colourModel.getAttributeName();
6629 String[] attributes = attributeName
6630 .toArray(new String[attributeName.size()]);
6631 if (attributes != null && attributes.length > 0)
6633 colour.setAttributeName(attributes);
6635 if (colourModel.isAutoScale() != null)
6637 colour.setAutoScaled(colourModel.isAutoScale().booleanValue());
6639 if (colourModel.isColourByLabel() != null)
6641 colour.setColourByLabel(
6642 colourModel.isColourByLabel().booleanValue());
6644 if (colourModel.getThreshold() != null)
6646 colour.setThreshold(colourModel.getThreshold().floatValue());
6648 ThresholdType ttyp = colourModel.getThreshType();
6649 if (ttyp == ThresholdType.ABOVE)
6651 colour.setAboveThreshold(true);
6653 else if (ttyp == ThresholdType.BELOW)
6655 colour.setBelowThreshold(true);
6660 Color color = new Color(Integer.parseInt(colourModel.getRGB(), 16));
6661 colour = new FeatureColour(color);