2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 package jalview.project;
23 import static jalview.math.RotatableMatrix.Axis.X;
24 import static jalview.math.RotatableMatrix.Axis.Y;
25 import static jalview.math.RotatableMatrix.Axis.Z;
27 import jalview.analysis.Conservation;
28 import jalview.analysis.PCA;
29 import jalview.analysis.scoremodels.ScoreModels;
30 import jalview.analysis.scoremodels.SimilarityParams;
31 import jalview.api.FeatureColourI;
32 import jalview.api.ViewStyleI;
33 import jalview.api.analysis.ScoreModelI;
34 import jalview.api.analysis.SimilarityParamsI;
35 import jalview.api.structures.JalviewStructureDisplayI;
36 import jalview.bin.Cache;
37 import jalview.datamodel.AlignedCodonFrame;
38 import jalview.datamodel.Alignment;
39 import jalview.datamodel.AlignmentAnnotation;
40 import jalview.datamodel.AlignmentI;
41 import jalview.datamodel.DBRefEntry;
42 import jalview.datamodel.GraphLine;
43 import jalview.datamodel.PDBEntry;
44 import jalview.datamodel.Point;
45 import jalview.datamodel.RnaViewerModel;
46 import jalview.datamodel.SequenceFeature;
47 import jalview.datamodel.SequenceGroup;
48 import jalview.datamodel.SequenceI;
49 import jalview.datamodel.StructureViewerModel;
50 import jalview.datamodel.StructureViewerModel.StructureData;
51 import jalview.datamodel.features.FeatureMatcher;
52 import jalview.datamodel.features.FeatureMatcherI;
53 import jalview.datamodel.features.FeatureMatcherSet;
54 import jalview.datamodel.features.FeatureMatcherSetI;
55 import jalview.ext.varna.RnaModel;
56 import jalview.gui.AlignFrame;
57 import jalview.gui.AlignViewport;
58 import jalview.gui.AlignmentPanel;
59 import jalview.gui.AppVarna;
60 import jalview.gui.ChimeraViewFrame;
61 import jalview.gui.Desktop;
62 import jalview.gui.FeatureRenderer;
63 import jalview.gui.JvOptionPane;
64 import jalview.gui.OOMWarning;
65 import jalview.gui.PCAPanel;
66 import jalview.gui.PaintRefresher;
67 import jalview.gui.SplitFrame;
68 import jalview.gui.StructureViewer;
69 import jalview.gui.StructureViewer.ViewerType;
70 import jalview.gui.StructureViewerBase;
71 import jalview.gui.TreePanel;
72 import jalview.io.BackupFiles;
73 import jalview.io.DataSourceType;
74 import jalview.io.FileFormat;
75 import jalview.io.NewickFile;
76 import jalview.math.Matrix;
77 import jalview.math.MatrixI;
78 import jalview.renderer.ResidueShaderI;
79 import jalview.schemes.AnnotationColourGradient;
80 import jalview.schemes.ColourSchemeI;
81 import jalview.schemes.ColourSchemeProperty;
82 import jalview.schemes.FeatureColour;
83 import jalview.schemes.ResidueProperties;
84 import jalview.schemes.UserColourScheme;
85 import jalview.structure.StructureSelectionManager;
86 import jalview.structures.models.AAStructureBindingModel;
87 import jalview.util.Format;
88 import jalview.util.MessageManager;
89 import jalview.util.Platform;
90 import jalview.util.StringUtils;
91 import jalview.util.jarInputStreamProvider;
92 import jalview.util.matcher.Condition;
93 import jalview.viewmodel.AlignmentViewport;
94 import jalview.viewmodel.PCAModel;
95 import jalview.viewmodel.ViewportRanges;
96 import jalview.viewmodel.seqfeatures.FeatureRendererSettings;
97 import jalview.viewmodel.seqfeatures.FeaturesDisplayed;
98 import jalview.ws.jws2.Jws2Discoverer;
99 import jalview.ws.jws2.dm.AAConSettings;
100 import jalview.ws.jws2.jabaws2.Jws2Instance;
101 import jalview.ws.params.ArgumentI;
102 import jalview.ws.params.AutoCalcSetting;
103 import jalview.ws.params.WsParamSetI;
104 import jalview.xml.binding.jalview.AlcodonFrame;
105 import jalview.xml.binding.jalview.AlcodonFrame.AlcodMap;
106 import jalview.xml.binding.jalview.Annotation;
107 import jalview.xml.binding.jalview.Annotation.ThresholdLine;
108 import jalview.xml.binding.jalview.AnnotationColourScheme;
109 import jalview.xml.binding.jalview.AnnotationElement;
110 import jalview.xml.binding.jalview.DoubleMatrix;
111 import jalview.xml.binding.jalview.DoubleVector;
112 import jalview.xml.binding.jalview.Feature;
113 import jalview.xml.binding.jalview.Feature.OtherData;
114 import jalview.xml.binding.jalview.FeatureMatcherSet.CompoundMatcher;
115 import jalview.xml.binding.jalview.FilterBy;
116 import jalview.xml.binding.jalview.JalviewModel;
117 import jalview.xml.binding.jalview.JalviewModel.FeatureSettings;
118 import jalview.xml.binding.jalview.JalviewModel.FeatureSettings.Group;
119 import jalview.xml.binding.jalview.JalviewModel.FeatureSettings.Setting;
120 import jalview.xml.binding.jalview.JalviewModel.JGroup;
121 import jalview.xml.binding.jalview.JalviewModel.JSeq;
122 import jalview.xml.binding.jalview.JalviewModel.JSeq.Pdbids;
123 import jalview.xml.binding.jalview.JalviewModel.JSeq.Pdbids.StructureState;
124 import jalview.xml.binding.jalview.JalviewModel.JSeq.RnaViewer;
125 import jalview.xml.binding.jalview.JalviewModel.JSeq.RnaViewer.SecondaryStructure;
126 import jalview.xml.binding.jalview.JalviewModel.PcaViewer;
127 import jalview.xml.binding.jalview.JalviewModel.PcaViewer.Axis;
128 import jalview.xml.binding.jalview.JalviewModel.PcaViewer.SeqPointMax;
129 import jalview.xml.binding.jalview.JalviewModel.PcaViewer.SeqPointMin;
130 import jalview.xml.binding.jalview.JalviewModel.PcaViewer.SequencePoint;
131 import jalview.xml.binding.jalview.JalviewModel.Tree;
132 import jalview.xml.binding.jalview.JalviewModel.UserColours;
133 import jalview.xml.binding.jalview.JalviewModel.Viewport;
134 import jalview.xml.binding.jalview.JalviewModel.Viewport.CalcIdParam;
135 import jalview.xml.binding.jalview.JalviewModel.Viewport.HiddenColumns;
136 import jalview.xml.binding.jalview.JalviewUserColours;
137 import jalview.xml.binding.jalview.JalviewUserColours.Colour;
138 import jalview.xml.binding.jalview.MapListType.MapListFrom;
139 import jalview.xml.binding.jalview.MapListType.MapListTo;
140 import jalview.xml.binding.jalview.Mapping;
141 import jalview.xml.binding.jalview.NoValueColour;
142 import jalview.xml.binding.jalview.ObjectFactory;
143 import jalview.xml.binding.jalview.PcaDataType;
144 import jalview.xml.binding.jalview.Pdbentry.Property;
145 import jalview.xml.binding.jalview.Sequence;
146 import jalview.xml.binding.jalview.Sequence.DBRef;
147 import jalview.xml.binding.jalview.SequenceSet;
148 import jalview.xml.binding.jalview.SequenceSet.SequenceSetProperties;
149 import jalview.xml.binding.jalview.ThresholdType;
150 import jalview.xml.binding.jalview.VAMSAS;
152 import java.awt.Color;
153 import java.awt.Font;
154 import java.awt.Rectangle;
155 import java.io.BufferedReader;
156 import java.io.ByteArrayInputStream;
157 import java.io.DataInputStream;
158 import java.io.DataOutputStream;
160 import java.io.FileInputStream;
161 import java.io.FileOutputStream;
162 import java.io.IOException;
163 import java.io.InputStreamReader;
164 import java.io.OutputStreamWriter;
165 import java.io.PrintWriter;
166 import java.lang.reflect.InvocationTargetException;
167 import java.math.BigInteger;
168 import java.net.MalformedURLException;
170 import java.util.ArrayList;
171 import java.util.Arrays;
172 import java.util.Collections;
173 import java.util.Enumeration;
174 import java.util.GregorianCalendar;
175 import java.util.HashMap;
176 import java.util.HashSet;
177 import java.util.Hashtable;
178 import java.util.IdentityHashMap;
179 import java.util.Iterator;
180 import java.util.LinkedHashMap;
181 import java.util.List;
182 import java.util.Map;
183 import java.util.Map.Entry;
184 import java.util.Set;
185 import java.util.Vector;
186 import java.util.jar.JarEntry;
187 import java.util.jar.JarInputStream;
188 import java.util.jar.JarOutputStream;
190 import javax.swing.JInternalFrame;
191 import javax.swing.SwingUtilities;
192 import javax.xml.bind.JAXBContext;
193 import javax.xml.bind.JAXBElement;
194 import javax.xml.bind.Marshaller;
195 import javax.xml.datatype.DatatypeConfigurationException;
196 import javax.xml.datatype.DatatypeFactory;
197 import javax.xml.datatype.XMLGregorianCalendar;
198 import javax.xml.stream.XMLInputFactory;
199 import javax.xml.stream.XMLStreamReader;
202 * Write out the current jalview desktop state as a Jalview XML stream.
204 * Note: the vamsas objects referred to here are primitive versions of the
205 * VAMSAS project schema elements - they are not the same and most likely never
209 * @version $Revision: 1.134 $
211 public class Jalview2XML
214 // BH 2018 we add the .jvp binary extension to J2S so that
215 // it will declare that binary when we do the file save from the browser
219 Platform.addJ2SBinaryType(".jvp?");
222 private static final String VIEWER_PREFIX = "viewer_";
224 private static final String RNA_PREFIX = "rna_";
226 private static final String UTF_8 = "UTF-8";
229 * prefix for recovering datasets for alignments with multiple views where
230 * non-existent dataset IDs were written for some views
232 private static final String UNIQSEQSETID = "uniqueSeqSetId.";
234 // use this with nextCounter() to make unique names for entities
235 private int counter = 0;
238 * SequenceI reference -> XML ID string in jalview XML. Populated as XML reps
239 * of sequence objects are created.
241 IdentityHashMap<SequenceI, String> seqsToIds = null;
244 * jalview XML Sequence ID to jalview sequence object reference (both dataset
245 * and alignment sequences. Populated as XML reps of sequence objects are
248 Map<String, SequenceI> seqRefIds = null;
250 Map<String, SequenceI> incompleteSeqs = null;
252 List<SeqFref> frefedSequence = null;
254 boolean raiseGUI = true; // whether errors are raised in dialog boxes or not
257 * Map of reconstructed AlignFrame objects that appear to have come from
258 * SplitFrame objects (have a dna/protein complement view).
260 private Map<Viewport, AlignFrame> splitFrameCandidates = new HashMap<>();
263 * Map from displayed rna structure models to their saved session state jar
266 private Map<RnaModel, String> rnaSessions = new HashMap<>();
269 * A helper method for safely using the value of an optional attribute that
270 * may be null if not present in the XML. Answers the boolean value, or false
276 public static boolean safeBoolean(Boolean b)
278 return b == null ? false : b.booleanValue();
282 * A helper method for safely using the value of an optional attribute that
283 * may be null if not present in the XML. Answers the integer value, or zero
289 public static int safeInt(Integer i)
291 return i == null ? 0 : i.intValue();
295 * A helper method for safely using the value of an optional attribute that
296 * may be null if not present in the XML. Answers the float value, or zero if
302 public static float safeFloat(Float f)
304 return f == null ? 0f : f.floatValue();
308 * create/return unique hash string for sq
311 * @return new or existing unique string for sq
313 String seqHash(SequenceI sq)
315 if (seqsToIds == null)
319 if (seqsToIds.containsKey(sq))
321 return seqsToIds.get(sq);
325 // create sequential key
326 String key = "sq" + (seqsToIds.size() + 1);
327 key = makeHashCode(sq, key); // check we don't have an external reference
329 seqsToIds.put(sq, key);
336 if (seqsToIds == null)
338 seqsToIds = new IdentityHashMap<>();
340 if (seqRefIds == null)
342 seqRefIds = new HashMap<>();
344 if (incompleteSeqs == null)
346 incompleteSeqs = new HashMap<>();
348 if (frefedSequence == null)
350 frefedSequence = new ArrayList<>();
358 public Jalview2XML(boolean raiseGUI)
360 this.raiseGUI = raiseGUI;
364 * base class for resolving forward references to sequences by their ID
369 abstract class SeqFref
375 public SeqFref(String _sref, String type)
381 public String getSref()
386 public SequenceI getSrefSeq()
388 return seqRefIds.get(sref);
391 public boolean isResolvable()
393 return seqRefIds.get(sref) != null;
396 public SequenceI getSrefDatasetSeq()
398 SequenceI sq = seqRefIds.get(sref);
401 while (sq.getDatasetSequence() != null)
403 sq = sq.getDatasetSequence();
410 * @return true if the forward reference was fully resolved
412 abstract boolean resolve();
415 public String toString()
417 return type + " reference to " + sref;
422 * create forward reference for a mapping
428 public SeqFref newMappingRef(final String sref,
429 final jalview.datamodel.Mapping _jmap)
431 SeqFref fref = new SeqFref(sref, "Mapping")
433 public jalview.datamodel.Mapping jmap = _jmap;
438 SequenceI seq = getSrefDatasetSeq();
450 public SeqFref newAlcodMapRef(final String sref,
451 final AlignedCodonFrame _cf,
452 final jalview.datamodel.Mapping _jmap)
455 SeqFref fref = new SeqFref(sref, "Codon Frame")
457 AlignedCodonFrame cf = _cf;
459 public jalview.datamodel.Mapping mp = _jmap;
462 public boolean isResolvable()
464 return super.isResolvable() && mp.getTo() != null;
470 SequenceI seq = getSrefDatasetSeq();
475 cf.addMap(seq, mp.getTo(), mp.getMap());
482 public void resolveFrefedSequences()
484 Iterator<SeqFref> nextFref = frefedSequence.iterator();
485 int toresolve = frefedSequence.size();
486 int unresolved = 0, failedtoresolve = 0;
487 while (nextFref.hasNext())
489 SeqFref ref = nextFref.next();
490 if (ref.isResolvable())
502 } catch (Exception x)
505 "IMPLEMENTATION ERROR: Failed to resolve forward reference for sequence "
518 System.err.println("Jalview Project Import: There were " + unresolved
519 + " forward references left unresolved on the stack.");
521 if (failedtoresolve > 0)
523 System.err.println("SERIOUS! " + failedtoresolve
524 + " resolvable forward references failed to resolve.");
526 if (incompleteSeqs != null && incompleteSeqs.size() > 0)
529 "Jalview Project Import: There are " + incompleteSeqs.size()
530 + " sequences which may have incomplete metadata.");
531 if (incompleteSeqs.size() < 10)
533 for (SequenceI s : incompleteSeqs.values())
535 System.err.println(s.toString());
541 "Too many to report. Skipping output of incomplete sequences.");
547 * This maintains a map of viewports, the key being the seqSetId. Important to
548 * set historyItem and redoList for multiple views
550 Map<String, AlignViewport> viewportsAdded = new HashMap<>();
552 Map<String, AlignmentAnnotation> annotationIds = new HashMap<>();
554 String uniqueSetSuffix = "";
557 * List of pdbfiles added to Jar
559 List<String> pdbfiles = null;
561 // SAVES SEVERAL ALIGNMENT WINDOWS TO SAME JARFILE
562 public void saveState(File statefile)
564 FileOutputStream fos = null;
569 fos = new FileOutputStream(statefile);
571 JarOutputStream jout = new JarOutputStream(fos);
575 } catch (Exception e)
577 Cache.log.error("Couln't write Jalview state to " + statefile, e);
578 // TODO: inform user of the problem - they need to know if their data was
580 if (errorMessage == null)
582 errorMessage = "Did't write Jalview Archive to output file '"
583 + statefile + "' - See console error log for details";
587 errorMessage += "(Didn't write Jalview Archive to output file '"
598 } catch (IOException e)
608 * Writes a jalview project archive to the given Jar output stream.
612 public void saveState(JarOutputStream jout)
614 AlignFrame[] frames = Desktop.getAlignFrames();
620 saveAllFrames(Arrays.asList(frames), jout);
624 * core method for storing state for a set of AlignFrames.
627 * - frames involving all data to be exported (including containing
630 * - project output stream
632 private void saveAllFrames(List<AlignFrame> frames, JarOutputStream jout)
634 Hashtable<String, AlignFrame> dsses = new Hashtable<>();
637 * ensure cached data is clear before starting
639 // todo tidy up seqRefIds, seqsToIds initialisation / reset
641 splitFrameCandidates.clear();
646 // NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS
647 // //////////////////////////////////////////////////
649 List<String> shortNames = new ArrayList<>();
650 List<String> viewIds = new ArrayList<>();
653 for (int i = frames.size() - 1; i > -1; i--)
655 AlignFrame af = frames.get(i);
657 if (skipList != null && skipList
658 .containsKey(af.getViewport().getSequenceSetId()))
663 String shortName = makeFilename(af, shortNames);
665 int apSize = af.getAlignPanels().size();
667 for (int ap = 0; ap < apSize; ap++)
669 AlignmentPanel apanel = (AlignmentPanel) af.getAlignPanels()
671 String fileName = apSize == 1 ? shortName : ap + shortName;
672 if (!fileName.endsWith(".xml"))
674 fileName = fileName + ".xml";
677 saveState(apanel, fileName, jout, viewIds);
679 String dssid = getDatasetIdRef(
680 af.getViewport().getAlignment().getDataset());
681 if (!dsses.containsKey(dssid))
683 dsses.put(dssid, af);
688 writeDatasetFor(dsses, "" + jout.hashCode() + " " + uniqueSetSuffix,
694 } catch (Exception foo)
699 } catch (Exception ex)
701 // TODO: inform user of the problem - they need to know if their data was
703 if (errorMessage == null)
705 errorMessage = "Couldn't write Jalview Archive - see error output for details";
707 ex.printStackTrace();
712 * Generates a distinct file name, based on the title of the AlignFrame, by
713 * appending _n for increasing n until an unused name is generated. The new
714 * name (without its extension) is added to the list.
718 * @return the generated name, with .xml extension
720 protected String makeFilename(AlignFrame af, List<String> namesUsed)
722 String shortName = af.getTitle();
724 if (shortName.indexOf(File.separatorChar) > -1)
726 shortName = shortName
727 .substring(shortName.lastIndexOf(File.separatorChar) + 1);
732 while (namesUsed.contains(shortName))
734 if (shortName.endsWith("_" + (count - 1)))
736 shortName = shortName.substring(0, shortName.lastIndexOf("_"));
739 shortName = shortName.concat("_" + count);
743 namesUsed.add(shortName);
745 if (!shortName.endsWith(".xml"))
747 shortName = shortName + ".xml";
752 // USE THIS METHOD TO SAVE A SINGLE ALIGNMENT WINDOW
753 public boolean saveAlignment(AlignFrame af, String jarFile,
758 // create backupfiles object and get new temp filename destination
759 boolean doBackup = BackupFiles.getEnabled();
760 BackupFiles backupfiles = doBackup ? new BackupFiles(jarFile) : null;
761 FileOutputStream fos = new FileOutputStream(doBackup ?
762 backupfiles.getTempFilePath() : jarFile);
764 JarOutputStream jout = new JarOutputStream(fos);
765 List<AlignFrame> frames = new ArrayList<>();
767 // resolve splitframes
768 if (af.getViewport().getCodingComplement() != null)
770 frames = ((SplitFrame) af.getSplitViewContainer()).getAlignFrames();
776 saveAllFrames(frames, jout);
780 } catch (Exception foo)
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 Enumeration en = jal.getProperties().keys();
918 while (en.hasMoreElements())
920 String key = en.nextElement().toString();
921 SequenceSetProperties ssp = new SequenceSetProperties();
923 ssp.setValue(jal.getProperties().get(key).toString());
924 // vamsasSet.addSequenceSetProperties(ssp);
925 vamsasSet.getSequenceSetProperties().add(ssp);
930 Set<String> calcIdSet = new HashSet<>();
931 // record the set of vamsas sequence XML POJO we create.
932 HashMap<String, Sequence> vamsasSetIds = new HashMap<>();
934 for (final SequenceI jds : rjal.getSequences())
936 final SequenceI jdatasq = jds.getDatasetSequence() == null ? jds
937 : jds.getDatasetSequence();
938 String id = seqHash(jds);
939 if (vamsasSetIds.get(id) == null)
941 if (seqRefIds.get(id) != null && !storeDS)
943 // This happens for two reasons: 1. multiple views are being
945 // 2. the hashCode has collided with another sequence's code. This
947 // HAPPEN! (PF00072.15.stk does this)
948 // JBPNote: Uncomment to debug writing out of files that do not read
949 // back in due to ArrayOutOfBoundExceptions.
950 // System.err.println("vamsasSeq backref: "+id+"");
951 // System.err.println(jds.getName()+"
952 // "+jds.getStart()+"-"+jds.getEnd()+" "+jds.getSequenceAsString());
953 // System.err.println("Hashcode: "+seqHash(jds));
954 // SequenceI rsq = (SequenceI) seqRefIds.get(id + "");
955 // System.err.println(rsq.getName()+"
956 // "+rsq.getStart()+"-"+rsq.getEnd()+" "+rsq.getSequenceAsString());
957 // System.err.println("Hashcode: "+seqHash(rsq));
961 vamsasSeq = createVamsasSequence(id, jds);
962 // vamsasSet.addSequence(vamsasSeq);
963 vamsasSet.getSequence().add(vamsasSeq);
964 vamsasSetIds.put(id, vamsasSeq);
965 seqRefIds.put(id, jds);
969 jseq.setStart(jds.getStart());
970 jseq.setEnd(jds.getEnd());
971 jseq.setColour(av.getSequenceColour(jds).getRGB());
973 jseq.setId(id); // jseq id should be a string not a number
976 // Store any sequences this sequence represents
977 if (av.hasHiddenRows())
979 // use rjal, contains the full height alignment
981 av.getAlignment().getHiddenSequences().isHidden(jds));
983 if (av.isHiddenRepSequence(jds))
985 jalview.datamodel.SequenceI[] reps = av
986 .getRepresentedSequences(jds).getSequencesInOrder(rjal);
988 for (int h = 0; h < reps.length; h++)
992 // jseq.addHiddenSequences(rjal.findIndex(reps[h]));
993 jseq.getHiddenSequences().add(rjal.findIndex(reps[h]));
998 // mark sequence as reference - if it is the reference for this view
1001 jseq.setViewreference(jds == jal.getSeqrep());
1005 // TODO: omit sequence features from each alignment view's XML dump if we
1006 // are storing dataset
1007 List<SequenceFeature> sfs = jds.getSequenceFeatures();
1008 for (SequenceFeature sf : sfs)
1010 // Features features = new Features();
1011 Feature features = new Feature();
1013 features.setBegin(sf.getBegin());
1014 features.setEnd(sf.getEnd());
1015 features.setDescription(sf.getDescription());
1016 features.setType(sf.getType());
1017 features.setFeatureGroup(sf.getFeatureGroup());
1018 features.setScore(sf.getScore());
1019 if (sf.links != null)
1021 for (int l = 0; l < sf.links.size(); l++)
1023 OtherData keyValue = new OtherData();
1024 keyValue.setKey("LINK_" + l);
1025 keyValue.setValue(sf.links.elementAt(l).toString());
1026 // features.addOtherData(keyValue);
1027 features.getOtherData().add(keyValue);
1030 if (sf.otherDetails != null)
1033 * save feature attributes, which may be simple strings or
1034 * map valued (have sub-attributes)
1036 for (Entry<String, Object> entry : sf.otherDetails.entrySet())
1038 String key = entry.getKey();
1039 Object value = entry.getValue();
1040 if (value instanceof Map<?, ?>)
1042 for (Entry<String, Object> subAttribute : ((Map<String, Object>) value)
1045 OtherData otherData = new OtherData();
1046 otherData.setKey(key);
1047 otherData.setKey2(subAttribute.getKey());
1048 otherData.setValue(subAttribute.getValue().toString());
1049 // features.addOtherData(otherData);
1050 features.getOtherData().add(otherData);
1055 OtherData otherData = new OtherData();
1056 otherData.setKey(key);
1057 otherData.setValue(value.toString());
1058 // features.addOtherData(otherData);
1059 features.getOtherData().add(otherData);
1064 // jseq.addFeatures(features);
1065 jseq.getFeatures().add(features);
1068 if (jdatasq.getAllPDBEntries() != null)
1070 Enumeration<PDBEntry> en = jdatasq.getAllPDBEntries().elements();
1071 while (en.hasMoreElements())
1073 Pdbids pdb = new Pdbids();
1074 jalview.datamodel.PDBEntry entry = en.nextElement();
1076 String pdbId = entry.getId();
1078 pdb.setType(entry.getType());
1081 * Store any structure views associated with this sequence. This
1082 * section copes with duplicate entries in the project, so a dataset
1083 * only view *should* be coped with sensibly.
1085 // This must have been loaded, is it still visible?
1086 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1087 String matchedFile = null;
1088 for (int f = frames.length - 1; f > -1; f--)
1090 if (frames[f] instanceof StructureViewerBase)
1092 StructureViewerBase viewFrame = (StructureViewerBase) frames[f];
1093 matchedFile = saveStructureState(ap, jds, pdb, entry, viewIds,
1094 matchedFile, viewFrame);
1096 * Only store each structure viewer's state once in the project
1097 * jar. First time through only (storeDS==false)
1099 String viewId = viewFrame.getViewId();
1100 if (!storeDS && !viewIds.contains(viewId))
1102 viewIds.add(viewId);
1105 String viewerState = viewFrame.getStateInfo();
1106 writeJarEntry(jout, getViewerJarEntryName(viewId),
1107 viewerState.getBytes());
1108 } catch (IOException e)
1111 "Error saving viewer state: " + e.getMessage());
1117 if (matchedFile != null || entry.getFile() != null)
1119 if (entry.getFile() != null)
1122 matchedFile = entry.getFile();
1124 pdb.setFile(matchedFile); // entry.getFile());
1125 if (pdbfiles == null)
1127 pdbfiles = new ArrayList<>();
1130 if (!pdbfiles.contains(pdbId))
1132 pdbfiles.add(pdbId);
1133 copyFileToJar(jout, matchedFile, pdbId);
1137 Enumeration<String> props = entry.getProperties();
1138 if (props.hasMoreElements())
1140 // PdbentryItem item = new PdbentryItem();
1141 while (props.hasMoreElements())
1143 Property prop = new Property();
1144 String key = props.nextElement();
1146 prop.setValue(entry.getProperty(key).toString());
1147 // item.addProperty(prop);
1148 pdb.getProperty().add(prop);
1150 // pdb.addPdbentryItem(item);
1153 // jseq.addPdbids(pdb);
1154 jseq.getPdbids().add(pdb);
1158 saveRnaViewers(jout, jseq, jds, viewIds, ap, storeDS);
1160 // jms.addJSeq(jseq);
1161 object.getJSeq().add(jseq);
1164 if (!storeDS && av.hasHiddenRows())
1166 jal = av.getAlignment();
1170 if (storeDS && jal.getCodonFrames() != null)
1172 List<AlignedCodonFrame> jac = jal.getCodonFrames();
1173 for (AlignedCodonFrame acf : jac)
1175 AlcodonFrame alc = new AlcodonFrame();
1176 if (acf.getProtMappings() != null
1177 && acf.getProtMappings().length > 0)
1179 boolean hasMap = false;
1180 SequenceI[] dnas = acf.getdnaSeqs();
1181 jalview.datamodel.Mapping[] pmaps = acf.getProtMappings();
1182 for (int m = 0; m < pmaps.length; m++)
1184 AlcodMap alcmap = new AlcodMap();
1185 alcmap.setDnasq(seqHash(dnas[m]));
1187 createVamsasMapping(pmaps[m], dnas[m], null, false));
1188 // alc.addAlcodMap(alcmap);
1189 alc.getAlcodMap().add(alcmap);
1194 // vamsasSet.addAlcodonFrame(alc);
1195 vamsasSet.getAlcodonFrame().add(alc);
1198 // TODO: delete this ? dead code from 2.8.3->2.9 ?
1200 // AlcodonFrame alc = new AlcodonFrame();
1201 // vamsasSet.addAlcodonFrame(alc);
1202 // for (int p = 0; p < acf.aaWidth; p++)
1204 // Alcodon cmap = new Alcodon();
1205 // if (acf.codons[p] != null)
1207 // // Null codons indicate a gapped column in the translated peptide
1209 // cmap.setPos1(acf.codons[p][0]);
1210 // cmap.setPos2(acf.codons[p][1]);
1211 // cmap.setPos3(acf.codons[p][2]);
1213 // alc.addAlcodon(cmap);
1215 // if (acf.getProtMappings() != null
1216 // && acf.getProtMappings().length > 0)
1218 // SequenceI[] dnas = acf.getdnaSeqs();
1219 // jalview.datamodel.Mapping[] pmaps = acf.getProtMappings();
1220 // for (int m = 0; m < pmaps.length; m++)
1222 // AlcodMap alcmap = new AlcodMap();
1223 // alcmap.setDnasq(seqHash(dnas[m]));
1224 // alcmap.setMapping(createVamsasMapping(pmaps[m], dnas[m], null,
1226 // alc.addAlcodMap(alcmap);
1233 // /////////////////////////////////
1234 if (!storeDS && av.getCurrentTree() != null)
1236 // FIND ANY ASSOCIATED TREES
1237 // NOT IMPLEMENTED FOR HEADLESS STATE AT PRESENT
1238 if (Desktop.desktop != null)
1240 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1242 for (int t = 0; t < frames.length; t++)
1244 if (frames[t] instanceof TreePanel)
1246 TreePanel tp = (TreePanel) frames[t];
1248 if (tp.getTreeCanvas().getViewport().getAlignment() == jal)
1250 JalviewModel.Tree tree = new JalviewModel.Tree();
1251 tree.setTitle(tp.getTitle());
1252 tree.setCurrentTree((av.getCurrentTree() == tp.getTree()));
1253 tree.setNewick(tp.getTree().print());
1254 tree.setThreshold(tp.getTreeCanvas().getThreshold());
1256 tree.setFitToWindow(tp.fitToWindow.getState());
1257 tree.setFontName(tp.getTreeFont().getName());
1258 tree.setFontSize(tp.getTreeFont().getSize());
1259 tree.setFontStyle(tp.getTreeFont().getStyle());
1260 tree.setMarkUnlinked(tp.placeholdersMenu.getState());
1262 tree.setShowBootstrap(tp.bootstrapMenu.getState());
1263 tree.setShowDistances(tp.distanceMenu.getState());
1265 tree.setHeight(tp.getHeight());
1266 tree.setWidth(tp.getWidth());
1267 tree.setXpos(tp.getX());
1268 tree.setYpos(tp.getY());
1269 tree.setId(makeHashCode(tp, null));
1270 tree.setLinkToAllViews(
1271 tp.getTreeCanvas().isApplyToAllViews());
1273 // jms.addTree(tree);
1274 object.getTree().add(tree);
1284 if (!storeDS && Desktop.desktop != null)
1286 for (JInternalFrame frame : Desktop.desktop.getAllFrames())
1288 if (frame instanceof PCAPanel)
1290 PCAPanel panel = (PCAPanel) frame;
1291 if (panel.getAlignViewport().getAlignment() == jal)
1293 savePCA(panel, object);
1301 * store forward refs from an annotationRow to any groups
1303 IdentityHashMap<SequenceGroup, String> groupRefs = new IdentityHashMap<>();
1306 for (SequenceI sq : jal.getSequences())
1308 // Store annotation on dataset sequences only
1309 AlignmentAnnotation[] aa = sq.getAnnotation();
1310 if (aa != null && aa.length > 0)
1312 storeAlignmentAnnotation(aa, groupRefs, av, calcIdSet, storeDS,
1319 if (jal.getAlignmentAnnotation() != null)
1321 // Store the annotation shown on the alignment.
1322 AlignmentAnnotation[] aa = jal.getAlignmentAnnotation();
1323 storeAlignmentAnnotation(aa, groupRefs, av, calcIdSet, storeDS,
1328 if (jal.getGroups() != null)
1330 JGroup[] groups = new JGroup[jal.getGroups().size()];
1332 for (jalview.datamodel.SequenceGroup sg : jal.getGroups())
1334 JGroup jGroup = new JGroup();
1335 groups[++i] = jGroup;
1337 jGroup.setStart(sg.getStartRes());
1338 jGroup.setEnd(sg.getEndRes());
1339 jGroup.setName(sg.getName());
1340 if (groupRefs.containsKey(sg))
1342 // group has references so set its ID field
1343 jGroup.setId(groupRefs.get(sg));
1345 ColourSchemeI colourScheme = sg.getColourScheme();
1346 if (colourScheme != null)
1348 ResidueShaderI groupColourScheme = sg.getGroupColourScheme();
1349 if (groupColourScheme.conservationApplied())
1351 jGroup.setConsThreshold(groupColourScheme.getConservationInc());
1353 if (colourScheme instanceof jalview.schemes.UserColourScheme)
1356 setUserColourScheme(colourScheme, userColours,
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 if (av.getFeaturesDisplayed() != null)
1519 FeatureSettings fs = new FeatureSettings();
1521 FeatureRenderer fr = ap.getSeqPanel().seqCanvas
1522 .getFeatureRenderer();
1523 String[] renderOrder = fr.getRenderOrder().toArray(new String[0]);
1525 Vector<String> settingsAdded = new Vector<>();
1526 if (renderOrder != null)
1528 for (String featureType : renderOrder)
1530 FeatureSettings.Setting setting = new FeatureSettings.Setting();
1531 setting.setType(featureType);
1534 * save any filter for the feature type
1536 FeatureMatcherSetI filter = fr.getFeatureFilter(featureType);
1537 if (filter != null) {
1538 Iterator<FeatureMatcherI> filters = filter.getMatchers().iterator();
1539 FeatureMatcherI firstFilter = filters.next();
1540 setting.setMatcherSet(Jalview2XML.marshalFilter(
1541 firstFilter, filters, filter.isAnded()));
1545 * save colour scheme for the feature type
1547 FeatureColourI fcol = fr.getFeatureStyle(featureType);
1548 if (!fcol.isSimpleColour())
1550 setting.setColour(fcol.getMaxColour().getRGB());
1551 setting.setMincolour(fcol.getMinColour().getRGB());
1552 setting.setMin(fcol.getMin());
1553 setting.setMax(fcol.getMax());
1554 setting.setColourByLabel(fcol.isColourByLabel());
1555 if (fcol.isColourByAttribute())
1557 String[] attName = fcol.getAttributeName();
1558 setting.getAttributeName().add(attName[0]);
1559 if (attName.length > 1)
1561 setting.getAttributeName().add(attName[1]);
1564 setting.setAutoScale(fcol.isAutoScaled());
1565 setting.setThreshold(fcol.getThreshold());
1566 Color noColour = fcol.getNoColour();
1567 if (noColour == null)
1569 setting.setNoValueColour(NoValueColour.NONE);
1571 else if (noColour.equals(fcol.getMaxColour()))
1573 setting.setNoValueColour(NoValueColour.MAX);
1577 setting.setNoValueColour(NoValueColour.MIN);
1579 // -1 = No threshold, 0 = Below, 1 = Above
1580 setting.setThreshstate(fcol.isAboveThreshold() ? 1
1581 : (fcol.isBelowThreshold() ? 0 : -1));
1585 setting.setColour(fcol.getColour().getRGB());
1589 av.getFeaturesDisplayed().isVisible(featureType));
1591 .getOrder(featureType);
1594 setting.setOrder(rorder);
1596 /// fs.addSetting(setting);
1597 fs.getSetting().add(setting);
1598 settingsAdded.addElement(featureType);
1602 // is groups actually supposed to be a map here ?
1603 Iterator<String> en = fr.getFeatureGroups().iterator();
1604 Vector<String> groupsAdded = new Vector<>();
1605 while (en.hasNext())
1607 String grp = en.next();
1608 if (groupsAdded.contains(grp))
1612 Group g = new Group();
1614 g.setDisplay(((Boolean) fr.checkGroupVisibility(grp, false))
1617 fs.getGroup().add(g);
1618 groupsAdded.addElement(grp);
1620 // jms.setFeatureSettings(fs);
1621 object.setFeatureSettings(fs);
1624 if (av.hasHiddenColumns())
1626 jalview.datamodel.HiddenColumns hidden = av.getAlignment()
1627 .getHiddenColumns();
1630 warn("REPORT BUG: avoided null columnselection bug (DMAM reported). Please contact Jim about this.");
1634 Iterator<int[]> hiddenRegions = hidden.iterator();
1635 while (hiddenRegions.hasNext())
1637 int[] region = hiddenRegions.next();
1638 HiddenColumns hc = new HiddenColumns();
1639 hc.setStart(region[0]);
1640 hc.setEnd(region[1]);
1641 // view.addHiddenColumns(hc);
1642 view.getHiddenColumns().add(hc);
1646 if (calcIdSet.size() > 0)
1648 for (String calcId : calcIdSet)
1650 if (calcId.trim().length() > 0)
1652 CalcIdParam cidp = createCalcIdParam(calcId, av);
1653 // Some calcIds have no parameters.
1656 // view.addCalcIdParam(cidp);
1657 view.getCalcIdParam().add(cidp);
1663 // jms.addViewport(view);
1664 object.getViewport().add(view);
1666 // object.setJalviewModelSequence(jms);
1667 // object.getVamsasModel().addSequenceSet(vamsasSet);
1668 object.getVamsasModel().getSequenceSet().add(vamsasSet);
1670 if (jout != null && fileName != null)
1672 // We may not want to write the object to disk,
1673 // eg we can copy the alignViewport to a new view object
1674 // using save and then load
1677 fileName = fileName.replace('\\', '/');
1678 System.out.println("Writing jar entry " + fileName);
1679 JarEntry entry = new JarEntry(fileName);
1680 jout.putNextEntry(entry);
1681 PrintWriter pout = new PrintWriter(
1682 new OutputStreamWriter(jout, UTF_8));
1683 JAXBContext jaxbContext = JAXBContext
1684 .newInstance(JalviewModel.class);
1685 Marshaller jaxbMarshaller = jaxbContext.createMarshaller();
1687 // output pretty printed
1688 // jaxbMarshaller.setProperty(Marshaller.JAXB_FORMATTED_OUTPUT, true);
1689 jaxbMarshaller.marshal(
1690 new ObjectFactory().createJalviewModel(object), pout);
1692 // jaxbMarshaller.marshal(object, pout);
1693 // marshaller.marshal(object);
1696 } catch (Exception ex)
1698 // TODO: raise error in GUI if marshalling failed.
1699 System.err.println("Error writing Jalview project");
1700 ex.printStackTrace();
1707 * Writes PCA viewer attributes and computed values to an XML model object and
1708 * adds it to the JalviewModel. Any exceptions are reported by logging.
1710 protected void savePCA(PCAPanel panel, JalviewModel object)
1714 PcaViewer viewer = new PcaViewer();
1715 viewer.setHeight(panel.getHeight());
1716 viewer.setWidth(panel.getWidth());
1717 viewer.setXpos(panel.getX());
1718 viewer.setYpos(panel.getY());
1719 viewer.setTitle(panel.getTitle());
1720 PCAModel pcaModel = panel.getPcaModel();
1721 viewer.setScoreModelName(pcaModel.getScoreModelName());
1722 viewer.setXDim(panel.getSelectedDimensionIndex(X));
1723 viewer.setYDim(panel.getSelectedDimensionIndex(Y));
1724 viewer.setZDim(panel.getSelectedDimensionIndex(Z));
1726 panel.getRotatableCanvas().getBackgroundColour().getRGB());
1727 viewer.setScaleFactor(panel.getRotatableCanvas().getScaleFactor());
1728 float[] spMin = panel.getRotatableCanvas().getSeqMin();
1729 SeqPointMin spmin = new SeqPointMin();
1730 spmin.setXPos(spMin[0]);
1731 spmin.setYPos(spMin[1]);
1732 spmin.setZPos(spMin[2]);
1733 viewer.setSeqPointMin(spmin);
1734 float[] spMax = panel.getRotatableCanvas().getSeqMax();
1735 SeqPointMax spmax = new SeqPointMax();
1736 spmax.setXPos(spMax[0]);
1737 spmax.setYPos(spMax[1]);
1738 spmax.setZPos(spMax[2]);
1739 viewer.setSeqPointMax(spmax);
1740 viewer.setShowLabels(panel.getRotatableCanvas().isShowLabels());
1741 viewer.setLinkToAllViews(
1742 panel.getRotatableCanvas().isApplyToAllViews());
1743 SimilarityParamsI sp = pcaModel.getSimilarityParameters();
1744 viewer.setIncludeGaps(sp.includeGaps());
1745 viewer.setMatchGaps(sp.matchGaps());
1746 viewer.setIncludeGappedColumns(sp.includeGappedColumns());
1747 viewer.setDenominateByShortestLength(sp.denominateByShortestLength());
1750 * sequence points on display
1752 for (jalview.datamodel.SequencePoint spt : pcaModel
1753 .getSequencePoints())
1755 SequencePoint point = new SequencePoint();
1756 point.setSequenceRef(seqHash(spt.getSequence()));
1757 point.setXPos(spt.coord.x);
1758 point.setYPos(spt.coord.y);
1759 point.setZPos(spt.coord.z);
1760 viewer.getSequencePoint().add(point);
1764 * (end points of) axes on display
1766 for (Point p : panel.getRotatableCanvas().getAxisEndPoints())
1769 Axis axis = new Axis();
1773 viewer.getAxis().add(axis);
1777 * raw PCA data (note we are not restoring PCA inputs here -
1778 * alignment view, score model, similarity parameters)
1780 PcaDataType data = new PcaDataType();
1781 viewer.setPcaData(data);
1782 PCA pca = pcaModel.getPcaData();
1784 DoubleMatrix pm = new DoubleMatrix();
1785 saveDoubleMatrix(pca.getPairwiseScores(), pm);
1786 data.setPairwiseMatrix(pm);
1788 DoubleMatrix tm = new DoubleMatrix();
1789 saveDoubleMatrix(pca.getTridiagonal(), tm);
1790 data.setTridiagonalMatrix(tm);
1792 DoubleMatrix eigenMatrix = new DoubleMatrix();
1793 data.setEigenMatrix(eigenMatrix);
1794 saveDoubleMatrix(pca.getEigenmatrix(), eigenMatrix);
1796 object.getPcaViewer().add(viewer);
1797 } catch (Throwable t)
1799 Cache.log.error("Error saving PCA: " + t.getMessage());
1804 * Stores values from a matrix into an XML element, including (if present) the
1809 * @see #loadDoubleMatrix(DoubleMatrix)
1811 protected void saveDoubleMatrix(MatrixI m, DoubleMatrix xmlMatrix)
1813 xmlMatrix.setRows(m.height());
1814 xmlMatrix.setColumns(m.width());
1815 for (int i = 0; i < m.height(); i++)
1817 DoubleVector row = new DoubleVector();
1818 for (int j = 0; j < m.width(); j++)
1820 row.getV().add(m.getValue(i, j));
1822 xmlMatrix.getRow().add(row);
1824 if (m.getD() != null)
1826 DoubleVector dVector = new DoubleVector();
1827 for (double d : m.getD())
1829 dVector.getV().add(d);
1831 xmlMatrix.setD(dVector);
1833 if (m.getE() != null)
1835 DoubleVector eVector = new DoubleVector();
1836 for (double e : m.getE())
1838 eVector.getV().add(e);
1840 xmlMatrix.setE(eVector);
1845 * Loads XML matrix data into a new Matrix object, including the D and/or E
1846 * vectors (if present)
1850 * @see Jalview2XML#saveDoubleMatrix(MatrixI, DoubleMatrix)
1852 protected MatrixI loadDoubleMatrix(DoubleMatrix mData)
1854 int rows = mData.getRows();
1855 double[][] vals = new double[rows][];
1857 for (int i = 0; i < rows; i++)
1859 List<Double> dVector = mData.getRow().get(i).getV();
1860 vals[i] = new double[dVector.size()];
1862 for (Double d : dVector)
1868 MatrixI m = new Matrix(vals);
1870 if (mData.getD() != null)
1872 List<Double> dVector = mData.getD().getV();
1873 double[] vec = new double[dVector.size()];
1875 for (Double d : dVector)
1881 if (mData.getE() != null)
1883 List<Double> dVector = mData.getE().getV();
1884 double[] vec = new double[dVector.size()];
1886 for (Double d : dVector)
1897 * Save any Varna viewers linked to this sequence. Writes an rnaViewer element
1898 * for each viewer, with
1900 * <li>viewer geometry (position, size, split pane divider location)</li>
1901 * <li>index of the selected structure in the viewer (currently shows gapped
1903 * <li>the id of the annotation holding RNA secondary structure</li>
1904 * <li>(currently only one SS is shown per viewer, may be more in future)</li>
1906 * Varna viewer state is also written out (in native Varna XML) to separate
1907 * project jar entries. A separate entry is written for each RNA structure
1908 * displayed, with the naming convention
1910 * <li>rna_viewId_sequenceId_annotationId_[gapped|trimmed]</li>
1918 * @param storeDataset
1920 protected void saveRnaViewers(JarOutputStream jout, JSeq jseq,
1921 final SequenceI jds, List<String> viewIds, AlignmentPanel ap,
1922 boolean storeDataset)
1924 if (Desktop.desktop == null)
1928 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1929 for (int f = frames.length - 1; f > -1; f--)
1931 if (frames[f] instanceof AppVarna)
1933 AppVarna varna = (AppVarna) frames[f];
1935 * link the sequence to every viewer that is showing it and is linked to
1936 * its alignment panel
1938 if (varna.isListeningFor(jds) && ap == varna.getAlignmentPanel())
1940 String viewId = varna.getViewId();
1941 RnaViewer rna = new RnaViewer();
1942 rna.setViewId(viewId);
1943 rna.setTitle(varna.getTitle());
1944 rna.setXpos(varna.getX());
1945 rna.setYpos(varna.getY());
1946 rna.setWidth(varna.getWidth());
1947 rna.setHeight(varna.getHeight());
1948 rna.setDividerLocation(varna.getDividerLocation());
1949 rna.setSelectedRna(varna.getSelectedIndex());
1950 // jseq.addRnaViewer(rna);
1951 jseq.getRnaViewer().add(rna);
1954 * Store each Varna panel's state once in the project per sequence.
1955 * First time through only (storeDataset==false)
1957 // boolean storeSessions = false;
1958 // String sequenceViewId = viewId + seqsToIds.get(jds);
1959 // if (!storeDataset && !viewIds.contains(sequenceViewId))
1961 // viewIds.add(sequenceViewId);
1962 // storeSessions = true;
1964 for (RnaModel model : varna.getModels())
1966 if (model.seq == jds)
1969 * VARNA saves each view (sequence or alignment secondary
1970 * structure, gapped or trimmed) as a separate XML file
1972 String jarEntryName = rnaSessions.get(model);
1973 if (jarEntryName == null)
1976 String varnaStateFile = varna.getStateInfo(model.rna);
1977 jarEntryName = RNA_PREFIX + viewId + "_" + nextCounter();
1978 copyFileToJar(jout, varnaStateFile, jarEntryName);
1979 rnaSessions.put(model, jarEntryName);
1981 SecondaryStructure ss = new SecondaryStructure();
1982 String annotationId = varna.getAnnotation(jds).annotationId;
1983 ss.setAnnotationId(annotationId);
1984 ss.setViewerState(jarEntryName);
1985 ss.setGapped(model.gapped);
1986 ss.setTitle(model.title);
1987 // rna.addSecondaryStructure(ss);
1988 rna.getSecondaryStructure().add(ss);
1997 * Copy the contents of a file to a new entry added to the output jar
2001 * @param jarEntryName
2003 protected void copyFileToJar(JarOutputStream jout, String infilePath,
2004 String jarEntryName)
2006 DataInputStream dis = null;
2009 File file = new File(infilePath);
2010 if (file.exists() && jout != null)
2012 dis = new DataInputStream(new FileInputStream(file));
2013 byte[] data = new byte[(int) file.length()];
2014 dis.readFully(data);
2015 writeJarEntry(jout, jarEntryName, data);
2017 } catch (Exception ex)
2019 ex.printStackTrace();
2027 } catch (IOException e)
2036 * Write the data to a new entry of given name in the output jar file
2039 * @param jarEntryName
2041 * @throws IOException
2043 protected void writeJarEntry(JarOutputStream jout, String jarEntryName,
2044 byte[] data) throws IOException
2048 jarEntryName = jarEntryName.replace('\\','/');
2049 System.out.println("Writing jar entry " + jarEntryName);
2050 jout.putNextEntry(new JarEntry(jarEntryName));
2051 DataOutputStream dout = new DataOutputStream(jout);
2052 dout.write(data, 0, data.length);
2059 * Save the state of a structure viewer
2064 * the archive XML element under which to save the state
2067 * @param matchedFile
2071 protected String saveStructureState(AlignmentPanel ap, SequenceI jds,
2072 Pdbids pdb, PDBEntry entry, List<String> viewIds,
2073 String matchedFile, StructureViewerBase viewFrame)
2075 final AAStructureBindingModel bindingModel = viewFrame.getBinding();
2078 * Look for any bindings for this viewer to the PDB file of interest
2079 * (including part matches excluding chain id)
2081 for (int peid = 0; peid < bindingModel.getPdbCount(); peid++)
2083 final PDBEntry pdbentry = bindingModel.getPdbEntry(peid);
2084 final String pdbId = pdbentry.getId();
2085 if (!pdbId.equals(entry.getId())
2086 && !(entry.getId().length() > 4 && entry.getId().toLowerCase()
2087 .startsWith(pdbId.toLowerCase())))
2090 * not interested in a binding to a different PDB entry here
2094 if (matchedFile == null)
2096 matchedFile = pdbentry.getFile();
2098 else if (!matchedFile.equals(pdbentry.getFile()))
2101 "Probably lost some PDB-Sequence mappings for this structure file (which apparently has same PDB Entry code): "
2102 + pdbentry.getFile());
2106 // can get at it if the ID
2107 // match is ambiguous (e.g.
2110 for (int smap = 0; smap < viewFrame.getBinding()
2111 .getSequence()[peid].length; smap++)
2113 // if (jal.findIndex(jmol.jmb.sequence[peid][smap]) > -1)
2114 if (jds == viewFrame.getBinding().getSequence()[peid][smap])
2116 StructureState state = new StructureState();
2117 state.setVisible(true);
2118 state.setXpos(viewFrame.getX());
2119 state.setYpos(viewFrame.getY());
2120 state.setWidth(viewFrame.getWidth());
2121 state.setHeight(viewFrame.getHeight());
2122 final String viewId = viewFrame.getViewId();
2123 state.setViewId(viewId);
2124 state.setAlignwithAlignPanel(viewFrame.isUsedforaligment(ap));
2125 state.setColourwithAlignPanel(viewFrame.isUsedforcolourby(ap));
2126 state.setColourByJmol(viewFrame.isColouredByViewer());
2127 state.setType(viewFrame.getViewerType().toString());
2128 // pdb.addStructureState(state);
2129 pdb.getStructureState().add(state);
2137 * Populates the AnnotationColourScheme xml for save. This captures the
2138 * settings of the options in the 'Colour by Annotation' dialog.
2141 * @param userColours
2145 private AnnotationColourScheme constructAnnotationColours(
2146 AnnotationColourGradient acg, List<UserColourScheme> userColours,
2149 AnnotationColourScheme ac = new AnnotationColourScheme();
2150 ac.setAboveThreshold(acg.getAboveThreshold());
2151 ac.setThreshold(acg.getAnnotationThreshold());
2152 // 2.10.2 save annotationId (unique) not annotation label
2153 ac.setAnnotation(acg.getAnnotation().annotationId);
2154 if (acg.getBaseColour() instanceof UserColourScheme)
2157 setUserColourScheme(acg.getBaseColour(), userColours, jm));
2162 ColourSchemeProperty.getColourName(acg.getBaseColour()));
2165 ac.setMaxColour(acg.getMaxColour().getRGB());
2166 ac.setMinColour(acg.getMinColour().getRGB());
2167 ac.setPerSequence(acg.isSeqAssociated());
2168 ac.setPredefinedColours(acg.isPredefinedColours());
2172 private void storeAlignmentAnnotation(AlignmentAnnotation[] aa,
2173 IdentityHashMap<SequenceGroup, String> groupRefs,
2174 AlignmentViewport av, Set<String> calcIdSet, boolean storeDS,
2175 SequenceSet vamsasSet)
2178 for (int i = 0; i < aa.length; i++)
2180 Annotation an = new Annotation();
2182 AlignmentAnnotation annotation = aa[i];
2183 if (annotation.annotationId != null)
2185 annotationIds.put(annotation.annotationId, annotation);
2188 an.setId(annotation.annotationId);
2190 an.setVisible(annotation.visible);
2192 an.setDescription(annotation.description);
2194 if (annotation.sequenceRef != null)
2196 // 2.9 JAL-1781 xref on sequence id rather than name
2197 an.setSequenceRef(seqsToIds.get(annotation.sequenceRef));
2199 if (annotation.groupRef != null)
2201 String groupIdr = groupRefs.get(annotation.groupRef);
2202 if (groupIdr == null)
2204 // make a locally unique String
2205 groupRefs.put(annotation.groupRef,
2206 groupIdr = ("" + System.currentTimeMillis()
2207 + annotation.groupRef.getName()
2208 + groupRefs.size()));
2210 an.setGroupRef(groupIdr.toString());
2213 // store all visualization attributes for annotation
2214 an.setGraphHeight(annotation.graphHeight);
2215 an.setCentreColLabels(annotation.centreColLabels);
2216 an.setScaleColLabels(annotation.scaleColLabel);
2217 an.setShowAllColLabels(annotation.showAllColLabels);
2218 an.setBelowAlignment(annotation.belowAlignment);
2220 if (annotation.graph > 0)
2223 an.setGraphType(annotation.graph);
2224 an.setGraphGroup(annotation.graphGroup);
2225 if (annotation.getThreshold() != null)
2227 ThresholdLine line = new ThresholdLine();
2228 line.setLabel(annotation.getThreshold().label);
2229 line.setValue(annotation.getThreshold().value);
2230 line.setColour(annotation.getThreshold().colour.getRGB());
2231 an.setThresholdLine(line);
2239 an.setLabel(annotation.label);
2241 if (annotation == av.getAlignmentQualityAnnot()
2242 || annotation == av.getAlignmentConservationAnnotation()
2243 || annotation == av.getAlignmentConsensusAnnotation()
2244 || annotation.autoCalculated)
2246 // new way of indicating autocalculated annotation -
2247 an.setAutoCalculated(annotation.autoCalculated);
2249 if (annotation.hasScore())
2251 an.setScore(annotation.getScore());
2254 if (annotation.getCalcId() != null)
2256 calcIdSet.add(annotation.getCalcId());
2257 an.setCalcId(annotation.getCalcId());
2259 if (annotation.hasProperties())
2261 for (String pr : annotation.getProperties())
2263 jalview.xml.binding.jalview.Annotation.Property prop = new jalview.xml.binding.jalview.Annotation.Property();
2265 prop.setValue(annotation.getProperty(pr));
2266 // an.addProperty(prop);
2267 an.getProperty().add(prop);
2271 AnnotationElement ae;
2272 if (annotation.annotations != null)
2274 an.setScoreOnly(false);
2275 for (int a = 0; a < annotation.annotations.length; a++)
2277 if ((annotation == null) || (annotation.annotations[a] == null))
2282 ae = new AnnotationElement();
2283 if (annotation.annotations[a].description != null)
2285 ae.setDescription(annotation.annotations[a].description);
2287 if (annotation.annotations[a].displayCharacter != null)
2289 ae.setDisplayCharacter(
2290 annotation.annotations[a].displayCharacter);
2293 if (!Float.isNaN(annotation.annotations[a].value))
2295 ae.setValue(annotation.annotations[a].value);
2299 if (annotation.annotations[a].secondaryStructure > ' ')
2301 ae.setSecondaryStructure(
2302 annotation.annotations[a].secondaryStructure + "");
2305 if (annotation.annotations[a].colour != null
2306 && annotation.annotations[a].colour != java.awt.Color.black)
2308 ae.setColour(annotation.annotations[a].colour.getRGB());
2311 // an.addAnnotationElement(ae);
2312 an.getAnnotationElement().add(ae);
2313 if (annotation.autoCalculated)
2315 // only write one non-null entry into the annotation row -
2316 // sufficient to get the visualization attributes necessary to
2324 an.setScoreOnly(true);
2326 if (!storeDS || (storeDS && !annotation.autoCalculated))
2328 // skip autocalculated annotation - these are only provided for
2330 // vamsasSet.addAnnotation(an);
2331 vamsasSet.getAnnotation().add(an);
2337 private CalcIdParam createCalcIdParam(String calcId, AlignViewport av)
2339 AutoCalcSetting settings = av.getCalcIdSettingsFor(calcId);
2340 if (settings != null)
2342 CalcIdParam vCalcIdParam = new CalcIdParam();
2343 vCalcIdParam.setCalcId(calcId);
2344 // vCalcIdParam.addServiceURL(settings.getServiceURI());
2345 vCalcIdParam.getServiceURL().add(settings.getServiceURI());
2346 // generic URI allowing a third party to resolve another instance of the
2347 // service used for this calculation
2348 for (String url : settings.getServiceURLs())
2350 // vCalcIdParam.addServiceURL(urls);
2351 vCalcIdParam.getServiceURL().add(url);
2353 vCalcIdParam.setVersion("1.0");
2354 if (settings.getPreset() != null)
2356 WsParamSetI setting = settings.getPreset();
2357 vCalcIdParam.setName(setting.getName());
2358 vCalcIdParam.setDescription(setting.getDescription());
2362 vCalcIdParam.setName("");
2363 vCalcIdParam.setDescription("Last used parameters");
2365 // need to be able to recover 1) settings 2) user-defined presets or
2366 // recreate settings from preset 3) predefined settings provided by
2367 // service - or settings that can be transferred (or discarded)
2368 vCalcIdParam.setParameters(
2369 settings.getWsParamFile().replace("\n", "|\\n|"));
2370 vCalcIdParam.setAutoUpdate(settings.isAutoUpdate());
2371 // todo - decide if updateImmediately is needed for any projects.
2373 return vCalcIdParam;
2378 private boolean recoverCalcIdParam(CalcIdParam calcIdParam,
2381 if (calcIdParam.getVersion().equals("1.0"))
2383 final String[] calcIds = calcIdParam.getServiceURL().toArray(new String[0]);
2384 Jws2Instance service = Jws2Discoverer.getDiscoverer()
2385 .getPreferredServiceFor(calcIds);
2386 if (service != null)
2388 WsParamSetI parmSet = null;
2391 parmSet = service.getParamStore().parseServiceParameterFile(
2392 calcIdParam.getName(), calcIdParam.getDescription(),
2394 calcIdParam.getParameters().replace("|\\n|", "\n"));
2395 } catch (IOException x)
2397 warn("Couldn't parse parameter data for "
2398 + calcIdParam.getCalcId(), x);
2401 List<ArgumentI> argList = null;
2402 if (calcIdParam.getName().length() > 0)
2404 parmSet = service.getParamStore()
2405 .getPreset(calcIdParam.getName());
2406 if (parmSet != null)
2408 // TODO : check we have a good match with settings in AACon -
2409 // otherwise we'll need to create a new preset
2414 argList = parmSet.getArguments();
2417 AAConSettings settings = new AAConSettings(
2418 calcIdParam.isAutoUpdate(), service, parmSet, argList);
2419 av.setCalcIdSettingsFor(calcIdParam.getCalcId(), settings,
2420 calcIdParam.isNeedsUpdate());
2425 warn("Cannot resolve a service for the parameters used in this project. Try configuring a JABAWS server.");
2429 throw new Error(MessageManager.formatMessage(
2430 "error.unsupported_version_calcIdparam", new Object[]
2431 { calcIdParam.toString() }));
2435 * External mapping between jalview objects and objects yielding a valid and
2436 * unique object ID string. This is null for normal Jalview project IO, but
2437 * non-null when a jalview project is being read or written as part of a
2440 IdentityHashMap jv2vobj = null;
2443 * Construct a unique ID for jvobj using either existing bindings or if none
2444 * exist, the result of the hashcode call for the object.
2447 * jalview data object
2448 * @return unique ID for referring to jvobj
2450 private String makeHashCode(Object jvobj, String altCode)
2452 if (jv2vobj != null)
2454 Object id = jv2vobj.get(jvobj);
2457 return id.toString();
2459 // check string ID mappings
2460 if (jvids2vobj != null && jvobj instanceof String)
2462 id = jvids2vobj.get(jvobj);
2466 return id.toString();
2468 // give up and warn that something has gone wrong
2469 warn("Cannot find ID for object in external mapping : " + jvobj);
2475 * return local jalview object mapped to ID, if it exists
2479 * @return null or object bound to idcode
2481 private Object retrieveExistingObj(String idcode)
2483 if (idcode != null && vobj2jv != null)
2485 return vobj2jv.get(idcode);
2491 * binding from ID strings from external mapping table to jalview data model
2494 private Hashtable vobj2jv;
2496 private Sequence createVamsasSequence(String id, SequenceI jds)
2498 return createVamsasSequence(true, id, jds, null);
2501 private Sequence createVamsasSequence(boolean recurse, String id,
2502 SequenceI jds, SequenceI parentseq)
2504 Sequence vamsasSeq = new Sequence();
2505 vamsasSeq.setId(id);
2506 vamsasSeq.setName(jds.getName());
2507 vamsasSeq.setSequence(jds.getSequenceAsString());
2508 vamsasSeq.setDescription(jds.getDescription());
2509 List<DBRefEntry> dbrefs = null;
2510 if (jds.getDatasetSequence() != null)
2512 vamsasSeq.setDsseqid(seqHash(jds.getDatasetSequence()));
2516 // seqId==dsseqid so we can tell which sequences really are
2517 // dataset sequences only
2518 vamsasSeq.setDsseqid(id);
2519 dbrefs = jds.getDBRefs();
2520 if (parentseq == null)
2527 for (int d = 0, nd = dbrefs.size(); d < nd; d++)
2529 DBRef dbref = new DBRef();
2530 DBRefEntry ref = dbrefs.get(d);
2531 dbref.setSource(ref.getSource());
2532 dbref.setVersion(ref.getVersion());
2533 dbref.setAccessionId(ref.getAccessionId());
2536 Mapping mp = createVamsasMapping(ref.getMap(), parentseq,
2538 dbref.setMapping(mp);
2540 // vamsasSeq.addDBRef(dbref);
2541 vamsasSeq.getDBRef().add(dbref);
2547 private Mapping createVamsasMapping(jalview.datamodel.Mapping jmp,
2548 SequenceI parentseq, SequenceI jds, boolean recurse)
2551 if (jmp.getMap() != null)
2555 jalview.util.MapList mlst = jmp.getMap();
2556 List<int[]> r = mlst.getFromRanges();
2557 for (int[] range : r)
2559 MapListFrom mfrom = new MapListFrom();
2560 mfrom.setStart(range[0]);
2561 mfrom.setEnd(range[1]);
2562 // mp.addMapListFrom(mfrom);
2563 mp.getMapListFrom().add(mfrom);
2565 r = mlst.getToRanges();
2566 for (int[] range : r)
2568 MapListTo mto = new MapListTo();
2569 mto.setStart(range[0]);
2570 mto.setEnd(range[1]);
2571 // mp.addMapListTo(mto);
2572 mp.getMapListTo().add(mto);
2574 mp.setMapFromUnit(BigInteger.valueOf(mlst.getFromRatio()));
2575 mp.setMapToUnit(BigInteger.valueOf(mlst.getToRatio()));
2576 if (jmp.getTo() != null)
2578 // MappingChoice mpc = new MappingChoice();
2580 // check/create ID for the sequence referenced by getTo()
2583 SequenceI ps = null;
2584 if (parentseq != jmp.getTo()
2585 && parentseq.getDatasetSequence() != jmp.getTo())
2587 // chaining dbref rather than a handshaking one
2588 jmpid = seqHash(ps = jmp.getTo());
2592 jmpid = seqHash(ps = parentseq);
2594 // mpc.setDseqFor(jmpid);
2595 mp.setDseqFor(jmpid);
2596 if (!seqRefIds.containsKey(jmpid))
2598 jalview.bin.Cache.log.debug("creatign new DseqFor ID");
2599 seqRefIds.put(jmpid, ps);
2603 jalview.bin.Cache.log.debug("reusing DseqFor ID");
2606 // mp.setMappingChoice(mpc);
2612 String setUserColourScheme(jalview.schemes.ColourSchemeI cs,
2613 List<UserColourScheme> userColours, JalviewModel jm)
2616 jalview.schemes.UserColourScheme ucs = (jalview.schemes.UserColourScheme) cs;
2617 boolean newucs = false;
2618 if (!userColours.contains(ucs))
2620 userColours.add(ucs);
2623 id = "ucs" + userColours.indexOf(ucs);
2626 // actually create the scheme's entry in the XML model
2627 java.awt.Color[] colours = ucs.getColours();
2628 UserColours uc = new UserColours();
2629 // UserColourScheme jbucs = new UserColourScheme();
2630 JalviewUserColours jbucs = new JalviewUserColours();
2632 for (int i = 0; i < colours.length; i++)
2634 Colour col = new Colour();
2635 col.setName(ResidueProperties.aa[i]);
2636 col.setRGB(jalview.util.Format.getHexString(colours[i]));
2637 // jbucs.addColour(col);
2638 jbucs.getColour().add(col);
2640 if (ucs.getLowerCaseColours() != null)
2642 colours = ucs.getLowerCaseColours();
2643 for (int i = 0; i < colours.length; i++)
2645 Colour col = new Colour();
2646 col.setName(ResidueProperties.aa[i].toLowerCase());
2647 col.setRGB(jalview.util.Format.getHexString(colours[i]));
2648 // jbucs.addColour(col);
2649 jbucs.getColour().add(col);
2654 uc.setUserColourScheme(jbucs);
2655 // jm.addUserColours(uc);
2656 jm.getUserColours().add(uc);
2662 jalview.schemes.UserColourScheme getUserColourScheme(
2663 JalviewModel jm, String id)
2665 List<UserColours> uc = jm.getUserColours();
2666 UserColours colours = null;
2668 for (int i = 0; i < uc.length; i++)
2670 if (uc[i].getId().equals(id))
2677 for (UserColours c : uc)
2679 if (c.getId().equals(id))
2686 java.awt.Color[] newColours = new java.awt.Color[24];
2688 for (int i = 0; i < 24; i++)
2690 newColours[i] = new java.awt.Color(Integer.parseInt(
2691 // colours.getUserColourScheme().getColour(i).getRGB(), 16));
2692 colours.getUserColourScheme().getColour().get(i).getRGB(),
2696 jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(
2699 if (colours.getUserColourScheme().getColour().size()/*Count()*/ > 24)
2701 newColours = new java.awt.Color[23];
2702 for (int i = 0; i < 23; i++)
2704 newColours[i] = new java.awt.Color(Integer.parseInt(
2705 colours.getUserColourScheme().getColour().get(i + 24)
2709 ucs.setLowerCaseColours(newColours);
2716 * contains last error message (if any) encountered by XML loader.
2718 String errorMessage = null;
2721 * flag to control whether the Jalview2XML_V1 parser should be deferred to if
2722 * exceptions are raised during project XML parsing
2724 public boolean attemptversion1parse = false;
2727 * Load a jalview project archive from a jar file
2730 * - HTTP URL or filename
2732 public AlignFrame loadJalviewAlign(final Object file)
2735 jalview.gui.AlignFrame af = null;
2739 // create list to store references for any new Jmol viewers created
2740 newStructureViewers = new Vector<>();
2741 // UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
2742 // Workaround is to make sure caller implements the JarInputStreamProvider
2744 // so we can re-open the jar input stream for each entry.
2746 jarInputStreamProvider jprovider = createjarInputStreamProvider(file);
2747 af = loadJalviewAlign(jprovider);
2750 af.setMenusForViewport();
2752 } catch (MalformedURLException e)
2754 errorMessage = "Invalid URL format for '" + file + "'";
2760 SwingUtilities.invokeAndWait(new Runnable()
2765 setLoadingFinishedForNewStructureViewers();
2768 } catch (Exception x)
2770 System.err.println("Error loading alignment: " + x.getMessage());
2776 @SuppressWarnings("unused")
2777 private jarInputStreamProvider createjarInputStreamProvider(final Object ofile) throws MalformedURLException {
2779 // BH 2018 allow for bytes already attached to File object
2781 String file = (ofile instanceof File ? ((File) ofile).getCanonicalPath() : ofile.toString());
2782 byte[] bytes = Platform.getFileBytes((File) ofile);
2784 errorMessage = null;
2785 uniqueSetSuffix = null;
2787 viewportsAdded.clear();
2788 frefedSequence = null;
2790 if (file.startsWith("http://")) {
2791 url = new URL(file);
2793 final URL _url = url;
2794 return new jarInputStreamProvider() {
2797 public JarInputStream getJarInputStream() throws IOException {
2798 if (bytes != null) {
2799 // System.out.println("Jalview2XML: opening byte jarInputStream for bytes.length=" + bytes.length);
2800 return new JarInputStream(new ByteArrayInputStream(bytes));
2803 // System.out.println("Jalview2XML: opening url jarInputStream for " + _url);
2804 return new JarInputStream(_url.openStream());
2806 // System.out.println("Jalview2XML: opening file jarInputStream for " + file);
2807 return new JarInputStream(new FileInputStream(file));
2812 public String getFilename() {
2816 } catch (IOException e) {
2817 e.printStackTrace();
2823 * Recover jalview session from a jalview project archive. Caller may
2824 * initialise uniqueSetSuffix, seqRefIds, viewportsAdded and frefedSequence
2825 * themselves. Any null fields will be initialised with default values,
2826 * non-null fields are left alone.
2831 public AlignFrame loadJalviewAlign(final jarInputStreamProvider jprovider)
2833 errorMessage = null;
2834 if (uniqueSetSuffix == null)
2836 uniqueSetSuffix = System.currentTimeMillis() % 100000 + "";
2838 if (seqRefIds == null)
2842 AlignFrame af = null, _af = null;
2843 IdentityHashMap<AlignmentI, AlignmentI> importedDatasets = new IdentityHashMap<>();
2844 Map<String, AlignFrame> gatherToThisFrame = new HashMap<>();
2845 final String file = jprovider.getFilename();
2848 JarInputStream jin = null;
2849 JarEntry jarentry = null;
2854 jin = jprovider.getJarInputStream();
2855 for (int i = 0; i < entryCount; i++)
2857 jarentry = jin.getNextJarEntry();
2860 if (jarentry != null && jarentry.getName().endsWith(".xml"))
2862 JAXBContext jc = JAXBContext
2863 .newInstance("jalview.xml.binding.jalview");
2864 XMLStreamReader streamReader = XMLInputFactory.newInstance()
2865 .createXMLStreamReader(jin);
2866 javax.xml.bind.Unmarshaller um = jc.createUnmarshaller();
2867 JAXBElement<JalviewModel> jbe = um
2868 .unmarshal(streamReader, JalviewModel.class);
2869 JalviewModel object = jbe.getValue();
2871 if (true) // !skipViewport(object))
2873 _af = loadFromObject(object, file, true, jprovider);
2874 if (_af != null && object.getViewport().size() > 0)
2875 // getJalviewModelSequence().getViewportCount() > 0)
2879 // store a reference to the first view
2882 if (_af.getViewport().isGatherViewsHere())
2884 // if this is a gathered view, keep its reference since
2885 // after gathering views, only this frame will remain
2887 gatherToThisFrame.put(_af.getViewport().getSequenceSetId(),
2890 // Save dataset to register mappings once all resolved
2891 importedDatasets.put(
2892 af.getViewport().getAlignment().getDataset(),
2893 af.getViewport().getAlignment().getDataset());
2898 else if (jarentry != null)
2900 // Some other file here.
2903 } while (jarentry != null);
2904 resolveFrefedSequences();
2905 } catch (IOException ex)
2907 ex.printStackTrace();
2908 errorMessage = "Couldn't locate Jalview XML file : " + file;
2910 "Exception whilst loading jalview XML file : " + ex + "\n");
2911 } catch (Exception ex)
2913 System.err.println("Parsing as Jalview Version 2 file failed.");
2914 ex.printStackTrace(System.err);
2915 if (attemptversion1parse)
2917 // used to attempt to parse as V1 castor-generated xml
2919 if (Desktop.instance != null)
2921 Desktop.instance.stopLoading();
2925 System.out.println("Successfully loaded archive file");
2928 ex.printStackTrace();
2931 "Exception whilst loading jalview XML file : " + ex + "\n");
2932 } catch (OutOfMemoryError e)
2934 // Don't use the OOM Window here
2935 errorMessage = "Out of memory loading jalview XML file";
2936 System.err.println("Out of memory whilst loading jalview XML file");
2937 e.printStackTrace();
2941 * Regather multiple views (with the same sequence set id) to the frame (if
2942 * any) that is flagged as the one to gather to, i.e. convert them to tabbed
2943 * views instead of separate frames. Note this doesn't restore a state where
2944 * some expanded views in turn have tabbed views - the last "first tab" read
2945 * in will play the role of gatherer for all.
2947 for (AlignFrame fr : gatherToThisFrame.values())
2949 Desktop.instance.gatherViews(fr);
2952 restoreSplitFrames();
2953 for (AlignmentI ds : importedDatasets.keySet())
2955 if (ds.getCodonFrames() != null)
2957 StructureSelectionManager
2958 .getStructureSelectionManager(Desktop.instance)
2959 .registerMappings(ds.getCodonFrames());
2962 if (errorMessage != null)
2967 if (Desktop.instance != null)
2969 Desktop.instance.stopLoading();
2976 * Try to reconstruct and display SplitFrame windows, where each contains
2977 * complementary dna and protein alignments. Done by pairing up AlignFrame
2978 * objects (created earlier) which have complementary viewport ids associated.
2980 protected void restoreSplitFrames()
2982 List<SplitFrame> gatherTo = new ArrayList<>();
2983 List<AlignFrame> addedToSplitFrames = new ArrayList<>();
2984 Map<String, AlignFrame> dna = new HashMap<>();
2987 * Identify the DNA alignments
2989 for (Entry<Viewport, AlignFrame> candidate : splitFrameCandidates
2992 AlignFrame af = candidate.getValue();
2993 if (af.getViewport().getAlignment().isNucleotide())
2995 dna.put(candidate.getKey().getId(), af);
3000 * Try to match up the protein complements
3002 for (Entry<Viewport, AlignFrame> candidate : splitFrameCandidates
3005 AlignFrame af = candidate.getValue();
3006 if (!af.getViewport().getAlignment().isNucleotide())
3008 String complementId = candidate.getKey().getComplementId();
3009 // only non-null complements should be in the Map
3010 if (complementId != null && dna.containsKey(complementId))
3012 final AlignFrame dnaFrame = dna.get(complementId);
3013 SplitFrame sf = createSplitFrame(dnaFrame, af);
3014 addedToSplitFrames.add(dnaFrame);
3015 addedToSplitFrames.add(af);
3016 dnaFrame.setMenusForViewport();
3017 af.setMenusForViewport();
3018 if (af.getViewport().isGatherViewsHere())
3027 * Open any that we failed to pair up (which shouldn't happen!) as
3028 * standalone AlignFrame's.
3030 for (Entry<Viewport, AlignFrame> candidate : splitFrameCandidates
3033 AlignFrame af = candidate.getValue();
3034 if (!addedToSplitFrames.contains(af))
3036 Viewport view = candidate.getKey();
3037 Desktop.addInternalFrame(af, view.getTitle(),
3038 safeInt(view.getWidth()), safeInt(view.getHeight()));
3039 af.setMenusForViewport();
3040 System.err.println("Failed to restore view " + view.getTitle()
3041 + " to split frame");
3046 * Gather back into tabbed views as flagged.
3048 for (SplitFrame sf : gatherTo)
3050 Desktop.instance.gatherViews(sf);
3053 splitFrameCandidates.clear();
3057 * Construct and display one SplitFrame holding DNA and protein alignments.
3060 * @param proteinFrame
3063 protected SplitFrame createSplitFrame(AlignFrame dnaFrame,
3064 AlignFrame proteinFrame)
3066 SplitFrame splitFrame = new SplitFrame(dnaFrame, proteinFrame);
3067 String title = MessageManager.getString("label.linked_view_title");
3068 int width = (int) dnaFrame.getBounds().getWidth();
3069 int height = (int) (dnaFrame.getBounds().getHeight()
3070 + proteinFrame.getBounds().getHeight() + 50);
3073 * SplitFrame location is saved to both enclosed frames
3075 splitFrame.setLocation(dnaFrame.getX(), dnaFrame.getY());
3076 Desktop.addInternalFrame(splitFrame, title, width, height);
3079 * And compute cDNA consensus (couldn't do earlier with consensus as
3080 * mappings were not yet present)
3082 proteinFrame.getViewport().alignmentChanged(proteinFrame.alignPanel);
3088 * check errorMessage for a valid error message and raise an error box in the
3089 * GUI or write the current errorMessage to stderr and then clear the error
3092 protected void reportErrors()
3094 reportErrors(false);
3097 protected void reportErrors(final boolean saving)
3099 if (errorMessage != null)
3101 final String finalErrorMessage = errorMessage;
3104 javax.swing.SwingUtilities.invokeLater(new Runnable()
3109 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
3111 "Error " + (saving ? "saving" : "loading")
3113 JvOptionPane.WARNING_MESSAGE);
3119 System.err.println("Problem loading Jalview file: " + errorMessage);
3122 errorMessage = null;
3125 Map<String, String> alreadyLoadedPDB = new HashMap<>();
3128 * when set, local views will be updated from view stored in JalviewXML
3129 * Currently (28th Sep 2008) things will go horribly wrong in vamsas document
3130 * sync if this is set to true.
3132 private final boolean updateLocalViews = false;
3135 * Returns the path to a temporary file holding the PDB file for the given PDB
3136 * id. The first time of asking, searches for a file of that name in the
3137 * Jalview project jar, and copies it to a new temporary file. Any repeat
3138 * requests just return the path to the file previously created.
3144 String loadPDBFile(jarInputStreamProvider jprovider, String pdbId,
3147 if (alreadyLoadedPDB.containsKey(pdbId))
3149 return alreadyLoadedPDB.get(pdbId).toString();
3152 String tempFile = copyJarEntry(jprovider, pdbId, "jalview_pdb",
3154 if (tempFile != null)
3156 alreadyLoadedPDB.put(pdbId, tempFile);
3162 * Copies the jar entry of given name to a new temporary file and returns the
3163 * path to the file, or null if the entry is not found.
3166 * @param jarEntryName
3168 * a prefix for the temporary file name, must be at least three
3171 * null or original file - so new file can be given the same suffix
3175 protected String copyJarEntry(jarInputStreamProvider jprovider,
3176 String jarEntryName, String prefix, String origFile)
3178 BufferedReader in = null;
3179 PrintWriter out = null;
3180 String suffix = ".tmp";
3181 if (origFile == null)
3183 origFile = jarEntryName;
3185 int sfpos = origFile.lastIndexOf(".");
3186 if (sfpos > -1 && sfpos < (origFile.length() - 3))
3188 suffix = "." + origFile.substring(sfpos + 1);
3192 JarInputStream jin = jprovider.getJarInputStream();
3194 * if (jprovider.startsWith("http://")) { jin = new JarInputStream(new
3195 * URL(jprovider).openStream()); } else { jin = new JarInputStream(new
3196 * FileInputStream(jprovider)); }
3199 JarEntry entry = null;
3202 entry = jin.getNextJarEntry();
3203 } while (entry != null && !entry.getName().equals(jarEntryName));
3206 in = new BufferedReader(new InputStreamReader(jin, UTF_8));
3207 File outFile = File.createTempFile(prefix, suffix);
3208 outFile.deleteOnExit();
3209 out = new PrintWriter(new FileOutputStream(outFile));
3212 while ((data = in.readLine()) != null)
3217 String t = outFile.getAbsolutePath();
3222 warn("Couldn't find entry in Jalview Jar for " + jarEntryName);
3224 } catch (Exception ex)
3226 ex.printStackTrace();
3234 } catch (IOException e)
3248 private class JvAnnotRow
3250 public JvAnnotRow(int i, AlignmentAnnotation jaa)
3257 * persisted version of annotation row from which to take vis properties
3259 public jalview.datamodel.AlignmentAnnotation template;
3262 * original position of the annotation row in the alignment
3268 * Load alignment frame from jalview XML DOM object
3270 * @param jalviewModel
3273 * filename source string
3274 * @param loadTreesAndStructures
3275 * when false only create Viewport
3277 * data source provider
3278 * @return alignment frame created from view stored in DOM
3280 AlignFrame loadFromObject(JalviewModel jalviewModel, String file,
3281 boolean loadTreesAndStructures, jarInputStreamProvider jprovider)
3283 SequenceSet vamsasSet = jalviewModel.getVamsasModel().getSequenceSet().get(0);
3284 List<Sequence> vamsasSeqs = vamsasSet.getSequence();
3286 // JalviewModelSequence jms = object.getJalviewModelSequence();
3288 // Viewport view = (jms.getViewportCount() > 0) ? jms.getViewport(0)
3290 Viewport view = (jalviewModel.getViewport().size() > 0)
3291 ? jalviewModel.getViewport().get(0)
3294 // ////////////////////////////////
3295 // INITIALISE ALIGNMENT SEQUENCESETID AND VIEWID
3298 // If we just load in the same jar file again, the sequenceSetId
3299 // will be the same, and we end up with multiple references
3300 // to the same sequenceSet. We must modify this id on load
3301 // so that each load of the file gives a unique id
3304 * used to resolve correct alignment dataset for alignments with multiple
3307 String uniqueSeqSetId = null;
3308 String viewId = null;
3311 uniqueSeqSetId = view.getSequenceSetId() + uniqueSetSuffix;
3312 viewId = (view.getId() == null ? null
3313 : view.getId() + uniqueSetSuffix);
3316 // ////////////////////////////////
3319 List<SequenceI> hiddenSeqs = null;
3321 List<SequenceI> tmpseqs = new ArrayList<>();
3323 boolean multipleView = false;
3324 SequenceI referenceseqForView = null;
3325 // JSeq[] jseqs = object.getJalviewModelSequence().getJSeq();
3326 List<JSeq> jseqs = jalviewModel.getJSeq();
3327 int vi = 0; // counter in vamsasSeq array
3328 for (int i = 0; i < jseqs.size(); i++)
3330 JSeq jseq = jseqs.get(i);
3331 String seqId = jseq.getId();
3333 SequenceI tmpSeq = seqRefIds.get(seqId);
3336 if (!incompleteSeqs.containsKey(seqId))
3338 // may not need this check, but keep it for at least 2.9,1 release
3339 if (tmpSeq.getStart() != jseq.getStart()
3340 || tmpSeq.getEnd() != jseq.getEnd())
3343 "Warning JAL-2154 regression: updating start/end for sequence "
3344 + tmpSeq.toString() + " to " + jseq);
3349 incompleteSeqs.remove(seqId);
3351 if (vamsasSeqs.size() > vi
3352 && vamsasSeqs.get(vi).getId().equals(seqId))
3354 // most likely we are reading a dataset XML document so
3355 // update from vamsasSeq section of XML for this sequence
3356 tmpSeq.setName(vamsasSeqs.get(vi).getName());
3357 tmpSeq.setDescription(vamsasSeqs.get(vi).getDescription());
3358 tmpSeq.setSequence(vamsasSeqs.get(vi).getSequence());
3363 // reading multiple views, so vamsasSeq set is a subset of JSeq
3364 multipleView = true;
3366 tmpSeq.setStart(jseq.getStart());
3367 tmpSeq.setEnd(jseq.getEnd());
3368 tmpseqs.add(tmpSeq);
3372 Sequence vamsasSeq = vamsasSeqs.get(vi);
3373 tmpSeq = new jalview.datamodel.Sequence(vamsasSeq.getName(),
3374 vamsasSeq.getSequence());
3375 tmpSeq.setDescription(vamsasSeq.getDescription());
3376 tmpSeq.setStart(jseq.getStart());
3377 tmpSeq.setEnd(jseq.getEnd());
3378 tmpSeq.setVamsasId(uniqueSetSuffix + seqId);
3379 seqRefIds.put(vamsasSeq.getId(), tmpSeq);
3380 tmpseqs.add(tmpSeq);
3384 if (safeBoolean(jseq.isViewreference()))
3386 referenceseqForView = tmpseqs.get(tmpseqs.size() - 1);
3389 if (jseq.isHidden() != null && jseq.isHidden().booleanValue())
3391 if (hiddenSeqs == null)
3393 hiddenSeqs = new ArrayList<>();
3396 hiddenSeqs.add(tmpSeq);
3401 // Create the alignment object from the sequence set
3402 // ///////////////////////////////
3403 SequenceI[] orderedSeqs = tmpseqs
3404 .toArray(new SequenceI[tmpseqs.size()]);
3406 AlignmentI al = null;
3407 // so we must create or recover the dataset alignment before going further
3408 // ///////////////////////////////
3409 if (vamsasSet.getDatasetId() == null || vamsasSet.getDatasetId() == "")
3411 // older jalview projects do not have a dataset - so creat alignment and
3413 al = new Alignment(orderedSeqs);
3414 al.setDataset(null);
3418 boolean isdsal = jalviewModel.getViewport().isEmpty();
3421 // we are importing a dataset record, so
3422 // recover reference to an alignment already materialsed as dataset
3423 al = getDatasetFor(vamsasSet.getDatasetId());
3427 // materialse the alignment
3428 al = new Alignment(orderedSeqs);
3432 addDatasetRef(vamsasSet.getDatasetId(), al);
3435 // finally, verify all data in vamsasSet is actually present in al
3436 // passing on flag indicating if it is actually a stored dataset
3437 recoverDatasetFor(vamsasSet, al, isdsal, uniqueSeqSetId);
3440 if (referenceseqForView != null)
3442 al.setSeqrep(referenceseqForView);
3444 // / Add the alignment properties
3445 for (int i = 0; i < vamsasSet.getSequenceSetProperties().size(); i++)
3447 SequenceSetProperties ssp = vamsasSet.getSequenceSetProperties()
3449 al.setProperty(ssp.getKey(), ssp.getValue());
3452 // ///////////////////////////////
3454 Hashtable pdbloaded = new Hashtable(); // TODO nothing writes to this??
3457 // load sequence features, database references and any associated PDB
3458 // structures for the alignment
3460 // prior to 2.10, this part would only be executed the first time a
3461 // sequence was encountered, but not afterwards.
3462 // now, for 2.10 projects, this is also done if the xml doc includes
3463 // dataset sequences not actually present in any particular view.
3465 for (int i = 0; i < vamsasSeqs.size(); i++)
3467 JSeq jseq = jseqs.get(i);
3468 if (jseq.getFeatures().size() > 0)
3470 List<Feature> features = jseq.getFeatures();
3471 for (int f = 0; f < features.size(); f++)
3473 Feature feat = features.get(f);
3474 SequenceFeature sf = new SequenceFeature(feat.getType(),
3475 feat.getDescription(), feat.getBegin(), feat.getEnd(),
3476 safeFloat(feat.getScore()), feat.getFeatureGroup());
3477 sf.setStatus(feat.getStatus());
3480 * load any feature attributes - include map-valued attributes
3482 Map<String, Map<String, String>> mapAttributes = new HashMap<>();
3483 for (int od = 0; od < feat.getOtherData().size(); od++)
3485 OtherData keyValue = feat.getOtherData().get(od);
3486 String attributeName = keyValue.getKey();
3487 String attributeValue = keyValue.getValue();
3488 if (attributeName.startsWith("LINK"))
3490 sf.addLink(attributeValue);
3494 String subAttribute = keyValue.getKey2();
3495 if (subAttribute == null)
3497 // simple string-valued attribute
3498 sf.setValue(attributeName, attributeValue);
3502 // attribute 'key' has sub-attribute 'key2'
3503 if (!mapAttributes.containsKey(attributeName))
3505 mapAttributes.put(attributeName, new HashMap<>());
3507 mapAttributes.get(attributeName).put(subAttribute,
3512 for (Entry<String, Map<String, String>> mapAttribute : mapAttributes
3515 sf.setValue(mapAttribute.getKey(), mapAttribute.getValue());
3518 // adds feature to datasequence's feature set (since Jalview 2.10)
3519 al.getSequenceAt(i).addSequenceFeature(sf);
3522 if (vamsasSeqs.get(i).getDBRef().size() > 0)
3524 // adds dbrefs to datasequence's set (since Jalview 2.10)
3526 al.getSequenceAt(i).getDatasetSequence() == null
3527 ? al.getSequenceAt(i)
3528 : al.getSequenceAt(i).getDatasetSequence(),
3531 if (jseq.getPdbids().size() > 0)
3533 List<Pdbids> ids = jseq.getPdbids();
3534 for (int p = 0; p < ids.size(); p++)
3536 Pdbids pdbid = ids.get(p);
3537 jalview.datamodel.PDBEntry entry = new jalview.datamodel.PDBEntry();
3538 entry.setId(pdbid.getId());
3539 if (pdbid.getType() != null)
3541 if (PDBEntry.Type.getType(pdbid.getType()) != null)
3543 entry.setType(PDBEntry.Type.getType(pdbid.getType()));
3547 entry.setType(PDBEntry.Type.FILE);
3550 // jprovider is null when executing 'New View'
3551 if (pdbid.getFile() != null && jprovider != null)
3553 if (!pdbloaded.containsKey(pdbid.getFile()))
3555 entry.setFile(loadPDBFile(jprovider, pdbid.getId(),
3560 entry.setFile(pdbloaded.get(pdbid.getId()).toString());
3564 if (pdbid.getPdbentryItem() != null)
3566 for (PdbentryItem item : pdbid.getPdbentryItem())
3568 for (Property pr : item.getProperty())
3570 entry.setProperty(pr.getName(), pr.getValue());
3575 for (Property prop : pdbid.getProperty())
3577 entry.setProperty(prop.getName(), prop.getValue());
3579 StructureSelectionManager
3580 .getStructureSelectionManager(Desktop.instance)
3581 .registerPDBEntry(entry);
3582 // adds PDBEntry to datasequence's set (since Jalview 2.10)
3583 if (al.getSequenceAt(i).getDatasetSequence() != null)
3585 al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
3589 al.getSequenceAt(i).addPDBId(entry);
3594 } // end !multipleview
3596 // ///////////////////////////////
3597 // LOAD SEQUENCE MAPPINGS
3599 if (vamsasSet.getAlcodonFrame().size() > 0)
3601 // TODO Potentially this should only be done once for all views of an
3603 List<AlcodonFrame> alc = vamsasSet.getAlcodonFrame();
3604 for (int i = 0; i < alc.size(); i++)
3606 AlignedCodonFrame cf = new AlignedCodonFrame();
3607 if (alc.get(i).getAlcodMap().size() > 0)
3609 List<AlcodMap> maps = alc.get(i).getAlcodMap();
3610 for (int m = 0; m < maps.size(); m++)
3612 AlcodMap map = maps.get(m);
3613 SequenceI dnaseq = seqRefIds.get(map.getDnasq());
3615 jalview.datamodel.Mapping mapping = null;
3616 // attach to dna sequence reference.
3617 if (map.getMapping() != null)
3619 mapping = addMapping(map.getMapping());
3620 if (dnaseq != null && mapping.getTo() != null)
3622 cf.addMap(dnaseq, mapping.getTo(), mapping.getMap());
3628 newAlcodMapRef(map.getDnasq(), cf, mapping));
3632 al.addCodonFrame(cf);
3637 // ////////////////////////////////
3639 List<JvAnnotRow> autoAlan = new ArrayList<>();
3642 * store any annotations which forward reference a group's ID
3644 Map<String, List<AlignmentAnnotation>> groupAnnotRefs = new Hashtable<>();
3646 if (vamsasSet.getAnnotation().size()/*Count()*/ > 0)
3648 List<Annotation> an = vamsasSet.getAnnotation();
3650 for (int i = 0; i < an.size(); i++)
3652 Annotation annotation = an.get(i);
3655 * test if annotation is automatically calculated for this view only
3657 boolean autoForView = false;
3658 if (annotation.getLabel().equals("Quality")
3659 || annotation.getLabel().equals("Conservation")
3660 || annotation.getLabel().equals("Consensus"))
3662 // Kludge for pre 2.5 projects which lacked the autocalculated flag
3664 // JAXB has no has() test; schema defaults value to false
3665 // if (!annotation.hasAutoCalculated())
3667 // annotation.setAutoCalculated(true);
3670 if (autoForView || annotation.isAutoCalculated())
3672 // remove ID - we don't recover annotation from other views for
3673 // view-specific annotation
3674 annotation.setId(null);
3677 // set visibility for other annotation in this view
3678 String annotationId = annotation.getId();
3679 if (annotationId != null && annotationIds.containsKey(annotationId))
3681 AlignmentAnnotation jda = annotationIds.get(annotationId);
3682 // in principle Visible should always be true for annotation displayed
3683 // in multiple views
3684 if (annotation.isVisible() != null)
3686 jda.visible = annotation.isVisible();
3689 al.addAnnotation(jda);
3693 // Construct new annotation from model.
3694 List<AnnotationElement> ae = annotation.getAnnotationElement();
3695 jalview.datamodel.Annotation[] anot = null;
3696 java.awt.Color firstColour = null;
3698 if (!annotation.isScoreOnly())
3700 anot = new jalview.datamodel.Annotation[al.getWidth()];
3701 for (int aa = 0; aa < ae.size() && aa < anot.length; aa++)
3703 AnnotationElement annElement = ae.get(aa);
3704 anpos = annElement.getPosition();
3706 if (anpos >= anot.length)
3711 float value = safeFloat(annElement.getValue());
3712 anot[anpos] = new jalview.datamodel.Annotation(
3713 annElement.getDisplayCharacter(),
3714 annElement.getDescription(),
3715 (annElement.getSecondaryStructure() == null
3716 || annElement.getSecondaryStructure()
3720 .getSecondaryStructure()
3723 anot[anpos].colour = new Color(safeInt(annElement.getColour()));
3724 if (firstColour == null)
3726 firstColour = anot[anpos].colour;
3730 jalview.datamodel.AlignmentAnnotation jaa = null;
3732 if (annotation.isGraph())
3734 float llim = 0, hlim = 0;
3735 // if (autoForView || an[i].isAutoCalculated()) {
3738 jaa = new jalview.datamodel.AlignmentAnnotation(
3739 annotation.getLabel(), annotation.getDescription(), anot,
3740 llim, hlim, safeInt(annotation.getGraphType()));
3742 jaa.graphGroup = safeInt(annotation.getGraphGroup());
3743 jaa._linecolour = firstColour;
3744 if (annotation.getThresholdLine() != null)
3746 jaa.setThreshold(new jalview.datamodel.GraphLine(
3747 safeFloat(annotation.getThresholdLine().getValue()),
3748 annotation.getThresholdLine().getLabel(),
3749 new java.awt.Color(safeInt(
3750 annotation.getThresholdLine().getColour()))));
3752 if (autoForView || annotation.isAutoCalculated())
3754 // Hardwire the symbol display line to ensure that labels for
3755 // histograms are displayed
3761 jaa = new jalview.datamodel.AlignmentAnnotation(
3762 annotation.getLabel(), annotation.getDescription(), anot);
3763 jaa._linecolour = firstColour;
3765 // register new annotation
3766 if (annotation.getId() != null)
3768 annotationIds.put(annotation.getId(), jaa);
3769 jaa.annotationId = annotation.getId();
3771 // recover sequence association
3772 String sequenceRef = annotation.getSequenceRef();
3773 if (sequenceRef != null)
3775 // from 2.9 sequenceRef is to sequence id (JAL-1781)
3776 SequenceI sequence = seqRefIds.get(sequenceRef);
3777 if (sequence == null)
3779 // in pre-2.9 projects sequence ref is to sequence name
3780 sequence = al.findName(sequenceRef);
3782 if (sequence != null)
3784 jaa.createSequenceMapping(sequence, 1, true);
3785 sequence.addAlignmentAnnotation(jaa);
3788 // and make a note of any group association
3789 if (annotation.getGroupRef() != null
3790 && annotation.getGroupRef().length() > 0)
3792 List<jalview.datamodel.AlignmentAnnotation> aal = groupAnnotRefs
3793 .get(annotation.getGroupRef());
3796 aal = new ArrayList<>();
3797 groupAnnotRefs.put(annotation.getGroupRef(), aal);
3802 if (annotation.getScore() != null)
3804 jaa.setScore(annotation.getScore().doubleValue());
3806 if (annotation.isVisible() != null)
3808 jaa.visible = annotation.isVisible().booleanValue();
3811 if (annotation.isCentreColLabels() != null)
3813 jaa.centreColLabels = annotation.isCentreColLabels()
3817 if (annotation.isScaleColLabels() != null)
3819 jaa.scaleColLabel = annotation.isScaleColLabels().booleanValue();
3821 if (annotation.isAutoCalculated())
3823 // newer files have an 'autoCalculated' flag and store calculation
3824 // state in viewport properties
3825 jaa.autoCalculated = true; // means annotation will be marked for
3826 // update at end of load.
3828 if (annotation.getGraphHeight() != null)
3830 jaa.graphHeight = annotation.getGraphHeight().intValue();
3832 jaa.belowAlignment = annotation.isBelowAlignment();
3833 jaa.setCalcId(annotation.getCalcId());
3834 if (annotation.getProperty().size() > 0)
3836 for (Annotation.Property prop : annotation
3839 jaa.setProperty(prop.getName(), prop.getValue());
3842 if (jaa.autoCalculated)
3844 autoAlan.add(new JvAnnotRow(i, jaa));
3847 // if (!autoForView)
3849 // add autocalculated group annotation and any user created annotation
3851 al.addAnnotation(jaa);
3855 // ///////////////////////
3857 // Create alignment markup and styles for this view
3858 if (jalviewModel.getJGroup().size() > 0)
3860 List<JGroup> groups = jalviewModel.getJGroup();
3861 boolean addAnnotSchemeGroup = false;
3862 for (int i = 0; i < groups.size(); i++)
3864 JGroup jGroup = groups.get(i);
3865 ColourSchemeI cs = null;
3866 if (jGroup.getColour() != null)
3868 if (jGroup.getColour().startsWith("ucs"))
3870 cs = getUserColourScheme(jalviewModel, jGroup.getColour());
3872 else if (jGroup.getColour().equals("AnnotationColourGradient")
3873 && jGroup.getAnnotationColours() != null)
3875 addAnnotSchemeGroup = true;
3879 cs = ColourSchemeProperty.getColourScheme(null, al,
3880 jGroup.getColour());
3883 int pidThreshold = safeInt(jGroup.getPidThreshold());
3885 Vector<SequenceI> seqs = new Vector<>();
3887 for (int s = 0; s < jGroup.getSeq().size(); s++)
3889 String seqId = jGroup.getSeq().get(s);
3890 SequenceI ts = seqRefIds.get(seqId);
3894 seqs.addElement(ts);
3898 if (seqs.size() < 1)
3903 SequenceGroup sg = new SequenceGroup(seqs, jGroup.getName(), cs,
3904 safeBoolean(jGroup.isDisplayBoxes()),
3905 safeBoolean(jGroup.isDisplayText()),
3906 safeBoolean(jGroup.isColourText()),
3907 safeInt(jGroup.getStart()), safeInt(jGroup.getEnd()));
3908 sg.getGroupColourScheme().setThreshold(pidThreshold, true);
3909 sg.getGroupColourScheme()
3910 .setConservationInc(safeInt(jGroup.getConsThreshold()));
3911 sg.setOutlineColour(new Color(safeInt(jGroup.getOutlineColour())));
3913 sg.textColour = new Color(safeInt(jGroup.getTextCol1()));
3914 sg.textColour2 = new Color(safeInt(jGroup.getTextCol2()));
3915 sg.setShowNonconserved(safeBoolean(jGroup.isShowUnconserved()));
3916 sg.thresholdTextColour = safeInt(jGroup.getTextColThreshold());
3917 // attributes with a default in the schema are never null
3918 sg.setShowConsensusHistogram(jGroup.isShowConsensusHistogram());
3919 sg.setshowSequenceLogo(jGroup.isShowSequenceLogo());
3920 sg.setNormaliseSequenceLogo(jGroup.isNormaliseSequenceLogo());
3921 sg.setIgnoreGapsConsensus(jGroup.isIgnoreGapsinConsensus());
3922 if (jGroup.getConsThreshold() != null
3923 && jGroup.getConsThreshold().intValue() != 0)
3925 Conservation c = new Conservation("All", sg.getSequences(null), 0,
3928 c.verdict(false, 25);
3929 sg.cs.setConservation(c);
3932 if (jGroup.getId() != null && groupAnnotRefs.size() > 0)
3934 // re-instate unique group/annotation row reference
3935 List<AlignmentAnnotation> jaal = groupAnnotRefs
3936 .get(jGroup.getId());
3939 for (AlignmentAnnotation jaa : jaal)
3942 if (jaa.autoCalculated)
3944 // match up and try to set group autocalc alignment row for this
3946 if (jaa.label.startsWith("Consensus for "))
3948 sg.setConsensus(jaa);
3950 // match up and try to set group autocalc alignment row for this
3952 if (jaa.label.startsWith("Conservation for "))
3954 sg.setConservationRow(jaa);
3961 if (addAnnotSchemeGroup)
3963 // reconstruct the annotation colourscheme
3964 sg.setColourScheme(constructAnnotationColour(
3965 jGroup.getAnnotationColours(), null, al, jalviewModel, false));
3971 // only dataset in this model, so just return.
3974 // ///////////////////////////////
3977 AlignFrame af = null;
3978 AlignViewport av = null;
3979 // now check to see if we really need to create a new viewport.
3980 if (multipleView && viewportsAdded.size() == 0)
3982 // We recovered an alignment for which a viewport already exists.
3983 // TODO: fix up any settings necessary for overlaying stored state onto
3984 // state recovered from another document. (may not be necessary).
3985 // we may need a binding from a viewport in memory to one recovered from
3987 // and then recover its containing af to allow the settings to be applied.
3988 // TODO: fix for vamsas demo
3990 "About to recover a viewport for existing alignment: Sequence set ID is "
3992 Object seqsetobj = retrieveExistingObj(uniqueSeqSetId);
3993 if (seqsetobj != null)
3995 if (seqsetobj instanceof String)
3997 uniqueSeqSetId = (String) seqsetobj;
3999 "Recovered extant sequence set ID mapping for ID : New Sequence set ID is "
4005 "Warning : Collision between sequence set ID string and existing jalview object mapping.");
4011 * indicate that annotation colours are applied across all groups (pre
4012 * Jalview 2.8.1 behaviour)
4014 boolean doGroupAnnColour = Jalview2XML.isVersionStringLaterThan("2.8.1",
4015 jalviewModel.getVersion());
4017 AlignmentPanel ap = null;
4018 boolean isnewview = true;
4021 // Check to see if this alignment already has a view id == viewId
4022 jalview.gui.AlignmentPanel views[] = Desktop
4023 .getAlignmentPanels(uniqueSeqSetId);
4024 if (views != null && views.length > 0)
4026 for (int v = 0; v < views.length; v++)
4028 if (views[v].av.getViewId().equalsIgnoreCase(viewId))
4030 // recover the existing alignpanel, alignframe, viewport
4031 af = views[v].alignFrame;
4034 // TODO: could even skip resetting view settings if we don't want to
4035 // change the local settings from other jalview processes
4044 af = loadViewport(file, jseqs, hiddenSeqs, al, jalviewModel, view,
4045 uniqueSeqSetId, viewId, autoAlan);
4046 av = af.getViewport();
4051 * Load any trees, PDB structures and viewers
4053 * Not done if flag is false (when this method is used for New View)
4055 if (loadTreesAndStructures)
4057 loadTrees(jalviewModel, view, af, av, ap);
4058 loadPCAViewers(jalviewModel, ap);
4059 loadPDBStructures(jprovider, jseqs, af, ap);
4060 loadRnaViewers(jprovider, jseqs, ap);
4062 // and finally return.
4067 * Instantiate and link any saved RNA (Varna) viewers. The state of the Varna
4068 * panel is restored from separate jar entries, two (gapped and trimmed) per
4069 * sequence and secondary structure.
4071 * Currently each viewer shows just one sequence and structure (gapped and
4072 * trimmed), however this method is designed to support multiple sequences or
4073 * structures in viewers if wanted in future.
4079 private void loadRnaViewers(jarInputStreamProvider jprovider,
4080 List<JSeq> jseqs, AlignmentPanel ap)
4083 * scan the sequences for references to viewers; create each one the first
4084 * time it is referenced, add Rna models to existing viewers
4086 for (JSeq jseq : jseqs)
4088 for (int i = 0; i < jseq.getRnaViewer().size(); i++)
4090 RnaViewer viewer = jseq.getRnaViewer().get(i);
4091 AppVarna appVarna = findOrCreateVarnaViewer(viewer, uniqueSetSuffix,
4094 for (int j = 0; j < viewer.getSecondaryStructure().size(); j++)
4096 SecondaryStructure ss = viewer.getSecondaryStructure().get(j);
4097 SequenceI seq = seqRefIds.get(jseq.getId());
4098 AlignmentAnnotation ann = this.annotationIds
4099 .get(ss.getAnnotationId());
4102 * add the structure to the Varna display (with session state copied
4103 * from the jar to a temporary file)
4105 boolean gapped = safeBoolean(ss.isGapped());
4106 String rnaTitle = ss.getTitle();
4107 String sessionState = ss.getViewerState();
4108 String tempStateFile = copyJarEntry(jprovider, sessionState,
4110 RnaModel rna = new RnaModel(rnaTitle, ann, seq, null, gapped);
4111 appVarna.addModelSession(rna, rnaTitle, tempStateFile);
4113 appVarna.setInitialSelection(safeInt(viewer.getSelectedRna()));
4119 * Locate and return an already instantiated matching AppVarna, or create one
4123 * @param viewIdSuffix
4127 protected AppVarna findOrCreateVarnaViewer(RnaViewer viewer,
4128 String viewIdSuffix, AlignmentPanel ap)
4131 * on each load a suffix is appended to the saved viewId, to avoid conflicts
4132 * if load is repeated
4134 String postLoadId = viewer.getViewId() + viewIdSuffix;
4135 for (JInternalFrame frame : getAllFrames())
4137 if (frame instanceof AppVarna)
4139 AppVarna varna = (AppVarna) frame;
4140 if (postLoadId.equals(varna.getViewId()))
4142 // this viewer is already instantiated
4143 // could in future here add ap as another 'parent' of the
4144 // AppVarna window; currently just 1-to-many
4151 * viewer not found - make it
4153 RnaViewerModel model = new RnaViewerModel(postLoadId, viewer.getTitle(),
4154 safeInt(viewer.getXpos()), safeInt(viewer.getYpos()),
4155 safeInt(viewer.getWidth()), safeInt(viewer.getHeight()),
4156 safeInt(viewer.getDividerLocation()));
4157 AppVarna varna = new AppVarna(model, ap);
4163 * Load any saved trees
4171 protected void loadTrees(JalviewModel jm, Viewport view,
4172 AlignFrame af, AlignViewport av, AlignmentPanel ap)
4174 // TODO result of automated refactoring - are all these parameters needed?
4177 for (int t = 0; t < jm.getTree().size(); t++)
4180 Tree tree = jm.getTree().get(t);
4182 TreePanel tp = (TreePanel) retrieveExistingObj(tree.getId());
4185 tp = af.showNewickTree(new NewickFile(tree.getNewick()),
4186 tree.getTitle(), safeInt(tree.getWidth()),
4187 safeInt(tree.getHeight()), safeInt(tree.getXpos()),
4188 safeInt(tree.getYpos()));
4189 if (tree.getId() != null)
4191 // perhaps bind the tree id to something ?
4196 // update local tree attributes ?
4197 // TODO: should check if tp has been manipulated by user - if so its
4198 // settings shouldn't be modified
4199 tp.setTitle(tree.getTitle());
4200 tp.setBounds(new Rectangle(safeInt(tree.getXpos()),
4201 safeInt(tree.getYpos()), safeInt(tree.getWidth()),
4202 safeInt(tree.getHeight())));
4203 tp.setViewport(av); // af.viewport;
4204 // TODO: verify 'associate with all views' works still
4205 tp.getTreeCanvas().setViewport(av); // af.viewport;
4206 tp.getTreeCanvas().setAssociatedPanel(ap); // af.alignPanel;
4208 tp.getTreeCanvas().setApplyToAllViews(tree.isLinkToAllViews());
4211 warn("There was a problem recovering stored Newick tree: \n"
4212 + tree.getNewick());
4216 tp.fitToWindow.setState(safeBoolean(tree.isFitToWindow()));
4217 tp.fitToWindow_actionPerformed(null);
4219 if (tree.getFontName() != null)
4222 new Font(tree.getFontName(), safeInt(tree.getFontStyle()),
4223 safeInt(tree.getFontSize())));
4228 new Font(view.getFontName(), safeInt(view.getFontStyle()),
4229 safeInt(view.getFontSize())));
4232 tp.showPlaceholders(safeBoolean(tree.isMarkUnlinked()));
4233 tp.showBootstrap(safeBoolean(tree.isShowBootstrap()));
4234 tp.showDistances(safeBoolean(tree.isShowDistances()));
4236 tp.getTreeCanvas().setThreshold(safeFloat(tree.getThreshold()));
4238 if (safeBoolean(tree.isCurrentTree()))
4240 af.getViewport().setCurrentTree(tp.getTree());
4244 } catch (Exception ex)
4246 ex.printStackTrace();
4251 * Load and link any saved structure viewers.
4258 protected void loadPDBStructures(jarInputStreamProvider jprovider,
4259 List<JSeq> jseqs, AlignFrame af, AlignmentPanel ap)
4262 * Run through all PDB ids on the alignment, and collect mappings between
4263 * distinct view ids and all sequences referring to that view.
4265 Map<String, StructureViewerModel> structureViewers = new LinkedHashMap<>();
4267 for (int i = 0; i < jseqs.size(); i++)
4269 JSeq jseq = jseqs.get(i);
4270 if (jseq.getPdbids().size() > 0)
4272 List<Pdbids> ids = jseq.getPdbids();
4273 for (int p = 0; p < ids.size(); p++)
4275 Pdbids pdbid = ids.get(p);
4276 final int structureStateCount = pdbid.getStructureState().size();
4277 for (int s = 0; s < structureStateCount; s++)
4279 // check to see if we haven't already created this structure view
4280 final StructureState structureState = pdbid
4281 .getStructureState().get(s);
4282 String sviewid = (structureState.getViewId() == null) ? null
4283 : structureState.getViewId() + uniqueSetSuffix;
4284 jalview.datamodel.PDBEntry jpdb = new jalview.datamodel.PDBEntry();
4285 // Originally : pdbid.getFile()
4286 // : TODO: verify external PDB file recovery still works in normal
4287 // jalview project load
4289 loadPDBFile(jprovider, pdbid.getId(), pdbid.getFile()));
4290 jpdb.setId(pdbid.getId());
4292 int x = safeInt(structureState.getXpos());
4293 int y = safeInt(structureState.getYpos());
4294 int width = safeInt(structureState.getWidth());
4295 int height = safeInt(structureState.getHeight());
4297 // Probably don't need to do this anymore...
4298 // Desktop.desktop.getComponentAt(x, y);
4299 // TODO: NOW: check that this recovers the PDB file correctly.
4300 String pdbFile = loadPDBFile(jprovider, pdbid.getId(),
4302 jalview.datamodel.SequenceI seq = seqRefIds
4303 .get(jseq.getId() + "");
4304 if (sviewid == null)
4306 sviewid = "_jalview_pre2_4_" + x + "," + y + "," + width + ","
4309 if (!structureViewers.containsKey(sviewid))
4311 structureViewers.put(sviewid,
4312 new StructureViewerModel(x, y, width, height, false,
4313 false, true, structureState.getViewId(),
4314 structureState.getType()));
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
4345 .getValue()/*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);
4416 * From 2.9: stateData.type contains JMOL or CHIMERA, data is in jar entry
4417 * "viewer_"+stateData.viewId
4419 if (ViewerType.CHIMERA.toString().equals(stateData.getType()))
4421 createChimeraViewer(viewerData, af, jprovider);
4426 * else Jmol (if pre-2.9, stateData contains JMOL state string)
4428 createJmolViewer(viewerData, af, jprovider);
4433 * Create a new Chimera viewer.
4439 protected void createChimeraViewer(
4440 Entry<String, StructureViewerModel> viewerData, AlignFrame af,
4441 jarInputStreamProvider jprovider)
4443 StructureViewerModel data = viewerData.getValue();
4444 String chimeraSessionFile = data.getStateData();
4447 * Copy Chimera session from jar entry "viewer_"+viewId to a temporary file
4449 * NB this is the 'saved' viewId as in the project file XML, _not_ the
4450 * 'uniquified' sviewid used to reconstruct the viewer here
4452 String viewerJarEntryName = getViewerJarEntryName(data.getViewId());
4453 chimeraSessionFile = copyJarEntry(jprovider, viewerJarEntryName,
4456 Set<Entry<File, StructureData>> fileData = data.getFileData()
4458 List<PDBEntry> pdbs = new ArrayList<>();
4459 List<SequenceI[]> allseqs = new ArrayList<>();
4460 for (Entry<File, StructureData> pdb : fileData)
4462 String filePath = pdb.getValue().getFilePath();
4463 String pdbId = pdb.getValue().getPdbId();
4464 // pdbs.add(new PDBEntry(filePath, pdbId));
4465 pdbs.add(new PDBEntry(pdbId, null, PDBEntry.Type.PDB, filePath));
4466 final List<SequenceI> seqList = pdb.getValue().getSeqList();
4467 SequenceI[] seqs = seqList.toArray(new SequenceI[seqList.size()]);
4471 boolean colourByChimera = data.isColourByViewer();
4472 boolean colourBySequence = data.isColourWithAlignPanel();
4474 // TODO use StructureViewer as a factory here, see JAL-1761
4475 final PDBEntry[] pdbArray = pdbs.toArray(new PDBEntry[pdbs.size()]);
4476 final SequenceI[][] seqsArray = allseqs
4477 .toArray(new SequenceI[allseqs.size()][]);
4478 String newViewId = viewerData.getKey();
4480 ChimeraViewFrame cvf = new ChimeraViewFrame(chimeraSessionFile,
4481 af.alignPanel, pdbArray, seqsArray, colourByChimera,
4482 colourBySequence, newViewId);
4483 cvf.setSize(data.getWidth(), data.getHeight());
4484 cvf.setLocation(data.getX(), data.getY());
4488 * Create a new Jmol window. First parse the Jmol state to translate filenames
4489 * loaded into the view, and record the order in which files are shown in the
4490 * Jmol view, so we can add the sequence mappings in same order.
4496 protected void createJmolViewer(
4497 final Entry<String, StructureViewerModel> viewerData,
4498 AlignFrame af, jarInputStreamProvider jprovider)
4500 final StructureViewerModel svattrib = viewerData.getValue();
4501 String state = svattrib.getStateData();
4504 * Pre-2.9: state element value is the Jmol state string
4506 * 2.9+: @type is "JMOL", state data is in a Jar file member named "viewer_"
4509 if (ViewerType.JMOL.toString().equals(svattrib.getType()))
4511 state = readJarEntry(jprovider,
4512 getViewerJarEntryName(svattrib.getViewId()));
4515 List<String> pdbfilenames = new ArrayList<>();
4516 List<SequenceI[]> seqmaps = new ArrayList<>();
4517 List<String> pdbids = new ArrayList<>();
4518 StringBuilder newFileLoc = new StringBuilder(64);
4519 int cp = 0, ncp, ecp;
4520 Map<File, StructureData> oldFiles = svattrib.getFileData();
4521 while ((ncp = state.indexOf("load ", cp)) > -1)
4525 // look for next filename in load statement
4526 newFileLoc.append(state.substring(cp,
4527 ncp = (state.indexOf("\"", ncp + 1) + 1)));
4528 String oldfilenam = state.substring(ncp,
4529 ecp = state.indexOf("\"", ncp));
4530 // recover the new mapping data for this old filename
4531 // have to normalize filename - since Jmol and jalview do
4533 // translation differently.
4534 StructureData filedat = oldFiles.get(new File(oldfilenam));
4535 if (filedat == null)
4537 String reformatedOldFilename = oldfilenam.replaceAll("/", "\\\\");
4538 filedat = oldFiles.get(new File(reformatedOldFilename));
4540 newFileLoc.append(Platform.escapeString(filedat.getFilePath()));
4541 pdbfilenames.add(filedat.getFilePath());
4542 pdbids.add(filedat.getPdbId());
4543 seqmaps.add(filedat.getSeqList().toArray(new SequenceI[0]));
4544 newFileLoc.append("\"");
4545 cp = ecp + 1; // advance beyond last \" and set cursor so we can
4546 // look for next file statement.
4547 } while ((ncp = state.indexOf("/*file*/", cp)) > -1);
4551 // just append rest of state
4552 newFileLoc.append(state.substring(cp));
4556 System.err.print("Ignoring incomplete Jmol state for PDB ids: ");
4557 newFileLoc = new StringBuilder(state);
4558 newFileLoc.append("; load append ");
4559 for (File id : oldFiles.keySet())
4561 // add this and any other pdb files that should be present in
4563 StructureData filedat = oldFiles.get(id);
4564 newFileLoc.append(filedat.getFilePath());
4565 pdbfilenames.add(filedat.getFilePath());
4566 pdbids.add(filedat.getPdbId());
4567 seqmaps.add(filedat.getSeqList().toArray(new SequenceI[0]));
4568 newFileLoc.append(" \"");
4569 newFileLoc.append(filedat.getFilePath());
4570 newFileLoc.append("\"");
4573 newFileLoc.append(";");
4576 if (newFileLoc.length() == 0)
4580 int histbug = newFileLoc.indexOf("history = ");
4584 * change "history = [true|false];" to "history = [1|0];"
4587 int diff = histbug == -1 ? -1 : newFileLoc.indexOf(";", histbug);
4588 String val = (diff == -1) ? null
4589 : newFileLoc.substring(histbug, diff);
4590 if (val != null && val.length() >= 4)
4592 if (val.contains("e")) // eh? what can it be?
4594 if (val.trim().equals("true"))
4602 newFileLoc.replace(histbug, diff, val);
4607 final String[] pdbf = pdbfilenames
4608 .toArray(new String[pdbfilenames.size()]);
4609 final String[] id = pdbids.toArray(new String[pdbids.size()]);
4610 final SequenceI[][] sq = seqmaps
4611 .toArray(new SequenceI[seqmaps.size()][]);
4612 final String fileloc = newFileLoc.toString();
4613 final String sviewid = viewerData.getKey();
4614 final AlignFrame alf = af;
4615 final Rectangle rect = new Rectangle(svattrib.getX(), svattrib.getY(),
4616 svattrib.getWidth(), svattrib.getHeight());
4619 javax.swing.SwingUtilities.invokeAndWait(new Runnable()
4624 JalviewStructureDisplayI sview = null;
4627 sview = new StructureViewer(
4628 alf.alignPanel.getStructureSelectionManager())
4629 .createView(StructureViewer.ViewerType.JMOL,
4630 pdbf, id, sq, alf.alignPanel, svattrib,
4631 fileloc, rect, sviewid);
4632 addNewStructureViewer(sview);
4633 } catch (OutOfMemoryError ex)
4635 new OOMWarning("restoring structure view for PDB id " + id,
4636 (OutOfMemoryError) ex.getCause());
4637 if (sview != null && sview.isVisible())
4639 sview.closeViewer(false);
4640 sview.setVisible(false);
4646 } catch (InvocationTargetException ex)
4648 warn("Unexpected error when opening Jmol view.", ex);
4650 } catch (InterruptedException e)
4652 // e.printStackTrace();
4658 * Generates a name for the entry in the project jar file to hold state
4659 * information for a structure viewer
4664 protected String getViewerJarEntryName(String viewId)
4666 return VIEWER_PREFIX + viewId;
4670 * Returns any open frame that matches given structure viewer data. The match
4671 * is based on the unique viewId, or (for older project versions) the frame's
4677 protected StructureViewerBase findMatchingViewer(
4678 Entry<String, StructureViewerModel> viewerData)
4680 final String sviewid = viewerData.getKey();
4681 final StructureViewerModel svattrib = viewerData.getValue();
4682 StructureViewerBase comp = null;
4683 JInternalFrame[] frames = getAllFrames();
4684 for (JInternalFrame frame : frames)
4686 if (frame instanceof StructureViewerBase)
4689 * Post jalview 2.4 schema includes structure view id
4691 if (sviewid != null && ((StructureViewerBase) frame).getViewId()
4694 comp = (StructureViewerBase) frame;
4695 break; // break added in 2.9
4698 * Otherwise test for matching position and size of viewer frame
4700 else if (frame.getX() == svattrib.getX()
4701 && frame.getY() == svattrib.getY()
4702 && frame.getHeight() == svattrib.getHeight()
4703 && frame.getWidth() == svattrib.getWidth())
4705 comp = (StructureViewerBase) frame;
4706 // no break in faint hope of an exact match on viewId
4714 * Link an AlignmentPanel to an existing structure viewer.
4719 * @param useinViewerSuperpos
4720 * @param usetoColourbyseq
4721 * @param viewerColouring
4723 protected void linkStructureViewer(AlignmentPanel ap,
4724 StructureViewerBase viewer, StructureViewerModel stateData)
4726 // NOTE: if the jalview project is part of a shared session then
4727 // view synchronization should/could be done here.
4729 final boolean useinViewerSuperpos = stateData.isAlignWithPanel();
4730 final boolean usetoColourbyseq = stateData.isColourWithAlignPanel();
4731 final boolean viewerColouring = stateData.isColourByViewer();
4732 Map<File, StructureData> oldFiles = stateData.getFileData();
4735 * Add mapping for sequences in this view to an already open viewer
4737 final AAStructureBindingModel binding = viewer.getBinding();
4738 for (File id : oldFiles.keySet())
4740 // add this and any other pdb files that should be present in the
4742 StructureData filedat = oldFiles.get(id);
4743 String pdbFile = filedat.getFilePath();
4744 SequenceI[] seq = filedat.getSeqList().toArray(new SequenceI[0]);
4745 binding.getSsm().setMapping(seq, null, pdbFile, DataSourceType.FILE,
4747 binding.addSequenceForStructFile(pdbFile, seq);
4749 // and add the AlignmentPanel's reference to the view panel
4750 viewer.addAlignmentPanel(ap);
4751 if (useinViewerSuperpos)
4753 viewer.useAlignmentPanelForSuperposition(ap);
4757 viewer.excludeAlignmentPanelForSuperposition(ap);
4759 if (usetoColourbyseq)
4761 viewer.useAlignmentPanelForColourbyseq(ap, !viewerColouring);
4765 viewer.excludeAlignmentPanelForColourbyseq(ap);
4770 * Get all frames within the Desktop.
4774 protected JInternalFrame[] getAllFrames()
4776 JInternalFrame[] frames = null;
4777 // TODO is this necessary - is it safe - risk of hanging?
4782 frames = Desktop.desktop.getAllFrames();
4783 } catch (ArrayIndexOutOfBoundsException e)
4785 // occasional No such child exceptions are thrown here...
4789 } catch (InterruptedException f)
4793 } while (frames == null);
4798 * Answers true if 'version' is equal to or later than 'supported', where each
4799 * is formatted as major/minor versions like "2.8.3" or "2.3.4b1" for bugfix
4800 * changes. Development and test values for 'version' are leniently treated
4804 * - minimum version we are comparing against
4806 * - version of data being processsed
4809 public static boolean isVersionStringLaterThan(String supported,
4812 if (supported == null || version == null
4813 || version.equalsIgnoreCase("DEVELOPMENT BUILD")
4814 || version.equalsIgnoreCase("Test")
4815 || version.equalsIgnoreCase("AUTOMATED BUILD"))
4817 System.err.println("Assuming project file with "
4818 + (version == null ? "null" : version)
4819 + " is compatible with Jalview version " + supported);
4824 return StringUtils.compareVersions(version, supported, "b") >= 0;
4828 Vector<JalviewStructureDisplayI> newStructureViewers = null;
4830 protected void addNewStructureViewer(JalviewStructureDisplayI sview)
4832 if (newStructureViewers != null)
4834 sview.getBinding().setFinishedLoadingFromArchive(false);
4835 newStructureViewers.add(sview);
4839 protected void setLoadingFinishedForNewStructureViewers()
4841 if (newStructureViewers != null)
4843 for (JalviewStructureDisplayI sview : newStructureViewers)
4845 sview.getBinding().setFinishedLoadingFromArchive(true);
4847 newStructureViewers.clear();
4848 newStructureViewers = null;
4852 AlignFrame loadViewport(String file, List<JSeq> JSEQ,
4853 List<SequenceI> hiddenSeqs, AlignmentI al,
4854 JalviewModel jm, Viewport view, String uniqueSeqSetId,
4855 String viewId, List<JvAnnotRow> autoAlan)
4857 AlignFrame af = null;
4858 af = new AlignFrame(al, safeInt(view.getWidth()),
4859 safeInt(view.getHeight()), uniqueSeqSetId, viewId)
4863 // protected void processKeyEvent(java.awt.event.KeyEvent e) {
4864 // System.out.println("Jalview2XML AF " + e);
4865 // super.processKeyEvent(e);
4872 af.setFileName(file, FileFormat.Jalview);
4874 final AlignViewport viewport = af.getViewport();
4875 for (int i = 0; i < JSEQ.size(); i++)
4877 int colour = safeInt(JSEQ.get(i).getColour());
4878 viewport.setSequenceColour(viewport.getAlignment().getSequenceAt(i),
4884 viewport.setColourByReferenceSeq(true);
4885 viewport.setDisplayReferenceSeq(true);
4888 viewport.setGatherViewsHere(safeBoolean(view.isGatheredViews()));
4890 if (view.getSequenceSetId() != null)
4892 AlignmentViewport av = viewportsAdded.get(uniqueSeqSetId);
4894 viewport.setSequenceSetId(uniqueSeqSetId);
4897 // propagate shared settings to this new view
4898 viewport.setHistoryList(av.getHistoryList());
4899 viewport.setRedoList(av.getRedoList());
4903 viewportsAdded.put(uniqueSeqSetId, viewport);
4905 // TODO: check if this method can be called repeatedly without
4906 // side-effects if alignpanel already registered.
4907 PaintRefresher.Register(af.alignPanel, uniqueSeqSetId);
4909 // apply Hidden regions to view.
4910 if (hiddenSeqs != null)
4912 for (int s = 0; s < JSEQ.size(); s++)
4914 SequenceGroup hidden = new SequenceGroup();
4915 boolean isRepresentative = false;
4916 for (int r = 0; r < JSEQ.get(s).getHiddenSequences().size(); r++)
4918 isRepresentative = true;
4919 SequenceI sequenceToHide = al
4920 .getSequenceAt(JSEQ.get(s).getHiddenSequences().get(r));
4921 hidden.addSequence(sequenceToHide, false);
4922 // remove from hiddenSeqs list so we don't try to hide it twice
4923 hiddenSeqs.remove(sequenceToHide);
4925 if (isRepresentative)
4927 SequenceI representativeSequence = al.getSequenceAt(s);
4928 hidden.addSequence(representativeSequence, false);
4929 viewport.hideRepSequences(representativeSequence, hidden);
4933 SequenceI[] hseqs = hiddenSeqs
4934 .toArray(new SequenceI[hiddenSeqs.size()]);
4935 viewport.hideSequence(hseqs);
4938 // recover view properties and display parameters
4940 viewport.setShowAnnotation(safeBoolean(view.isShowAnnotation()));
4941 viewport.setAbovePIDThreshold(safeBoolean(view.isPidSelected()));
4942 final int pidThreshold = safeInt(view.getPidThreshold());
4943 viewport.setThreshold(pidThreshold);
4945 viewport.setColourText(safeBoolean(view.isShowColourText()));
4948 .setConservationSelected(
4949 safeBoolean(view.isConservationSelected()));
4950 viewport.setIncrement(safeInt(view.getConsThreshold()));
4951 viewport.setShowJVSuffix(safeBoolean(view.isShowFullId()));
4952 viewport.setRightAlignIds(safeBoolean(view.isRightAlignIds()));
4953 viewport.setFont(new Font(view.getFontName(),
4954 safeInt(view.getFontStyle()), safeInt(view.getFontSize())),
4956 ViewStyleI vs = viewport.getViewStyle();
4957 vs.setScaleProteinAsCdna(view.isScaleProteinAsCdna());
4958 viewport.setViewStyle(vs);
4959 // TODO: allow custom charWidth/Heights to be restored by updating them
4960 // after setting font - which means set above to false
4961 viewport.setRenderGaps(safeBoolean(view.isRenderGaps()));
4962 viewport.setWrapAlignment(safeBoolean(view.isWrapAlignment()));
4963 viewport.setShowAnnotation(safeBoolean(view.isShowAnnotation()));
4965 viewport.setShowBoxes(safeBoolean(view.isShowBoxes()));
4967 viewport.setShowText(safeBoolean(view.isShowText()));
4969 viewport.setTextColour(new Color(safeInt(view.getTextCol1())));
4970 viewport.setTextColour2(new Color(safeInt(view.getTextCol2())));
4971 viewport.setThresholdTextColour(safeInt(view.getTextColThreshold()));
4972 viewport.setShowUnconserved(view.isShowUnconserved());
4973 viewport.getRanges().setStartRes(safeInt(view.getStartRes()));
4975 if (view.getViewName() != null)
4977 viewport.setViewName(view.getViewName());
4978 af.setInitialTabVisible();
4980 af.setBounds(safeInt(view.getXpos()), safeInt(view.getYpos()),
4981 safeInt(view.getWidth()), safeInt(view.getHeight()));
4982 // startSeq set in af.alignPanel.updateLayout below
4983 af.alignPanel.updateLayout();
4984 ColourSchemeI cs = null;
4985 // apply colourschemes
4986 if (view.getBgColour() != null)
4988 if (view.getBgColour().startsWith("ucs"))
4990 cs = getUserColourScheme(jm, view.getBgColour());
4992 else if (view.getBgColour().startsWith("Annotation"))
4994 AnnotationColourScheme viewAnnColour = view.getAnnotationColours();
4995 cs = constructAnnotationColour(viewAnnColour, af, al, jm, true);
5002 cs = ColourSchemeProperty.getColourScheme(af.getViewport(), al,
5003 view.getBgColour());
5008 * turn off 'alignment colour applies to all groups'
5009 * while restoring global colour scheme
5011 viewport.setColourAppliesToAllGroups(false);
5012 viewport.setGlobalColourScheme(cs);
5013 viewport.getResidueShading().setThreshold(pidThreshold,
5014 view.isIgnoreGapsinConsensus());
5015 viewport.getResidueShading()
5016 .setConsensus(viewport.getSequenceConsensusHash());
5017 if (safeBoolean(view.isConservationSelected()) && cs != null)
5019 viewport.getResidueShading()
5020 .setConservationInc(safeInt(view.getConsThreshold()));
5022 af.changeColour(cs);
5023 viewport.setColourAppliesToAllGroups(true);
5026 .setShowSequenceFeatures(
5027 safeBoolean(view.isShowSequenceFeatures()));
5029 viewport.setCentreColumnLabels(view.isCentreColumnLabels());
5030 viewport.setIgnoreGapsConsensus(view.isIgnoreGapsinConsensus(), null);
5031 viewport.setFollowHighlight(view.isFollowHighlight());
5032 viewport.followSelection = view.isFollowSelection();
5033 viewport.setShowConsensusHistogram(view.isShowConsensusHistogram());
5034 viewport.setShowSequenceLogo(view.isShowSequenceLogo());
5035 viewport.setNormaliseSequenceLogo(view.isNormaliseSequenceLogo());
5036 viewport.setShowDBRefs(safeBoolean(view.isShowDbRefTooltip()));
5037 viewport.setShowNPFeats(safeBoolean(view.isShowNPfeatureTooltip()));
5038 viewport.setShowGroupConsensus(view.isShowGroupConsensus());
5039 viewport.setShowGroupConservation(view.isShowGroupConservation());
5041 // recover feature settings
5042 if (jm.getFeatureSettings() != null)
5044 FeatureRenderer fr = af.alignPanel.getSeqPanel().seqCanvas
5045 .getFeatureRenderer();
5046 FeaturesDisplayed fdi;
5047 viewport.setFeaturesDisplayed(fdi = new FeaturesDisplayed());
5048 String[] renderOrder = new String[jm.getFeatureSettings()
5049 .getSetting().size()];
5050 Map<String, FeatureColourI> featureColours = new Hashtable<>();
5051 Map<String, Float> featureOrder = new Hashtable<>();
5053 for (int fs = 0; fs < jm.getFeatureSettings()
5054 .getSetting().size(); fs++)
5056 Setting setting = jm.getFeatureSettings().getSetting().get(fs);
5057 String featureType = setting.getType();
5060 * restore feature filters (if any)
5062 jalview.xml.binding.jalview.FeatureMatcherSet filters = setting
5064 if (filters != null)
5066 FeatureMatcherSetI filter = Jalview2XML
5067 .parseFilter(featureType, filters);
5068 if (!filter.isEmpty())
5070 fr.setFeatureFilter(featureType, filter);
5075 * restore feature colour scheme
5077 Color maxColour = new Color(setting.getColour());
5078 if (setting.getMincolour() != null)
5081 * minColour is always set unless a simple colour
5082 * (including for colour by label though it doesn't use it)
5084 Color minColour = new Color(setting.getMincolour().intValue());
5085 Color noValueColour = minColour;
5086 NoValueColour noColour = setting.getNoValueColour();
5087 if (noColour == NoValueColour.NONE)
5089 noValueColour = null;
5091 else if (noColour == NoValueColour.MAX)
5093 noValueColour = maxColour;
5095 float min = safeFloat(safeFloat(setting.getMin()));
5096 float max = setting.getMax() == null ? 1f
5097 : setting.getMax().floatValue();
5098 FeatureColourI gc = new FeatureColour(maxColour, minColour,
5100 noValueColour, min, max);
5101 if (setting.getAttributeName().size() > 0)
5103 gc.setAttributeName(setting.getAttributeName().toArray(
5104 new String[setting.getAttributeName().size()]));
5106 if (setting.getThreshold() != null)
5108 gc.setThreshold(setting.getThreshold().floatValue());
5109 int threshstate = safeInt(setting.getThreshstate());
5110 // -1 = None, 0 = Below, 1 = Above threshold
5111 if (threshstate == 0)
5113 gc.setBelowThreshold(true);
5115 else if (threshstate == 1)
5117 gc.setAboveThreshold(true);
5120 gc.setAutoScaled(true); // default
5121 if (setting.isAutoScale() != null)
5123 gc.setAutoScaled(setting.isAutoScale());
5125 if (setting.isColourByLabel() != null)
5127 gc.setColourByLabel(setting.isColourByLabel());
5129 // and put in the feature colour table.
5130 featureColours.put(featureType, gc);
5134 featureColours.put(featureType,
5135 new FeatureColour(maxColour));
5137 renderOrder[fs] = featureType;
5138 if (setting.getOrder() != null)
5140 featureOrder.put(featureType, setting.getOrder().floatValue());
5144 featureOrder.put(featureType, new Float(
5145 fs / jm.getFeatureSettings().getSetting().size()));
5147 if (safeBoolean(setting.isDisplay()))
5149 fdi.setVisible(featureType);
5152 Map<String, Boolean> fgtable = new Hashtable<>();
5153 for (int gs = 0; gs < jm.getFeatureSettings().getGroup().size(); gs++)
5155 Group grp = jm.getFeatureSettings().getGroup().get(gs);
5156 fgtable.put(grp.getName(), new Boolean(grp.isDisplay()));
5158 // FeatureRendererSettings frs = new FeatureRendererSettings(renderOrder,
5159 // fgtable, featureColours, jms.getFeatureSettings().hasTransparency() ?
5160 // jms.getFeatureSettings().getTransparency() : 0.0, featureOrder);
5161 FeatureRendererSettings frs = new FeatureRendererSettings(renderOrder,
5162 fgtable, featureColours, 1.0f, featureOrder);
5163 fr.transferSettings(frs);
5166 if (view.getHiddenColumns().size() > 0)
5168 for (int c = 0; c < view.getHiddenColumns().size(); c++)
5170 final HiddenColumns hc = view.getHiddenColumns().get(c);
5171 viewport.hideColumns(safeInt(hc.getStart()),
5172 safeInt(hc.getEnd()) /* +1 */);
5175 if (view.getCalcIdParam() != null)
5177 for (CalcIdParam calcIdParam : view.getCalcIdParam())
5179 if (calcIdParam != null)
5181 if (recoverCalcIdParam(calcIdParam, viewport))
5186 warn("Couldn't recover parameters for "
5187 + calcIdParam.getCalcId());
5192 af.setMenusFromViewport(viewport);
5193 af.setTitle(view.getTitle());
5194 // TODO: we don't need to do this if the viewport is aready visible.
5196 * Add the AlignFrame to the desktop (it may be 'gathered' later), unless it
5197 * has a 'cdna/protein complement' view, in which case save it in order to
5198 * populate a SplitFrame once all views have been read in.
5200 String complementaryViewId = view.getComplementId();
5201 if (complementaryViewId == null)
5203 Desktop.addInternalFrame(af, view.getTitle(),
5204 safeInt(view.getWidth()), safeInt(view.getHeight()));
5205 // recompute any autoannotation
5206 af.alignPanel.updateAnnotation(false, true);
5207 reorderAutoannotation(af, al, autoAlan);
5208 af.alignPanel.alignmentChanged();
5212 splitFrameCandidates.put(view, af);
5218 * Reads saved data to restore Colour by Annotation settings
5220 * @param viewAnnColour
5224 * @param checkGroupAnnColour
5227 private ColourSchemeI constructAnnotationColour(
5228 AnnotationColourScheme viewAnnColour, AlignFrame af,
5229 AlignmentI al, JalviewModel model, boolean checkGroupAnnColour)
5231 boolean propagateAnnColour = false;
5232 AlignmentI annAlignment = af != null ? af.getViewport().getAlignment()
5234 if (checkGroupAnnColour && al.getGroups() != null
5235 && al.getGroups().size() > 0)
5237 // pre 2.8.1 behaviour
5238 // check to see if we should transfer annotation colours
5239 propagateAnnColour = true;
5240 for (SequenceGroup sg : al.getGroups())
5242 if (sg.getColourScheme() instanceof AnnotationColourGradient)
5244 propagateAnnColour = false;
5250 * 2.10.2- : saved annotationId is AlignmentAnnotation.annotationId
5252 String annotationId = viewAnnColour.getAnnotation();
5253 AlignmentAnnotation matchedAnnotation = annotationIds.get(annotationId);
5256 * pre 2.10.2: saved annotationId is AlignmentAnnotation.label
5258 if (matchedAnnotation == null
5259 && annAlignment.getAlignmentAnnotation() != null)
5261 for (int i = 0; i < annAlignment.getAlignmentAnnotation().length; i++)
5264 .equals(annAlignment.getAlignmentAnnotation()[i].label))
5266 matchedAnnotation = annAlignment.getAlignmentAnnotation()[i];
5271 if (matchedAnnotation == null)
5273 System.err.println("Failed to match annotation colour scheme for "
5277 if (matchedAnnotation.getThreshold() == null)
5279 matchedAnnotation.setThreshold(
5280 new GraphLine(safeFloat(viewAnnColour.getThreshold()),
5281 "Threshold", Color.black));
5284 AnnotationColourGradient cs = null;
5285 if (viewAnnColour.getColourScheme().equals("None"))
5287 cs = new AnnotationColourGradient(matchedAnnotation,
5288 new Color(safeInt(viewAnnColour.getMinColour())),
5289 new Color(safeInt(viewAnnColour.getMaxColour())),
5290 safeInt(viewAnnColour.getAboveThreshold()));
5292 else if (viewAnnColour.getColourScheme().startsWith("ucs"))
5294 cs = new AnnotationColourGradient(matchedAnnotation,
5295 getUserColourScheme(model, viewAnnColour.getColourScheme()),
5296 safeInt(viewAnnColour.getAboveThreshold()));
5300 cs = new AnnotationColourGradient(matchedAnnotation,
5301 ColourSchemeProperty.getColourScheme(af.getViewport(), al,
5302 viewAnnColour.getColourScheme()),
5303 safeInt(viewAnnColour.getAboveThreshold()));
5306 boolean perSequenceOnly = safeBoolean(viewAnnColour.isPerSequence());
5307 boolean useOriginalColours = safeBoolean(
5308 viewAnnColour.isPredefinedColours());
5309 cs.setSeqAssociated(perSequenceOnly);
5310 cs.setPredefinedColours(useOriginalColours);
5312 if (propagateAnnColour && al.getGroups() != null)
5314 // Also use these settings for all the groups
5315 for (int g = 0; g < al.getGroups().size(); g++)
5317 SequenceGroup sg = al.getGroups().get(g);
5318 if (sg.getGroupColourScheme() == null)
5323 AnnotationColourGradient groupScheme = new AnnotationColourGradient(
5324 matchedAnnotation, sg.getColourScheme(),
5325 safeInt(viewAnnColour.getAboveThreshold()));
5326 sg.setColourScheme(groupScheme);
5327 groupScheme.setSeqAssociated(perSequenceOnly);
5328 groupScheme.setPredefinedColours(useOriginalColours);
5334 private void reorderAutoannotation(AlignFrame af, AlignmentI al,
5335 List<JvAnnotRow> autoAlan)
5337 // copy over visualization settings for autocalculated annotation in the
5339 if (al.getAlignmentAnnotation() != null)
5342 * Kludge for magic autoannotation names (see JAL-811)
5344 String[] magicNames = new String[] { "Consensus", "Quality",
5346 JvAnnotRow nullAnnot = new JvAnnotRow(-1, null);
5347 Hashtable<String, JvAnnotRow> visan = new Hashtable<>();
5348 for (String nm : magicNames)
5350 visan.put(nm, nullAnnot);
5352 for (JvAnnotRow auan : autoAlan)
5354 visan.put(auan.template.label
5355 + (auan.template.getCalcId() == null ? ""
5356 : "\t" + auan.template.getCalcId()),
5359 int hSize = al.getAlignmentAnnotation().length;
5360 List<JvAnnotRow> reorder = new ArrayList<>();
5361 // work through any autoCalculated annotation already on the view
5362 // removing it if it should be placed in a different location on the
5363 // annotation panel.
5364 List<String> remains = new ArrayList<>(visan.keySet());
5365 for (int h = 0; h < hSize; h++)
5367 jalview.datamodel.AlignmentAnnotation jalan = al
5368 .getAlignmentAnnotation()[h];
5369 if (jalan.autoCalculated)
5372 JvAnnotRow valan = visan.get(k = jalan.label);
5373 if (jalan.getCalcId() != null)
5375 valan = visan.get(k = jalan.label + "\t" + jalan.getCalcId());
5380 // delete the auto calculated row from the alignment
5381 al.deleteAnnotation(jalan, false);
5385 if (valan != nullAnnot)
5387 if (jalan != valan.template)
5389 // newly created autoannotation row instance
5390 // so keep a reference to the visible annotation row
5391 // and copy over all relevant attributes
5392 if (valan.template.graphHeight >= 0)
5395 jalan.graphHeight = valan.template.graphHeight;
5397 jalan.visible = valan.template.visible;
5399 reorder.add(new JvAnnotRow(valan.order, jalan));
5404 // Add any (possibly stale) autocalculated rows that were not appended to
5405 // the view during construction
5406 for (String other : remains)
5408 JvAnnotRow othera = visan.get(other);
5409 if (othera != nullAnnot && othera.template.getCalcId() != null
5410 && othera.template.getCalcId().length() > 0)
5412 reorder.add(othera);
5415 // now put the automatic annotation in its correct place
5416 int s = 0, srt[] = new int[reorder.size()];
5417 JvAnnotRow[] rws = new JvAnnotRow[reorder.size()];
5418 for (JvAnnotRow jvar : reorder)
5421 srt[s++] = jvar.order;
5424 jalview.util.QuickSort.sort(srt, rws);
5425 // and re-insert the annotation at its correct position
5426 for (JvAnnotRow jvar : rws)
5428 al.addAnnotation(jvar.template, jvar.order);
5430 af.alignPanel.adjustAnnotationHeight();
5434 Hashtable skipList = null;
5437 * TODO remove this method
5440 * @return AlignFrame bound to sequenceSetId from view, if one exists. private
5441 * AlignFrame getSkippedFrame(Viewport view) { if (skipList==null) {
5442 * throw new Error("Implementation Error. No skipList defined for this
5443 * Jalview2XML instance."); } return (AlignFrame)
5444 * skipList.get(view.getSequenceSetId()); }
5448 * Check if the Jalview view contained in object should be skipped or not.
5451 * @return true if view's sequenceSetId is a key in skipList
5453 private boolean skipViewport(JalviewModel object)
5455 if (skipList == null)
5459 String id = object.getViewport().get(0).getSequenceSetId();
5460 if (skipList.containsKey(id))
5462 if (Cache.log != null && Cache.log.isDebugEnabled())
5464 Cache.log.debug("Skipping seuqence set id " + id);
5471 public void addToSkipList(AlignFrame af)
5473 if (skipList == null)
5475 skipList = new Hashtable();
5477 skipList.put(af.getViewport().getSequenceSetId(), af);
5480 public void clearSkipList()
5482 if (skipList != null)
5489 private void recoverDatasetFor(SequenceSet vamsasSet, AlignmentI al,
5490 boolean ignoreUnrefed, String uniqueSeqSetId)
5492 jalview.datamodel.AlignmentI ds = getDatasetFor(
5493 vamsasSet.getDatasetId());
5494 AlignmentI xtant_ds = ds;
5495 if (xtant_ds == null)
5497 // good chance we are about to create a new dataset, but check if we've
5498 // seen some of the dataset sequence IDs before.
5499 // TODO: skip this check if we are working with project generated by
5500 // version 2.11 or later
5501 xtant_ds = checkIfHasDataset(vamsasSet.getSequence());
5502 if (xtant_ds != null)
5505 addDatasetRef(vamsasSet.getDatasetId(), ds);
5508 Vector dseqs = null;
5511 // recovering an alignment View
5512 AlignmentI seqSetDS = getDatasetFor(UNIQSEQSETID + uniqueSeqSetId);
5513 if (seqSetDS != null)
5515 if (ds != null && ds != seqSetDS)
5517 warn("JAL-3171 regression: Overwriting a dataset reference for an alignment"
5518 + " - CDS/Protein crossreference data may be lost");
5519 if (xtant_ds != null)
5521 // This can only happen if the unique sequence set ID was bound to a
5522 // dataset that did not contain any of the sequences in the view
5523 // currently being restored.
5524 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.");
5528 addDatasetRef(vamsasSet.getDatasetId(), ds);
5533 // try even harder to restore dataset
5534 AlignmentI xtantDS = checkIfHasDataset(vamsasSet.getSequence());
5535 // create a list of new dataset sequences
5536 dseqs = new Vector();
5538 for (int i = 0, iSize = vamsasSet.getSequence().size(); i < iSize; i++)
5540 Sequence vamsasSeq = vamsasSet.getSequence().get(i);
5541 ensureJalviewDatasetSequence(vamsasSeq, ds, dseqs, ignoreUnrefed, i);
5543 // create a new dataset
5546 SequenceI[] dsseqs = new SequenceI[dseqs.size()];
5547 dseqs.copyInto(dsseqs);
5548 ds = new jalview.datamodel.Alignment(dsseqs);
5549 debug("Created new dataset " + vamsasSet.getDatasetId()
5550 + " for alignment " + System.identityHashCode(al));
5551 addDatasetRef(vamsasSet.getDatasetId(), ds);
5553 // set the dataset for the newly imported alignment.
5554 if (al.getDataset() == null && !ignoreUnrefed)
5557 // register dataset for the alignment's uniqueSeqSetId for legacy projects
5558 addDatasetRef(UNIQSEQSETID + uniqueSeqSetId, ds);
5560 updateSeqDatasetBinding(vamsasSet.getSequence(), ds);
5564 * XML dataset sequence ID to materialised dataset reference
5566 HashMap<String, AlignmentI> seqToDataset = new HashMap<>();
5569 * @return the first materialised dataset reference containing a dataset
5570 * sequence referenced in the given view
5572 * - sequences from the view
5574 AlignmentI checkIfHasDataset(List<Sequence> list)
5576 for (Sequence restoredSeq : list)
5578 AlignmentI datasetFor = seqToDataset.get(restoredSeq.getDsseqid());
5579 if (datasetFor != null)
5588 * Register ds as the containing dataset for the dataset sequences referenced
5589 * by sequences in list
5592 * - sequences in a view
5595 void updateSeqDatasetBinding(List<Sequence> list, AlignmentI ds)
5597 for (Sequence restoredSeq : list)
5599 AlignmentI prevDS = seqToDataset.put(restoredSeq.getDsseqid(), ds);
5600 if (prevDS != null && prevDS != ds)
5602 warn("Dataset sequence appears in many datasets: "
5603 + restoredSeq.getDsseqid());
5604 // TODO: try to merge!
5611 * sequence definition to create/merge dataset sequence for
5615 * vector to add new dataset sequence to
5616 * @param ignoreUnrefed
5617 * - when true, don't create new sequences from vamsasSeq if it's id
5618 * doesn't already have an asssociated Jalview sequence.
5620 * - used to reorder the sequence in the alignment according to the
5621 * vamsasSeq array ordering, to preserve ordering of dataset
5623 private void ensureJalviewDatasetSequence(Sequence vamsasSeq,
5624 AlignmentI ds, Vector dseqs, boolean ignoreUnrefed, int vseqpos)
5626 // JBP TODO: Check this is called for AlCodonFrames to support recovery of
5628 SequenceI sq = seqRefIds.get(vamsasSeq.getId());
5629 boolean reorder = false;
5630 SequenceI dsq = null;
5631 if (sq != null && sq.getDatasetSequence() != null)
5633 dsq = sq.getDatasetSequence();
5639 if (sq == null && ignoreUnrefed)
5643 String sqid = vamsasSeq.getDsseqid();
5646 // need to create or add a new dataset sequence reference to this sequence
5649 dsq = seqRefIds.get(sqid);
5654 // make a new dataset sequence
5655 dsq = sq.createDatasetSequence();
5658 // make up a new dataset reference for this sequence
5659 sqid = seqHash(dsq);
5661 dsq.setVamsasId(uniqueSetSuffix + sqid);
5662 seqRefIds.put(sqid, dsq);
5667 dseqs.addElement(dsq);
5672 ds.addSequence(dsq);
5678 { // make this dataset sequence sq's dataset sequence
5679 sq.setDatasetSequence(dsq);
5680 // and update the current dataset alignment
5685 if (!dseqs.contains(dsq))
5692 if (ds.findIndex(dsq) < 0)
5694 ds.addSequence(dsq);
5701 // TODO: refactor this as a merge dataset sequence function
5702 // now check that sq (the dataset sequence) sequence really is the union of
5703 // all references to it
5704 // boolean pre = sq.getStart() < dsq.getStart();
5705 // boolean post = sq.getEnd() > dsq.getEnd();
5709 // StringBuffer sb = new StringBuffer();
5710 String newres = jalview.analysis.AlignSeq.extractGaps(
5711 jalview.util.Comparison.GapChars, sq.getSequenceAsString());
5712 if (!newres.equalsIgnoreCase(dsq.getSequenceAsString())
5713 && newres.length() > dsq.getLength())
5715 // Update with the longer sequence.
5719 * if (pre) { sb.insert(0, newres .substring(0, dsq.getStart() -
5720 * sq.getStart())); dsq.setStart(sq.getStart()); } if (post) {
5721 * sb.append(newres.substring(newres.length() - sq.getEnd() -
5722 * dsq.getEnd())); dsq.setEnd(sq.getEnd()); }
5724 dsq.setSequence(newres);
5726 // TODO: merges will never happen if we 'know' we have the real dataset
5727 // sequence - this should be detected when id==dssid
5729 "DEBUG Notice: Merged dataset sequence (if you see this often, post at http://issues.jalview.org/browse/JAL-1474)"); // ("
5730 // + (pre ? "prepended" : "") + " "
5731 // + (post ? "appended" : ""));
5736 // sequence refs are identical. We may need to update the existing dataset
5737 // alignment with this one, though.
5738 if (ds != null && dseqs == null)
5740 int opos = ds.findIndex(dsq);
5741 SequenceI tseq = null;
5742 if (opos != -1 && vseqpos != opos)
5744 // remove from old position
5745 ds.deleteSequence(dsq);
5747 if (vseqpos < ds.getHeight())
5749 if (vseqpos != opos)
5751 // save sequence at destination position
5752 tseq = ds.getSequenceAt(vseqpos);
5753 ds.replaceSequenceAt(vseqpos, dsq);
5754 ds.addSequence(tseq);
5759 ds.addSequence(dsq);
5766 * TODO use AlignmentI here and in related methods - needs
5767 * AlignmentI.getDataset() changed to return AlignmentI instead of Alignment
5769 Hashtable<String, AlignmentI> datasetIds = null;
5771 IdentityHashMap<AlignmentI, String> dataset2Ids = null;
5773 private AlignmentI getDatasetFor(String datasetId)
5775 if (datasetIds == null)
5777 datasetIds = new Hashtable<>();
5780 if (datasetIds.containsKey(datasetId))
5782 return datasetIds.get(datasetId);
5787 private void addDatasetRef(String datasetId, AlignmentI dataset)
5789 if (datasetIds == null)
5791 datasetIds = new Hashtable<>();
5793 datasetIds.put(datasetId, dataset);
5797 * make a new dataset ID for this jalview dataset alignment
5802 private String getDatasetIdRef(AlignmentI dataset)
5804 if (dataset.getDataset() != null)
5806 warn("Serious issue! Dataset Object passed to getDatasetIdRef is not a Jalview DATASET alignment...");
5808 String datasetId = makeHashCode(dataset, null);
5809 if (datasetId == null)
5811 // make a new datasetId and record it
5812 if (dataset2Ids == null)
5814 dataset2Ids = new IdentityHashMap<>();
5818 datasetId = dataset2Ids.get(dataset);
5820 if (datasetId == null)
5822 datasetId = "ds" + dataset2Ids.size() + 1;
5823 dataset2Ids.put(dataset, datasetId);
5829 private void addDBRefs(SequenceI datasetSequence, Sequence sequence)
5831 for (int d = 0; d < sequence.getDBRef().size(); d++)
5833 DBRef dr = sequence.getDBRef().get(d);
5834 jalview.datamodel.DBRefEntry entry = new jalview.datamodel.DBRefEntry(
5835 dr.getSource(), dr.getVersion(), dr.getAccessionId());
5836 if (dr.getMapping() != null)
5838 entry.setMap(addMapping(dr.getMapping()));
5840 datasetSequence.addDBRef(entry);
5844 private jalview.datamodel.Mapping addMapping(Mapping m)
5846 SequenceI dsto = null;
5847 // Mapping m = dr.getMapping();
5848 int fr[] = new int[m.getMapListFrom().size() * 2];
5849 Iterator<MapListFrom> from = m.getMapListFrom().iterator();// enumerateMapListFrom();
5850 for (int _i = 0; from.hasNext(); _i += 2)
5852 MapListFrom mf = from.next();
5853 fr[_i] = mf.getStart();
5854 fr[_i + 1] = mf.getEnd();
5856 int fto[] = new int[m.getMapListTo().size() * 2];
5857 Iterator<MapListTo> to = m.getMapListTo().iterator();// enumerateMapListTo();
5858 for (int _i = 0; to.hasNext(); _i += 2)
5860 MapListTo mf = to.next();
5861 fto[_i] = mf.getStart();
5862 fto[_i + 1] = mf.getEnd();
5864 jalview.datamodel.Mapping jmap = new jalview.datamodel.Mapping(dsto, fr,
5865 fto, m.getMapFromUnit().intValue(),
5866 m.getMapToUnit().intValue());
5869 * (optional) choice of dseqFor or Sequence
5871 if (m.getDseqFor() != null)
5873 String dsfor = m.getDseqFor();
5874 if (seqRefIds.containsKey(dsfor))
5879 jmap.setTo(seqRefIds.get(dsfor));
5883 frefedSequence.add(newMappingRef(dsfor, jmap));
5886 else if (m.getSequence() != null)
5889 * local sequence definition
5891 Sequence ms = m.getSequence();
5892 SequenceI djs = null;
5893 String sqid = ms.getDsseqid();
5894 if (sqid != null && sqid.length() > 0)
5897 * recover dataset sequence
5899 djs = seqRefIds.get(sqid);
5904 "Warning - making up dataset sequence id for DbRef sequence map reference");
5905 sqid = ((Object) ms).toString(); // make up a new hascode for
5906 // undefined dataset sequence hash
5907 // (unlikely to happen)
5913 * make a new dataset sequence and add it to refIds hash
5915 djs = new jalview.datamodel.Sequence(ms.getName(),
5917 djs.setStart(jmap.getMap().getToLowest());
5918 djs.setEnd(jmap.getMap().getToHighest());
5919 djs.setVamsasId(uniqueSetSuffix + sqid);
5921 incompleteSeqs.put(sqid, djs);
5922 seqRefIds.put(sqid, djs);
5925 jalview.bin.Cache.log.debug("about to recurse on addDBRefs.");
5934 * Provides a 'copy' of an alignment view (on action New View) by 'saving' the
5935 * view as XML (but not to file), and then reloading it
5940 public AlignmentPanel copyAlignPanel(AlignmentPanel ap)
5943 JalviewModel jm = saveState(ap, null, null, null);
5946 jm.getVamsasModel().getSequenceSet().get(0).getDatasetId(),
5947 ap.getAlignment().getDataset());
5949 uniqueSetSuffix = "";
5950 // jm.getJalviewModelSequence().getViewport(0).setId(null);
5951 jm.getViewport().get(0).setId(null);
5952 // we don't overwrite the view we just copied
5954 if (this.frefedSequence == null)
5956 frefedSequence = new Vector<>();
5959 viewportsAdded.clear();
5961 AlignFrame af = loadFromObject(jm, null, false, null);
5962 af.getAlignPanels().clear();
5963 af.closeMenuItem_actionPerformed(true);
5966 * if(ap.av.getAlignment().getAlignmentAnnotation()!=null) { for(int i=0;
5967 * i<ap.av.getAlignment().getAlignmentAnnotation().length; i++) {
5968 * if(!ap.av.getAlignment().getAlignmentAnnotation()[i].autoCalculated) {
5969 * af.alignPanel.av.getAlignment().getAlignmentAnnotation()[i] =
5970 * ap.av.getAlignment().getAlignmentAnnotation()[i]; } } }
5973 return af.alignPanel;
5976 private Hashtable jvids2vobj;
5978 private void warn(String msg)
5983 private void warn(String msg, Exception e)
5985 if (Cache.log != null)
5989 Cache.log.warn(msg, e);
5993 Cache.log.warn(msg);
5998 System.err.println("Warning: " + msg);
6001 e.printStackTrace();
6006 private void debug(String string)
6008 debug(string, null);
6011 private void debug(String msg, Exception e)
6013 if (Cache.log != null)
6017 Cache.log.debug(msg, e);
6021 Cache.log.debug(msg);
6026 System.err.println("Warning: " + msg);
6029 e.printStackTrace();
6035 * set the object to ID mapping tables used to write/recover objects and XML
6036 * ID strings for the jalview project. If external tables are provided then
6037 * finalize and clearSeqRefs will not clear the tables when the Jalview2XML
6038 * object goes out of scope. - also populates the datasetIds hashtable with
6039 * alignment objects containing dataset sequences
6042 * Map from ID strings to jalview datamodel
6044 * Map from jalview datamodel to ID strings
6048 public void setObjectMappingTables(Hashtable vobj2jv,
6049 IdentityHashMap jv2vobj)
6051 this.jv2vobj = jv2vobj;
6052 this.vobj2jv = vobj2jv;
6053 Iterator ds = jv2vobj.keySet().iterator();
6055 while (ds.hasNext())
6057 Object jvobj = ds.next();
6058 id = jv2vobj.get(jvobj).toString();
6059 if (jvobj instanceof jalview.datamodel.Alignment)
6061 if (((jalview.datamodel.Alignment) jvobj).getDataset() == null)
6063 addDatasetRef(id, (jalview.datamodel.Alignment) jvobj);
6066 else if (jvobj instanceof jalview.datamodel.Sequence)
6068 // register sequence object so the XML parser can recover it.
6069 if (seqRefIds == null)
6071 seqRefIds = new HashMap<>();
6073 if (seqsToIds == null)
6075 seqsToIds = new IdentityHashMap<>();
6077 seqRefIds.put(jv2vobj.get(jvobj).toString(), (SequenceI) jvobj);
6078 seqsToIds.put((SequenceI) jvobj, id);
6080 else if (jvobj instanceof jalview.datamodel.AlignmentAnnotation)
6083 AlignmentAnnotation jvann = (AlignmentAnnotation) jvobj;
6084 annotationIds.put(anid = jv2vobj.get(jvobj).toString(), jvann);
6085 if (jvann.annotationId == null)
6087 jvann.annotationId = anid;
6089 if (!jvann.annotationId.equals(anid))
6091 // TODO verify that this is the correct behaviour
6092 this.warn("Overriding Annotation ID for " + anid
6093 + " from different id : " + jvann.annotationId);
6094 jvann.annotationId = anid;
6097 else if (jvobj instanceof String)
6099 if (jvids2vobj == null)
6101 jvids2vobj = new Hashtable();
6102 jvids2vobj.put(jvobj, jv2vobj.get(jvobj).toString());
6107 Cache.log.debug("Ignoring " + jvobj.getClass() + " (ID = " + id);
6113 * set the uniqueSetSuffix used to prefix/suffix object IDs for jalview
6114 * objects created from the project archive. If string is null (default for
6115 * construction) then suffix will be set automatically.
6119 public void setUniqueSetSuffix(String string)
6121 uniqueSetSuffix = string;
6126 * uses skipList2 as the skipList for skipping views on sequence sets
6127 * associated with keys in the skipList
6131 public void setSkipList(Hashtable skipList2)
6133 skipList = skipList2;
6137 * Reads the jar entry of given name and returns its contents, or null if the
6138 * entry is not found.
6141 * @param jarEntryName
6144 protected String readJarEntry(jarInputStreamProvider jprovider,
6145 String jarEntryName)
6147 String result = null;
6148 BufferedReader in = null;
6153 * Reopen the jar input stream and traverse its entries to find a matching
6156 JarInputStream jin = jprovider.getJarInputStream();
6157 JarEntry entry = null;
6160 entry = jin.getNextJarEntry();
6161 } while (entry != null && !entry.getName().equals(jarEntryName));
6165 StringBuilder out = new StringBuilder(256);
6166 in = new BufferedReader(new InputStreamReader(jin, UTF_8));
6169 while ((data = in.readLine()) != null)
6173 result = out.toString();
6177 warn("Couldn't find entry in Jalview Jar for " + jarEntryName);
6179 } catch (Exception ex)
6181 ex.printStackTrace();
6189 } catch (IOException e)
6200 * Returns an incrementing counter (0, 1, 2...)
6204 private synchronized int nextCounter()
6210 * Loads any saved PCA viewers
6215 protected void loadPCAViewers(JalviewModel model, AlignmentPanel ap)
6219 List<PcaViewer> pcaviewers = model.getPcaViewer();
6220 for (PcaViewer viewer : pcaviewers)
6222 String modelName = viewer.getScoreModelName();
6223 SimilarityParamsI params = new SimilarityParams(
6224 viewer.isIncludeGappedColumns(), viewer.isMatchGaps(),
6225 viewer.isIncludeGaps(),
6226 viewer.isDenominateByShortestLength());
6229 * create the panel (without computing the PCA)
6231 PCAPanel panel = new PCAPanel(ap, modelName, params);
6233 panel.setTitle(viewer.getTitle());
6234 panel.setBounds(new Rectangle(viewer.getXpos(), viewer.getYpos(),
6235 viewer.getWidth(), viewer.getHeight()));
6237 boolean showLabels = viewer.isShowLabels();
6238 panel.setShowLabels(showLabels);
6239 panel.getRotatableCanvas().setShowLabels(showLabels);
6240 panel.getRotatableCanvas()
6241 .setBgColour(new Color(viewer.getBgColour()));
6242 panel.getRotatableCanvas()
6243 .setApplyToAllViews(viewer.isLinkToAllViews());
6246 * load PCA output data
6248 ScoreModelI scoreModel = ScoreModels.getInstance()
6249 .getScoreModel(modelName, ap);
6250 PCA pca = new PCA(null, scoreModel, params);
6251 PcaDataType pcaData = viewer.getPcaData();
6253 MatrixI pairwise = loadDoubleMatrix(pcaData.getPairwiseMatrix());
6254 pca.setPairwiseScores(pairwise);
6256 MatrixI triDiag = loadDoubleMatrix(pcaData.getTridiagonalMatrix());
6257 pca.setTridiagonal(triDiag);
6259 MatrixI result = loadDoubleMatrix(pcaData.getEigenMatrix());
6260 pca.setEigenmatrix(result);
6262 panel.getPcaModel().setPCA(pca);
6265 * we haven't saved the input data! (JAL-2647 to do)
6267 panel.setInputData(null);
6270 * add the sequence points for the PCA display
6272 List<jalview.datamodel.SequencePoint> seqPoints = new ArrayList<>();
6273 for (SequencePoint sp : viewer.getSequencePoint())
6275 String seqId = sp.getSequenceRef();
6276 SequenceI seq = seqRefIds.get(seqId);
6279 throw new IllegalStateException(
6280 "Unmatched seqref for PCA: " + seqId);
6282 Point pt = new Point(sp.getXPos(), sp.getYPos(), sp.getZPos());
6283 jalview.datamodel.SequencePoint seqPoint = new jalview.datamodel.SequencePoint(
6285 seqPoints.add(seqPoint);
6287 panel.getRotatableCanvas().setPoints(seqPoints, seqPoints.size());
6290 * set min-max ranges and scale after setPoints (which recomputes them)
6292 panel.getRotatableCanvas().setScaleFactor(viewer.getScaleFactor());
6293 SeqPointMin spMin = viewer.getSeqPointMin();
6294 float[] min = new float[] { spMin.getXPos(), spMin.getYPos(),
6296 SeqPointMax spMax = viewer.getSeqPointMax();
6297 float[] max = new float[] { spMax.getXPos(), spMax.getYPos(),
6299 panel.getRotatableCanvas().setSeqMinMax(min, max);
6301 // todo: hold points list in PCAModel only
6302 panel.getPcaModel().setSequencePoints(seqPoints);
6304 panel.setSelectedDimensionIndex(viewer.getXDim(), X);
6305 panel.setSelectedDimensionIndex(viewer.getYDim(), Y);
6306 panel.setSelectedDimensionIndex(viewer.getZDim(), Z);
6308 // is this duplication needed?
6309 panel.setTop(seqPoints.size() - 1);
6310 panel.getPcaModel().setTop(seqPoints.size() - 1);
6313 * add the axes' end points for the display
6315 for (int i = 0; i < 3; i++)
6317 Axis axis = viewer.getAxis().get(i);
6318 panel.getRotatableCanvas().getAxisEndPoints()[i] = new Point(
6319 axis.getXPos(), axis.getYPos(), axis.getZPos());
6322 Desktop.addInternalFrame(panel, MessageManager.formatMessage(
6323 "label.calc_title", "PCA", modelName), 475, 450);
6325 } catch (Exception ex)
6327 Cache.log.error("Error loading PCA: " + ex.toString());
6332 * Populates an XML model of the feature colour scheme for one feature type
6334 * @param featureType
6338 public static Colour marshalColour(
6339 String featureType, FeatureColourI fcol)
6341 Colour col = new Colour();
6342 if (fcol.isSimpleColour())
6344 col.setRGB(Format.getHexString(fcol.getColour()));
6348 col.setRGB(Format.getHexString(fcol.getMaxColour()));
6349 col.setMin(fcol.getMin());
6350 col.setMax(fcol.getMax());
6351 col.setMinRGB(jalview.util.Format.getHexString(fcol.getMinColour()));
6352 col.setAutoScale(fcol.isAutoScaled());
6353 col.setThreshold(fcol.getThreshold());
6354 col.setColourByLabel(fcol.isColourByLabel());
6355 col.setThreshType(fcol.isAboveThreshold() ? ThresholdType.ABOVE
6356 : (fcol.isBelowThreshold() ? ThresholdType.BELOW
6357 : ThresholdType.NONE));
6358 if (fcol.isColourByAttribute())
6360 final String[] attName = fcol.getAttributeName();
6361 col.getAttributeName().add(attName[0]);
6362 if (attName.length > 1)
6364 col.getAttributeName().add(attName[1]);
6367 Color noColour = fcol.getNoColour();
6368 if (noColour == null)
6370 col.setNoValueColour(NoValueColour.NONE);
6372 else if (noColour == fcol.getMaxColour())
6374 col.setNoValueColour(NoValueColour.MAX);
6378 col.setNoValueColour(NoValueColour.MIN);
6381 col.setName(featureType);
6386 * Populates an XML model of the feature filter(s) for one feature type
6388 * @param firstMatcher
6389 * the first (or only) match condition)
6391 * remaining match conditions (if any)
6393 * if true, conditions are and-ed, else or-ed
6395 public static jalview.xml.binding.jalview.FeatureMatcherSet marshalFilter(
6396 FeatureMatcherI firstMatcher, Iterator<FeatureMatcherI> filters,
6399 jalview.xml.binding.jalview.FeatureMatcherSet result = new jalview.xml.binding.jalview.FeatureMatcherSet();
6401 if (filters.hasNext())
6406 CompoundMatcher compound = new CompoundMatcher();
6407 compound.setAnd(and);
6408 jalview.xml.binding.jalview.FeatureMatcherSet matcher1 = marshalFilter(
6409 firstMatcher, Collections.emptyIterator(), and);
6410 // compound.addMatcherSet(matcher1);
6411 compound.getMatcherSet().add(matcher1);
6412 FeatureMatcherI nextMatcher = filters.next();
6413 jalview.xml.binding.jalview.FeatureMatcherSet matcher2 = marshalFilter(
6414 nextMatcher, filters, and);
6415 // compound.addMatcherSet(matcher2);
6416 compound.getMatcherSet().add(matcher2);
6417 result.setCompoundMatcher(compound);
6422 * single condition matcher
6424 // MatchCondition matcherModel = new MatchCondition();
6425 jalview.xml.binding.jalview.FeatureMatcher matcherModel = new jalview.xml.binding.jalview.FeatureMatcher();
6426 matcherModel.setCondition(
6427 firstMatcher.getMatcher().getCondition().getStableName());
6428 matcherModel.setValue(firstMatcher.getMatcher().getPattern());
6429 if (firstMatcher.isByAttribute())
6431 matcherModel.setBy(FilterBy.BY_ATTRIBUTE);
6432 // matcherModel.setAttributeName(firstMatcher.getAttribute());
6433 String[] attName = firstMatcher.getAttribute();
6434 matcherModel.getAttributeName().add(attName[0]); // attribute
6435 if (attName.length > 1)
6437 matcherModel.getAttributeName().add(attName[1]); // sub-attribute
6440 else if (firstMatcher.isByLabel())
6442 matcherModel.setBy(FilterBy.BY_LABEL);
6444 else if (firstMatcher.isByScore())
6446 matcherModel.setBy(FilterBy.BY_SCORE);
6448 result.setMatchCondition(matcherModel);
6455 * Loads one XML model of a feature filter to a Jalview object
6457 * @param featureType
6458 * @param matcherSetModel
6461 public static FeatureMatcherSetI parseFilter(
6463 jalview.xml.binding.jalview.FeatureMatcherSet matcherSetModel)
6465 FeatureMatcherSetI result = new FeatureMatcherSet();
6468 parseFilterConditions(result, matcherSetModel, true);
6469 } catch (IllegalStateException e)
6471 // mixing AND and OR conditions perhaps
6473 String.format("Error reading filter conditions for '%s': %s",
6474 featureType, e.getMessage()));
6475 // return as much as was parsed up to the error
6482 * Adds feature match conditions to matcherSet as unmarshalled from XML
6483 * (possibly recursively for compound conditions)
6486 * @param matcherSetModel
6488 * if true, multiple conditions are AND-ed, else they are OR-ed
6489 * @throws IllegalStateException
6490 * if AND and OR conditions are mixed
6492 protected static void parseFilterConditions(
6493 FeatureMatcherSetI matcherSet,
6494 jalview.xml.binding.jalview.FeatureMatcherSet matcherSetModel,
6497 jalview.xml.binding.jalview.FeatureMatcher mc = matcherSetModel
6498 .getMatchCondition();
6504 FilterBy filterBy = mc.getBy();
6505 Condition cond = Condition.fromString(mc.getCondition());
6506 String pattern = mc.getValue();
6507 FeatureMatcherI matchCondition = null;
6508 if (filterBy == FilterBy.BY_LABEL)
6510 matchCondition = FeatureMatcher.byLabel(cond, pattern);
6512 else if (filterBy == FilterBy.BY_SCORE)
6514 matchCondition = FeatureMatcher.byScore(cond, pattern);
6517 else if (filterBy == FilterBy.BY_ATTRIBUTE)
6519 final List<String> attributeName = mc.getAttributeName();
6520 String[] attNames = attributeName
6521 .toArray(new String[attributeName.size()]);
6522 matchCondition = FeatureMatcher.byAttribute(cond, pattern,
6527 * note this throws IllegalStateException if AND-ing to a
6528 * previously OR-ed compound condition, or vice versa
6532 matcherSet.and(matchCondition);
6536 matcherSet.or(matchCondition);
6542 * compound condition
6544 List<jalview.xml.binding.jalview.FeatureMatcherSet> matchers = matcherSetModel
6545 .getCompoundMatcher().getMatcherSet();
6546 boolean anded = matcherSetModel.getCompoundMatcher().isAnd();
6547 if (matchers.size() == 2)
6549 parseFilterConditions(matcherSet, matchers.get(0), anded);
6550 parseFilterConditions(matcherSet, matchers.get(1), anded);
6554 System.err.println("Malformed compound filter condition");
6560 * Loads one XML model of a feature colour to a Jalview object
6562 * @param colourModel
6565 public static FeatureColourI parseColour(Colour colourModel)
6567 FeatureColourI colour = null;
6569 if (colourModel.getMax() != null)
6571 Color mincol = null;
6572 Color maxcol = null;
6573 Color noValueColour = null;
6577 mincol = new Color(Integer.parseInt(colourModel.getMinRGB(), 16));
6578 maxcol = new Color(Integer.parseInt(colourModel.getRGB(), 16));
6579 } catch (Exception e)
6581 Cache.log.warn("Couldn't parse out graduated feature color.", e);
6584 NoValueColour noCol = colourModel.getNoValueColour();
6585 if (noCol == NoValueColour.MIN)
6587 noValueColour = mincol;
6589 else if (noCol == NoValueColour.MAX)
6591 noValueColour = maxcol;
6594 colour = new FeatureColour(maxcol, mincol, maxcol, noValueColour,
6595 safeFloat(colourModel.getMin()),
6596 safeFloat(colourModel.getMax()));
6597 final List<String> attributeName = colourModel.getAttributeName();
6598 String[] attributes = attributeName
6599 .toArray(new String[attributeName.size()]);
6600 if (attributes != null && attributes.length > 0)
6602 colour.setAttributeName(attributes);
6604 if (colourModel.isAutoScale() != null)
6606 colour.setAutoScaled(colourModel.isAutoScale().booleanValue());
6608 if (colourModel.isColourByLabel() != null)
6610 colour.setColourByLabel(
6611 colourModel.isColourByLabel().booleanValue());
6613 if (colourModel.getThreshold() != null)
6615 colour.setThreshold(colourModel.getThreshold().floatValue());
6617 ThresholdType ttyp = colourModel.getThreshType();
6618 if (ttyp == ThresholdType.ABOVE)
6620 colour.setAboveThreshold(true);
6622 else if (ttyp == ThresholdType.BELOW)
6624 colour.setBelowThreshold(true);
6629 Color color = new Color(Integer.parseInt(colourModel.getRGB(), 16));
6630 colour = new FeatureColour(color);