2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 package jalview.project;
23 import static jalview.math.RotatableMatrix.Axis.X;
24 import static jalview.math.RotatableMatrix.Axis.Y;
25 import static jalview.math.RotatableMatrix.Axis.Z;
27 import java.awt.Color;
29 import java.awt.Rectangle;
30 import java.io.BufferedReader;
31 import java.io.ByteArrayInputStream;
33 import java.io.FileInputStream;
34 import java.io.FileOutputStream;
35 import java.io.IOException;
36 import java.io.InputStream;
37 import java.io.InputStreamReader;
38 import java.io.OutputStream;
39 import java.io.OutputStreamWriter;
40 import java.io.PrintWriter;
41 import java.lang.reflect.InvocationTargetException;
42 import java.math.BigInteger;
43 import java.net.MalformedURLException;
45 import java.util.ArrayList;
46 import java.util.Arrays;
47 import java.util.Collections;
48 import java.util.Enumeration;
49 import java.util.GregorianCalendar;
50 import java.util.HashMap;
51 import java.util.HashSet;
52 import java.util.Hashtable;
53 import java.util.IdentityHashMap;
54 import java.util.Iterator;
55 import java.util.LinkedHashMap;
56 import java.util.List;
58 import java.util.Map.Entry;
60 import java.util.Vector;
61 import java.util.jar.JarEntry;
62 import java.util.jar.JarInputStream;
63 import java.util.jar.JarOutputStream;
65 import javax.swing.JInternalFrame;
66 import javax.swing.SwingUtilities;
67 import javax.xml.bind.JAXBContext;
68 import javax.xml.bind.JAXBElement;
69 import javax.xml.bind.Marshaller;
70 import javax.xml.datatype.DatatypeConfigurationException;
71 import javax.xml.datatype.DatatypeFactory;
72 import javax.xml.datatype.XMLGregorianCalendar;
73 import javax.xml.stream.XMLInputFactory;
74 import javax.xml.stream.XMLStreamReader;
76 import jalview.analysis.Conservation;
77 import jalview.analysis.PCA;
78 import jalview.analysis.scoremodels.ScoreModels;
79 import jalview.analysis.scoremodels.SimilarityParams;
80 import jalview.api.FeatureColourI;
81 import jalview.api.ViewStyleI;
82 import jalview.api.analysis.ScoreModelI;
83 import jalview.api.analysis.SimilarityParamsI;
84 import jalview.api.structures.JalviewStructureDisplayI;
85 import jalview.bin.Cache;
86 import jalview.datamodel.AlignedCodonFrame;
87 import jalview.datamodel.Alignment;
88 import jalview.datamodel.AlignmentAnnotation;
89 import jalview.datamodel.AlignmentI;
90 import jalview.datamodel.DBRefEntry;
91 import jalview.datamodel.GeneLocus;
92 import jalview.datamodel.GraphLine;
93 import jalview.datamodel.PDBEntry;
94 import jalview.datamodel.Point;
95 import jalview.datamodel.RnaViewerModel;
96 import jalview.datamodel.SequenceFeature;
97 import jalview.datamodel.SequenceGroup;
98 import jalview.datamodel.SequenceI;
99 import jalview.datamodel.StructureViewerModel;
100 import jalview.datamodel.StructureViewerModel.StructureData;
101 import jalview.datamodel.features.FeatureMatcher;
102 import jalview.datamodel.features.FeatureMatcherI;
103 import jalview.datamodel.features.FeatureMatcherSet;
104 import jalview.datamodel.features.FeatureMatcherSetI;
105 import jalview.ext.varna.RnaModel;
106 import jalview.gui.AlignFrame;
107 import jalview.gui.AlignViewport;
108 import jalview.gui.AlignmentPanel;
109 import jalview.gui.AppVarna;
110 import jalview.gui.Desktop;
111 import jalview.gui.JvOptionPane;
112 import jalview.gui.OOMWarning;
113 import jalview.gui.PCAPanel;
114 import jalview.gui.PaintRefresher;
115 import jalview.gui.SplitFrame;
116 import jalview.gui.StructureViewer;
117 import jalview.gui.StructureViewer.ViewerType;
118 import jalview.gui.StructureViewerBase;
119 import jalview.gui.TreePanel;
120 import jalview.io.BackupFiles;
121 import jalview.io.DataSourceType;
122 import jalview.io.FileFormat;
123 import jalview.io.NewickFile;
124 import jalview.math.Matrix;
125 import jalview.math.MatrixI;
126 import jalview.renderer.ResidueShaderI;
127 import jalview.schemes.AnnotationColourGradient;
128 import jalview.schemes.ColourSchemeI;
129 import jalview.schemes.ColourSchemeProperty;
130 import jalview.schemes.FeatureColour;
131 import jalview.schemes.ResidueProperties;
132 import jalview.schemes.UserColourScheme;
133 import jalview.structure.StructureSelectionManager;
134 import jalview.structures.models.AAStructureBindingModel;
135 import jalview.util.Format;
136 import jalview.util.HttpUtils;
137 import jalview.util.MessageManager;
138 import jalview.util.Platform;
139 import jalview.util.StringUtils;
140 import jalview.util.jarInputStreamProvider;
141 import jalview.util.matcher.Condition;
142 import jalview.viewmodel.AlignmentViewport;
143 import jalview.viewmodel.PCAModel;
144 import jalview.viewmodel.ViewportRanges;
145 import jalview.viewmodel.seqfeatures.FeatureRendererModel;
146 import jalview.viewmodel.seqfeatures.FeatureRendererSettings;
147 import jalview.viewmodel.seqfeatures.FeaturesDisplayed;
148 import jalview.ws.jws2.Jws2Discoverer;
149 import jalview.ws.jws2.dm.AAConSettings;
150 import jalview.ws.jws2.jabaws2.Jws2Instance;
151 import jalview.ws.params.ArgumentI;
152 import jalview.ws.params.AutoCalcSetting;
153 import jalview.ws.params.WsParamSetI;
154 import jalview.xml.binding.jalview.AlcodonFrame;
155 import jalview.xml.binding.jalview.AlcodonFrame.AlcodMap;
156 import jalview.xml.binding.jalview.Annotation;
157 import jalview.xml.binding.jalview.Annotation.ThresholdLine;
158 import jalview.xml.binding.jalview.AnnotationColourScheme;
159 import jalview.xml.binding.jalview.AnnotationElement;
160 import jalview.xml.binding.jalview.DoubleMatrix;
161 import jalview.xml.binding.jalview.DoubleVector;
162 import jalview.xml.binding.jalview.Feature;
163 import jalview.xml.binding.jalview.Feature.OtherData;
164 import jalview.xml.binding.jalview.FeatureMatcherSet.CompoundMatcher;
165 import jalview.xml.binding.jalview.FilterBy;
166 import jalview.xml.binding.jalview.JalviewModel;
167 import jalview.xml.binding.jalview.JalviewModel.FeatureSettings;
168 import jalview.xml.binding.jalview.JalviewModel.FeatureSettings.Group;
169 import jalview.xml.binding.jalview.JalviewModel.FeatureSettings.Setting;
170 import jalview.xml.binding.jalview.JalviewModel.JGroup;
171 import jalview.xml.binding.jalview.JalviewModel.JSeq;
172 import jalview.xml.binding.jalview.JalviewModel.JSeq.Pdbids;
173 import jalview.xml.binding.jalview.JalviewModel.JSeq.Pdbids.StructureState;
174 import jalview.xml.binding.jalview.JalviewModel.JSeq.RnaViewer;
175 import jalview.xml.binding.jalview.JalviewModel.JSeq.RnaViewer.SecondaryStructure;
176 import jalview.xml.binding.jalview.JalviewModel.PcaViewer;
177 import jalview.xml.binding.jalview.JalviewModel.PcaViewer.Axis;
178 import jalview.xml.binding.jalview.JalviewModel.PcaViewer.SeqPointMax;
179 import jalview.xml.binding.jalview.JalviewModel.PcaViewer.SeqPointMin;
180 import jalview.xml.binding.jalview.JalviewModel.PcaViewer.SequencePoint;
181 import jalview.xml.binding.jalview.JalviewModel.Tree;
182 import jalview.xml.binding.jalview.JalviewModel.UserColours;
183 import jalview.xml.binding.jalview.JalviewModel.Viewport;
184 import jalview.xml.binding.jalview.JalviewModel.Viewport.CalcIdParam;
185 import jalview.xml.binding.jalview.JalviewModel.Viewport.HiddenColumns;
186 import jalview.xml.binding.jalview.JalviewUserColours;
187 import jalview.xml.binding.jalview.JalviewUserColours.Colour;
188 import jalview.xml.binding.jalview.MapListType.MapListFrom;
189 import jalview.xml.binding.jalview.MapListType.MapListTo;
190 import jalview.xml.binding.jalview.Mapping;
191 import jalview.xml.binding.jalview.NoValueColour;
192 import jalview.xml.binding.jalview.ObjectFactory;
193 import jalview.xml.binding.jalview.PcaDataType;
194 import jalview.xml.binding.jalview.Pdbentry.Property;
195 import jalview.xml.binding.jalview.Sequence;
196 import jalview.xml.binding.jalview.Sequence.DBRef;
197 import jalview.xml.binding.jalview.SequenceSet;
198 import jalview.xml.binding.jalview.SequenceSet.SequenceSetProperties;
199 import jalview.xml.binding.jalview.ThresholdType;
200 import jalview.xml.binding.jalview.VAMSAS;
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(
762 doBackup ? 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 = saveStructureViewer(ap, jds, pdb, entry,
1093 viewIds, 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 String viewerType = viewFrame.getViewerType().toString();
1100 if (!storeDS && !viewIds.contains(viewId))
1102 viewIds.add(viewId);
1103 File viewerState = viewFrame.saveSession();
1104 if (viewerState != null)
1106 copyFileToJar(jout, viewerState.getPath(),
1107 getViewerJarEntryName(viewId), viewerType);
1112 "Failed to save viewer state for " + viewerType);
1118 if (matchedFile != null || entry.getFile() != null)
1120 if (entry.getFile() != null)
1123 matchedFile = entry.getFile();
1125 pdb.setFile(matchedFile); // entry.getFile());
1126 if (pdbfiles == null)
1128 pdbfiles = new ArrayList<>();
1131 if (!pdbfiles.contains(pdbId))
1133 pdbfiles.add(pdbId);
1134 copyFileToJar(jout, matchedFile, pdbId, pdbId);
1138 Enumeration<String> props = entry.getProperties();
1139 if (props.hasMoreElements())
1141 // PdbentryItem item = new PdbentryItem();
1142 while (props.hasMoreElements())
1144 Property prop = new Property();
1145 String key = props.nextElement();
1147 prop.setValue(entry.getProperty(key).toString());
1148 // item.addProperty(prop);
1149 pdb.getProperty().add(prop);
1151 // pdb.addPdbentryItem(item);
1154 // jseq.addPdbids(pdb);
1155 jseq.getPdbids().add(pdb);
1159 saveRnaViewers(jout, jseq, jds, viewIds, ap, storeDS);
1161 // jms.addJSeq(jseq);
1162 object.getJSeq().add(jseq);
1165 if (!storeDS && av.hasHiddenRows())
1167 jal = av.getAlignment();
1171 if (storeDS && jal.getCodonFrames() != null)
1173 List<AlignedCodonFrame> jac = jal.getCodonFrames();
1174 for (AlignedCodonFrame acf : jac)
1176 AlcodonFrame alc = new AlcodonFrame();
1177 if (acf.getProtMappings() != null
1178 && acf.getProtMappings().length > 0)
1180 boolean hasMap = false;
1181 SequenceI[] dnas = acf.getdnaSeqs();
1182 jalview.datamodel.Mapping[] pmaps = acf.getProtMappings();
1183 for (int m = 0; m < pmaps.length; m++)
1185 AlcodMap alcmap = new AlcodMap();
1186 alcmap.setDnasq(seqHash(dnas[m]));
1188 createVamsasMapping(pmaps[m], dnas[m], null, false));
1189 // alc.addAlcodMap(alcmap);
1190 alc.getAlcodMap().add(alcmap);
1195 // vamsasSet.addAlcodonFrame(alc);
1196 vamsasSet.getAlcodonFrame().add(alc);
1199 // TODO: delete this ? dead code from 2.8.3->2.9 ?
1201 // AlcodonFrame alc = new AlcodonFrame();
1202 // vamsasSet.addAlcodonFrame(alc);
1203 // for (int p = 0; p < acf.aaWidth; p++)
1205 // Alcodon cmap = new Alcodon();
1206 // if (acf.codons[p] != null)
1208 // // Null codons indicate a gapped column in the translated peptide
1210 // cmap.setPos1(acf.codons[p][0]);
1211 // cmap.setPos2(acf.codons[p][1]);
1212 // cmap.setPos3(acf.codons[p][2]);
1214 // alc.addAlcodon(cmap);
1216 // if (acf.getProtMappings() != null
1217 // && acf.getProtMappings().length > 0)
1219 // SequenceI[] dnas = acf.getdnaSeqs();
1220 // jalview.datamodel.Mapping[] pmaps = acf.getProtMappings();
1221 // for (int m = 0; m < pmaps.length; m++)
1223 // AlcodMap alcmap = new AlcodMap();
1224 // alcmap.setDnasq(seqHash(dnas[m]));
1225 // alcmap.setMapping(createVamsasMapping(pmaps[m], dnas[m], null,
1227 // alc.addAlcodMap(alcmap);
1234 // /////////////////////////////////
1235 if (!storeDS && av.getCurrentTree() != null)
1237 // FIND ANY ASSOCIATED TREES
1238 // NOT IMPLEMENTED FOR HEADLESS STATE AT PRESENT
1239 if (Desktop.desktop != null)
1241 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1243 for (int t = 0; t < frames.length; t++)
1245 if (frames[t] instanceof TreePanel)
1247 TreePanel tp = (TreePanel) frames[t];
1249 if (tp.getTreeCanvas().getViewport().getAlignment() == jal)
1251 JalviewModel.Tree tree = new JalviewModel.Tree();
1252 tree.setTitle(tp.getTitle());
1253 tree.setCurrentTree((av.getCurrentTree() == tp.getTree()));
1254 tree.setNewick(tp.getTree().print());
1255 tree.setThreshold(tp.getTreeCanvas().getThreshold());
1257 tree.setFitToWindow(tp.fitToWindow.getState());
1258 tree.setFontName(tp.getTreeFont().getName());
1259 tree.setFontSize(tp.getTreeFont().getSize());
1260 tree.setFontStyle(tp.getTreeFont().getStyle());
1261 tree.setMarkUnlinked(tp.placeholdersMenu.getState());
1263 tree.setShowBootstrap(tp.bootstrapMenu.getState());
1264 tree.setShowDistances(tp.distanceMenu.getState());
1266 tree.setHeight(tp.getHeight());
1267 tree.setWidth(tp.getWidth());
1268 tree.setXpos(tp.getX());
1269 tree.setYpos(tp.getY());
1270 tree.setId(makeHashCode(tp, null));
1271 tree.setLinkToAllViews(
1272 tp.getTreeCanvas().isApplyToAllViews());
1274 // jms.addTree(tree);
1275 object.getTree().add(tree);
1285 if (!storeDS && Desktop.desktop != null)
1287 for (JInternalFrame frame : Desktop.desktop.getAllFrames())
1289 if (frame instanceof PCAPanel)
1291 PCAPanel panel = (PCAPanel) frame;
1292 if (panel.getAlignViewport().getAlignment() == jal)
1294 savePCA(panel, object);
1302 * store forward refs from an annotationRow to any groups
1304 IdentityHashMap<SequenceGroup, String> groupRefs = new IdentityHashMap<>();
1307 for (SequenceI sq : jal.getSequences())
1309 // Store annotation on dataset sequences only
1310 AlignmentAnnotation[] aa = sq.getAnnotation();
1311 if (aa != null && aa.length > 0)
1313 storeAlignmentAnnotation(aa, groupRefs, av, calcIdSet, storeDS,
1320 if (jal.getAlignmentAnnotation() != null)
1322 // Store the annotation shown on the alignment.
1323 AlignmentAnnotation[] aa = jal.getAlignmentAnnotation();
1324 storeAlignmentAnnotation(aa, groupRefs, av, calcIdSet, storeDS,
1329 if (jal.getGroups() != null)
1331 JGroup[] groups = new JGroup[jal.getGroups().size()];
1333 for (jalview.datamodel.SequenceGroup sg : jal.getGroups())
1335 JGroup jGroup = new JGroup();
1336 groups[++i] = jGroup;
1338 jGroup.setStart(sg.getStartRes());
1339 jGroup.setEnd(sg.getEndRes());
1340 jGroup.setName(sg.getName());
1341 if (groupRefs.containsKey(sg))
1343 // group has references so set its ID field
1344 jGroup.setId(groupRefs.get(sg));
1346 ColourSchemeI colourScheme = sg.getColourScheme();
1347 if (colourScheme != null)
1349 ResidueShaderI groupColourScheme = sg.getGroupColourScheme();
1350 if (groupColourScheme.conservationApplied())
1352 jGroup.setConsThreshold(groupColourScheme.getConservationInc());
1354 if (colourScheme instanceof jalview.schemes.UserColourScheme)
1356 jGroup.setColour(setUserColourScheme(colourScheme,
1357 userColours, object));
1361 jGroup.setColour(colourScheme.getSchemeName());
1364 else if (colourScheme instanceof jalview.schemes.AnnotationColourGradient)
1366 jGroup.setColour("AnnotationColourGradient");
1367 jGroup.setAnnotationColours(constructAnnotationColours(
1368 (jalview.schemes.AnnotationColourGradient) colourScheme,
1369 userColours, object));
1371 else if (colourScheme instanceof jalview.schemes.UserColourScheme)
1374 setUserColourScheme(colourScheme, userColours, object));
1378 jGroup.setColour(colourScheme.getSchemeName());
1381 jGroup.setPidThreshold(groupColourScheme.getThreshold());
1384 jGroup.setOutlineColour(sg.getOutlineColour().getRGB());
1385 jGroup.setDisplayBoxes(sg.getDisplayBoxes());
1386 jGroup.setDisplayText(sg.getDisplayText());
1387 jGroup.setColourText(sg.getColourText());
1388 jGroup.setTextCol1(sg.textColour.getRGB());
1389 jGroup.setTextCol2(sg.textColour2.getRGB());
1390 jGroup.setTextColThreshold(sg.thresholdTextColour);
1391 jGroup.setShowUnconserved(sg.getShowNonconserved());
1392 jGroup.setIgnoreGapsinConsensus(sg.getIgnoreGapsConsensus());
1393 jGroup.setShowConsensusHistogram(sg.isShowConsensusHistogram());
1394 jGroup.setShowSequenceLogo(sg.isShowSequenceLogo());
1395 jGroup.setNormaliseSequenceLogo(sg.isNormaliseSequenceLogo());
1396 for (SequenceI seq : sg.getSequences())
1398 // jGroup.addSeq(seqHash(seq));
1399 jGroup.getSeq().add(seqHash(seq));
1403 // jms.setJGroup(groups);
1405 for (JGroup grp : groups)
1407 object.getJGroup().add(grp);
1412 // /////////SAVE VIEWPORT
1413 Viewport view = new Viewport();
1414 view.setTitle(ap.alignFrame.getTitle());
1415 view.setSequenceSetId(
1416 makeHashCode(av.getSequenceSetId(), av.getSequenceSetId()));
1417 view.setId(av.getViewId());
1418 if (av.getCodingComplement() != null)
1420 view.setComplementId(av.getCodingComplement().getViewId());
1422 view.setViewName(av.getViewName());
1423 view.setGatheredViews(av.isGatherViewsHere());
1425 Rectangle size = ap.av.getExplodedGeometry();
1426 Rectangle position = size;
1429 size = ap.alignFrame.getBounds();
1430 if (av.getCodingComplement() != null)
1432 position = ((SplitFrame) ap.alignFrame.getSplitViewContainer())
1440 view.setXpos(position.x);
1441 view.setYpos(position.y);
1443 view.setWidth(size.width);
1444 view.setHeight(size.height);
1446 view.setStartRes(vpRanges.getStartRes());
1447 view.setStartSeq(vpRanges.getStartSeq());
1449 if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme)
1451 view.setBgColour(setUserColourScheme(av.getGlobalColourScheme(),
1452 userColours, object));
1455 .getGlobalColourScheme() instanceof jalview.schemes.AnnotationColourGradient)
1457 AnnotationColourScheme ac = constructAnnotationColours(
1458 (jalview.schemes.AnnotationColourGradient) av
1459 .getGlobalColourScheme(),
1460 userColours, object);
1462 view.setAnnotationColours(ac);
1463 view.setBgColour("AnnotationColourGradient");
1467 view.setBgColour(ColourSchemeProperty
1468 .getColourName(av.getGlobalColourScheme()));
1471 ResidueShaderI vcs = av.getResidueShading();
1472 ColourSchemeI cs = av.getGlobalColourScheme();
1476 if (vcs.conservationApplied())
1478 view.setConsThreshold(vcs.getConservationInc());
1479 if (cs instanceof jalview.schemes.UserColourScheme)
1481 view.setBgColour(setUserColourScheme(cs, userColours, object));
1484 view.setPidThreshold(vcs.getThreshold());
1487 view.setConservationSelected(av.getConservationSelected());
1488 view.setPidSelected(av.getAbovePIDThreshold());
1489 final Font font = av.getFont();
1490 view.setFontName(font.getName());
1491 view.setFontSize(font.getSize());
1492 view.setFontStyle(font.getStyle());
1493 view.setScaleProteinAsCdna(av.getViewStyle().isScaleProteinAsCdna());
1494 view.setRenderGaps(av.isRenderGaps());
1495 view.setShowAnnotation(av.isShowAnnotation());
1496 view.setShowBoxes(av.getShowBoxes());
1497 view.setShowColourText(av.getColourText());
1498 view.setShowFullId(av.getShowJVSuffix());
1499 view.setRightAlignIds(av.isRightAlignIds());
1500 view.setShowSequenceFeatures(av.isShowSequenceFeatures());
1501 view.setShowText(av.getShowText());
1502 view.setShowUnconserved(av.getShowUnconserved());
1503 view.setWrapAlignment(av.getWrapAlignment());
1504 view.setTextCol1(av.getTextColour().getRGB());
1505 view.setTextCol2(av.getTextColour2().getRGB());
1506 view.setTextColThreshold(av.getThresholdTextColour());
1507 view.setShowConsensusHistogram(av.isShowConsensusHistogram());
1508 view.setShowSequenceLogo(av.isShowSequenceLogo());
1509 view.setNormaliseSequenceLogo(av.isNormaliseSequenceLogo());
1510 view.setShowGroupConsensus(av.isShowGroupConsensus());
1511 view.setShowGroupConservation(av.isShowGroupConservation());
1512 view.setShowNPfeatureTooltip(av.isShowNPFeats());
1513 view.setShowDbRefTooltip(av.isShowDBRefs());
1514 view.setFollowHighlight(av.isFollowHighlight());
1515 view.setFollowSelection(av.followSelection);
1516 view.setIgnoreGapsinConsensus(av.isIgnoreGapsConsensus());
1517 view.setShowComplementFeatures(av.isShowComplementFeatures());
1518 view.setShowComplementFeaturesOnTop(
1519 av.isShowComplementFeaturesOnTop());
1520 if (av.getFeaturesDisplayed() != null)
1522 FeatureSettings fs = new FeatureSettings();
1524 FeatureRendererModel fr = ap.getSeqPanel().seqCanvas
1525 .getFeatureRenderer();
1526 String[] renderOrder = fr.getRenderOrder().toArray(new String[0]);
1528 Vector<String> settingsAdded = new Vector<>();
1529 if (renderOrder != null)
1531 for (String featureType : renderOrder)
1533 FeatureSettings.Setting setting = new FeatureSettings.Setting();
1534 setting.setType(featureType);
1537 * save any filter for the feature type
1539 FeatureMatcherSetI filter = fr.getFeatureFilter(featureType);
1542 Iterator<FeatureMatcherI> filters = filter.getMatchers()
1544 FeatureMatcherI firstFilter = filters.next();
1545 setting.setMatcherSet(Jalview2XML.marshalFilter(firstFilter,
1546 filters, filter.isAnded()));
1550 * save colour scheme for the feature type
1552 FeatureColourI fcol = fr.getFeatureStyle(featureType);
1553 if (!fcol.isSimpleColour())
1555 setting.setColour(fcol.getMaxColour().getRGB());
1556 setting.setMincolour(fcol.getMinColour().getRGB());
1557 setting.setMin(fcol.getMin());
1558 setting.setMax(fcol.getMax());
1559 setting.setColourByLabel(fcol.isColourByLabel());
1560 if (fcol.isColourByAttribute())
1562 String[] attName = fcol.getAttributeName();
1563 setting.getAttributeName().add(attName[0]);
1564 if (attName.length > 1)
1566 setting.getAttributeName().add(attName[1]);
1569 setting.setAutoScale(fcol.isAutoScaled());
1570 setting.setThreshold(fcol.getThreshold());
1571 Color noColour = fcol.getNoColour();
1572 if (noColour == null)
1574 setting.setNoValueColour(NoValueColour.NONE);
1576 else if (noColour.equals(fcol.getMaxColour()))
1578 setting.setNoValueColour(NoValueColour.MAX);
1582 setting.setNoValueColour(NoValueColour.MIN);
1584 // -1 = No threshold, 0 = Below, 1 = Above
1585 setting.setThreshstate(fcol.isAboveThreshold() ? 1
1586 : (fcol.isBelowThreshold() ? 0 : -1));
1590 setting.setColour(fcol.getColour().getRGB());
1594 av.getFeaturesDisplayed().isVisible(featureType));
1595 float rorder = fr.getOrder(featureType);
1598 setting.setOrder(rorder);
1600 /// fs.addSetting(setting);
1601 fs.getSetting().add(setting);
1602 settingsAdded.addElement(featureType);
1606 // is groups actually supposed to be a map here ?
1607 Iterator<String> en = fr.getFeatureGroups().iterator();
1608 Vector<String> groupsAdded = new Vector<>();
1609 while (en.hasNext())
1611 String grp = en.next();
1612 if (groupsAdded.contains(grp))
1616 Group g = new Group();
1618 g.setDisplay(((Boolean) fr.checkGroupVisibility(grp, false))
1621 fs.getGroup().add(g);
1622 groupsAdded.addElement(grp);
1624 // jms.setFeatureSettings(fs);
1625 object.setFeatureSettings(fs);
1628 if (av.hasHiddenColumns())
1630 jalview.datamodel.HiddenColumns hidden = av.getAlignment()
1631 .getHiddenColumns();
1634 warn("REPORT BUG: avoided null columnselection bug (DMAM reported). Please contact Jim about this.");
1638 Iterator<int[]> hiddenRegions = hidden.iterator();
1639 while (hiddenRegions.hasNext())
1641 int[] region = hiddenRegions.next();
1642 HiddenColumns hc = new HiddenColumns();
1643 hc.setStart(region[0]);
1644 hc.setEnd(region[1]);
1645 // view.addHiddenColumns(hc);
1646 view.getHiddenColumns().add(hc);
1650 if (calcIdSet.size() > 0)
1652 for (String calcId : calcIdSet)
1654 if (calcId.trim().length() > 0)
1656 CalcIdParam cidp = createCalcIdParam(calcId, av);
1657 // Some calcIds have no parameters.
1660 // view.addCalcIdParam(cidp);
1661 view.getCalcIdParam().add(cidp);
1667 // jms.addViewport(view);
1668 object.getViewport().add(view);
1670 // object.setJalviewModelSequence(jms);
1671 // object.getVamsasModel().addSequenceSet(vamsasSet);
1672 object.getVamsasModel().getSequenceSet().add(vamsasSet);
1674 if (jout != null && fileName != null)
1676 // We may not want to write the object to disk,
1677 // eg we can copy the alignViewport to a new view object
1678 // using save and then load
1681 fileName = fileName.replace('\\', '/');
1682 System.out.println("Writing jar entry " + fileName);
1683 JarEntry entry = new JarEntry(fileName);
1684 jout.putNextEntry(entry);
1685 PrintWriter pout = new PrintWriter(
1686 new OutputStreamWriter(jout, UTF_8));
1687 JAXBContext jaxbContext = JAXBContext
1688 .newInstance(JalviewModel.class);
1689 Marshaller jaxbMarshaller = jaxbContext.createMarshaller();
1691 // output pretty printed
1692 // jaxbMarshaller.setProperty(Marshaller.JAXB_FORMATTED_OUTPUT, true);
1693 jaxbMarshaller.marshal(
1694 new ObjectFactory().createJalviewModel(object), pout);
1696 // jaxbMarshaller.marshal(object, pout);
1697 // marshaller.marshal(object);
1700 } catch (Exception ex)
1702 // TODO: raise error in GUI if marshalling failed.
1703 System.err.println("Error writing Jalview project");
1704 ex.printStackTrace();
1711 * Writes PCA viewer attributes and computed values to an XML model object and
1712 * adds it to the JalviewModel. Any exceptions are reported by logging.
1714 protected void savePCA(PCAPanel panel, JalviewModel object)
1718 PcaViewer viewer = new PcaViewer();
1719 viewer.setHeight(panel.getHeight());
1720 viewer.setWidth(panel.getWidth());
1721 viewer.setXpos(panel.getX());
1722 viewer.setYpos(panel.getY());
1723 viewer.setTitle(panel.getTitle());
1724 PCAModel pcaModel = panel.getPcaModel();
1725 viewer.setScoreModelName(pcaModel.getScoreModelName());
1726 viewer.setXDim(panel.getSelectedDimensionIndex(X));
1727 viewer.setYDim(panel.getSelectedDimensionIndex(Y));
1728 viewer.setZDim(panel.getSelectedDimensionIndex(Z));
1730 panel.getRotatableCanvas().getBackgroundColour().getRGB());
1731 viewer.setScaleFactor(panel.getRotatableCanvas().getScaleFactor());
1732 float[] spMin = panel.getRotatableCanvas().getSeqMin();
1733 SeqPointMin spmin = new SeqPointMin();
1734 spmin.setXPos(spMin[0]);
1735 spmin.setYPos(spMin[1]);
1736 spmin.setZPos(spMin[2]);
1737 viewer.setSeqPointMin(spmin);
1738 float[] spMax = panel.getRotatableCanvas().getSeqMax();
1739 SeqPointMax spmax = new SeqPointMax();
1740 spmax.setXPos(spMax[0]);
1741 spmax.setYPos(spMax[1]);
1742 spmax.setZPos(spMax[2]);
1743 viewer.setSeqPointMax(spmax);
1744 viewer.setShowLabels(panel.getRotatableCanvas().isShowLabels());
1745 viewer.setLinkToAllViews(
1746 panel.getRotatableCanvas().isApplyToAllViews());
1747 SimilarityParamsI sp = pcaModel.getSimilarityParameters();
1748 viewer.setIncludeGaps(sp.includeGaps());
1749 viewer.setMatchGaps(sp.matchGaps());
1750 viewer.setIncludeGappedColumns(sp.includeGappedColumns());
1751 viewer.setDenominateByShortestLength(sp.denominateByShortestLength());
1754 * sequence points on display
1756 for (jalview.datamodel.SequencePoint spt : pcaModel
1757 .getSequencePoints())
1759 SequencePoint point = new SequencePoint();
1760 point.setSequenceRef(seqHash(spt.getSequence()));
1761 point.setXPos(spt.coord.x);
1762 point.setYPos(spt.coord.y);
1763 point.setZPos(spt.coord.z);
1764 viewer.getSequencePoint().add(point);
1768 * (end points of) axes on display
1770 for (Point p : panel.getRotatableCanvas().getAxisEndPoints())
1773 Axis axis = new Axis();
1777 viewer.getAxis().add(axis);
1781 * raw PCA data (note we are not restoring PCA inputs here -
1782 * alignment view, score model, similarity parameters)
1784 PcaDataType data = new PcaDataType();
1785 viewer.setPcaData(data);
1786 PCA pca = pcaModel.getPcaData();
1788 DoubleMatrix pm = new DoubleMatrix();
1789 saveDoubleMatrix(pca.getPairwiseScores(), pm);
1790 data.setPairwiseMatrix(pm);
1792 DoubleMatrix tm = new DoubleMatrix();
1793 saveDoubleMatrix(pca.getTridiagonal(), tm);
1794 data.setTridiagonalMatrix(tm);
1796 DoubleMatrix eigenMatrix = new DoubleMatrix();
1797 data.setEigenMatrix(eigenMatrix);
1798 saveDoubleMatrix(pca.getEigenmatrix(), eigenMatrix);
1800 object.getPcaViewer().add(viewer);
1801 } catch (Throwable t)
1803 Cache.log.error("Error saving PCA: " + t.getMessage());
1808 * Stores values from a matrix into an XML element, including (if present) the
1813 * @see #loadDoubleMatrix(DoubleMatrix)
1815 protected void saveDoubleMatrix(MatrixI m, DoubleMatrix xmlMatrix)
1817 xmlMatrix.setRows(m.height());
1818 xmlMatrix.setColumns(m.width());
1819 for (int i = 0; i < m.height(); i++)
1821 DoubleVector row = new DoubleVector();
1822 for (int j = 0; j < m.width(); j++)
1824 row.getV().add(m.getValue(i, j));
1826 xmlMatrix.getRow().add(row);
1828 if (m.getD() != null)
1830 DoubleVector dVector = new DoubleVector();
1831 for (double d : m.getD())
1833 dVector.getV().add(d);
1835 xmlMatrix.setD(dVector);
1837 if (m.getE() != null)
1839 DoubleVector eVector = new DoubleVector();
1840 for (double e : m.getE())
1842 eVector.getV().add(e);
1844 xmlMatrix.setE(eVector);
1849 * Loads XML matrix data into a new Matrix object, including the D and/or E
1850 * vectors (if present)
1854 * @see Jalview2XML#saveDoubleMatrix(MatrixI, DoubleMatrix)
1856 protected MatrixI loadDoubleMatrix(DoubleMatrix mData)
1858 int rows = mData.getRows();
1859 double[][] vals = new double[rows][];
1861 for (int i = 0; i < rows; i++)
1863 List<Double> dVector = mData.getRow().get(i).getV();
1864 vals[i] = new double[dVector.size()];
1866 for (Double d : dVector)
1872 MatrixI m = new Matrix(vals);
1874 if (mData.getD() != null)
1876 List<Double> dVector = mData.getD().getV();
1877 double[] vec = new double[dVector.size()];
1879 for (Double d : dVector)
1885 if (mData.getE() != null)
1887 List<Double> dVector = mData.getE().getV();
1888 double[] vec = new double[dVector.size()];
1890 for (Double d : dVector)
1901 * Save any Varna viewers linked to this sequence. Writes an rnaViewer element
1902 * for each viewer, with
1904 * <li>viewer geometry (position, size, split pane divider location)</li>
1905 * <li>index of the selected structure in the viewer (currently shows gapped
1907 * <li>the id of the annotation holding RNA secondary structure</li>
1908 * <li>(currently only one SS is shown per viewer, may be more in future)</li>
1910 * Varna viewer state is also written out (in native Varna XML) to separate
1911 * project jar entries. A separate entry is written for each RNA structure
1912 * displayed, with the naming convention
1914 * <li>rna_viewId_sequenceId_annotationId_[gapped|trimmed]</li>
1922 * @param storeDataset
1924 protected void saveRnaViewers(JarOutputStream jout, JSeq jseq,
1925 final SequenceI jds, List<String> viewIds, AlignmentPanel ap,
1926 boolean storeDataset)
1928 if (Desktop.desktop == null)
1932 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1933 for (int f = frames.length - 1; f > -1; f--)
1935 if (frames[f] instanceof AppVarna)
1937 AppVarna varna = (AppVarna) frames[f];
1939 * link the sequence to every viewer that is showing it and is linked to
1940 * its alignment panel
1942 if (varna.isListeningFor(jds) && ap == varna.getAlignmentPanel())
1944 String viewId = varna.getViewId();
1945 RnaViewer rna = new RnaViewer();
1946 rna.setViewId(viewId);
1947 rna.setTitle(varna.getTitle());
1948 rna.setXpos(varna.getX());
1949 rna.setYpos(varna.getY());
1950 rna.setWidth(varna.getWidth());
1951 rna.setHeight(varna.getHeight());
1952 rna.setDividerLocation(varna.getDividerLocation());
1953 rna.setSelectedRna(varna.getSelectedIndex());
1954 // jseq.addRnaViewer(rna);
1955 jseq.getRnaViewer().add(rna);
1958 * Store each Varna panel's state once in the project per sequence.
1959 * First time through only (storeDataset==false)
1961 // boolean storeSessions = false;
1962 // String sequenceViewId = viewId + seqsToIds.get(jds);
1963 // if (!storeDataset && !viewIds.contains(sequenceViewId))
1965 // viewIds.add(sequenceViewId);
1966 // storeSessions = true;
1968 for (RnaModel model : varna.getModels())
1970 if (model.seq == jds)
1973 * VARNA saves each view (sequence or alignment secondary
1974 * structure, gapped or trimmed) as a separate XML file
1976 String jarEntryName = rnaSessions.get(model);
1977 if (jarEntryName == null)
1980 String varnaStateFile = varna.getStateInfo(model.rna);
1981 jarEntryName = RNA_PREFIX + viewId + "_" + nextCounter();
1982 copyFileToJar(jout, varnaStateFile, jarEntryName, "Varna");
1983 rnaSessions.put(model, jarEntryName);
1985 SecondaryStructure ss = new SecondaryStructure();
1986 String annotationId = varna.getAnnotation(jds).annotationId;
1987 ss.setAnnotationId(annotationId);
1988 ss.setViewerState(jarEntryName);
1989 ss.setGapped(model.gapped);
1990 ss.setTitle(model.title);
1991 // rna.addSecondaryStructure(ss);
1992 rna.getSecondaryStructure().add(ss);
2001 * Copy the contents of a file to a new entry added to the output jar
2005 * @param jarEntryName
2007 * additional identifying info to log to the console
2009 protected void copyFileToJar(JarOutputStream jout, String infilePath,
2010 String jarEntryName, String msg)
2012 try (InputStream is = new FileInputStream(infilePath))
2014 File file = new File(infilePath);
2015 if (file.exists() && jout != null)
2018 "Writing jar entry " + jarEntryName + " (" + msg + ")");
2019 jout.putNextEntry(new JarEntry(jarEntryName));
2022 // dis = new DataInputStream(new FileInputStream(file));
2023 // byte[] data = new byte[(int) file.length()];
2024 // dis.readFully(data);
2025 // writeJarEntry(jout, jarEntryName, data);
2027 } catch (Exception ex)
2029 ex.printStackTrace();
2034 * Copies input to output, in 4K buffers; handles any data (text or binary)
2038 * @throws IOException
2040 protected void copyAll(InputStream in, OutputStream out)
2043 byte[] buffer = new byte[4096];
2045 while ((bytesRead = in.read(buffer)) != -1)
2047 out.write(buffer, 0, bytesRead);
2052 * Save the state of a structure viewer
2057 * the archive XML element under which to save the state
2060 * @param matchedFile
2064 protected String saveStructureViewer(AlignmentPanel ap, SequenceI jds,
2065 Pdbids pdb, PDBEntry entry, List<String> viewIds,
2066 String matchedFile, StructureViewerBase viewFrame)
2068 final AAStructureBindingModel bindingModel = viewFrame.getBinding();
2071 * Look for any bindings for this viewer to the PDB file of interest
2072 * (including part matches excluding chain id)
2074 for (int peid = 0; peid < bindingModel.getPdbCount(); peid++)
2076 final PDBEntry pdbentry = bindingModel.getPdbEntry(peid);
2077 final String pdbId = pdbentry.getId();
2078 if (!pdbId.equals(entry.getId())
2079 && !(entry.getId().length() > 4 && entry.getId().toLowerCase()
2080 .startsWith(pdbId.toLowerCase())))
2083 * not interested in a binding to a different PDB entry here
2087 if (matchedFile == null)
2089 matchedFile = pdbentry.getFile();
2091 else if (!matchedFile.equals(pdbentry.getFile()))
2094 "Probably lost some PDB-Sequence mappings for this structure file (which apparently has same PDB Entry code): "
2095 + pdbentry.getFile());
2099 // can get at it if the ID
2100 // match is ambiguous (e.g.
2103 for (int smap = 0; smap < viewFrame.getBinding()
2104 .getSequence()[peid].length; smap++)
2106 // if (jal.findIndex(jmol.jmb.sequence[peid][smap]) > -1)
2107 if (jds == viewFrame.getBinding().getSequence()[peid][smap])
2109 StructureState state = new StructureState();
2110 state.setVisible(true);
2111 state.setXpos(viewFrame.getX());
2112 state.setYpos(viewFrame.getY());
2113 state.setWidth(viewFrame.getWidth());
2114 state.setHeight(viewFrame.getHeight());
2115 final String viewId = viewFrame.getViewId();
2116 state.setViewId(viewId);
2117 state.setAlignwithAlignPanel(viewFrame.isUsedforaligment(ap));
2118 state.setColourwithAlignPanel(viewFrame.isUsedForColourBy(ap));
2119 state.setColourByJmol(viewFrame.isColouredByViewer());
2120 state.setType(viewFrame.getViewerType().toString());
2121 // pdb.addStructureState(state);
2122 pdb.getStructureState().add(state);
2130 * Populates the AnnotationColourScheme xml for save. This captures the
2131 * settings of the options in the 'Colour by Annotation' dialog.
2134 * @param userColours
2138 private AnnotationColourScheme constructAnnotationColours(
2139 AnnotationColourGradient acg, List<UserColourScheme> userColours,
2142 AnnotationColourScheme ac = new AnnotationColourScheme();
2143 ac.setAboveThreshold(acg.getAboveThreshold());
2144 ac.setThreshold(acg.getAnnotationThreshold());
2145 // 2.10.2 save annotationId (unique) not annotation label
2146 ac.setAnnotation(acg.getAnnotation().annotationId);
2147 if (acg.getBaseColour() instanceof UserColourScheme)
2150 setUserColourScheme(acg.getBaseColour(), userColours, jm));
2155 ColourSchemeProperty.getColourName(acg.getBaseColour()));
2158 ac.setMaxColour(acg.getMaxColour().getRGB());
2159 ac.setMinColour(acg.getMinColour().getRGB());
2160 ac.setPerSequence(acg.isSeqAssociated());
2161 ac.setPredefinedColours(acg.isPredefinedColours());
2165 private void storeAlignmentAnnotation(AlignmentAnnotation[] aa,
2166 IdentityHashMap<SequenceGroup, String> groupRefs,
2167 AlignmentViewport av, Set<String> calcIdSet, boolean storeDS,
2168 SequenceSet vamsasSet)
2171 for (int i = 0; i < aa.length; i++)
2173 Annotation an = new Annotation();
2175 AlignmentAnnotation annotation = aa[i];
2176 if (annotation.annotationId != null)
2178 annotationIds.put(annotation.annotationId, annotation);
2181 an.setId(annotation.annotationId);
2183 an.setVisible(annotation.visible);
2185 an.setDescription(annotation.description);
2187 if (annotation.sequenceRef != null)
2189 // 2.9 JAL-1781 xref on sequence id rather than name
2190 an.setSequenceRef(seqsToIds.get(annotation.sequenceRef));
2192 if (annotation.groupRef != null)
2194 String groupIdr = groupRefs.get(annotation.groupRef);
2195 if (groupIdr == null)
2197 // make a locally unique String
2198 groupRefs.put(annotation.groupRef,
2199 groupIdr = ("" + System.currentTimeMillis()
2200 + annotation.groupRef.getName()
2201 + groupRefs.size()));
2203 an.setGroupRef(groupIdr.toString());
2206 // store all visualization attributes for annotation
2207 an.setGraphHeight(annotation.graphHeight);
2208 an.setCentreColLabels(annotation.centreColLabels);
2209 an.setScaleColLabels(annotation.scaleColLabel);
2210 an.setShowAllColLabels(annotation.showAllColLabels);
2211 an.setBelowAlignment(annotation.belowAlignment);
2213 if (annotation.graph > 0)
2216 an.setGraphType(annotation.graph);
2217 an.setGraphGroup(annotation.graphGroup);
2218 if (annotation.getThreshold() != null)
2220 ThresholdLine line = new ThresholdLine();
2221 line.setLabel(annotation.getThreshold().label);
2222 line.setValue(annotation.getThreshold().value);
2223 line.setColour(annotation.getThreshold().colour.getRGB());
2224 an.setThresholdLine(line);
2232 an.setLabel(annotation.label);
2234 if (annotation == av.getAlignmentQualityAnnot()
2235 || annotation == av.getAlignmentConservationAnnotation()
2236 || annotation == av.getAlignmentConsensusAnnotation()
2237 || annotation.autoCalculated)
2239 // new way of indicating autocalculated annotation -
2240 an.setAutoCalculated(annotation.autoCalculated);
2242 if (annotation.hasScore())
2244 an.setScore(annotation.getScore());
2247 if (annotation.getCalcId() != null)
2249 calcIdSet.add(annotation.getCalcId());
2250 an.setCalcId(annotation.getCalcId());
2252 if (annotation.hasProperties())
2254 for (String pr : annotation.getProperties())
2256 jalview.xml.binding.jalview.Annotation.Property prop = new jalview.xml.binding.jalview.Annotation.Property();
2258 prop.setValue(annotation.getProperty(pr));
2259 // an.addProperty(prop);
2260 an.getProperty().add(prop);
2264 AnnotationElement ae;
2265 if (annotation.annotations != null)
2267 an.setScoreOnly(false);
2268 for (int a = 0; a < annotation.annotations.length; a++)
2270 if ((annotation == null) || (annotation.annotations[a] == null))
2275 ae = new AnnotationElement();
2276 if (annotation.annotations[a].description != null)
2278 ae.setDescription(annotation.annotations[a].description);
2280 if (annotation.annotations[a].displayCharacter != null)
2282 ae.setDisplayCharacter(
2283 annotation.annotations[a].displayCharacter);
2286 if (!Float.isNaN(annotation.annotations[a].value))
2288 ae.setValue(annotation.annotations[a].value);
2292 if (annotation.annotations[a].secondaryStructure > ' ')
2294 ae.setSecondaryStructure(
2295 annotation.annotations[a].secondaryStructure + "");
2298 if (annotation.annotations[a].colour != null
2299 && annotation.annotations[a].colour != java.awt.Color.black)
2301 ae.setColour(annotation.annotations[a].colour.getRGB());
2304 // an.addAnnotationElement(ae);
2305 an.getAnnotationElement().add(ae);
2306 if (annotation.autoCalculated)
2308 // only write one non-null entry into the annotation row -
2309 // sufficient to get the visualization attributes necessary to
2317 an.setScoreOnly(true);
2319 if (!storeDS || (storeDS && !annotation.autoCalculated))
2321 // skip autocalculated annotation - these are only provided for
2323 // vamsasSet.addAnnotation(an);
2324 vamsasSet.getAnnotation().add(an);
2330 private CalcIdParam createCalcIdParam(String calcId, AlignViewport av)
2332 AutoCalcSetting settings = av.getCalcIdSettingsFor(calcId);
2333 if (settings != null)
2335 CalcIdParam vCalcIdParam = new CalcIdParam();
2336 vCalcIdParam.setCalcId(calcId);
2337 // vCalcIdParam.addServiceURL(settings.getServiceURI());
2338 vCalcIdParam.getServiceURL().add(settings.getServiceURI());
2339 // generic URI allowing a third party to resolve another instance of the
2340 // service used for this calculation
2341 for (String url : settings.getServiceURLs())
2343 // vCalcIdParam.addServiceURL(urls);
2344 vCalcIdParam.getServiceURL().add(url);
2346 vCalcIdParam.setVersion("1.0");
2347 if (settings.getPreset() != null)
2349 WsParamSetI setting = settings.getPreset();
2350 vCalcIdParam.setName(setting.getName());
2351 vCalcIdParam.setDescription(setting.getDescription());
2355 vCalcIdParam.setName("");
2356 vCalcIdParam.setDescription("Last used parameters");
2358 // need to be able to recover 1) settings 2) user-defined presets or
2359 // recreate settings from preset 3) predefined settings provided by
2360 // service - or settings that can be transferred (or discarded)
2361 vCalcIdParam.setParameters(
2362 settings.getWsParamFile().replace("\n", "|\\n|"));
2363 vCalcIdParam.setAutoUpdate(settings.isAutoUpdate());
2364 // todo - decide if updateImmediately is needed for any projects.
2366 return vCalcIdParam;
2371 private boolean recoverCalcIdParam(CalcIdParam calcIdParam,
2374 if (calcIdParam.getVersion().equals("1.0"))
2376 final String[] calcIds = calcIdParam.getServiceURL()
2377 .toArray(new String[0]);
2378 Jws2Instance service = Jws2Discoverer.getDiscoverer()
2379 .getPreferredServiceFor(calcIds);
2380 if (service != null)
2382 WsParamSetI parmSet = null;
2385 parmSet = service.getParamStore().parseServiceParameterFile(
2386 calcIdParam.getName(), calcIdParam.getDescription(),
2388 calcIdParam.getParameters().replace("|\\n|", "\n"));
2389 } catch (IOException x)
2391 warn("Couldn't parse parameter data for "
2392 + calcIdParam.getCalcId(), x);
2395 List<ArgumentI> argList = null;
2396 if (calcIdParam.getName().length() > 0)
2398 parmSet = service.getParamStore()
2399 .getPreset(calcIdParam.getName());
2400 if (parmSet != null)
2402 // TODO : check we have a good match with settings in AACon -
2403 // otherwise we'll need to create a new preset
2408 argList = parmSet.getArguments();
2411 AAConSettings settings = new AAConSettings(
2412 calcIdParam.isAutoUpdate(), service, parmSet, argList);
2413 av.setCalcIdSettingsFor(calcIdParam.getCalcId(), settings,
2414 calcIdParam.isNeedsUpdate());
2419 warn("Cannot resolve a service for the parameters used in this project. Try configuring a JABAWS server.");
2423 throw new Error(MessageManager.formatMessage(
2424 "error.unsupported_version_calcIdparam", new Object[]
2425 { calcIdParam.toString() }));
2429 * External mapping between jalview objects and objects yielding a valid and
2430 * unique object ID string. This is null for normal Jalview project IO, but
2431 * non-null when a jalview project is being read or written as part of a
2434 IdentityHashMap jv2vobj = null;
2437 * Construct a unique ID for jvobj using either existing bindings or if none
2438 * exist, the result of the hashcode call for the object.
2441 * jalview data object
2442 * @return unique ID for referring to jvobj
2444 private String makeHashCode(Object jvobj, String altCode)
2446 if (jv2vobj != null)
2448 Object id = jv2vobj.get(jvobj);
2451 return id.toString();
2453 // check string ID mappings
2454 if (jvids2vobj != null && jvobj instanceof String)
2456 id = jvids2vobj.get(jvobj);
2460 return id.toString();
2462 // give up and warn that something has gone wrong
2463 warn("Cannot find ID for object in external mapping : " + jvobj);
2469 * return local jalview object mapped to ID, if it exists
2473 * @return null or object bound to idcode
2475 private Object retrieveExistingObj(String idcode)
2477 if (idcode != null && vobj2jv != null)
2479 return vobj2jv.get(idcode);
2485 * binding from ID strings from external mapping table to jalview data model
2488 private Hashtable vobj2jv;
2490 private Sequence createVamsasSequence(String id, SequenceI jds)
2492 return createVamsasSequence(true, id, jds, null);
2495 private Sequence createVamsasSequence(boolean recurse, String id,
2496 SequenceI jds, SequenceI parentseq)
2498 Sequence vamsasSeq = new Sequence();
2499 vamsasSeq.setId(id);
2500 vamsasSeq.setName(jds.getName());
2501 vamsasSeq.setSequence(jds.getSequenceAsString());
2502 vamsasSeq.setDescription(jds.getDescription());
2503 List<DBRefEntry> dbrefs = null;
2504 if (jds.getDatasetSequence() != null)
2506 vamsasSeq.setDsseqid(seqHash(jds.getDatasetSequence()));
2510 // seqId==dsseqid so we can tell which sequences really are
2511 // dataset sequences only
2512 vamsasSeq.setDsseqid(id);
2513 dbrefs = jds.getDBRefs();
2514 if (parentseq == null)
2521 * save any dbrefs; special subclass GeneLocus is flagged as 'locus'
2525 for (int d = 0, nd = dbrefs.size(); d < nd; d++)
2527 DBRef dbref = new DBRef();
2528 DBRefEntry ref = dbrefs.get(d);
2529 dbref.setSource(ref.getSource());
2530 dbref.setVersion(ref.getVersion());
2531 dbref.setAccessionId(ref.getAccessionId());
2532 dbref.setCanonical(ref.isCanonical());
2533 if (ref instanceof GeneLocus)
2535 dbref.setLocus(true);
2539 Mapping mp = createVamsasMapping(ref.getMap(), parentseq, jds,
2541 dbref.setMapping(mp);
2543 vamsasSeq.getDBRef().add(dbref);
2549 private Mapping createVamsasMapping(jalview.datamodel.Mapping jmp,
2550 SequenceI parentseq, SequenceI jds, boolean recurse)
2553 if (jmp.getMap() != null)
2557 jalview.util.MapList mlst = jmp.getMap();
2558 List<int[]> r = mlst.getFromRanges();
2559 for (int[] range : r)
2561 MapListFrom mfrom = new MapListFrom();
2562 mfrom.setStart(range[0]);
2563 mfrom.setEnd(range[1]);
2564 // mp.addMapListFrom(mfrom);
2565 mp.getMapListFrom().add(mfrom);
2567 r = mlst.getToRanges();
2568 for (int[] range : r)
2570 MapListTo mto = new MapListTo();
2571 mto.setStart(range[0]);
2572 mto.setEnd(range[1]);
2573 // mp.addMapListTo(mto);
2574 mp.getMapListTo().add(mto);
2576 mp.setMapFromUnit(BigInteger.valueOf(mlst.getFromRatio()));
2577 mp.setMapToUnit(BigInteger.valueOf(mlst.getToRatio()));
2578 if (jmp.getTo() != null)
2580 // MappingChoice mpc = new MappingChoice();
2582 // check/create ID for the sequence referenced by getTo()
2585 SequenceI ps = null;
2586 if (parentseq != jmp.getTo()
2587 && parentseq.getDatasetSequence() != jmp.getTo())
2589 // chaining dbref rather than a handshaking one
2590 jmpid = seqHash(ps = jmp.getTo());
2594 jmpid = seqHash(ps = parentseq);
2596 // mpc.setDseqFor(jmpid);
2597 mp.setDseqFor(jmpid);
2598 if (!seqRefIds.containsKey(jmpid))
2600 jalview.bin.Cache.log.debug("creatign new DseqFor ID");
2601 seqRefIds.put(jmpid, ps);
2605 jalview.bin.Cache.log.debug("reusing DseqFor ID");
2608 // mp.setMappingChoice(mpc);
2614 String setUserColourScheme(jalview.schemes.ColourSchemeI cs,
2615 List<UserColourScheme> userColours, JalviewModel jm)
2618 jalview.schemes.UserColourScheme ucs = (jalview.schemes.UserColourScheme) cs;
2619 boolean newucs = false;
2620 if (!userColours.contains(ucs))
2622 userColours.add(ucs);
2625 id = "ucs" + userColours.indexOf(ucs);
2628 // actually create the scheme's entry in the XML model
2629 java.awt.Color[] colours = ucs.getColours();
2630 UserColours uc = new UserColours();
2631 // UserColourScheme jbucs = new UserColourScheme();
2632 JalviewUserColours jbucs = new JalviewUserColours();
2634 for (int i = 0; i < colours.length; i++)
2636 Colour col = new Colour();
2637 col.setName(ResidueProperties.aa[i]);
2638 col.setRGB(jalview.util.Format.getHexString(colours[i]));
2639 // jbucs.addColour(col);
2640 jbucs.getColour().add(col);
2642 if (ucs.getLowerCaseColours() != null)
2644 colours = ucs.getLowerCaseColours();
2645 for (int i = 0; i < colours.length; i++)
2647 Colour col = new Colour();
2648 col.setName(ResidueProperties.aa[i].toLowerCase());
2649 col.setRGB(jalview.util.Format.getHexString(colours[i]));
2650 // jbucs.addColour(col);
2651 jbucs.getColour().add(col);
2656 uc.setUserColourScheme(jbucs);
2657 // jm.addUserColours(uc);
2658 jm.getUserColours().add(uc);
2664 jalview.schemes.UserColourScheme getUserColourScheme(JalviewModel jm,
2667 List<UserColours> uc = jm.getUserColours();
2668 UserColours colours = null;
2670 for (int i = 0; i < uc.length; i++)
2672 if (uc[i].getId().equals(id))
2679 for (UserColours c : uc)
2681 if (c.getId().equals(id))
2688 java.awt.Color[] newColours = new java.awt.Color[24];
2690 for (int i = 0; i < 24; i++)
2692 newColours[i] = new java.awt.Color(Integer.parseInt(
2693 // colours.getUserColourScheme().getColour(i).getRGB(), 16));
2694 colours.getUserColourScheme().getColour().get(i).getRGB(),
2698 jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(
2701 if (colours.getUserColourScheme().getColour().size()/*Count()*/ > 24)
2703 newColours = new java.awt.Color[23];
2704 for (int i = 0; i < 23; i++)
2706 newColours[i] = new java.awt.Color(
2707 Integer.parseInt(colours.getUserColourScheme().getColour()
2708 .get(i + 24).getRGB(), 16));
2710 ucs.setLowerCaseColours(newColours);
2717 * contains last error message (if any) encountered by XML loader.
2719 String errorMessage = null;
2722 * flag to control whether the Jalview2XML_V1 parser should be deferred to if
2723 * exceptions are raised during project XML parsing
2725 public boolean attemptversion1parse = false;
2728 * Load a jalview project archive from a jar file
2731 * - HTTP URL or filename
2733 public AlignFrame loadJalviewAlign(final Object file)
2736 jalview.gui.AlignFrame af = null;
2740 // create list to store references for any new Jmol viewers created
2741 newStructureViewers = new Vector<>();
2742 // UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
2743 // Workaround is to make sure caller implements the JarInputStreamProvider
2745 // so we can re-open the jar input stream for each entry.
2747 jarInputStreamProvider jprovider = createjarInputStreamProvider(file);
2748 af = loadJalviewAlign(jprovider);
2751 af.setMenusForViewport();
2753 } catch (MalformedURLException e)
2755 errorMessage = "Invalid URL format for '" + file + "'";
2761 SwingUtilities.invokeAndWait(new Runnable()
2766 setLoadingFinishedForNewStructureViewers();
2769 } catch (Exception x)
2771 System.err.println("Error loading alignment: " + x.getMessage());
2777 @SuppressWarnings("unused")
2778 private jarInputStreamProvider createjarInputStreamProvider(
2779 final Object ofile) throws MalformedURLException
2782 // BH 2018 allow for bytes already attached to File object
2785 String file = (ofile instanceof File
2786 ? ((File) ofile).getCanonicalPath()
2787 : ofile.toString());
2788 byte[] bytes = Platform.isJS() ? Platform.getFileBytes((File) ofile)
2791 errorMessage = null;
2792 uniqueSetSuffix = null;
2794 viewportsAdded.clear();
2795 frefedSequence = null;
2797 if (HttpUtils.startsWithHttpOrHttps(file))
2799 url = new URL(file);
2801 final URL _url = url;
2802 return new jarInputStreamProvider()
2806 public JarInputStream getJarInputStream() throws IOException
2810 // System.out.println("Jalview2XML: opening byte jarInputStream for
2811 // bytes.length=" + bytes.length);
2812 return new JarInputStream(new ByteArrayInputStream(bytes));
2816 // System.out.println("Jalview2XML: opening url jarInputStream for "
2818 return new JarInputStream(_url.openStream());
2822 // System.out.println("Jalview2XML: opening file jarInputStream for
2824 return new JarInputStream(new FileInputStream(file));
2829 public String getFilename()
2834 } catch (IOException e)
2836 e.printStackTrace();
2842 * Recover jalview session from a jalview project archive. Caller may
2843 * initialise uniqueSetSuffix, seqRefIds, viewportsAdded and frefedSequence
2844 * themselves. Any null fields will be initialised with default values,
2845 * non-null fields are left alone.
2850 public AlignFrame loadJalviewAlign(final jarInputStreamProvider jprovider)
2852 errorMessage = null;
2853 if (uniqueSetSuffix == null)
2855 uniqueSetSuffix = System.currentTimeMillis() % 100000 + "";
2857 if (seqRefIds == null)
2861 AlignFrame af = null, _af = null;
2862 IdentityHashMap<AlignmentI, AlignmentI> importedDatasets = new IdentityHashMap<>();
2863 Map<String, AlignFrame> gatherToThisFrame = new HashMap<>();
2864 final String file = jprovider.getFilename();
2867 JarInputStream jin = null;
2868 JarEntry jarentry = null;
2873 jin = jprovider.getJarInputStream();
2874 for (int i = 0; i < entryCount; i++)
2876 jarentry = jin.getNextJarEntry();
2879 if (jarentry != null && jarentry.getName().endsWith(".xml"))
2881 JAXBContext jc = JAXBContext
2882 .newInstance("jalview.xml.binding.jalview");
2883 XMLStreamReader streamReader = XMLInputFactory.newInstance()
2884 .createXMLStreamReader(jin);
2885 javax.xml.bind.Unmarshaller um = jc.createUnmarshaller();
2886 JAXBElement<JalviewModel> jbe = um.unmarshal(streamReader,
2887 JalviewModel.class);
2888 JalviewModel object = jbe.getValue();
2890 if (true) // !skipViewport(object))
2892 _af = loadFromObject(object, file, true, jprovider);
2893 if (_af != null && object.getViewport().size() > 0)
2894 // getJalviewModelSequence().getViewportCount() > 0)
2898 // store a reference to the first view
2901 if (_af.getViewport().isGatherViewsHere())
2903 // if this is a gathered view, keep its reference since
2904 // after gathering views, only this frame will remain
2906 gatherToThisFrame.put(_af.getViewport().getSequenceSetId(),
2909 // Save dataset to register mappings once all resolved
2910 importedDatasets.put(
2911 af.getViewport().getAlignment().getDataset(),
2912 af.getViewport().getAlignment().getDataset());
2917 else if (jarentry != null)
2919 // Some other file here.
2922 } while (jarentry != null);
2923 resolveFrefedSequences();
2924 } catch (IOException ex)
2926 ex.printStackTrace();
2927 errorMessage = "Couldn't locate Jalview XML file : " + file;
2929 "Exception whilst loading jalview XML file : " + ex + "\n");
2930 } catch (Exception ex)
2932 System.err.println("Parsing as Jalview Version 2 file failed.");
2933 ex.printStackTrace(System.err);
2934 if (attemptversion1parse)
2936 // used to attempt to parse as V1 castor-generated xml
2938 if (Desktop.instance != null)
2940 Desktop.instance.stopLoading();
2944 System.out.println("Successfully loaded archive file");
2947 ex.printStackTrace();
2950 "Exception whilst loading jalview XML file : " + ex + "\n");
2951 } catch (OutOfMemoryError e)
2953 // Don't use the OOM Window here
2954 errorMessage = "Out of memory loading jalview XML file";
2955 System.err.println("Out of memory whilst loading jalview XML file");
2956 e.printStackTrace();
2960 * Regather multiple views (with the same sequence set id) to the frame (if
2961 * any) that is flagged as the one to gather to, i.e. convert them to tabbed
2962 * views instead of separate frames. Note this doesn't restore a state where
2963 * some expanded views in turn have tabbed views - the last "first tab" read
2964 * in will play the role of gatherer for all.
2966 for (AlignFrame fr : gatherToThisFrame.values())
2968 Desktop.instance.gatherViews(fr);
2971 restoreSplitFrames();
2972 for (AlignmentI ds : importedDatasets.keySet())
2974 if (ds.getCodonFrames() != null)
2976 StructureSelectionManager
2977 .getStructureSelectionManager(Desktop.instance)
2978 .registerMappings(ds.getCodonFrames());
2981 if (errorMessage != null)
2986 if (Desktop.instance != null)
2988 Desktop.instance.stopLoading();
2995 * Try to reconstruct and display SplitFrame windows, where each contains
2996 * complementary dna and protein alignments. Done by pairing up AlignFrame
2997 * objects (created earlier) which have complementary viewport ids associated.
2999 protected void restoreSplitFrames()
3001 List<SplitFrame> gatherTo = new ArrayList<>();
3002 List<AlignFrame> addedToSplitFrames = new ArrayList<>();
3003 Map<String, AlignFrame> dna = new HashMap<>();
3006 * Identify the DNA alignments
3008 for (Entry<Viewport, AlignFrame> candidate : splitFrameCandidates
3011 AlignFrame af = candidate.getValue();
3012 if (af.getViewport().getAlignment().isNucleotide())
3014 dna.put(candidate.getKey().getId(), af);
3019 * Try to match up the protein complements
3021 for (Entry<Viewport, AlignFrame> candidate : splitFrameCandidates
3024 AlignFrame af = candidate.getValue();
3025 if (!af.getViewport().getAlignment().isNucleotide())
3027 String complementId = candidate.getKey().getComplementId();
3028 // only non-null complements should be in the Map
3029 if (complementId != null && dna.containsKey(complementId))
3031 final AlignFrame dnaFrame = dna.get(complementId);
3032 SplitFrame sf = createSplitFrame(dnaFrame, af);
3033 addedToSplitFrames.add(dnaFrame);
3034 addedToSplitFrames.add(af);
3035 dnaFrame.setMenusForViewport();
3036 af.setMenusForViewport();
3037 if (af.getViewport().isGatherViewsHere())
3046 * Open any that we failed to pair up (which shouldn't happen!) as
3047 * standalone AlignFrame's.
3049 for (Entry<Viewport, AlignFrame> candidate : splitFrameCandidates
3052 AlignFrame af = candidate.getValue();
3053 if (!addedToSplitFrames.contains(af))
3055 Viewport view = candidate.getKey();
3056 Desktop.addInternalFrame(af, view.getTitle(),
3057 safeInt(view.getWidth()), safeInt(view.getHeight()));
3058 af.setMenusForViewport();
3059 System.err.println("Failed to restore view " + view.getTitle()
3060 + " to split frame");
3065 * Gather back into tabbed views as flagged.
3067 for (SplitFrame sf : gatherTo)
3069 Desktop.instance.gatherViews(sf);
3072 splitFrameCandidates.clear();
3076 * Construct and display one SplitFrame holding DNA and protein alignments.
3079 * @param proteinFrame
3082 protected SplitFrame createSplitFrame(AlignFrame dnaFrame,
3083 AlignFrame proteinFrame)
3085 SplitFrame splitFrame = new SplitFrame(dnaFrame, proteinFrame);
3086 String title = MessageManager.getString("label.linked_view_title");
3087 int width = (int) dnaFrame.getBounds().getWidth();
3088 int height = (int) (dnaFrame.getBounds().getHeight()
3089 + proteinFrame.getBounds().getHeight() + 50);
3092 * SplitFrame location is saved to both enclosed frames
3094 splitFrame.setLocation(dnaFrame.getX(), dnaFrame.getY());
3095 Desktop.addInternalFrame(splitFrame, title, width, height);
3098 * And compute cDNA consensus (couldn't do earlier with consensus as
3099 * mappings were not yet present)
3101 proteinFrame.getViewport().alignmentChanged(proteinFrame.alignPanel);
3107 * check errorMessage for a valid error message and raise an error box in the
3108 * GUI or write the current errorMessage to stderr and then clear the error
3111 protected void reportErrors()
3113 reportErrors(false);
3116 protected void reportErrors(final boolean saving)
3118 if (errorMessage != null)
3120 final String finalErrorMessage = errorMessage;
3123 javax.swing.SwingUtilities.invokeLater(new Runnable()
3128 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
3130 "Error " + (saving ? "saving" : "loading")
3132 JvOptionPane.WARNING_MESSAGE);
3138 System.err.println("Problem loading Jalview file: " + errorMessage);
3141 errorMessage = null;
3144 Map<String, String> alreadyLoadedPDB = new HashMap<>();
3147 * when set, local views will be updated from view stored in JalviewXML
3148 * Currently (28th Sep 2008) things will go horribly wrong in vamsas document
3149 * sync if this is set to true.
3151 private final boolean updateLocalViews = false;
3154 * Returns the path to a temporary file holding the PDB file for the given PDB
3155 * id. The first time of asking, searches for a file of that name in the
3156 * Jalview project jar, and copies it to a new temporary file. Any repeat
3157 * requests just return the path to the file previously created.
3163 String loadPDBFile(jarInputStreamProvider jprovider, String pdbId,
3166 if (alreadyLoadedPDB.containsKey(pdbId))
3168 return alreadyLoadedPDB.get(pdbId).toString();
3171 String tempFile = copyJarEntry(jprovider, pdbId, "jalview_pdb",
3173 if (tempFile != null)
3175 alreadyLoadedPDB.put(pdbId, tempFile);
3181 * Copies the jar entry of given name to a new temporary file and returns the
3182 * path to the file, or null if the entry is not found.
3185 * @param jarEntryName
3187 * a prefix for the temporary file name, must be at least three
3189 * @param suffixModel
3190 * null or original file - so new file can be given the same suffix
3194 protected String copyJarEntry(jarInputStreamProvider jprovider,
3195 String jarEntryName, String prefix, String suffixModel)
3197 String suffix = ".tmp";
3198 if (suffixModel == null)
3200 suffixModel = jarEntryName;
3202 int sfpos = suffixModel.lastIndexOf(".");
3203 if (sfpos > -1 && sfpos < (suffixModel.length() - 1))
3205 suffix = "." + suffixModel.substring(sfpos + 1);
3208 try (JarInputStream jin = jprovider.getJarInputStream())
3210 JarEntry entry = null;
3213 entry = jin.getNextJarEntry();
3214 } while (entry != null && !entry.getName().equals(jarEntryName));
3218 // in = new BufferedReader(new InputStreamReader(jin, UTF_8));
3219 File outFile = File.createTempFile(prefix, suffix);
3220 outFile.deleteOnExit();
3221 try (OutputStream os = new FileOutputStream(outFile))
3225 String t = outFile.getAbsolutePath();
3230 warn("Couldn't find entry in Jalview Jar for " + jarEntryName);
3232 } catch (Exception ex)
3234 ex.printStackTrace();
3240 private class JvAnnotRow
3242 public JvAnnotRow(int i, AlignmentAnnotation jaa)
3249 * persisted version of annotation row from which to take vis properties
3251 public jalview.datamodel.AlignmentAnnotation template;
3254 * original position of the annotation row in the alignment
3260 * Load alignment frame from jalview XML DOM object
3262 * @param jalviewModel
3265 * filename source string
3266 * @param loadTreesAndStructures
3267 * when false only create Viewport
3269 * data source provider
3270 * @return alignment frame created from view stored in DOM
3272 AlignFrame loadFromObject(JalviewModel jalviewModel, String file,
3273 boolean loadTreesAndStructures, jarInputStreamProvider jprovider)
3275 SequenceSet vamsasSet = jalviewModel.getVamsasModel().getSequenceSet()
3277 List<Sequence> vamsasSeqs = vamsasSet.getSequence();
3279 // JalviewModelSequence jms = object.getJalviewModelSequence();
3281 // Viewport view = (jms.getViewportCount() > 0) ? jms.getViewport(0)
3283 Viewport view = (jalviewModel.getViewport().size() > 0)
3284 ? jalviewModel.getViewport().get(0)
3287 // ////////////////////////////////
3288 // INITIALISE ALIGNMENT SEQUENCESETID AND VIEWID
3291 // If we just load in the same jar file again, the sequenceSetId
3292 // will be the same, and we end up with multiple references
3293 // to the same sequenceSet. We must modify this id on load
3294 // so that each load of the file gives a unique id
3297 * used to resolve correct alignment dataset for alignments with multiple
3300 String uniqueSeqSetId = null;
3301 String viewId = null;
3304 uniqueSeqSetId = view.getSequenceSetId() + uniqueSetSuffix;
3305 viewId = (view.getId() == null ? null
3306 : view.getId() + uniqueSetSuffix);
3309 // ////////////////////////////////
3312 List<SequenceI> hiddenSeqs = null;
3314 List<SequenceI> tmpseqs = new ArrayList<>();
3316 boolean multipleView = false;
3317 SequenceI referenceseqForView = null;
3318 // JSeq[] jseqs = object.getJalviewModelSequence().getJSeq();
3319 List<JSeq> jseqs = jalviewModel.getJSeq();
3320 int vi = 0; // counter in vamsasSeq array
3321 for (int i = 0; i < jseqs.size(); i++)
3323 JSeq jseq = jseqs.get(i);
3324 String seqId = jseq.getId();
3326 SequenceI tmpSeq = seqRefIds.get(seqId);
3329 if (!incompleteSeqs.containsKey(seqId))
3331 // may not need this check, but keep it for at least 2.9,1 release
3332 if (tmpSeq.getStart() != jseq.getStart()
3333 || tmpSeq.getEnd() != jseq.getEnd())
3335 System.err.println(String.format(
3336 "Warning JAL-2154 regression: updating start/end for sequence %s from %d/%d to %d/%d",
3337 tmpSeq.getName(), tmpSeq.getStart(), tmpSeq.getEnd(),
3338 jseq.getStart(), jseq.getEnd()));
3343 incompleteSeqs.remove(seqId);
3345 if (vamsasSeqs.size() > vi
3346 && vamsasSeqs.get(vi).getId().equals(seqId))
3348 // most likely we are reading a dataset XML document so
3349 // update from vamsasSeq section of XML for this sequence
3350 tmpSeq.setName(vamsasSeqs.get(vi).getName());
3351 tmpSeq.setDescription(vamsasSeqs.get(vi).getDescription());
3352 tmpSeq.setSequence(vamsasSeqs.get(vi).getSequence());
3357 // reading multiple views, so vamsasSeq set is a subset of JSeq
3358 multipleView = true;
3360 tmpSeq.setStart(jseq.getStart());
3361 tmpSeq.setEnd(jseq.getEnd());
3362 tmpseqs.add(tmpSeq);
3366 Sequence vamsasSeq = vamsasSeqs.get(vi);
3367 tmpSeq = new jalview.datamodel.Sequence(vamsasSeq.getName(),
3368 vamsasSeq.getSequence());
3369 tmpSeq.setDescription(vamsasSeq.getDescription());
3370 tmpSeq.setStart(jseq.getStart());
3371 tmpSeq.setEnd(jseq.getEnd());
3372 tmpSeq.setVamsasId(uniqueSetSuffix + seqId);
3373 seqRefIds.put(vamsasSeq.getId(), tmpSeq);
3374 tmpseqs.add(tmpSeq);
3378 if (safeBoolean(jseq.isViewreference()))
3380 referenceseqForView = tmpseqs.get(tmpseqs.size() - 1);
3383 if (jseq.isHidden() != null && jseq.isHidden().booleanValue())
3385 if (hiddenSeqs == null)
3387 hiddenSeqs = new ArrayList<>();
3390 hiddenSeqs.add(tmpSeq);
3395 // Create the alignment object from the sequence set
3396 // ///////////////////////////////
3397 SequenceI[] orderedSeqs = tmpseqs
3398 .toArray(new SequenceI[tmpseqs.size()]);
3400 AlignmentI al = null;
3401 // so we must create or recover the dataset alignment before going further
3402 // ///////////////////////////////
3403 if (vamsasSet.getDatasetId() == null || vamsasSet.getDatasetId() == "")
3405 // older jalview projects do not have a dataset - so creat alignment and
3407 al = new Alignment(orderedSeqs);
3408 al.setDataset(null);
3412 boolean isdsal = jalviewModel.getViewport().isEmpty();
3415 // we are importing a dataset record, so
3416 // recover reference to an alignment already materialsed as dataset
3417 al = getDatasetFor(vamsasSet.getDatasetId());
3421 // materialse the alignment
3422 al = new Alignment(orderedSeqs);
3426 addDatasetRef(vamsasSet.getDatasetId(), al);
3429 // finally, verify all data in vamsasSet is actually present in al
3430 // passing on flag indicating if it is actually a stored dataset
3431 recoverDatasetFor(vamsasSet, al, isdsal, uniqueSeqSetId);
3434 if (referenceseqForView != null)
3436 al.setSeqrep(referenceseqForView);
3438 // / Add the alignment properties
3439 for (int i = 0; i < vamsasSet.getSequenceSetProperties().size(); i++)
3441 SequenceSetProperties ssp = vamsasSet.getSequenceSetProperties()
3443 al.setProperty(ssp.getKey(), ssp.getValue());
3446 // ///////////////////////////////
3448 Hashtable pdbloaded = new Hashtable(); // TODO nothing writes to this??
3451 // load sequence features, database references and any associated PDB
3452 // structures for the alignment
3454 // prior to 2.10, this part would only be executed the first time a
3455 // sequence was encountered, but not afterwards.
3456 // now, for 2.10 projects, this is also done if the xml doc includes
3457 // dataset sequences not actually present in any particular view.
3459 for (int i = 0; i < vamsasSeqs.size(); i++)
3461 JSeq jseq = jseqs.get(i);
3462 if (jseq.getFeatures().size() > 0)
3464 List<Feature> features = jseq.getFeatures();
3465 for (int f = 0; f < features.size(); f++)
3467 Feature feat = features.get(f);
3468 SequenceFeature sf = new SequenceFeature(feat.getType(),
3469 feat.getDescription(), feat.getBegin(), feat.getEnd(),
3470 safeFloat(feat.getScore()), feat.getFeatureGroup());
3471 sf.setStatus(feat.getStatus());
3474 * load any feature attributes - include map-valued attributes
3476 Map<String, Map<String, String>> mapAttributes = new HashMap<>();
3477 for (int od = 0; od < feat.getOtherData().size(); od++)
3479 OtherData keyValue = feat.getOtherData().get(od);
3480 String attributeName = keyValue.getKey();
3481 String attributeValue = keyValue.getValue();
3482 if (attributeName.startsWith("LINK"))
3484 sf.addLink(attributeValue);
3488 String subAttribute = keyValue.getKey2();
3489 if (subAttribute == null)
3491 // simple string-valued attribute
3492 sf.setValue(attributeName, attributeValue);
3496 // attribute 'key' has sub-attribute 'key2'
3497 if (!mapAttributes.containsKey(attributeName))
3499 mapAttributes.put(attributeName, new HashMap<>());
3501 mapAttributes.get(attributeName).put(subAttribute,
3506 for (Entry<String, Map<String, String>> mapAttribute : mapAttributes
3509 sf.setValue(mapAttribute.getKey(), mapAttribute.getValue());
3512 // adds feature to datasequence's feature set (since Jalview 2.10)
3513 al.getSequenceAt(i).addSequenceFeature(sf);
3516 if (vamsasSeqs.get(i).getDBRef().size() > 0)
3518 // adds dbrefs to datasequence's set (since Jalview 2.10)
3520 al.getSequenceAt(i).getDatasetSequence() == null
3521 ? al.getSequenceAt(i)
3522 : al.getSequenceAt(i).getDatasetSequence(),
3525 if (jseq.getPdbids().size() > 0)
3527 List<Pdbids> ids = jseq.getPdbids();
3528 for (int p = 0; p < ids.size(); p++)
3530 Pdbids pdbid = ids.get(p);
3531 jalview.datamodel.PDBEntry entry = new jalview.datamodel.PDBEntry();
3532 entry.setId(pdbid.getId());
3533 if (pdbid.getType() != null)
3535 if (PDBEntry.Type.getType(pdbid.getType()) != null)
3537 entry.setType(PDBEntry.Type.getType(pdbid.getType()));
3541 entry.setType(PDBEntry.Type.FILE);
3544 // jprovider is null when executing 'New View'
3545 if (pdbid.getFile() != null && jprovider != null)
3547 if (!pdbloaded.containsKey(pdbid.getFile()))
3549 entry.setFile(loadPDBFile(jprovider, pdbid.getId(),
3554 entry.setFile(pdbloaded.get(pdbid.getId()).toString());
3558 if (pdbid.getPdbentryItem() != null)
3560 for (PdbentryItem item : pdbid.getPdbentryItem())
3562 for (Property pr : item.getProperty())
3564 entry.setProperty(pr.getName(), pr.getValue());
3569 for (Property prop : pdbid.getProperty())
3571 entry.setProperty(prop.getName(), prop.getValue());
3573 StructureSelectionManager
3574 .getStructureSelectionManager(Desktop.instance)
3575 .registerPDBEntry(entry);
3576 // adds PDBEntry to datasequence's set (since Jalview 2.10)
3577 if (al.getSequenceAt(i).getDatasetSequence() != null)
3579 al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
3583 al.getSequenceAt(i).addPDBId(entry);
3588 } // end !multipleview
3590 // ///////////////////////////////
3591 // LOAD SEQUENCE MAPPINGS
3593 if (vamsasSet.getAlcodonFrame().size() > 0)
3595 // TODO Potentially this should only be done once for all views of an
3597 List<AlcodonFrame> alc = vamsasSet.getAlcodonFrame();
3598 for (int i = 0; i < alc.size(); i++)
3600 AlignedCodonFrame cf = new AlignedCodonFrame();
3601 if (alc.get(i).getAlcodMap().size() > 0)
3603 List<AlcodMap> maps = alc.get(i).getAlcodMap();
3604 for (int m = 0; m < maps.size(); m++)
3606 AlcodMap map = maps.get(m);
3607 SequenceI dnaseq = seqRefIds.get(map.getDnasq());
3609 jalview.datamodel.Mapping mapping = null;
3610 // attach to dna sequence reference.
3611 if (map.getMapping() != null)
3613 mapping = addMapping(map.getMapping());
3614 if (dnaseq != null && mapping.getTo() != null)
3616 cf.addMap(dnaseq, mapping.getTo(), mapping.getMap());
3622 .add(newAlcodMapRef(map.getDnasq(), cf, mapping));
3626 al.addCodonFrame(cf);
3631 // ////////////////////////////////
3633 List<JvAnnotRow> autoAlan = new ArrayList<>();
3636 * store any annotations which forward reference a group's ID
3638 Map<String, List<AlignmentAnnotation>> groupAnnotRefs = new Hashtable<>();
3640 if (vamsasSet.getAnnotation().size()/*Count()*/ > 0)
3642 List<Annotation> an = vamsasSet.getAnnotation();
3644 for (int i = 0; i < an.size(); i++)
3646 Annotation annotation = an.get(i);
3649 * test if annotation is automatically calculated for this view only
3651 boolean autoForView = false;
3652 if (annotation.getLabel().equals("Quality")
3653 || annotation.getLabel().equals("Conservation")
3654 || annotation.getLabel().equals("Consensus"))
3656 // Kludge for pre 2.5 projects which lacked the autocalculated flag
3658 // JAXB has no has() test; schema defaults value to false
3659 // if (!annotation.hasAutoCalculated())
3661 // annotation.setAutoCalculated(true);
3664 if (autoForView || annotation.isAutoCalculated())
3666 // remove ID - we don't recover annotation from other views for
3667 // view-specific annotation
3668 annotation.setId(null);
3671 // set visibility for other annotation in this view
3672 String annotationId = annotation.getId();
3673 if (annotationId != null && annotationIds.containsKey(annotationId))
3675 AlignmentAnnotation jda = annotationIds.get(annotationId);
3676 // in principle Visible should always be true for annotation displayed
3677 // in multiple views
3678 if (annotation.isVisible() != null)
3680 jda.visible = annotation.isVisible();
3683 al.addAnnotation(jda);
3687 // Construct new annotation from model.
3688 List<AnnotationElement> ae = annotation.getAnnotationElement();
3689 jalview.datamodel.Annotation[] anot = null;
3690 java.awt.Color firstColour = null;
3692 if (!annotation.isScoreOnly())
3694 anot = new jalview.datamodel.Annotation[al.getWidth()];
3695 for (int aa = 0; aa < ae.size() && aa < anot.length; aa++)
3697 AnnotationElement annElement = ae.get(aa);
3698 anpos = annElement.getPosition();
3700 if (anpos >= anot.length)
3705 float value = safeFloat(annElement.getValue());
3706 anot[anpos] = new jalview.datamodel.Annotation(
3707 annElement.getDisplayCharacter(),
3708 annElement.getDescription(),
3709 (annElement.getSecondaryStructure() == null
3710 || annElement.getSecondaryStructure()
3714 .getSecondaryStructure()
3717 anot[anpos].colour = new Color(safeInt(annElement.getColour()));
3718 if (firstColour == null)
3720 firstColour = anot[anpos].colour;
3724 jalview.datamodel.AlignmentAnnotation jaa = null;
3726 if (annotation.isGraph())
3728 float llim = 0, hlim = 0;
3729 // if (autoForView || an[i].isAutoCalculated()) {
3732 jaa = new jalview.datamodel.AlignmentAnnotation(
3733 annotation.getLabel(), annotation.getDescription(), anot,
3734 llim, hlim, safeInt(annotation.getGraphType()));
3736 jaa.graphGroup = safeInt(annotation.getGraphGroup());
3737 jaa._linecolour = firstColour;
3738 if (annotation.getThresholdLine() != null)
3740 jaa.setThreshold(new jalview.datamodel.GraphLine(
3741 safeFloat(annotation.getThresholdLine().getValue()),
3742 annotation.getThresholdLine().getLabel(),
3743 new java.awt.Color(safeInt(
3744 annotation.getThresholdLine().getColour()))));
3746 if (autoForView || annotation.isAutoCalculated())
3748 // Hardwire the symbol display line to ensure that labels for
3749 // histograms are displayed
3755 jaa = new jalview.datamodel.AlignmentAnnotation(
3756 annotation.getLabel(), annotation.getDescription(), anot);
3757 jaa._linecolour = firstColour;
3759 // register new annotation
3760 if (annotation.getId() != null)
3762 annotationIds.put(annotation.getId(), jaa);
3763 jaa.annotationId = annotation.getId();
3765 // recover sequence association
3766 String sequenceRef = annotation.getSequenceRef();
3767 if (sequenceRef != null)
3769 // from 2.9 sequenceRef is to sequence id (JAL-1781)
3770 SequenceI sequence = seqRefIds.get(sequenceRef);
3771 if (sequence == null)
3773 // in pre-2.9 projects sequence ref is to sequence name
3774 sequence = al.findName(sequenceRef);
3776 if (sequence != null)
3778 jaa.createSequenceMapping(sequence, 1, true);
3779 sequence.addAlignmentAnnotation(jaa);
3782 // and make a note of any group association
3783 if (annotation.getGroupRef() != null
3784 && annotation.getGroupRef().length() > 0)
3786 List<jalview.datamodel.AlignmentAnnotation> aal = groupAnnotRefs
3787 .get(annotation.getGroupRef());
3790 aal = new ArrayList<>();
3791 groupAnnotRefs.put(annotation.getGroupRef(), aal);
3796 if (annotation.getScore() != null)
3798 jaa.setScore(annotation.getScore().doubleValue());
3800 if (annotation.isVisible() != null)
3802 jaa.visible = annotation.isVisible().booleanValue();
3805 if (annotation.isCentreColLabels() != null)
3807 jaa.centreColLabels = annotation.isCentreColLabels()
3811 if (annotation.isScaleColLabels() != null)
3813 jaa.scaleColLabel = annotation.isScaleColLabels().booleanValue();
3815 if (annotation.isAutoCalculated())
3817 // newer files have an 'autoCalculated' flag and store calculation
3818 // state in viewport properties
3819 jaa.autoCalculated = true; // means annotation will be marked for
3820 // update at end of load.
3822 if (annotation.getGraphHeight() != null)
3824 jaa.graphHeight = annotation.getGraphHeight().intValue();
3826 jaa.belowAlignment = annotation.isBelowAlignment();
3827 jaa.setCalcId(annotation.getCalcId());
3828 if (annotation.getProperty().size() > 0)
3830 for (Annotation.Property prop : annotation.getProperty())
3832 jaa.setProperty(prop.getName(), prop.getValue());
3835 if (jaa.autoCalculated)
3837 autoAlan.add(new JvAnnotRow(i, jaa));
3840 // if (!autoForView)
3842 // add autocalculated group annotation and any user created annotation
3844 al.addAnnotation(jaa);
3848 // ///////////////////////
3850 // Create alignment markup and styles for this view
3851 if (jalviewModel.getJGroup().size() > 0)
3853 List<JGroup> groups = jalviewModel.getJGroup();
3854 boolean addAnnotSchemeGroup = false;
3855 for (int i = 0; i < groups.size(); i++)
3857 JGroup jGroup = groups.get(i);
3858 ColourSchemeI cs = null;
3859 if (jGroup.getColour() != null)
3861 if (jGroup.getColour().startsWith("ucs"))
3863 cs = getUserColourScheme(jalviewModel, jGroup.getColour());
3865 else if (jGroup.getColour().equals("AnnotationColourGradient")
3866 && jGroup.getAnnotationColours() != null)
3868 addAnnotSchemeGroup = true;
3872 cs = ColourSchemeProperty.getColourScheme(null, al,
3873 jGroup.getColour());
3876 int pidThreshold = safeInt(jGroup.getPidThreshold());
3878 Vector<SequenceI> seqs = new Vector<>();
3880 for (int s = 0; s < jGroup.getSeq().size(); s++)
3882 String seqId = jGroup.getSeq().get(s);
3883 SequenceI ts = seqRefIds.get(seqId);
3887 seqs.addElement(ts);
3891 if (seqs.size() < 1)
3896 SequenceGroup sg = new SequenceGroup(seqs, jGroup.getName(), cs,
3897 safeBoolean(jGroup.isDisplayBoxes()),
3898 safeBoolean(jGroup.isDisplayText()),
3899 safeBoolean(jGroup.isColourText()),
3900 safeInt(jGroup.getStart()), safeInt(jGroup.getEnd()));
3901 sg.getGroupColourScheme().setThreshold(pidThreshold, true);
3902 sg.getGroupColourScheme()
3903 .setConservationInc(safeInt(jGroup.getConsThreshold()));
3904 sg.setOutlineColour(new Color(safeInt(jGroup.getOutlineColour())));
3906 sg.textColour = new Color(safeInt(jGroup.getTextCol1()));
3907 sg.textColour2 = new Color(safeInt(jGroup.getTextCol2()));
3908 sg.setShowNonconserved(safeBoolean(jGroup.isShowUnconserved()));
3909 sg.thresholdTextColour = safeInt(jGroup.getTextColThreshold());
3910 // attributes with a default in the schema are never null
3911 sg.setShowConsensusHistogram(jGroup.isShowConsensusHistogram());
3912 sg.setshowSequenceLogo(jGroup.isShowSequenceLogo());
3913 sg.setNormaliseSequenceLogo(jGroup.isNormaliseSequenceLogo());
3914 sg.setIgnoreGapsConsensus(jGroup.isIgnoreGapsinConsensus());
3915 if (jGroup.getConsThreshold() != null
3916 && jGroup.getConsThreshold().intValue() != 0)
3918 Conservation c = new Conservation("All", sg.getSequences(null), 0,
3921 c.verdict(false, 25);
3922 sg.cs.setConservation(c);
3925 if (jGroup.getId() != null && groupAnnotRefs.size() > 0)
3927 // re-instate unique group/annotation row reference
3928 List<AlignmentAnnotation> jaal = groupAnnotRefs
3929 .get(jGroup.getId());
3932 for (AlignmentAnnotation jaa : jaal)
3935 if (jaa.autoCalculated)
3937 // match up and try to set group autocalc alignment row for this
3939 if (jaa.label.startsWith("Consensus for "))
3941 sg.setConsensus(jaa);
3943 // match up and try to set group autocalc alignment row for this
3945 if (jaa.label.startsWith("Conservation for "))
3947 sg.setConservationRow(jaa);
3954 if (addAnnotSchemeGroup)
3956 // reconstruct the annotation colourscheme
3958 constructAnnotationColour(jGroup.getAnnotationColours(),
3959 null, al, jalviewModel, false));
3965 // only dataset in this model, so just return.
3968 // ///////////////////////////////
3971 AlignFrame af = null;
3972 AlignViewport av = null;
3973 // now check to see if we really need to create a new viewport.
3974 if (multipleView && viewportsAdded.size() == 0)
3976 // We recovered an alignment for which a viewport already exists.
3977 // TODO: fix up any settings necessary for overlaying stored state onto
3978 // state recovered from another document. (may not be necessary).
3979 // we may need a binding from a viewport in memory to one recovered from
3981 // and then recover its containing af to allow the settings to be applied.
3982 // TODO: fix for vamsas demo
3984 "About to recover a viewport for existing alignment: Sequence set ID is "
3986 Object seqsetobj = retrieveExistingObj(uniqueSeqSetId);
3987 if (seqsetobj != null)
3989 if (seqsetobj instanceof String)
3991 uniqueSeqSetId = (String) seqsetobj;
3993 "Recovered extant sequence set ID mapping for ID : New Sequence set ID is "
3999 "Warning : Collision between sequence set ID string and existing jalview object mapping.");
4005 * indicate that annotation colours are applied across all groups (pre
4006 * Jalview 2.8.1 behaviour)
4008 boolean doGroupAnnColour = Jalview2XML.isVersionStringLaterThan("2.8.1",
4009 jalviewModel.getVersion());
4011 AlignmentPanel ap = null;
4012 boolean isnewview = true;
4015 // Check to see if this alignment already has a view id == viewId
4016 jalview.gui.AlignmentPanel views[] = Desktop
4017 .getAlignmentPanels(uniqueSeqSetId);
4018 if (views != null && views.length > 0)
4020 for (int v = 0; v < views.length; v++)
4022 if (views[v].av.getViewId().equalsIgnoreCase(viewId))
4024 // recover the existing alignpanel, alignframe, viewport
4025 af = views[v].alignFrame;
4028 // TODO: could even skip resetting view settings if we don't want to
4029 // change the local settings from other jalview processes
4038 af = loadViewport(file, jseqs, hiddenSeqs, al, jalviewModel, view,
4039 uniqueSeqSetId, viewId, autoAlan);
4040 av = af.getViewport();
4045 * Load any trees, PDB structures and viewers
4047 * Not done if flag is false (when this method is used for New View)
4049 if (loadTreesAndStructures)
4051 loadTrees(jalviewModel, view, af, av, ap);
4052 loadPCAViewers(jalviewModel, ap);
4053 loadPDBStructures(jprovider, jseqs, af, ap);
4054 loadRnaViewers(jprovider, jseqs, ap);
4056 // and finally return.
4061 * Instantiate and link any saved RNA (Varna) viewers. The state of the Varna
4062 * panel is restored from separate jar entries, two (gapped and trimmed) per
4063 * sequence and secondary structure.
4065 * Currently each viewer shows just one sequence and structure (gapped and
4066 * trimmed), however this method is designed to support multiple sequences or
4067 * structures in viewers if wanted in future.
4073 private void loadRnaViewers(jarInputStreamProvider jprovider,
4074 List<JSeq> jseqs, AlignmentPanel ap)
4077 * scan the sequences for references to viewers; create each one the first
4078 * time it is referenced, add Rna models to existing viewers
4080 for (JSeq jseq : jseqs)
4082 for (int i = 0; i < jseq.getRnaViewer().size(); i++)
4084 RnaViewer viewer = jseq.getRnaViewer().get(i);
4085 AppVarna appVarna = findOrCreateVarnaViewer(viewer, uniqueSetSuffix,
4088 for (int j = 0; j < viewer.getSecondaryStructure().size(); j++)
4090 SecondaryStructure ss = viewer.getSecondaryStructure().get(j);
4091 SequenceI seq = seqRefIds.get(jseq.getId());
4092 AlignmentAnnotation ann = this.annotationIds
4093 .get(ss.getAnnotationId());
4096 * add the structure to the Varna display (with session state copied
4097 * from the jar to a temporary file)
4099 boolean gapped = safeBoolean(ss.isGapped());
4100 String rnaTitle = ss.getTitle();
4101 String sessionState = ss.getViewerState();
4102 String tempStateFile = copyJarEntry(jprovider, sessionState,
4104 RnaModel rna = new RnaModel(rnaTitle, ann, seq, null, gapped);
4105 appVarna.addModelSession(rna, rnaTitle, tempStateFile);
4107 appVarna.setInitialSelection(safeInt(viewer.getSelectedRna()));
4113 * Locate and return an already instantiated matching AppVarna, or create one
4117 * @param viewIdSuffix
4121 protected AppVarna findOrCreateVarnaViewer(RnaViewer viewer,
4122 String viewIdSuffix, AlignmentPanel ap)
4125 * on each load a suffix is appended to the saved viewId, to avoid conflicts
4126 * if load is repeated
4128 String postLoadId = viewer.getViewId() + viewIdSuffix;
4129 for (JInternalFrame frame : getAllFrames())
4131 if (frame instanceof AppVarna)
4133 AppVarna varna = (AppVarna) frame;
4134 if (postLoadId.equals(varna.getViewId()))
4136 // this viewer is already instantiated
4137 // could in future here add ap as another 'parent' of the
4138 // AppVarna window; currently just 1-to-many
4145 * viewer not found - make it
4147 RnaViewerModel model = new RnaViewerModel(postLoadId, viewer.getTitle(),
4148 safeInt(viewer.getXpos()), safeInt(viewer.getYpos()),
4149 safeInt(viewer.getWidth()), safeInt(viewer.getHeight()),
4150 safeInt(viewer.getDividerLocation()));
4151 AppVarna varna = new AppVarna(model, ap);
4157 * Load any saved trees
4165 protected void loadTrees(JalviewModel jm, Viewport view, AlignFrame af,
4166 AlignViewport av, AlignmentPanel ap)
4168 // TODO result of automated refactoring - are all these parameters needed?
4171 for (int t = 0; t < jm.getTree().size(); t++)
4174 Tree tree = jm.getTree().get(t);
4176 TreePanel tp = (TreePanel) retrieveExistingObj(tree.getId());
4179 tp = af.showNewickTree(new NewickFile(tree.getNewick()),
4180 tree.getTitle(), safeInt(tree.getWidth()),
4181 safeInt(tree.getHeight()), safeInt(tree.getXpos()),
4182 safeInt(tree.getYpos()));
4183 if (tree.getId() != null)
4185 // perhaps bind the tree id to something ?
4190 // update local tree attributes ?
4191 // TODO: should check if tp has been manipulated by user - if so its
4192 // settings shouldn't be modified
4193 tp.setTitle(tree.getTitle());
4194 tp.setBounds(new Rectangle(safeInt(tree.getXpos()),
4195 safeInt(tree.getYpos()), safeInt(tree.getWidth()),
4196 safeInt(tree.getHeight())));
4197 tp.setViewport(av); // af.viewport;
4198 // TODO: verify 'associate with all views' works still
4199 tp.getTreeCanvas().setViewport(av); // af.viewport;
4200 tp.getTreeCanvas().setAssociatedPanel(ap); // af.alignPanel;
4202 tp.getTreeCanvas().setApplyToAllViews(tree.isLinkToAllViews());
4205 warn("There was a problem recovering stored Newick tree: \n"
4206 + tree.getNewick());
4210 tp.fitToWindow.setState(safeBoolean(tree.isFitToWindow()));
4211 tp.fitToWindow_actionPerformed(null);
4213 if (tree.getFontName() != null)
4216 new Font(tree.getFontName(), safeInt(tree.getFontStyle()),
4217 safeInt(tree.getFontSize())));
4222 new Font(view.getFontName(), safeInt(view.getFontStyle()),
4223 safeInt(view.getFontSize())));
4226 tp.showPlaceholders(safeBoolean(tree.isMarkUnlinked()));
4227 tp.showBootstrap(safeBoolean(tree.isShowBootstrap()));
4228 tp.showDistances(safeBoolean(tree.isShowDistances()));
4230 tp.getTreeCanvas().setThreshold(safeFloat(tree.getThreshold()));
4232 if (safeBoolean(tree.isCurrentTree()))
4234 af.getViewport().setCurrentTree(tp.getTree());
4238 } catch (Exception ex)
4240 ex.printStackTrace();
4245 * Load and link any saved structure viewers.
4252 protected void loadPDBStructures(jarInputStreamProvider jprovider,
4253 List<JSeq> jseqs, AlignFrame af, AlignmentPanel ap)
4256 * Run through all PDB ids on the alignment, and collect mappings between
4257 * distinct view ids and all sequences referring to that view.
4259 Map<String, StructureViewerModel> structureViewers = new LinkedHashMap<>();
4261 for (int i = 0; i < jseqs.size(); i++)
4263 JSeq jseq = jseqs.get(i);
4264 if (jseq.getPdbids().size() > 0)
4266 List<Pdbids> ids = jseq.getPdbids();
4267 for (int p = 0; p < ids.size(); p++)
4269 Pdbids pdbid = ids.get(p);
4270 final int structureStateCount = pdbid.getStructureState().size();
4271 for (int s = 0; s < structureStateCount; s++)
4273 // check to see if we haven't already created this structure view
4274 final StructureState structureState = pdbid.getStructureState()
4276 String sviewid = (structureState.getViewId() == null) ? null
4277 : structureState.getViewId() + uniqueSetSuffix;
4278 jalview.datamodel.PDBEntry jpdb = new jalview.datamodel.PDBEntry();
4279 // Originally : pdbid.getFile()
4280 // : TODO: verify external PDB file recovery still works in normal
4281 // jalview project load
4283 loadPDBFile(jprovider, pdbid.getId(), pdbid.getFile()));
4284 jpdb.setId(pdbid.getId());
4286 int x = safeInt(structureState.getXpos());
4287 int y = safeInt(structureState.getYpos());
4288 int width = safeInt(structureState.getWidth());
4289 int height = safeInt(structureState.getHeight());
4291 // Probably don't need to do this anymore...
4292 // Desktop.desktop.getComponentAt(x, y);
4293 // TODO: NOW: check that this recovers the PDB file correctly.
4294 String pdbFile = loadPDBFile(jprovider, pdbid.getId(),
4296 jalview.datamodel.SequenceI seq = seqRefIds
4297 .get(jseq.getId() + "");
4298 if (sviewid == null)
4300 sviewid = "_jalview_pre2_4_" + x + "," + y + "," + width + ","
4303 if (!structureViewers.containsKey(sviewid))
4305 String viewerType = structureState.getType();
4306 if (viewerType == null) // pre Jalview 2.9
4308 viewerType = ViewerType.JMOL.toString();
4310 structureViewers.put(sviewid,
4311 new StructureViewerModel(x, y, width, height, false,
4312 false, true, structureState.getViewId(),
4314 // Legacy pre-2.7 conversion JAL-823 :
4315 // do not assume any view has to be linked for colour by
4319 // assemble String[] { pdb files }, String[] { id for each
4320 // file }, orig_fileloc, SequenceI[][] {{ seqs_file 1 }, {
4321 // seqs_file 2}, boolean[] {
4322 // linkAlignPanel,superposeWithAlignpanel}} from hash
4323 StructureViewerModel jmoldat = structureViewers.get(sviewid);
4324 jmoldat.setAlignWithPanel(jmoldat.isAlignWithPanel()
4325 || structureState.isAlignwithAlignPanel());
4328 * Default colour by linked panel to false if not specified (e.g.
4329 * for pre-2.7 projects)
4331 boolean colourWithAlignPanel = jmoldat.isColourWithAlignPanel();
4332 colourWithAlignPanel |= structureState.isColourwithAlignPanel();
4333 jmoldat.setColourWithAlignPanel(colourWithAlignPanel);
4336 * Default colour by viewer to true if not specified (e.g. for
4339 boolean colourByViewer = jmoldat.isColourByViewer();
4340 colourByViewer &= structureState.isColourByJmol();
4341 jmoldat.setColourByViewer(colourByViewer);
4343 if (jmoldat.getStateData().length() < structureState.getValue()
4344 /*Content()*/.length())
4346 jmoldat.setStateData(structureState.getValue());// Content());
4348 if (pdbid.getFile() != null)
4350 File mapkey = new File(pdbid.getFile());
4351 StructureData seqstrmaps = jmoldat.getFileData().get(mapkey);
4352 if (seqstrmaps == null)
4354 jmoldat.getFileData().put(mapkey,
4355 seqstrmaps = jmoldat.new StructureData(pdbFile,
4358 if (!seqstrmaps.getSeqList().contains(seq))
4360 seqstrmaps.getSeqList().add(seq);
4366 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");
4373 // Instantiate the associated structure views
4374 for (Entry<String, StructureViewerModel> entry : structureViewers
4379 createOrLinkStructureViewer(entry, af, ap, jprovider);
4380 } catch (Exception e)
4383 "Error loading structure viewer: " + e.getMessage());
4384 // failed - try the next one
4396 protected void createOrLinkStructureViewer(
4397 Entry<String, StructureViewerModel> viewerData, AlignFrame af,
4398 AlignmentPanel ap, jarInputStreamProvider jprovider)
4400 final StructureViewerModel stateData = viewerData.getValue();
4403 * Search for any viewer windows already open from other alignment views
4404 * that exactly match the stored structure state
4406 StructureViewerBase comp = findMatchingViewer(viewerData);
4410 linkStructureViewer(ap, comp, stateData);
4414 String type = stateData.getType();
4417 ViewerType viewerType = ViewerType.valueOf(type);
4418 createStructureViewer(viewerType, viewerData, af, jprovider);
4419 } catch (IllegalArgumentException | NullPointerException e)
4421 // TODO JAL-3619 show error dialog / offer an alternative viewer
4422 Cache.log.error("Invalid structure viewer type: " + type);
4427 * Generates a name for the entry in the project jar file to hold state
4428 * information for a structure viewer
4433 protected String getViewerJarEntryName(String viewId)
4435 return VIEWER_PREFIX + viewId;
4439 * Returns any open frame that matches given structure viewer data. The match
4440 * is based on the unique viewId, or (for older project versions) the frame's
4446 protected StructureViewerBase findMatchingViewer(
4447 Entry<String, StructureViewerModel> viewerData)
4449 final String sviewid = viewerData.getKey();
4450 final StructureViewerModel svattrib = viewerData.getValue();
4451 StructureViewerBase comp = null;
4452 JInternalFrame[] frames = getAllFrames();
4453 for (JInternalFrame frame : frames)
4455 if (frame instanceof StructureViewerBase)
4458 * Post jalview 2.4 schema includes structure view id
4460 if (sviewid != null && ((StructureViewerBase) frame).getViewId()
4463 comp = (StructureViewerBase) frame;
4464 break; // break added in 2.9
4467 * Otherwise test for matching position and size of viewer frame
4469 else if (frame.getX() == svattrib.getX()
4470 && frame.getY() == svattrib.getY()
4471 && frame.getHeight() == svattrib.getHeight()
4472 && frame.getWidth() == svattrib.getWidth())
4474 comp = (StructureViewerBase) frame;
4475 // no break in faint hope of an exact match on viewId
4483 * Link an AlignmentPanel to an existing structure viewer.
4488 * @param useinViewerSuperpos
4489 * @param usetoColourbyseq
4490 * @param viewerColouring
4492 protected void linkStructureViewer(AlignmentPanel ap,
4493 StructureViewerBase viewer, StructureViewerModel stateData)
4495 // NOTE: if the jalview project is part of a shared session then
4496 // view synchronization should/could be done here.
4498 final boolean useinViewerSuperpos = stateData.isAlignWithPanel();
4499 final boolean usetoColourbyseq = stateData.isColourWithAlignPanel();
4500 final boolean viewerColouring = stateData.isColourByViewer();
4501 Map<File, StructureData> oldFiles = stateData.getFileData();
4504 * Add mapping for sequences in this view to an already open viewer
4506 final AAStructureBindingModel binding = viewer.getBinding();
4507 for (File id : oldFiles.keySet())
4509 // add this and any other pdb files that should be present in the
4511 StructureData filedat = oldFiles.get(id);
4512 String pdbFile = filedat.getFilePath();
4513 SequenceI[] seq = filedat.getSeqList().toArray(new SequenceI[0]);
4514 binding.getSsm().setMapping(seq, null, pdbFile, DataSourceType.FILE,
4516 binding.addSequenceForStructFile(pdbFile, seq);
4518 // and add the AlignmentPanel's reference to the view panel
4519 viewer.addAlignmentPanel(ap);
4520 if (useinViewerSuperpos)
4522 viewer.useAlignmentPanelForSuperposition(ap);
4526 viewer.excludeAlignmentPanelForSuperposition(ap);
4528 if (usetoColourbyseq)
4530 viewer.useAlignmentPanelForColourbyseq(ap, !viewerColouring);
4534 viewer.excludeAlignmentPanelForColourbyseq(ap);
4539 * Get all frames within the Desktop.
4543 protected JInternalFrame[] getAllFrames()
4545 JInternalFrame[] frames = null;
4546 // TODO is this necessary - is it safe - risk of hanging?
4551 frames = Desktop.desktop.getAllFrames();
4552 } catch (ArrayIndexOutOfBoundsException e)
4554 // occasional No such child exceptions are thrown here...
4558 } catch (InterruptedException f)
4562 } while (frames == null);
4567 * Answers true if 'version' is equal to or later than 'supported', where each
4568 * is formatted as major/minor versions like "2.8.3" or "2.3.4b1" for bugfix
4569 * changes. Development and test values for 'version' are leniently treated
4573 * - minimum version we are comparing against
4575 * - version of data being processsed
4578 public static boolean isVersionStringLaterThan(String supported,
4581 if (supported == null || version == null
4582 || version.equalsIgnoreCase("DEVELOPMENT BUILD")
4583 || version.equalsIgnoreCase("Test")
4584 || version.equalsIgnoreCase("AUTOMATED BUILD"))
4586 System.err.println("Assuming project file with "
4587 + (version == null ? "null" : version)
4588 + " is compatible with Jalview version " + supported);
4593 return StringUtils.compareVersions(version, supported, "b") >= 0;
4597 Vector<JalviewStructureDisplayI> newStructureViewers = null;
4599 protected void addNewStructureViewer(JalviewStructureDisplayI sview)
4601 if (newStructureViewers != null)
4603 sview.getBinding().setFinishedLoadingFromArchive(false);
4604 newStructureViewers.add(sview);
4608 protected void setLoadingFinishedForNewStructureViewers()
4610 if (newStructureViewers != null)
4612 for (JalviewStructureDisplayI sview : newStructureViewers)
4614 sview.getBinding().setFinishedLoadingFromArchive(true);
4616 newStructureViewers.clear();
4617 newStructureViewers = null;
4621 AlignFrame loadViewport(String file, List<JSeq> JSEQ,
4622 List<SequenceI> hiddenSeqs, AlignmentI al, JalviewModel jm,
4623 Viewport view, String uniqueSeqSetId, String viewId,
4624 List<JvAnnotRow> autoAlan)
4626 AlignFrame af = null;
4627 af = new AlignFrame(al, safeInt(view.getWidth()),
4628 safeInt(view.getHeight()), uniqueSeqSetId, viewId)
4632 // protected void processKeyEvent(java.awt.event.KeyEvent e) {
4633 // System.out.println("Jalview2XML AF " + e);
4634 // super.processKeyEvent(e);
4641 af.setFileName(file, FileFormat.Jalview);
4643 final AlignViewport viewport = af.getViewport();
4644 for (int i = 0; i < JSEQ.size(); i++)
4646 int colour = safeInt(JSEQ.get(i).getColour());
4647 viewport.setSequenceColour(viewport.getAlignment().getSequenceAt(i),
4653 viewport.setColourByReferenceSeq(true);
4654 viewport.setDisplayReferenceSeq(true);
4657 viewport.setGatherViewsHere(safeBoolean(view.isGatheredViews()));
4659 if (view.getSequenceSetId() != null)
4661 AlignmentViewport av = viewportsAdded.get(uniqueSeqSetId);
4663 viewport.setSequenceSetId(uniqueSeqSetId);
4666 // propagate shared settings to this new view
4667 viewport.setHistoryList(av.getHistoryList());
4668 viewport.setRedoList(av.getRedoList());
4672 viewportsAdded.put(uniqueSeqSetId, viewport);
4674 // TODO: check if this method can be called repeatedly without
4675 // side-effects if alignpanel already registered.
4676 PaintRefresher.Register(af.alignPanel, uniqueSeqSetId);
4678 // apply Hidden regions to view.
4679 if (hiddenSeqs != null)
4681 for (int s = 0; s < JSEQ.size(); s++)
4683 SequenceGroup hidden = new SequenceGroup();
4684 boolean isRepresentative = false;
4685 for (int r = 0; r < JSEQ.get(s).getHiddenSequences().size(); r++)
4687 isRepresentative = true;
4688 SequenceI sequenceToHide = al
4689 .getSequenceAt(JSEQ.get(s).getHiddenSequences().get(r));
4690 hidden.addSequence(sequenceToHide, false);
4691 // remove from hiddenSeqs list so we don't try to hide it twice
4692 hiddenSeqs.remove(sequenceToHide);
4694 if (isRepresentative)
4696 SequenceI representativeSequence = al.getSequenceAt(s);
4697 hidden.addSequence(representativeSequence, false);
4698 viewport.hideRepSequences(representativeSequence, hidden);
4702 SequenceI[] hseqs = hiddenSeqs
4703 .toArray(new SequenceI[hiddenSeqs.size()]);
4704 viewport.hideSequence(hseqs);
4707 // recover view properties and display parameters
4709 viewport.setShowAnnotation(safeBoolean(view.isShowAnnotation()));
4710 viewport.setAbovePIDThreshold(safeBoolean(view.isPidSelected()));
4711 final int pidThreshold = safeInt(view.getPidThreshold());
4712 viewport.setThreshold(pidThreshold);
4714 viewport.setColourText(safeBoolean(view.isShowColourText()));
4716 viewport.setConservationSelected(
4717 safeBoolean(view.isConservationSelected()));
4718 viewport.setIncrement(safeInt(view.getConsThreshold()));
4719 viewport.setShowJVSuffix(safeBoolean(view.isShowFullId()));
4720 viewport.setRightAlignIds(safeBoolean(view.isRightAlignIds()));
4721 viewport.setFont(new Font(view.getFontName(),
4722 safeInt(view.getFontStyle()), safeInt(view.getFontSize())),
4724 ViewStyleI vs = viewport.getViewStyle();
4725 vs.setScaleProteinAsCdna(view.isScaleProteinAsCdna());
4726 viewport.setViewStyle(vs);
4727 // TODO: allow custom charWidth/Heights to be restored by updating them
4728 // after setting font - which means set above to false
4729 viewport.setRenderGaps(safeBoolean(view.isRenderGaps()));
4730 viewport.setWrapAlignment(safeBoolean(view.isWrapAlignment()));
4731 viewport.setShowAnnotation(safeBoolean(view.isShowAnnotation()));
4733 viewport.setShowBoxes(safeBoolean(view.isShowBoxes()));
4735 viewport.setShowText(safeBoolean(view.isShowText()));
4737 viewport.setTextColour(new Color(safeInt(view.getTextCol1())));
4738 viewport.setTextColour2(new Color(safeInt(view.getTextCol2())));
4739 viewport.setThresholdTextColour(safeInt(view.getTextColThreshold()));
4740 viewport.setShowUnconserved(view.isShowUnconserved());
4741 viewport.getRanges().setStartRes(safeInt(view.getStartRes()));
4743 if (view.getViewName() != null)
4745 viewport.setViewName(view.getViewName());
4746 af.setInitialTabVisible();
4748 af.setBounds(safeInt(view.getXpos()), safeInt(view.getYpos()),
4749 safeInt(view.getWidth()), safeInt(view.getHeight()));
4750 // startSeq set in af.alignPanel.updateLayout below
4751 af.alignPanel.updateLayout();
4752 ColourSchemeI cs = null;
4753 // apply colourschemes
4754 if (view.getBgColour() != null)
4756 if (view.getBgColour().startsWith("ucs"))
4758 cs = getUserColourScheme(jm, view.getBgColour());
4760 else if (view.getBgColour().startsWith("Annotation"))
4762 AnnotationColourScheme viewAnnColour = view.getAnnotationColours();
4763 cs = constructAnnotationColour(viewAnnColour, af, al, jm, true);
4770 cs = ColourSchemeProperty.getColourScheme(af.getViewport(), al,
4771 view.getBgColour());
4776 * turn off 'alignment colour applies to all groups'
4777 * while restoring global colour scheme
4779 viewport.setColourAppliesToAllGroups(false);
4780 viewport.setGlobalColourScheme(cs);
4781 viewport.getResidueShading().setThreshold(pidThreshold,
4782 view.isIgnoreGapsinConsensus());
4783 viewport.getResidueShading()
4784 .setConsensus(viewport.getSequenceConsensusHash());
4785 if (safeBoolean(view.isConservationSelected()) && cs != null)
4787 viewport.getResidueShading()
4788 .setConservationInc(safeInt(view.getConsThreshold()));
4790 af.changeColour(cs);
4791 viewport.setColourAppliesToAllGroups(true);
4793 viewport.setShowSequenceFeatures(
4794 safeBoolean(view.isShowSequenceFeatures()));
4796 viewport.setCentreColumnLabels(view.isCentreColumnLabels());
4797 viewport.setIgnoreGapsConsensus(view.isIgnoreGapsinConsensus(), null);
4798 viewport.setFollowHighlight(view.isFollowHighlight());
4799 viewport.followSelection = view.isFollowSelection();
4800 viewport.setShowConsensusHistogram(view.isShowConsensusHistogram());
4801 viewport.setShowSequenceLogo(view.isShowSequenceLogo());
4802 viewport.setNormaliseSequenceLogo(view.isNormaliseSequenceLogo());
4803 viewport.setShowDBRefs(safeBoolean(view.isShowDbRefTooltip()));
4804 viewport.setShowNPFeats(safeBoolean(view.isShowNPfeatureTooltip()));
4805 viewport.setShowGroupConsensus(view.isShowGroupConsensus());
4806 viewport.setShowGroupConservation(view.isShowGroupConservation());
4807 viewport.setShowComplementFeatures(view.isShowComplementFeatures());
4808 viewport.setShowComplementFeaturesOnTop(
4809 view.isShowComplementFeaturesOnTop());
4811 // recover feature settings
4812 if (jm.getFeatureSettings() != null)
4814 FeatureRendererModel fr = af.alignPanel.getSeqPanel().seqCanvas
4815 .getFeatureRenderer();
4816 FeaturesDisplayed fdi;
4817 viewport.setFeaturesDisplayed(fdi = new FeaturesDisplayed());
4818 String[] renderOrder = new String[jm.getFeatureSettings().getSetting()
4820 Map<String, FeatureColourI> featureColours = new Hashtable<>();
4821 Map<String, Float> featureOrder = new Hashtable<>();
4823 for (int fs = 0; fs < jm.getFeatureSettings().getSetting()
4826 Setting setting = jm.getFeatureSettings().getSetting().get(fs);
4827 String featureType = setting.getType();
4830 * restore feature filters (if any)
4832 jalview.xml.binding.jalview.FeatureMatcherSet filters = setting
4834 if (filters != null)
4836 FeatureMatcherSetI filter = Jalview2XML.parseFilter(featureType,
4838 if (!filter.isEmpty())
4840 fr.setFeatureFilter(featureType, filter);
4845 * restore feature colour scheme
4847 Color maxColour = new Color(setting.getColour());
4848 if (setting.getMincolour() != null)
4851 * minColour is always set unless a simple colour
4852 * (including for colour by label though it doesn't use it)
4854 Color minColour = new Color(setting.getMincolour().intValue());
4855 Color noValueColour = minColour;
4856 NoValueColour noColour = setting.getNoValueColour();
4857 if (noColour == NoValueColour.NONE)
4859 noValueColour = null;
4861 else if (noColour == NoValueColour.MAX)
4863 noValueColour = maxColour;
4865 float min = safeFloat(safeFloat(setting.getMin()));
4866 float max = setting.getMax() == null ? 1f
4867 : setting.getMax().floatValue();
4868 FeatureColourI gc = new FeatureColour(maxColour, minColour,
4869 maxColour, noValueColour, min, max);
4870 if (setting.getAttributeName().size() > 0)
4872 gc.setAttributeName(setting.getAttributeName().toArray(
4873 new String[setting.getAttributeName().size()]));
4875 if (setting.getThreshold() != null)
4877 gc.setThreshold(setting.getThreshold().floatValue());
4878 int threshstate = safeInt(setting.getThreshstate());
4879 // -1 = None, 0 = Below, 1 = Above threshold
4880 if (threshstate == 0)
4882 gc.setBelowThreshold(true);
4884 else if (threshstate == 1)
4886 gc.setAboveThreshold(true);
4889 gc.setAutoScaled(true); // default
4890 if (setting.isAutoScale() != null)
4892 gc.setAutoScaled(setting.isAutoScale());
4894 if (setting.isColourByLabel() != null)
4896 gc.setColourByLabel(setting.isColourByLabel());
4898 // and put in the feature colour table.
4899 featureColours.put(featureType, gc);
4903 featureColours.put(featureType, new FeatureColour(maxColour));
4905 renderOrder[fs] = featureType;
4906 if (setting.getOrder() != null)
4908 featureOrder.put(featureType, setting.getOrder().floatValue());
4912 featureOrder.put(featureType, Float.valueOf(
4913 fs / jm.getFeatureSettings().getSetting().size()));
4915 if (safeBoolean(setting.isDisplay()))
4917 fdi.setVisible(featureType);
4920 Map<String, Boolean> fgtable = new Hashtable<>();
4921 for (int gs = 0; gs < jm.getFeatureSettings().getGroup().size(); gs++)
4923 Group grp = jm.getFeatureSettings().getGroup().get(gs);
4924 fgtable.put(grp.getName(), Boolean.valueOf(grp.isDisplay()));
4926 // FeatureRendererSettings frs = new FeatureRendererSettings(renderOrder,
4927 // fgtable, featureColours, jms.getFeatureSettings().hasTransparency() ?
4928 // jms.getFeatureSettings().getTransparency() : 0.0, featureOrder);
4929 FeatureRendererSettings frs = new FeatureRendererSettings(renderOrder,
4930 fgtable, featureColours, 1.0f, featureOrder);
4931 fr.transferSettings(frs);
4934 if (view.getHiddenColumns().size() > 0)
4936 for (int c = 0; c < view.getHiddenColumns().size(); c++)
4938 final HiddenColumns hc = view.getHiddenColumns().get(c);
4939 viewport.hideColumns(safeInt(hc.getStart()),
4940 safeInt(hc.getEnd()) /* +1 */);
4943 if (view.getCalcIdParam() != null)
4945 for (CalcIdParam calcIdParam : view.getCalcIdParam())
4947 if (calcIdParam != null)
4949 if (recoverCalcIdParam(calcIdParam, viewport))
4954 warn("Couldn't recover parameters for "
4955 + calcIdParam.getCalcId());
4960 af.setMenusFromViewport(viewport);
4961 af.setTitle(view.getTitle());
4962 // TODO: we don't need to do this if the viewport is aready visible.
4964 * Add the AlignFrame to the desktop (it may be 'gathered' later), unless it
4965 * has a 'cdna/protein complement' view, in which case save it in order to
4966 * populate a SplitFrame once all views have been read in.
4968 String complementaryViewId = view.getComplementId();
4969 if (complementaryViewId == null)
4971 Desktop.addInternalFrame(af, view.getTitle(),
4972 safeInt(view.getWidth()), safeInt(view.getHeight()));
4973 // recompute any autoannotation
4974 af.alignPanel.updateAnnotation(false, true);
4975 reorderAutoannotation(af, al, autoAlan);
4976 af.alignPanel.alignmentChanged();
4980 splitFrameCandidates.put(view, af);
4986 * Reads saved data to restore Colour by Annotation settings
4988 * @param viewAnnColour
4992 * @param checkGroupAnnColour
4995 private ColourSchemeI constructAnnotationColour(
4996 AnnotationColourScheme viewAnnColour, AlignFrame af,
4997 AlignmentI al, JalviewModel model, boolean checkGroupAnnColour)
4999 boolean propagateAnnColour = false;
5000 AlignmentI annAlignment = af != null ? af.getViewport().getAlignment()
5002 if (checkGroupAnnColour && al.getGroups() != null
5003 && al.getGroups().size() > 0)
5005 // pre 2.8.1 behaviour
5006 // check to see if we should transfer annotation colours
5007 propagateAnnColour = true;
5008 for (SequenceGroup sg : al.getGroups())
5010 if (sg.getColourScheme() instanceof AnnotationColourGradient)
5012 propagateAnnColour = false;
5018 * 2.10.2- : saved annotationId is AlignmentAnnotation.annotationId
5020 String annotationId = viewAnnColour.getAnnotation();
5021 AlignmentAnnotation matchedAnnotation = annotationIds.get(annotationId);
5024 * pre 2.10.2: saved annotationId is AlignmentAnnotation.label
5026 if (matchedAnnotation == null
5027 && annAlignment.getAlignmentAnnotation() != null)
5029 for (int i = 0; i < annAlignment.getAlignmentAnnotation().length; i++)
5032 .equals(annAlignment.getAlignmentAnnotation()[i].label))
5034 matchedAnnotation = annAlignment.getAlignmentAnnotation()[i];
5039 if (matchedAnnotation == null)
5041 System.err.println("Failed to match annotation colour scheme for "
5045 if (matchedAnnotation.getThreshold() == null)
5047 matchedAnnotation.setThreshold(
5048 new GraphLine(safeFloat(viewAnnColour.getThreshold()),
5049 "Threshold", Color.black));
5052 AnnotationColourGradient cs = null;
5053 if (viewAnnColour.getColourScheme().equals("None"))
5055 cs = new AnnotationColourGradient(matchedAnnotation,
5056 new Color(safeInt(viewAnnColour.getMinColour())),
5057 new Color(safeInt(viewAnnColour.getMaxColour())),
5058 safeInt(viewAnnColour.getAboveThreshold()));
5060 else if (viewAnnColour.getColourScheme().startsWith("ucs"))
5062 cs = new AnnotationColourGradient(matchedAnnotation,
5063 getUserColourScheme(model, viewAnnColour.getColourScheme()),
5064 safeInt(viewAnnColour.getAboveThreshold()));
5068 cs = new AnnotationColourGradient(matchedAnnotation,
5069 ColourSchemeProperty.getColourScheme(af.getViewport(), al,
5070 viewAnnColour.getColourScheme()),
5071 safeInt(viewAnnColour.getAboveThreshold()));
5074 boolean perSequenceOnly = safeBoolean(viewAnnColour.isPerSequence());
5075 boolean useOriginalColours = safeBoolean(
5076 viewAnnColour.isPredefinedColours());
5077 cs.setSeqAssociated(perSequenceOnly);
5078 cs.setPredefinedColours(useOriginalColours);
5080 if (propagateAnnColour && al.getGroups() != null)
5082 // Also use these settings for all the groups
5083 for (int g = 0; g < al.getGroups().size(); g++)
5085 SequenceGroup sg = al.getGroups().get(g);
5086 if (sg.getGroupColourScheme() == null)
5091 AnnotationColourGradient groupScheme = new AnnotationColourGradient(
5092 matchedAnnotation, sg.getColourScheme(),
5093 safeInt(viewAnnColour.getAboveThreshold()));
5094 sg.setColourScheme(groupScheme);
5095 groupScheme.setSeqAssociated(perSequenceOnly);
5096 groupScheme.setPredefinedColours(useOriginalColours);
5102 private void reorderAutoannotation(AlignFrame af, AlignmentI al,
5103 List<JvAnnotRow> autoAlan)
5105 // copy over visualization settings for autocalculated annotation in the
5107 if (al.getAlignmentAnnotation() != null)
5110 * Kludge for magic autoannotation names (see JAL-811)
5112 String[] magicNames = new String[] { "Consensus", "Quality",
5114 JvAnnotRow nullAnnot = new JvAnnotRow(-1, null);
5115 Hashtable<String, JvAnnotRow> visan = new Hashtable<>();
5116 for (String nm : magicNames)
5118 visan.put(nm, nullAnnot);
5120 for (JvAnnotRow auan : autoAlan)
5122 visan.put(auan.template.label
5123 + (auan.template.getCalcId() == null ? ""
5124 : "\t" + auan.template.getCalcId()),
5127 int hSize = al.getAlignmentAnnotation().length;
5128 List<JvAnnotRow> reorder = new ArrayList<>();
5129 // work through any autoCalculated annotation already on the view
5130 // removing it if it should be placed in a different location on the
5131 // annotation panel.
5132 List<String> remains = new ArrayList<>(visan.keySet());
5133 for (int h = 0; h < hSize; h++)
5135 jalview.datamodel.AlignmentAnnotation jalan = al
5136 .getAlignmentAnnotation()[h];
5137 if (jalan.autoCalculated)
5140 JvAnnotRow valan = visan.get(k = jalan.label);
5141 if (jalan.getCalcId() != null)
5143 valan = visan.get(k = jalan.label + "\t" + jalan.getCalcId());
5148 // delete the auto calculated row from the alignment
5149 al.deleteAnnotation(jalan, false);
5153 if (valan != nullAnnot)
5155 if (jalan != valan.template)
5157 // newly created autoannotation row instance
5158 // so keep a reference to the visible annotation row
5159 // and copy over all relevant attributes
5160 if (valan.template.graphHeight >= 0)
5163 jalan.graphHeight = valan.template.graphHeight;
5165 jalan.visible = valan.template.visible;
5167 reorder.add(new JvAnnotRow(valan.order, jalan));
5172 // Add any (possibly stale) autocalculated rows that were not appended to
5173 // the view during construction
5174 for (String other : remains)
5176 JvAnnotRow othera = visan.get(other);
5177 if (othera != nullAnnot && othera.template.getCalcId() != null
5178 && othera.template.getCalcId().length() > 0)
5180 reorder.add(othera);
5183 // now put the automatic annotation in its correct place
5184 int s = 0, srt[] = new int[reorder.size()];
5185 JvAnnotRow[] rws = new JvAnnotRow[reorder.size()];
5186 for (JvAnnotRow jvar : reorder)
5189 srt[s++] = jvar.order;
5192 jalview.util.QuickSort.sort(srt, rws);
5193 // and re-insert the annotation at its correct position
5194 for (JvAnnotRow jvar : rws)
5196 al.addAnnotation(jvar.template, jvar.order);
5198 af.alignPanel.adjustAnnotationHeight();
5202 Hashtable skipList = null;
5205 * TODO remove this method
5208 * @return AlignFrame bound to sequenceSetId from view, if one exists. private
5209 * AlignFrame getSkippedFrame(Viewport view) { if (skipList==null) {
5210 * throw new Error("Implementation Error. No skipList defined for this
5211 * Jalview2XML instance."); } return (AlignFrame)
5212 * skipList.get(view.getSequenceSetId()); }
5216 * Check if the Jalview view contained in object should be skipped or not.
5219 * @return true if view's sequenceSetId is a key in skipList
5221 private boolean skipViewport(JalviewModel object)
5223 if (skipList == null)
5227 String id = object.getViewport().get(0).getSequenceSetId();
5228 if (skipList.containsKey(id))
5230 if (Cache.log != null && Cache.log.isDebugEnabled())
5232 Cache.log.debug("Skipping seuqence set id " + id);
5239 public void addToSkipList(AlignFrame af)
5241 if (skipList == null)
5243 skipList = new Hashtable();
5245 skipList.put(af.getViewport().getSequenceSetId(), af);
5248 public void clearSkipList()
5250 if (skipList != null)
5257 private void recoverDatasetFor(SequenceSet vamsasSet, AlignmentI al,
5258 boolean ignoreUnrefed, String uniqueSeqSetId)
5260 jalview.datamodel.AlignmentI ds = getDatasetFor(
5261 vamsasSet.getDatasetId());
5262 AlignmentI xtant_ds = ds;
5263 if (xtant_ds == null)
5265 // good chance we are about to create a new dataset, but check if we've
5266 // seen some of the dataset sequence IDs before.
5267 // TODO: skip this check if we are working with project generated by
5268 // version 2.11 or later
5269 xtant_ds = checkIfHasDataset(vamsasSet.getSequence());
5270 if (xtant_ds != null)
5273 addDatasetRef(vamsasSet.getDatasetId(), ds);
5276 Vector<SequenceI> dseqs = null;
5279 // recovering an alignment View
5280 AlignmentI seqSetDS = getDatasetFor(UNIQSEQSETID + uniqueSeqSetId);
5281 if (seqSetDS != null)
5283 if (ds != null && ds != seqSetDS)
5285 warn("JAL-3171 regression: Overwriting a dataset reference for an alignment"
5286 + " - CDS/Protein crossreference data may be lost");
5287 if (xtant_ds != null)
5289 // This can only happen if the unique sequence set ID was bound to a
5290 // dataset that did not contain any of the sequences in the view
5291 // currently being restored.
5292 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.");
5296 addDatasetRef(vamsasSet.getDatasetId(), ds);
5301 // try even harder to restore dataset
5302 AlignmentI xtantDS = checkIfHasDataset(vamsasSet.getSequence());
5303 // create a list of new dataset sequences
5304 dseqs = new Vector<>();
5306 for (int i = 0, iSize = vamsasSet.getSequence().size(); i < iSize; i++)
5308 Sequence vamsasSeq = vamsasSet.getSequence().get(i);
5309 ensureJalviewDatasetSequence(vamsasSeq, ds, dseqs, ignoreUnrefed, i);
5311 // create a new dataset
5314 SequenceI[] dsseqs = new SequenceI[dseqs.size()];
5315 dseqs.copyInto(dsseqs);
5316 ds = new jalview.datamodel.Alignment(dsseqs);
5317 debug("Created new dataset " + vamsasSet.getDatasetId()
5318 + " for alignment " + System.identityHashCode(al));
5319 addDatasetRef(vamsasSet.getDatasetId(), ds);
5321 // set the dataset for the newly imported alignment.
5322 if (al.getDataset() == null && !ignoreUnrefed)
5325 // register dataset for the alignment's uniqueSeqSetId for legacy projects
5326 addDatasetRef(UNIQSEQSETID + uniqueSeqSetId, ds);
5328 updateSeqDatasetBinding(vamsasSet.getSequence(), ds);
5332 * XML dataset sequence ID to materialised dataset reference
5334 HashMap<String, AlignmentI> seqToDataset = new HashMap<>();
5337 * @return the first materialised dataset reference containing a dataset
5338 * sequence referenced in the given view
5340 * - sequences from the view
5342 AlignmentI checkIfHasDataset(List<Sequence> list)
5344 for (Sequence restoredSeq : list)
5346 AlignmentI datasetFor = seqToDataset.get(restoredSeq.getDsseqid());
5347 if (datasetFor != null)
5356 * Register ds as the containing dataset for the dataset sequences referenced
5357 * by sequences in list
5360 * - sequences in a view
5363 void updateSeqDatasetBinding(List<Sequence> list, AlignmentI ds)
5365 for (Sequence restoredSeq : list)
5367 AlignmentI prevDS = seqToDataset.put(restoredSeq.getDsseqid(), ds);
5368 if (prevDS != null && prevDS != ds)
5370 warn("Dataset sequence appears in many datasets: "
5371 + restoredSeq.getDsseqid());
5372 // TODO: try to merge!
5380 * sequence definition to create/merge dataset sequence for
5384 * vector to add new dataset sequence to
5385 * @param ignoreUnrefed
5386 * - when true, don't create new sequences from vamsasSeq if it's id
5387 * doesn't already have an asssociated Jalview sequence.
5389 * - used to reorder the sequence in the alignment according to the
5390 * vamsasSeq array ordering, to preserve ordering of dataset
5392 private void ensureJalviewDatasetSequence(Sequence vamsasSeq,
5393 AlignmentI ds, Vector<SequenceI> dseqs, boolean ignoreUnrefed,
5396 // JBP TODO: Check this is called for AlCodonFrames to support recovery of
5398 SequenceI sq = seqRefIds.get(vamsasSeq.getId());
5399 boolean reorder = false;
5400 SequenceI dsq = null;
5401 if (sq != null && sq.getDatasetSequence() != null)
5403 dsq = sq.getDatasetSequence();
5409 if (sq == null && ignoreUnrefed)
5413 String sqid = vamsasSeq.getDsseqid();
5416 // need to create or add a new dataset sequence reference to this sequence
5419 dsq = seqRefIds.get(sqid);
5424 // make a new dataset sequence
5425 dsq = sq.createDatasetSequence();
5428 // make up a new dataset reference for this sequence
5429 sqid = seqHash(dsq);
5431 dsq.setVamsasId(uniqueSetSuffix + sqid);
5432 seqRefIds.put(sqid, dsq);
5437 dseqs.addElement(dsq);
5442 ds.addSequence(dsq);
5448 { // make this dataset sequence sq's dataset sequence
5449 sq.setDatasetSequence(dsq);
5450 // and update the current dataset alignment
5455 if (!dseqs.contains(dsq))
5462 if (ds.findIndex(dsq) < 0)
5464 ds.addSequence(dsq);
5471 // TODO: refactor this as a merge dataset sequence function
5472 // now check that sq (the dataset sequence) sequence really is the union of
5473 // all references to it
5474 // boolean pre = sq.getStart() < dsq.getStart();
5475 // boolean post = sq.getEnd() > dsq.getEnd();
5479 // StringBuffer sb = new StringBuffer();
5480 String newres = jalview.analysis.AlignSeq.extractGaps(
5481 jalview.util.Comparison.GapChars, sq.getSequenceAsString());
5482 if (!newres.equalsIgnoreCase(dsq.getSequenceAsString())
5483 && newres.length() > dsq.getLength())
5485 // Update with the longer sequence.
5489 * if (pre) { sb.insert(0, newres .substring(0, dsq.getStart() -
5490 * sq.getStart())); dsq.setStart(sq.getStart()); } if (post) {
5491 * sb.append(newres.substring(newres.length() - sq.getEnd() -
5492 * dsq.getEnd())); dsq.setEnd(sq.getEnd()); }
5494 dsq.setSequence(newres);
5496 // TODO: merges will never happen if we 'know' we have the real dataset
5497 // sequence - this should be detected when id==dssid
5499 "DEBUG Notice: Merged dataset sequence (if you see this often, post at http://issues.jalview.org/browse/JAL-1474)"); // ("
5500 // + (pre ? "prepended" : "") + " "
5501 // + (post ? "appended" : ""));
5506 // sequence refs are identical. We may need to update the existing dataset
5507 // alignment with this one, though.
5508 if (ds != null && dseqs == null)
5510 int opos = ds.findIndex(dsq);
5511 SequenceI tseq = null;
5512 if (opos != -1 && vseqpos != opos)
5514 // remove from old position
5515 ds.deleteSequence(dsq);
5517 if (vseqpos < ds.getHeight())
5519 if (vseqpos != opos)
5521 // save sequence at destination position
5522 tseq = ds.getSequenceAt(vseqpos);
5523 ds.replaceSequenceAt(vseqpos, dsq);
5524 ds.addSequence(tseq);
5529 ds.addSequence(dsq);
5536 * TODO use AlignmentI here and in related methods - needs
5537 * AlignmentI.getDataset() changed to return AlignmentI instead of Alignment
5539 Hashtable<String, AlignmentI> datasetIds = null;
5541 IdentityHashMap<AlignmentI, String> dataset2Ids = null;
5543 private AlignmentI getDatasetFor(String datasetId)
5545 if (datasetIds == null)
5547 datasetIds = new Hashtable<>();
5550 if (datasetIds.containsKey(datasetId))
5552 return datasetIds.get(datasetId);
5557 private void addDatasetRef(String datasetId, AlignmentI dataset)
5559 if (datasetIds == null)
5561 datasetIds = new Hashtable<>();
5563 datasetIds.put(datasetId, dataset);
5567 * make a new dataset ID for this jalview dataset alignment
5572 private String getDatasetIdRef(AlignmentI dataset)
5574 if (dataset.getDataset() != null)
5576 warn("Serious issue! Dataset Object passed to getDatasetIdRef is not a Jalview DATASET alignment...");
5578 String datasetId = makeHashCode(dataset, null);
5579 if (datasetId == null)
5581 // make a new datasetId and record it
5582 if (dataset2Ids == null)
5584 dataset2Ids = new IdentityHashMap<>();
5588 datasetId = dataset2Ids.get(dataset);
5590 if (datasetId == null)
5592 datasetId = "ds" + dataset2Ids.size() + 1;
5593 dataset2Ids.put(dataset, datasetId);
5600 * Add any saved DBRefEntry's to the sequence. An entry flagged as 'locus' is
5601 * constructed as a special subclass GeneLocus.
5603 * @param datasetSequence
5606 private void addDBRefs(SequenceI datasetSequence, Sequence sequence)
5608 for (int d = 0; d < sequence.getDBRef().size(); d++)
5610 DBRef dr = sequence.getDBRef().get(d);
5614 entry = new GeneLocus(dr.getSource(), dr.getVersion(),
5615 dr.getAccessionId());
5619 entry = new DBRefEntry(dr.getSource(), dr.getVersion(),
5620 dr.getAccessionId());
5622 if (dr.getMapping() != null)
5624 entry.setMap(addMapping(dr.getMapping()));
5626 entry.setCanonical(dr.isCanonical());
5627 datasetSequence.addDBRef(entry);
5631 private jalview.datamodel.Mapping addMapping(Mapping m)
5633 SequenceI dsto = null;
5634 // Mapping m = dr.getMapping();
5635 int fr[] = new int[m.getMapListFrom().size() * 2];
5636 Iterator<MapListFrom> from = m.getMapListFrom().iterator();// enumerateMapListFrom();
5637 for (int _i = 0; from.hasNext(); _i += 2)
5639 MapListFrom mf = from.next();
5640 fr[_i] = mf.getStart();
5641 fr[_i + 1] = mf.getEnd();
5643 int fto[] = new int[m.getMapListTo().size() * 2];
5644 Iterator<MapListTo> to = m.getMapListTo().iterator();// enumerateMapListTo();
5645 for (int _i = 0; to.hasNext(); _i += 2)
5647 MapListTo mf = to.next();
5648 fto[_i] = mf.getStart();
5649 fto[_i + 1] = mf.getEnd();
5651 jalview.datamodel.Mapping jmap = new jalview.datamodel.Mapping(dsto, fr,
5652 fto, m.getMapFromUnit().intValue(),
5653 m.getMapToUnit().intValue());
5656 * (optional) choice of dseqFor or Sequence
5658 if (m.getDseqFor() != null)
5660 String dsfor = m.getDseqFor();
5661 if (seqRefIds.containsKey(dsfor))
5666 jmap.setTo(seqRefIds.get(dsfor));
5670 frefedSequence.add(newMappingRef(dsfor, jmap));
5673 else if (m.getSequence() != null)
5676 * local sequence definition
5678 Sequence ms = m.getSequence();
5679 SequenceI djs = null;
5680 String sqid = ms.getDsseqid();
5681 if (sqid != null && sqid.length() > 0)
5684 * recover dataset sequence
5686 djs = seqRefIds.get(sqid);
5691 "Warning - making up dataset sequence id for DbRef sequence map reference");
5692 sqid = ((Object) ms).toString(); // make up a new hascode for
5693 // undefined dataset sequence hash
5694 // (unlikely to happen)
5700 * make a new dataset sequence and add it to refIds hash
5702 djs = new jalview.datamodel.Sequence(ms.getName(),
5704 djs.setStart(jmap.getMap().getToLowest());
5705 djs.setEnd(jmap.getMap().getToHighest());
5706 djs.setVamsasId(uniqueSetSuffix + sqid);
5708 incompleteSeqs.put(sqid, djs);
5709 seqRefIds.put(sqid, djs);
5712 jalview.bin.Cache.log.debug("about to recurse on addDBRefs.");
5721 * Provides a 'copy' of an alignment view (on action New View) by 'saving' the
5722 * view as XML (but not to file), and then reloading it
5727 public AlignmentPanel copyAlignPanel(AlignmentPanel ap)
5730 JalviewModel jm = saveState(ap, null, null, null);
5733 jm.getVamsasModel().getSequenceSet().get(0).getDatasetId(),
5734 ap.getAlignment().getDataset());
5736 uniqueSetSuffix = "";
5737 // jm.getJalviewModelSequence().getViewport(0).setId(null);
5738 jm.getViewport().get(0).setId(null);
5739 // we don't overwrite the view we just copied
5741 if (this.frefedSequence == null)
5743 frefedSequence = new Vector<>();
5746 viewportsAdded.clear();
5748 AlignFrame af = loadFromObject(jm, null, false, null);
5749 af.getAlignPanels().clear();
5750 af.closeMenuItem_actionPerformed(true);
5753 * if(ap.av.getAlignment().getAlignmentAnnotation()!=null) { for(int i=0;
5754 * i<ap.av.getAlignment().getAlignmentAnnotation().length; i++) {
5755 * if(!ap.av.getAlignment().getAlignmentAnnotation()[i].autoCalculated) {
5756 * af.alignPanel.av.getAlignment().getAlignmentAnnotation()[i] =
5757 * ap.av.getAlignment().getAlignmentAnnotation()[i]; } } }
5760 return af.alignPanel;
5763 private Hashtable jvids2vobj;
5765 private void warn(String msg)
5770 private void warn(String msg, Exception e)
5772 if (Cache.log != null)
5776 Cache.log.warn(msg, e);
5780 Cache.log.warn(msg);
5785 System.err.println("Warning: " + msg);
5788 e.printStackTrace();
5793 private void debug(String string)
5795 debug(string, null);
5798 private void debug(String msg, Exception e)
5800 if (Cache.log != null)
5804 Cache.log.debug(msg, e);
5808 Cache.log.debug(msg);
5813 System.err.println("Warning: " + msg);
5816 e.printStackTrace();
5822 * set the object to ID mapping tables used to write/recover objects and XML
5823 * ID strings for the jalview project. If external tables are provided then
5824 * finalize and clearSeqRefs will not clear the tables when the Jalview2XML
5825 * object goes out of scope. - also populates the datasetIds hashtable with
5826 * alignment objects containing dataset sequences
5829 * Map from ID strings to jalview datamodel
5831 * Map from jalview datamodel to ID strings
5835 public void setObjectMappingTables(Hashtable vobj2jv,
5836 IdentityHashMap jv2vobj)
5838 this.jv2vobj = jv2vobj;
5839 this.vobj2jv = vobj2jv;
5840 Iterator ds = jv2vobj.keySet().iterator();
5842 while (ds.hasNext())
5844 Object jvobj = ds.next();
5845 id = jv2vobj.get(jvobj).toString();
5846 if (jvobj instanceof jalview.datamodel.Alignment)
5848 if (((jalview.datamodel.Alignment) jvobj).getDataset() == null)
5850 addDatasetRef(id, (jalview.datamodel.Alignment) jvobj);
5853 else if (jvobj instanceof jalview.datamodel.Sequence)
5855 // register sequence object so the XML parser can recover it.
5856 if (seqRefIds == null)
5858 seqRefIds = new HashMap<>();
5860 if (seqsToIds == null)
5862 seqsToIds = new IdentityHashMap<>();
5864 seqRefIds.put(jv2vobj.get(jvobj).toString(), (SequenceI) jvobj);
5865 seqsToIds.put((SequenceI) jvobj, id);
5867 else if (jvobj instanceof jalview.datamodel.AlignmentAnnotation)
5870 AlignmentAnnotation jvann = (AlignmentAnnotation) jvobj;
5871 annotationIds.put(anid = jv2vobj.get(jvobj).toString(), jvann);
5872 if (jvann.annotationId == null)
5874 jvann.annotationId = anid;
5876 if (!jvann.annotationId.equals(anid))
5878 // TODO verify that this is the correct behaviour
5879 this.warn("Overriding Annotation ID for " + anid
5880 + " from different id : " + jvann.annotationId);
5881 jvann.annotationId = anid;
5884 else if (jvobj instanceof String)
5886 if (jvids2vobj == null)
5888 jvids2vobj = new Hashtable();
5889 jvids2vobj.put(jvobj, jv2vobj.get(jvobj).toString());
5894 Cache.log.debug("Ignoring " + jvobj.getClass() + " (ID = " + id);
5900 * set the uniqueSetSuffix used to prefix/suffix object IDs for jalview
5901 * objects created from the project archive. If string is null (default for
5902 * construction) then suffix will be set automatically.
5906 public void setUniqueSetSuffix(String string)
5908 uniqueSetSuffix = string;
5913 * uses skipList2 as the skipList for skipping views on sequence sets
5914 * associated with keys in the skipList
5918 public void setSkipList(Hashtable skipList2)
5920 skipList = skipList2;
5924 * Reads the jar entry of given name and returns its contents, or null if the
5925 * entry is not found.
5928 * @param jarEntryName
5931 protected String readJarEntry(jarInputStreamProvider jprovider,
5932 String jarEntryName)
5934 String result = null;
5935 BufferedReader in = null;
5940 * Reopen the jar input stream and traverse its entries to find a matching
5943 JarInputStream jin = jprovider.getJarInputStream();
5944 JarEntry entry = null;
5947 entry = jin.getNextJarEntry();
5948 } while (entry != null && !entry.getName().equals(jarEntryName));
5952 StringBuilder out = new StringBuilder(256);
5953 in = new BufferedReader(new InputStreamReader(jin, UTF_8));
5956 while ((data = in.readLine()) != null)
5960 result = out.toString();
5964 warn("Couldn't find entry in Jalview Jar for " + jarEntryName);
5966 } catch (Exception ex)
5968 ex.printStackTrace();
5976 } catch (IOException e)
5987 * Returns an incrementing counter (0, 1, 2...)
5991 private synchronized int nextCounter()
5997 * Loads any saved PCA viewers
6002 protected void loadPCAViewers(JalviewModel model, AlignmentPanel ap)
6006 List<PcaViewer> pcaviewers = model.getPcaViewer();
6007 for (PcaViewer viewer : pcaviewers)
6009 String modelName = viewer.getScoreModelName();
6010 SimilarityParamsI params = new SimilarityParams(
6011 viewer.isIncludeGappedColumns(), viewer.isMatchGaps(),
6012 viewer.isIncludeGaps(),
6013 viewer.isDenominateByShortestLength());
6016 * create the panel (without computing the PCA)
6018 PCAPanel panel = new PCAPanel(ap, modelName, params);
6020 panel.setTitle(viewer.getTitle());
6021 panel.setBounds(new Rectangle(viewer.getXpos(), viewer.getYpos(),
6022 viewer.getWidth(), viewer.getHeight()));
6024 boolean showLabels = viewer.isShowLabels();
6025 panel.setShowLabels(showLabels);
6026 panel.getRotatableCanvas().setShowLabels(showLabels);
6027 panel.getRotatableCanvas()
6028 .setBgColour(new Color(viewer.getBgColour()));
6029 panel.getRotatableCanvas()
6030 .setApplyToAllViews(viewer.isLinkToAllViews());
6033 * load PCA output data
6035 ScoreModelI scoreModel = ScoreModels.getInstance()
6036 .getScoreModel(modelName, ap);
6037 PCA pca = new PCA(null, scoreModel, params);
6038 PcaDataType pcaData = viewer.getPcaData();
6040 MatrixI pairwise = loadDoubleMatrix(pcaData.getPairwiseMatrix());
6041 pca.setPairwiseScores(pairwise);
6043 MatrixI triDiag = loadDoubleMatrix(pcaData.getTridiagonalMatrix());
6044 pca.setTridiagonal(triDiag);
6046 MatrixI result = loadDoubleMatrix(pcaData.getEigenMatrix());
6047 pca.setEigenmatrix(result);
6049 panel.getPcaModel().setPCA(pca);
6052 * we haven't saved the input data! (JAL-2647 to do)
6054 panel.setInputData(null);
6057 * add the sequence points for the PCA display
6059 List<jalview.datamodel.SequencePoint> seqPoints = new ArrayList<>();
6060 for (SequencePoint sp : viewer.getSequencePoint())
6062 String seqId = sp.getSequenceRef();
6063 SequenceI seq = seqRefIds.get(seqId);
6066 throw new IllegalStateException(
6067 "Unmatched seqref for PCA: " + seqId);
6069 Point pt = new Point(sp.getXPos(), sp.getYPos(), sp.getZPos());
6070 jalview.datamodel.SequencePoint seqPoint = new jalview.datamodel.SequencePoint(
6072 seqPoints.add(seqPoint);
6074 panel.getRotatableCanvas().setPoints(seqPoints, seqPoints.size());
6077 * set min-max ranges and scale after setPoints (which recomputes them)
6079 panel.getRotatableCanvas().setScaleFactor(viewer.getScaleFactor());
6080 SeqPointMin spMin = viewer.getSeqPointMin();
6081 float[] min = new float[] { spMin.getXPos(), spMin.getYPos(),
6083 SeqPointMax spMax = viewer.getSeqPointMax();
6084 float[] max = new float[] { spMax.getXPos(), spMax.getYPos(),
6086 panel.getRotatableCanvas().setSeqMinMax(min, max);
6088 // todo: hold points list in PCAModel only
6089 panel.getPcaModel().setSequencePoints(seqPoints);
6091 panel.setSelectedDimensionIndex(viewer.getXDim(), X);
6092 panel.setSelectedDimensionIndex(viewer.getYDim(), Y);
6093 panel.setSelectedDimensionIndex(viewer.getZDim(), Z);
6095 // is this duplication needed?
6096 panel.setTop(seqPoints.size() - 1);
6097 panel.getPcaModel().setTop(seqPoints.size() - 1);
6100 * add the axes' end points for the display
6102 for (int i = 0; i < 3; i++)
6104 Axis axis = viewer.getAxis().get(i);
6105 panel.getRotatableCanvas().getAxisEndPoints()[i] = new Point(
6106 axis.getXPos(), axis.getYPos(), axis.getZPos());
6109 Desktop.addInternalFrame(panel, MessageManager.formatMessage(
6110 "label.calc_title", "PCA", modelName), 475, 450);
6112 } catch (Exception ex)
6114 Cache.log.error("Error loading PCA: " + ex.toString());
6119 * Creates a new structure viewer window
6126 protected void createStructureViewer(ViewerType viewerType,
6127 final Entry<String, StructureViewerModel> viewerData,
6128 AlignFrame af, jarInputStreamProvider jprovider)
6130 final StructureViewerModel viewerModel = viewerData.getValue();
6131 String sessionFilePath = null;
6133 if (viewerType == ViewerType.JMOL)
6135 sessionFilePath = rewriteJmolSession(viewerModel, jprovider);
6139 String viewerJarEntryName = getViewerJarEntryName(
6140 viewerModel.getViewId());
6141 sessionFilePath = copyJarEntry(jprovider, viewerJarEntryName,
6142 "viewerSession", ".tmp");
6144 final String sessionPath = sessionFilePath;
6145 final String sviewid = viewerData.getKey();
6148 SwingUtilities.invokeAndWait(new Runnable()
6153 JalviewStructureDisplayI sview = null;
6156 sview = StructureViewer.createView(viewerType, af.alignPanel,
6157 viewerModel, sessionPath, sviewid);
6158 addNewStructureViewer(sview);
6159 } catch (OutOfMemoryError ex)
6161 new OOMWarning("Restoring structure view for " + viewerType,
6162 (OutOfMemoryError) ex.getCause());
6163 if (sview != null && sview.isVisible())
6165 sview.closeViewer(false);
6166 sview.setVisible(false);
6172 } catch (InvocationTargetException | InterruptedException ex)
6174 warn("Unexpected error when opening " + viewerType
6175 + " structure viewer", ex);
6180 * Rewrites a Jmol session script, saves it to a temporary file, and returns
6181 * the path of the file. "load file" commands are rewritten to change the
6182 * original PDB file names to those created as the Jalview project is loaded.
6188 private String rewriteJmolSession(StructureViewerModel svattrib,
6189 jarInputStreamProvider jprovider)
6191 String state = svattrib.getStateData(); // Jalview < 2.9
6192 if (state == null || state.isEmpty()) // Jalview >= 2.9
6194 String jarEntryName = getViewerJarEntryName(svattrib.getViewId());
6195 state = readJarEntry(jprovider, jarEntryName);
6197 // TODO or simpler? for each key in oldFiles,
6198 // replace key.getPath() in state with oldFiles.get(key).getFilePath()
6199 // (allowing for different path escapings)
6200 StringBuilder rewritten = new StringBuilder(state.length());
6201 int cp = 0, ncp, ecp;
6202 Map<File, StructureData> oldFiles = svattrib.getFileData();
6203 while ((ncp = state.indexOf("load ", cp)) > -1)
6207 // look for next filename in load statement
6208 rewritten.append(state.substring(cp,
6209 ncp = (state.indexOf("\"", ncp + 1) + 1)));
6210 String oldfilenam = state.substring(ncp,
6211 ecp = state.indexOf("\"", ncp));
6212 // recover the new mapping data for this old filename
6213 // have to normalize filename - since Jmol and jalview do
6214 // filename translation differently.
6215 StructureData filedat = oldFiles.get(new File(oldfilenam));
6216 if (filedat == null)
6218 String reformatedOldFilename = oldfilenam.replaceAll("/", "\\\\");
6219 filedat = oldFiles.get(new File(reformatedOldFilename));
6221 rewritten.append(Platform.escapeBackslashes(filedat.getFilePath()));
6222 rewritten.append("\"");
6223 cp = ecp + 1; // advance beyond last \" and set cursor so we can
6224 // look for next file statement.
6225 } while ((ncp = state.indexOf("/*file*/", cp)) > -1);
6229 // just append rest of state
6230 rewritten.append(state.substring(cp));
6234 System.err.print("Ignoring incomplete Jmol state for PDB ids: ");
6235 rewritten = new StringBuilder(state);
6236 rewritten.append("; load append ");
6237 for (File id : oldFiles.keySet())
6239 // add pdb files that should be present in the viewer
6240 StructureData filedat = oldFiles.get(id);
6241 rewritten.append(" \"").append(filedat.getFilePath()).append("\"");
6243 rewritten.append(";");
6246 if (rewritten.length() == 0)
6250 final String history = "history = ";
6251 int historyIndex = rewritten.indexOf(history);
6252 if (historyIndex > -1)
6255 * change "history = [true|false];" to "history = [1|0];"
6257 historyIndex += history.length();
6258 String val = rewritten.substring(historyIndex, historyIndex + 5);
6259 if (val.startsWith("true"))
6261 rewritten.replace(historyIndex, historyIndex + 4, "1");
6263 else if (val.startsWith("false"))
6265 rewritten.replace(historyIndex, historyIndex + 5, "0");
6271 File tmp = File.createTempFile("viewerSession", ".tmp");
6272 try (OutputStream os = new FileOutputStream(tmp))
6274 InputStream is = new ByteArrayInputStream(
6275 rewritten.toString().getBytes());
6277 return tmp.getAbsolutePath();
6279 } catch (IOException e)
6281 Cache.log.error("Error restoring Jmol session: " + e.toString());
6287 * Populates an XML model of the feature colour scheme for one feature type
6289 * @param featureType
6293 public static Colour marshalColour(String featureType,
6294 FeatureColourI fcol)
6296 Colour col = new Colour();
6297 if (fcol.isSimpleColour())
6299 col.setRGB(Format.getHexString(fcol.getColour()));
6303 col.setRGB(Format.getHexString(fcol.getMaxColour()));
6304 col.setMin(fcol.getMin());
6305 col.setMax(fcol.getMax());
6306 col.setMinRGB(jalview.util.Format.getHexString(fcol.getMinColour()));
6307 col.setAutoScale(fcol.isAutoScaled());
6308 col.setThreshold(fcol.getThreshold());
6309 col.setColourByLabel(fcol.isColourByLabel());
6310 col.setThreshType(fcol.isAboveThreshold() ? ThresholdType.ABOVE
6311 : (fcol.isBelowThreshold() ? ThresholdType.BELOW
6312 : ThresholdType.NONE));
6313 if (fcol.isColourByAttribute())
6315 final String[] attName = fcol.getAttributeName();
6316 col.getAttributeName().add(attName[0]);
6317 if (attName.length > 1)
6319 col.getAttributeName().add(attName[1]);
6322 Color noColour = fcol.getNoColour();
6323 if (noColour == null)
6325 col.setNoValueColour(NoValueColour.NONE);
6327 else if (noColour == fcol.getMaxColour())
6329 col.setNoValueColour(NoValueColour.MAX);
6333 col.setNoValueColour(NoValueColour.MIN);
6336 col.setName(featureType);
6341 * Populates an XML model of the feature filter(s) for one feature type
6343 * @param firstMatcher
6344 * the first (or only) match condition)
6346 * remaining match conditions (if any)
6348 * if true, conditions are and-ed, else or-ed
6350 public static jalview.xml.binding.jalview.FeatureMatcherSet marshalFilter(
6351 FeatureMatcherI firstMatcher, Iterator<FeatureMatcherI> filters,
6354 jalview.xml.binding.jalview.FeatureMatcherSet result = new jalview.xml.binding.jalview.FeatureMatcherSet();
6356 if (filters.hasNext())
6361 CompoundMatcher compound = new CompoundMatcher();
6362 compound.setAnd(and);
6363 jalview.xml.binding.jalview.FeatureMatcherSet matcher1 = marshalFilter(
6364 firstMatcher, Collections.emptyIterator(), and);
6365 // compound.addMatcherSet(matcher1);
6366 compound.getMatcherSet().add(matcher1);
6367 FeatureMatcherI nextMatcher = filters.next();
6368 jalview.xml.binding.jalview.FeatureMatcherSet matcher2 = marshalFilter(
6369 nextMatcher, filters, and);
6370 // compound.addMatcherSet(matcher2);
6371 compound.getMatcherSet().add(matcher2);
6372 result.setCompoundMatcher(compound);
6377 * single condition matcher
6379 // MatchCondition matcherModel = new MatchCondition();
6380 jalview.xml.binding.jalview.FeatureMatcher matcherModel = new jalview.xml.binding.jalview.FeatureMatcher();
6381 matcherModel.setCondition(
6382 firstMatcher.getMatcher().getCondition().getStableName());
6383 matcherModel.setValue(firstMatcher.getMatcher().getPattern());
6384 if (firstMatcher.isByAttribute())
6386 matcherModel.setBy(FilterBy.BY_ATTRIBUTE);
6387 // matcherModel.setAttributeName(firstMatcher.getAttribute());
6388 String[] attName = firstMatcher.getAttribute();
6389 matcherModel.getAttributeName().add(attName[0]); // attribute
6390 if (attName.length > 1)
6392 matcherModel.getAttributeName().add(attName[1]); // sub-attribute
6395 else if (firstMatcher.isByLabel())
6397 matcherModel.setBy(FilterBy.BY_LABEL);
6399 else if (firstMatcher.isByScore())
6401 matcherModel.setBy(FilterBy.BY_SCORE);
6403 result.setMatchCondition(matcherModel);
6410 * Loads one XML model of a feature filter to a Jalview object
6412 * @param featureType
6413 * @param matcherSetModel
6416 public static FeatureMatcherSetI parseFilter(String featureType,
6417 jalview.xml.binding.jalview.FeatureMatcherSet matcherSetModel)
6419 FeatureMatcherSetI result = new FeatureMatcherSet();
6422 parseFilterConditions(result, matcherSetModel, true);
6423 } catch (IllegalStateException e)
6425 // mixing AND and OR conditions perhaps
6427 String.format("Error reading filter conditions for '%s': %s",
6428 featureType, e.getMessage()));
6429 // return as much as was parsed up to the error
6436 * Adds feature match conditions to matcherSet as unmarshalled from XML
6437 * (possibly recursively for compound conditions)
6440 * @param matcherSetModel
6442 * if true, multiple conditions are AND-ed, else they are OR-ed
6443 * @throws IllegalStateException
6444 * if AND and OR conditions are mixed
6446 protected static void parseFilterConditions(FeatureMatcherSetI matcherSet,
6447 jalview.xml.binding.jalview.FeatureMatcherSet matcherSetModel,
6450 jalview.xml.binding.jalview.FeatureMatcher mc = matcherSetModel
6451 .getMatchCondition();
6457 FilterBy filterBy = mc.getBy();
6458 Condition cond = Condition.fromString(mc.getCondition());
6459 String pattern = mc.getValue();
6460 FeatureMatcherI matchCondition = null;
6461 if (filterBy == FilterBy.BY_LABEL)
6463 matchCondition = FeatureMatcher.byLabel(cond, pattern);
6465 else if (filterBy == FilterBy.BY_SCORE)
6467 matchCondition = FeatureMatcher.byScore(cond, pattern);
6470 else if (filterBy == FilterBy.BY_ATTRIBUTE)
6472 final List<String> attributeName = mc.getAttributeName();
6473 String[] attNames = attributeName
6474 .toArray(new String[attributeName.size()]);
6475 matchCondition = FeatureMatcher.byAttribute(cond, pattern,
6480 * note this throws IllegalStateException if AND-ing to a
6481 * previously OR-ed compound condition, or vice versa
6485 matcherSet.and(matchCondition);
6489 matcherSet.or(matchCondition);
6495 * compound condition
6497 List<jalview.xml.binding.jalview.FeatureMatcherSet> matchers = matcherSetModel
6498 .getCompoundMatcher().getMatcherSet();
6499 boolean anded = matcherSetModel.getCompoundMatcher().isAnd();
6500 if (matchers.size() == 2)
6502 parseFilterConditions(matcherSet, matchers.get(0), anded);
6503 parseFilterConditions(matcherSet, matchers.get(1), anded);
6507 System.err.println("Malformed compound filter condition");
6513 * Loads one XML model of a feature colour to a Jalview object
6515 * @param colourModel
6518 public static FeatureColourI parseColour(Colour colourModel)
6520 FeatureColourI colour = null;
6522 if (colourModel.getMax() != null)
6524 Color mincol = null;
6525 Color maxcol = null;
6526 Color noValueColour = null;
6530 mincol = new Color(Integer.parseInt(colourModel.getMinRGB(), 16));
6531 maxcol = new Color(Integer.parseInt(colourModel.getRGB(), 16));
6532 } catch (Exception e)
6534 Cache.log.warn("Couldn't parse out graduated feature color.", e);
6537 NoValueColour noCol = colourModel.getNoValueColour();
6538 if (noCol == NoValueColour.MIN)
6540 noValueColour = mincol;
6542 else if (noCol == NoValueColour.MAX)
6544 noValueColour = maxcol;
6547 colour = new FeatureColour(maxcol, mincol, maxcol, noValueColour,
6548 safeFloat(colourModel.getMin()),
6549 safeFloat(colourModel.getMax()));
6550 final List<String> attributeName = colourModel.getAttributeName();
6551 String[] attributes = attributeName
6552 .toArray(new String[attributeName.size()]);
6553 if (attributes != null && attributes.length > 0)
6555 colour.setAttributeName(attributes);
6557 if (colourModel.isAutoScale() != null)
6559 colour.setAutoScaled(colourModel.isAutoScale().booleanValue());
6561 if (colourModel.isColourByLabel() != null)
6563 colour.setColourByLabel(
6564 colourModel.isColourByLabel().booleanValue());
6566 if (colourModel.getThreshold() != null)
6568 colour.setThreshold(colourModel.getThreshold().floatValue());
6570 ThresholdType ttyp = colourModel.getThreshType();
6571 if (ttyp == ThresholdType.ABOVE)
6573 colour.setAboveThreshold(true);
6575 else if (ttyp == ThresholdType.BELOW)
6577 colour.setBelowThreshold(true);
6582 Color color = new Color(Integer.parseInt(colourModel.getRGB(), 16));
6583 colour = new FeatureColour(color);