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;
57 import java.util.Locale;
59 import java.util.Map.Entry;
61 import java.util.Vector;
62 import java.util.jar.JarEntry;
63 import java.util.jar.JarInputStream;
64 import java.util.jar.JarOutputStream;
66 import javax.swing.JInternalFrame;
67 import javax.swing.SwingUtilities;
68 import javax.xml.bind.JAXBContext;
69 import javax.xml.bind.JAXBElement;
70 import javax.xml.bind.Marshaller;
71 import javax.xml.datatype.DatatypeConfigurationException;
72 import javax.xml.datatype.DatatypeFactory;
73 import javax.xml.datatype.XMLGregorianCalendar;
74 import javax.xml.stream.XMLInputFactory;
75 import javax.xml.stream.XMLStreamReader;
77 import jalview.analysis.Conservation;
78 import jalview.analysis.PCA;
79 import jalview.analysis.scoremodels.ScoreModels;
80 import jalview.analysis.scoremodels.SimilarityParams;
81 import jalview.api.FeatureColourI;
82 import jalview.api.ViewStyleI;
83 import jalview.api.analysis.ScoreModelI;
84 import jalview.api.analysis.SimilarityParamsI;
85 import jalview.api.structures.JalviewStructureDisplayI;
86 import jalview.bin.Cache;
87 import jalview.datamodel.AlignedCodonFrame;
88 import jalview.datamodel.Alignment;
89 import jalview.datamodel.AlignmentAnnotation;
90 import jalview.datamodel.AlignmentI;
91 import jalview.datamodel.DBRefEntry;
92 import jalview.datamodel.GeneLocus;
93 import jalview.datamodel.GraphLine;
94 import jalview.datamodel.PDBEntry;
95 import jalview.datamodel.Point;
96 import jalview.datamodel.RnaViewerModel;
97 import jalview.datamodel.SequenceFeature;
98 import jalview.datamodel.SequenceGroup;
99 import jalview.datamodel.SequenceI;
100 import jalview.datamodel.StructureViewerModel;
101 import jalview.datamodel.StructureViewerModel.StructureData;
102 import jalview.datamodel.features.FeatureMatcher;
103 import jalview.datamodel.features.FeatureMatcherI;
104 import jalview.datamodel.features.FeatureMatcherSet;
105 import jalview.datamodel.features.FeatureMatcherSetI;
106 import jalview.ext.varna.RnaModel;
107 import jalview.gui.AlignFrame;
108 import jalview.gui.AlignViewport;
109 import jalview.gui.AlignmentPanel;
110 import jalview.gui.AppVarna;
111 import jalview.gui.Desktop;
112 import jalview.gui.JvOptionPane;
113 import jalview.gui.OOMWarning;
114 import jalview.gui.PCAPanel;
115 import jalview.gui.PaintRefresher;
116 import jalview.gui.SplitFrame;
117 import jalview.gui.StructureViewer;
118 import jalview.gui.StructureViewer.ViewerType;
119 import jalview.gui.StructureViewerBase;
120 import jalview.gui.TreePanel;
121 import jalview.io.BackupFiles;
122 import jalview.io.DataSourceType;
123 import jalview.io.FileFormat;
124 import jalview.io.NewickFile;
125 import jalview.math.Matrix;
126 import jalview.math.MatrixI;
127 import jalview.renderer.ResidueShaderI;
128 import jalview.schemes.AnnotationColourGradient;
129 import jalview.schemes.ColourSchemeI;
130 import jalview.schemes.ColourSchemeProperty;
131 import jalview.schemes.FeatureColour;
132 import jalview.schemes.ResidueProperties;
133 import jalview.schemes.UserColourScheme;
134 import jalview.structure.StructureSelectionManager;
135 import jalview.structures.models.AAStructureBindingModel;
136 import jalview.util.Format;
137 import jalview.util.HttpUtils;
138 import jalview.util.MessageManager;
139 import jalview.util.Platform;
140 import jalview.util.StringUtils;
141 import jalview.util.jarInputStreamProvider;
142 import jalview.util.matcher.Condition;
143 import jalview.viewmodel.AlignmentViewport;
144 import jalview.viewmodel.PCAModel;
145 import jalview.viewmodel.ViewportRanges;
146 import jalview.viewmodel.seqfeatures.FeatureRendererModel;
147 import jalview.viewmodel.seqfeatures.FeatureRendererSettings;
148 import jalview.viewmodel.seqfeatures.FeaturesDisplayed;
149 import jalview.ws.jws2.Jws2Discoverer;
150 import jalview.ws.jws2.dm.AAConSettings;
151 import jalview.ws.jws2.jabaws2.Jws2Instance;
152 import jalview.ws.params.ArgumentI;
153 import jalview.ws.params.AutoCalcSetting;
154 import jalview.ws.params.WsParamSetI;
155 import jalview.xml.binding.jalview.AlcodonFrame;
156 import jalview.xml.binding.jalview.AlcodonFrame.AlcodMap;
157 import jalview.xml.binding.jalview.Annotation;
158 import jalview.xml.binding.jalview.Annotation.ThresholdLine;
159 import jalview.xml.binding.jalview.AnnotationColourScheme;
160 import jalview.xml.binding.jalview.AnnotationElement;
161 import jalview.xml.binding.jalview.DoubleMatrix;
162 import jalview.xml.binding.jalview.DoubleVector;
163 import jalview.xml.binding.jalview.Feature;
164 import jalview.xml.binding.jalview.Feature.OtherData;
165 import jalview.xml.binding.jalview.FeatureMatcherSet.CompoundMatcher;
166 import jalview.xml.binding.jalview.FilterBy;
167 import jalview.xml.binding.jalview.JalviewModel;
168 import jalview.xml.binding.jalview.JalviewModel.FeatureSettings;
169 import jalview.xml.binding.jalview.JalviewModel.FeatureSettings.Group;
170 import jalview.xml.binding.jalview.JalviewModel.FeatureSettings.Setting;
171 import jalview.xml.binding.jalview.JalviewModel.JGroup;
172 import jalview.xml.binding.jalview.JalviewModel.JSeq;
173 import jalview.xml.binding.jalview.JalviewModel.JSeq.Pdbids;
174 import jalview.xml.binding.jalview.JalviewModel.JSeq.Pdbids.StructureState;
175 import jalview.xml.binding.jalview.JalviewModel.JSeq.RnaViewer;
176 import jalview.xml.binding.jalview.JalviewModel.JSeq.RnaViewer.SecondaryStructure;
177 import jalview.xml.binding.jalview.JalviewModel.PcaViewer;
178 import jalview.xml.binding.jalview.JalviewModel.PcaViewer.Axis;
179 import jalview.xml.binding.jalview.JalviewModel.PcaViewer.SeqPointMax;
180 import jalview.xml.binding.jalview.JalviewModel.PcaViewer.SeqPointMin;
181 import jalview.xml.binding.jalview.JalviewModel.PcaViewer.SequencePoint;
182 import jalview.xml.binding.jalview.JalviewModel.Tree;
183 import jalview.xml.binding.jalview.JalviewModel.UserColours;
184 import jalview.xml.binding.jalview.JalviewModel.Viewport;
185 import jalview.xml.binding.jalview.JalviewModel.Viewport.CalcIdParam;
186 import jalview.xml.binding.jalview.JalviewModel.Viewport.HiddenColumns;
187 import jalview.xml.binding.jalview.JalviewUserColours;
188 import jalview.xml.binding.jalview.JalviewUserColours.Colour;
189 import jalview.xml.binding.jalview.MapListType.MapListFrom;
190 import jalview.xml.binding.jalview.MapListType.MapListTo;
191 import jalview.xml.binding.jalview.Mapping;
192 import jalview.xml.binding.jalview.NoValueColour;
193 import jalview.xml.binding.jalview.ObjectFactory;
194 import jalview.xml.binding.jalview.PcaDataType;
195 import jalview.xml.binding.jalview.Pdbentry.Property;
196 import jalview.xml.binding.jalview.Sequence;
197 import jalview.xml.binding.jalview.Sequence.DBRef;
198 import jalview.xml.binding.jalview.SequenceSet;
199 import jalview.xml.binding.jalview.SequenceSet.SequenceSetProperties;
200 import jalview.xml.binding.jalview.ThresholdType;
201 import jalview.xml.binding.jalview.VAMSAS;
204 * Write out the current jalview desktop state as a Jalview XML stream.
206 * Note: the vamsas objects referred to here are primitive versions of the
207 * VAMSAS project schema elements - they are not the same and most likely never
211 * @version $Revision: 1.134 $
213 public class Jalview2XML
216 // BH 2018 we add the .jvp binary extension to J2S so that
217 // it will declare that binary when we do the file save from the browser
221 Platform.addJ2SBinaryType(".jvp?");
224 private static final String VIEWER_PREFIX = "viewer_";
226 private static final String RNA_PREFIX = "rna_";
228 private static final String UTF_8 = "UTF-8";
231 * prefix for recovering datasets for alignments with multiple views where
232 * non-existent dataset IDs were written for some views
234 private static final String UNIQSEQSETID = "uniqueSeqSetId.";
236 // use this with nextCounter() to make unique names for entities
237 private int counter = 0;
240 * SequenceI reference -> XML ID string in jalview XML. Populated as XML reps
241 * of sequence objects are created.
243 IdentityHashMap<SequenceI, String> seqsToIds = null;
246 * jalview XML Sequence ID to jalview sequence object reference (both dataset
247 * and alignment sequences. Populated as XML reps of sequence objects are
250 Map<String, SequenceI> seqRefIds = null;
252 Map<String, SequenceI> incompleteSeqs = null;
254 List<SeqFref> frefedSequence = null;
256 boolean raiseGUI = true; // whether errors are raised in dialog boxes or not
259 * Map of reconstructed AlignFrame objects that appear to have come from
260 * SplitFrame objects (have a dna/protein complement view).
262 private Map<Viewport, AlignFrame> splitFrameCandidates = new HashMap<>();
265 * Map from displayed rna structure models to their saved session state jar
268 private Map<RnaModel, String> rnaSessions = new HashMap<>();
271 * A helper method for safely using the value of an optional attribute that
272 * may be null if not present in the XML. Answers the boolean value, or false
278 public static boolean safeBoolean(Boolean b)
280 return b == null ? false : b.booleanValue();
284 * A helper method for safely using the value of an optional attribute that
285 * may be null if not present in the XML. Answers the integer value, or zero
291 public static int safeInt(Integer i)
293 return i == null ? 0 : i.intValue();
297 * A helper method for safely using the value of an optional attribute that
298 * may be null if not present in the XML. Answers the float value, or zero if
304 public static float safeFloat(Float f)
306 return f == null ? 0f : f.floatValue();
310 * create/return unique hash string for sq
313 * @return new or existing unique string for sq
315 String seqHash(SequenceI sq)
317 if (seqsToIds == null)
321 if (seqsToIds.containsKey(sq))
323 return seqsToIds.get(sq);
327 // create sequential key
328 String key = "sq" + (seqsToIds.size() + 1);
329 key = makeHashCode(sq, key); // check we don't have an external reference
331 seqsToIds.put(sq, key);
338 if (seqsToIds == null)
340 seqsToIds = new IdentityHashMap<>();
342 if (seqRefIds == null)
344 seqRefIds = new HashMap<>();
346 if (incompleteSeqs == null)
348 incompleteSeqs = new HashMap<>();
350 if (frefedSequence == null)
352 frefedSequence = new ArrayList<>();
360 public Jalview2XML(boolean raiseGUI)
362 this.raiseGUI = raiseGUI;
366 * base class for resolving forward references to sequences by their ID
371 abstract class SeqFref
377 public SeqFref(String _sref, String type)
383 public String getSref()
388 public SequenceI getSrefSeq()
390 return seqRefIds.get(sref);
393 public boolean isResolvable()
395 return seqRefIds.get(sref) != null;
398 public SequenceI getSrefDatasetSeq()
400 SequenceI sq = seqRefIds.get(sref);
403 while (sq.getDatasetSequence() != null)
405 sq = sq.getDatasetSequence();
412 * @return true if the forward reference was fully resolved
414 abstract boolean resolve();
417 public String toString()
419 return type + " reference to " + sref;
424 * create forward reference for a mapping
430 public SeqFref newMappingRef(final String sref,
431 final jalview.datamodel.Mapping _jmap)
433 SeqFref fref = new SeqFref(sref, "Mapping")
435 public jalview.datamodel.Mapping jmap = _jmap;
440 SequenceI seq = getSrefDatasetSeq();
452 public SeqFref newAlcodMapRef(final String sref,
453 final AlignedCodonFrame _cf,
454 final jalview.datamodel.Mapping _jmap)
457 SeqFref fref = new SeqFref(sref, "Codon Frame")
459 AlignedCodonFrame cf = _cf;
461 public jalview.datamodel.Mapping mp = _jmap;
464 public boolean isResolvable()
466 return super.isResolvable() && mp.getTo() != null;
472 SequenceI seq = getSrefDatasetSeq();
477 cf.addMap(seq, mp.getTo(), mp.getMap());
484 public void resolveFrefedSequences()
486 Iterator<SeqFref> nextFref = frefedSequence.iterator();
487 int toresolve = frefedSequence.size();
488 int unresolved = 0, failedtoresolve = 0;
489 while (nextFref.hasNext())
491 SeqFref ref = nextFref.next();
492 if (ref.isResolvable())
504 } catch (Exception x)
507 "IMPLEMENTATION ERROR: Failed to resolve forward reference for sequence "
520 System.err.println("Jalview Project Import: There were " + unresolved
521 + " forward references left unresolved on the stack.");
523 if (failedtoresolve > 0)
525 System.err.println("SERIOUS! " + failedtoresolve
526 + " resolvable forward references failed to resolve.");
528 if (incompleteSeqs != null && incompleteSeqs.size() > 0)
531 "Jalview Project Import: There are " + incompleteSeqs.size()
532 + " sequences which may have incomplete metadata.");
533 if (incompleteSeqs.size() < 10)
535 for (SequenceI s : incompleteSeqs.values())
537 System.err.println(s.toString());
543 "Too many to report. Skipping output of incomplete sequences.");
549 * This maintains a map of viewports, the key being the seqSetId. Important to
550 * set historyItem and redoList for multiple views
552 Map<String, AlignViewport> viewportsAdded = new HashMap<>();
554 Map<String, AlignmentAnnotation> annotationIds = new HashMap<>();
556 String uniqueSetSuffix = "";
559 * List of pdbfiles added to Jar
561 List<String> pdbfiles = null;
563 // SAVES SEVERAL ALIGNMENT WINDOWS TO SAME JARFILE
564 public void saveState(File statefile)
566 FileOutputStream fos = null;
571 fos = new FileOutputStream(statefile);
573 JarOutputStream jout = new JarOutputStream(fos);
577 } catch (Exception e)
579 Cache.log.error("Couln't write Jalview state to " + statefile, e);
580 // TODO: inform user of the problem - they need to know if their data was
582 if (errorMessage == null)
584 errorMessage = "Did't write Jalview Archive to output file '"
585 + statefile + "' - See console error log for details";
589 errorMessage += "(Didn't write Jalview Archive to output file '"
600 } catch (IOException e)
610 * Writes a jalview project archive to the given Jar output stream.
614 public void saveState(JarOutputStream jout)
616 AlignFrame[] frames = Desktop.getAlignFrames();
622 saveAllFrames(Arrays.asList(frames), jout);
626 * core method for storing state for a set of AlignFrames.
629 * - frames involving all data to be exported (including containing
632 * - project output stream
634 private void saveAllFrames(List<AlignFrame> frames, JarOutputStream jout)
636 Hashtable<String, AlignFrame> dsses = new Hashtable<>();
639 * ensure cached data is clear before starting
641 // todo tidy up seqRefIds, seqsToIds initialisation / reset
643 splitFrameCandidates.clear();
648 // NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS
649 // //////////////////////////////////////////////////
651 List<String> shortNames = new ArrayList<>();
652 List<String> viewIds = new ArrayList<>();
655 for (int i = frames.size() - 1; i > -1; i--)
657 AlignFrame af = frames.get(i);
659 if (skipList != null && skipList
660 .containsKey(af.getViewport().getSequenceSetId()))
665 String shortName = makeFilename(af, shortNames);
667 int apSize = af.getAlignPanels().size();
669 for (int ap = 0; ap < apSize; ap++)
671 AlignmentPanel apanel = (AlignmentPanel) af.getAlignPanels()
673 String fileName = apSize == 1 ? shortName : ap + shortName;
674 if (!fileName.endsWith(".xml"))
676 fileName = fileName + ".xml";
679 saveState(apanel, fileName, jout, viewIds);
681 String dssid = getDatasetIdRef(
682 af.getViewport().getAlignment().getDataset());
683 if (!dsses.containsKey(dssid))
685 dsses.put(dssid, af);
690 writeDatasetFor(dsses, "" + jout.hashCode() + " " + uniqueSetSuffix,
696 } catch (Exception foo)
700 } catch (Exception ex)
702 // TODO: inform user of the problem - they need to know if their data was
704 if (errorMessage == null)
706 errorMessage = "Couldn't write Jalview Archive - see error output for details";
708 ex.printStackTrace();
713 * Generates a distinct file name, based on the title of the AlignFrame, by
714 * appending _n for increasing n until an unused name is generated. The new
715 * name (without its extension) is added to the list.
719 * @return the generated name, with .xml extension
721 protected String makeFilename(AlignFrame af, List<String> namesUsed)
723 String shortName = af.getTitle();
725 if (shortName.indexOf(File.separatorChar) > -1)
727 shortName = shortName
728 .substring(shortName.lastIndexOf(File.separatorChar) + 1);
733 while (namesUsed.contains(shortName))
735 if (shortName.endsWith("_" + (count - 1)))
737 shortName = shortName.substring(0, shortName.lastIndexOf("_"));
740 shortName = shortName.concat("_" + count);
744 namesUsed.add(shortName);
746 if (!shortName.endsWith(".xml"))
748 shortName = shortName + ".xml";
753 // USE THIS METHOD TO SAVE A SINGLE ALIGNMENT WINDOW
754 public boolean saveAlignment(AlignFrame af, String jarFile,
759 // create backupfiles object and get new temp filename destination
760 boolean doBackup = BackupFiles.getEnabled();
761 BackupFiles backupfiles = doBackup ? new BackupFiles(jarFile) : null;
762 FileOutputStream fos = new FileOutputStream(
763 doBackup ? backupfiles.getTempFilePath() : jarFile);
765 JarOutputStream jout = new JarOutputStream(fos);
766 List<AlignFrame> frames = new ArrayList<>();
768 // resolve splitframes
769 if (af.getViewport().getCodingComplement() != null)
771 frames = ((SplitFrame) af.getSplitViewContainer()).getAlignFrames();
777 saveAllFrames(frames, jout);
781 } catch (Exception foo)
785 boolean success = true;
789 backupfiles.setWriteSuccess(success);
790 success = backupfiles.rollBackupsAndRenameTempFile();
794 } catch (Exception ex)
796 errorMessage = "Couldn't Write alignment view to Jalview Archive - see error output for details";
797 ex.printStackTrace();
802 private void writeDatasetFor(Hashtable<String, AlignFrame> dsses,
803 String fileName, JarOutputStream jout)
806 for (String dssids : dsses.keySet())
808 AlignFrame _af = dsses.get(dssids);
809 String jfileName = fileName + " Dataset for " + _af.getTitle();
810 if (!jfileName.endsWith(".xml"))
812 jfileName = jfileName + ".xml";
814 saveState(_af.alignPanel, jfileName, true, jout, null);
819 * create a JalviewModel from an alignment view and marshall it to a
823 * panel to create jalview model for
825 * name of alignment panel written to output stream
832 public JalviewModel saveState(AlignmentPanel ap, String fileName,
833 JarOutputStream jout, List<String> viewIds)
835 return saveState(ap, fileName, false, jout, viewIds);
839 * create a JalviewModel from an alignment view and marshall it to a
843 * panel to create jalview model for
845 * name of alignment panel written to output stream
847 * when true, only write the dataset for the alignment, not the data
848 * associated with the view.
854 public JalviewModel saveState(AlignmentPanel ap, String fileName,
855 boolean storeDS, JarOutputStream jout, List<String> viewIds)
859 viewIds = new ArrayList<>();
864 List<UserColourScheme> userColours = new ArrayList<>();
866 AlignViewport av = ap.av;
867 ViewportRanges vpRanges = av.getRanges();
869 final ObjectFactory objectFactory = new ObjectFactory();
870 JalviewModel object = objectFactory.createJalviewModel();
871 object.setVamsasModel(new VAMSAS());
873 // object.setCreationDate(new java.util.Date(System.currentTimeMillis()));
876 GregorianCalendar c = new GregorianCalendar();
877 DatatypeFactory datatypeFactory = DatatypeFactory.newInstance();
878 XMLGregorianCalendar now = datatypeFactory.newXMLGregorianCalendar(c);// gregorianCalendar);
879 object.setCreationDate(now);
880 } catch (DatatypeConfigurationException e)
882 System.err.println("error writing date: " + e.toString());
885 jalview.bin.Cache.getDefault("VERSION", "Development Build"));
888 * rjal is full height alignment, jal is actual alignment with full metadata
889 * but excludes hidden sequences.
891 jalview.datamodel.AlignmentI rjal = av.getAlignment(), jal = rjal;
893 if (av.hasHiddenRows())
895 rjal = jal.getHiddenSequences().getFullAlignment();
898 SequenceSet vamsasSet = new SequenceSet();
900 // JalviewModelSequence jms = new JalviewModelSequence();
902 vamsasSet.setGapChar(jal.getGapCharacter() + "");
904 if (jal.getDataset() != null)
906 // dataset id is the dataset's hashcode
907 vamsasSet.setDatasetId(getDatasetIdRef(jal.getDataset()));
910 // switch jal and the dataset
911 jal = jal.getDataset();
915 if (jal.getProperties() != null)
917 for (Entry<Object, Object> prop : jal.getProperties().entrySet())
919 String key = prop.getKey().toString();
920 SequenceSetProperties ssp = new SequenceSetProperties();
922 ssp.setValue(prop.getValue().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()) && !(entry.getId().length() > 4
2079 && entry.getId().toLowerCase(Locale.ROOT)
2080 .startsWith(pdbId.toLowerCase(Locale.ROOT))))
2083 * not interested in a binding to a different PDB entry here
2087 if (matchedFile == null)
2089 matchedFile = pdbentry.getFile();
2091 else if (!matchedFile.equals(pdbentry.getFile()))
2094 "Probably lost some PDB-Sequence mappings for this structure file (which apparently has same PDB Entry code): "
2095 + pdbentry.getFile());
2099 // can get at it if the ID
2100 // match is ambiguous (e.g.
2103 for (int smap = 0; smap < viewFrame.getBinding()
2104 .getSequence()[peid].length; smap++)
2106 // if (jal.findIndex(jmol.jmb.sequence[peid][smap]) > -1)
2107 if (jds == viewFrame.getBinding().getSequence()[peid][smap])
2109 StructureState state = new StructureState();
2110 state.setVisible(true);
2111 state.setXpos(viewFrame.getX());
2112 state.setYpos(viewFrame.getY());
2113 state.setWidth(viewFrame.getWidth());
2114 state.setHeight(viewFrame.getHeight());
2115 final String viewId = viewFrame.getViewId();
2116 state.setViewId(viewId);
2117 state.setAlignwithAlignPanel(viewFrame.isUsedforaligment(ap));
2118 state.setColourwithAlignPanel(viewFrame.isUsedForColourBy(ap));
2119 state.setColourByJmol(viewFrame.isColouredByViewer());
2120 state.setType(viewFrame.getViewerType().toString());
2121 // pdb.addStructureState(state);
2122 pdb.getStructureState().add(state);
2130 * Populates the AnnotationColourScheme xml for save. This captures the
2131 * settings of the options in the 'Colour by Annotation' dialog.
2134 * @param userColours
2138 private AnnotationColourScheme constructAnnotationColours(
2139 AnnotationColourGradient acg, List<UserColourScheme> userColours,
2142 AnnotationColourScheme ac = new AnnotationColourScheme();
2143 ac.setAboveThreshold(acg.getAboveThreshold());
2144 ac.setThreshold(acg.getAnnotationThreshold());
2145 // 2.10.2 save annotationId (unique) not annotation label
2146 ac.setAnnotation(acg.getAnnotation().annotationId);
2147 if (acg.getBaseColour() instanceof UserColourScheme)
2150 setUserColourScheme(acg.getBaseColour(), userColours, jm));
2155 ColourSchemeProperty.getColourName(acg.getBaseColour()));
2158 ac.setMaxColour(acg.getMaxColour().getRGB());
2159 ac.setMinColour(acg.getMinColour().getRGB());
2160 ac.setPerSequence(acg.isSeqAssociated());
2161 ac.setPredefinedColours(acg.isPredefinedColours());
2165 private void storeAlignmentAnnotation(AlignmentAnnotation[] aa,
2166 IdentityHashMap<SequenceGroup, String> groupRefs,
2167 AlignmentViewport av, Set<String> calcIdSet, boolean storeDS,
2168 SequenceSet vamsasSet)
2171 for (int i = 0; i < aa.length; i++)
2173 Annotation an = new Annotation();
2175 AlignmentAnnotation annotation = aa[i];
2176 if (annotation.annotationId != null)
2178 annotationIds.put(annotation.annotationId, annotation);
2181 an.setId(annotation.annotationId);
2183 an.setVisible(annotation.visible);
2185 an.setDescription(annotation.description);
2187 if (annotation.sequenceRef != null)
2189 // 2.9 JAL-1781 xref on sequence id rather than name
2190 an.setSequenceRef(seqsToIds.get(annotation.sequenceRef));
2192 if (annotation.groupRef != null)
2194 String groupIdr = groupRefs.get(annotation.groupRef);
2195 if (groupIdr == null)
2197 // make a locally unique String
2198 groupRefs.put(annotation.groupRef,
2199 groupIdr = ("" + System.currentTimeMillis()
2200 + annotation.groupRef.getName()
2201 + groupRefs.size()));
2203 an.setGroupRef(groupIdr.toString());
2206 // store all visualization attributes for annotation
2207 an.setGraphHeight(annotation.graphHeight);
2208 an.setCentreColLabels(annotation.centreColLabels);
2209 an.setScaleColLabels(annotation.scaleColLabel);
2210 an.setShowAllColLabels(annotation.showAllColLabels);
2211 an.setBelowAlignment(annotation.belowAlignment);
2213 if (annotation.graph > 0)
2216 an.setGraphType(annotation.graph);
2217 an.setGraphGroup(annotation.graphGroup);
2218 if (annotation.getThreshold() != null)
2220 ThresholdLine line = new ThresholdLine();
2221 line.setLabel(annotation.getThreshold().label);
2222 line.setValue(annotation.getThreshold().value);
2223 line.setColour(annotation.getThreshold().colour.getRGB());
2224 an.setThresholdLine(line);
2232 an.setLabel(annotation.label);
2234 if (annotation == av.getAlignmentQualityAnnot()
2235 || annotation == av.getAlignmentConservationAnnotation()
2236 || annotation == av.getAlignmentConsensusAnnotation()
2237 || annotation.autoCalculated)
2239 // new way of indicating autocalculated annotation -
2240 an.setAutoCalculated(annotation.autoCalculated);
2242 if (annotation.hasScore())
2244 an.setScore(annotation.getScore());
2247 if (annotation.getCalcId() != null)
2249 calcIdSet.add(annotation.getCalcId());
2250 an.setCalcId(annotation.getCalcId());
2252 if (annotation.hasProperties())
2254 for (String pr : annotation.getProperties())
2256 jalview.xml.binding.jalview.Annotation.Property prop = new jalview.xml.binding.jalview.Annotation.Property();
2258 prop.setValue(annotation.getProperty(pr));
2259 // an.addProperty(prop);
2260 an.getProperty().add(prop);
2264 AnnotationElement ae;
2265 if (annotation.annotations != null)
2267 an.setScoreOnly(false);
2268 for (int a = 0; a < annotation.annotations.length; a++)
2270 if ((annotation == null) || (annotation.annotations[a] == null))
2275 ae = new AnnotationElement();
2276 if (annotation.annotations[a].description != null)
2278 ae.setDescription(annotation.annotations[a].description);
2280 if (annotation.annotations[a].displayCharacter != null)
2282 ae.setDisplayCharacter(
2283 annotation.annotations[a].displayCharacter);
2286 if (!Float.isNaN(annotation.annotations[a].value))
2288 ae.setValue(annotation.annotations[a].value);
2292 if (annotation.annotations[a].secondaryStructure > ' ')
2294 ae.setSecondaryStructure(
2295 annotation.annotations[a].secondaryStructure + "");
2298 if (annotation.annotations[a].colour != null
2299 && annotation.annotations[a].colour != java.awt.Color.black)
2301 ae.setColour(annotation.annotations[a].colour.getRGB());
2304 // an.addAnnotationElement(ae);
2305 an.getAnnotationElement().add(ae);
2306 if (annotation.autoCalculated)
2308 // only write one non-null entry into the annotation row -
2309 // sufficient to get the visualization attributes necessary to
2317 an.setScoreOnly(true);
2319 if (!storeDS || (storeDS && !annotation.autoCalculated))
2321 // skip autocalculated annotation - these are only provided for
2323 // vamsasSet.addAnnotation(an);
2324 vamsasSet.getAnnotation().add(an);
2330 private CalcIdParam createCalcIdParam(String calcId, AlignViewport av)
2332 AutoCalcSetting settings = av.getCalcIdSettingsFor(calcId);
2333 if (settings != null)
2335 CalcIdParam vCalcIdParam = new CalcIdParam();
2336 vCalcIdParam.setCalcId(calcId);
2337 // vCalcIdParam.addServiceURL(settings.getServiceURI());
2338 vCalcIdParam.getServiceURL().add(settings.getServiceURI());
2339 // generic URI allowing a third party to resolve another instance of the
2340 // service used for this calculation
2341 for (String url : settings.getServiceURLs())
2343 // vCalcIdParam.addServiceURL(urls);
2344 vCalcIdParam.getServiceURL().add(url);
2346 vCalcIdParam.setVersion("1.0");
2347 if (settings.getPreset() != null)
2349 WsParamSetI setting = settings.getPreset();
2350 vCalcIdParam.setName(setting.getName());
2351 vCalcIdParam.setDescription(setting.getDescription());
2355 vCalcIdParam.setName("");
2356 vCalcIdParam.setDescription("Last used parameters");
2358 // need to be able to recover 1) settings 2) user-defined presets or
2359 // recreate settings from preset 3) predefined settings provided by
2360 // service - or settings that can be transferred (or discarded)
2361 vCalcIdParam.setParameters(
2362 settings.getWsParamFile().replace("\n", "|\\n|"));
2363 vCalcIdParam.setAutoUpdate(settings.isAutoUpdate());
2364 // todo - decide if updateImmediately is needed for any projects.
2366 return vCalcIdParam;
2371 private boolean recoverCalcIdParam(CalcIdParam calcIdParam,
2374 if (calcIdParam.getVersion().equals("1.0"))
2376 final String[] calcIds = calcIdParam.getServiceURL()
2377 .toArray(new String[0]);
2378 Jws2Instance service = Jws2Discoverer.getDiscoverer()
2379 .getPreferredServiceFor(calcIds);
2380 if (service != null)
2382 WsParamSetI parmSet = null;
2385 parmSet = service.getParamStore().parseServiceParameterFile(
2386 calcIdParam.getName(), calcIdParam.getDescription(),
2388 calcIdParam.getParameters().replace("|\\n|", "\n"));
2389 } catch (IOException x)
2391 warn("Couldn't parse parameter data for "
2392 + calcIdParam.getCalcId(), x);
2395 List<ArgumentI> argList = null;
2396 if (calcIdParam.getName().length() > 0)
2398 parmSet = service.getParamStore()
2399 .getPreset(calcIdParam.getName());
2400 if (parmSet != null)
2402 // TODO : check we have a good match with settings in AACon -
2403 // otherwise we'll need to create a new preset
2408 argList = parmSet.getArguments();
2411 AAConSettings settings = new AAConSettings(
2412 calcIdParam.isAutoUpdate(), service, parmSet, argList);
2413 av.setCalcIdSettingsFor(calcIdParam.getCalcId(), settings,
2414 calcIdParam.isNeedsUpdate());
2419 warn("Cannot resolve a service for the parameters used in this project. Try configuring a JABAWS server.");
2423 throw new Error(MessageManager.formatMessage(
2424 "error.unsupported_version_calcIdparam", new Object[]
2425 { calcIdParam.toString() }));
2429 * External mapping between jalview objects and objects yielding a valid and
2430 * unique object ID string. This is null for normal Jalview project IO, but
2431 * non-null when a jalview project is being read or written as part of a
2434 IdentityHashMap jv2vobj = null;
2437 * Construct a unique ID for jvobj using either existing bindings or if none
2438 * exist, the result of the hashcode call for the object.
2441 * jalview data object
2442 * @return unique ID for referring to jvobj
2444 private String makeHashCode(Object jvobj, String altCode)
2446 if (jv2vobj != null)
2448 Object id = jv2vobj.get(jvobj);
2451 return id.toString();
2453 // check string ID mappings
2454 if (jvids2vobj != null && jvobj instanceof String)
2456 id = jvids2vobj.get(jvobj);
2460 return id.toString();
2462 // give up and warn that something has gone wrong
2463 warn("Cannot find ID for object in external mapping : " + jvobj);
2469 * return local jalview object mapped to ID, if it exists
2473 * @return null or object bound to idcode
2475 private Object retrieveExistingObj(String idcode)
2477 if (idcode != null && vobj2jv != null)
2479 return vobj2jv.get(idcode);
2485 * binding from ID strings from external mapping table to jalview data model
2488 private Hashtable vobj2jv;
2490 private Sequence createVamsasSequence(String id, SequenceI jds)
2492 return createVamsasSequence(true, id, jds, null);
2495 private Sequence createVamsasSequence(boolean recurse, String id,
2496 SequenceI jds, SequenceI parentseq)
2498 Sequence vamsasSeq = new Sequence();
2499 vamsasSeq.setId(id);
2500 vamsasSeq.setName(jds.getName());
2501 vamsasSeq.setSequence(jds.getSequenceAsString());
2502 vamsasSeq.setDescription(jds.getDescription());
2503 List<DBRefEntry> dbrefs = null;
2504 if (jds.getDatasetSequence() != null)
2506 vamsasSeq.setDsseqid(seqHash(jds.getDatasetSequence()));
2510 // seqId==dsseqid so we can tell which sequences really are
2511 // dataset sequences only
2512 vamsasSeq.setDsseqid(id);
2513 dbrefs = jds.getDBRefs();
2514 if (parentseq == null)
2521 * save any dbrefs; special subclass GeneLocus is flagged as 'locus'
2525 for (int d = 0, nd = dbrefs.size(); d < nd; d++)
2527 DBRef dbref = new DBRef();
2528 DBRefEntry ref = dbrefs.get(d);
2529 dbref.setSource(ref.getSource());
2530 dbref.setVersion(ref.getVersion());
2531 dbref.setAccessionId(ref.getAccessionId());
2532 dbref.setCanonical(ref.isCanonical());
2533 if (ref instanceof GeneLocus)
2535 dbref.setLocus(true);
2539 Mapping mp = createVamsasMapping(ref.getMap(), parentseq, jds,
2541 dbref.setMapping(mp);
2543 vamsasSeq.getDBRef().add(dbref);
2549 private Mapping createVamsasMapping(jalview.datamodel.Mapping jmp,
2550 SequenceI parentseq, SequenceI jds, boolean recurse)
2553 if (jmp.getMap() != null)
2557 jalview.util.MapList mlst = jmp.getMap();
2558 List<int[]> r = mlst.getFromRanges();
2559 for (int[] range : r)
2561 MapListFrom mfrom = new MapListFrom();
2562 mfrom.setStart(range[0]);
2563 mfrom.setEnd(range[1]);
2564 // mp.addMapListFrom(mfrom);
2565 mp.getMapListFrom().add(mfrom);
2567 r = mlst.getToRanges();
2568 for (int[] range : r)
2570 MapListTo mto = new MapListTo();
2571 mto.setStart(range[0]);
2572 mto.setEnd(range[1]);
2573 // mp.addMapListTo(mto);
2574 mp.getMapListTo().add(mto);
2576 mp.setMapFromUnit(BigInteger.valueOf(mlst.getFromRatio()));
2577 mp.setMapToUnit(BigInteger.valueOf(mlst.getToRatio()));
2578 if (jmp.getTo() != null)
2580 // MappingChoice mpc = new MappingChoice();
2582 // check/create ID for the sequence referenced by getTo()
2585 SequenceI ps = null;
2586 if (parentseq != jmp.getTo()
2587 && parentseq.getDatasetSequence() != jmp.getTo())
2589 // chaining dbref rather than a handshaking one
2590 jmpid = seqHash(ps = jmp.getTo());
2594 jmpid = seqHash(ps = parentseq);
2596 // mpc.setDseqFor(jmpid);
2597 mp.setDseqFor(jmpid);
2598 if (!seqRefIds.containsKey(jmpid))
2600 jalview.bin.Cache.log.debug("creatign new DseqFor ID");
2601 seqRefIds.put(jmpid, ps);
2605 jalview.bin.Cache.log.debug("reusing DseqFor ID");
2608 // mp.setMappingChoice(mpc);
2614 String setUserColourScheme(jalview.schemes.ColourSchemeI cs,
2615 List<UserColourScheme> userColours, JalviewModel jm)
2618 jalview.schemes.UserColourScheme ucs = (jalview.schemes.UserColourScheme) cs;
2619 boolean newucs = false;
2620 if (!userColours.contains(ucs))
2622 userColours.add(ucs);
2625 id = "ucs" + userColours.indexOf(ucs);
2628 // actually create the scheme's entry in the XML model
2629 java.awt.Color[] colours = ucs.getColours();
2630 UserColours uc = new UserColours();
2631 // UserColourScheme jbucs = new UserColourScheme();
2632 JalviewUserColours jbucs = new JalviewUserColours();
2634 for (int i = 0; i < colours.length; i++)
2636 Colour col = new Colour();
2637 col.setName(ResidueProperties.aa[i]);
2638 col.setRGB(jalview.util.Format.getHexString(colours[i]));
2639 // jbucs.addColour(col);
2640 jbucs.getColour().add(col);
2642 if (ucs.getLowerCaseColours() != null)
2644 colours = ucs.getLowerCaseColours();
2645 for (int i = 0; i < colours.length; i++)
2647 Colour col = new Colour();
2648 col.setName(ResidueProperties.aa[i].toLowerCase(Locale.ROOT));
2649 col.setRGB(jalview.util.Format.getHexString(colours[i]));
2650 // jbucs.addColour(col);
2651 jbucs.getColour().add(col);
2656 uc.setUserColourScheme(jbucs);
2657 // jm.addUserColours(uc);
2658 jm.getUserColours().add(uc);
2664 jalview.schemes.UserColourScheme getUserColourScheme(JalviewModel jm,
2667 List<UserColours> uc = jm.getUserColours();
2668 UserColours colours = null;
2670 for (int i = 0; i < uc.length; i++)
2672 if (uc[i].getId().equals(id))
2679 for (UserColours c : uc)
2681 if (c.getId().equals(id))
2688 java.awt.Color[] newColours = new java.awt.Color[24];
2690 for (int i = 0; i < 24; i++)
2692 newColours[i] = new java.awt.Color(Integer.parseInt(
2693 // colours.getUserColourScheme().getColour(i).getRGB(), 16));
2694 colours.getUserColourScheme().getColour().get(i).getRGB(),
2698 jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(
2701 if (colours.getUserColourScheme().getColour().size()/*Count()*/ > 24)
2703 newColours = new java.awt.Color[23];
2704 for (int i = 0; i < 23; i++)
2706 newColours[i] = new java.awt.Color(
2707 Integer.parseInt(colours.getUserColourScheme().getColour()
2708 .get(i + 24).getRGB(), 16));
2710 ucs.setLowerCaseColours(newColours);
2717 * contains last error message (if any) encountered by XML loader.
2719 String errorMessage = null;
2722 * flag to control whether the Jalview2XML_V1 parser should be deferred to if
2723 * exceptions are raised during project XML parsing
2725 public boolean attemptversion1parse = false;
2728 * Load a jalview project archive from a jar file
2731 * - HTTP URL or filename
2733 public AlignFrame loadJalviewAlign(final Object file)
2736 jalview.gui.AlignFrame af = null;
2740 // create list to store references for any new Jmol viewers created
2741 newStructureViewers = new Vector<>();
2742 // UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
2743 // Workaround is to make sure caller implements the JarInputStreamProvider
2745 // so we can re-open the jar input stream for each entry.
2747 jarInputStreamProvider jprovider = createjarInputStreamProvider(file);
2748 af = loadJalviewAlign(jprovider);
2751 af.setMenusForViewport();
2753 } catch (MalformedURLException e)
2755 errorMessage = "Invalid URL format for '" + file + "'";
2761 SwingUtilities.invokeAndWait(new Runnable()
2766 setLoadingFinishedForNewStructureViewers();
2769 } catch (Exception x)
2771 System.err.println("Error loading alignment: " + x.getMessage());
2777 @SuppressWarnings("unused")
2778 private jarInputStreamProvider createjarInputStreamProvider(
2779 final Object ofile) throws MalformedURLException
2782 // BH 2018 allow for bytes already attached to File object
2785 String file = (ofile instanceof File
2786 ? ((File) ofile).getCanonicalPath()
2787 : ofile.toString());
2788 byte[] bytes = Platform.isJS() ? Platform.getFileBytes((File) ofile)
2791 errorMessage = null;
2792 uniqueSetSuffix = null;
2794 viewportsAdded.clear();
2795 frefedSequence = null;
2797 if (HttpUtils.startsWithHttpOrHttps(file))
2799 url = new URL(file);
2801 final URL _url = url;
2802 return new jarInputStreamProvider()
2806 public JarInputStream getJarInputStream() throws IOException
2810 // System.out.println("Jalview2XML: opening byte jarInputStream for
2811 // bytes.length=" + bytes.length);
2812 return new JarInputStream(new ByteArrayInputStream(bytes));
2816 // System.out.println("Jalview2XML: opening url jarInputStream for "
2818 return new JarInputStream(_url.openStream());
2822 // System.out.println("Jalview2XML: opening file jarInputStream for
2824 return new JarInputStream(new FileInputStream(file));
2829 public String getFilename()
2834 } catch (IOException e)
2836 e.printStackTrace();
2842 * Recover jalview session from a jalview project archive. Caller may
2843 * initialise uniqueSetSuffix, seqRefIds, viewportsAdded and frefedSequence
2844 * themselves. Any null fields will be initialised with default values,
2845 * non-null fields are left alone.
2850 public AlignFrame loadJalviewAlign(final jarInputStreamProvider jprovider)
2852 errorMessage = null;
2853 if (uniqueSetSuffix == null)
2855 uniqueSetSuffix = System.currentTimeMillis() % 100000 + "";
2857 if (seqRefIds == null)
2861 AlignFrame af = null, _af = null;
2862 IdentityHashMap<AlignmentI, AlignmentI> importedDatasets = new IdentityHashMap<>();
2863 Map<String, AlignFrame> gatherToThisFrame = new HashMap<>();
2864 final String file = jprovider.getFilename();
2867 JarInputStream jin = null;
2868 JarEntry jarentry = null;
2873 jin = jprovider.getJarInputStream();
2874 for (int i = 0; i < entryCount; i++)
2876 jarentry = jin.getNextJarEntry();
2879 if (jarentry != null && jarentry.getName().endsWith(".xml"))
2881 JAXBContext jc = JAXBContext
2882 .newInstance("jalview.xml.binding.jalview");
2883 XMLStreamReader streamReader = XMLInputFactory.newInstance()
2884 .createXMLStreamReader(jin);
2885 javax.xml.bind.Unmarshaller um = jc.createUnmarshaller();
2886 JAXBElement<JalviewModel> jbe = um.unmarshal(streamReader,
2887 JalviewModel.class);
2888 JalviewModel object = jbe.getValue();
2890 if (true) // !skipViewport(object))
2892 _af = loadFromObject(object, file, true, jprovider);
2893 if (_af != null && object.getViewport().size() > 0)
2894 // getJalviewModelSequence().getViewportCount() > 0)
2898 // store a reference to the first view
2901 if (_af.getViewport().isGatherViewsHere())
2903 // if this is a gathered view, keep its reference since
2904 // after gathering views, only this frame will remain
2906 gatherToThisFrame.put(_af.getViewport().getSequenceSetId(),
2909 // Save dataset to register mappings once all resolved
2910 importedDatasets.put(
2911 af.getViewport().getAlignment().getDataset(),
2912 af.getViewport().getAlignment().getDataset());
2917 else if (jarentry != null)
2919 // Some other file here.
2922 } while (jarentry != null);
2924 resolveFrefedSequences();
2925 } catch (IOException ex)
2927 ex.printStackTrace();
2928 errorMessage = "Couldn't locate Jalview XML file : " + file;
2930 "Exception whilst loading jalview XML file : " + ex + "\n");
2931 } catch (Exception ex)
2933 System.err.println("Parsing as Jalview Version 2 file failed.");
2934 ex.printStackTrace(System.err);
2935 if (attemptversion1parse)
2937 // used to attempt to parse as V1 castor-generated xml
2939 if (Desktop.instance != null)
2941 Desktop.instance.stopLoading();
2945 System.out.println("Successfully loaded archive file");
2948 ex.printStackTrace();
2951 "Exception whilst loading jalview XML file : " + ex + "\n");
2952 } catch (OutOfMemoryError e)
2954 // Don't use the OOM Window here
2955 errorMessage = "Out of memory loading jalview XML file";
2956 System.err.println("Out of memory whilst loading jalview XML file");
2957 e.printStackTrace();
2961 * Regather multiple views (with the same sequence set id) to the frame (if
2962 * any) that is flagged as the one to gather to, i.e. convert them to tabbed
2963 * views instead of separate frames. Note this doesn't restore a state where
2964 * some expanded views in turn have tabbed views - the last "first tab" read
2965 * in will play the role of gatherer for all.
2967 for (AlignFrame fr : gatherToThisFrame.values())
2969 Desktop.instance.gatherViews(fr);
2972 restoreSplitFrames();
2973 for (AlignmentI ds : importedDatasets.keySet())
2975 if (ds.getCodonFrames() != null)
2977 StructureSelectionManager
2978 .getStructureSelectionManager(Desktop.instance)
2979 .registerMappings(ds.getCodonFrames());
2982 if (errorMessage != null)
2987 if (Desktop.instance != null)
2989 Desktop.instance.stopLoading();
2996 * Try to reconstruct and display SplitFrame windows, where each contains
2997 * complementary dna and protein alignments. Done by pairing up AlignFrame
2998 * objects (created earlier) which have complementary viewport ids associated.
3000 protected void restoreSplitFrames()
3002 List<SplitFrame> gatherTo = new ArrayList<>();
3003 List<AlignFrame> addedToSplitFrames = new ArrayList<>();
3004 Map<String, AlignFrame> dna = new HashMap<>();
3007 * Identify the DNA alignments
3009 for (Entry<Viewport, AlignFrame> candidate : splitFrameCandidates
3012 AlignFrame af = candidate.getValue();
3013 if (af.getViewport().getAlignment().isNucleotide())
3015 dna.put(candidate.getKey().getId(), af);
3020 * Try to match up the protein complements
3022 for (Entry<Viewport, AlignFrame> candidate : splitFrameCandidates
3025 AlignFrame af = candidate.getValue();
3026 if (!af.getViewport().getAlignment().isNucleotide())
3028 String complementId = candidate.getKey().getComplementId();
3029 // only non-null complements should be in the Map
3030 if (complementId != null && dna.containsKey(complementId))
3032 final AlignFrame dnaFrame = dna.get(complementId);
3033 SplitFrame sf = createSplitFrame(dnaFrame, af);
3034 addedToSplitFrames.add(dnaFrame);
3035 addedToSplitFrames.add(af);
3036 dnaFrame.setMenusForViewport();
3037 af.setMenusForViewport();
3038 if (af.getViewport().isGatherViewsHere())
3047 * Open any that we failed to pair up (which shouldn't happen!) as
3048 * standalone AlignFrame's.
3050 for (Entry<Viewport, AlignFrame> candidate : splitFrameCandidates
3053 AlignFrame af = candidate.getValue();
3054 if (!addedToSplitFrames.contains(af))
3056 Viewport view = candidate.getKey();
3057 Desktop.addInternalFrame(af, view.getTitle(),
3058 safeInt(view.getWidth()), safeInt(view.getHeight()));
3059 af.setMenusForViewport();
3060 System.err.println("Failed to restore view " + view.getTitle()
3061 + " to split frame");
3066 * Gather back into tabbed views as flagged.
3068 for (SplitFrame sf : gatherTo)
3070 Desktop.instance.gatherViews(sf);
3073 splitFrameCandidates.clear();
3077 * Construct and display one SplitFrame holding DNA and protein alignments.
3080 * @param proteinFrame
3083 protected SplitFrame createSplitFrame(AlignFrame dnaFrame,
3084 AlignFrame proteinFrame)
3086 SplitFrame splitFrame = new SplitFrame(dnaFrame, proteinFrame);
3087 String title = MessageManager.getString("label.linked_view_title");
3088 int width = (int) dnaFrame.getBounds().getWidth();
3089 int height = (int) (dnaFrame.getBounds().getHeight()
3090 + proteinFrame.getBounds().getHeight() + 50);
3093 * SplitFrame location is saved to both enclosed frames
3095 splitFrame.setLocation(dnaFrame.getX(), dnaFrame.getY());
3096 Desktop.addInternalFrame(splitFrame, title, width, height);
3099 * And compute cDNA consensus (couldn't do earlier with consensus as
3100 * mappings were not yet present)
3102 proteinFrame.getViewport().alignmentChanged(proteinFrame.alignPanel);
3108 * check errorMessage for a valid error message and raise an error box in the
3109 * GUI or write the current errorMessage to stderr and then clear the error
3112 protected void reportErrors()
3114 reportErrors(false);
3117 protected void reportErrors(final boolean saving)
3119 if (errorMessage != null)
3121 final String finalErrorMessage = errorMessage;
3124 javax.swing.SwingUtilities.invokeLater(new Runnable()
3129 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
3131 "Error " + (saving ? "saving" : "loading")
3133 JvOptionPane.WARNING_MESSAGE);
3139 System.err.println("Problem loading Jalview file: " + errorMessage);
3142 errorMessage = null;
3145 Map<String, String> alreadyLoadedPDB = new HashMap<>();
3148 * when set, local views will be updated from view stored in JalviewXML
3149 * Currently (28th Sep 2008) things will go horribly wrong in vamsas document
3150 * sync if this is set to true.
3152 private final boolean updateLocalViews = false;
3155 * Returns the path to a temporary file holding the PDB file for the given PDB
3156 * id. The first time of asking, searches for a file of that name in the
3157 * Jalview project jar, and copies it to a new temporary file. Any repeat
3158 * requests just return the path to the file previously created.
3164 String loadPDBFile(jarInputStreamProvider jprovider, String pdbId,
3167 if (alreadyLoadedPDB.containsKey(pdbId))
3169 return alreadyLoadedPDB.get(pdbId).toString();
3172 String tempFile = copyJarEntry(jprovider, pdbId, "jalview_pdb",
3174 if (tempFile != null)
3176 alreadyLoadedPDB.put(pdbId, tempFile);
3182 * Copies the jar entry of given name to a new temporary file and returns the
3183 * path to the file, or null if the entry is not found.
3186 * @param jarEntryName
3188 * a prefix for the temporary file name, must be at least three
3190 * @param suffixModel
3191 * null or original file - so new file can be given the same suffix
3195 protected String copyJarEntry(jarInputStreamProvider jprovider,
3196 String jarEntryName, String prefix, String suffixModel)
3198 String suffix = ".tmp";
3199 if (suffixModel == null)
3201 suffixModel = jarEntryName;
3203 int sfpos = suffixModel.lastIndexOf(".");
3204 if (sfpos > -1 && sfpos < (suffixModel.length() - 1))
3206 suffix = "." + suffixModel.substring(sfpos + 1);
3209 try (JarInputStream jin = jprovider.getJarInputStream())
3211 JarEntry entry = null;
3214 entry = jin.getNextJarEntry();
3215 } while (entry != null && !entry.getName().equals(jarEntryName));
3219 // in = new BufferedReader(new InputStreamReader(jin, UTF_8));
3220 File outFile = File.createTempFile(prefix, suffix);
3221 outFile.deleteOnExit();
3222 try (OutputStream os = new FileOutputStream(outFile))
3226 String t = outFile.getAbsolutePath();
3231 warn("Couldn't find entry in Jalview Jar for " + jarEntryName);
3233 } catch (Exception ex)
3235 ex.printStackTrace();
3241 private class JvAnnotRow
3243 public JvAnnotRow(int i, AlignmentAnnotation jaa)
3250 * persisted version of annotation row from which to take vis properties
3252 public jalview.datamodel.AlignmentAnnotation template;
3255 * original position of the annotation row in the alignment
3261 * Load alignment frame from jalview XML DOM object
3263 * @param jalviewModel
3266 * filename source string
3267 * @param loadTreesAndStructures
3268 * when false only create Viewport
3270 * data source provider
3271 * @return alignment frame created from view stored in DOM
3273 AlignFrame loadFromObject(JalviewModel jalviewModel, String file,
3274 boolean loadTreesAndStructures, jarInputStreamProvider jprovider)
3276 SequenceSet vamsasSet = jalviewModel.getVamsasModel().getSequenceSet()
3278 List<Sequence> vamsasSeqs = vamsasSet.getSequence();
3280 // JalviewModelSequence jms = object.getJalviewModelSequence();
3282 // Viewport view = (jms.getViewportCount() > 0) ? jms.getViewport(0)
3284 Viewport view = (jalviewModel.getViewport().size() > 0)
3285 ? jalviewModel.getViewport().get(0)
3288 // ////////////////////////////////
3289 // INITIALISE ALIGNMENT SEQUENCESETID AND VIEWID
3292 // If we just load in the same jar file again, the sequenceSetId
3293 // will be the same, and we end up with multiple references
3294 // to the same sequenceSet. We must modify this id on load
3295 // so that each load of the file gives a unique id
3298 * used to resolve correct alignment dataset for alignments with multiple
3301 String uniqueSeqSetId = null;
3302 String viewId = null;
3305 uniqueSeqSetId = view.getSequenceSetId() + uniqueSetSuffix;
3306 viewId = (view.getId() == null ? null
3307 : view.getId() + uniqueSetSuffix);
3310 // ////////////////////////////////
3313 List<SequenceI> hiddenSeqs = null;
3315 List<SequenceI> tmpseqs = new ArrayList<>();
3317 boolean multipleView = false;
3318 SequenceI referenceseqForView = null;
3319 // JSeq[] jseqs = object.getJalviewModelSequence().getJSeq();
3320 List<JSeq> jseqs = jalviewModel.getJSeq();
3321 int vi = 0; // counter in vamsasSeq array
3322 for (int i = 0; i < jseqs.size(); i++)
3324 JSeq jseq = jseqs.get(i);
3325 String seqId = jseq.getId();
3327 SequenceI tmpSeq = seqRefIds.get(seqId);
3330 if (!incompleteSeqs.containsKey(seqId))
3332 // may not need this check, but keep it for at least 2.9,1 release
3333 if (tmpSeq.getStart() != jseq.getStart()
3334 || tmpSeq.getEnd() != jseq.getEnd())
3336 System.err.println(String.format(
3337 "Warning JAL-2154 regression: updating start/end for sequence %s from %d/%d to %d/%d",
3338 tmpSeq.getName(), tmpSeq.getStart(), tmpSeq.getEnd(),
3339 jseq.getStart(), jseq.getEnd()));
3344 incompleteSeqs.remove(seqId);
3346 if (vamsasSeqs.size() > vi
3347 && vamsasSeqs.get(vi).getId().equals(seqId))
3349 // most likely we are reading a dataset XML document so
3350 // update from vamsasSeq section of XML for this sequence
3351 tmpSeq.setName(vamsasSeqs.get(vi).getName());
3352 tmpSeq.setDescription(vamsasSeqs.get(vi).getDescription());
3353 tmpSeq.setSequence(vamsasSeqs.get(vi).getSequence());
3358 // reading multiple views, so vamsasSeq set is a subset of JSeq
3359 multipleView = true;
3361 tmpSeq.setStart(jseq.getStart());
3362 tmpSeq.setEnd(jseq.getEnd());
3363 tmpseqs.add(tmpSeq);
3367 Sequence vamsasSeq = vamsasSeqs.get(vi);
3368 tmpSeq = new jalview.datamodel.Sequence(vamsasSeq.getName(),
3369 vamsasSeq.getSequence());
3370 tmpSeq.setDescription(vamsasSeq.getDescription());
3371 tmpSeq.setStart(jseq.getStart());
3372 tmpSeq.setEnd(jseq.getEnd());
3373 tmpSeq.setVamsasId(uniqueSetSuffix + seqId);
3374 seqRefIds.put(vamsasSeq.getId(), tmpSeq);
3375 tmpseqs.add(tmpSeq);
3379 if (safeBoolean(jseq.isViewreference()))
3381 referenceseqForView = tmpseqs.get(tmpseqs.size() - 1);
3384 if (jseq.isHidden() != null && jseq.isHidden().booleanValue())
3386 if (hiddenSeqs == null)
3388 hiddenSeqs = new ArrayList<>();
3391 hiddenSeqs.add(tmpSeq);
3396 // Create the alignment object from the sequence set
3397 // ///////////////////////////////
3398 SequenceI[] orderedSeqs = tmpseqs
3399 .toArray(new SequenceI[tmpseqs.size()]);
3401 AlignmentI al = null;
3402 // so we must create or recover the dataset alignment before going further
3403 // ///////////////////////////////
3404 if (vamsasSet.getDatasetId() == null || vamsasSet.getDatasetId() == "")
3406 // older jalview projects do not have a dataset - so creat alignment and
3408 al = new Alignment(orderedSeqs);
3409 al.setDataset(null);
3413 boolean isdsal = jalviewModel.getViewport().isEmpty();
3416 // we are importing a dataset record, so
3417 // recover reference to an alignment already materialsed as dataset
3418 al = getDatasetFor(vamsasSet.getDatasetId());
3422 // materialse the alignment
3423 al = new Alignment(orderedSeqs);
3427 addDatasetRef(vamsasSet.getDatasetId(), al);
3430 // finally, verify all data in vamsasSet is actually present in al
3431 // passing on flag indicating if it is actually a stored dataset
3432 recoverDatasetFor(vamsasSet, al, isdsal, uniqueSeqSetId);
3435 if (referenceseqForView != null)
3437 al.setSeqrep(referenceseqForView);
3439 // / Add the alignment properties
3440 for (int i = 0; i < vamsasSet.getSequenceSetProperties().size(); i++)
3442 SequenceSetProperties ssp = vamsasSet.getSequenceSetProperties()
3444 al.setProperty(ssp.getKey(), ssp.getValue());
3447 // ///////////////////////////////
3449 Hashtable pdbloaded = new Hashtable(); // TODO nothing writes to this??
3452 // load sequence features, database references and any associated PDB
3453 // structures for the alignment
3455 // prior to 2.10, this part would only be executed the first time a
3456 // sequence was encountered, but not afterwards.
3457 // now, for 2.10 projects, this is also done if the xml doc includes
3458 // dataset sequences not actually present in any particular view.
3460 for (int i = 0; i < vamsasSeqs.size(); i++)
3462 JSeq jseq = jseqs.get(i);
3463 if (jseq.getFeatures().size() > 0)
3465 List<Feature> features = jseq.getFeatures();
3466 for (int f = 0; f < features.size(); f++)
3468 Feature feat = features.get(f);
3469 SequenceFeature sf = new SequenceFeature(feat.getType(),
3470 feat.getDescription(), feat.getBegin(), feat.getEnd(),
3471 safeFloat(feat.getScore()), feat.getFeatureGroup());
3472 sf.setStatus(feat.getStatus());
3475 * load any feature attributes - include map-valued attributes
3477 Map<String, Map<String, String>> mapAttributes = new HashMap<>();
3478 for (int od = 0; od < feat.getOtherData().size(); od++)
3480 OtherData keyValue = feat.getOtherData().get(od);
3481 String attributeName = keyValue.getKey();
3482 String attributeValue = keyValue.getValue();
3483 if (attributeName.startsWith("LINK"))
3485 sf.addLink(attributeValue);
3489 String subAttribute = keyValue.getKey2();
3490 if (subAttribute == null)
3492 // simple string-valued attribute
3493 sf.setValue(attributeName, attributeValue);
3497 // attribute 'key' has sub-attribute 'key2'
3498 if (!mapAttributes.containsKey(attributeName))
3500 mapAttributes.put(attributeName, new HashMap<>());
3502 mapAttributes.get(attributeName).put(subAttribute,
3507 for (Entry<String, Map<String, String>> mapAttribute : mapAttributes
3510 sf.setValue(mapAttribute.getKey(), mapAttribute.getValue());
3513 // adds feature to datasequence's feature set (since Jalview 2.10)
3514 al.getSequenceAt(i).addSequenceFeature(sf);
3517 if (vamsasSeqs.get(i).getDBRef().size() > 0)
3519 // adds dbrefs to datasequence's set (since Jalview 2.10)
3521 al.getSequenceAt(i).getDatasetSequence() == null
3522 ? al.getSequenceAt(i)
3523 : al.getSequenceAt(i).getDatasetSequence(),
3526 if (jseq.getPdbids().size() > 0)
3528 List<Pdbids> ids = jseq.getPdbids();
3529 for (int p = 0; p < ids.size(); p++)
3531 Pdbids pdbid = ids.get(p);
3532 jalview.datamodel.PDBEntry entry = new jalview.datamodel.PDBEntry();
3533 entry.setId(pdbid.getId());
3534 if (pdbid.getType() != null)
3536 if (PDBEntry.Type.getType(pdbid.getType()) != null)
3538 entry.setType(PDBEntry.Type.getType(pdbid.getType()));
3542 entry.setType(PDBEntry.Type.FILE);
3545 // jprovider is null when executing 'New View'
3546 if (pdbid.getFile() != null && jprovider != null)
3548 if (!pdbloaded.containsKey(pdbid.getFile()))
3550 entry.setFile(loadPDBFile(jprovider, pdbid.getId(),
3555 entry.setFile(pdbloaded.get(pdbid.getId()).toString());
3559 if (pdbid.getPdbentryItem() != null)
3561 for (PdbentryItem item : pdbid.getPdbentryItem())
3563 for (Property pr : item.getProperty())
3565 entry.setProperty(pr.getName(), pr.getValue());
3570 for (Property prop : pdbid.getProperty())
3572 entry.setProperty(prop.getName(), prop.getValue());
3574 StructureSelectionManager
3575 .getStructureSelectionManager(Desktop.instance)
3576 .registerPDBEntry(entry);
3577 // adds PDBEntry to datasequence's set (since Jalview 2.10)
3578 if (al.getSequenceAt(i).getDatasetSequence() != null)
3580 al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
3584 al.getSequenceAt(i).addPDBId(entry);
3589 } // end !multipleview
3591 // ///////////////////////////////
3592 // LOAD SEQUENCE MAPPINGS
3594 if (vamsasSet.getAlcodonFrame().size() > 0)
3596 // TODO Potentially this should only be done once for all views of an
3598 List<AlcodonFrame> alc = vamsasSet.getAlcodonFrame();
3599 for (int i = 0; i < alc.size(); i++)
3601 AlignedCodonFrame cf = new AlignedCodonFrame();
3602 if (alc.get(i).getAlcodMap().size() > 0)
3604 List<AlcodMap> maps = alc.get(i).getAlcodMap();
3605 for (int m = 0; m < maps.size(); m++)
3607 AlcodMap map = maps.get(m);
3608 SequenceI dnaseq = seqRefIds.get(map.getDnasq());
3610 jalview.datamodel.Mapping mapping = null;
3611 // attach to dna sequence reference.
3612 if (map.getMapping() != null)
3614 mapping = addMapping(map.getMapping());
3615 if (dnaseq != null && mapping.getTo() != null)
3617 cf.addMap(dnaseq, mapping.getTo(), mapping.getMap());
3623 .add(newAlcodMapRef(map.getDnasq(), cf, mapping));
3627 al.addCodonFrame(cf);
3632 // ////////////////////////////////
3634 List<JvAnnotRow> autoAlan = new ArrayList<>();
3637 * store any annotations which forward reference a group's ID
3639 Map<String, List<AlignmentAnnotation>> groupAnnotRefs = new Hashtable<>();
3641 if (vamsasSet.getAnnotation().size()/*Count()*/ > 0)
3643 List<Annotation> an = vamsasSet.getAnnotation();
3645 for (int i = 0; i < an.size(); i++)
3647 Annotation annotation = an.get(i);
3650 * test if annotation is automatically calculated for this view only
3652 boolean autoForView = false;
3653 if (annotation.getLabel().equals("Quality")
3654 || annotation.getLabel().equals("Conservation")
3655 || annotation.getLabel().equals("Consensus"))
3657 // Kludge for pre 2.5 projects which lacked the autocalculated flag
3659 // JAXB has no has() test; schema defaults value to false
3660 // if (!annotation.hasAutoCalculated())
3662 // annotation.setAutoCalculated(true);
3665 if (autoForView || annotation.isAutoCalculated())
3667 // remove ID - we don't recover annotation from other views for
3668 // view-specific annotation
3669 annotation.setId(null);
3672 // set visibility for other annotation in this view
3673 String annotationId = annotation.getId();
3674 if (annotationId != null && annotationIds.containsKey(annotationId))
3676 AlignmentAnnotation jda = annotationIds.get(annotationId);
3677 // in principle Visible should always be true for annotation displayed
3678 // in multiple views
3679 if (annotation.isVisible() != null)
3681 jda.visible = annotation.isVisible();
3684 al.addAnnotation(jda);
3688 // Construct new annotation from model.
3689 List<AnnotationElement> ae = annotation.getAnnotationElement();
3690 jalview.datamodel.Annotation[] anot = null;
3691 java.awt.Color firstColour = null;
3693 if (!annotation.isScoreOnly())
3695 anot = new jalview.datamodel.Annotation[al.getWidth()];
3696 for (int aa = 0; aa < ae.size() && aa < anot.length; aa++)
3698 AnnotationElement annElement = ae.get(aa);
3699 anpos = annElement.getPosition();
3701 if (anpos >= anot.length)
3706 float value = safeFloat(annElement.getValue());
3707 anot[anpos] = new jalview.datamodel.Annotation(
3708 annElement.getDisplayCharacter(),
3709 annElement.getDescription(),
3710 (annElement.getSecondaryStructure() == null
3711 || annElement.getSecondaryStructure()
3715 .getSecondaryStructure()
3718 anot[anpos].colour = new Color(safeInt(annElement.getColour()));
3719 if (firstColour == null)
3721 firstColour = anot[anpos].colour;
3725 jalview.datamodel.AlignmentAnnotation jaa = null;
3727 if (annotation.isGraph())
3729 float llim = 0, hlim = 0;
3730 // if (autoForView || an[i].isAutoCalculated()) {
3733 jaa = new jalview.datamodel.AlignmentAnnotation(
3734 annotation.getLabel(), annotation.getDescription(), anot,
3735 llim, hlim, safeInt(annotation.getGraphType()));
3737 jaa.graphGroup = safeInt(annotation.getGraphGroup());
3738 jaa._linecolour = firstColour;
3739 if (annotation.getThresholdLine() != null)
3741 jaa.setThreshold(new jalview.datamodel.GraphLine(
3742 safeFloat(annotation.getThresholdLine().getValue()),
3743 annotation.getThresholdLine().getLabel(),
3744 new java.awt.Color(safeInt(
3745 annotation.getThresholdLine().getColour()))));
3747 if (autoForView || annotation.isAutoCalculated())
3749 // Hardwire the symbol display line to ensure that labels for
3750 // histograms are displayed
3756 jaa = new jalview.datamodel.AlignmentAnnotation(
3757 annotation.getLabel(), annotation.getDescription(), anot);
3758 jaa._linecolour = firstColour;
3760 // register new annotation
3761 if (annotation.getId() != null)
3763 annotationIds.put(annotation.getId(), jaa);
3764 jaa.annotationId = annotation.getId();
3766 // recover sequence association
3767 String sequenceRef = annotation.getSequenceRef();
3768 if (sequenceRef != null)
3770 // from 2.9 sequenceRef is to sequence id (JAL-1781)
3771 SequenceI sequence = seqRefIds.get(sequenceRef);
3772 if (sequence == null)
3774 // in pre-2.9 projects sequence ref is to sequence name
3775 sequence = al.findName(sequenceRef);
3777 if (sequence != null)
3779 jaa.createSequenceMapping(sequence, 1, true);
3780 sequence.addAlignmentAnnotation(jaa);
3783 // and make a note of any group association
3784 if (annotation.getGroupRef() != null
3785 && annotation.getGroupRef().length() > 0)
3787 List<jalview.datamodel.AlignmentAnnotation> aal = groupAnnotRefs
3788 .get(annotation.getGroupRef());
3791 aal = new ArrayList<>();
3792 groupAnnotRefs.put(annotation.getGroupRef(), aal);
3797 if (annotation.getScore() != null)
3799 jaa.setScore(annotation.getScore().doubleValue());
3801 if (annotation.isVisible() != null)
3803 jaa.visible = annotation.isVisible().booleanValue();
3806 if (annotation.isCentreColLabels() != null)
3808 jaa.centreColLabels = annotation.isCentreColLabels()
3812 if (annotation.isScaleColLabels() != null)
3814 jaa.scaleColLabel = annotation.isScaleColLabels().booleanValue();
3816 if (annotation.isAutoCalculated())
3818 // newer files have an 'autoCalculated' flag and store calculation
3819 // state in viewport properties
3820 jaa.autoCalculated = true; // means annotation will be marked for
3821 // update at end of load.
3823 if (annotation.getGraphHeight() != null)
3825 jaa.graphHeight = annotation.getGraphHeight().intValue();
3827 jaa.belowAlignment = annotation.isBelowAlignment();
3828 jaa.setCalcId(annotation.getCalcId());
3829 if (annotation.getProperty().size() > 0)
3831 for (Annotation.Property prop : annotation.getProperty())
3833 jaa.setProperty(prop.getName(), prop.getValue());
3836 if (jaa.autoCalculated)
3838 autoAlan.add(new JvAnnotRow(i, jaa));
3841 // if (!autoForView)
3843 // add autocalculated group annotation and any user created annotation
3845 al.addAnnotation(jaa);
3849 // ///////////////////////
3851 // Create alignment markup and styles for this view
3852 if (jalviewModel.getJGroup().size() > 0)
3854 List<JGroup> groups = jalviewModel.getJGroup();
3855 boolean addAnnotSchemeGroup = false;
3856 for (int i = 0; i < groups.size(); i++)
3858 JGroup jGroup = groups.get(i);
3859 ColourSchemeI cs = null;
3860 if (jGroup.getColour() != null)
3862 if (jGroup.getColour().startsWith("ucs"))
3864 cs = getUserColourScheme(jalviewModel, jGroup.getColour());
3866 else if (jGroup.getColour().equals("AnnotationColourGradient")
3867 && jGroup.getAnnotationColours() != null)
3869 addAnnotSchemeGroup = true;
3873 cs = ColourSchemeProperty.getColourScheme(null, al,
3874 jGroup.getColour());
3877 int pidThreshold = safeInt(jGroup.getPidThreshold());
3879 Vector<SequenceI> seqs = new Vector<>();
3881 for (int s = 0; s < jGroup.getSeq().size(); s++)
3883 String seqId = jGroup.getSeq().get(s);
3884 SequenceI ts = seqRefIds.get(seqId);
3888 seqs.addElement(ts);
3892 if (seqs.size() < 1)
3897 SequenceGroup sg = new SequenceGroup(seqs, jGroup.getName(), cs,
3898 safeBoolean(jGroup.isDisplayBoxes()),
3899 safeBoolean(jGroup.isDisplayText()),
3900 safeBoolean(jGroup.isColourText()),
3901 safeInt(jGroup.getStart()), safeInt(jGroup.getEnd()));
3902 sg.getGroupColourScheme().setThreshold(pidThreshold, true);
3903 sg.getGroupColourScheme()
3904 .setConservationInc(safeInt(jGroup.getConsThreshold()));
3905 sg.setOutlineColour(new Color(safeInt(jGroup.getOutlineColour())));
3907 sg.textColour = new Color(safeInt(jGroup.getTextCol1()));
3908 sg.textColour2 = new Color(safeInt(jGroup.getTextCol2()));
3909 sg.setShowNonconserved(safeBoolean(jGroup.isShowUnconserved()));
3910 sg.thresholdTextColour = safeInt(jGroup.getTextColThreshold());
3911 // attributes with a default in the schema are never null
3912 sg.setShowConsensusHistogram(jGroup.isShowConsensusHistogram());
3913 sg.setshowSequenceLogo(jGroup.isShowSequenceLogo());
3914 sg.setNormaliseSequenceLogo(jGroup.isNormaliseSequenceLogo());
3915 sg.setIgnoreGapsConsensus(jGroup.isIgnoreGapsinConsensus());
3916 if (jGroup.getConsThreshold() != null
3917 && jGroup.getConsThreshold().intValue() != 0)
3919 Conservation c = new Conservation("All", sg.getSequences(null), 0,
3922 c.verdict(false, 25);
3923 sg.cs.setConservation(c);
3926 if (jGroup.getId() != null && groupAnnotRefs.size() > 0)
3928 // re-instate unique group/annotation row reference
3929 List<AlignmentAnnotation> jaal = groupAnnotRefs
3930 .get(jGroup.getId());
3933 for (AlignmentAnnotation jaa : jaal)
3936 if (jaa.autoCalculated)
3938 // match up and try to set group autocalc alignment row for this
3940 if (jaa.label.startsWith("Consensus for "))
3942 sg.setConsensus(jaa);
3944 // match up and try to set group autocalc alignment row for this
3946 if (jaa.label.startsWith("Conservation for "))
3948 sg.setConservationRow(jaa);
3955 if (addAnnotSchemeGroup)
3957 // reconstruct the annotation colourscheme
3959 constructAnnotationColour(jGroup.getAnnotationColours(),
3960 null, al, jalviewModel, false));
3966 // only dataset in this model, so just return.
3969 // ///////////////////////////////
3972 AlignFrame af = null;
3973 AlignViewport av = null;
3974 // now check to see if we really need to create a new viewport.
3975 if (multipleView && viewportsAdded.size() == 0)
3977 // We recovered an alignment for which a viewport already exists.
3978 // TODO: fix up any settings necessary for overlaying stored state onto
3979 // state recovered from another document. (may not be necessary).
3980 // we may need a binding from a viewport in memory to one recovered from
3982 // and then recover its containing af to allow the settings to be applied.
3983 // TODO: fix for vamsas demo
3985 "About to recover a viewport for existing alignment: Sequence set ID is "
3987 Object seqsetobj = retrieveExistingObj(uniqueSeqSetId);
3988 if (seqsetobj != null)
3990 if (seqsetobj instanceof String)
3992 uniqueSeqSetId = (String) seqsetobj;
3994 "Recovered extant sequence set ID mapping for ID : New Sequence set ID is "
4000 "Warning : Collision between sequence set ID string and existing jalview object mapping.");
4006 * indicate that annotation colours are applied across all groups (pre
4007 * Jalview 2.8.1 behaviour)
4009 boolean doGroupAnnColour = Jalview2XML.isVersionStringLaterThan("2.8.1",
4010 jalviewModel.getVersion());
4012 AlignmentPanel ap = null;
4013 boolean isnewview = true;
4016 // Check to see if this alignment already has a view id == viewId
4017 jalview.gui.AlignmentPanel views[] = Desktop
4018 .getAlignmentPanels(uniqueSeqSetId);
4019 if (views != null && views.length > 0)
4021 for (int v = 0; v < views.length; v++)
4023 if (views[v].av.getViewId().equalsIgnoreCase(viewId))
4025 // recover the existing alignpanel, alignframe, viewport
4026 af = views[v].alignFrame;
4029 // TODO: could even skip resetting view settings if we don't want to
4030 // change the local settings from other jalview processes
4039 af = loadViewport(file, jseqs, hiddenSeqs, al, jalviewModel, view,
4040 uniqueSeqSetId, viewId, autoAlan);
4041 av = af.getViewport();
4046 * Load any trees, PDB structures and viewers
4048 * Not done if flag is false (when this method is used for New View)
4050 if (loadTreesAndStructures)
4052 loadTrees(jalviewModel, view, af, av, ap);
4053 loadPCAViewers(jalviewModel, ap);
4054 loadPDBStructures(jprovider, jseqs, af, ap);
4055 loadRnaViewers(jprovider, jseqs, ap);
4057 // and finally return.
4062 * Instantiate and link any saved RNA (Varna) viewers. The state of the Varna
4063 * panel is restored from separate jar entries, two (gapped and trimmed) per
4064 * sequence and secondary structure.
4066 * Currently each viewer shows just one sequence and structure (gapped and
4067 * trimmed), however this method is designed to support multiple sequences or
4068 * structures in viewers if wanted in future.
4074 private void loadRnaViewers(jarInputStreamProvider jprovider,
4075 List<JSeq> jseqs, AlignmentPanel ap)
4078 * scan the sequences for references to viewers; create each one the first
4079 * time it is referenced, add Rna models to existing viewers
4081 for (JSeq jseq : jseqs)
4083 for (int i = 0; i < jseq.getRnaViewer().size(); i++)
4085 RnaViewer viewer = jseq.getRnaViewer().get(i);
4086 AppVarna appVarna = findOrCreateVarnaViewer(viewer, uniqueSetSuffix,
4089 for (int j = 0; j < viewer.getSecondaryStructure().size(); j++)
4091 SecondaryStructure ss = viewer.getSecondaryStructure().get(j);
4092 SequenceI seq = seqRefIds.get(jseq.getId());
4093 AlignmentAnnotation ann = this.annotationIds
4094 .get(ss.getAnnotationId());
4097 * add the structure to the Varna display (with session state copied
4098 * from the jar to a temporary file)
4100 boolean gapped = safeBoolean(ss.isGapped());
4101 String rnaTitle = ss.getTitle();
4102 String sessionState = ss.getViewerState();
4103 String tempStateFile = copyJarEntry(jprovider, sessionState,
4105 RnaModel rna = new RnaModel(rnaTitle, ann, seq, null, gapped);
4106 appVarna.addModelSession(rna, rnaTitle, tempStateFile);
4108 appVarna.setInitialSelection(safeInt(viewer.getSelectedRna()));
4114 * Locate and return an already instantiated matching AppVarna, or create one
4118 * @param viewIdSuffix
4122 protected AppVarna findOrCreateVarnaViewer(RnaViewer viewer,
4123 String viewIdSuffix, AlignmentPanel ap)
4126 * on each load a suffix is appended to the saved viewId, to avoid conflicts
4127 * if load is repeated
4129 String postLoadId = viewer.getViewId() + viewIdSuffix;
4130 for (JInternalFrame frame : getAllFrames())
4132 if (frame instanceof AppVarna)
4134 AppVarna varna = (AppVarna) frame;
4135 if (postLoadId.equals(varna.getViewId()))
4137 // this viewer is already instantiated
4138 // could in future here add ap as another 'parent' of the
4139 // AppVarna window; currently just 1-to-many
4146 * viewer not found - make it
4148 RnaViewerModel model = new RnaViewerModel(postLoadId, viewer.getTitle(),
4149 safeInt(viewer.getXpos()), safeInt(viewer.getYpos()),
4150 safeInt(viewer.getWidth()), safeInt(viewer.getHeight()),
4151 safeInt(viewer.getDividerLocation()));
4152 AppVarna varna = new AppVarna(model, ap);
4158 * Load any saved trees
4166 protected void loadTrees(JalviewModel jm, Viewport view, AlignFrame af,
4167 AlignViewport av, AlignmentPanel ap)
4169 // TODO result of automated refactoring - are all these parameters needed?
4172 for (int t = 0; t < jm.getTree().size(); t++)
4175 Tree tree = jm.getTree().get(t);
4177 TreePanel tp = (TreePanel) retrieveExistingObj(tree.getId());
4180 tp = af.showNewickTree(new NewickFile(tree.getNewick()),
4181 tree.getTitle(), safeInt(tree.getWidth()),
4182 safeInt(tree.getHeight()), safeInt(tree.getXpos()),
4183 safeInt(tree.getYpos()));
4184 if (tree.getId() != null)
4186 // perhaps bind the tree id to something ?
4191 // update local tree attributes ?
4192 // TODO: should check if tp has been manipulated by user - if so its
4193 // settings shouldn't be modified
4194 tp.setTitle(tree.getTitle());
4195 tp.setBounds(new Rectangle(safeInt(tree.getXpos()),
4196 safeInt(tree.getYpos()), safeInt(tree.getWidth()),
4197 safeInt(tree.getHeight())));
4198 tp.setViewport(av); // af.viewport;
4199 // TODO: verify 'associate with all views' works still
4200 tp.getTreeCanvas().setViewport(av); // af.viewport;
4201 tp.getTreeCanvas().setAssociatedPanel(ap); // af.alignPanel;
4203 tp.getTreeCanvas().setApplyToAllViews(tree.isLinkToAllViews());
4206 warn("There was a problem recovering stored Newick tree: \n"
4207 + tree.getNewick());
4211 tp.fitToWindow.setState(safeBoolean(tree.isFitToWindow()));
4212 tp.fitToWindow_actionPerformed(null);
4214 if (tree.getFontName() != null)
4217 new Font(tree.getFontName(), safeInt(tree.getFontStyle()),
4218 safeInt(tree.getFontSize())));
4223 new Font(view.getFontName(), safeInt(view.getFontStyle()),
4224 safeInt(view.getFontSize())));
4227 tp.showPlaceholders(safeBoolean(tree.isMarkUnlinked()));
4228 tp.showBootstrap(safeBoolean(tree.isShowBootstrap()));
4229 tp.showDistances(safeBoolean(tree.isShowDistances()));
4231 tp.getTreeCanvas().setThreshold(safeFloat(tree.getThreshold()));
4233 if (safeBoolean(tree.isCurrentTree()))
4235 af.getViewport().setCurrentTree(tp.getTree());
4239 } catch (Exception ex)
4241 ex.printStackTrace();
4246 * Load and link any saved structure viewers.
4253 protected void loadPDBStructures(jarInputStreamProvider jprovider,
4254 List<JSeq> jseqs, AlignFrame af, AlignmentPanel ap)
4257 * Run through all PDB ids on the alignment, and collect mappings between
4258 * distinct view ids and all sequences referring to that view.
4260 Map<String, StructureViewerModel> structureViewers = new LinkedHashMap<>();
4262 for (int i = 0; i < jseqs.size(); i++)
4264 JSeq jseq = jseqs.get(i);
4265 if (jseq.getPdbids().size() > 0)
4267 List<Pdbids> ids = jseq.getPdbids();
4268 for (int p = 0; p < ids.size(); p++)
4270 Pdbids pdbid = ids.get(p);
4271 final int structureStateCount = pdbid.getStructureState().size();
4272 for (int s = 0; s < structureStateCount; s++)
4274 // check to see if we haven't already created this structure view
4275 final StructureState structureState = pdbid.getStructureState()
4277 String sviewid = (structureState.getViewId() == null) ? null
4278 : structureState.getViewId() + uniqueSetSuffix;
4279 jalview.datamodel.PDBEntry jpdb = new jalview.datamodel.PDBEntry();
4280 // Originally : pdbid.getFile()
4281 // : TODO: verify external PDB file recovery still works in normal
4282 // jalview project load
4284 loadPDBFile(jprovider, pdbid.getId(), pdbid.getFile()));
4285 jpdb.setId(pdbid.getId());
4287 int x = safeInt(structureState.getXpos());
4288 int y = safeInt(structureState.getYpos());
4289 int width = safeInt(structureState.getWidth());
4290 int height = safeInt(structureState.getHeight());
4292 // Probably don't need to do this anymore...
4293 // Desktop.desktop.getComponentAt(x, y);
4294 // TODO: NOW: check that this recovers the PDB file correctly.
4295 String pdbFile = loadPDBFile(jprovider, pdbid.getId(),
4297 jalview.datamodel.SequenceI seq = seqRefIds
4298 .get(jseq.getId() + "");
4299 if (sviewid == null)
4301 sviewid = "_jalview_pre2_4_" + x + "," + y + "," + width + ","
4304 if (!structureViewers.containsKey(sviewid))
4306 String viewerType = structureState.getType();
4307 if (viewerType == null) // pre Jalview 2.9
4309 viewerType = ViewerType.JMOL.toString();
4311 structureViewers.put(sviewid,
4312 new StructureViewerModel(x, y, width, height, false,
4313 false, true, structureState.getViewId(),
4315 // Legacy pre-2.7 conversion JAL-823 :
4316 // do not assume any view has to be linked for colour by
4320 // assemble String[] { pdb files }, String[] { id for each
4321 // file }, orig_fileloc, SequenceI[][] {{ seqs_file 1 }, {
4322 // seqs_file 2}, boolean[] {
4323 // linkAlignPanel,superposeWithAlignpanel}} from hash
4324 StructureViewerModel jmoldat = structureViewers.get(sviewid);
4325 jmoldat.setAlignWithPanel(jmoldat.isAlignWithPanel()
4326 || structureState.isAlignwithAlignPanel());
4329 * Default colour by linked panel to false if not specified (e.g.
4330 * for pre-2.7 projects)
4332 boolean colourWithAlignPanel = jmoldat.isColourWithAlignPanel();
4333 colourWithAlignPanel |= structureState.isColourwithAlignPanel();
4334 jmoldat.setColourWithAlignPanel(colourWithAlignPanel);
4337 * Default colour by viewer to true if not specified (e.g. for
4340 boolean colourByViewer = jmoldat.isColourByViewer();
4341 colourByViewer &= structureState.isColourByJmol();
4342 jmoldat.setColourByViewer(colourByViewer);
4344 if (jmoldat.getStateData().length() < structureState.getValue()
4345 /*Content()*/.length())
4347 jmoldat.setStateData(structureState.getValue());// Content());
4349 if (pdbid.getFile() != null)
4351 File mapkey = new File(pdbid.getFile());
4352 StructureData seqstrmaps = jmoldat.getFileData().get(mapkey);
4353 if (seqstrmaps == null)
4355 jmoldat.getFileData().put(mapkey,
4356 seqstrmaps = jmoldat.new StructureData(pdbFile,
4359 if (!seqstrmaps.getSeqList().contains(seq))
4361 seqstrmaps.getSeqList().add(seq);
4367 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");
4374 // Instantiate the associated structure views
4375 for (Entry<String, StructureViewerModel> entry : structureViewers
4380 createOrLinkStructureViewer(entry, af, ap, jprovider);
4381 } catch (Exception e)
4384 "Error loading structure viewer: " + e.getMessage());
4385 // failed - try the next one
4397 protected void createOrLinkStructureViewer(
4398 Entry<String, StructureViewerModel> viewerData, AlignFrame af,
4399 AlignmentPanel ap, jarInputStreamProvider jprovider)
4401 final StructureViewerModel stateData = viewerData.getValue();
4404 * Search for any viewer windows already open from other alignment views
4405 * that exactly match the stored structure state
4407 StructureViewerBase comp = findMatchingViewer(viewerData);
4411 linkStructureViewer(ap, comp, stateData);
4415 String type = stateData.getType();
4418 ViewerType viewerType = ViewerType.valueOf(type);
4419 createStructureViewer(viewerType, viewerData, af, jprovider);
4420 } catch (IllegalArgumentException | NullPointerException e)
4422 // TODO JAL-3619 show error dialog / offer an alternative viewer
4423 Cache.log.error("Invalid structure viewer type: " + type);
4428 * Generates a name for the entry in the project jar file to hold state
4429 * information for a structure viewer
4434 protected String getViewerJarEntryName(String viewId)
4436 return VIEWER_PREFIX + viewId;
4440 * Returns any open frame that matches given structure viewer data. The match
4441 * is based on the unique viewId, or (for older project versions) the frame's
4447 protected StructureViewerBase findMatchingViewer(
4448 Entry<String, StructureViewerModel> viewerData)
4450 final String sviewid = viewerData.getKey();
4451 final StructureViewerModel svattrib = viewerData.getValue();
4452 StructureViewerBase comp = null;
4453 JInternalFrame[] frames = getAllFrames();
4454 for (JInternalFrame frame : frames)
4456 if (frame instanceof StructureViewerBase)
4459 * Post jalview 2.4 schema includes structure view id
4461 if (sviewid != null && ((StructureViewerBase) frame).getViewId()
4464 comp = (StructureViewerBase) frame;
4465 break; // break added in 2.9
4468 * Otherwise test for matching position and size of viewer frame
4470 else if (frame.getX() == svattrib.getX()
4471 && frame.getY() == svattrib.getY()
4472 && frame.getHeight() == svattrib.getHeight()
4473 && frame.getWidth() == svattrib.getWidth())
4475 comp = (StructureViewerBase) frame;
4476 // no break in faint hope of an exact match on viewId
4484 * Link an AlignmentPanel to an existing structure viewer.
4489 * @param useinViewerSuperpos
4490 * @param usetoColourbyseq
4491 * @param viewerColouring
4493 protected void linkStructureViewer(AlignmentPanel ap,
4494 StructureViewerBase viewer, StructureViewerModel stateData)
4496 // NOTE: if the jalview project is part of a shared session then
4497 // view synchronization should/could be done here.
4499 final boolean useinViewerSuperpos = stateData.isAlignWithPanel();
4500 final boolean usetoColourbyseq = stateData.isColourWithAlignPanel();
4501 final boolean viewerColouring = stateData.isColourByViewer();
4502 Map<File, StructureData> oldFiles = stateData.getFileData();
4505 * Add mapping for sequences in this view to an already open viewer
4507 final AAStructureBindingModel binding = viewer.getBinding();
4508 for (File id : oldFiles.keySet())
4510 // add this and any other pdb files that should be present in the
4512 StructureData filedat = oldFiles.get(id);
4513 String pdbFile = filedat.getFilePath();
4514 SequenceI[] seq = filedat.getSeqList().toArray(new SequenceI[0]);
4515 binding.getSsm().setMapping(seq, null, pdbFile, DataSourceType.FILE,
4517 binding.addSequenceForStructFile(pdbFile, seq);
4519 // and add the AlignmentPanel's reference to the view panel
4520 viewer.addAlignmentPanel(ap);
4521 if (useinViewerSuperpos)
4523 viewer.useAlignmentPanelForSuperposition(ap);
4527 viewer.excludeAlignmentPanelForSuperposition(ap);
4529 if (usetoColourbyseq)
4531 viewer.useAlignmentPanelForColourbyseq(ap, !viewerColouring);
4535 viewer.excludeAlignmentPanelForColourbyseq(ap);
4540 * Get all frames within the Desktop.
4544 protected JInternalFrame[] getAllFrames()
4546 JInternalFrame[] frames = null;
4547 // TODO is this necessary - is it safe - risk of hanging?
4552 frames = Desktop.desktop.getAllFrames();
4553 } catch (ArrayIndexOutOfBoundsException e)
4555 // occasional No such child exceptions are thrown here...
4559 } catch (InterruptedException f)
4563 } while (frames == null);
4568 * Answers true if 'version' is equal to or later than 'supported', where each
4569 * is formatted as major/minor versions like "2.8.3" or "2.3.4b1" for bugfix
4570 * changes. Development and test values for 'version' are leniently treated
4574 * - minimum version we are comparing against
4576 * - version of data being processsed
4579 public static boolean isVersionStringLaterThan(String supported,
4582 if (supported == null || version == null
4583 || version.equalsIgnoreCase("DEVELOPMENT BUILD")
4584 || version.equalsIgnoreCase("Test")
4585 || version.equalsIgnoreCase("AUTOMATED BUILD"))
4587 System.err.println("Assuming project file with "
4588 + (version == null ? "null" : version)
4589 + " is compatible with Jalview version " + supported);
4594 return StringUtils.compareVersions(version, supported, "b") >= 0;
4598 Vector<JalviewStructureDisplayI> newStructureViewers = null;
4600 protected void addNewStructureViewer(JalviewStructureDisplayI sview)
4602 if (newStructureViewers != null)
4604 sview.getBinding().setFinishedLoadingFromArchive(false);
4605 newStructureViewers.add(sview);
4609 protected void setLoadingFinishedForNewStructureViewers()
4611 if (newStructureViewers != null)
4613 for (JalviewStructureDisplayI sview : newStructureViewers)
4615 sview.getBinding().setFinishedLoadingFromArchive(true);
4617 newStructureViewers.clear();
4618 newStructureViewers = null;
4622 AlignFrame loadViewport(String file, List<JSeq> JSEQ,
4623 List<SequenceI> hiddenSeqs, AlignmentI al, JalviewModel jm,
4624 Viewport view, String uniqueSeqSetId, String viewId,
4625 List<JvAnnotRow> autoAlan)
4627 AlignFrame af = null;
4628 af = new AlignFrame(al, safeInt(view.getWidth()),
4629 safeInt(view.getHeight()), uniqueSeqSetId, viewId)
4633 // protected void processKeyEvent(java.awt.event.KeyEvent e) {
4634 // System.out.println("Jalview2XML AF " + e);
4635 // super.processKeyEvent(e);
4642 af.setFileName(file, FileFormat.Jalview);
4644 final AlignViewport viewport = af.getViewport();
4645 for (int i = 0; i < JSEQ.size(); i++)
4647 int colour = safeInt(JSEQ.get(i).getColour());
4648 viewport.setSequenceColour(viewport.getAlignment().getSequenceAt(i),
4654 viewport.setColourByReferenceSeq(true);
4655 viewport.setDisplayReferenceSeq(true);
4658 viewport.setGatherViewsHere(safeBoolean(view.isGatheredViews()));
4660 if (view.getSequenceSetId() != null)
4662 AlignmentViewport av = viewportsAdded.get(uniqueSeqSetId);
4664 viewport.setSequenceSetId(uniqueSeqSetId);
4667 // propagate shared settings to this new view
4668 viewport.setHistoryList(av.getHistoryList());
4669 viewport.setRedoList(av.getRedoList());
4673 viewportsAdded.put(uniqueSeqSetId, viewport);
4675 // TODO: check if this method can be called repeatedly without
4676 // side-effects if alignpanel already registered.
4677 PaintRefresher.Register(af.alignPanel, uniqueSeqSetId);
4679 // apply Hidden regions to view.
4680 if (hiddenSeqs != null)
4682 for (int s = 0; s < JSEQ.size(); s++)
4684 SequenceGroup hidden = new SequenceGroup();
4685 boolean isRepresentative = false;
4686 for (int r = 0; r < JSEQ.get(s).getHiddenSequences().size(); r++)
4688 isRepresentative = true;
4689 SequenceI sequenceToHide = al
4690 .getSequenceAt(JSEQ.get(s).getHiddenSequences().get(r));
4691 hidden.addSequence(sequenceToHide, false);
4692 // remove from hiddenSeqs list so we don't try to hide it twice
4693 hiddenSeqs.remove(sequenceToHide);
4695 if (isRepresentative)
4697 SequenceI representativeSequence = al.getSequenceAt(s);
4698 hidden.addSequence(representativeSequence, false);
4699 viewport.hideRepSequences(representativeSequence, hidden);
4703 SequenceI[] hseqs = hiddenSeqs
4704 .toArray(new SequenceI[hiddenSeqs.size()]);
4705 viewport.hideSequence(hseqs);
4708 // recover view properties and display parameters
4710 viewport.setShowAnnotation(safeBoolean(view.isShowAnnotation()));
4711 viewport.setAbovePIDThreshold(safeBoolean(view.isPidSelected()));
4712 final int pidThreshold = safeInt(view.getPidThreshold());
4713 viewport.setThreshold(pidThreshold);
4715 viewport.setColourText(safeBoolean(view.isShowColourText()));
4717 viewport.setConservationSelected(
4718 safeBoolean(view.isConservationSelected()));
4719 viewport.setIncrement(safeInt(view.getConsThreshold()));
4720 viewport.setShowJVSuffix(safeBoolean(view.isShowFullId()));
4721 viewport.setRightAlignIds(safeBoolean(view.isRightAlignIds()));
4722 viewport.setFont(new Font(view.getFontName(),
4723 safeInt(view.getFontStyle()), safeInt(view.getFontSize())),
4725 ViewStyleI vs = viewport.getViewStyle();
4726 vs.setScaleProteinAsCdna(view.isScaleProteinAsCdna());
4727 viewport.setViewStyle(vs);
4728 // TODO: allow custom charWidth/Heights to be restored by updating them
4729 // after setting font - which means set above to false
4730 viewport.setRenderGaps(safeBoolean(view.isRenderGaps()));
4731 viewport.setWrapAlignment(safeBoolean(view.isWrapAlignment()));
4732 viewport.setShowAnnotation(safeBoolean(view.isShowAnnotation()));
4734 viewport.setShowBoxes(safeBoolean(view.isShowBoxes()));
4736 viewport.setShowText(safeBoolean(view.isShowText()));
4738 viewport.setTextColour(new Color(safeInt(view.getTextCol1())));
4739 viewport.setTextColour2(new Color(safeInt(view.getTextCol2())));
4740 viewport.setThresholdTextColour(safeInt(view.getTextColThreshold()));
4741 viewport.setShowUnconserved(view.isShowUnconserved());
4742 viewport.getRanges().setStartRes(safeInt(view.getStartRes()));
4744 if (view.getViewName() != null)
4746 viewport.setViewName(view.getViewName());
4747 af.setInitialTabVisible();
4749 af.setBounds(safeInt(view.getXpos()), safeInt(view.getYpos()),
4750 safeInt(view.getWidth()), safeInt(view.getHeight()));
4751 // startSeq set in af.alignPanel.updateLayout below
4752 af.alignPanel.updateLayout();
4753 ColourSchemeI cs = null;
4754 // apply colourschemes
4755 if (view.getBgColour() != null)
4757 if (view.getBgColour().startsWith("ucs"))
4759 cs = getUserColourScheme(jm, view.getBgColour());
4761 else if (view.getBgColour().startsWith("Annotation"))
4763 AnnotationColourScheme viewAnnColour = view.getAnnotationColours();
4764 cs = constructAnnotationColour(viewAnnColour, af, al, jm, true);
4771 cs = ColourSchemeProperty.getColourScheme(af.getViewport(), al,
4772 view.getBgColour());
4777 * turn off 'alignment colour applies to all groups'
4778 * while restoring global colour scheme
4780 viewport.setColourAppliesToAllGroups(false);
4781 viewport.setGlobalColourScheme(cs);
4782 viewport.getResidueShading().setThreshold(pidThreshold,
4783 view.isIgnoreGapsinConsensus());
4784 viewport.getResidueShading()
4785 .setConsensus(viewport.getSequenceConsensusHash());
4786 if (safeBoolean(view.isConservationSelected()) && cs != null)
4788 viewport.getResidueShading()
4789 .setConservationInc(safeInt(view.getConsThreshold()));
4791 af.changeColour(cs);
4792 viewport.setColourAppliesToAllGroups(true);
4794 viewport.setShowSequenceFeatures(
4795 safeBoolean(view.isShowSequenceFeatures()));
4797 viewport.setCentreColumnLabels(view.isCentreColumnLabels());
4798 viewport.setIgnoreGapsConsensus(view.isIgnoreGapsinConsensus(), null);
4799 viewport.setFollowHighlight(view.isFollowHighlight());
4800 viewport.followSelection = view.isFollowSelection();
4801 viewport.setShowConsensusHistogram(view.isShowConsensusHistogram());
4802 viewport.setShowSequenceLogo(view.isShowSequenceLogo());
4803 viewport.setNormaliseSequenceLogo(view.isNormaliseSequenceLogo());
4804 viewport.setShowDBRefs(safeBoolean(view.isShowDbRefTooltip()));
4805 viewport.setShowNPFeats(safeBoolean(view.isShowNPfeatureTooltip()));
4806 viewport.setShowGroupConsensus(view.isShowGroupConsensus());
4807 viewport.setShowGroupConservation(view.isShowGroupConservation());
4808 viewport.setShowComplementFeatures(view.isShowComplementFeatures());
4809 viewport.setShowComplementFeaturesOnTop(
4810 view.isShowComplementFeaturesOnTop());
4812 // recover feature settings
4813 if (jm.getFeatureSettings() != null)
4815 FeatureRendererModel fr = af.alignPanel.getSeqPanel().seqCanvas
4816 .getFeatureRenderer();
4817 FeaturesDisplayed fdi;
4818 viewport.setFeaturesDisplayed(fdi = new FeaturesDisplayed());
4819 String[] renderOrder = new String[jm.getFeatureSettings().getSetting()
4821 Map<String, FeatureColourI> featureColours = new Hashtable<>();
4822 Map<String, Float> featureOrder = new Hashtable<>();
4824 for (int fs = 0; fs < jm.getFeatureSettings().getSetting()
4827 Setting setting = jm.getFeatureSettings().getSetting().get(fs);
4828 String featureType = setting.getType();
4831 * restore feature filters (if any)
4833 jalview.xml.binding.jalview.FeatureMatcherSet filters = setting
4835 if (filters != null)
4837 FeatureMatcherSetI filter = Jalview2XML.parseFilter(featureType,
4839 if (!filter.isEmpty())
4841 fr.setFeatureFilter(featureType, filter);
4846 * restore feature colour scheme
4848 Color maxColour = new Color(setting.getColour());
4849 if (setting.getMincolour() != null)
4852 * minColour is always set unless a simple colour
4853 * (including for colour by label though it doesn't use it)
4855 Color minColour = new Color(setting.getMincolour().intValue());
4856 Color noValueColour = minColour;
4857 NoValueColour noColour = setting.getNoValueColour();
4858 if (noColour == NoValueColour.NONE)
4860 noValueColour = null;
4862 else if (noColour == NoValueColour.MAX)
4864 noValueColour = maxColour;
4866 float min = safeFloat(safeFloat(setting.getMin()));
4867 float max = setting.getMax() == null ? 1f
4868 : setting.getMax().floatValue();
4869 FeatureColourI gc = new FeatureColour(maxColour, minColour,
4870 maxColour, noValueColour, min, max);
4871 if (setting.getAttributeName().size() > 0)
4873 gc.setAttributeName(setting.getAttributeName().toArray(
4874 new String[setting.getAttributeName().size()]));
4876 if (setting.getThreshold() != null)
4878 gc.setThreshold(setting.getThreshold().floatValue());
4879 int threshstate = safeInt(setting.getThreshstate());
4880 // -1 = None, 0 = Below, 1 = Above threshold
4881 if (threshstate == 0)
4883 gc.setBelowThreshold(true);
4885 else if (threshstate == 1)
4887 gc.setAboveThreshold(true);
4890 gc.setAutoScaled(true); // default
4891 if (setting.isAutoScale() != null)
4893 gc.setAutoScaled(setting.isAutoScale());
4895 if (setting.isColourByLabel() != null)
4897 gc.setColourByLabel(setting.isColourByLabel());
4899 // and put in the feature colour table.
4900 featureColours.put(featureType, gc);
4904 featureColours.put(featureType, new FeatureColour(maxColour));
4906 renderOrder[fs] = featureType;
4907 if (setting.getOrder() != null)
4909 featureOrder.put(featureType, setting.getOrder().floatValue());
4913 featureOrder.put(featureType, Float.valueOf(
4914 fs / jm.getFeatureSettings().getSetting().size()));
4916 if (safeBoolean(setting.isDisplay()))
4918 fdi.setVisible(featureType);
4921 Map<String, Boolean> fgtable = new Hashtable<>();
4922 for (int gs = 0; gs < jm.getFeatureSettings().getGroup().size(); gs++)
4924 Group grp = jm.getFeatureSettings().getGroup().get(gs);
4925 fgtable.put(grp.getName(), Boolean.valueOf(grp.isDisplay()));
4927 // FeatureRendererSettings frs = new FeatureRendererSettings(renderOrder,
4928 // fgtable, featureColours, jms.getFeatureSettings().hasTransparency() ?
4929 // jms.getFeatureSettings().getTransparency() : 0.0, featureOrder);
4930 FeatureRendererSettings frs = new FeatureRendererSettings(renderOrder,
4931 fgtable, featureColours, 1.0f, featureOrder);
4932 fr.transferSettings(frs);
4935 if (view.getHiddenColumns().size() > 0)
4937 for (int c = 0; c < view.getHiddenColumns().size(); c++)
4939 final HiddenColumns hc = view.getHiddenColumns().get(c);
4940 viewport.hideColumns(safeInt(hc.getStart()),
4941 safeInt(hc.getEnd()) /* +1 */);
4944 if (view.getCalcIdParam() != null)
4946 for (CalcIdParam calcIdParam : view.getCalcIdParam())
4948 if (calcIdParam != null)
4950 if (recoverCalcIdParam(calcIdParam, viewport))
4955 warn("Couldn't recover parameters for "
4956 + calcIdParam.getCalcId());
4961 af.setMenusFromViewport(viewport);
4962 af.setTitle(view.getTitle());
4963 // TODO: we don't need to do this if the viewport is aready visible.
4965 * Add the AlignFrame to the desktop (it may be 'gathered' later), unless it
4966 * has a 'cdna/protein complement' view, in which case save it in order to
4967 * populate a SplitFrame once all views have been read in.
4969 String complementaryViewId = view.getComplementId();
4970 if (complementaryViewId == null)
4972 Desktop.addInternalFrame(af, view.getTitle(),
4973 safeInt(view.getWidth()), safeInt(view.getHeight()));
4974 // recompute any autoannotation
4975 af.alignPanel.updateAnnotation(false, true);
4976 reorderAutoannotation(af, al, autoAlan);
4977 af.alignPanel.alignmentChanged();
4981 splitFrameCandidates.put(view, af);
4987 * Reads saved data to restore Colour by Annotation settings
4989 * @param viewAnnColour
4993 * @param checkGroupAnnColour
4996 private ColourSchemeI constructAnnotationColour(
4997 AnnotationColourScheme viewAnnColour, AlignFrame af,
4998 AlignmentI al, JalviewModel model, boolean checkGroupAnnColour)
5000 boolean propagateAnnColour = false;
5001 AlignmentI annAlignment = af != null ? af.getViewport().getAlignment()
5003 if (checkGroupAnnColour && al.getGroups() != null
5004 && al.getGroups().size() > 0)
5006 // pre 2.8.1 behaviour
5007 // check to see if we should transfer annotation colours
5008 propagateAnnColour = true;
5009 for (SequenceGroup sg : al.getGroups())
5011 if (sg.getColourScheme() instanceof AnnotationColourGradient)
5013 propagateAnnColour = false;
5019 * 2.10.2- : saved annotationId is AlignmentAnnotation.annotationId
5021 String annotationId = viewAnnColour.getAnnotation();
5022 AlignmentAnnotation matchedAnnotation = annotationIds.get(annotationId);
5025 * pre 2.10.2: saved annotationId is AlignmentAnnotation.label
5027 if (matchedAnnotation == null
5028 && annAlignment.getAlignmentAnnotation() != null)
5030 for (int i = 0; i < annAlignment.getAlignmentAnnotation().length; i++)
5033 .equals(annAlignment.getAlignmentAnnotation()[i].label))
5035 matchedAnnotation = annAlignment.getAlignmentAnnotation()[i];
5040 if (matchedAnnotation == null)
5042 System.err.println("Failed to match annotation colour scheme for "
5046 if (matchedAnnotation.getThreshold() == null)
5048 matchedAnnotation.setThreshold(
5049 new GraphLine(safeFloat(viewAnnColour.getThreshold()),
5050 "Threshold", Color.black));
5053 AnnotationColourGradient cs = null;
5054 if (viewAnnColour.getColourScheme().equals("None"))
5056 cs = new AnnotationColourGradient(matchedAnnotation,
5057 new Color(safeInt(viewAnnColour.getMinColour())),
5058 new Color(safeInt(viewAnnColour.getMaxColour())),
5059 safeInt(viewAnnColour.getAboveThreshold()));
5061 else if (viewAnnColour.getColourScheme().startsWith("ucs"))
5063 cs = new AnnotationColourGradient(matchedAnnotation,
5064 getUserColourScheme(model, viewAnnColour.getColourScheme()),
5065 safeInt(viewAnnColour.getAboveThreshold()));
5069 cs = new AnnotationColourGradient(matchedAnnotation,
5070 ColourSchemeProperty.getColourScheme(af.getViewport(), al,
5071 viewAnnColour.getColourScheme()),
5072 safeInt(viewAnnColour.getAboveThreshold()));
5075 boolean perSequenceOnly = safeBoolean(viewAnnColour.isPerSequence());
5076 boolean useOriginalColours = safeBoolean(
5077 viewAnnColour.isPredefinedColours());
5078 cs.setSeqAssociated(perSequenceOnly);
5079 cs.setPredefinedColours(useOriginalColours);
5081 if (propagateAnnColour && al.getGroups() != null)
5083 // Also use these settings for all the groups
5084 for (int g = 0; g < al.getGroups().size(); g++)
5086 SequenceGroup sg = al.getGroups().get(g);
5087 if (sg.getGroupColourScheme() == null)
5092 AnnotationColourGradient groupScheme = new AnnotationColourGradient(
5093 matchedAnnotation, sg.getColourScheme(),
5094 safeInt(viewAnnColour.getAboveThreshold()));
5095 sg.setColourScheme(groupScheme);
5096 groupScheme.setSeqAssociated(perSequenceOnly);
5097 groupScheme.setPredefinedColours(useOriginalColours);
5103 private void reorderAutoannotation(AlignFrame af, AlignmentI al,
5104 List<JvAnnotRow> autoAlan)
5106 // copy over visualization settings for autocalculated annotation in the
5108 if (al.getAlignmentAnnotation() != null)
5111 * Kludge for magic autoannotation names (see JAL-811)
5113 String[] magicNames = new String[] { "Consensus", "Quality",
5115 JvAnnotRow nullAnnot = new JvAnnotRow(-1, null);
5116 Hashtable<String, JvAnnotRow> visan = new Hashtable<>();
5117 for (String nm : magicNames)
5119 visan.put(nm, nullAnnot);
5121 for (JvAnnotRow auan : autoAlan)
5123 visan.put(auan.template.label
5124 + (auan.template.getCalcId() == null ? ""
5125 : "\t" + auan.template.getCalcId()),
5128 int hSize = al.getAlignmentAnnotation().length;
5129 List<JvAnnotRow> reorder = new ArrayList<>();
5130 // work through any autoCalculated annotation already on the view
5131 // removing it if it should be placed in a different location on the
5132 // annotation panel.
5133 List<String> remains = new ArrayList<>(visan.keySet());
5134 for (int h = 0; h < hSize; h++)
5136 jalview.datamodel.AlignmentAnnotation jalan = al
5137 .getAlignmentAnnotation()[h];
5138 if (jalan.autoCalculated)
5141 JvAnnotRow valan = visan.get(k = jalan.label);
5142 if (jalan.getCalcId() != null)
5144 valan = visan.get(k = jalan.label + "\t" + jalan.getCalcId());
5149 // delete the auto calculated row from the alignment
5150 al.deleteAnnotation(jalan, false);
5154 if (valan != nullAnnot)
5156 if (jalan != valan.template)
5158 // newly created autoannotation row instance
5159 // so keep a reference to the visible annotation row
5160 // and copy over all relevant attributes
5161 if (valan.template.graphHeight >= 0)
5164 jalan.graphHeight = valan.template.graphHeight;
5166 jalan.visible = valan.template.visible;
5168 reorder.add(new JvAnnotRow(valan.order, jalan));
5173 // Add any (possibly stale) autocalculated rows that were not appended to
5174 // the view during construction
5175 for (String other : remains)
5177 JvAnnotRow othera = visan.get(other);
5178 if (othera != nullAnnot && othera.template.getCalcId() != null
5179 && othera.template.getCalcId().length() > 0)
5181 reorder.add(othera);
5184 // now put the automatic annotation in its correct place
5185 int s = 0, srt[] = new int[reorder.size()];
5186 JvAnnotRow[] rws = new JvAnnotRow[reorder.size()];
5187 for (JvAnnotRow jvar : reorder)
5190 srt[s++] = jvar.order;
5193 jalview.util.QuickSort.sort(srt, rws);
5194 // and re-insert the annotation at its correct position
5195 for (JvAnnotRow jvar : rws)
5197 al.addAnnotation(jvar.template, jvar.order);
5199 af.alignPanel.adjustAnnotationHeight();
5203 Hashtable skipList = null;
5206 * TODO remove this method
5209 * @return AlignFrame bound to sequenceSetId from view, if one exists. private
5210 * AlignFrame getSkippedFrame(Viewport view) { if (skipList==null) {
5211 * throw new Error("Implementation Error. No skipList defined for this
5212 * Jalview2XML instance."); } return (AlignFrame)
5213 * skipList.get(view.getSequenceSetId()); }
5217 * Check if the Jalview view contained in object should be skipped or not.
5220 * @return true if view's sequenceSetId is a key in skipList
5222 private boolean skipViewport(JalviewModel object)
5224 if (skipList == null)
5228 String id = object.getViewport().get(0).getSequenceSetId();
5229 if (skipList.containsKey(id))
5231 if (Cache.log != null && Cache.log.isDebugEnabled())
5233 Cache.log.debug("Skipping seuqence set id " + id);
5240 public void addToSkipList(AlignFrame af)
5242 if (skipList == null)
5244 skipList = new Hashtable();
5246 skipList.put(af.getViewport().getSequenceSetId(), af);
5249 public void clearSkipList()
5251 if (skipList != null)
5258 private void recoverDatasetFor(SequenceSet vamsasSet, AlignmentI al,
5259 boolean ignoreUnrefed, String uniqueSeqSetId)
5261 jalview.datamodel.AlignmentI ds = getDatasetFor(
5262 vamsasSet.getDatasetId());
5263 AlignmentI xtant_ds = ds;
5264 if (xtant_ds == null)
5266 // good chance we are about to create a new dataset, but check if we've
5267 // seen some of the dataset sequence IDs before.
5268 // TODO: skip this check if we are working with project generated by
5269 // version 2.11 or later
5270 xtant_ds = checkIfHasDataset(vamsasSet.getSequence());
5271 if (xtant_ds != null)
5274 addDatasetRef(vamsasSet.getDatasetId(), ds);
5277 Vector<SequenceI> dseqs = null;
5280 // recovering an alignment View
5281 AlignmentI seqSetDS = getDatasetFor(UNIQSEQSETID + uniqueSeqSetId);
5282 if (seqSetDS != null)
5284 if (ds != null && ds != seqSetDS)
5286 warn("JAL-3171 regression: Overwriting a dataset reference for an alignment"
5287 + " - CDS/Protein crossreference data may be lost");
5288 if (xtant_ds != null)
5290 // This can only happen if the unique sequence set ID was bound to a
5291 // dataset that did not contain any of the sequences in the view
5292 // currently being restored.
5293 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.");
5297 addDatasetRef(vamsasSet.getDatasetId(), ds);
5302 // try even harder to restore dataset
5303 AlignmentI xtantDS = checkIfHasDataset(vamsasSet.getSequence());
5304 // create a list of new dataset sequences
5305 dseqs = new Vector<>();
5307 for (int i = 0, iSize = vamsasSet.getSequence().size(); i < iSize; i++)
5309 Sequence vamsasSeq = vamsasSet.getSequence().get(i);
5310 ensureJalviewDatasetSequence(vamsasSeq, ds, dseqs, ignoreUnrefed, i);
5312 // create a new dataset
5315 SequenceI[] dsseqs = new SequenceI[dseqs.size()];
5316 dseqs.copyInto(dsseqs);
5317 ds = new jalview.datamodel.Alignment(dsseqs);
5318 debug("Created new dataset " + vamsasSet.getDatasetId()
5319 + " for alignment " + System.identityHashCode(al));
5320 addDatasetRef(vamsasSet.getDatasetId(), ds);
5322 // set the dataset for the newly imported alignment.
5323 if (al.getDataset() == null && !ignoreUnrefed)
5326 // register dataset for the alignment's uniqueSeqSetId for legacy projects
5327 addDatasetRef(UNIQSEQSETID + uniqueSeqSetId, ds);
5329 updateSeqDatasetBinding(vamsasSet.getSequence(), ds);
5333 * XML dataset sequence ID to materialised dataset reference
5335 HashMap<String, AlignmentI> seqToDataset = new HashMap<>();
5338 * @return the first materialised dataset reference containing a dataset
5339 * sequence referenced in the given view
5341 * - sequences from the view
5343 AlignmentI checkIfHasDataset(List<Sequence> list)
5345 for (Sequence restoredSeq : list)
5347 AlignmentI datasetFor = seqToDataset.get(restoredSeq.getDsseqid());
5348 if (datasetFor != null)
5357 * Register ds as the containing dataset for the dataset sequences referenced
5358 * by sequences in list
5361 * - sequences in a view
5364 void updateSeqDatasetBinding(List<Sequence> list, AlignmentI ds)
5366 for (Sequence restoredSeq : list)
5368 AlignmentI prevDS = seqToDataset.put(restoredSeq.getDsseqid(), ds);
5369 if (prevDS != null && prevDS != ds)
5371 warn("Dataset sequence appears in many datasets: "
5372 + restoredSeq.getDsseqid());
5373 // TODO: try to merge!
5381 * sequence definition to create/merge dataset sequence for
5385 * vector to add new dataset sequence to
5386 * @param ignoreUnrefed
5387 * - when true, don't create new sequences from vamsasSeq if it's id
5388 * doesn't already have an asssociated Jalview sequence.
5390 * - used to reorder the sequence in the alignment according to the
5391 * vamsasSeq array ordering, to preserve ordering of dataset
5393 private void ensureJalviewDatasetSequence(Sequence vamsasSeq,
5394 AlignmentI ds, Vector<SequenceI> dseqs, boolean ignoreUnrefed,
5397 // JBP TODO: Check this is called for AlCodonFrames to support recovery of
5399 SequenceI sq = seqRefIds.get(vamsasSeq.getId());
5400 boolean reorder = false;
5401 SequenceI dsq = null;
5402 if (sq != null && sq.getDatasetSequence() != null)
5404 dsq = sq.getDatasetSequence();
5410 if (sq == null && ignoreUnrefed)
5414 String sqid = vamsasSeq.getDsseqid();
5417 // need to create or add a new dataset sequence reference to this sequence
5420 dsq = seqRefIds.get(sqid);
5425 // make a new dataset sequence
5426 dsq = sq.createDatasetSequence();
5429 // make up a new dataset reference for this sequence
5430 sqid = seqHash(dsq);
5432 dsq.setVamsasId(uniqueSetSuffix + sqid);
5433 seqRefIds.put(sqid, dsq);
5438 dseqs.addElement(dsq);
5443 ds.addSequence(dsq);
5449 { // make this dataset sequence sq's dataset sequence
5450 sq.setDatasetSequence(dsq);
5451 // and update the current dataset alignment
5456 if (!dseqs.contains(dsq))
5463 if (ds.findIndex(dsq) < 0)
5465 ds.addSequence(dsq);
5472 // TODO: refactor this as a merge dataset sequence function
5473 // now check that sq (the dataset sequence) sequence really is the union of
5474 // all references to it
5475 // boolean pre = sq.getStart() < dsq.getStart();
5476 // boolean post = sq.getEnd() > dsq.getEnd();
5480 // StringBuffer sb = new StringBuffer();
5481 String newres = jalview.analysis.AlignSeq.extractGaps(
5482 jalview.util.Comparison.GapChars, sq.getSequenceAsString());
5483 if (!newres.equalsIgnoreCase(dsq.getSequenceAsString())
5484 && newres.length() > dsq.getLength())
5486 // Update with the longer sequence.
5490 * if (pre) { sb.insert(0, newres .substring(0, dsq.getStart() -
5491 * sq.getStart())); dsq.setStart(sq.getStart()); } if (post) {
5492 * sb.append(newres.substring(newres.length() - sq.getEnd() -
5493 * dsq.getEnd())); dsq.setEnd(sq.getEnd()); }
5495 dsq.setSequence(newres);
5497 // TODO: merges will never happen if we 'know' we have the real dataset
5498 // sequence - this should be detected when id==dssid
5500 "DEBUG Notice: Merged dataset sequence (if you see this often, post at http://issues.jalview.org/browse/JAL-1474)"); // ("
5501 // + (pre ? "prepended" : "") + " "
5502 // + (post ? "appended" : ""));
5507 // sequence refs are identical. We may need to update the existing dataset
5508 // alignment with this one, though.
5509 if (ds != null && dseqs == null)
5511 int opos = ds.findIndex(dsq);
5512 SequenceI tseq = null;
5513 if (opos != -1 && vseqpos != opos)
5515 // remove from old position
5516 ds.deleteSequence(dsq);
5518 if (vseqpos < ds.getHeight())
5520 if (vseqpos != opos)
5522 // save sequence at destination position
5523 tseq = ds.getSequenceAt(vseqpos);
5524 ds.replaceSequenceAt(vseqpos, dsq);
5525 ds.addSequence(tseq);
5530 ds.addSequence(dsq);
5537 * TODO use AlignmentI here and in related methods - needs
5538 * AlignmentI.getDataset() changed to return AlignmentI instead of Alignment
5540 Hashtable<String, AlignmentI> datasetIds = null;
5542 IdentityHashMap<AlignmentI, String> dataset2Ids = null;
5544 private AlignmentI getDatasetFor(String datasetId)
5546 if (datasetIds == null)
5548 datasetIds = new Hashtable<>();
5551 if (datasetIds.containsKey(datasetId))
5553 return datasetIds.get(datasetId);
5558 private void addDatasetRef(String datasetId, AlignmentI dataset)
5560 if (datasetIds == null)
5562 datasetIds = new Hashtable<>();
5564 datasetIds.put(datasetId, dataset);
5568 * make a new dataset ID for this jalview dataset alignment
5573 private String getDatasetIdRef(AlignmentI dataset)
5575 if (dataset.getDataset() != null)
5577 warn("Serious issue! Dataset Object passed to getDatasetIdRef is not a Jalview DATASET alignment...");
5579 String datasetId = makeHashCode(dataset, null);
5580 if (datasetId == null)
5582 // make a new datasetId and record it
5583 if (dataset2Ids == null)
5585 dataset2Ids = new IdentityHashMap<>();
5589 datasetId = dataset2Ids.get(dataset);
5591 if (datasetId == null)
5593 datasetId = "ds" + dataset2Ids.size() + 1;
5594 dataset2Ids.put(dataset, datasetId);
5601 * Add any saved DBRefEntry's to the sequence. An entry flagged as 'locus' is
5602 * constructed as a special subclass GeneLocus.
5604 * @param datasetSequence
5607 private void addDBRefs(SequenceI datasetSequence, Sequence sequence)
5609 for (int d = 0; d < sequence.getDBRef().size(); d++)
5611 DBRef dr = sequence.getDBRef().get(d);
5615 entry = new GeneLocus(dr.getSource(), dr.getVersion(),
5616 dr.getAccessionId());
5620 entry = new DBRefEntry(dr.getSource(), dr.getVersion(),
5621 dr.getAccessionId());
5623 if (dr.getMapping() != null)
5625 entry.setMap(addMapping(dr.getMapping()));
5627 entry.setCanonical(dr.isCanonical());
5628 datasetSequence.addDBRef(entry);
5632 private jalview.datamodel.Mapping addMapping(Mapping m)
5634 SequenceI dsto = null;
5635 // Mapping m = dr.getMapping();
5636 int fr[] = new int[m.getMapListFrom().size() * 2];
5637 Iterator<MapListFrom> from = m.getMapListFrom().iterator();// enumerateMapListFrom();
5638 for (int _i = 0; from.hasNext(); _i += 2)
5640 MapListFrom mf = from.next();
5641 fr[_i] = mf.getStart();
5642 fr[_i + 1] = mf.getEnd();
5644 int fto[] = new int[m.getMapListTo().size() * 2];
5645 Iterator<MapListTo> to = m.getMapListTo().iterator();// enumerateMapListTo();
5646 for (int _i = 0; to.hasNext(); _i += 2)
5648 MapListTo mf = to.next();
5649 fto[_i] = mf.getStart();
5650 fto[_i + 1] = mf.getEnd();
5652 jalview.datamodel.Mapping jmap = new jalview.datamodel.Mapping(dsto, fr,
5653 fto, m.getMapFromUnit().intValue(),
5654 m.getMapToUnit().intValue());
5657 * (optional) choice of dseqFor or Sequence
5659 if (m.getDseqFor() != null)
5661 String dsfor = m.getDseqFor();
5662 if (seqRefIds.containsKey(dsfor))
5667 jmap.setTo(seqRefIds.get(dsfor));
5671 frefedSequence.add(newMappingRef(dsfor, jmap));
5674 else if (m.getSequence() != null)
5677 * local sequence definition
5679 Sequence ms = m.getSequence();
5680 SequenceI djs = null;
5681 String sqid = ms.getDsseqid();
5682 if (sqid != null && sqid.length() > 0)
5685 * recover dataset sequence
5687 djs = seqRefIds.get(sqid);
5692 "Warning - making up dataset sequence id for DbRef sequence map reference");
5693 sqid = ((Object) ms).toString(); // make up a new hascode for
5694 // undefined dataset sequence hash
5695 // (unlikely to happen)
5701 * make a new dataset sequence and add it to refIds hash
5703 djs = new jalview.datamodel.Sequence(ms.getName(),
5705 djs.setStart(jmap.getMap().getToLowest());
5706 djs.setEnd(jmap.getMap().getToHighest());
5707 djs.setVamsasId(uniqueSetSuffix + sqid);
5709 incompleteSeqs.put(sqid, djs);
5710 seqRefIds.put(sqid, djs);
5713 jalview.bin.Cache.log.debug("about to recurse on addDBRefs.");
5722 * Provides a 'copy' of an alignment view (on action New View) by 'saving' the
5723 * view as XML (but not to file), and then reloading it
5728 public AlignmentPanel copyAlignPanel(AlignmentPanel ap)
5731 JalviewModel jm = saveState(ap, null, null, null);
5734 jm.getVamsasModel().getSequenceSet().get(0).getDatasetId(),
5735 ap.getAlignment().getDataset());
5737 uniqueSetSuffix = "";
5738 // jm.getJalviewModelSequence().getViewport(0).setId(null);
5739 jm.getViewport().get(0).setId(null);
5740 // we don't overwrite the view we just copied
5742 if (this.frefedSequence == null)
5744 frefedSequence = new Vector<>();
5747 viewportsAdded.clear();
5749 AlignFrame af = loadFromObject(jm, null, false, null);
5750 af.getAlignPanels().clear();
5751 af.closeMenuItem_actionPerformed(true);
5754 * if(ap.av.getAlignment().getAlignmentAnnotation()!=null) { for(int i=0;
5755 * i<ap.av.getAlignment().getAlignmentAnnotation().length; i++) {
5756 * if(!ap.av.getAlignment().getAlignmentAnnotation()[i].autoCalculated) {
5757 * af.alignPanel.av.getAlignment().getAlignmentAnnotation()[i] =
5758 * ap.av.getAlignment().getAlignmentAnnotation()[i]; } } }
5761 return af.alignPanel;
5764 private Hashtable jvids2vobj;
5766 private void warn(String msg)
5771 private void warn(String msg, Exception e)
5773 if (Cache.log != null)
5777 Cache.log.warn(msg, e);
5781 Cache.log.warn(msg);
5786 System.err.println("Warning: " + msg);
5789 e.printStackTrace();
5794 private void debug(String string)
5796 debug(string, null);
5799 private void debug(String msg, Exception e)
5801 if (Cache.log != null)
5805 Cache.log.debug(msg, e);
5809 Cache.log.debug(msg);
5814 System.err.println("Warning: " + msg);
5817 e.printStackTrace();
5823 * set the object to ID mapping tables used to write/recover objects and XML
5824 * ID strings for the jalview project. If external tables are provided then
5825 * finalize and clearSeqRefs will not clear the tables when the Jalview2XML
5826 * object goes out of scope. - also populates the datasetIds hashtable with
5827 * alignment objects containing dataset sequences
5830 * Map from ID strings to jalview datamodel
5832 * Map from jalview datamodel to ID strings
5836 public void setObjectMappingTables(Hashtable vobj2jv,
5837 IdentityHashMap jv2vobj)
5839 this.jv2vobj = jv2vobj;
5840 this.vobj2jv = vobj2jv;
5841 Iterator ds = jv2vobj.keySet().iterator();
5843 while (ds.hasNext())
5845 Object jvobj = ds.next();
5846 id = jv2vobj.get(jvobj).toString();
5847 if (jvobj instanceof jalview.datamodel.Alignment)
5849 if (((jalview.datamodel.Alignment) jvobj).getDataset() == null)
5851 addDatasetRef(id, (jalview.datamodel.Alignment) jvobj);
5854 else if (jvobj instanceof jalview.datamodel.Sequence)
5856 // register sequence object so the XML parser can recover it.
5857 if (seqRefIds == null)
5859 seqRefIds = new HashMap<>();
5861 if (seqsToIds == null)
5863 seqsToIds = new IdentityHashMap<>();
5865 seqRefIds.put(jv2vobj.get(jvobj).toString(), (SequenceI) jvobj);
5866 seqsToIds.put((SequenceI) jvobj, id);
5868 else if (jvobj instanceof jalview.datamodel.AlignmentAnnotation)
5871 AlignmentAnnotation jvann = (AlignmentAnnotation) jvobj;
5872 annotationIds.put(anid = jv2vobj.get(jvobj).toString(), jvann);
5873 if (jvann.annotationId == null)
5875 jvann.annotationId = anid;
5877 if (!jvann.annotationId.equals(anid))
5879 // TODO verify that this is the correct behaviour
5880 this.warn("Overriding Annotation ID for " + anid
5881 + " from different id : " + jvann.annotationId);
5882 jvann.annotationId = anid;
5885 else if (jvobj instanceof String)
5887 if (jvids2vobj == null)
5889 jvids2vobj = new Hashtable();
5890 jvids2vobj.put(jvobj, jv2vobj.get(jvobj).toString());
5895 Cache.log.debug("Ignoring " + jvobj.getClass() + " (ID = " + id);
5901 * set the uniqueSetSuffix used to prefix/suffix object IDs for jalview
5902 * objects created from the project archive. If string is null (default for
5903 * construction) then suffix will be set automatically.
5907 public void setUniqueSetSuffix(String string)
5909 uniqueSetSuffix = string;
5914 * uses skipList2 as the skipList for skipping views on sequence sets
5915 * associated with keys in the skipList
5919 public void setSkipList(Hashtable skipList2)
5921 skipList = skipList2;
5925 * Reads the jar entry of given name and returns its contents, or null if the
5926 * entry is not found.
5929 * @param jarEntryName
5932 protected String readJarEntry(jarInputStreamProvider jprovider,
5933 String jarEntryName)
5935 String result = null;
5936 BufferedReader in = null;
5941 * Reopen the jar input stream and traverse its entries to find a matching
5944 JarInputStream jin = jprovider.getJarInputStream();
5945 JarEntry entry = null;
5948 entry = jin.getNextJarEntry();
5949 } while (entry != null && !entry.getName().equals(jarEntryName));
5953 StringBuilder out = new StringBuilder(256);
5954 in = new BufferedReader(new InputStreamReader(jin, UTF_8));
5957 while ((data = in.readLine()) != null)
5961 result = out.toString();
5965 warn("Couldn't find entry in Jalview Jar for " + jarEntryName);
5967 } catch (Exception ex)
5969 ex.printStackTrace();
5977 } catch (IOException e)
5988 * Returns an incrementing counter (0, 1, 2...)
5992 private synchronized int nextCounter()
5998 * Loads any saved PCA viewers
6003 protected void loadPCAViewers(JalviewModel model, AlignmentPanel ap)
6007 List<PcaViewer> pcaviewers = model.getPcaViewer();
6008 for (PcaViewer viewer : pcaviewers)
6010 String modelName = viewer.getScoreModelName();
6011 SimilarityParamsI params = new SimilarityParams(
6012 viewer.isIncludeGappedColumns(), viewer.isMatchGaps(),
6013 viewer.isIncludeGaps(),
6014 viewer.isDenominateByShortestLength());
6017 * create the panel (without computing the PCA)
6019 PCAPanel panel = new PCAPanel(ap, modelName, params);
6021 panel.setTitle(viewer.getTitle());
6022 panel.setBounds(new Rectangle(viewer.getXpos(), viewer.getYpos(),
6023 viewer.getWidth(), viewer.getHeight()));
6025 boolean showLabels = viewer.isShowLabels();
6026 panel.setShowLabels(showLabels);
6027 panel.getRotatableCanvas().setShowLabels(showLabels);
6028 panel.getRotatableCanvas()
6029 .setBgColour(new Color(viewer.getBgColour()));
6030 panel.getRotatableCanvas()
6031 .setApplyToAllViews(viewer.isLinkToAllViews());
6034 * load PCA output data
6036 ScoreModelI scoreModel = ScoreModels.getInstance()
6037 .getScoreModel(modelName, ap);
6038 PCA pca = new PCA(null, scoreModel, params);
6039 PcaDataType pcaData = viewer.getPcaData();
6041 MatrixI pairwise = loadDoubleMatrix(pcaData.getPairwiseMatrix());
6042 pca.setPairwiseScores(pairwise);
6044 MatrixI triDiag = loadDoubleMatrix(pcaData.getTridiagonalMatrix());
6045 pca.setTridiagonal(triDiag);
6047 MatrixI result = loadDoubleMatrix(pcaData.getEigenMatrix());
6048 pca.setEigenmatrix(result);
6050 panel.getPcaModel().setPCA(pca);
6053 * we haven't saved the input data! (JAL-2647 to do)
6055 panel.setInputData(null);
6058 * add the sequence points for the PCA display
6060 List<jalview.datamodel.SequencePoint> seqPoints = new ArrayList<>();
6061 for (SequencePoint sp : viewer.getSequencePoint())
6063 String seqId = sp.getSequenceRef();
6064 SequenceI seq = seqRefIds.get(seqId);
6067 throw new IllegalStateException(
6068 "Unmatched seqref for PCA: " + seqId);
6070 Point pt = new Point(sp.getXPos(), sp.getYPos(), sp.getZPos());
6071 jalview.datamodel.SequencePoint seqPoint = new jalview.datamodel.SequencePoint(
6073 seqPoints.add(seqPoint);
6075 panel.getRotatableCanvas().setPoints(seqPoints, seqPoints.size());
6078 * set min-max ranges and scale after setPoints (which recomputes them)
6080 panel.getRotatableCanvas().setScaleFactor(viewer.getScaleFactor());
6081 SeqPointMin spMin = viewer.getSeqPointMin();
6082 float[] min = new float[] { spMin.getXPos(), spMin.getYPos(),
6084 SeqPointMax spMax = viewer.getSeqPointMax();
6085 float[] max = new float[] { spMax.getXPos(), spMax.getYPos(),
6087 panel.getRotatableCanvas().setSeqMinMax(min, max);
6089 // todo: hold points list in PCAModel only
6090 panel.getPcaModel().setSequencePoints(seqPoints);
6092 panel.setSelectedDimensionIndex(viewer.getXDim(), X);
6093 panel.setSelectedDimensionIndex(viewer.getYDim(), Y);
6094 panel.setSelectedDimensionIndex(viewer.getZDim(), Z);
6096 // is this duplication needed?
6097 panel.setTop(seqPoints.size() - 1);
6098 panel.getPcaModel().setTop(seqPoints.size() - 1);
6101 * add the axes' end points for the display
6103 for (int i = 0; i < 3; i++)
6105 Axis axis = viewer.getAxis().get(i);
6106 panel.getRotatableCanvas().getAxisEndPoints()[i] = new Point(
6107 axis.getXPos(), axis.getYPos(), axis.getZPos());
6110 Desktop.addInternalFrame(panel, MessageManager.formatMessage(
6111 "label.calc_title", "PCA", modelName), 475, 450);
6113 } catch (Exception ex)
6115 Cache.log.error("Error loading PCA: " + ex.toString());
6120 * Creates a new structure viewer window
6127 protected void createStructureViewer(ViewerType viewerType,
6128 final Entry<String, StructureViewerModel> viewerData,
6129 AlignFrame af, jarInputStreamProvider jprovider)
6131 final StructureViewerModel viewerModel = viewerData.getValue();
6132 String sessionFilePath = null;
6134 if (viewerType == ViewerType.JMOL)
6136 sessionFilePath = rewriteJmolSession(viewerModel, jprovider);
6140 String viewerJarEntryName = getViewerJarEntryName(
6141 viewerModel.getViewId());
6142 sessionFilePath = copyJarEntry(jprovider, viewerJarEntryName,
6143 "viewerSession", ".tmp");
6145 final String sessionPath = sessionFilePath;
6146 final String sviewid = viewerData.getKey();
6149 SwingUtilities.invokeAndWait(new Runnable()
6154 JalviewStructureDisplayI sview = null;
6157 sview = StructureViewer.createView(viewerType, af.alignPanel,
6158 viewerModel, sessionPath, sviewid);
6159 addNewStructureViewer(sview);
6160 } catch (OutOfMemoryError ex)
6162 new OOMWarning("Restoring structure view for " + viewerType,
6163 (OutOfMemoryError) ex.getCause());
6164 if (sview != null && sview.isVisible())
6166 sview.closeViewer(false);
6167 sview.setVisible(false);
6173 } catch (InvocationTargetException | InterruptedException ex)
6175 warn("Unexpected error when opening " + viewerType
6176 + " structure viewer", ex);
6181 * Rewrites a Jmol session script, saves it to a temporary file, and returns
6182 * the path of the file. "load file" commands are rewritten to change the
6183 * original PDB file names to those created as the Jalview project is loaded.
6189 private String rewriteJmolSession(StructureViewerModel svattrib,
6190 jarInputStreamProvider jprovider)
6192 String state = svattrib.getStateData(); // Jalview < 2.9
6193 if (state == null || state.isEmpty()) // Jalview >= 2.9
6195 String jarEntryName = getViewerJarEntryName(svattrib.getViewId());
6196 state = readJarEntry(jprovider, jarEntryName);
6198 // TODO or simpler? for each key in oldFiles,
6199 // replace key.getPath() in state with oldFiles.get(key).getFilePath()
6200 // (allowing for different path escapings)
6201 StringBuilder rewritten = new StringBuilder(state.length());
6202 int cp = 0, ncp, ecp;
6203 Map<File, StructureData> oldFiles = svattrib.getFileData();
6204 while ((ncp = state.indexOf("load ", cp)) > -1)
6208 // look for next filename in load statement
6209 rewritten.append(state.substring(cp,
6210 ncp = (state.indexOf("\"", ncp + 1) + 1)));
6211 String oldfilenam = state.substring(ncp,
6212 ecp = state.indexOf("\"", ncp));
6213 // recover the new mapping data for this old filename
6214 // have to normalize filename - since Jmol and jalview do
6215 // filename translation differently.
6216 StructureData filedat = oldFiles.get(new File(oldfilenam));
6217 if (filedat == null)
6219 String reformatedOldFilename = oldfilenam.replaceAll("/", "\\\\");
6220 filedat = oldFiles.get(new File(reformatedOldFilename));
6222 rewritten.append(Platform.escapeBackslashes(filedat.getFilePath()));
6223 rewritten.append("\"");
6224 cp = ecp + 1; // advance beyond last \" and set cursor so we can
6225 // look for next file statement.
6226 } while ((ncp = state.indexOf("/*file*/", cp)) > -1);
6230 // just append rest of state
6231 rewritten.append(state.substring(cp));
6235 System.err.print("Ignoring incomplete Jmol state for PDB ids: ");
6236 rewritten = new StringBuilder(state);
6237 rewritten.append("; load append ");
6238 for (File id : oldFiles.keySet())
6240 // add pdb files that should be present in the viewer
6241 StructureData filedat = oldFiles.get(id);
6242 rewritten.append(" \"").append(filedat.getFilePath()).append("\"");
6244 rewritten.append(";");
6247 if (rewritten.length() == 0)
6251 final String history = "history = ";
6252 int historyIndex = rewritten.indexOf(history);
6253 if (historyIndex > -1)
6256 * change "history = [true|false];" to "history = [1|0];"
6258 historyIndex += history.length();
6259 String val = rewritten.substring(historyIndex, historyIndex + 5);
6260 if (val.startsWith("true"))
6262 rewritten.replace(historyIndex, historyIndex + 4, "1");
6264 else if (val.startsWith("false"))
6266 rewritten.replace(historyIndex, historyIndex + 5, "0");
6272 File tmp = File.createTempFile("viewerSession", ".tmp");
6273 try (OutputStream os = new FileOutputStream(tmp))
6275 InputStream is = new ByteArrayInputStream(
6276 rewritten.toString().getBytes());
6278 return tmp.getAbsolutePath();
6280 } catch (IOException e)
6282 Cache.log.error("Error restoring Jmol session: " + e.toString());
6288 * Populates an XML model of the feature colour scheme for one feature type
6290 * @param featureType
6294 public static Colour marshalColour(String featureType,
6295 FeatureColourI fcol)
6297 Colour col = new Colour();
6298 if (fcol.isSimpleColour())
6300 col.setRGB(Format.getHexString(fcol.getColour()));
6304 col.setRGB(Format.getHexString(fcol.getMaxColour()));
6305 col.setMin(fcol.getMin());
6306 col.setMax(fcol.getMax());
6307 col.setMinRGB(jalview.util.Format.getHexString(fcol.getMinColour()));
6308 col.setAutoScale(fcol.isAutoScaled());
6309 col.setThreshold(fcol.getThreshold());
6310 col.setColourByLabel(fcol.isColourByLabel());
6311 col.setThreshType(fcol.isAboveThreshold() ? ThresholdType.ABOVE
6312 : (fcol.isBelowThreshold() ? ThresholdType.BELOW
6313 : ThresholdType.NONE));
6314 if (fcol.isColourByAttribute())
6316 final String[] attName = fcol.getAttributeName();
6317 col.getAttributeName().add(attName[0]);
6318 if (attName.length > 1)
6320 col.getAttributeName().add(attName[1]);
6323 Color noColour = fcol.getNoColour();
6324 if (noColour == null)
6326 col.setNoValueColour(NoValueColour.NONE);
6328 else if (noColour == fcol.getMaxColour())
6330 col.setNoValueColour(NoValueColour.MAX);
6334 col.setNoValueColour(NoValueColour.MIN);
6337 col.setName(featureType);
6342 * Populates an XML model of the feature filter(s) for one feature type
6344 * @param firstMatcher
6345 * the first (or only) match condition)
6347 * remaining match conditions (if any)
6349 * if true, conditions are and-ed, else or-ed
6351 public static jalview.xml.binding.jalview.FeatureMatcherSet marshalFilter(
6352 FeatureMatcherI firstMatcher, Iterator<FeatureMatcherI> filters,
6355 jalview.xml.binding.jalview.FeatureMatcherSet result = new jalview.xml.binding.jalview.FeatureMatcherSet();
6357 if (filters.hasNext())
6362 CompoundMatcher compound = new CompoundMatcher();
6363 compound.setAnd(and);
6364 jalview.xml.binding.jalview.FeatureMatcherSet matcher1 = marshalFilter(
6365 firstMatcher, Collections.emptyIterator(), and);
6366 // compound.addMatcherSet(matcher1);
6367 compound.getMatcherSet().add(matcher1);
6368 FeatureMatcherI nextMatcher = filters.next();
6369 jalview.xml.binding.jalview.FeatureMatcherSet matcher2 = marshalFilter(
6370 nextMatcher, filters, and);
6371 // compound.addMatcherSet(matcher2);
6372 compound.getMatcherSet().add(matcher2);
6373 result.setCompoundMatcher(compound);
6378 * single condition matcher
6380 // MatchCondition matcherModel = new MatchCondition();
6381 jalview.xml.binding.jalview.FeatureMatcher matcherModel = new jalview.xml.binding.jalview.FeatureMatcher();
6382 matcherModel.setCondition(
6383 firstMatcher.getMatcher().getCondition().getStableName());
6384 matcherModel.setValue(firstMatcher.getMatcher().getPattern());
6385 if (firstMatcher.isByAttribute())
6387 matcherModel.setBy(FilterBy.BY_ATTRIBUTE);
6388 // matcherModel.setAttributeName(firstMatcher.getAttribute());
6389 String[] attName = firstMatcher.getAttribute();
6390 matcherModel.getAttributeName().add(attName[0]); // attribute
6391 if (attName.length > 1)
6393 matcherModel.getAttributeName().add(attName[1]); // sub-attribute
6396 else if (firstMatcher.isByLabel())
6398 matcherModel.setBy(FilterBy.BY_LABEL);
6400 else if (firstMatcher.isByScore())
6402 matcherModel.setBy(FilterBy.BY_SCORE);
6404 result.setMatchCondition(matcherModel);
6411 * Loads one XML model of a feature filter to a Jalview object
6413 * @param featureType
6414 * @param matcherSetModel
6417 public static FeatureMatcherSetI parseFilter(String featureType,
6418 jalview.xml.binding.jalview.FeatureMatcherSet matcherSetModel)
6420 FeatureMatcherSetI result = new FeatureMatcherSet();
6423 parseFilterConditions(result, matcherSetModel, true);
6424 } catch (IllegalStateException e)
6426 // mixing AND and OR conditions perhaps
6428 String.format("Error reading filter conditions for '%s': %s",
6429 featureType, e.getMessage()));
6430 // return as much as was parsed up to the error
6437 * Adds feature match conditions to matcherSet as unmarshalled from XML
6438 * (possibly recursively for compound conditions)
6441 * @param matcherSetModel
6443 * if true, multiple conditions are AND-ed, else they are OR-ed
6444 * @throws IllegalStateException
6445 * if AND and OR conditions are mixed
6447 protected static void parseFilterConditions(FeatureMatcherSetI matcherSet,
6448 jalview.xml.binding.jalview.FeatureMatcherSet matcherSetModel,
6451 jalview.xml.binding.jalview.FeatureMatcher mc = matcherSetModel
6452 .getMatchCondition();
6458 FilterBy filterBy = mc.getBy();
6459 Condition cond = Condition.fromString(mc.getCondition());
6460 String pattern = mc.getValue();
6461 FeatureMatcherI matchCondition = null;
6462 if (filterBy == FilterBy.BY_LABEL)
6464 matchCondition = FeatureMatcher.byLabel(cond, pattern);
6466 else if (filterBy == FilterBy.BY_SCORE)
6468 matchCondition = FeatureMatcher.byScore(cond, pattern);
6471 else if (filterBy == FilterBy.BY_ATTRIBUTE)
6473 final List<String> attributeName = mc.getAttributeName();
6474 String[] attNames = attributeName
6475 .toArray(new String[attributeName.size()]);
6476 matchCondition = FeatureMatcher.byAttribute(cond, pattern,
6481 * note this throws IllegalStateException if AND-ing to a
6482 * previously OR-ed compound condition, or vice versa
6486 matcherSet.and(matchCondition);
6490 matcherSet.or(matchCondition);
6496 * compound condition
6498 List<jalview.xml.binding.jalview.FeatureMatcherSet> matchers = matcherSetModel
6499 .getCompoundMatcher().getMatcherSet();
6500 boolean anded = matcherSetModel.getCompoundMatcher().isAnd();
6501 if (matchers.size() == 2)
6503 parseFilterConditions(matcherSet, matchers.get(0), anded);
6504 parseFilterConditions(matcherSet, matchers.get(1), anded);
6508 System.err.println("Malformed compound filter condition");
6514 * Loads one XML model of a feature colour to a Jalview object
6516 * @param colourModel
6519 public static FeatureColourI parseColour(Colour colourModel)
6521 FeatureColourI colour = null;
6523 if (colourModel.getMax() != null)
6525 Color mincol = null;
6526 Color maxcol = null;
6527 Color noValueColour = null;
6531 mincol = new Color(Integer.parseInt(colourModel.getMinRGB(), 16));
6532 maxcol = new Color(Integer.parseInt(colourModel.getRGB(), 16));
6533 } catch (Exception e)
6535 Cache.log.warn("Couldn't parse out graduated feature color.", e);
6538 NoValueColour noCol = colourModel.getNoValueColour();
6539 if (noCol == NoValueColour.MIN)
6541 noValueColour = mincol;
6543 else if (noCol == NoValueColour.MAX)
6545 noValueColour = maxcol;
6548 colour = new FeatureColour(maxcol, mincol, maxcol, noValueColour,
6549 safeFloat(colourModel.getMin()),
6550 safeFloat(colourModel.getMax()));
6551 final List<String> attributeName = colourModel.getAttributeName();
6552 String[] attributes = attributeName
6553 .toArray(new String[attributeName.size()]);
6554 if (attributes != null && attributes.length > 0)
6556 colour.setAttributeName(attributes);
6558 if (colourModel.isAutoScale() != null)
6560 colour.setAutoScaled(colourModel.isAutoScale().booleanValue());
6562 if (colourModel.isColourByLabel() != null)
6564 colour.setColourByLabel(
6565 colourModel.isColourByLabel().booleanValue());
6567 if (colourModel.getThreshold() != null)
6569 colour.setThreshold(colourModel.getThreshold().floatValue());
6571 ThresholdType ttyp = colourModel.getThreshType();
6572 if (ttyp == ThresholdType.ABOVE)
6574 colour.setAboveThreshold(true);
6576 else if (ttyp == ThresholdType.BELOW)
6578 colour.setBelowThreshold(true);
6583 Color color = new Color(Integer.parseInt(colourModel.getRGB(), 16));
6584 colour = new FeatureColour(color);