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 if (ref instanceof GeneLocus)
2534 dbref.setLocus(true);
2538 Mapping mp = createVamsasMapping(ref.getMap(), parentseq, jds,
2540 dbref.setMapping(mp);
2542 vamsasSeq.getDBRef().add(dbref);
2548 private Mapping createVamsasMapping(jalview.datamodel.Mapping jmp,
2549 SequenceI parentseq, SequenceI jds, boolean recurse)
2552 if (jmp.getMap() != null)
2556 jalview.util.MapList mlst = jmp.getMap();
2557 List<int[]> r = mlst.getFromRanges();
2558 for (int[] range : r)
2560 MapListFrom mfrom = new MapListFrom();
2561 mfrom.setStart(range[0]);
2562 mfrom.setEnd(range[1]);
2563 // mp.addMapListFrom(mfrom);
2564 mp.getMapListFrom().add(mfrom);
2566 r = mlst.getToRanges();
2567 for (int[] range : r)
2569 MapListTo mto = new MapListTo();
2570 mto.setStart(range[0]);
2571 mto.setEnd(range[1]);
2572 // mp.addMapListTo(mto);
2573 mp.getMapListTo().add(mto);
2575 mp.setMapFromUnit(BigInteger.valueOf(mlst.getFromRatio()));
2576 mp.setMapToUnit(BigInteger.valueOf(mlst.getToRatio()));
2577 if (jmp.getTo() != null)
2579 // MappingChoice mpc = new MappingChoice();
2581 // check/create ID for the sequence referenced by getTo()
2584 SequenceI ps = null;
2585 if (parentseq != jmp.getTo()
2586 && parentseq.getDatasetSequence() != jmp.getTo())
2588 // chaining dbref rather than a handshaking one
2589 jmpid = seqHash(ps = jmp.getTo());
2593 jmpid = seqHash(ps = parentseq);
2595 // mpc.setDseqFor(jmpid);
2596 mp.setDseqFor(jmpid);
2597 if (!seqRefIds.containsKey(jmpid))
2599 jalview.bin.Cache.log.debug("creatign new DseqFor ID");
2600 seqRefIds.put(jmpid, ps);
2604 jalview.bin.Cache.log.debug("reusing DseqFor ID");
2607 // mp.setMappingChoice(mpc);
2613 String setUserColourScheme(jalview.schemes.ColourSchemeI cs,
2614 List<UserColourScheme> userColours, JalviewModel jm)
2617 jalview.schemes.UserColourScheme ucs = (jalview.schemes.UserColourScheme) cs;
2618 boolean newucs = false;
2619 if (!userColours.contains(ucs))
2621 userColours.add(ucs);
2624 id = "ucs" + userColours.indexOf(ucs);
2627 // actually create the scheme's entry in the XML model
2628 java.awt.Color[] colours = ucs.getColours();
2629 UserColours uc = new UserColours();
2630 // UserColourScheme jbucs = new UserColourScheme();
2631 JalviewUserColours jbucs = new JalviewUserColours();
2633 for (int i = 0; i < colours.length; i++)
2635 Colour col = new Colour();
2636 col.setName(ResidueProperties.aa[i]);
2637 col.setRGB(jalview.util.Format.getHexString(colours[i]));
2638 // jbucs.addColour(col);
2639 jbucs.getColour().add(col);
2641 if (ucs.getLowerCaseColours() != null)
2643 colours = ucs.getLowerCaseColours();
2644 for (int i = 0; i < colours.length; i++)
2646 Colour col = new Colour();
2647 col.setName(ResidueProperties.aa[i].toLowerCase());
2648 col.setRGB(jalview.util.Format.getHexString(colours[i]));
2649 // jbucs.addColour(col);
2650 jbucs.getColour().add(col);
2655 uc.setUserColourScheme(jbucs);
2656 // jm.addUserColours(uc);
2657 jm.getUserColours().add(uc);
2663 jalview.schemes.UserColourScheme getUserColourScheme(JalviewModel jm,
2666 List<UserColours> uc = jm.getUserColours();
2667 UserColours colours = null;
2669 for (int i = 0; i < uc.length; i++)
2671 if (uc[i].getId().equals(id))
2678 for (UserColours c : uc)
2680 if (c.getId().equals(id))
2687 java.awt.Color[] newColours = new java.awt.Color[24];
2689 for (int i = 0; i < 24; i++)
2691 newColours[i] = new java.awt.Color(Integer.parseInt(
2692 // colours.getUserColourScheme().getColour(i).getRGB(), 16));
2693 colours.getUserColourScheme().getColour().get(i).getRGB(),
2697 jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(
2700 if (colours.getUserColourScheme().getColour().size()/*Count()*/ > 24)
2702 newColours = new java.awt.Color[23];
2703 for (int i = 0; i < 23; i++)
2705 newColours[i] = new java.awt.Color(
2706 Integer.parseInt(colours.getUserColourScheme().getColour()
2707 .get(i + 24).getRGB(), 16));
2709 ucs.setLowerCaseColours(newColours);
2716 * contains last error message (if any) encountered by XML loader.
2718 String errorMessage = null;
2721 * flag to control whether the Jalview2XML_V1 parser should be deferred to if
2722 * exceptions are raised during project XML parsing
2724 public boolean attemptversion1parse = false;
2727 * Load a jalview project archive from a jar file
2730 * - HTTP URL or filename
2732 public AlignFrame loadJalviewAlign(final Object file)
2735 jalview.gui.AlignFrame af = null;
2739 // create list to store references for any new Jmol viewers created
2740 newStructureViewers = new Vector<>();
2741 // UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
2742 // Workaround is to make sure caller implements the JarInputStreamProvider
2744 // so we can re-open the jar input stream for each entry.
2746 jarInputStreamProvider jprovider = createjarInputStreamProvider(file);
2747 af = loadJalviewAlign(jprovider);
2750 af.setMenusForViewport();
2752 } catch (MalformedURLException e)
2754 errorMessage = "Invalid URL format for '" + file + "'";
2760 SwingUtilities.invokeAndWait(new Runnable()
2765 setLoadingFinishedForNewStructureViewers();
2768 } catch (Exception x)
2770 System.err.println("Error loading alignment: " + x.getMessage());
2776 @SuppressWarnings("unused")
2777 private jarInputStreamProvider createjarInputStreamProvider(
2778 final Object ofile) throws MalformedURLException
2781 // BH 2018 allow for bytes already attached to File object
2784 String file = (ofile instanceof File
2785 ? ((File) ofile).getCanonicalPath()
2786 : ofile.toString());
2787 byte[] bytes = Platform.isJS() ? Platform.getFileBytes((File) ofile)
2790 errorMessage = null;
2791 uniqueSetSuffix = null;
2793 viewportsAdded.clear();
2794 frefedSequence = null;
2796 if (HttpUtils.startsWithHttpOrHttps(file))
2798 url = new URL(file);
2800 final URL _url = url;
2801 return new jarInputStreamProvider()
2805 public JarInputStream getJarInputStream() throws IOException
2809 // System.out.println("Jalview2XML: opening byte jarInputStream for
2810 // bytes.length=" + bytes.length);
2811 return new JarInputStream(new ByteArrayInputStream(bytes));
2815 // System.out.println("Jalview2XML: opening url jarInputStream for "
2817 return new JarInputStream(_url.openStream());
2821 // System.out.println("Jalview2XML: opening file jarInputStream for
2823 return new JarInputStream(new FileInputStream(file));
2828 public String getFilename()
2833 } catch (IOException e)
2835 e.printStackTrace();
2841 * Recover jalview session from a jalview project archive. Caller may
2842 * initialise uniqueSetSuffix, seqRefIds, viewportsAdded and frefedSequence
2843 * themselves. Any null fields will be initialised with default values,
2844 * non-null fields are left alone.
2849 public AlignFrame loadJalviewAlign(final jarInputStreamProvider jprovider)
2851 errorMessage = null;
2852 if (uniqueSetSuffix == null)
2854 uniqueSetSuffix = System.currentTimeMillis() % 100000 + "";
2856 if (seqRefIds == null)
2860 AlignFrame af = null, _af = null;
2861 IdentityHashMap<AlignmentI, AlignmentI> importedDatasets = new IdentityHashMap<>();
2862 Map<String, AlignFrame> gatherToThisFrame = new HashMap<>();
2863 final String file = jprovider.getFilename();
2866 JarInputStream jin = null;
2867 JarEntry jarentry = null;
2872 jin = jprovider.getJarInputStream();
2873 for (int i = 0; i < entryCount; i++)
2875 jarentry = jin.getNextJarEntry();
2878 if (jarentry != null && jarentry.getName().endsWith(".xml"))
2880 JAXBContext jc = JAXBContext
2881 .newInstance("jalview.xml.binding.jalview");
2882 XMLStreamReader streamReader = XMLInputFactory.newInstance()
2883 .createXMLStreamReader(jin);
2884 javax.xml.bind.Unmarshaller um = jc.createUnmarshaller();
2885 JAXBElement<JalviewModel> jbe = um.unmarshal(streamReader,
2886 JalviewModel.class);
2887 JalviewModel object = jbe.getValue();
2889 if (true) // !skipViewport(object))
2891 _af = loadFromObject(object, file, true, jprovider);
2892 if (_af != null && object.getViewport().size() > 0)
2893 // getJalviewModelSequence().getViewportCount() > 0)
2897 // store a reference to the first view
2900 if (_af.getViewport().isGatherViewsHere())
2902 // if this is a gathered view, keep its reference since
2903 // after gathering views, only this frame will remain
2905 gatherToThisFrame.put(_af.getViewport().getSequenceSetId(),
2908 // Save dataset to register mappings once all resolved
2909 importedDatasets.put(
2910 af.getViewport().getAlignment().getDataset(),
2911 af.getViewport().getAlignment().getDataset());
2916 else if (jarentry != null)
2918 // Some other file here.
2921 } while (jarentry != null);
2922 resolveFrefedSequences();
2923 } catch (IOException ex)
2925 ex.printStackTrace();
2926 errorMessage = "Couldn't locate Jalview XML file : " + file;
2928 "Exception whilst loading jalview XML file : " + ex + "\n");
2929 } catch (Exception ex)
2931 System.err.println("Parsing as Jalview Version 2 file failed.");
2932 ex.printStackTrace(System.err);
2933 if (attemptversion1parse)
2935 // used to attempt to parse as V1 castor-generated xml
2937 if (Desktop.instance != null)
2939 Desktop.instance.stopLoading();
2943 System.out.println("Successfully loaded archive file");
2946 ex.printStackTrace();
2949 "Exception whilst loading jalview XML file : " + ex + "\n");
2950 } catch (OutOfMemoryError e)
2952 // Don't use the OOM Window here
2953 errorMessage = "Out of memory loading jalview XML file";
2954 System.err.println("Out of memory whilst loading jalview XML file");
2955 e.printStackTrace();
2959 * Regather multiple views (with the same sequence set id) to the frame (if
2960 * any) that is flagged as the one to gather to, i.e. convert them to tabbed
2961 * views instead of separate frames. Note this doesn't restore a state where
2962 * some expanded views in turn have tabbed views - the last "first tab" read
2963 * in will play the role of gatherer for all.
2965 for (AlignFrame fr : gatherToThisFrame.values())
2967 Desktop.instance.gatherViews(fr);
2970 restoreSplitFrames();
2971 for (AlignmentI ds : importedDatasets.keySet())
2973 if (ds.getCodonFrames() != null)
2975 StructureSelectionManager
2976 .getStructureSelectionManager(Desktop.instance)
2977 .registerMappings(ds.getCodonFrames());
2980 if (errorMessage != null)
2985 if (Desktop.instance != null)
2987 Desktop.instance.stopLoading();
2994 * Try to reconstruct and display SplitFrame windows, where each contains
2995 * complementary dna and protein alignments. Done by pairing up AlignFrame
2996 * objects (created earlier) which have complementary viewport ids associated.
2998 protected void restoreSplitFrames()
3000 List<SplitFrame> gatherTo = new ArrayList<>();
3001 List<AlignFrame> addedToSplitFrames = new ArrayList<>();
3002 Map<String, AlignFrame> dna = new HashMap<>();
3005 * Identify the DNA alignments
3007 for (Entry<Viewport, AlignFrame> candidate : splitFrameCandidates
3010 AlignFrame af = candidate.getValue();
3011 if (af.getViewport().getAlignment().isNucleotide())
3013 dna.put(candidate.getKey().getId(), af);
3018 * Try to match up the protein complements
3020 for (Entry<Viewport, AlignFrame> candidate : splitFrameCandidates
3023 AlignFrame af = candidate.getValue();
3024 if (!af.getViewport().getAlignment().isNucleotide())
3026 String complementId = candidate.getKey().getComplementId();
3027 // only non-null complements should be in the Map
3028 if (complementId != null && dna.containsKey(complementId))
3030 final AlignFrame dnaFrame = dna.get(complementId);
3031 SplitFrame sf = createSplitFrame(dnaFrame, af);
3032 addedToSplitFrames.add(dnaFrame);
3033 addedToSplitFrames.add(af);
3034 dnaFrame.setMenusForViewport();
3035 af.setMenusForViewport();
3036 if (af.getViewport().isGatherViewsHere())
3045 * Open any that we failed to pair up (which shouldn't happen!) as
3046 * standalone AlignFrame's.
3048 for (Entry<Viewport, AlignFrame> candidate : splitFrameCandidates
3051 AlignFrame af = candidate.getValue();
3052 if (!addedToSplitFrames.contains(af))
3054 Viewport view = candidate.getKey();
3055 Desktop.addInternalFrame(af, view.getTitle(),
3056 safeInt(view.getWidth()), safeInt(view.getHeight()));
3057 af.setMenusForViewport();
3058 System.err.println("Failed to restore view " + view.getTitle()
3059 + " to split frame");
3064 * Gather back into tabbed views as flagged.
3066 for (SplitFrame sf : gatherTo)
3068 Desktop.instance.gatherViews(sf);
3071 splitFrameCandidates.clear();
3075 * Construct and display one SplitFrame holding DNA and protein alignments.
3078 * @param proteinFrame
3081 protected SplitFrame createSplitFrame(AlignFrame dnaFrame,
3082 AlignFrame proteinFrame)
3084 SplitFrame splitFrame = new SplitFrame(dnaFrame, proteinFrame);
3085 String title = MessageManager.getString("label.linked_view_title");
3086 int width = (int) dnaFrame.getBounds().getWidth();
3087 int height = (int) (dnaFrame.getBounds().getHeight()
3088 + proteinFrame.getBounds().getHeight() + 50);
3091 * SplitFrame location is saved to both enclosed frames
3093 splitFrame.setLocation(dnaFrame.getX(), dnaFrame.getY());
3094 Desktop.addInternalFrame(splitFrame, title, width, height);
3097 * And compute cDNA consensus (couldn't do earlier with consensus as
3098 * mappings were not yet present)
3100 proteinFrame.getViewport().alignmentChanged(proteinFrame.alignPanel);
3106 * check errorMessage for a valid error message and raise an error box in the
3107 * GUI or write the current errorMessage to stderr and then clear the error
3110 protected void reportErrors()
3112 reportErrors(false);
3115 protected void reportErrors(final boolean saving)
3117 if (errorMessage != null)
3119 final String finalErrorMessage = errorMessage;
3122 javax.swing.SwingUtilities.invokeLater(new Runnable()
3127 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
3129 "Error " + (saving ? "saving" : "loading")
3131 JvOptionPane.WARNING_MESSAGE);
3137 System.err.println("Problem loading Jalview file: " + errorMessage);
3140 errorMessage = null;
3143 Map<String, String> alreadyLoadedPDB = new HashMap<>();
3146 * when set, local views will be updated from view stored in JalviewXML
3147 * Currently (28th Sep 2008) things will go horribly wrong in vamsas document
3148 * sync if this is set to true.
3150 private final boolean updateLocalViews = false;
3153 * Returns the path to a temporary file holding the PDB file for the given PDB
3154 * id. The first time of asking, searches for a file of that name in the
3155 * Jalview project jar, and copies it to a new temporary file. Any repeat
3156 * requests just return the path to the file previously created.
3162 String loadPDBFile(jarInputStreamProvider jprovider, String pdbId,
3165 if (alreadyLoadedPDB.containsKey(pdbId))
3167 return alreadyLoadedPDB.get(pdbId).toString();
3170 String tempFile = copyJarEntry(jprovider, pdbId, "jalview_pdb",
3172 if (tempFile != null)
3174 alreadyLoadedPDB.put(pdbId, tempFile);
3180 * Copies the jar entry of given name to a new temporary file and returns the
3181 * path to the file, or null if the entry is not found.
3184 * @param jarEntryName
3186 * a prefix for the temporary file name, must be at least three
3188 * @param suffixModel
3189 * null or original file - so new file can be given the same suffix
3193 protected String copyJarEntry(jarInputStreamProvider jprovider,
3194 String jarEntryName, String prefix, String suffixModel)
3196 String suffix = ".tmp";
3197 if (suffixModel == null)
3199 suffixModel = jarEntryName;
3201 int sfpos = suffixModel.lastIndexOf(".");
3202 if (sfpos > -1 && sfpos < (suffixModel.length() - 1))
3204 suffix = "." + suffixModel.substring(sfpos + 1);
3207 try (JarInputStream jin = jprovider.getJarInputStream())
3209 JarEntry entry = null;
3212 entry = jin.getNextJarEntry();
3213 } while (entry != null && !entry.getName().equals(jarEntryName));
3217 // in = new BufferedReader(new InputStreamReader(jin, UTF_8));
3218 File outFile = File.createTempFile(prefix, suffix);
3219 outFile.deleteOnExit();
3220 try (OutputStream os = new FileOutputStream(outFile))
3224 String t = outFile.getAbsolutePath();
3229 warn("Couldn't find entry in Jalview Jar for " + jarEntryName);
3231 } catch (Exception ex)
3233 ex.printStackTrace();
3239 private class JvAnnotRow
3241 public JvAnnotRow(int i, AlignmentAnnotation jaa)
3248 * persisted version of annotation row from which to take vis properties
3250 public jalview.datamodel.AlignmentAnnotation template;
3253 * original position of the annotation row in the alignment
3259 * Load alignment frame from jalview XML DOM object
3261 * @param jalviewModel
3264 * filename source string
3265 * @param loadTreesAndStructures
3266 * when false only create Viewport
3268 * data source provider
3269 * @return alignment frame created from view stored in DOM
3271 AlignFrame loadFromObject(JalviewModel jalviewModel, String file,
3272 boolean loadTreesAndStructures, jarInputStreamProvider jprovider)
3274 SequenceSet vamsasSet = jalviewModel.getVamsasModel().getSequenceSet()
3276 List<Sequence> vamsasSeqs = vamsasSet.getSequence();
3278 // JalviewModelSequence jms = object.getJalviewModelSequence();
3280 // Viewport view = (jms.getViewportCount() > 0) ? jms.getViewport(0)
3282 Viewport view = (jalviewModel.getViewport().size() > 0)
3283 ? jalviewModel.getViewport().get(0)
3286 // ////////////////////////////////
3287 // INITIALISE ALIGNMENT SEQUENCESETID AND VIEWID
3290 // If we just load in the same jar file again, the sequenceSetId
3291 // will be the same, and we end up with multiple references
3292 // to the same sequenceSet. We must modify this id on load
3293 // so that each load of the file gives a unique id
3296 * used to resolve correct alignment dataset for alignments with multiple
3299 String uniqueSeqSetId = null;
3300 String viewId = null;
3303 uniqueSeqSetId = view.getSequenceSetId() + uniqueSetSuffix;
3304 viewId = (view.getId() == null ? null
3305 : view.getId() + uniqueSetSuffix);
3308 // ////////////////////////////////
3311 List<SequenceI> hiddenSeqs = null;
3313 List<SequenceI> tmpseqs = new ArrayList<>();
3315 boolean multipleView = false;
3316 SequenceI referenceseqForView = null;
3317 // JSeq[] jseqs = object.getJalviewModelSequence().getJSeq();
3318 List<JSeq> jseqs = jalviewModel.getJSeq();
3319 int vi = 0; // counter in vamsasSeq array
3320 for (int i = 0; i < jseqs.size(); i++)
3322 JSeq jseq = jseqs.get(i);
3323 String seqId = jseq.getId();
3325 SequenceI tmpSeq = seqRefIds.get(seqId);
3328 if (!incompleteSeqs.containsKey(seqId))
3330 // may not need this check, but keep it for at least 2.9,1 release
3331 if (tmpSeq.getStart() != jseq.getStart()
3332 || tmpSeq.getEnd() != jseq.getEnd())
3334 System.err.println(String.format(
3335 "Warning JAL-2154 regression: updating start/end for sequence %s from %d/%d to %d/%d",
3336 tmpSeq.getName(), tmpSeq.getStart(), tmpSeq.getEnd(),
3337 jseq.getStart(), jseq.getEnd()));
3342 incompleteSeqs.remove(seqId);
3344 if (vamsasSeqs.size() > vi
3345 && vamsasSeqs.get(vi).getId().equals(seqId))
3347 // most likely we are reading a dataset XML document so
3348 // update from vamsasSeq section of XML for this sequence
3349 tmpSeq.setName(vamsasSeqs.get(vi).getName());
3350 tmpSeq.setDescription(vamsasSeqs.get(vi).getDescription());
3351 tmpSeq.setSequence(vamsasSeqs.get(vi).getSequence());
3356 // reading multiple views, so vamsasSeq set is a subset of JSeq
3357 multipleView = true;
3359 tmpSeq.setStart(jseq.getStart());
3360 tmpSeq.setEnd(jseq.getEnd());
3361 tmpseqs.add(tmpSeq);
3365 Sequence vamsasSeq = vamsasSeqs.get(vi);
3366 tmpSeq = new jalview.datamodel.Sequence(vamsasSeq.getName(),
3367 vamsasSeq.getSequence());
3368 tmpSeq.setDescription(vamsasSeq.getDescription());
3369 tmpSeq.setStart(jseq.getStart());
3370 tmpSeq.setEnd(jseq.getEnd());
3371 tmpSeq.setVamsasId(uniqueSetSuffix + seqId);
3372 seqRefIds.put(vamsasSeq.getId(), tmpSeq);
3373 tmpseqs.add(tmpSeq);
3377 if (safeBoolean(jseq.isViewreference()))
3379 referenceseqForView = tmpseqs.get(tmpseqs.size() - 1);
3382 if (jseq.isHidden() != null && jseq.isHidden().booleanValue())
3384 if (hiddenSeqs == null)
3386 hiddenSeqs = new ArrayList<>();
3389 hiddenSeqs.add(tmpSeq);
3394 // Create the alignment object from the sequence set
3395 // ///////////////////////////////
3396 SequenceI[] orderedSeqs = tmpseqs
3397 .toArray(new SequenceI[tmpseqs.size()]);
3399 AlignmentI al = null;
3400 // so we must create or recover the dataset alignment before going further
3401 // ///////////////////////////////
3402 if (vamsasSet.getDatasetId() == null || vamsasSet.getDatasetId() == "")
3404 // older jalview projects do not have a dataset - so creat alignment and
3406 al = new Alignment(orderedSeqs);
3407 al.setDataset(null);
3411 boolean isdsal = jalviewModel.getViewport().isEmpty();
3414 // we are importing a dataset record, so
3415 // recover reference to an alignment already materialsed as dataset
3416 al = getDatasetFor(vamsasSet.getDatasetId());
3420 // materialse the alignment
3421 al = new Alignment(orderedSeqs);
3425 addDatasetRef(vamsasSet.getDatasetId(), al);
3428 // finally, verify all data in vamsasSet is actually present in al
3429 // passing on flag indicating if it is actually a stored dataset
3430 recoverDatasetFor(vamsasSet, al, isdsal, uniqueSeqSetId);
3433 if (referenceseqForView != null)
3435 al.setSeqrep(referenceseqForView);
3437 // / Add the alignment properties
3438 for (int i = 0; i < vamsasSet.getSequenceSetProperties().size(); i++)
3440 SequenceSetProperties ssp = vamsasSet.getSequenceSetProperties()
3442 al.setProperty(ssp.getKey(), ssp.getValue());
3445 // ///////////////////////////////
3447 Hashtable pdbloaded = new Hashtable(); // TODO nothing writes to this??
3450 // load sequence features, database references and any associated PDB
3451 // structures for the alignment
3453 // prior to 2.10, this part would only be executed the first time a
3454 // sequence was encountered, but not afterwards.
3455 // now, for 2.10 projects, this is also done if the xml doc includes
3456 // dataset sequences not actually present in any particular view.
3458 for (int i = 0; i < vamsasSeqs.size(); i++)
3460 JSeq jseq = jseqs.get(i);
3461 if (jseq.getFeatures().size() > 0)
3463 List<Feature> features = jseq.getFeatures();
3464 for (int f = 0; f < features.size(); f++)
3466 Feature feat = features.get(f);
3467 SequenceFeature sf = new SequenceFeature(feat.getType(),
3468 feat.getDescription(), feat.getBegin(), feat.getEnd(),
3469 safeFloat(feat.getScore()), feat.getFeatureGroup());
3470 sf.setStatus(feat.getStatus());
3473 * load any feature attributes - include map-valued attributes
3475 Map<String, Map<String, String>> mapAttributes = new HashMap<>();
3476 for (int od = 0; od < feat.getOtherData().size(); od++)
3478 OtherData keyValue = feat.getOtherData().get(od);
3479 String attributeName = keyValue.getKey();
3480 String attributeValue = keyValue.getValue();
3481 if (attributeName.startsWith("LINK"))
3483 sf.addLink(attributeValue);
3487 String subAttribute = keyValue.getKey2();
3488 if (subAttribute == null)
3490 // simple string-valued attribute
3491 sf.setValue(attributeName, attributeValue);
3495 // attribute 'key' has sub-attribute 'key2'
3496 if (!mapAttributes.containsKey(attributeName))
3498 mapAttributes.put(attributeName, new HashMap<>());
3500 mapAttributes.get(attributeName).put(subAttribute,
3505 for (Entry<String, Map<String, String>> mapAttribute : mapAttributes
3508 sf.setValue(mapAttribute.getKey(), mapAttribute.getValue());
3511 // adds feature to datasequence's feature set (since Jalview 2.10)
3512 al.getSequenceAt(i).addSequenceFeature(sf);
3515 if (vamsasSeqs.get(i).getDBRef().size() > 0)
3517 // adds dbrefs to datasequence's set (since Jalview 2.10)
3519 al.getSequenceAt(i).getDatasetSequence() == null
3520 ? al.getSequenceAt(i)
3521 : al.getSequenceAt(i).getDatasetSequence(),
3524 if (jseq.getPdbids().size() > 0)
3526 List<Pdbids> ids = jseq.getPdbids();
3527 for (int p = 0; p < ids.size(); p++)
3529 Pdbids pdbid = ids.get(p);
3530 jalview.datamodel.PDBEntry entry = new jalview.datamodel.PDBEntry();
3531 entry.setId(pdbid.getId());
3532 if (pdbid.getType() != null)
3534 if (PDBEntry.Type.getType(pdbid.getType()) != null)
3536 entry.setType(PDBEntry.Type.getType(pdbid.getType()));
3540 entry.setType(PDBEntry.Type.FILE);
3543 // jprovider is null when executing 'New View'
3544 if (pdbid.getFile() != null && jprovider != null)
3546 if (!pdbloaded.containsKey(pdbid.getFile()))
3548 entry.setFile(loadPDBFile(jprovider, pdbid.getId(),
3553 entry.setFile(pdbloaded.get(pdbid.getId()).toString());
3557 if (pdbid.getPdbentryItem() != null)
3559 for (PdbentryItem item : pdbid.getPdbentryItem())
3561 for (Property pr : item.getProperty())
3563 entry.setProperty(pr.getName(), pr.getValue());
3568 for (Property prop : pdbid.getProperty())
3570 entry.setProperty(prop.getName(), prop.getValue());
3572 StructureSelectionManager
3573 .getStructureSelectionManager(Desktop.instance)
3574 .registerPDBEntry(entry);
3575 // adds PDBEntry to datasequence's set (since Jalview 2.10)
3576 if (al.getSequenceAt(i).getDatasetSequence() != null)
3578 al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
3582 al.getSequenceAt(i).addPDBId(entry);
3587 } // end !multipleview
3589 // ///////////////////////////////
3590 // LOAD SEQUENCE MAPPINGS
3592 if (vamsasSet.getAlcodonFrame().size() > 0)
3594 // TODO Potentially this should only be done once for all views of an
3596 List<AlcodonFrame> alc = vamsasSet.getAlcodonFrame();
3597 for (int i = 0; i < alc.size(); i++)
3599 AlignedCodonFrame cf = new AlignedCodonFrame();
3600 if (alc.get(i).getAlcodMap().size() > 0)
3602 List<AlcodMap> maps = alc.get(i).getAlcodMap();
3603 for (int m = 0; m < maps.size(); m++)
3605 AlcodMap map = maps.get(m);
3606 SequenceI dnaseq = seqRefIds.get(map.getDnasq());
3608 jalview.datamodel.Mapping mapping = null;
3609 // attach to dna sequence reference.
3610 if (map.getMapping() != null)
3612 mapping = addMapping(map.getMapping());
3613 if (dnaseq != null && mapping.getTo() != null)
3615 cf.addMap(dnaseq, mapping.getTo(), mapping.getMap());
3621 .add(newAlcodMapRef(map.getDnasq(), cf, mapping));
3625 al.addCodonFrame(cf);
3630 // ////////////////////////////////
3632 List<JvAnnotRow> autoAlan = new ArrayList<>();
3635 * store any annotations which forward reference a group's ID
3637 Map<String, List<AlignmentAnnotation>> groupAnnotRefs = new Hashtable<>();
3639 if (vamsasSet.getAnnotation().size()/*Count()*/ > 0)
3641 List<Annotation> an = vamsasSet.getAnnotation();
3643 for (int i = 0; i < an.size(); i++)
3645 Annotation annotation = an.get(i);
3648 * test if annotation is automatically calculated for this view only
3650 boolean autoForView = false;
3651 if (annotation.getLabel().equals("Quality")
3652 || annotation.getLabel().equals("Conservation")
3653 || annotation.getLabel().equals("Consensus"))
3655 // Kludge for pre 2.5 projects which lacked the autocalculated flag
3657 // JAXB has no has() test; schema defaults value to false
3658 // if (!annotation.hasAutoCalculated())
3660 // annotation.setAutoCalculated(true);
3663 if (autoForView || annotation.isAutoCalculated())
3665 // remove ID - we don't recover annotation from other views for
3666 // view-specific annotation
3667 annotation.setId(null);
3670 // set visibility for other annotation in this view
3671 String annotationId = annotation.getId();
3672 if (annotationId != null && annotationIds.containsKey(annotationId))
3674 AlignmentAnnotation jda = annotationIds.get(annotationId);
3675 // in principle Visible should always be true for annotation displayed
3676 // in multiple views
3677 if (annotation.isVisible() != null)
3679 jda.visible = annotation.isVisible();
3682 al.addAnnotation(jda);
3686 // Construct new annotation from model.
3687 List<AnnotationElement> ae = annotation.getAnnotationElement();
3688 jalview.datamodel.Annotation[] anot = null;
3689 java.awt.Color firstColour = null;
3691 if (!annotation.isScoreOnly())
3693 anot = new jalview.datamodel.Annotation[al.getWidth()];
3694 for (int aa = 0; aa < ae.size() && aa < anot.length; aa++)
3696 AnnotationElement annElement = ae.get(aa);
3697 anpos = annElement.getPosition();
3699 if (anpos >= anot.length)
3704 float value = safeFloat(annElement.getValue());
3705 anot[anpos] = new jalview.datamodel.Annotation(
3706 annElement.getDisplayCharacter(),
3707 annElement.getDescription(),
3708 (annElement.getSecondaryStructure() == null
3709 || annElement.getSecondaryStructure()
3713 .getSecondaryStructure()
3716 anot[anpos].colour = new Color(safeInt(annElement.getColour()));
3717 if (firstColour == null)
3719 firstColour = anot[anpos].colour;
3723 jalview.datamodel.AlignmentAnnotation jaa = null;
3725 if (annotation.isGraph())
3727 float llim = 0, hlim = 0;
3728 // if (autoForView || an[i].isAutoCalculated()) {
3731 jaa = new jalview.datamodel.AlignmentAnnotation(
3732 annotation.getLabel(), annotation.getDescription(), anot,
3733 llim, hlim, safeInt(annotation.getGraphType()));
3735 jaa.graphGroup = safeInt(annotation.getGraphGroup());
3736 jaa._linecolour = firstColour;
3737 if (annotation.getThresholdLine() != null)
3739 jaa.setThreshold(new jalview.datamodel.GraphLine(
3740 safeFloat(annotation.getThresholdLine().getValue()),
3741 annotation.getThresholdLine().getLabel(),
3742 new java.awt.Color(safeInt(
3743 annotation.getThresholdLine().getColour()))));
3745 if (autoForView || annotation.isAutoCalculated())
3747 // Hardwire the symbol display line to ensure that labels for
3748 // histograms are displayed
3754 jaa = new jalview.datamodel.AlignmentAnnotation(
3755 annotation.getLabel(), annotation.getDescription(), anot);
3756 jaa._linecolour = firstColour;
3758 // register new annotation
3759 if (annotation.getId() != null)
3761 annotationIds.put(annotation.getId(), jaa);
3762 jaa.annotationId = annotation.getId();
3764 // recover sequence association
3765 String sequenceRef = annotation.getSequenceRef();
3766 if (sequenceRef != null)
3768 // from 2.9 sequenceRef is to sequence id (JAL-1781)
3769 SequenceI sequence = seqRefIds.get(sequenceRef);
3770 if (sequence == null)
3772 // in pre-2.9 projects sequence ref is to sequence name
3773 sequence = al.findName(sequenceRef);
3775 if (sequence != null)
3777 jaa.createSequenceMapping(sequence, 1, true);
3778 sequence.addAlignmentAnnotation(jaa);
3781 // and make a note of any group association
3782 if (annotation.getGroupRef() != null
3783 && annotation.getGroupRef().length() > 0)
3785 List<jalview.datamodel.AlignmentAnnotation> aal = groupAnnotRefs
3786 .get(annotation.getGroupRef());
3789 aal = new ArrayList<>();
3790 groupAnnotRefs.put(annotation.getGroupRef(), aal);
3795 if (annotation.getScore() != null)
3797 jaa.setScore(annotation.getScore().doubleValue());
3799 if (annotation.isVisible() != null)
3801 jaa.visible = annotation.isVisible().booleanValue();
3804 if (annotation.isCentreColLabels() != null)
3806 jaa.centreColLabels = annotation.isCentreColLabels()
3810 if (annotation.isScaleColLabels() != null)
3812 jaa.scaleColLabel = annotation.isScaleColLabels().booleanValue();
3814 if (annotation.isAutoCalculated())
3816 // newer files have an 'autoCalculated' flag and store calculation
3817 // state in viewport properties
3818 jaa.autoCalculated = true; // means annotation will be marked for
3819 // update at end of load.
3821 if (annotation.getGraphHeight() != null)
3823 jaa.graphHeight = annotation.getGraphHeight().intValue();
3825 jaa.belowAlignment = annotation.isBelowAlignment();
3826 jaa.setCalcId(annotation.getCalcId());
3827 if (annotation.getProperty().size() > 0)
3829 for (Annotation.Property prop : annotation.getProperty())
3831 jaa.setProperty(prop.getName(), prop.getValue());
3834 if (jaa.autoCalculated)
3836 autoAlan.add(new JvAnnotRow(i, jaa));
3839 // if (!autoForView)
3841 // add autocalculated group annotation and any user created annotation
3843 al.addAnnotation(jaa);
3847 // ///////////////////////
3849 // Create alignment markup and styles for this view
3850 if (jalviewModel.getJGroup().size() > 0)
3852 List<JGroup> groups = jalviewModel.getJGroup();
3853 boolean addAnnotSchemeGroup = false;
3854 for (int i = 0; i < groups.size(); i++)
3856 JGroup jGroup = groups.get(i);
3857 ColourSchemeI cs = null;
3858 if (jGroup.getColour() != null)
3860 if (jGroup.getColour().startsWith("ucs"))
3862 cs = getUserColourScheme(jalviewModel, jGroup.getColour());
3864 else if (jGroup.getColour().equals("AnnotationColourGradient")
3865 && jGroup.getAnnotationColours() != null)
3867 addAnnotSchemeGroup = true;
3871 cs = ColourSchemeProperty.getColourScheme(null, al,
3872 jGroup.getColour());
3875 int pidThreshold = safeInt(jGroup.getPidThreshold());
3877 Vector<SequenceI> seqs = new Vector<>();
3879 for (int s = 0; s < jGroup.getSeq().size(); s++)
3881 String seqId = jGroup.getSeq().get(s);
3882 SequenceI ts = seqRefIds.get(seqId);
3886 seqs.addElement(ts);
3890 if (seqs.size() < 1)
3895 SequenceGroup sg = new SequenceGroup(seqs, jGroup.getName(), cs,
3896 safeBoolean(jGroup.isDisplayBoxes()),
3897 safeBoolean(jGroup.isDisplayText()),
3898 safeBoolean(jGroup.isColourText()),
3899 safeInt(jGroup.getStart()), safeInt(jGroup.getEnd()));
3900 sg.getGroupColourScheme().setThreshold(pidThreshold, true);
3901 sg.getGroupColourScheme()
3902 .setConservationInc(safeInt(jGroup.getConsThreshold()));
3903 sg.setOutlineColour(new Color(safeInt(jGroup.getOutlineColour())));
3905 sg.textColour = new Color(safeInt(jGroup.getTextCol1()));
3906 sg.textColour2 = new Color(safeInt(jGroup.getTextCol2()));
3907 sg.setShowNonconserved(safeBoolean(jGroup.isShowUnconserved()));
3908 sg.thresholdTextColour = safeInt(jGroup.getTextColThreshold());
3909 // attributes with a default in the schema are never null
3910 sg.setShowConsensusHistogram(jGroup.isShowConsensusHistogram());
3911 sg.setshowSequenceLogo(jGroup.isShowSequenceLogo());
3912 sg.setNormaliseSequenceLogo(jGroup.isNormaliseSequenceLogo());
3913 sg.setIgnoreGapsConsensus(jGroup.isIgnoreGapsinConsensus());
3914 if (jGroup.getConsThreshold() != null
3915 && jGroup.getConsThreshold().intValue() != 0)
3917 Conservation c = new Conservation("All", sg.getSequences(null), 0,
3920 c.verdict(false, 25);
3921 sg.cs.setConservation(c);
3924 if (jGroup.getId() != null && groupAnnotRefs.size() > 0)
3926 // re-instate unique group/annotation row reference
3927 List<AlignmentAnnotation> jaal = groupAnnotRefs
3928 .get(jGroup.getId());
3931 for (AlignmentAnnotation jaa : jaal)
3934 if (jaa.autoCalculated)
3936 // match up and try to set group autocalc alignment row for this
3938 if (jaa.label.startsWith("Consensus for "))
3940 sg.setConsensus(jaa);
3942 // match up and try to set group autocalc alignment row for this
3944 if (jaa.label.startsWith("Conservation for "))
3946 sg.setConservationRow(jaa);
3953 if (addAnnotSchemeGroup)
3955 // reconstruct the annotation colourscheme
3957 constructAnnotationColour(jGroup.getAnnotationColours(),
3958 null, al, jalviewModel, false));
3964 // only dataset in this model, so just return.
3967 // ///////////////////////////////
3970 AlignFrame af = null;
3971 AlignViewport av = null;
3972 // now check to see if we really need to create a new viewport.
3973 if (multipleView && viewportsAdded.size() == 0)
3975 // We recovered an alignment for which a viewport already exists.
3976 // TODO: fix up any settings necessary for overlaying stored state onto
3977 // state recovered from another document. (may not be necessary).
3978 // we may need a binding from a viewport in memory to one recovered from
3980 // and then recover its containing af to allow the settings to be applied.
3981 // TODO: fix for vamsas demo
3983 "About to recover a viewport for existing alignment: Sequence set ID is "
3985 Object seqsetobj = retrieveExistingObj(uniqueSeqSetId);
3986 if (seqsetobj != null)
3988 if (seqsetobj instanceof String)
3990 uniqueSeqSetId = (String) seqsetobj;
3992 "Recovered extant sequence set ID mapping for ID : New Sequence set ID is "
3998 "Warning : Collision between sequence set ID string and existing jalview object mapping.");
4004 * indicate that annotation colours are applied across all groups (pre
4005 * Jalview 2.8.1 behaviour)
4007 boolean doGroupAnnColour = Jalview2XML.isVersionStringLaterThan("2.8.1",
4008 jalviewModel.getVersion());
4010 AlignmentPanel ap = null;
4011 boolean isnewview = true;
4014 // Check to see if this alignment already has a view id == viewId
4015 jalview.gui.AlignmentPanel views[] = Desktop
4016 .getAlignmentPanels(uniqueSeqSetId);
4017 if (views != null && views.length > 0)
4019 for (int v = 0; v < views.length; v++)
4021 if (views[v].av.getViewId().equalsIgnoreCase(viewId))
4023 // recover the existing alignpanel, alignframe, viewport
4024 af = views[v].alignFrame;
4027 // TODO: could even skip resetting view settings if we don't want to
4028 // change the local settings from other jalview processes
4037 af = loadViewport(file, jseqs, hiddenSeqs, al, jalviewModel, view,
4038 uniqueSeqSetId, viewId, autoAlan);
4039 av = af.getViewport();
4044 * Load any trees, PDB structures and viewers
4046 * Not done if flag is false (when this method is used for New View)
4048 if (loadTreesAndStructures)
4050 loadTrees(jalviewModel, view, af, av, ap);
4051 loadPCAViewers(jalviewModel, ap);
4052 loadPDBStructures(jprovider, jseqs, af, ap);
4053 loadRnaViewers(jprovider, jseqs, ap);
4055 // and finally return.
4060 * Instantiate and link any saved RNA (Varna) viewers. The state of the Varna
4061 * panel is restored from separate jar entries, two (gapped and trimmed) per
4062 * sequence and secondary structure.
4064 * Currently each viewer shows just one sequence and structure (gapped and
4065 * trimmed), however this method is designed to support multiple sequences or
4066 * structures in viewers if wanted in future.
4072 private void loadRnaViewers(jarInputStreamProvider jprovider,
4073 List<JSeq> jseqs, AlignmentPanel ap)
4076 * scan the sequences for references to viewers; create each one the first
4077 * time it is referenced, add Rna models to existing viewers
4079 for (JSeq jseq : jseqs)
4081 for (int i = 0; i < jseq.getRnaViewer().size(); i++)
4083 RnaViewer viewer = jseq.getRnaViewer().get(i);
4084 AppVarna appVarna = findOrCreateVarnaViewer(viewer, uniqueSetSuffix,
4087 for (int j = 0; j < viewer.getSecondaryStructure().size(); j++)
4089 SecondaryStructure ss = viewer.getSecondaryStructure().get(j);
4090 SequenceI seq = seqRefIds.get(jseq.getId());
4091 AlignmentAnnotation ann = this.annotationIds
4092 .get(ss.getAnnotationId());
4095 * add the structure to the Varna display (with session state copied
4096 * from the jar to a temporary file)
4098 boolean gapped = safeBoolean(ss.isGapped());
4099 String rnaTitle = ss.getTitle();
4100 String sessionState = ss.getViewerState();
4101 String tempStateFile = copyJarEntry(jprovider, sessionState,
4103 RnaModel rna = new RnaModel(rnaTitle, ann, seq, null, gapped);
4104 appVarna.addModelSession(rna, rnaTitle, tempStateFile);
4106 appVarna.setInitialSelection(safeInt(viewer.getSelectedRna()));
4112 * Locate and return an already instantiated matching AppVarna, or create one
4116 * @param viewIdSuffix
4120 protected AppVarna findOrCreateVarnaViewer(RnaViewer viewer,
4121 String viewIdSuffix, AlignmentPanel ap)
4124 * on each load a suffix is appended to the saved viewId, to avoid conflicts
4125 * if load is repeated
4127 String postLoadId = viewer.getViewId() + viewIdSuffix;
4128 for (JInternalFrame frame : getAllFrames())
4130 if (frame instanceof AppVarna)
4132 AppVarna varna = (AppVarna) frame;
4133 if (postLoadId.equals(varna.getViewId()))
4135 // this viewer is already instantiated
4136 // could in future here add ap as another 'parent' of the
4137 // AppVarna window; currently just 1-to-many
4144 * viewer not found - make it
4146 RnaViewerModel model = new RnaViewerModel(postLoadId, viewer.getTitle(),
4147 safeInt(viewer.getXpos()), safeInt(viewer.getYpos()),
4148 safeInt(viewer.getWidth()), safeInt(viewer.getHeight()),
4149 safeInt(viewer.getDividerLocation()));
4150 AppVarna varna = new AppVarna(model, ap);
4156 * Load any saved trees
4164 protected void loadTrees(JalviewModel jm, Viewport view, AlignFrame af,
4165 AlignViewport av, AlignmentPanel ap)
4167 // TODO result of automated refactoring - are all these parameters needed?
4170 for (int t = 0; t < jm.getTree().size(); t++)
4173 Tree tree = jm.getTree().get(t);
4175 TreePanel tp = (TreePanel) retrieveExistingObj(tree.getId());
4178 tp = af.showNewickTree(new NewickFile(tree.getNewick()),
4179 tree.getTitle(), safeInt(tree.getWidth()),
4180 safeInt(tree.getHeight()), safeInt(tree.getXpos()),
4181 safeInt(tree.getYpos()));
4182 if (tree.getId() != null)
4184 // perhaps bind the tree id to something ?
4189 // update local tree attributes ?
4190 // TODO: should check if tp has been manipulated by user - if so its
4191 // settings shouldn't be modified
4192 tp.setTitle(tree.getTitle());
4193 tp.setBounds(new Rectangle(safeInt(tree.getXpos()),
4194 safeInt(tree.getYpos()), safeInt(tree.getWidth()),
4195 safeInt(tree.getHeight())));
4196 tp.setViewport(av); // af.viewport;
4197 // TODO: verify 'associate with all views' works still
4198 tp.getTreeCanvas().setViewport(av); // af.viewport;
4199 tp.getTreeCanvas().setAssociatedPanel(ap); // af.alignPanel;
4201 tp.getTreeCanvas().setApplyToAllViews(tree.isLinkToAllViews());
4204 warn("There was a problem recovering stored Newick tree: \n"
4205 + tree.getNewick());
4209 tp.fitToWindow.setState(safeBoolean(tree.isFitToWindow()));
4210 tp.fitToWindow_actionPerformed(null);
4212 if (tree.getFontName() != null)
4215 new Font(tree.getFontName(), safeInt(tree.getFontStyle()),
4216 safeInt(tree.getFontSize())));
4221 new Font(view.getFontName(), safeInt(view.getFontStyle()),
4222 safeInt(view.getFontSize())));
4225 tp.showPlaceholders(safeBoolean(tree.isMarkUnlinked()));
4226 tp.showBootstrap(safeBoolean(tree.isShowBootstrap()));
4227 tp.showDistances(safeBoolean(tree.isShowDistances()));
4229 tp.getTreeCanvas().setThreshold(safeFloat(tree.getThreshold()));
4231 if (safeBoolean(tree.isCurrentTree()))
4233 af.getViewport().setCurrentTree(tp.getTree());
4237 } catch (Exception ex)
4239 ex.printStackTrace();
4244 * Load and link any saved structure viewers.
4251 protected void loadPDBStructures(jarInputStreamProvider jprovider,
4252 List<JSeq> jseqs, AlignFrame af, AlignmentPanel ap)
4255 * Run through all PDB ids on the alignment, and collect mappings between
4256 * distinct view ids and all sequences referring to that view.
4258 Map<String, StructureViewerModel> structureViewers = new LinkedHashMap<>();
4260 for (int i = 0; i < jseqs.size(); i++)
4262 JSeq jseq = jseqs.get(i);
4263 if (jseq.getPdbids().size() > 0)
4265 List<Pdbids> ids = jseq.getPdbids();
4266 for (int p = 0; p < ids.size(); p++)
4268 Pdbids pdbid = ids.get(p);
4269 final int structureStateCount = pdbid.getStructureState().size();
4270 for (int s = 0; s < structureStateCount; s++)
4272 // check to see if we haven't already created this structure view
4273 final StructureState structureState = pdbid.getStructureState()
4275 String sviewid = (structureState.getViewId() == null) ? null
4276 : structureState.getViewId() + uniqueSetSuffix;
4277 jalview.datamodel.PDBEntry jpdb = new jalview.datamodel.PDBEntry();
4278 // Originally : pdbid.getFile()
4279 // : TODO: verify external PDB file recovery still works in normal
4280 // jalview project load
4282 loadPDBFile(jprovider, pdbid.getId(), pdbid.getFile()));
4283 jpdb.setId(pdbid.getId());
4285 int x = safeInt(structureState.getXpos());
4286 int y = safeInt(structureState.getYpos());
4287 int width = safeInt(structureState.getWidth());
4288 int height = safeInt(structureState.getHeight());
4290 // Probably don't need to do this anymore...
4291 // Desktop.desktop.getComponentAt(x, y);
4292 // TODO: NOW: check that this recovers the PDB file correctly.
4293 String pdbFile = loadPDBFile(jprovider, pdbid.getId(),
4295 jalview.datamodel.SequenceI seq = seqRefIds
4296 .get(jseq.getId() + "");
4297 if (sviewid == null)
4299 sviewid = "_jalview_pre2_4_" + x + "," + y + "," + width + ","
4302 if (!structureViewers.containsKey(sviewid))
4304 String viewerType = structureState.getType();
4305 if (viewerType == null) // pre Jalview 2.9
4307 viewerType = ViewerType.JMOL.toString();
4309 structureViewers.put(sviewid,
4310 new StructureViewerModel(x, y, width, height, false,
4311 false, true, structureState.getViewId(),
4313 // Legacy pre-2.7 conversion JAL-823 :
4314 // do not assume any view has to be linked for colour by
4318 // assemble String[] { pdb files }, String[] { id for each
4319 // file }, orig_fileloc, SequenceI[][] {{ seqs_file 1 }, {
4320 // seqs_file 2}, boolean[] {
4321 // linkAlignPanel,superposeWithAlignpanel}} from hash
4322 StructureViewerModel jmoldat = structureViewers.get(sviewid);
4323 jmoldat.setAlignWithPanel(jmoldat.isAlignWithPanel()
4324 || structureState.isAlignwithAlignPanel());
4327 * Default colour by linked panel to false if not specified (e.g.
4328 * for pre-2.7 projects)
4330 boolean colourWithAlignPanel = jmoldat.isColourWithAlignPanel();
4331 colourWithAlignPanel |= structureState.isColourwithAlignPanel();
4332 jmoldat.setColourWithAlignPanel(colourWithAlignPanel);
4335 * Default colour by viewer to true if not specified (e.g. for
4338 boolean colourByViewer = jmoldat.isColourByViewer();
4339 colourByViewer &= structureState.isColourByJmol();
4340 jmoldat.setColourByViewer(colourByViewer);
4342 if (jmoldat.getStateData().length() < structureState.getValue()
4343 /*Content()*/.length())
4345 jmoldat.setStateData(structureState.getValue());// Content());
4347 if (pdbid.getFile() != null)
4349 File mapkey = new File(pdbid.getFile());
4350 StructureData seqstrmaps = jmoldat.getFileData().get(mapkey);
4351 if (seqstrmaps == null)
4353 jmoldat.getFileData().put(mapkey,
4354 seqstrmaps = jmoldat.new StructureData(pdbFile,
4357 if (!seqstrmaps.getSeqList().contains(seq))
4359 seqstrmaps.getSeqList().add(seq);
4365 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");
4372 // Instantiate the associated structure views
4373 for (Entry<String, StructureViewerModel> entry : structureViewers
4378 createOrLinkStructureViewer(entry, af, ap, jprovider);
4379 } catch (Exception e)
4382 "Error loading structure viewer: " + e.getMessage());
4383 // failed - try the next one
4395 protected void createOrLinkStructureViewer(
4396 Entry<String, StructureViewerModel> viewerData, AlignFrame af,
4397 AlignmentPanel ap, jarInputStreamProvider jprovider)
4399 final StructureViewerModel stateData = viewerData.getValue();
4402 * Search for any viewer windows already open from other alignment views
4403 * that exactly match the stored structure state
4405 StructureViewerBase comp = findMatchingViewer(viewerData);
4409 linkStructureViewer(ap, comp, stateData);
4413 String type = stateData.getType();
4416 ViewerType viewerType = ViewerType.valueOf(type);
4417 createStructureViewer(viewerType, viewerData, af, jprovider);
4418 } catch (IllegalArgumentException | NullPointerException e)
4420 // TODO JAL-3619 show error dialog / offer an alternative viewer
4421 Cache.log.error("Invalid structure viewer type: " + type);
4426 * Generates a name for the entry in the project jar file to hold state
4427 * information for a structure viewer
4432 protected String getViewerJarEntryName(String viewId)
4434 return VIEWER_PREFIX + viewId;
4438 * Returns any open frame that matches given structure viewer data. The match
4439 * is based on the unique viewId, or (for older project versions) the frame's
4445 protected StructureViewerBase findMatchingViewer(
4446 Entry<String, StructureViewerModel> viewerData)
4448 final String sviewid = viewerData.getKey();
4449 final StructureViewerModel svattrib = viewerData.getValue();
4450 StructureViewerBase comp = null;
4451 JInternalFrame[] frames = getAllFrames();
4452 for (JInternalFrame frame : frames)
4454 if (frame instanceof StructureViewerBase)
4457 * Post jalview 2.4 schema includes structure view id
4459 if (sviewid != null && ((StructureViewerBase) frame).getViewId()
4462 comp = (StructureViewerBase) frame;
4463 break; // break added in 2.9
4466 * Otherwise test for matching position and size of viewer frame
4468 else if (frame.getX() == svattrib.getX()
4469 && frame.getY() == svattrib.getY()
4470 && frame.getHeight() == svattrib.getHeight()
4471 && frame.getWidth() == svattrib.getWidth())
4473 comp = (StructureViewerBase) frame;
4474 // no break in faint hope of an exact match on viewId
4482 * Link an AlignmentPanel to an existing structure viewer.
4487 * @param useinViewerSuperpos
4488 * @param usetoColourbyseq
4489 * @param viewerColouring
4491 protected void linkStructureViewer(AlignmentPanel ap,
4492 StructureViewerBase viewer, StructureViewerModel stateData)
4494 // NOTE: if the jalview project is part of a shared session then
4495 // view synchronization should/could be done here.
4497 final boolean useinViewerSuperpos = stateData.isAlignWithPanel();
4498 final boolean usetoColourbyseq = stateData.isColourWithAlignPanel();
4499 final boolean viewerColouring = stateData.isColourByViewer();
4500 Map<File, StructureData> oldFiles = stateData.getFileData();
4503 * Add mapping for sequences in this view to an already open viewer
4505 final AAStructureBindingModel binding = viewer.getBinding();
4506 for (File id : oldFiles.keySet())
4508 // add this and any other pdb files that should be present in the
4510 StructureData filedat = oldFiles.get(id);
4511 String pdbFile = filedat.getFilePath();
4512 SequenceI[] seq = filedat.getSeqList().toArray(new SequenceI[0]);
4513 binding.getSsm().setMapping(seq, null, pdbFile, DataSourceType.FILE,
4515 binding.addSequenceForStructFile(pdbFile, seq);
4517 // and add the AlignmentPanel's reference to the view panel
4518 viewer.addAlignmentPanel(ap);
4519 if (useinViewerSuperpos)
4521 viewer.useAlignmentPanelForSuperposition(ap);
4525 viewer.excludeAlignmentPanelForSuperposition(ap);
4527 if (usetoColourbyseq)
4529 viewer.useAlignmentPanelForColourbyseq(ap, !viewerColouring);
4533 viewer.excludeAlignmentPanelForColourbyseq(ap);
4538 * Get all frames within the Desktop.
4542 protected JInternalFrame[] getAllFrames()
4544 JInternalFrame[] frames = null;
4545 // TODO is this necessary - is it safe - risk of hanging?
4550 frames = Desktop.desktop.getAllFrames();
4551 } catch (ArrayIndexOutOfBoundsException e)
4553 // occasional No such child exceptions are thrown here...
4557 } catch (InterruptedException f)
4561 } while (frames == null);
4566 * Answers true if 'version' is equal to or later than 'supported', where each
4567 * is formatted as major/minor versions like "2.8.3" or "2.3.4b1" for bugfix
4568 * changes. Development and test values for 'version' are leniently treated
4572 * - minimum version we are comparing against
4574 * - version of data being processsed
4577 public static boolean isVersionStringLaterThan(String supported,
4580 if (supported == null || version == null
4581 || version.equalsIgnoreCase("DEVELOPMENT BUILD")
4582 || version.equalsIgnoreCase("Test")
4583 || version.equalsIgnoreCase("AUTOMATED BUILD"))
4585 System.err.println("Assuming project file with "
4586 + (version == null ? "null" : version)
4587 + " is compatible with Jalview version " + supported);
4592 return StringUtils.compareVersions(version, supported, "b") >= 0;
4596 Vector<JalviewStructureDisplayI> newStructureViewers = null;
4598 protected void addNewStructureViewer(JalviewStructureDisplayI sview)
4600 if (newStructureViewers != null)
4602 sview.getBinding().setFinishedLoadingFromArchive(false);
4603 newStructureViewers.add(sview);
4607 protected void setLoadingFinishedForNewStructureViewers()
4609 if (newStructureViewers != null)
4611 for (JalviewStructureDisplayI sview : newStructureViewers)
4613 sview.getBinding().setFinishedLoadingFromArchive(true);
4615 newStructureViewers.clear();
4616 newStructureViewers = null;
4620 AlignFrame loadViewport(String file, List<JSeq> JSEQ,
4621 List<SequenceI> hiddenSeqs, AlignmentI al, JalviewModel jm,
4622 Viewport view, String uniqueSeqSetId, String viewId,
4623 List<JvAnnotRow> autoAlan)
4625 AlignFrame af = null;
4626 af = new AlignFrame(al, safeInt(view.getWidth()),
4627 safeInt(view.getHeight()), uniqueSeqSetId, viewId)
4631 // protected void processKeyEvent(java.awt.event.KeyEvent e) {
4632 // System.out.println("Jalview2XML AF " + e);
4633 // super.processKeyEvent(e);
4640 af.setFileName(file, FileFormat.Jalview);
4642 final AlignViewport viewport = af.getViewport();
4643 for (int i = 0; i < JSEQ.size(); i++)
4645 int colour = safeInt(JSEQ.get(i).getColour());
4646 viewport.setSequenceColour(viewport.getAlignment().getSequenceAt(i),
4652 viewport.setColourByReferenceSeq(true);
4653 viewport.setDisplayReferenceSeq(true);
4656 viewport.setGatherViewsHere(safeBoolean(view.isGatheredViews()));
4658 if (view.getSequenceSetId() != null)
4660 AlignmentViewport av = viewportsAdded.get(uniqueSeqSetId);
4662 viewport.setSequenceSetId(uniqueSeqSetId);
4665 // propagate shared settings to this new view
4666 viewport.setHistoryList(av.getHistoryList());
4667 viewport.setRedoList(av.getRedoList());
4671 viewportsAdded.put(uniqueSeqSetId, viewport);
4673 // TODO: check if this method can be called repeatedly without
4674 // side-effects if alignpanel already registered.
4675 PaintRefresher.Register(af.alignPanel, uniqueSeqSetId);
4677 // apply Hidden regions to view.
4678 if (hiddenSeqs != null)
4680 for (int s = 0; s < JSEQ.size(); s++)
4682 SequenceGroup hidden = new SequenceGroup();
4683 boolean isRepresentative = false;
4684 for (int r = 0; r < JSEQ.get(s).getHiddenSequences().size(); r++)
4686 isRepresentative = true;
4687 SequenceI sequenceToHide = al
4688 .getSequenceAt(JSEQ.get(s).getHiddenSequences().get(r));
4689 hidden.addSequence(sequenceToHide, false);
4690 // remove from hiddenSeqs list so we don't try to hide it twice
4691 hiddenSeqs.remove(sequenceToHide);
4693 if (isRepresentative)
4695 SequenceI representativeSequence = al.getSequenceAt(s);
4696 hidden.addSequence(representativeSequence, false);
4697 viewport.hideRepSequences(representativeSequence, hidden);
4701 SequenceI[] hseqs = hiddenSeqs
4702 .toArray(new SequenceI[hiddenSeqs.size()]);
4703 viewport.hideSequence(hseqs);
4706 // recover view properties and display parameters
4708 viewport.setShowAnnotation(safeBoolean(view.isShowAnnotation()));
4709 viewport.setAbovePIDThreshold(safeBoolean(view.isPidSelected()));
4710 final int pidThreshold = safeInt(view.getPidThreshold());
4711 viewport.setThreshold(pidThreshold);
4713 viewport.setColourText(safeBoolean(view.isShowColourText()));
4715 viewport.setConservationSelected(
4716 safeBoolean(view.isConservationSelected()));
4717 viewport.setIncrement(safeInt(view.getConsThreshold()));
4718 viewport.setShowJVSuffix(safeBoolean(view.isShowFullId()));
4719 viewport.setRightAlignIds(safeBoolean(view.isRightAlignIds()));
4720 viewport.setFont(new Font(view.getFontName(),
4721 safeInt(view.getFontStyle()), safeInt(view.getFontSize())),
4723 ViewStyleI vs = viewport.getViewStyle();
4724 vs.setScaleProteinAsCdna(view.isScaleProteinAsCdna());
4725 viewport.setViewStyle(vs);
4726 // TODO: allow custom charWidth/Heights to be restored by updating them
4727 // after setting font - which means set above to false
4728 viewport.setRenderGaps(safeBoolean(view.isRenderGaps()));
4729 viewport.setWrapAlignment(safeBoolean(view.isWrapAlignment()));
4730 viewport.setShowAnnotation(safeBoolean(view.isShowAnnotation()));
4732 viewport.setShowBoxes(safeBoolean(view.isShowBoxes()));
4734 viewport.setShowText(safeBoolean(view.isShowText()));
4736 viewport.setTextColour(new Color(safeInt(view.getTextCol1())));
4737 viewport.setTextColour2(new Color(safeInt(view.getTextCol2())));
4738 viewport.setThresholdTextColour(safeInt(view.getTextColThreshold()));
4739 viewport.setShowUnconserved(view.isShowUnconserved());
4740 viewport.getRanges().setStartRes(safeInt(view.getStartRes()));
4742 if (view.getViewName() != null)
4744 viewport.setViewName(view.getViewName());
4745 af.setInitialTabVisible();
4747 af.setBounds(safeInt(view.getXpos()), safeInt(view.getYpos()),
4748 safeInt(view.getWidth()), safeInt(view.getHeight()));
4749 // startSeq set in af.alignPanel.updateLayout below
4750 af.alignPanel.updateLayout();
4751 ColourSchemeI cs = null;
4752 // apply colourschemes
4753 if (view.getBgColour() != null)
4755 if (view.getBgColour().startsWith("ucs"))
4757 cs = getUserColourScheme(jm, view.getBgColour());
4759 else if (view.getBgColour().startsWith("Annotation"))
4761 AnnotationColourScheme viewAnnColour = view.getAnnotationColours();
4762 cs = constructAnnotationColour(viewAnnColour, af, al, jm, true);
4769 cs = ColourSchemeProperty.getColourScheme(af.getViewport(), al,
4770 view.getBgColour());
4775 * turn off 'alignment colour applies to all groups'
4776 * while restoring global colour scheme
4778 viewport.setColourAppliesToAllGroups(false);
4779 viewport.setGlobalColourScheme(cs);
4780 viewport.getResidueShading().setThreshold(pidThreshold,
4781 view.isIgnoreGapsinConsensus());
4782 viewport.getResidueShading()
4783 .setConsensus(viewport.getSequenceConsensusHash());
4784 if (safeBoolean(view.isConservationSelected()) && cs != null)
4786 viewport.getResidueShading()
4787 .setConservationInc(safeInt(view.getConsThreshold()));
4789 af.changeColour(cs);
4790 viewport.setColourAppliesToAllGroups(true);
4792 viewport.setShowSequenceFeatures(
4793 safeBoolean(view.isShowSequenceFeatures()));
4795 viewport.setCentreColumnLabels(view.isCentreColumnLabels());
4796 viewport.setIgnoreGapsConsensus(view.isIgnoreGapsinConsensus(), null);
4797 viewport.setFollowHighlight(view.isFollowHighlight());
4798 viewport.followSelection = view.isFollowSelection();
4799 viewport.setShowConsensusHistogram(view.isShowConsensusHistogram());
4800 viewport.setShowSequenceLogo(view.isShowSequenceLogo());
4801 viewport.setNormaliseSequenceLogo(view.isNormaliseSequenceLogo());
4802 viewport.setShowDBRefs(safeBoolean(view.isShowDbRefTooltip()));
4803 viewport.setShowNPFeats(safeBoolean(view.isShowNPfeatureTooltip()));
4804 viewport.setShowGroupConsensus(view.isShowGroupConsensus());
4805 viewport.setShowGroupConservation(view.isShowGroupConservation());
4806 viewport.setShowComplementFeatures(view.isShowComplementFeatures());
4807 viewport.setShowComplementFeaturesOnTop(
4808 view.isShowComplementFeaturesOnTop());
4810 // recover feature settings
4811 if (jm.getFeatureSettings() != null)
4813 FeatureRendererModel fr = af.alignPanel.getSeqPanel().seqCanvas
4814 .getFeatureRenderer();
4815 FeaturesDisplayed fdi;
4816 viewport.setFeaturesDisplayed(fdi = new FeaturesDisplayed());
4817 String[] renderOrder = new String[jm.getFeatureSettings().getSetting()
4819 Map<String, FeatureColourI> featureColours = new Hashtable<>();
4820 Map<String, Float> featureOrder = new Hashtable<>();
4822 for (int fs = 0; fs < jm.getFeatureSettings().getSetting()
4825 Setting setting = jm.getFeatureSettings().getSetting().get(fs);
4826 String featureType = setting.getType();
4829 * restore feature filters (if any)
4831 jalview.xml.binding.jalview.FeatureMatcherSet filters = setting
4833 if (filters != null)
4835 FeatureMatcherSetI filter = Jalview2XML.parseFilter(featureType,
4837 if (!filter.isEmpty())
4839 fr.setFeatureFilter(featureType, filter);
4844 * restore feature colour scheme
4846 Color maxColour = new Color(setting.getColour());
4847 if (setting.getMincolour() != null)
4850 * minColour is always set unless a simple colour
4851 * (including for colour by label though it doesn't use it)
4853 Color minColour = new Color(setting.getMincolour().intValue());
4854 Color noValueColour = minColour;
4855 NoValueColour noColour = setting.getNoValueColour();
4856 if (noColour == NoValueColour.NONE)
4858 noValueColour = null;
4860 else if (noColour == NoValueColour.MAX)
4862 noValueColour = maxColour;
4864 float min = safeFloat(safeFloat(setting.getMin()));
4865 float max = setting.getMax() == null ? 1f
4866 : setting.getMax().floatValue();
4867 FeatureColourI gc = new FeatureColour(maxColour, minColour,
4868 maxColour, noValueColour, min, max);
4869 if (setting.getAttributeName().size() > 0)
4871 gc.setAttributeName(setting.getAttributeName().toArray(
4872 new String[setting.getAttributeName().size()]));
4874 if (setting.getThreshold() != null)
4876 gc.setThreshold(setting.getThreshold().floatValue());
4877 int threshstate = safeInt(setting.getThreshstate());
4878 // -1 = None, 0 = Below, 1 = Above threshold
4879 if (threshstate == 0)
4881 gc.setBelowThreshold(true);
4883 else if (threshstate == 1)
4885 gc.setAboveThreshold(true);
4888 gc.setAutoScaled(true); // default
4889 if (setting.isAutoScale() != null)
4891 gc.setAutoScaled(setting.isAutoScale());
4893 if (setting.isColourByLabel() != null)
4895 gc.setColourByLabel(setting.isColourByLabel());
4897 // and put in the feature colour table.
4898 featureColours.put(featureType, gc);
4902 featureColours.put(featureType, new FeatureColour(maxColour));
4904 renderOrder[fs] = featureType;
4905 if (setting.getOrder() != null)
4907 featureOrder.put(featureType, setting.getOrder().floatValue());
4911 featureOrder.put(featureType, Float.valueOf(
4912 fs / jm.getFeatureSettings().getSetting().size()));
4914 if (safeBoolean(setting.isDisplay()))
4916 fdi.setVisible(featureType);
4919 Map<String, Boolean> fgtable = new Hashtable<>();
4920 for (int gs = 0; gs < jm.getFeatureSettings().getGroup().size(); gs++)
4922 Group grp = jm.getFeatureSettings().getGroup().get(gs);
4923 fgtable.put(grp.getName(), Boolean.valueOf(grp.isDisplay()));
4925 // FeatureRendererSettings frs = new FeatureRendererSettings(renderOrder,
4926 // fgtable, featureColours, jms.getFeatureSettings().hasTransparency() ?
4927 // jms.getFeatureSettings().getTransparency() : 0.0, featureOrder);
4928 FeatureRendererSettings frs = new FeatureRendererSettings(renderOrder,
4929 fgtable, featureColours, 1.0f, featureOrder);
4930 fr.transferSettings(frs);
4933 if (view.getHiddenColumns().size() > 0)
4935 for (int c = 0; c < view.getHiddenColumns().size(); c++)
4937 final HiddenColumns hc = view.getHiddenColumns().get(c);
4938 viewport.hideColumns(safeInt(hc.getStart()),
4939 safeInt(hc.getEnd()) /* +1 */);
4942 if (view.getCalcIdParam() != null)
4944 for (CalcIdParam calcIdParam : view.getCalcIdParam())
4946 if (calcIdParam != null)
4948 if (recoverCalcIdParam(calcIdParam, viewport))
4953 warn("Couldn't recover parameters for "
4954 + calcIdParam.getCalcId());
4959 af.setMenusFromViewport(viewport);
4960 af.setTitle(view.getTitle());
4961 // TODO: we don't need to do this if the viewport is aready visible.
4963 * Add the AlignFrame to the desktop (it may be 'gathered' later), unless it
4964 * has a 'cdna/protein complement' view, in which case save it in order to
4965 * populate a SplitFrame once all views have been read in.
4967 String complementaryViewId = view.getComplementId();
4968 if (complementaryViewId == null)
4970 Desktop.addInternalFrame(af, view.getTitle(),
4971 safeInt(view.getWidth()), safeInt(view.getHeight()));
4972 // recompute any autoannotation
4973 af.alignPanel.updateAnnotation(false, true);
4974 reorderAutoannotation(af, al, autoAlan);
4975 af.alignPanel.alignmentChanged();
4979 splitFrameCandidates.put(view, af);
4985 * Reads saved data to restore Colour by Annotation settings
4987 * @param viewAnnColour
4991 * @param checkGroupAnnColour
4994 private ColourSchemeI constructAnnotationColour(
4995 AnnotationColourScheme viewAnnColour, AlignFrame af,
4996 AlignmentI al, JalviewModel model, boolean checkGroupAnnColour)
4998 boolean propagateAnnColour = false;
4999 AlignmentI annAlignment = af != null ? af.getViewport().getAlignment()
5001 if (checkGroupAnnColour && al.getGroups() != null
5002 && al.getGroups().size() > 0)
5004 // pre 2.8.1 behaviour
5005 // check to see if we should transfer annotation colours
5006 propagateAnnColour = true;
5007 for (SequenceGroup sg : al.getGroups())
5009 if (sg.getColourScheme() instanceof AnnotationColourGradient)
5011 propagateAnnColour = false;
5017 * 2.10.2- : saved annotationId is AlignmentAnnotation.annotationId
5019 String annotationId = viewAnnColour.getAnnotation();
5020 AlignmentAnnotation matchedAnnotation = annotationIds.get(annotationId);
5023 * pre 2.10.2: saved annotationId is AlignmentAnnotation.label
5025 if (matchedAnnotation == null
5026 && annAlignment.getAlignmentAnnotation() != null)
5028 for (int i = 0; i < annAlignment.getAlignmentAnnotation().length; i++)
5031 .equals(annAlignment.getAlignmentAnnotation()[i].label))
5033 matchedAnnotation = annAlignment.getAlignmentAnnotation()[i];
5038 if (matchedAnnotation == null)
5040 System.err.println("Failed to match annotation colour scheme for "
5044 if (matchedAnnotation.getThreshold() == null)
5046 matchedAnnotation.setThreshold(
5047 new GraphLine(safeFloat(viewAnnColour.getThreshold()),
5048 "Threshold", Color.black));
5051 AnnotationColourGradient cs = null;
5052 if (viewAnnColour.getColourScheme().equals("None"))
5054 cs = new AnnotationColourGradient(matchedAnnotation,
5055 new Color(safeInt(viewAnnColour.getMinColour())),
5056 new Color(safeInt(viewAnnColour.getMaxColour())),
5057 safeInt(viewAnnColour.getAboveThreshold()));
5059 else if (viewAnnColour.getColourScheme().startsWith("ucs"))
5061 cs = new AnnotationColourGradient(matchedAnnotation,
5062 getUserColourScheme(model, viewAnnColour.getColourScheme()),
5063 safeInt(viewAnnColour.getAboveThreshold()));
5067 cs = new AnnotationColourGradient(matchedAnnotation,
5068 ColourSchemeProperty.getColourScheme(af.getViewport(), al,
5069 viewAnnColour.getColourScheme()),
5070 safeInt(viewAnnColour.getAboveThreshold()));
5073 boolean perSequenceOnly = safeBoolean(viewAnnColour.isPerSequence());
5074 boolean useOriginalColours = safeBoolean(
5075 viewAnnColour.isPredefinedColours());
5076 cs.setSeqAssociated(perSequenceOnly);
5077 cs.setPredefinedColours(useOriginalColours);
5079 if (propagateAnnColour && al.getGroups() != null)
5081 // Also use these settings for all the groups
5082 for (int g = 0; g < al.getGroups().size(); g++)
5084 SequenceGroup sg = al.getGroups().get(g);
5085 if (sg.getGroupColourScheme() == null)
5090 AnnotationColourGradient groupScheme = new AnnotationColourGradient(
5091 matchedAnnotation, sg.getColourScheme(),
5092 safeInt(viewAnnColour.getAboveThreshold()));
5093 sg.setColourScheme(groupScheme);
5094 groupScheme.setSeqAssociated(perSequenceOnly);
5095 groupScheme.setPredefinedColours(useOriginalColours);
5101 private void reorderAutoannotation(AlignFrame af, AlignmentI al,
5102 List<JvAnnotRow> autoAlan)
5104 // copy over visualization settings for autocalculated annotation in the
5106 if (al.getAlignmentAnnotation() != null)
5109 * Kludge for magic autoannotation names (see JAL-811)
5111 String[] magicNames = new String[] { "Consensus", "Quality",
5113 JvAnnotRow nullAnnot = new JvAnnotRow(-1, null);
5114 Hashtable<String, JvAnnotRow> visan = new Hashtable<>();
5115 for (String nm : magicNames)
5117 visan.put(nm, nullAnnot);
5119 for (JvAnnotRow auan : autoAlan)
5121 visan.put(auan.template.label
5122 + (auan.template.getCalcId() == null ? ""
5123 : "\t" + auan.template.getCalcId()),
5126 int hSize = al.getAlignmentAnnotation().length;
5127 List<JvAnnotRow> reorder = new ArrayList<>();
5128 // work through any autoCalculated annotation already on the view
5129 // removing it if it should be placed in a different location on the
5130 // annotation panel.
5131 List<String> remains = new ArrayList<>(visan.keySet());
5132 for (int h = 0; h < hSize; h++)
5134 jalview.datamodel.AlignmentAnnotation jalan = al
5135 .getAlignmentAnnotation()[h];
5136 if (jalan.autoCalculated)
5139 JvAnnotRow valan = visan.get(k = jalan.label);
5140 if (jalan.getCalcId() != null)
5142 valan = visan.get(k = jalan.label + "\t" + jalan.getCalcId());
5147 // delete the auto calculated row from the alignment
5148 al.deleteAnnotation(jalan, false);
5152 if (valan != nullAnnot)
5154 if (jalan != valan.template)
5156 // newly created autoannotation row instance
5157 // so keep a reference to the visible annotation row
5158 // and copy over all relevant attributes
5159 if (valan.template.graphHeight >= 0)
5162 jalan.graphHeight = valan.template.graphHeight;
5164 jalan.visible = valan.template.visible;
5166 reorder.add(new JvAnnotRow(valan.order, jalan));
5171 // Add any (possibly stale) autocalculated rows that were not appended to
5172 // the view during construction
5173 for (String other : remains)
5175 JvAnnotRow othera = visan.get(other);
5176 if (othera != nullAnnot && othera.template.getCalcId() != null
5177 && othera.template.getCalcId().length() > 0)
5179 reorder.add(othera);
5182 // now put the automatic annotation in its correct place
5183 int s = 0, srt[] = new int[reorder.size()];
5184 JvAnnotRow[] rws = new JvAnnotRow[reorder.size()];
5185 for (JvAnnotRow jvar : reorder)
5188 srt[s++] = jvar.order;
5191 jalview.util.QuickSort.sort(srt, rws);
5192 // and re-insert the annotation at its correct position
5193 for (JvAnnotRow jvar : rws)
5195 al.addAnnotation(jvar.template, jvar.order);
5197 af.alignPanel.adjustAnnotationHeight();
5201 Hashtable skipList = null;
5204 * TODO remove this method
5207 * @return AlignFrame bound to sequenceSetId from view, if one exists. private
5208 * AlignFrame getSkippedFrame(Viewport view) { if (skipList==null) {
5209 * throw new Error("Implementation Error. No skipList defined for this
5210 * Jalview2XML instance."); } return (AlignFrame)
5211 * skipList.get(view.getSequenceSetId()); }
5215 * Check if the Jalview view contained in object should be skipped or not.
5218 * @return true if view's sequenceSetId is a key in skipList
5220 private boolean skipViewport(JalviewModel object)
5222 if (skipList == null)
5226 String id = object.getViewport().get(0).getSequenceSetId();
5227 if (skipList.containsKey(id))
5229 if (Cache.log != null && Cache.log.isDebugEnabled())
5231 Cache.log.debug("Skipping seuqence set id " + id);
5238 public void addToSkipList(AlignFrame af)
5240 if (skipList == null)
5242 skipList = new Hashtable();
5244 skipList.put(af.getViewport().getSequenceSetId(), af);
5247 public void clearSkipList()
5249 if (skipList != null)
5256 private void recoverDatasetFor(SequenceSet vamsasSet, AlignmentI al,
5257 boolean ignoreUnrefed, String uniqueSeqSetId)
5259 jalview.datamodel.AlignmentI ds = getDatasetFor(
5260 vamsasSet.getDatasetId());
5261 AlignmentI xtant_ds = ds;
5262 if (xtant_ds == null)
5264 // good chance we are about to create a new dataset, but check if we've
5265 // seen some of the dataset sequence IDs before.
5266 // TODO: skip this check if we are working with project generated by
5267 // version 2.11 or later
5268 xtant_ds = checkIfHasDataset(vamsasSet.getSequence());
5269 if (xtant_ds != null)
5272 addDatasetRef(vamsasSet.getDatasetId(), ds);
5275 Vector<SequenceI> dseqs = null;
5278 // recovering an alignment View
5279 AlignmentI seqSetDS = getDatasetFor(UNIQSEQSETID + uniqueSeqSetId);
5280 if (seqSetDS != null)
5282 if (ds != null && ds != seqSetDS)
5284 warn("JAL-3171 regression: Overwriting a dataset reference for an alignment"
5285 + " - CDS/Protein crossreference data may be lost");
5286 if (xtant_ds != null)
5288 // This can only happen if the unique sequence set ID was bound to a
5289 // dataset that did not contain any of the sequences in the view
5290 // currently being restored.
5291 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.");
5295 addDatasetRef(vamsasSet.getDatasetId(), ds);
5300 // try even harder to restore dataset
5301 AlignmentI xtantDS = checkIfHasDataset(vamsasSet.getSequence());
5302 // create a list of new dataset sequences
5303 dseqs = new Vector<>();
5305 for (int i = 0, iSize = vamsasSet.getSequence().size(); i < iSize; i++)
5307 Sequence vamsasSeq = vamsasSet.getSequence().get(i);
5308 ensureJalviewDatasetSequence(vamsasSeq, ds, dseqs, ignoreUnrefed, i);
5310 // create a new dataset
5313 SequenceI[] dsseqs = new SequenceI[dseqs.size()];
5314 dseqs.copyInto(dsseqs);
5315 ds = new jalview.datamodel.Alignment(dsseqs);
5316 debug("Created new dataset " + vamsasSet.getDatasetId()
5317 + " for alignment " + System.identityHashCode(al));
5318 addDatasetRef(vamsasSet.getDatasetId(), ds);
5320 // set the dataset for the newly imported alignment.
5321 if (al.getDataset() == null && !ignoreUnrefed)
5324 // register dataset for the alignment's uniqueSeqSetId for legacy projects
5325 addDatasetRef(UNIQSEQSETID + uniqueSeqSetId, ds);
5327 updateSeqDatasetBinding(vamsasSet.getSequence(), ds);
5331 * XML dataset sequence ID to materialised dataset reference
5333 HashMap<String, AlignmentI> seqToDataset = new HashMap<>();
5336 * @return the first materialised dataset reference containing a dataset
5337 * sequence referenced in the given view
5339 * - sequences from the view
5341 AlignmentI checkIfHasDataset(List<Sequence> list)
5343 for (Sequence restoredSeq : list)
5345 AlignmentI datasetFor = seqToDataset.get(restoredSeq.getDsseqid());
5346 if (datasetFor != null)
5355 * Register ds as the containing dataset for the dataset sequences referenced
5356 * by sequences in list
5359 * - sequences in a view
5362 void updateSeqDatasetBinding(List<Sequence> list, AlignmentI ds)
5364 for (Sequence restoredSeq : list)
5366 AlignmentI prevDS = seqToDataset.put(restoredSeq.getDsseqid(), ds);
5367 if (prevDS != null && prevDS != ds)
5369 warn("Dataset sequence appears in many datasets: "
5370 + restoredSeq.getDsseqid());
5371 // TODO: try to merge!
5379 * sequence definition to create/merge dataset sequence for
5383 * vector to add new dataset sequence to
5384 * @param ignoreUnrefed
5385 * - when true, don't create new sequences from vamsasSeq if it's id
5386 * doesn't already have an asssociated Jalview sequence.
5388 * - used to reorder the sequence in the alignment according to the
5389 * vamsasSeq array ordering, to preserve ordering of dataset
5391 private void ensureJalviewDatasetSequence(Sequence vamsasSeq,
5392 AlignmentI ds, Vector<SequenceI> dseqs, boolean ignoreUnrefed,
5395 // JBP TODO: Check this is called for AlCodonFrames to support recovery of
5397 SequenceI sq = seqRefIds.get(vamsasSeq.getId());
5398 boolean reorder = false;
5399 SequenceI dsq = null;
5400 if (sq != null && sq.getDatasetSequence() != null)
5402 dsq = sq.getDatasetSequence();
5408 if (sq == null && ignoreUnrefed)
5412 String sqid = vamsasSeq.getDsseqid();
5415 // need to create or add a new dataset sequence reference to this sequence
5418 dsq = seqRefIds.get(sqid);
5423 // make a new dataset sequence
5424 dsq = sq.createDatasetSequence();
5427 // make up a new dataset reference for this sequence
5428 sqid = seqHash(dsq);
5430 dsq.setVamsasId(uniqueSetSuffix + sqid);
5431 seqRefIds.put(sqid, dsq);
5436 dseqs.addElement(dsq);
5441 ds.addSequence(dsq);
5447 { // make this dataset sequence sq's dataset sequence
5448 sq.setDatasetSequence(dsq);
5449 // and update the current dataset alignment
5454 if (!dseqs.contains(dsq))
5461 if (ds.findIndex(dsq) < 0)
5463 ds.addSequence(dsq);
5470 // TODO: refactor this as a merge dataset sequence function
5471 // now check that sq (the dataset sequence) sequence really is the union of
5472 // all references to it
5473 // boolean pre = sq.getStart() < dsq.getStart();
5474 // boolean post = sq.getEnd() > dsq.getEnd();
5478 // StringBuffer sb = new StringBuffer();
5479 String newres = jalview.analysis.AlignSeq.extractGaps(
5480 jalview.util.Comparison.GapChars, sq.getSequenceAsString());
5481 if (!newres.equalsIgnoreCase(dsq.getSequenceAsString())
5482 && newres.length() > dsq.getLength())
5484 // Update with the longer sequence.
5488 * if (pre) { sb.insert(0, newres .substring(0, dsq.getStart() -
5489 * sq.getStart())); dsq.setStart(sq.getStart()); } if (post) {
5490 * sb.append(newres.substring(newres.length() - sq.getEnd() -
5491 * dsq.getEnd())); dsq.setEnd(sq.getEnd()); }
5493 dsq.setSequence(newres);
5495 // TODO: merges will never happen if we 'know' we have the real dataset
5496 // sequence - this should be detected when id==dssid
5498 "DEBUG Notice: Merged dataset sequence (if you see this often, post at http://issues.jalview.org/browse/JAL-1474)"); // ("
5499 // + (pre ? "prepended" : "") + " "
5500 // + (post ? "appended" : ""));
5505 // sequence refs are identical. We may need to update the existing dataset
5506 // alignment with this one, though.
5507 if (ds != null && dseqs == null)
5509 int opos = ds.findIndex(dsq);
5510 SequenceI tseq = null;
5511 if (opos != -1 && vseqpos != opos)
5513 // remove from old position
5514 ds.deleteSequence(dsq);
5516 if (vseqpos < ds.getHeight())
5518 if (vseqpos != opos)
5520 // save sequence at destination position
5521 tseq = ds.getSequenceAt(vseqpos);
5522 ds.replaceSequenceAt(vseqpos, dsq);
5523 ds.addSequence(tseq);
5528 ds.addSequence(dsq);
5535 * TODO use AlignmentI here and in related methods - needs
5536 * AlignmentI.getDataset() changed to return AlignmentI instead of Alignment
5538 Hashtable<String, AlignmentI> datasetIds = null;
5540 IdentityHashMap<AlignmentI, String> dataset2Ids = null;
5542 private AlignmentI getDatasetFor(String datasetId)
5544 if (datasetIds == null)
5546 datasetIds = new Hashtable<>();
5549 if (datasetIds.containsKey(datasetId))
5551 return datasetIds.get(datasetId);
5556 private void addDatasetRef(String datasetId, AlignmentI dataset)
5558 if (datasetIds == null)
5560 datasetIds = new Hashtable<>();
5562 datasetIds.put(datasetId, dataset);
5566 * make a new dataset ID for this jalview dataset alignment
5571 private String getDatasetIdRef(AlignmentI dataset)
5573 if (dataset.getDataset() != null)
5575 warn("Serious issue! Dataset Object passed to getDatasetIdRef is not a Jalview DATASET alignment...");
5577 String datasetId = makeHashCode(dataset, null);
5578 if (datasetId == null)
5580 // make a new datasetId and record it
5581 if (dataset2Ids == null)
5583 dataset2Ids = new IdentityHashMap<>();
5587 datasetId = dataset2Ids.get(dataset);
5589 if (datasetId == null)
5591 datasetId = "ds" + dataset2Ids.size() + 1;
5592 dataset2Ids.put(dataset, datasetId);
5599 * Add any saved DBRefEntry's to the sequence. An entry flagged as 'locus' is
5600 * constructed as a special subclass GeneLocus.
5602 * @param datasetSequence
5605 private void addDBRefs(SequenceI datasetSequence, Sequence sequence)
5607 for (int d = 0; d < sequence.getDBRef().size(); d++)
5609 DBRef dr = sequence.getDBRef().get(d);
5613 entry = new GeneLocus(dr.getSource(), dr.getVersion(),
5614 dr.getAccessionId());
5618 entry = new DBRefEntry(dr.getSource(), dr.getVersion(),
5619 dr.getAccessionId());
5621 if (dr.getMapping() != null)
5623 entry.setMap(addMapping(dr.getMapping()));
5625 datasetSequence.addDBRef(entry);
5629 private jalview.datamodel.Mapping addMapping(Mapping m)
5631 SequenceI dsto = null;
5632 // Mapping m = dr.getMapping();
5633 int fr[] = new int[m.getMapListFrom().size() * 2];
5634 Iterator<MapListFrom> from = m.getMapListFrom().iterator();// enumerateMapListFrom();
5635 for (int _i = 0; from.hasNext(); _i += 2)
5637 MapListFrom mf = from.next();
5638 fr[_i] = mf.getStart();
5639 fr[_i + 1] = mf.getEnd();
5641 int fto[] = new int[m.getMapListTo().size() * 2];
5642 Iterator<MapListTo> to = m.getMapListTo().iterator();// enumerateMapListTo();
5643 for (int _i = 0; to.hasNext(); _i += 2)
5645 MapListTo mf = to.next();
5646 fto[_i] = mf.getStart();
5647 fto[_i + 1] = mf.getEnd();
5649 jalview.datamodel.Mapping jmap = new jalview.datamodel.Mapping(dsto, fr,
5650 fto, m.getMapFromUnit().intValue(),
5651 m.getMapToUnit().intValue());
5654 * (optional) choice of dseqFor or Sequence
5656 if (m.getDseqFor() != null)
5658 String dsfor = m.getDseqFor();
5659 if (seqRefIds.containsKey(dsfor))
5664 jmap.setTo(seqRefIds.get(dsfor));
5668 frefedSequence.add(newMappingRef(dsfor, jmap));
5671 else if (m.getSequence() != null)
5674 * local sequence definition
5676 Sequence ms = m.getSequence();
5677 SequenceI djs = null;
5678 String sqid = ms.getDsseqid();
5679 if (sqid != null && sqid.length() > 0)
5682 * recover dataset sequence
5684 djs = seqRefIds.get(sqid);
5689 "Warning - making up dataset sequence id for DbRef sequence map reference");
5690 sqid = ((Object) ms).toString(); // make up a new hascode for
5691 // undefined dataset sequence hash
5692 // (unlikely to happen)
5698 * make a new dataset sequence and add it to refIds hash
5700 djs = new jalview.datamodel.Sequence(ms.getName(),
5702 djs.setStart(jmap.getMap().getToLowest());
5703 djs.setEnd(jmap.getMap().getToHighest());
5704 djs.setVamsasId(uniqueSetSuffix + sqid);
5706 incompleteSeqs.put(sqid, djs);
5707 seqRefIds.put(sqid, djs);
5710 jalview.bin.Cache.log.debug("about to recurse on addDBRefs.");
5719 * Provides a 'copy' of an alignment view (on action New View) by 'saving' the
5720 * view as XML (but not to file), and then reloading it
5725 public AlignmentPanel copyAlignPanel(AlignmentPanel ap)
5728 JalviewModel jm = saveState(ap, null, null, null);
5731 jm.getVamsasModel().getSequenceSet().get(0).getDatasetId(),
5732 ap.getAlignment().getDataset());
5734 uniqueSetSuffix = "";
5735 // jm.getJalviewModelSequence().getViewport(0).setId(null);
5736 jm.getViewport().get(0).setId(null);
5737 // we don't overwrite the view we just copied
5739 if (this.frefedSequence == null)
5741 frefedSequence = new Vector<>();
5744 viewportsAdded.clear();
5746 AlignFrame af = loadFromObject(jm, null, false, null);
5747 af.getAlignPanels().clear();
5748 af.closeMenuItem_actionPerformed(true);
5751 * if(ap.av.getAlignment().getAlignmentAnnotation()!=null) { for(int i=0;
5752 * i<ap.av.getAlignment().getAlignmentAnnotation().length; i++) {
5753 * if(!ap.av.getAlignment().getAlignmentAnnotation()[i].autoCalculated) {
5754 * af.alignPanel.av.getAlignment().getAlignmentAnnotation()[i] =
5755 * ap.av.getAlignment().getAlignmentAnnotation()[i]; } } }
5758 return af.alignPanel;
5761 private Hashtable jvids2vobj;
5763 private void warn(String msg)
5768 private void warn(String msg, Exception e)
5770 if (Cache.log != null)
5774 Cache.log.warn(msg, e);
5778 Cache.log.warn(msg);
5783 System.err.println("Warning: " + msg);
5786 e.printStackTrace();
5791 private void debug(String string)
5793 debug(string, null);
5796 private void debug(String msg, Exception e)
5798 if (Cache.log != null)
5802 Cache.log.debug(msg, e);
5806 Cache.log.debug(msg);
5811 System.err.println("Warning: " + msg);
5814 e.printStackTrace();
5820 * set the object to ID mapping tables used to write/recover objects and XML
5821 * ID strings for the jalview project. If external tables are provided then
5822 * finalize and clearSeqRefs will not clear the tables when the Jalview2XML
5823 * object goes out of scope. - also populates the datasetIds hashtable with
5824 * alignment objects containing dataset sequences
5827 * Map from ID strings to jalview datamodel
5829 * Map from jalview datamodel to ID strings
5833 public void setObjectMappingTables(Hashtable vobj2jv,
5834 IdentityHashMap jv2vobj)
5836 this.jv2vobj = jv2vobj;
5837 this.vobj2jv = vobj2jv;
5838 Iterator ds = jv2vobj.keySet().iterator();
5840 while (ds.hasNext())
5842 Object jvobj = ds.next();
5843 id = jv2vobj.get(jvobj).toString();
5844 if (jvobj instanceof jalview.datamodel.Alignment)
5846 if (((jalview.datamodel.Alignment) jvobj).getDataset() == null)
5848 addDatasetRef(id, (jalview.datamodel.Alignment) jvobj);
5851 else if (jvobj instanceof jalview.datamodel.Sequence)
5853 // register sequence object so the XML parser can recover it.
5854 if (seqRefIds == null)
5856 seqRefIds = new HashMap<>();
5858 if (seqsToIds == null)
5860 seqsToIds = new IdentityHashMap<>();
5862 seqRefIds.put(jv2vobj.get(jvobj).toString(), (SequenceI) jvobj);
5863 seqsToIds.put((SequenceI) jvobj, id);
5865 else if (jvobj instanceof jalview.datamodel.AlignmentAnnotation)
5868 AlignmentAnnotation jvann = (AlignmentAnnotation) jvobj;
5869 annotationIds.put(anid = jv2vobj.get(jvobj).toString(), jvann);
5870 if (jvann.annotationId == null)
5872 jvann.annotationId = anid;
5874 if (!jvann.annotationId.equals(anid))
5876 // TODO verify that this is the correct behaviour
5877 this.warn("Overriding Annotation ID for " + anid
5878 + " from different id : " + jvann.annotationId);
5879 jvann.annotationId = anid;
5882 else if (jvobj instanceof String)
5884 if (jvids2vobj == null)
5886 jvids2vobj = new Hashtable();
5887 jvids2vobj.put(jvobj, jv2vobj.get(jvobj).toString());
5892 Cache.log.debug("Ignoring " + jvobj.getClass() + " (ID = " + id);
5898 * set the uniqueSetSuffix used to prefix/suffix object IDs for jalview
5899 * objects created from the project archive. If string is null (default for
5900 * construction) then suffix will be set automatically.
5904 public void setUniqueSetSuffix(String string)
5906 uniqueSetSuffix = string;
5911 * uses skipList2 as the skipList for skipping views on sequence sets
5912 * associated with keys in the skipList
5916 public void setSkipList(Hashtable skipList2)
5918 skipList = skipList2;
5922 * Reads the jar entry of given name and returns its contents, or null if the
5923 * entry is not found.
5926 * @param jarEntryName
5929 protected String readJarEntry(jarInputStreamProvider jprovider,
5930 String jarEntryName)
5932 String result = null;
5933 BufferedReader in = null;
5938 * Reopen the jar input stream and traverse its entries to find a matching
5941 JarInputStream jin = jprovider.getJarInputStream();
5942 JarEntry entry = null;
5945 entry = jin.getNextJarEntry();
5946 } while (entry != null && !entry.getName().equals(jarEntryName));
5950 StringBuilder out = new StringBuilder(256);
5951 in = new BufferedReader(new InputStreamReader(jin, UTF_8));
5954 while ((data = in.readLine()) != null)
5958 result = out.toString();
5962 warn("Couldn't find entry in Jalview Jar for " + jarEntryName);
5964 } catch (Exception ex)
5966 ex.printStackTrace();
5974 } catch (IOException e)
5985 * Returns an incrementing counter (0, 1, 2...)
5989 private synchronized int nextCounter()
5995 * Loads any saved PCA viewers
6000 protected void loadPCAViewers(JalviewModel model, AlignmentPanel ap)
6004 List<PcaViewer> pcaviewers = model.getPcaViewer();
6005 for (PcaViewer viewer : pcaviewers)
6007 String modelName = viewer.getScoreModelName();
6008 SimilarityParamsI params = new SimilarityParams(
6009 viewer.isIncludeGappedColumns(), viewer.isMatchGaps(),
6010 viewer.isIncludeGaps(),
6011 viewer.isDenominateByShortestLength());
6014 * create the panel (without computing the PCA)
6016 PCAPanel panel = new PCAPanel(ap, modelName, params);
6018 panel.setTitle(viewer.getTitle());
6019 panel.setBounds(new Rectangle(viewer.getXpos(), viewer.getYpos(),
6020 viewer.getWidth(), viewer.getHeight()));
6022 boolean showLabels = viewer.isShowLabels();
6023 panel.setShowLabels(showLabels);
6024 panel.getRotatableCanvas().setShowLabels(showLabels);
6025 panel.getRotatableCanvas()
6026 .setBgColour(new Color(viewer.getBgColour()));
6027 panel.getRotatableCanvas()
6028 .setApplyToAllViews(viewer.isLinkToAllViews());
6031 * load PCA output data
6033 ScoreModelI scoreModel = ScoreModels.getInstance()
6034 .getScoreModel(modelName, ap);
6035 PCA pca = new PCA(null, scoreModel, params);
6036 PcaDataType pcaData = viewer.getPcaData();
6038 MatrixI pairwise = loadDoubleMatrix(pcaData.getPairwiseMatrix());
6039 pca.setPairwiseScores(pairwise);
6041 MatrixI triDiag = loadDoubleMatrix(pcaData.getTridiagonalMatrix());
6042 pca.setTridiagonal(triDiag);
6044 MatrixI result = loadDoubleMatrix(pcaData.getEigenMatrix());
6045 pca.setEigenmatrix(result);
6047 panel.getPcaModel().setPCA(pca);
6050 * we haven't saved the input data! (JAL-2647 to do)
6052 panel.setInputData(null);
6055 * add the sequence points for the PCA display
6057 List<jalview.datamodel.SequencePoint> seqPoints = new ArrayList<>();
6058 for (SequencePoint sp : viewer.getSequencePoint())
6060 String seqId = sp.getSequenceRef();
6061 SequenceI seq = seqRefIds.get(seqId);
6064 throw new IllegalStateException(
6065 "Unmatched seqref for PCA: " + seqId);
6067 Point pt = new Point(sp.getXPos(), sp.getYPos(), sp.getZPos());
6068 jalview.datamodel.SequencePoint seqPoint = new jalview.datamodel.SequencePoint(
6070 seqPoints.add(seqPoint);
6072 panel.getRotatableCanvas().setPoints(seqPoints, seqPoints.size());
6075 * set min-max ranges and scale after setPoints (which recomputes them)
6077 panel.getRotatableCanvas().setScaleFactor(viewer.getScaleFactor());
6078 SeqPointMin spMin = viewer.getSeqPointMin();
6079 float[] min = new float[] { spMin.getXPos(), spMin.getYPos(),
6081 SeqPointMax spMax = viewer.getSeqPointMax();
6082 float[] max = new float[] { spMax.getXPos(), spMax.getYPos(),
6084 panel.getRotatableCanvas().setSeqMinMax(min, max);
6086 // todo: hold points list in PCAModel only
6087 panel.getPcaModel().setSequencePoints(seqPoints);
6089 panel.setSelectedDimensionIndex(viewer.getXDim(), X);
6090 panel.setSelectedDimensionIndex(viewer.getYDim(), Y);
6091 panel.setSelectedDimensionIndex(viewer.getZDim(), Z);
6093 // is this duplication needed?
6094 panel.setTop(seqPoints.size() - 1);
6095 panel.getPcaModel().setTop(seqPoints.size() - 1);
6098 * add the axes' end points for the display
6100 for (int i = 0; i < 3; i++)
6102 Axis axis = viewer.getAxis().get(i);
6103 panel.getRotatableCanvas().getAxisEndPoints()[i] = new Point(
6104 axis.getXPos(), axis.getYPos(), axis.getZPos());
6107 Desktop.addInternalFrame(panel, MessageManager.formatMessage(
6108 "label.calc_title", "PCA", modelName), 475, 450);
6110 } catch (Exception ex)
6112 Cache.log.error("Error loading PCA: " + ex.toString());
6117 * Creates a new structure viewer window
6124 protected void createStructureViewer(ViewerType viewerType,
6125 final Entry<String, StructureViewerModel> viewerData,
6126 AlignFrame af, jarInputStreamProvider jprovider)
6128 final StructureViewerModel viewerModel = viewerData.getValue();
6129 String sessionFilePath = null;
6131 if (viewerType == ViewerType.JMOL)
6133 sessionFilePath = rewriteJmolSession(viewerModel, jprovider);
6137 String viewerJarEntryName = getViewerJarEntryName(
6138 viewerModel.getViewId());
6139 sessionFilePath = copyJarEntry(jprovider, viewerJarEntryName,
6140 "viewerSession", ".tmp");
6142 final String sessionPath = sessionFilePath;
6143 final String sviewid = viewerData.getKey();
6146 SwingUtilities.invokeAndWait(new Runnable()
6151 JalviewStructureDisplayI sview = null;
6154 sview = StructureViewer.createView(viewerType, af.alignPanel,
6155 viewerModel, sessionPath, sviewid);
6156 addNewStructureViewer(sview);
6157 } catch (OutOfMemoryError ex)
6159 new OOMWarning("Restoring structure view for " + viewerType,
6160 (OutOfMemoryError) ex.getCause());
6161 if (sview != null && sview.isVisible())
6163 sview.closeViewer(false);
6164 sview.setVisible(false);
6170 } catch (InvocationTargetException | InterruptedException ex)
6172 warn("Unexpected error when opening " + viewerType
6173 + " structure viewer", ex);
6178 * Rewrites a Jmol session script, saves it to a temporary file, and returns
6179 * the path of the file. "load file" commands are rewritten to change the
6180 * original PDB file names to those created as the Jalview project is loaded.
6186 private String rewriteJmolSession(StructureViewerModel svattrib,
6187 jarInputStreamProvider jprovider)
6189 String state = svattrib.getStateData(); // Jalview < 2.9
6190 if (state == null || state.isEmpty()) // Jalview >= 2.9
6192 String jarEntryName = getViewerJarEntryName(svattrib.getViewId());
6193 state = readJarEntry(jprovider, jarEntryName);
6195 // TODO or simpler? for each key in oldFiles,
6196 // replace key.getPath() in state with oldFiles.get(key).getFilePath()
6197 // (allowing for different path escapings)
6198 StringBuilder rewritten = new StringBuilder(state.length());
6199 int cp = 0, ncp, ecp;
6200 Map<File, StructureData> oldFiles = svattrib.getFileData();
6201 while ((ncp = state.indexOf("load ", cp)) > -1)
6205 // look for next filename in load statement
6206 rewritten.append(state.substring(cp,
6207 ncp = (state.indexOf("\"", ncp + 1) + 1)));
6208 String oldfilenam = state.substring(ncp,
6209 ecp = state.indexOf("\"", ncp));
6210 // recover the new mapping data for this old filename
6211 // have to normalize filename - since Jmol and jalview do
6212 // filename translation differently.
6213 StructureData filedat = oldFiles.get(new File(oldfilenam));
6214 if (filedat == null)
6216 String reformatedOldFilename = oldfilenam.replaceAll("/", "\\\\");
6217 filedat = oldFiles.get(new File(reformatedOldFilename));
6219 rewritten.append(Platform.escapeBackslashes(filedat.getFilePath()));
6220 rewritten.append("\"");
6221 cp = ecp + 1; // advance beyond last \" and set cursor so we can
6222 // look for next file statement.
6223 } while ((ncp = state.indexOf("/*file*/", cp)) > -1);
6227 // just append rest of state
6228 rewritten.append(state.substring(cp));
6232 System.err.print("Ignoring incomplete Jmol state for PDB ids: ");
6233 rewritten = new StringBuilder(state);
6234 rewritten.append("; load append ");
6235 for (File id : oldFiles.keySet())
6237 // add pdb files that should be present in the viewer
6238 StructureData filedat = oldFiles.get(id);
6239 rewritten.append(" \"").append(filedat.getFilePath()).append("\"");
6241 rewritten.append(";");
6244 if (rewritten.length() == 0)
6248 final String history = "history = ";
6249 int historyIndex = rewritten.indexOf(history);
6250 if (historyIndex > -1)
6253 * change "history = [true|false];" to "history = [1|0];"
6255 historyIndex += history.length();
6256 String val = rewritten.substring(historyIndex, historyIndex + 5);
6257 if (val.startsWith("true"))
6259 rewritten.replace(historyIndex, historyIndex + 4, "1");
6261 else if (val.startsWith("false"))
6263 rewritten.replace(historyIndex, historyIndex + 5, "0");
6269 File tmp = File.createTempFile("viewerSession", ".tmp");
6270 try (OutputStream os = new FileOutputStream(tmp))
6272 InputStream is = new ByteArrayInputStream(
6273 rewritten.toString().getBytes());
6275 return tmp.getAbsolutePath();
6277 } catch (IOException e)
6279 Cache.log.error("Error restoring Jmol session: " + e.toString());
6285 * Populates an XML model of the feature colour scheme for one feature type
6287 * @param featureType
6291 public static Colour marshalColour(String featureType,
6292 FeatureColourI fcol)
6294 Colour col = new Colour();
6295 if (fcol.isSimpleColour())
6297 col.setRGB(Format.getHexString(fcol.getColour()));
6301 col.setRGB(Format.getHexString(fcol.getMaxColour()));
6302 col.setMin(fcol.getMin());
6303 col.setMax(fcol.getMax());
6304 col.setMinRGB(jalview.util.Format.getHexString(fcol.getMinColour()));
6305 col.setAutoScale(fcol.isAutoScaled());
6306 col.setThreshold(fcol.getThreshold());
6307 col.setColourByLabel(fcol.isColourByLabel());
6308 col.setThreshType(fcol.isAboveThreshold() ? ThresholdType.ABOVE
6309 : (fcol.isBelowThreshold() ? ThresholdType.BELOW
6310 : ThresholdType.NONE));
6311 if (fcol.isColourByAttribute())
6313 final String[] attName = fcol.getAttributeName();
6314 col.getAttributeName().add(attName[0]);
6315 if (attName.length > 1)
6317 col.getAttributeName().add(attName[1]);
6320 Color noColour = fcol.getNoColour();
6321 if (noColour == null)
6323 col.setNoValueColour(NoValueColour.NONE);
6325 else if (noColour == fcol.getMaxColour())
6327 col.setNoValueColour(NoValueColour.MAX);
6331 col.setNoValueColour(NoValueColour.MIN);
6334 col.setName(featureType);
6339 * Populates an XML model of the feature filter(s) for one feature type
6341 * @param firstMatcher
6342 * the first (or only) match condition)
6344 * remaining match conditions (if any)
6346 * if true, conditions are and-ed, else or-ed
6348 public static jalview.xml.binding.jalview.FeatureMatcherSet marshalFilter(
6349 FeatureMatcherI firstMatcher, Iterator<FeatureMatcherI> filters,
6352 jalview.xml.binding.jalview.FeatureMatcherSet result = new jalview.xml.binding.jalview.FeatureMatcherSet();
6354 if (filters.hasNext())
6359 CompoundMatcher compound = new CompoundMatcher();
6360 compound.setAnd(and);
6361 jalview.xml.binding.jalview.FeatureMatcherSet matcher1 = marshalFilter(
6362 firstMatcher, Collections.emptyIterator(), and);
6363 // compound.addMatcherSet(matcher1);
6364 compound.getMatcherSet().add(matcher1);
6365 FeatureMatcherI nextMatcher = filters.next();
6366 jalview.xml.binding.jalview.FeatureMatcherSet matcher2 = marshalFilter(
6367 nextMatcher, filters, and);
6368 // compound.addMatcherSet(matcher2);
6369 compound.getMatcherSet().add(matcher2);
6370 result.setCompoundMatcher(compound);
6375 * single condition matcher
6377 // MatchCondition matcherModel = new MatchCondition();
6378 jalview.xml.binding.jalview.FeatureMatcher matcherModel = new jalview.xml.binding.jalview.FeatureMatcher();
6379 matcherModel.setCondition(
6380 firstMatcher.getMatcher().getCondition().getStableName());
6381 matcherModel.setValue(firstMatcher.getMatcher().getPattern());
6382 if (firstMatcher.isByAttribute())
6384 matcherModel.setBy(FilterBy.BY_ATTRIBUTE);
6385 // matcherModel.setAttributeName(firstMatcher.getAttribute());
6386 String[] attName = firstMatcher.getAttribute();
6387 matcherModel.getAttributeName().add(attName[0]); // attribute
6388 if (attName.length > 1)
6390 matcherModel.getAttributeName().add(attName[1]); // sub-attribute
6393 else if (firstMatcher.isByLabel())
6395 matcherModel.setBy(FilterBy.BY_LABEL);
6397 else if (firstMatcher.isByScore())
6399 matcherModel.setBy(FilterBy.BY_SCORE);
6401 result.setMatchCondition(matcherModel);
6408 * Loads one XML model of a feature filter to a Jalview object
6410 * @param featureType
6411 * @param matcherSetModel
6414 public static FeatureMatcherSetI parseFilter(String featureType,
6415 jalview.xml.binding.jalview.FeatureMatcherSet matcherSetModel)
6417 FeatureMatcherSetI result = new FeatureMatcherSet();
6420 parseFilterConditions(result, matcherSetModel, true);
6421 } catch (IllegalStateException e)
6423 // mixing AND and OR conditions perhaps
6425 String.format("Error reading filter conditions for '%s': %s",
6426 featureType, e.getMessage()));
6427 // return as much as was parsed up to the error
6434 * Adds feature match conditions to matcherSet as unmarshalled from XML
6435 * (possibly recursively for compound conditions)
6438 * @param matcherSetModel
6440 * if true, multiple conditions are AND-ed, else they are OR-ed
6441 * @throws IllegalStateException
6442 * if AND and OR conditions are mixed
6444 protected static void parseFilterConditions(FeatureMatcherSetI matcherSet,
6445 jalview.xml.binding.jalview.FeatureMatcherSet matcherSetModel,
6448 jalview.xml.binding.jalview.FeatureMatcher mc = matcherSetModel
6449 .getMatchCondition();
6455 FilterBy filterBy = mc.getBy();
6456 Condition cond = Condition.fromString(mc.getCondition());
6457 String pattern = mc.getValue();
6458 FeatureMatcherI matchCondition = null;
6459 if (filterBy == FilterBy.BY_LABEL)
6461 matchCondition = FeatureMatcher.byLabel(cond, pattern);
6463 else if (filterBy == FilterBy.BY_SCORE)
6465 matchCondition = FeatureMatcher.byScore(cond, pattern);
6468 else if (filterBy == FilterBy.BY_ATTRIBUTE)
6470 final List<String> attributeName = mc.getAttributeName();
6471 String[] attNames = attributeName
6472 .toArray(new String[attributeName.size()]);
6473 matchCondition = FeatureMatcher.byAttribute(cond, pattern,
6478 * note this throws IllegalStateException if AND-ing to a
6479 * previously OR-ed compound condition, or vice versa
6483 matcherSet.and(matchCondition);
6487 matcherSet.or(matchCondition);
6493 * compound condition
6495 List<jalview.xml.binding.jalview.FeatureMatcherSet> matchers = matcherSetModel
6496 .getCompoundMatcher().getMatcherSet();
6497 boolean anded = matcherSetModel.getCompoundMatcher().isAnd();
6498 if (matchers.size() == 2)
6500 parseFilterConditions(matcherSet, matchers.get(0), anded);
6501 parseFilterConditions(matcherSet, matchers.get(1), anded);
6505 System.err.println("Malformed compound filter condition");
6511 * Loads one XML model of a feature colour to a Jalview object
6513 * @param colourModel
6516 public static FeatureColourI parseColour(Colour colourModel)
6518 FeatureColourI colour = null;
6520 if (colourModel.getMax() != null)
6522 Color mincol = null;
6523 Color maxcol = null;
6524 Color noValueColour = null;
6528 mincol = new Color(Integer.parseInt(colourModel.getMinRGB(), 16));
6529 maxcol = new Color(Integer.parseInt(colourModel.getRGB(), 16));
6530 } catch (Exception e)
6532 Cache.log.warn("Couldn't parse out graduated feature color.", e);
6535 NoValueColour noCol = colourModel.getNoValueColour();
6536 if (noCol == NoValueColour.MIN)
6538 noValueColour = mincol;
6540 else if (noCol == NoValueColour.MAX)
6542 noValueColour = maxcol;
6545 colour = new FeatureColour(maxcol, mincol, maxcol, noValueColour,
6546 safeFloat(colourModel.getMin()),
6547 safeFloat(colourModel.getMax()));
6548 final List<String> attributeName = colourModel.getAttributeName();
6549 String[] attributes = attributeName
6550 .toArray(new String[attributeName.size()]);
6551 if (attributes != null && attributes.length > 0)
6553 colour.setAttributeName(attributes);
6555 if (colourModel.isAutoScale() != null)
6557 colour.setAutoScaled(colourModel.isAutoScale().booleanValue());
6559 if (colourModel.isColourByLabel() != null)
6561 colour.setColourByLabel(
6562 colourModel.isColourByLabel().booleanValue());
6564 if (colourModel.getThreshold() != null)
6566 colour.setThreshold(colourModel.getThreshold().floatValue());
6568 ThresholdType ttyp = colourModel.getThreshType();
6569 if (ttyp == ThresholdType.ABOVE)
6571 colour.setAboveThreshold(true);
6573 else if (ttyp == ThresholdType.BELOW)
6575 colour.setBelowThreshold(true);
6580 Color color = new Color(Integer.parseInt(colourModel.getRGB(), 16));
6581 colour = new FeatureColour(color);