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.GraphLine;
42 import jalview.datamodel.PDBEntry;
43 import jalview.datamodel.Point;
44 import jalview.datamodel.RnaViewerModel;
45 import jalview.datamodel.SequenceFeature;
46 import jalview.datamodel.SequenceGroup;
47 import jalview.datamodel.SequenceI;
48 import jalview.datamodel.StructureViewerModel;
49 import jalview.datamodel.StructureViewerModel.StructureData;
50 import jalview.datamodel.features.FeatureMatcher;
51 import jalview.datamodel.features.FeatureMatcherI;
52 import jalview.datamodel.features.FeatureMatcherSet;
53 import jalview.datamodel.features.FeatureMatcherSetI;
54 import jalview.ext.varna.RnaModel;
55 import jalview.gui.AlignFrame;
56 import jalview.gui.AlignViewport;
57 import jalview.gui.AlignmentPanel;
58 import jalview.gui.AppVarna;
59 import jalview.gui.ChimeraViewFrame;
60 import jalview.gui.Desktop;
61 import jalview.gui.Jalview2XML_V1;
62 import jalview.gui.JvOptionPane;
63 import jalview.gui.OOMWarning;
64 import jalview.gui.PCAPanel;
65 import jalview.gui.PaintRefresher;
66 import jalview.gui.SplitFrame;
67 import jalview.gui.StructureViewer;
68 import jalview.gui.StructureViewer.ViewerType;
69 import jalview.gui.StructureViewerBase;
70 import jalview.gui.TreePanel;
71 import jalview.io.DataSourceType;
72 import jalview.io.FileFormat;
73 import jalview.io.NewickFile;
74 import jalview.math.Matrix;
75 import jalview.math.MatrixI;
76 import jalview.renderer.ResidueShaderI;
77 import jalview.schemes.AnnotationColourGradient;
78 import jalview.schemes.ColourSchemeI;
79 import jalview.schemes.ColourSchemeProperty;
80 import jalview.schemes.FeatureColour;
81 import jalview.schemes.ResidueProperties;
82 import jalview.schemes.UserColourScheme;
83 import jalview.structure.StructureSelectionManager;
84 import jalview.structures.models.AAStructureBindingModel;
85 import jalview.util.Format;
86 import jalview.util.MessageManager;
87 import jalview.util.Platform;
88 import jalview.util.StringUtils;
89 import jalview.util.jarInputStreamProvider;
90 import jalview.util.matcher.Condition;
91 import jalview.viewmodel.AlignmentViewport;
92 import jalview.viewmodel.PCAModel;
93 import jalview.viewmodel.ViewportRanges;
94 import jalview.viewmodel.seqfeatures.FeatureRendererModel;
95 import jalview.viewmodel.seqfeatures.FeatureRendererSettings;
96 import jalview.viewmodel.seqfeatures.FeaturesDisplayed;
97 import jalview.ws.jws2.Jws2Discoverer;
98 import jalview.ws.jws2.dm.AAConSettings;
99 import jalview.ws.jws2.jabaws2.Jws2Instance;
100 import jalview.ws.params.ArgumentI;
101 import jalview.ws.params.AutoCalcSetting;
102 import jalview.ws.params.WsParamSetI;
103 import jalview.xml.binding.jalview.AlcodonFrame;
104 import jalview.xml.binding.jalview.AlcodonFrame.AlcodMap;
105 import jalview.xml.binding.jalview.Annotation;
106 import jalview.xml.binding.jalview.Annotation.ThresholdLine;
107 import jalview.xml.binding.jalview.AnnotationColourScheme;
108 import jalview.xml.binding.jalview.AnnotationElement;
109 import jalview.xml.binding.jalview.DoubleMatrix;
110 import jalview.xml.binding.jalview.DoubleVector;
111 import jalview.xml.binding.jalview.Feature;
112 import jalview.xml.binding.jalview.Feature.OtherData;
113 import jalview.xml.binding.jalview.FeatureMatcherSet.CompoundMatcher;
114 import jalview.xml.binding.jalview.FilterBy;
115 import jalview.xml.binding.jalview.JalviewModel;
116 import jalview.xml.binding.jalview.JalviewModel.FeatureSettings;
117 import jalview.xml.binding.jalview.JalviewModel.FeatureSettings.Group;
118 import jalview.xml.binding.jalview.JalviewModel.FeatureSettings.Setting;
119 import jalview.xml.binding.jalview.JalviewModel.JGroup;
120 import jalview.xml.binding.jalview.JalviewModel.JSeq;
121 import jalview.xml.binding.jalview.JalviewModel.JSeq.Pdbids;
122 import jalview.xml.binding.jalview.JalviewModel.JSeq.Pdbids.StructureState;
123 import jalview.xml.binding.jalview.JalviewModel.JSeq.RnaViewer;
124 import jalview.xml.binding.jalview.JalviewModel.JSeq.RnaViewer.SecondaryStructure;
125 import jalview.xml.binding.jalview.JalviewModel.PcaViewer;
126 import jalview.xml.binding.jalview.JalviewModel.PcaViewer.Axis;
127 import jalview.xml.binding.jalview.JalviewModel.PcaViewer.SeqPointMax;
128 import jalview.xml.binding.jalview.JalviewModel.PcaViewer.SeqPointMin;
129 import jalview.xml.binding.jalview.JalviewModel.PcaViewer.SequencePoint;
130 import jalview.xml.binding.jalview.JalviewModel.Tree;
131 import jalview.xml.binding.jalview.JalviewModel.UserColours;
132 import jalview.xml.binding.jalview.JalviewModel.Viewport;
133 import jalview.xml.binding.jalview.JalviewModel.Viewport.CalcIdParam;
134 import jalview.xml.binding.jalview.JalviewModel.Viewport.HiddenColumns;
135 import jalview.xml.binding.jalview.JalviewUserColours;
136 import jalview.xml.binding.jalview.JalviewUserColours.Colour;
137 import jalview.xml.binding.jalview.MapListType.MapListFrom;
138 import jalview.xml.binding.jalview.MapListType.MapListTo;
139 import jalview.xml.binding.jalview.Mapping;
140 import jalview.xml.binding.jalview.NoValueColour;
141 import jalview.xml.binding.jalview.ObjectFactory;
142 import jalview.xml.binding.jalview.PcaDataType;
143 import jalview.xml.binding.jalview.Pdbentry.Property;
144 import jalview.xml.binding.jalview.Sequence;
145 import jalview.xml.binding.jalview.Sequence.DBRef;
146 import jalview.xml.binding.jalview.SequenceSet;
147 import jalview.xml.binding.jalview.SequenceSet.SequenceSetProperties;
148 import jalview.xml.binding.jalview.ThresholdType;
149 import jalview.xml.binding.jalview.VAMSAS;
151 import java.awt.Color;
152 import java.awt.Font;
153 import java.awt.Rectangle;
154 import java.io.BufferedReader;
155 import java.io.DataInputStream;
156 import java.io.DataOutputStream;
158 import java.io.FileInputStream;
159 import java.io.FileOutputStream;
160 import java.io.IOException;
161 import java.io.InputStreamReader;
162 import java.io.OutputStreamWriter;
163 import java.io.PrintWriter;
164 import java.lang.reflect.InvocationTargetException;
165 import java.math.BigInteger;
166 import java.net.MalformedURLException;
168 import java.util.ArrayList;
169 import java.util.Arrays;
170 import java.util.Collections;
171 import java.util.Enumeration;
172 import java.util.GregorianCalendar;
173 import java.util.HashMap;
174 import java.util.HashSet;
175 import java.util.Hashtable;
176 import java.util.IdentityHashMap;
177 import java.util.Iterator;
178 import java.util.LinkedHashMap;
179 import java.util.List;
180 import java.util.Map;
181 import java.util.Map.Entry;
182 import java.util.Set;
183 import java.util.Vector;
184 import java.util.jar.JarEntry;
185 import java.util.jar.JarInputStream;
186 import java.util.jar.JarOutputStream;
188 import javax.swing.JInternalFrame;
189 import javax.swing.SwingUtilities;
190 import javax.xml.bind.JAXBContext;
191 import javax.xml.bind.JAXBElement;
192 import javax.xml.bind.Marshaller;
193 import javax.xml.datatype.DatatypeConfigurationException;
194 import javax.xml.datatype.DatatypeFactory;
195 import javax.xml.datatype.XMLGregorianCalendar;
196 import javax.xml.stream.XMLInputFactory;
197 import javax.xml.stream.XMLStreamReader;
200 * Write out the current jalview desktop state as a Jalview XML stream.
202 * Note: the vamsas objects referred to here are primitive versions of the
203 * VAMSAS project schema elements - they are not the same and most likely never
207 * @version $Revision: 1.134 $
209 public class Jalview2XML
211 private static final String VIEWER_PREFIX = "viewer_";
213 private static final String RNA_PREFIX = "rna_";
215 private static final String UTF_8 = "UTF-8";
218 * prefix for recovering datasets for alignments with multiple views where
219 * non-existent dataset IDs were written for some views
221 private static final String UNIQSEQSETID = "uniqueSeqSetId.";
223 // use this with nextCounter() to make unique names for entities
224 private int counter = 0;
227 * SequenceI reference -> XML ID string in jalview XML. Populated as XML reps
228 * of sequence objects are created.
230 IdentityHashMap<SequenceI, String> seqsToIds = null;
233 * jalview XML Sequence ID to jalview sequence object reference (both dataset
234 * and alignment sequences. Populated as XML reps of sequence objects are
237 Map<String, SequenceI> seqRefIds = null;
239 Map<String, SequenceI> incompleteSeqs = null;
241 List<SeqFref> frefedSequence = null;
243 boolean raiseGUI = true; // whether errors are raised in dialog boxes or not
246 * Map of reconstructed AlignFrame objects that appear to have come from
247 * SplitFrame objects (have a dna/protein complement view).
249 private Map<Viewport, AlignFrame> splitFrameCandidates = new HashMap<>();
252 * Map from displayed rna structure models to their saved session state jar
255 private Map<RnaModel, String> rnaSessions = new HashMap<>();
258 * A helper method for safely using the value of an optional attribute that
259 * may be null if not present in the XML. Answers the boolean value, or false
265 public static boolean safeBoolean(Boolean b)
267 return b == null ? false : b.booleanValue();
271 * A helper method for safely using the value of an optional attribute that
272 * may be null if not present in the XML. Answers the integer value, or zero
278 public static int safeInt(Integer i)
280 return i == null ? 0 : i.intValue();
284 * A helper method for safely using the value of an optional attribute that
285 * may be null if not present in the XML. Answers the float value, or zero if
291 public static float safeFloat(Float f)
293 return f == null ? 0f : f.floatValue();
297 * create/return unique hash string for sq
300 * @return new or existing unique string for sq
302 String seqHash(SequenceI sq)
304 if (seqsToIds == null)
308 if (seqsToIds.containsKey(sq))
310 return seqsToIds.get(sq);
314 // create sequential key
315 String key = "sq" + (seqsToIds.size() + 1);
316 key = makeHashCode(sq, key); // check we don't have an external reference
318 seqsToIds.put(sq, key);
325 if (seqsToIds == null)
327 seqsToIds = new IdentityHashMap<>();
329 if (seqRefIds == null)
331 seqRefIds = new HashMap<>();
333 if (incompleteSeqs == null)
335 incompleteSeqs = new HashMap<>();
337 if (frefedSequence == null)
339 frefedSequence = new ArrayList<>();
347 public Jalview2XML(boolean raiseGUI)
349 this.raiseGUI = raiseGUI;
353 * base class for resolving forward references to sequences by their ID
358 abstract class SeqFref
364 public SeqFref(String _sref, String type)
370 public String getSref()
375 public SequenceI getSrefSeq()
377 return seqRefIds.get(sref);
380 public boolean isResolvable()
382 return seqRefIds.get(sref) != null;
385 public SequenceI getSrefDatasetSeq()
387 SequenceI sq = seqRefIds.get(sref);
390 while (sq.getDatasetSequence() != null)
392 sq = sq.getDatasetSequence();
399 * @return true if the forward reference was fully resolved
401 abstract boolean resolve();
404 public String toString()
406 return type + " reference to " + sref;
411 * create forward reference for a mapping
417 public SeqFref newMappingRef(final String sref,
418 final jalview.datamodel.Mapping _jmap)
420 SeqFref fref = new SeqFref(sref, "Mapping")
422 public jalview.datamodel.Mapping jmap = _jmap;
427 SequenceI seq = getSrefDatasetSeq();
439 public SeqFref newAlcodMapRef(final String sref,
440 final AlignedCodonFrame _cf,
441 final jalview.datamodel.Mapping _jmap)
444 SeqFref fref = new SeqFref(sref, "Codon Frame")
446 AlignedCodonFrame cf = _cf;
448 public jalview.datamodel.Mapping mp = _jmap;
451 public boolean isResolvable()
453 return super.isResolvable() && mp.getTo() != null;
459 SequenceI seq = getSrefDatasetSeq();
464 cf.addMap(seq, mp.getTo(), mp.getMap());
471 public void resolveFrefedSequences()
473 Iterator<SeqFref> nextFref = frefedSequence.iterator();
474 int toresolve = frefedSequence.size();
475 int unresolved = 0, failedtoresolve = 0;
476 while (nextFref.hasNext())
478 SeqFref ref = nextFref.next();
479 if (ref.isResolvable())
491 } catch (Exception x)
494 "IMPLEMENTATION ERROR: Failed to resolve forward reference for sequence "
507 System.err.println("Jalview Project Import: There were " + unresolved
508 + " forward references left unresolved on the stack.");
510 if (failedtoresolve > 0)
512 System.err.println("SERIOUS! " + failedtoresolve
513 + " resolvable forward references failed to resolve.");
515 if (incompleteSeqs != null && incompleteSeqs.size() > 0)
518 "Jalview Project Import: There are " + incompleteSeqs.size()
519 + " sequences which may have incomplete metadata.");
520 if (incompleteSeqs.size() < 10)
522 for (SequenceI s : incompleteSeqs.values())
524 System.err.println(s.toString());
530 "Too many to report. Skipping output of incomplete sequences.");
536 * This maintains a map of viewports, the key being the seqSetId. Important to
537 * set historyItem and redoList for multiple views
539 Map<String, AlignViewport> viewportsAdded = new HashMap<>();
541 Map<String, AlignmentAnnotation> annotationIds = new HashMap<>();
543 String uniqueSetSuffix = "";
546 * List of pdbfiles added to Jar
548 List<String> pdbfiles = null;
550 // SAVES SEVERAL ALIGNMENT WINDOWS TO SAME JARFILE
551 public void saveState(File statefile)
553 FileOutputStream fos = null;
556 fos = new FileOutputStream(statefile);
557 JarOutputStream jout = new JarOutputStream(fos);
560 } catch (Exception e)
562 // TODO: inform user of the problem - they need to know if their data was
564 if (errorMessage == null)
566 errorMessage = "Couldn't write Jalview Archive to output file '"
567 + statefile + "' - See console error log for details";
571 errorMessage += "(output file was '" + statefile + "')";
581 } catch (IOException e)
591 * Writes a jalview project archive to the given Jar output stream.
595 public void saveState(JarOutputStream jout)
597 AlignFrame[] frames = Desktop.getAlignFrames();
603 saveAllFrames(Arrays.asList(frames), jout);
607 * core method for storing state for a set of AlignFrames.
610 * - frames involving all data to be exported (including containing
613 * - project output stream
615 private void saveAllFrames(List<AlignFrame> frames, JarOutputStream jout)
617 Hashtable<String, AlignFrame> dsses = new Hashtable<>();
620 * ensure cached data is clear before starting
622 // todo tidy up seqRefIds, seqsToIds initialisation / reset
624 splitFrameCandidates.clear();
629 // NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS
630 // //////////////////////////////////////////////////
632 List<String> shortNames = new ArrayList<>();
633 List<String> viewIds = new ArrayList<>();
636 for (int i = frames.size() - 1; i > -1; i--)
638 AlignFrame af = frames.get(i);
640 if (skipList != null && skipList
641 .containsKey(af.getViewport().getSequenceSetId()))
646 String shortName = makeFilename(af, shortNames);
648 int apSize = af.getAlignPanels().size();
650 for (int ap = 0; ap < apSize; ap++)
652 AlignmentPanel apanel = (AlignmentPanel) af.getAlignPanels()
654 String fileName = apSize == 1 ? shortName : ap + shortName;
655 if (!fileName.endsWith(".xml"))
657 fileName = fileName + ".xml";
660 saveState(apanel, fileName, jout, viewIds);
662 String dssid = getDatasetIdRef(
663 af.getViewport().getAlignment().getDataset());
664 if (!dsses.containsKey(dssid))
666 dsses.put(dssid, af);
671 writeDatasetFor(dsses, "" + jout.hashCode() + " " + uniqueSetSuffix,
677 } catch (Exception foo)
682 } catch (Exception ex)
684 // TODO: inform user of the problem - they need to know if their data was
686 if (errorMessage == null)
688 errorMessage = "Couldn't write Jalview Archive - see error output for details";
690 ex.printStackTrace();
695 * Generates a distinct file name, based on the title of the AlignFrame, by
696 * appending _n for increasing n until an unused name is generated. The new
697 * name (without its extension) is added to the list.
701 * @return the generated name, with .xml extension
703 protected String makeFilename(AlignFrame af, List<String> namesUsed)
705 String shortName = af.getTitle();
707 if (shortName.indexOf(File.separatorChar) > -1)
709 shortName = shortName
710 .substring(shortName.lastIndexOf(File.separatorChar) + 1);
715 while (namesUsed.contains(shortName))
717 if (shortName.endsWith("_" + (count - 1)))
719 shortName = shortName.substring(0, shortName.lastIndexOf("_"));
722 shortName = shortName.concat("_" + count);
726 namesUsed.add(shortName);
728 if (!shortName.endsWith(".xml"))
730 shortName = shortName + ".xml";
735 // USE THIS METHOD TO SAVE A SINGLE ALIGNMENT WINDOW
736 public boolean saveAlignment(AlignFrame af, String jarFile,
741 FileOutputStream fos = new FileOutputStream(jarFile);
742 JarOutputStream jout = new JarOutputStream(fos);
743 List<AlignFrame> frames = new ArrayList<>();
745 // resolve splitframes
746 if (af.getViewport().getCodingComplement() != null)
748 frames = ((SplitFrame) af.getSplitViewContainer()).getAlignFrames();
754 saveAllFrames(frames, jout);
758 } catch (Exception foo)
764 } catch (Exception ex)
766 errorMessage = "Couldn't Write alignment view to Jalview Archive - see error output for details";
767 ex.printStackTrace();
772 private void writeDatasetFor(Hashtable<String, AlignFrame> dsses,
773 String fileName, JarOutputStream jout)
776 for (String dssids : dsses.keySet())
778 AlignFrame _af = dsses.get(dssids);
779 String jfileName = fileName + " Dataset for " + _af.getTitle();
780 if (!jfileName.endsWith(".xml"))
782 jfileName = jfileName + ".xml";
784 saveState(_af.alignPanel, jfileName, true, jout, null);
789 * create a JalviewModel from an alignment view and marshall it to a
793 * panel to create jalview model for
795 * name of alignment panel written to output stream
802 public JalviewModel saveState(AlignmentPanel ap, String fileName,
803 JarOutputStream jout, List<String> viewIds)
805 return saveState(ap, fileName, false, jout, viewIds);
809 * create a JalviewModel from an alignment view and marshall it to a
813 * panel to create jalview model for
815 * name of alignment panel written to output stream
817 * when true, only write the dataset for the alignment, not the data
818 * associated with the view.
824 public JalviewModel saveState(AlignmentPanel ap, String fileName,
825 boolean storeDS, JarOutputStream jout, List<String> viewIds)
829 viewIds = new ArrayList<>();
834 List<UserColourScheme> userColours = new ArrayList<>();
836 AlignViewport av = ap.av;
837 ViewportRanges vpRanges = av.getRanges();
839 final ObjectFactory objectFactory = new ObjectFactory();
840 JalviewModel object = objectFactory.createJalviewModel();
841 object.setVamsasModel(new VAMSAS());
843 // object.setCreationDate(new java.util.Date(System.currentTimeMillis()));
846 GregorianCalendar c = new GregorianCalendar();
847 DatatypeFactory datatypeFactory = DatatypeFactory.newInstance();
848 XMLGregorianCalendar now = datatypeFactory.newXMLGregorianCalendar(c);// gregorianCalendar);
849 object.setCreationDate(now);
850 } catch (DatatypeConfigurationException e)
852 System.err.println("error writing date: " + e.toString());
855 jalview.bin.Cache.getDefault("VERSION", "Development Build"));
858 * rjal is full height alignment, jal is actual alignment with full metadata
859 * but excludes hidden sequences.
861 jalview.datamodel.AlignmentI rjal = av.getAlignment(), jal = rjal;
863 if (av.hasHiddenRows())
865 rjal = jal.getHiddenSequences().getFullAlignment();
868 SequenceSet vamsasSet = new SequenceSet();
870 // JalviewModelSequence jms = new JalviewModelSequence();
872 vamsasSet.setGapChar(jal.getGapCharacter() + "");
874 if (jal.getDataset() != null)
876 // dataset id is the dataset's hashcode
877 vamsasSet.setDatasetId(getDatasetIdRef(jal.getDataset()));
880 // switch jal and the dataset
881 jal = jal.getDataset();
885 if (jal.getProperties() != null)
887 Enumeration en = jal.getProperties().keys();
888 while (en.hasMoreElements())
890 String key = en.nextElement().toString();
891 SequenceSetProperties ssp = new SequenceSetProperties();
893 ssp.setValue(jal.getProperties().get(key).toString());
894 // vamsasSet.addSequenceSetProperties(ssp);
895 vamsasSet.getSequenceSetProperties().add(ssp);
900 Set<String> calcIdSet = new HashSet<>();
901 // record the set of vamsas sequence XML POJO we create.
902 HashMap<String, Sequence> vamsasSetIds = new HashMap<>();
904 for (final SequenceI jds : rjal.getSequences())
906 final SequenceI jdatasq = jds.getDatasetSequence() == null ? jds
907 : jds.getDatasetSequence();
908 String id = seqHash(jds);
909 if (vamsasSetIds.get(id) == null)
911 if (seqRefIds.get(id) != null && !storeDS)
913 // This happens for two reasons: 1. multiple views are being
915 // 2. the hashCode has collided with another sequence's code. This
917 // HAPPEN! (PF00072.15.stk does this)
918 // JBPNote: Uncomment to debug writing out of files that do not read
919 // back in due to ArrayOutOfBoundExceptions.
920 // System.err.println("vamsasSeq backref: "+id+"");
921 // System.err.println(jds.getName()+"
922 // "+jds.getStart()+"-"+jds.getEnd()+" "+jds.getSequenceAsString());
923 // System.err.println("Hashcode: "+seqHash(jds));
924 // SequenceI rsq = (SequenceI) seqRefIds.get(id + "");
925 // System.err.println(rsq.getName()+"
926 // "+rsq.getStart()+"-"+rsq.getEnd()+" "+rsq.getSequenceAsString());
927 // System.err.println("Hashcode: "+seqHash(rsq));
931 vamsasSeq = createVamsasSequence(id, jds);
932 // vamsasSet.addSequence(vamsasSeq);
933 vamsasSet.getSequence().add(vamsasSeq);
934 vamsasSetIds.put(id, vamsasSeq);
935 seqRefIds.put(id, jds);
939 jseq.setStart(jds.getStart());
940 jseq.setEnd(jds.getEnd());
941 jseq.setColour(av.getSequenceColour(jds).getRGB());
943 jseq.setId(id); // jseq id should be a string not a number
946 // Store any sequences this sequence represents
947 if (av.hasHiddenRows())
949 // use rjal, contains the full height alignment
951 av.getAlignment().getHiddenSequences().isHidden(jds));
953 if (av.isHiddenRepSequence(jds))
955 jalview.datamodel.SequenceI[] reps = av
956 .getRepresentedSequences(jds).getSequencesInOrder(rjal);
958 for (int h = 0; h < reps.length; h++)
962 // jseq.addHiddenSequences(rjal.findIndex(reps[h]));
963 jseq.getHiddenSequences().add(rjal.findIndex(reps[h]));
968 // mark sequence as reference - if it is the reference for this view
971 jseq.setViewreference(jds == jal.getSeqrep());
975 // TODO: omit sequence features from each alignment view's XML dump if we
976 // are storing dataset
977 List<SequenceFeature> sfs = jds.getSequenceFeatures();
978 for (SequenceFeature sf : sfs)
980 // Features features = new Features();
981 Feature features = new Feature();
983 features.setBegin(sf.getBegin());
984 features.setEnd(sf.getEnd());
985 features.setDescription(sf.getDescription());
986 features.setType(sf.getType());
987 features.setFeatureGroup(sf.getFeatureGroup());
988 features.setScore(sf.getScore());
989 if (sf.links != null)
991 for (int l = 0; l < sf.links.size(); l++)
993 OtherData keyValue = new OtherData();
994 keyValue.setKey("LINK_" + l);
995 keyValue.setValue(sf.links.elementAt(l).toString());
996 // features.addOtherData(keyValue);
997 features.getOtherData().add(keyValue);
1000 if (sf.otherDetails != null)
1003 * save feature attributes, which may be simple strings or
1004 * map valued (have sub-attributes)
1006 for (Entry<String, Object> entry : sf.otherDetails.entrySet())
1008 String key = entry.getKey();
1009 Object value = entry.getValue();
1010 if (value instanceof Map<?, ?>)
1012 for (Entry<String, Object> subAttribute : ((Map<String, Object>) value)
1015 OtherData otherData = new OtherData();
1016 otherData.setKey(key);
1017 otherData.setKey2(subAttribute.getKey());
1018 otherData.setValue(subAttribute.getValue().toString());
1019 // features.addOtherData(otherData);
1020 features.getOtherData().add(otherData);
1025 OtherData otherData = new OtherData();
1026 otherData.setKey(key);
1027 otherData.setValue(value.toString());
1028 // features.addOtherData(otherData);
1029 features.getOtherData().add(otherData);
1034 // jseq.addFeatures(features);
1035 jseq.getFeatures().add(features);
1038 if (jdatasq.getAllPDBEntries() != null)
1040 Enumeration<PDBEntry> en = jdatasq.getAllPDBEntries().elements();
1041 while (en.hasMoreElements())
1043 Pdbids pdb = new Pdbids();
1044 jalview.datamodel.PDBEntry entry = en.nextElement();
1046 String pdbId = entry.getId();
1048 pdb.setType(entry.getType());
1051 * Store any structure views associated with this sequence. This
1052 * section copes with duplicate entries in the project, so a dataset
1053 * only view *should* be coped with sensibly.
1055 // This must have been loaded, is it still visible?
1056 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1057 String matchedFile = null;
1058 for (int f = frames.length - 1; f > -1; f--)
1060 if (frames[f] instanceof StructureViewerBase)
1062 StructureViewerBase viewFrame = (StructureViewerBase) frames[f];
1063 matchedFile = saveStructureState(ap, jds, pdb, entry, viewIds,
1064 matchedFile, viewFrame);
1066 * Only store each structure viewer's state once in the project
1067 * jar. First time through only (storeDS==false)
1069 String viewId = viewFrame.getViewId();
1070 if (!storeDS && !viewIds.contains(viewId))
1072 viewIds.add(viewId);
1075 String viewerState = viewFrame.getStateInfo();
1076 writeJarEntry(jout, getViewerJarEntryName(viewId),
1077 viewerState.getBytes());
1078 } catch (IOException e)
1081 "Error saving viewer state: " + e.getMessage());
1087 if (matchedFile != null || entry.getFile() != null)
1089 if (entry.getFile() != null)
1092 matchedFile = entry.getFile();
1094 pdb.setFile(matchedFile); // entry.getFile());
1095 if (pdbfiles == null)
1097 pdbfiles = new ArrayList<>();
1100 if (!pdbfiles.contains(pdbId))
1102 pdbfiles.add(pdbId);
1103 copyFileToJar(jout, matchedFile, pdbId);
1107 Enumeration<String> props = entry.getProperties();
1108 if (props.hasMoreElements())
1110 // PdbentryItem item = new PdbentryItem();
1111 while (props.hasMoreElements())
1113 Property prop = new Property();
1114 String key = props.nextElement();
1116 prop.setValue(entry.getProperty(key).toString());
1117 // item.addProperty(prop);
1118 pdb.getProperty().add(prop);
1120 // pdb.addPdbentryItem(item);
1123 // jseq.addPdbids(pdb);
1124 jseq.getPdbids().add(pdb);
1128 saveRnaViewers(jout, jseq, jds, viewIds, ap, storeDS);
1130 // jms.addJSeq(jseq);
1131 object.getJSeq().add(jseq);
1134 if (!storeDS && av.hasHiddenRows())
1136 jal = av.getAlignment();
1140 if (storeDS && jal.getCodonFrames() != null)
1142 List<AlignedCodonFrame> jac = jal.getCodonFrames();
1143 for (AlignedCodonFrame acf : jac)
1145 AlcodonFrame alc = new AlcodonFrame();
1146 if (acf.getProtMappings() != null
1147 && acf.getProtMappings().length > 0)
1149 boolean hasMap = false;
1150 SequenceI[] dnas = acf.getdnaSeqs();
1151 jalview.datamodel.Mapping[] pmaps = acf.getProtMappings();
1152 for (int m = 0; m < pmaps.length; m++)
1154 AlcodMap alcmap = new AlcodMap();
1155 alcmap.setDnasq(seqHash(dnas[m]));
1157 createVamsasMapping(pmaps[m], dnas[m], null, false));
1158 // alc.addAlcodMap(alcmap);
1159 alc.getAlcodMap().add(alcmap);
1164 // vamsasSet.addAlcodonFrame(alc);
1165 vamsasSet.getAlcodonFrame().add(alc);
1168 // TODO: delete this ? dead code from 2.8.3->2.9 ?
1170 // AlcodonFrame alc = new AlcodonFrame();
1171 // vamsasSet.addAlcodonFrame(alc);
1172 // for (int p = 0; p < acf.aaWidth; p++)
1174 // Alcodon cmap = new Alcodon();
1175 // if (acf.codons[p] != null)
1177 // // Null codons indicate a gapped column in the translated peptide
1179 // cmap.setPos1(acf.codons[p][0]);
1180 // cmap.setPos2(acf.codons[p][1]);
1181 // cmap.setPos3(acf.codons[p][2]);
1183 // alc.addAlcodon(cmap);
1185 // if (acf.getProtMappings() != null
1186 // && acf.getProtMappings().length > 0)
1188 // SequenceI[] dnas = acf.getdnaSeqs();
1189 // jalview.datamodel.Mapping[] pmaps = acf.getProtMappings();
1190 // for (int m = 0; m < pmaps.length; m++)
1192 // AlcodMap alcmap = new AlcodMap();
1193 // alcmap.setDnasq(seqHash(dnas[m]));
1194 // alcmap.setMapping(createVamsasMapping(pmaps[m], dnas[m], null,
1196 // alc.addAlcodMap(alcmap);
1203 // /////////////////////////////////
1204 if (!storeDS && av.getCurrentTree() != null)
1206 // FIND ANY ASSOCIATED TREES
1207 // NOT IMPLEMENTED FOR HEADLESS STATE AT PRESENT
1208 if (Desktop.desktop != null)
1210 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1212 for (int t = 0; t < frames.length; t++)
1214 if (frames[t] instanceof TreePanel)
1216 TreePanel tp = (TreePanel) frames[t];
1218 if (tp.getTreeCanvas().getViewport().getAlignment() == jal)
1220 JalviewModel.Tree tree = new JalviewModel.Tree();
1221 tree.setTitle(tp.getTitle());
1222 tree.setCurrentTree((av.getCurrentTree() == tp.getTree()));
1223 tree.setNewick(tp.getTree().print());
1224 tree.setThreshold(tp.getTreeCanvas().getThreshold());
1226 tree.setFitToWindow(tp.fitToWindow.getState());
1227 tree.setFontName(tp.getTreeFont().getName());
1228 tree.setFontSize(tp.getTreeFont().getSize());
1229 tree.setFontStyle(tp.getTreeFont().getStyle());
1230 tree.setMarkUnlinked(tp.placeholdersMenu.getState());
1232 tree.setShowBootstrap(tp.bootstrapMenu.getState());
1233 tree.setShowDistances(tp.distanceMenu.getState());
1235 tree.setHeight(tp.getHeight());
1236 tree.setWidth(tp.getWidth());
1237 tree.setXpos(tp.getX());
1238 tree.setYpos(tp.getY());
1239 tree.setId(makeHashCode(tp, null));
1240 tree.setLinkToAllViews(
1241 tp.getTreeCanvas().isApplyToAllViews());
1243 // jms.addTree(tree);
1244 object.getTree().add(tree);
1254 if (!storeDS && Desktop.desktop != null)
1256 for (JInternalFrame frame : Desktop.desktop.getAllFrames())
1258 if (frame instanceof PCAPanel)
1260 PCAPanel panel = (PCAPanel) frame;
1261 if (panel.getAlignViewport().getAlignment() == jal)
1263 savePCA(panel, object);
1271 * store forward refs from an annotationRow to any groups
1273 IdentityHashMap<SequenceGroup, String> groupRefs = new IdentityHashMap<>();
1276 for (SequenceI sq : jal.getSequences())
1278 // Store annotation on dataset sequences only
1279 AlignmentAnnotation[] aa = sq.getAnnotation();
1280 if (aa != null && aa.length > 0)
1282 storeAlignmentAnnotation(aa, groupRefs, av, calcIdSet, storeDS,
1289 if (jal.getAlignmentAnnotation() != null)
1291 // Store the annotation shown on the alignment.
1292 AlignmentAnnotation[] aa = jal.getAlignmentAnnotation();
1293 storeAlignmentAnnotation(aa, groupRefs, av, calcIdSet, storeDS,
1298 if (jal.getGroups() != null)
1300 JGroup[] groups = new JGroup[jal.getGroups().size()];
1302 for (jalview.datamodel.SequenceGroup sg : jal.getGroups())
1304 JGroup jGroup = new JGroup();
1305 groups[++i] = jGroup;
1307 jGroup.setStart(sg.getStartRes());
1308 jGroup.setEnd(sg.getEndRes());
1309 jGroup.setName(sg.getName());
1310 if (groupRefs.containsKey(sg))
1312 // group has references so set its ID field
1313 jGroup.setId(groupRefs.get(sg));
1315 ColourSchemeI colourScheme = sg.getColourScheme();
1316 if (colourScheme != null)
1318 ResidueShaderI groupColourScheme = sg.getGroupColourScheme();
1319 if (groupColourScheme.conservationApplied())
1321 jGroup.setConsThreshold(groupColourScheme.getConservationInc());
1323 if (colourScheme instanceof jalview.schemes.UserColourScheme)
1326 setUserColourScheme(colourScheme, userColours,
1331 jGroup.setColour(colourScheme.getSchemeName());
1334 else if (colourScheme instanceof jalview.schemes.AnnotationColourGradient)
1336 jGroup.setColour("AnnotationColourGradient");
1337 jGroup.setAnnotationColours(constructAnnotationColours(
1338 (jalview.schemes.AnnotationColourGradient) colourScheme,
1339 userColours, object));
1341 else if (colourScheme instanceof jalview.schemes.UserColourScheme)
1344 setUserColourScheme(colourScheme, userColours, object));
1348 jGroup.setColour(colourScheme.getSchemeName());
1351 jGroup.setPidThreshold(groupColourScheme.getThreshold());
1354 jGroup.setOutlineColour(sg.getOutlineColour().getRGB());
1355 jGroup.setDisplayBoxes(sg.getDisplayBoxes());
1356 jGroup.setDisplayText(sg.getDisplayText());
1357 jGroup.setColourText(sg.getColourText());
1358 jGroup.setTextCol1(sg.textColour.getRGB());
1359 jGroup.setTextCol2(sg.textColour2.getRGB());
1360 jGroup.setTextColThreshold(sg.thresholdTextColour);
1361 jGroup.setShowUnconserved(sg.getShowNonconserved());
1362 jGroup.setIgnoreGapsinConsensus(sg.getIgnoreGapsConsensus());
1363 jGroup.setShowConsensusHistogram(sg.isShowConsensusHistogram());
1364 jGroup.setShowSequenceLogo(sg.isShowSequenceLogo());
1365 jGroup.setNormaliseSequenceLogo(sg.isNormaliseSequenceLogo());
1366 for (SequenceI seq : sg.getSequences())
1368 // jGroup.addSeq(seqHash(seq));
1369 jGroup.getSeq().add(seqHash(seq));
1373 //jms.setJGroup(groups);
1375 for (JGroup grp : groups)
1377 object.getJGroup().add(grp);
1382 // /////////SAVE VIEWPORT
1383 Viewport view = new Viewport();
1384 view.setTitle(ap.alignFrame.getTitle());
1385 view.setSequenceSetId(
1386 makeHashCode(av.getSequenceSetId(), av.getSequenceSetId()));
1387 view.setId(av.getViewId());
1388 if (av.getCodingComplement() != null)
1390 view.setComplementId(av.getCodingComplement().getViewId());
1392 view.setViewName(av.getViewName());
1393 view.setGatheredViews(av.isGatherViewsHere());
1395 Rectangle size = ap.av.getExplodedGeometry();
1396 Rectangle position = size;
1399 size = ap.alignFrame.getBounds();
1400 if (av.getCodingComplement() != null)
1402 position = ((SplitFrame) ap.alignFrame.getSplitViewContainer())
1410 view.setXpos(position.x);
1411 view.setYpos(position.y);
1413 view.setWidth(size.width);
1414 view.setHeight(size.height);
1416 view.setStartRes(vpRanges.getStartRes());
1417 view.setStartSeq(vpRanges.getStartSeq());
1419 if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme)
1421 view.setBgColour(setUserColourScheme(av.getGlobalColourScheme(),
1422 userColours, object));
1425 .getGlobalColourScheme() instanceof jalview.schemes.AnnotationColourGradient)
1427 AnnotationColourScheme ac = constructAnnotationColours(
1428 (jalview.schemes.AnnotationColourGradient) av
1429 .getGlobalColourScheme(),
1430 userColours, object);
1432 view.setAnnotationColours(ac);
1433 view.setBgColour("AnnotationColourGradient");
1437 view.setBgColour(ColourSchemeProperty
1438 .getColourName(av.getGlobalColourScheme()));
1441 ResidueShaderI vcs = av.getResidueShading();
1442 ColourSchemeI cs = av.getGlobalColourScheme();
1446 if (vcs.conservationApplied())
1448 view.setConsThreshold(vcs.getConservationInc());
1449 if (cs instanceof jalview.schemes.UserColourScheme)
1451 view.setBgColour(setUserColourScheme(cs, userColours, object));
1454 view.setPidThreshold(vcs.getThreshold());
1457 view.setConservationSelected(av.getConservationSelected());
1458 view.setPidSelected(av.getAbovePIDThreshold());
1459 final Font font = av.getFont();
1460 view.setFontName(font.getName());
1461 view.setFontSize(font.getSize());
1462 view.setFontStyle(font.getStyle());
1463 view.setScaleProteinAsCdna(av.getViewStyle().isScaleProteinAsCdna());
1464 view.setRenderGaps(av.isRenderGaps());
1465 view.setShowAnnotation(av.isShowAnnotation());
1466 view.setShowBoxes(av.getShowBoxes());
1467 view.setShowColourText(av.getColourText());
1468 view.setShowFullId(av.getShowJVSuffix());
1469 view.setRightAlignIds(av.isRightAlignIds());
1470 view.setShowSequenceFeatures(av.isShowSequenceFeatures());
1471 view.setShowText(av.getShowText());
1472 view.setShowUnconserved(av.getShowUnconserved());
1473 view.setWrapAlignment(av.getWrapAlignment());
1474 view.setTextCol1(av.getTextColour().getRGB());
1475 view.setTextCol2(av.getTextColour2().getRGB());
1476 view.setTextColThreshold(av.getThresholdTextColour());
1477 view.setShowConsensusHistogram(av.isShowConsensusHistogram());
1478 view.setShowSequenceLogo(av.isShowSequenceLogo());
1479 view.setNormaliseSequenceLogo(av.isNormaliseSequenceLogo());
1480 view.setShowGroupConsensus(av.isShowGroupConsensus());
1481 view.setShowGroupConservation(av.isShowGroupConservation());
1482 view.setShowNPfeatureTooltip(av.isShowNPFeats());
1483 view.setShowDbRefTooltip(av.isShowDBRefs());
1484 view.setFollowHighlight(av.isFollowHighlight());
1485 view.setFollowSelection(av.followSelection);
1486 view.setIgnoreGapsinConsensus(av.isIgnoreGapsConsensus());
1487 if (av.getFeaturesDisplayed() != null)
1489 FeatureSettings fs = new FeatureSettings();
1491 FeatureRendererModel fr = ap.getSeqPanel().seqCanvas
1492 .getFeatureRenderer();
1493 String[] renderOrder = fr.getRenderOrder().toArray(new String[0]);
1495 Vector<String> settingsAdded = new Vector<>();
1496 if (renderOrder != null)
1498 for (String featureType : renderOrder)
1500 FeatureSettings.Setting setting = new FeatureSettings.Setting();
1501 setting.setType(featureType);
1504 * save any filter for the feature type
1506 FeatureMatcherSetI filter = fr.getFeatureFilter(featureType);
1507 if (filter != null) {
1508 Iterator<FeatureMatcherI> filters = filter.getMatchers().iterator();
1509 FeatureMatcherI firstFilter = filters.next();
1510 setting.setMatcherSet(Jalview2XML.marshalFilter(
1511 firstFilter, filters, filter.isAnded()));
1515 * save colour scheme for the feature type
1517 FeatureColourI fcol = fr.getFeatureStyle(featureType);
1518 if (!fcol.isSimpleColour())
1520 setting.setColour(fcol.getMaxColour().getRGB());
1521 setting.setMincolour(fcol.getMinColour().getRGB());
1522 setting.setMin(fcol.getMin());
1523 setting.setMax(fcol.getMax());
1524 setting.setColourByLabel(fcol.isColourByLabel());
1525 if (fcol.isColourByAttribute())
1527 String[] attName = fcol.getAttributeName();
1528 setting.getAttributeName().add(attName[0]);
1529 if (attName.length > 1)
1531 setting.getAttributeName().add(attName[1]);
1534 setting.setAutoScale(fcol.isAutoScaled());
1535 setting.setThreshold(fcol.getThreshold());
1536 Color noColour = fcol.getNoColour();
1537 if (noColour == null)
1539 setting.setNoValueColour(NoValueColour.NONE);
1541 else if (noColour.equals(fcol.getMaxColour()))
1543 setting.setNoValueColour(NoValueColour.MAX);
1547 setting.setNoValueColour(NoValueColour.MIN);
1549 // -1 = No threshold, 0 = Below, 1 = Above
1550 setting.setThreshstate(fcol.isAboveThreshold() ? 1
1551 : (fcol.isBelowThreshold() ? 0 : -1));
1555 setting.setColour(fcol.getColour().getRGB());
1559 av.getFeaturesDisplayed().isVisible(featureType));
1561 .getOrder(featureType);
1564 setting.setOrder(rorder);
1566 /// fs.addSetting(setting);
1567 fs.getSetting().add(setting);
1568 settingsAdded.addElement(featureType);
1572 // is groups actually supposed to be a map here ?
1573 Iterator<String> en = fr.getFeatureGroups().iterator();
1574 Vector<String> groupsAdded = new Vector<>();
1575 while (en.hasNext())
1577 String grp = en.next();
1578 if (groupsAdded.contains(grp))
1582 Group g = new Group();
1584 g.setDisplay(((Boolean) fr.checkGroupVisibility(grp, false))
1587 fs.getGroup().add(g);
1588 groupsAdded.addElement(grp);
1590 // jms.setFeatureSettings(fs);
1591 object.setFeatureSettings(fs);
1594 if (av.hasHiddenColumns())
1596 jalview.datamodel.HiddenColumns hidden = av.getAlignment()
1597 .getHiddenColumns();
1600 warn("REPORT BUG: avoided null columnselection bug (DMAM reported). Please contact Jim about this.");
1604 Iterator<int[]> hiddenRegions = hidden.iterator();
1605 while (hiddenRegions.hasNext())
1607 int[] region = hiddenRegions.next();
1608 HiddenColumns hc = new HiddenColumns();
1609 hc.setStart(region[0]);
1610 hc.setEnd(region[1]);
1611 // view.addHiddenColumns(hc);
1612 view.getHiddenColumns().add(hc);
1616 if (calcIdSet.size() > 0)
1618 for (String calcId : calcIdSet)
1620 if (calcId.trim().length() > 0)
1622 CalcIdParam cidp = createCalcIdParam(calcId, av);
1623 // Some calcIds have no parameters.
1626 // view.addCalcIdParam(cidp);
1627 view.getCalcIdParam().add(cidp);
1633 // jms.addViewport(view);
1634 object.getViewport().add(view);
1636 // object.setJalviewModelSequence(jms);
1637 // object.getVamsasModel().addSequenceSet(vamsasSet);
1638 object.getVamsasModel().getSequenceSet().add(vamsasSet);
1640 if (jout != null && fileName != null)
1642 // We may not want to write the object to disk,
1643 // eg we can copy the alignViewport to a new view object
1644 // using save and then load
1647 System.out.println("Writing jar entry " + fileName);
1648 JarEntry entry = new JarEntry(fileName);
1649 jout.putNextEntry(entry);
1650 PrintWriter pout = new PrintWriter(
1651 new OutputStreamWriter(jout, UTF_8));
1652 JAXBContext jaxbContext = JAXBContext
1653 .newInstance(JalviewModel.class);
1654 Marshaller jaxbMarshaller = jaxbContext.createMarshaller();
1656 // output pretty printed
1657 // jaxbMarshaller.setProperty(Marshaller.JAXB_FORMATTED_OUTPUT, true);
1658 jaxbMarshaller.marshal(
1659 new ObjectFactory().createJalviewModel(object), pout);
1661 // jaxbMarshaller.marshal(object, pout);
1662 // marshaller.marshal(object);
1665 } catch (Exception ex)
1667 // TODO: raise error in GUI if marshalling failed.
1668 System.err.println("Error writing Jalview project");
1669 ex.printStackTrace();
1676 * Writes PCA viewer attributes and computed values to an XML model object and
1677 * adds it to the JalviewModel. Any exceptions are reported by logging.
1679 protected void savePCA(PCAPanel panel, JalviewModel object)
1683 PcaViewer viewer = new PcaViewer();
1684 viewer.setHeight(panel.getHeight());
1685 viewer.setWidth(panel.getWidth());
1686 viewer.setXpos(panel.getX());
1687 viewer.setYpos(panel.getY());
1688 viewer.setTitle(panel.getTitle());
1689 PCAModel pcaModel = panel.getPcaModel();
1690 viewer.setScoreModelName(pcaModel.getScoreModelName());
1691 viewer.setXDim(panel.getSelectedDimensionIndex(X));
1692 viewer.setYDim(panel.getSelectedDimensionIndex(Y));
1693 viewer.setZDim(panel.getSelectedDimensionIndex(Z));
1695 panel.getRotatableCanvas().getBackgroundColour().getRGB());
1696 viewer.setScaleFactor(panel.getRotatableCanvas().getScaleFactor());
1697 float[] spMin = panel.getRotatableCanvas().getSeqMin();
1698 SeqPointMin spmin = new SeqPointMin();
1699 spmin.setXPos(spMin[0]);
1700 spmin.setYPos(spMin[1]);
1701 spmin.setZPos(spMin[2]);
1702 viewer.setSeqPointMin(spmin);
1703 float[] spMax = panel.getRotatableCanvas().getSeqMax();
1704 SeqPointMax spmax = new SeqPointMax();
1705 spmax.setXPos(spMax[0]);
1706 spmax.setYPos(spMax[1]);
1707 spmax.setZPos(spMax[2]);
1708 viewer.setSeqPointMax(spmax);
1709 viewer.setShowLabels(panel.getRotatableCanvas().isShowLabels());
1710 viewer.setLinkToAllViews(
1711 panel.getRotatableCanvas().isApplyToAllViews());
1712 SimilarityParamsI sp = pcaModel.getSimilarityParameters();
1713 viewer.setIncludeGaps(sp.includeGaps());
1714 viewer.setMatchGaps(sp.matchGaps());
1715 viewer.setIncludeGappedColumns(sp.includeGappedColumns());
1716 viewer.setDenominateByShortestLength(sp.denominateByShortestLength());
1719 * sequence points on display
1721 for (jalview.datamodel.SequencePoint spt : pcaModel
1722 .getSequencePoints())
1724 SequencePoint point = new SequencePoint();
1725 point.setSequenceRef(seqHash(spt.getSequence()));
1726 point.setXPos(spt.coord.x);
1727 point.setYPos(spt.coord.y);
1728 point.setZPos(spt.coord.z);
1729 viewer.getSequencePoint().add(point);
1733 * (end points of) axes on display
1735 for (Point p : panel.getRotatableCanvas().getAxisEndPoints())
1738 Axis axis = new Axis();
1742 viewer.getAxis().add(axis);
1746 * raw PCA data (note we are not restoring PCA inputs here -
1747 * alignment view, score model, similarity parameters)
1749 PcaDataType data = new PcaDataType();
1750 viewer.setPcaData(data);
1751 PCA pca = pcaModel.getPcaData();
1753 DoubleMatrix pm = new DoubleMatrix();
1754 saveDoubleMatrix(pca.getPairwiseScores(), pm);
1755 data.setPairwiseMatrix(pm);
1757 DoubleMatrix tm = new DoubleMatrix();
1758 saveDoubleMatrix(pca.getTridiagonal(), tm);
1759 data.setTridiagonalMatrix(tm);
1761 DoubleMatrix eigenMatrix = new DoubleMatrix();
1762 data.setEigenMatrix(eigenMatrix);
1763 saveDoubleMatrix(pca.getEigenmatrix(), eigenMatrix);
1765 object.getPcaViewer().add(viewer);
1766 } catch (Throwable t)
1768 Cache.log.error("Error saving PCA: " + t.getMessage());
1773 * Stores values from a matrix into an XML element, including (if present) the
1778 * @see #loadDoubleMatrix(DoubleMatrix)
1780 protected void saveDoubleMatrix(MatrixI m, DoubleMatrix xmlMatrix)
1782 xmlMatrix.setRows(m.height());
1783 xmlMatrix.setColumns(m.width());
1784 for (int i = 0; i < m.height(); i++)
1786 DoubleVector row = new DoubleVector();
1787 for (int j = 0; j < m.width(); j++)
1789 row.getV().add(m.getValue(i, j));
1791 xmlMatrix.getRow().add(row);
1793 if (m.getD() != null)
1795 DoubleVector dVector = new DoubleVector();
1796 for (double d : m.getD())
1798 dVector.getV().add(d);
1800 xmlMatrix.setD(dVector);
1802 if (m.getE() != null)
1804 DoubleVector eVector = new DoubleVector();
1805 for (double e : m.getE())
1807 eVector.getV().add(e);
1809 xmlMatrix.setE(eVector);
1814 * Loads XML matrix data into a new Matrix object, including the D and/or E
1815 * vectors (if present)
1819 * @see Jalview2XML#saveDoubleMatrix(MatrixI, DoubleMatrix)
1821 protected MatrixI loadDoubleMatrix(DoubleMatrix mData)
1823 int rows = mData.getRows();
1824 double[][] vals = new double[rows][];
1826 for (int i = 0; i < rows; i++)
1828 List<Double> dVector = mData.getRow().get(i).getV();
1829 vals[i] = new double[dVector.size()];
1831 for (Double d : dVector)
1837 MatrixI m = new Matrix(vals);
1839 if (mData.getD() != null)
1841 List<Double> dVector = mData.getD().getV();
1842 double[] vec = new double[dVector.size()];
1844 for (Double d : dVector)
1850 if (mData.getE() != null)
1852 List<Double> dVector = mData.getE().getV();
1853 double[] vec = new double[dVector.size()];
1855 for (Double d : dVector)
1866 * Save any Varna viewers linked to this sequence. Writes an rnaViewer element
1867 * for each viewer, with
1869 * <li>viewer geometry (position, size, split pane divider location)</li>
1870 * <li>index of the selected structure in the viewer (currently shows gapped
1872 * <li>the id of the annotation holding RNA secondary structure</li>
1873 * <li>(currently only one SS is shown per viewer, may be more in future)</li>
1875 * Varna viewer state is also written out (in native Varna XML) to separate
1876 * project jar entries. A separate entry is written for each RNA structure
1877 * displayed, with the naming convention
1879 * <li>rna_viewId_sequenceId_annotationId_[gapped|trimmed]</li>
1887 * @param storeDataset
1889 protected void saveRnaViewers(JarOutputStream jout, JSeq jseq,
1890 final SequenceI jds, List<String> viewIds, AlignmentPanel ap,
1891 boolean storeDataset)
1893 if (Desktop.desktop == null)
1897 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1898 for (int f = frames.length - 1; f > -1; f--)
1900 if (frames[f] instanceof AppVarna)
1902 AppVarna varna = (AppVarna) frames[f];
1904 * link the sequence to every viewer that is showing it and is linked to
1905 * its alignment panel
1907 if (varna.isListeningFor(jds) && ap == varna.getAlignmentPanel())
1909 String viewId = varna.getViewId();
1910 RnaViewer rna = new RnaViewer();
1911 rna.setViewId(viewId);
1912 rna.setTitle(varna.getTitle());
1913 rna.setXpos(varna.getX());
1914 rna.setYpos(varna.getY());
1915 rna.setWidth(varna.getWidth());
1916 rna.setHeight(varna.getHeight());
1917 rna.setDividerLocation(varna.getDividerLocation());
1918 rna.setSelectedRna(varna.getSelectedIndex());
1919 // jseq.addRnaViewer(rna);
1920 jseq.getRnaViewer().add(rna);
1923 * Store each Varna panel's state once in the project per sequence.
1924 * First time through only (storeDataset==false)
1926 // boolean storeSessions = false;
1927 // String sequenceViewId = viewId + seqsToIds.get(jds);
1928 // if (!storeDataset && !viewIds.contains(sequenceViewId))
1930 // viewIds.add(sequenceViewId);
1931 // storeSessions = true;
1933 for (RnaModel model : varna.getModels())
1935 if (model.seq == jds)
1938 * VARNA saves each view (sequence or alignment secondary
1939 * structure, gapped or trimmed) as a separate XML file
1941 String jarEntryName = rnaSessions.get(model);
1942 if (jarEntryName == null)
1945 String varnaStateFile = varna.getStateInfo(model.rna);
1946 jarEntryName = RNA_PREFIX + viewId + "_" + nextCounter();
1947 copyFileToJar(jout, varnaStateFile, jarEntryName);
1948 rnaSessions.put(model, jarEntryName);
1950 SecondaryStructure ss = new SecondaryStructure();
1951 String annotationId = varna.getAnnotation(jds).annotationId;
1952 ss.setAnnotationId(annotationId);
1953 ss.setViewerState(jarEntryName);
1954 ss.setGapped(model.gapped);
1955 ss.setTitle(model.title);
1956 // rna.addSecondaryStructure(ss);
1957 rna.getSecondaryStructure().add(ss);
1966 * Copy the contents of a file to a new entry added to the output jar
1970 * @param jarEntryName
1972 protected void copyFileToJar(JarOutputStream jout, String infilePath,
1973 String jarEntryName)
1975 DataInputStream dis = null;
1978 File file = new File(infilePath);
1979 if (file.exists() && jout != null)
1981 dis = new DataInputStream(new FileInputStream(file));
1982 byte[] data = new byte[(int) file.length()];
1983 dis.readFully(data);
1984 writeJarEntry(jout, jarEntryName, data);
1986 } catch (Exception ex)
1988 ex.printStackTrace();
1996 } catch (IOException e)
2005 * Write the data to a new entry of given name in the output jar file
2008 * @param jarEntryName
2010 * @throws IOException
2012 protected void writeJarEntry(JarOutputStream jout, String jarEntryName,
2013 byte[] data) throws IOException
2017 System.out.println("Writing jar entry " + jarEntryName);
2018 jout.putNextEntry(new JarEntry(jarEntryName));
2019 DataOutputStream dout = new DataOutputStream(jout);
2020 dout.write(data, 0, data.length);
2027 * Save the state of a structure viewer
2032 * the archive XML element under which to save the state
2035 * @param matchedFile
2039 protected String saveStructureState(AlignmentPanel ap, SequenceI jds,
2040 Pdbids pdb, PDBEntry entry, List<String> viewIds,
2041 String matchedFile, StructureViewerBase viewFrame)
2043 final AAStructureBindingModel bindingModel = viewFrame.getBinding();
2046 * Look for any bindings for this viewer to the PDB file of interest
2047 * (including part matches excluding chain id)
2049 for (int peid = 0; peid < bindingModel.getPdbCount(); peid++)
2051 final PDBEntry pdbentry = bindingModel.getPdbEntry(peid);
2052 final String pdbId = pdbentry.getId();
2053 if (!pdbId.equals(entry.getId())
2054 && !(entry.getId().length() > 4 && entry.getId().toLowerCase()
2055 .startsWith(pdbId.toLowerCase())))
2058 * not interested in a binding to a different PDB entry here
2062 if (matchedFile == null)
2064 matchedFile = pdbentry.getFile();
2066 else if (!matchedFile.equals(pdbentry.getFile()))
2069 "Probably lost some PDB-Sequence mappings for this structure file (which apparently has same PDB Entry code): "
2070 + pdbentry.getFile());
2074 // can get at it if the ID
2075 // match is ambiguous (e.g.
2078 for (int smap = 0; smap < viewFrame.getBinding()
2079 .getSequence()[peid].length; smap++)
2081 // if (jal.findIndex(jmol.jmb.sequence[peid][smap]) > -1)
2082 if (jds == viewFrame.getBinding().getSequence()[peid][smap])
2084 StructureState state = new StructureState();
2085 state.setVisible(true);
2086 state.setXpos(viewFrame.getX());
2087 state.setYpos(viewFrame.getY());
2088 state.setWidth(viewFrame.getWidth());
2089 state.setHeight(viewFrame.getHeight());
2090 final String viewId = viewFrame.getViewId();
2091 state.setViewId(viewId);
2092 state.setAlignwithAlignPanel(viewFrame.isUsedforaligment(ap));
2093 state.setColourwithAlignPanel(viewFrame.isUsedforcolourby(ap));
2094 state.setColourByJmol(viewFrame.isColouredByViewer());
2095 state.setType(viewFrame.getViewerType().toString());
2096 // pdb.addStructureState(state);
2097 pdb.getStructureState().add(state);
2105 * Populates the AnnotationColourScheme xml for save. This captures the
2106 * settings of the options in the 'Colour by Annotation' dialog.
2109 * @param userColours
2113 private AnnotationColourScheme constructAnnotationColours(
2114 AnnotationColourGradient acg, List<UserColourScheme> userColours,
2117 AnnotationColourScheme ac = new AnnotationColourScheme();
2118 ac.setAboveThreshold(acg.getAboveThreshold());
2119 ac.setThreshold(acg.getAnnotationThreshold());
2120 // 2.10.2 save annotationId (unique) not annotation label
2121 ac.setAnnotation(acg.getAnnotation().annotationId);
2122 if (acg.getBaseColour() instanceof UserColourScheme)
2125 setUserColourScheme(acg.getBaseColour(), userColours, jm));
2130 ColourSchemeProperty.getColourName(acg.getBaseColour()));
2133 ac.setMaxColour(acg.getMaxColour().getRGB());
2134 ac.setMinColour(acg.getMinColour().getRGB());
2135 ac.setPerSequence(acg.isSeqAssociated());
2136 ac.setPredefinedColours(acg.isPredefinedColours());
2140 private void storeAlignmentAnnotation(AlignmentAnnotation[] aa,
2141 IdentityHashMap<SequenceGroup, String> groupRefs,
2142 AlignmentViewport av, Set<String> calcIdSet, boolean storeDS,
2143 SequenceSet vamsasSet)
2146 for (int i = 0; i < aa.length; i++)
2148 Annotation an = new Annotation();
2150 AlignmentAnnotation annotation = aa[i];
2151 if (annotation.annotationId != null)
2153 annotationIds.put(annotation.annotationId, annotation);
2156 an.setId(annotation.annotationId);
2158 an.setVisible(annotation.visible);
2160 an.setDescription(annotation.description);
2162 if (annotation.sequenceRef != null)
2164 // 2.9 JAL-1781 xref on sequence id rather than name
2165 an.setSequenceRef(seqsToIds.get(annotation.sequenceRef));
2167 if (annotation.groupRef != null)
2169 String groupIdr = groupRefs.get(annotation.groupRef);
2170 if (groupIdr == null)
2172 // make a locally unique String
2173 groupRefs.put(annotation.groupRef,
2174 groupIdr = ("" + System.currentTimeMillis()
2175 + annotation.groupRef.getName()
2176 + groupRefs.size()));
2178 an.setGroupRef(groupIdr.toString());
2181 // store all visualization attributes for annotation
2182 an.setGraphHeight(annotation.graphHeight);
2183 an.setCentreColLabels(annotation.centreColLabels);
2184 an.setScaleColLabels(annotation.scaleColLabel);
2185 an.setShowAllColLabels(annotation.showAllColLabels);
2186 an.setBelowAlignment(annotation.belowAlignment);
2188 if (annotation.graph > 0)
2191 an.setGraphType(annotation.graph);
2192 an.setGraphGroup(annotation.graphGroup);
2193 if (annotation.getThreshold() != null)
2195 ThresholdLine line = new ThresholdLine();
2196 line.setLabel(annotation.getThreshold().label);
2197 line.setValue(annotation.getThreshold().value);
2198 line.setColour(annotation.getThreshold().colour.getRGB());
2199 an.setThresholdLine(line);
2207 an.setLabel(annotation.label);
2209 if (annotation == av.getAlignmentQualityAnnot()
2210 || annotation == av.getAlignmentConservationAnnotation()
2211 || annotation == av.getAlignmentConsensusAnnotation()
2212 || annotation.autoCalculated)
2214 // new way of indicating autocalculated annotation -
2215 an.setAutoCalculated(annotation.autoCalculated);
2217 if (annotation.hasScore())
2219 an.setScore(annotation.getScore());
2222 if (annotation.getCalcId() != null)
2224 calcIdSet.add(annotation.getCalcId());
2225 an.setCalcId(annotation.getCalcId());
2227 if (annotation.hasProperties())
2229 for (String pr : annotation.getProperties())
2231 jalview.xml.binding.jalview.Annotation.Property prop = new jalview.xml.binding.jalview.Annotation.Property();
2233 prop.setValue(annotation.getProperty(pr));
2234 // an.addProperty(prop);
2235 an.getProperty().add(prop);
2239 AnnotationElement ae;
2240 if (annotation.annotations != null)
2242 an.setScoreOnly(false);
2243 for (int a = 0; a < annotation.annotations.length; a++)
2245 if ((annotation == null) || (annotation.annotations[a] == null))
2250 ae = new AnnotationElement();
2251 if (annotation.annotations[a].description != null)
2253 ae.setDescription(annotation.annotations[a].description);
2255 if (annotation.annotations[a].displayCharacter != null)
2257 ae.setDisplayCharacter(
2258 annotation.annotations[a].displayCharacter);
2261 if (!Float.isNaN(annotation.annotations[a].value))
2263 ae.setValue(annotation.annotations[a].value);
2267 if (annotation.annotations[a].secondaryStructure > ' ')
2269 ae.setSecondaryStructure(
2270 annotation.annotations[a].secondaryStructure + "");
2273 if (annotation.annotations[a].colour != null
2274 && annotation.annotations[a].colour != java.awt.Color.black)
2276 ae.setColour(annotation.annotations[a].colour.getRGB());
2279 // an.addAnnotationElement(ae);
2280 an.getAnnotationElement().add(ae);
2281 if (annotation.autoCalculated)
2283 // only write one non-null entry into the annotation row -
2284 // sufficient to get the visualization attributes necessary to
2292 an.setScoreOnly(true);
2294 if (!storeDS || (storeDS && !annotation.autoCalculated))
2296 // skip autocalculated annotation - these are only provided for
2298 // vamsasSet.addAnnotation(an);
2299 vamsasSet.getAnnotation().add(an);
2305 private CalcIdParam createCalcIdParam(String calcId, AlignViewport av)
2307 AutoCalcSetting settings = av.getCalcIdSettingsFor(calcId);
2308 if (settings != null)
2310 CalcIdParam vCalcIdParam = new CalcIdParam();
2311 vCalcIdParam.setCalcId(calcId);
2312 // vCalcIdParam.addServiceURL(settings.getServiceURI());
2313 vCalcIdParam.getServiceURL().add(settings.getServiceURI());
2314 // generic URI allowing a third party to resolve another instance of the
2315 // service used for this calculation
2316 for (String url : settings.getServiceURLs())
2318 // vCalcIdParam.addServiceURL(urls);
2319 vCalcIdParam.getServiceURL().add(url);
2321 vCalcIdParam.setVersion("1.0");
2322 if (settings.getPreset() != null)
2324 WsParamSetI setting = settings.getPreset();
2325 vCalcIdParam.setName(setting.getName());
2326 vCalcIdParam.setDescription(setting.getDescription());
2330 vCalcIdParam.setName("");
2331 vCalcIdParam.setDescription("Last used parameters");
2333 // need to be able to recover 1) settings 2) user-defined presets or
2334 // recreate settings from preset 3) predefined settings provided by
2335 // service - or settings that can be transferred (or discarded)
2336 vCalcIdParam.setParameters(
2337 settings.getWsParamFile().replace("\n", "|\\n|"));
2338 vCalcIdParam.setAutoUpdate(settings.isAutoUpdate());
2339 // todo - decide if updateImmediately is needed for any projects.
2341 return vCalcIdParam;
2346 private boolean recoverCalcIdParam(CalcIdParam calcIdParam,
2349 if (calcIdParam.getVersion().equals("1.0"))
2351 final String[] calcIds = calcIdParam.getServiceURL().toArray(new String[0]);
2352 Jws2Instance service = Jws2Discoverer.getDiscoverer()
2353 .getPreferredServiceFor(calcIds);
2354 if (service != null)
2356 WsParamSetI parmSet = null;
2359 parmSet = service.getParamStore().parseServiceParameterFile(
2360 calcIdParam.getName(), calcIdParam.getDescription(),
2362 calcIdParam.getParameters().replace("|\\n|", "\n"));
2363 } catch (IOException x)
2365 warn("Couldn't parse parameter data for "
2366 + calcIdParam.getCalcId(), x);
2369 List<ArgumentI> argList = null;
2370 if (calcIdParam.getName().length() > 0)
2372 parmSet = service.getParamStore()
2373 .getPreset(calcIdParam.getName());
2374 if (parmSet != null)
2376 // TODO : check we have a good match with settings in AACon -
2377 // otherwise we'll need to create a new preset
2382 argList = parmSet.getArguments();
2385 AAConSettings settings = new AAConSettings(
2386 calcIdParam.isAutoUpdate(), service, parmSet, argList);
2387 av.setCalcIdSettingsFor(calcIdParam.getCalcId(), settings,
2388 calcIdParam.isNeedsUpdate());
2393 warn("Cannot resolve a service for the parameters used in this project. Try configuring a JABAWS server.");
2397 throw new Error(MessageManager.formatMessage(
2398 "error.unsupported_version_calcIdparam", new Object[]
2399 { calcIdParam.toString() }));
2403 * External mapping between jalview objects and objects yielding a valid and
2404 * unique object ID string. This is null for normal Jalview project IO, but
2405 * non-null when a jalview project is being read or written as part of a
2408 IdentityHashMap jv2vobj = null;
2411 * Construct a unique ID for jvobj using either existing bindings or if none
2412 * exist, the result of the hashcode call for the object.
2415 * jalview data object
2416 * @return unique ID for referring to jvobj
2418 private String makeHashCode(Object jvobj, String altCode)
2420 if (jv2vobj != null)
2422 Object id = jv2vobj.get(jvobj);
2425 return id.toString();
2427 // check string ID mappings
2428 if (jvids2vobj != null && jvobj instanceof String)
2430 id = jvids2vobj.get(jvobj);
2434 return id.toString();
2436 // give up and warn that something has gone wrong
2437 warn("Cannot find ID for object in external mapping : " + jvobj);
2443 * return local jalview object mapped to ID, if it exists
2447 * @return null or object bound to idcode
2449 private Object retrieveExistingObj(String idcode)
2451 if (idcode != null && vobj2jv != null)
2453 return vobj2jv.get(idcode);
2459 * binding from ID strings from external mapping table to jalview data model
2462 private Hashtable vobj2jv;
2464 private Sequence createVamsasSequence(String id, SequenceI jds)
2466 return createVamsasSequence(true, id, jds, null);
2469 private Sequence createVamsasSequence(boolean recurse, String id,
2470 SequenceI jds, SequenceI parentseq)
2472 Sequence vamsasSeq = new Sequence();
2473 vamsasSeq.setId(id);
2474 vamsasSeq.setName(jds.getName());
2475 vamsasSeq.setSequence(jds.getSequenceAsString());
2476 vamsasSeq.setDescription(jds.getDescription());
2477 jalview.datamodel.DBRefEntry[] dbrefs = null;
2478 if (jds.getDatasetSequence() != null)
2480 vamsasSeq.setDsseqid(seqHash(jds.getDatasetSequence()));
2484 // seqId==dsseqid so we can tell which sequences really are
2485 // dataset sequences only
2486 vamsasSeq.setDsseqid(id);
2487 dbrefs = jds.getDBRefs();
2488 if (parentseq == null)
2495 for (int d = 0; d < dbrefs.length; d++)
2497 DBRef dbref = new DBRef();
2498 dbref.setSource(dbrefs[d].getSource());
2499 dbref.setVersion(dbrefs[d].getVersion());
2500 dbref.setAccessionId(dbrefs[d].getAccessionId());
2501 if (dbrefs[d].hasMap())
2503 Mapping mp = createVamsasMapping(dbrefs[d].getMap(), parentseq,
2505 dbref.setMapping(mp);
2507 // vamsasSeq.addDBRef(dbref);
2508 vamsasSeq.getDBRef().add(dbref);
2514 private Mapping createVamsasMapping(jalview.datamodel.Mapping jmp,
2515 SequenceI parentseq, SequenceI jds, boolean recurse)
2518 if (jmp.getMap() != null)
2522 jalview.util.MapList mlst = jmp.getMap();
2523 List<int[]> r = mlst.getFromRanges();
2524 for (int[] range : r)
2526 MapListFrom mfrom = new MapListFrom();
2527 mfrom.setStart(range[0]);
2528 mfrom.setEnd(range[1]);
2529 // mp.addMapListFrom(mfrom);
2530 mp.getMapListFrom().add(mfrom);
2532 r = mlst.getToRanges();
2533 for (int[] range : r)
2535 MapListTo mto = new MapListTo();
2536 mto.setStart(range[0]);
2537 mto.setEnd(range[1]);
2538 // mp.addMapListTo(mto);
2539 mp.getMapListTo().add(mto);
2541 mp.setMapFromUnit(BigInteger.valueOf(mlst.getFromRatio()));
2542 mp.setMapToUnit(BigInteger.valueOf(mlst.getToRatio()));
2543 if (jmp.getTo() != null)
2545 // MappingChoice mpc = new MappingChoice();
2547 // check/create ID for the sequence referenced by getTo()
2550 SequenceI ps = null;
2551 if (parentseq != jmp.getTo()
2552 && parentseq.getDatasetSequence() != jmp.getTo())
2554 // chaining dbref rather than a handshaking one
2555 jmpid = seqHash(ps = jmp.getTo());
2559 jmpid = seqHash(ps = parentseq);
2561 // mpc.setDseqFor(jmpid);
2562 mp.setDseqFor(jmpid);
2563 if (!seqRefIds.containsKey(jmpid))
2565 jalview.bin.Cache.log.debug("creatign new DseqFor ID");
2566 seqRefIds.put(jmpid, ps);
2570 jalview.bin.Cache.log.debug("reusing DseqFor ID");
2573 // mp.setMappingChoice(mpc);
2579 String setUserColourScheme(jalview.schemes.ColourSchemeI cs,
2580 List<UserColourScheme> userColours, JalviewModel jm)
2583 jalview.schemes.UserColourScheme ucs = (jalview.schemes.UserColourScheme) cs;
2584 boolean newucs = false;
2585 if (!userColours.contains(ucs))
2587 userColours.add(ucs);
2590 id = "ucs" + userColours.indexOf(ucs);
2593 // actually create the scheme's entry in the XML model
2594 java.awt.Color[] colours = ucs.getColours();
2595 UserColours uc = new UserColours();
2596 // UserColourScheme jbucs = new UserColourScheme();
2597 JalviewUserColours jbucs = new JalviewUserColours();
2599 for (int i = 0; i < colours.length; i++)
2601 Colour col = new Colour();
2602 col.setName(ResidueProperties.aa[i]);
2603 col.setRGB(jalview.util.Format.getHexString(colours[i]));
2604 // jbucs.addColour(col);
2605 jbucs.getColour().add(col);
2607 if (ucs.getLowerCaseColours() != null)
2609 colours = ucs.getLowerCaseColours();
2610 for (int i = 0; i < colours.length; i++)
2612 Colour col = new Colour();
2613 col.setName(ResidueProperties.aa[i].toLowerCase());
2614 col.setRGB(jalview.util.Format.getHexString(colours[i]));
2615 // jbucs.addColour(col);
2616 jbucs.getColour().add(col);
2621 uc.setUserColourScheme(jbucs);
2622 // jm.addUserColours(uc);
2623 jm.getUserColours().add(uc);
2629 jalview.schemes.UserColourScheme getUserColourScheme(
2630 JalviewModel jm, String id)
2632 List<UserColours> uc = jm.getUserColours();
2633 UserColours colours = null;
2635 for (int i = 0; i < uc.length; i++)
2637 if (uc[i].getId().equals(id))
2644 for (UserColours c : uc)
2646 if (c.getId().equals(id))
2653 java.awt.Color[] newColours = new java.awt.Color[24];
2655 for (int i = 0; i < 24; i++)
2657 newColours[i] = new java.awt.Color(Integer.parseInt(
2658 // colours.getUserColourScheme().getColour(i).getRGB(), 16));
2659 colours.getUserColourScheme().getColour().get(i).getRGB(),
2663 jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(
2666 if (colours.getUserColourScheme().getColour().size()/*Count()*/ > 24)
2668 newColours = new java.awt.Color[23];
2669 for (int i = 0; i < 23; i++)
2671 newColours[i] = new java.awt.Color(Integer.parseInt(
2672 colours.getUserColourScheme().getColour().get(i + 24)
2676 ucs.setLowerCaseColours(newColours);
2683 * contains last error message (if any) encountered by XML loader.
2685 String errorMessage = null;
2688 * flag to control whether the Jalview2XML_V1 parser should be deferred to if
2689 * exceptions are raised during project XML parsing
2691 public boolean attemptversion1parse = false;
2694 * Load a jalview project archive from a jar file
2697 * - HTTP URL or filename
2699 public AlignFrame loadJalviewAlign(final String file)
2702 jalview.gui.AlignFrame af = null;
2706 // create list to store references for any new Jmol viewers created
2707 newStructureViewers = new Vector<>();
2708 // UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
2709 // Workaround is to make sure caller implements the JarInputStreamProvider
2711 // so we can re-open the jar input stream for each entry.
2713 jarInputStreamProvider jprovider = createjarInputStreamProvider(file);
2714 af = loadJalviewAlign(jprovider);
2717 af.setMenusForViewport();
2719 } catch (MalformedURLException e)
2721 errorMessage = "Invalid URL format for '" + file + "'";
2727 SwingUtilities.invokeAndWait(new Runnable()
2732 setLoadingFinishedForNewStructureViewers();
2735 } catch (Exception x)
2737 System.err.println("Error loading alignment: " + x.getMessage());
2743 private jarInputStreamProvider createjarInputStreamProvider(
2744 final String file) throws MalformedURLException
2747 errorMessage = null;
2748 uniqueSetSuffix = null;
2750 viewportsAdded.clear();
2751 frefedSequence = null;
2753 if (file.startsWith("http://"))
2755 url = new URL(file);
2757 final URL _url = url;
2758 return new jarInputStreamProvider()
2762 public JarInputStream getJarInputStream() throws IOException
2766 return new JarInputStream(_url.openStream());
2770 return new JarInputStream(new FileInputStream(file));
2775 public String getFilename()
2783 * Recover jalview session from a jalview project archive. Caller may
2784 * initialise uniqueSetSuffix, seqRefIds, viewportsAdded and frefedSequence
2785 * themselves. Any null fields will be initialised with default values,
2786 * non-null fields are left alone.
2791 public AlignFrame loadJalviewAlign(final jarInputStreamProvider jprovider)
2793 errorMessage = null;
2794 if (uniqueSetSuffix == null)
2796 uniqueSetSuffix = System.currentTimeMillis() % 100000 + "";
2798 if (seqRefIds == null)
2802 AlignFrame af = null, _af = null;
2803 IdentityHashMap<AlignmentI, AlignmentI> importedDatasets = new IdentityHashMap<>();
2804 Map<String, AlignFrame> gatherToThisFrame = new HashMap<>();
2805 final String file = jprovider.getFilename();
2808 JarInputStream jin = null;
2809 JarEntry jarentry = null;
2814 jin = jprovider.getJarInputStream();
2815 for (int i = 0; i < entryCount; i++)
2817 jarentry = jin.getNextJarEntry();
2820 if (jarentry != null && jarentry.getName().endsWith(".xml"))
2822 InputStreamReader in = new InputStreamReader(jin, UTF_8);
2823 // JalviewModel object = new JalviewModel();
2825 JAXBContext jc = JAXBContext
2826 .newInstance("jalview.xml.binding.jalview");
2827 XMLStreamReader streamReader = XMLInputFactory.newInstance()
2828 .createXMLStreamReader(jin);
2829 javax.xml.bind.Unmarshaller um = jc.createUnmarshaller();
2830 JAXBElement<JalviewModel> jbe = um
2831 .unmarshal(streamReader, JalviewModel.class);
2832 JalviewModel object = jbe.getValue();
2835 Unmarshaller unmar = new Unmarshaller(object);
2836 unmar.setValidation(false);
2837 object = (JalviewModel) unmar.unmarshal(in);
2839 if (true) // !skipViewport(object))
2841 _af = loadFromObject(object, file, true, jprovider);
2842 if (_af != null && object.getViewport().size() > 0)
2843 // getJalviewModelSequence().getViewportCount() > 0)
2847 // store a reference to the first view
2850 if (_af.getViewport().isGatherViewsHere())
2852 // if this is a gathered view, keep its reference since
2853 // after gathering views, only this frame will remain
2855 gatherToThisFrame.put(_af.getViewport().getSequenceSetId(),
2858 // Save dataset to register mappings once all resolved
2859 importedDatasets.put(
2860 af.getViewport().getAlignment().getDataset(),
2861 af.getViewport().getAlignment().getDataset());
2866 else if (jarentry != null)
2868 // Some other file here.
2871 } while (jarentry != null);
2872 resolveFrefedSequences();
2873 } catch (IOException ex)
2875 ex.printStackTrace();
2876 errorMessage = "Couldn't locate Jalview XML file : " + file;
2878 "Exception whilst loading jalview XML file : " + ex + "\n");
2879 } catch (Exception ex)
2881 System.err.println("Parsing as Jalview Version 2 file failed.");
2882 ex.printStackTrace(System.err);
2883 if (attemptversion1parse)
2885 // Is Version 1 Jar file?
2888 af = new Jalview2XML_V1(raiseGUI).LoadJalviewAlign(jprovider);
2889 } catch (Exception ex2)
2891 System.err.println("Exception whilst loading as jalviewXMLV1:");
2892 ex2.printStackTrace();
2896 if (Desktop.instance != null)
2898 Desktop.instance.stopLoading();
2902 System.out.println("Successfully loaded archive file");
2905 ex.printStackTrace();
2908 "Exception whilst loading jalview XML file : " + ex + "\n");
2909 } catch (OutOfMemoryError e)
2911 // Don't use the OOM Window here
2912 errorMessage = "Out of memory loading jalview XML file";
2913 System.err.println("Out of memory whilst loading jalview XML file");
2914 e.printStackTrace();
2918 * Regather multiple views (with the same sequence set id) to the frame (if
2919 * any) that is flagged as the one to gather to, i.e. convert them to tabbed
2920 * views instead of separate frames. Note this doesn't restore a state where
2921 * some expanded views in turn have tabbed views - the last "first tab" read
2922 * in will play the role of gatherer for all.
2924 for (AlignFrame fr : gatherToThisFrame.values())
2926 Desktop.instance.gatherViews(fr);
2929 restoreSplitFrames();
2930 for (AlignmentI ds : importedDatasets.keySet())
2932 if (ds.getCodonFrames() != null)
2934 StructureSelectionManager
2935 .getStructureSelectionManager(Desktop.instance)
2936 .registerMappings(ds.getCodonFrames());
2939 if (errorMessage != null)
2944 if (Desktop.instance != null)
2946 Desktop.instance.stopLoading();
2953 * Try to reconstruct and display SplitFrame windows, where each contains
2954 * complementary dna and protein alignments. Done by pairing up AlignFrame
2955 * objects (created earlier) which have complementary viewport ids associated.
2957 protected void restoreSplitFrames()
2959 List<SplitFrame> gatherTo = new ArrayList<>();
2960 List<AlignFrame> addedToSplitFrames = new ArrayList<>();
2961 Map<String, AlignFrame> dna = new HashMap<>();
2964 * Identify the DNA alignments
2966 for (Entry<Viewport, AlignFrame> candidate : splitFrameCandidates
2969 AlignFrame af = candidate.getValue();
2970 if (af.getViewport().getAlignment().isNucleotide())
2972 dna.put(candidate.getKey().getId(), af);
2977 * Try to match up the protein complements
2979 for (Entry<Viewport, AlignFrame> candidate : splitFrameCandidates
2982 AlignFrame af = candidate.getValue();
2983 if (!af.getViewport().getAlignment().isNucleotide())
2985 String complementId = candidate.getKey().getComplementId();
2986 // only non-null complements should be in the Map
2987 if (complementId != null && dna.containsKey(complementId))
2989 final AlignFrame dnaFrame = dna.get(complementId);
2990 SplitFrame sf = createSplitFrame(dnaFrame, af);
2991 addedToSplitFrames.add(dnaFrame);
2992 addedToSplitFrames.add(af);
2993 dnaFrame.setMenusForViewport();
2994 af.setMenusForViewport();
2995 if (af.getViewport().isGatherViewsHere())
3004 * Open any that we failed to pair up (which shouldn't happen!) as
3005 * standalone AlignFrame's.
3007 for (Entry<Viewport, AlignFrame> candidate : splitFrameCandidates
3010 AlignFrame af = candidate.getValue();
3011 if (!addedToSplitFrames.contains(af))
3013 Viewport view = candidate.getKey();
3014 Desktop.addInternalFrame(af, view.getTitle(),
3015 safeInt(view.getWidth()), safeInt(view.getHeight()));
3016 af.setMenusForViewport();
3017 System.err.println("Failed to restore view " + view.getTitle()
3018 + " to split frame");
3023 * Gather back into tabbed views as flagged.
3025 for (SplitFrame sf : gatherTo)
3027 Desktop.instance.gatherViews(sf);
3030 splitFrameCandidates.clear();
3034 * Construct and display one SplitFrame holding DNA and protein alignments.
3037 * @param proteinFrame
3040 protected SplitFrame createSplitFrame(AlignFrame dnaFrame,
3041 AlignFrame proteinFrame)
3043 SplitFrame splitFrame = new SplitFrame(dnaFrame, proteinFrame);
3044 String title = MessageManager.getString("label.linked_view_title");
3045 int width = (int) dnaFrame.getBounds().getWidth();
3046 int height = (int) (dnaFrame.getBounds().getHeight()
3047 + proteinFrame.getBounds().getHeight() + 50);
3050 * SplitFrame location is saved to both enclosed frames
3052 splitFrame.setLocation(dnaFrame.getX(), dnaFrame.getY());
3053 Desktop.addInternalFrame(splitFrame, title, width, height);
3056 * And compute cDNA consensus (couldn't do earlier with consensus as
3057 * mappings were not yet present)
3059 proteinFrame.getViewport().alignmentChanged(proteinFrame.alignPanel);
3065 * check errorMessage for a valid error message and raise an error box in the
3066 * GUI or write the current errorMessage to stderr and then clear the error
3069 protected void reportErrors()
3071 reportErrors(false);
3074 protected void reportErrors(final boolean saving)
3076 if (errorMessage != null)
3078 final String finalErrorMessage = errorMessage;
3081 javax.swing.SwingUtilities.invokeLater(new Runnable()
3086 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
3088 "Error " + (saving ? "saving" : "loading")
3090 JvOptionPane.WARNING_MESSAGE);
3096 System.err.println("Problem loading Jalview file: " + errorMessage);
3099 errorMessage = null;
3102 Map<String, String> alreadyLoadedPDB = new HashMap<>();
3105 * when set, local views will be updated from view stored in JalviewXML
3106 * Currently (28th Sep 2008) things will go horribly wrong in vamsas document
3107 * sync if this is set to true.
3109 private final boolean updateLocalViews = false;
3112 * Returns the path to a temporary file holding the PDB file for the given PDB
3113 * id. The first time of asking, searches for a file of that name in the
3114 * Jalview project jar, and copies it to a new temporary file. Any repeat
3115 * requests just return the path to the file previously created.
3121 String loadPDBFile(jarInputStreamProvider jprovider, String pdbId,
3124 if (alreadyLoadedPDB.containsKey(pdbId))
3126 return alreadyLoadedPDB.get(pdbId).toString();
3129 String tempFile = copyJarEntry(jprovider, pdbId, "jalview_pdb",
3131 if (tempFile != null)
3133 alreadyLoadedPDB.put(pdbId, tempFile);
3139 * Copies the jar entry of given name to a new temporary file and returns the
3140 * path to the file, or null if the entry is not found.
3143 * @param jarEntryName
3145 * a prefix for the temporary file name, must be at least three
3148 * null or original file - so new file can be given the same suffix
3152 protected String copyJarEntry(jarInputStreamProvider jprovider,
3153 String jarEntryName, String prefix, String origFile)
3155 BufferedReader in = null;
3156 PrintWriter out = null;
3157 String suffix = ".tmp";
3158 if (origFile == null)
3160 origFile = jarEntryName;
3162 int sfpos = origFile.lastIndexOf(".");
3163 if (sfpos > -1 && sfpos < (origFile.length() - 3))
3165 suffix = "." + origFile.substring(sfpos + 1);
3169 JarInputStream jin = jprovider.getJarInputStream();
3171 * if (jprovider.startsWith("http://")) { jin = new JarInputStream(new
3172 * URL(jprovider).openStream()); } else { jin = new JarInputStream(new
3173 * FileInputStream(jprovider)); }
3176 JarEntry entry = null;
3179 entry = jin.getNextJarEntry();
3180 } while (entry != null && !entry.getName().equals(jarEntryName));
3183 in = new BufferedReader(new InputStreamReader(jin, UTF_8));
3184 File outFile = File.createTempFile(prefix, suffix);
3185 outFile.deleteOnExit();
3186 out = new PrintWriter(new FileOutputStream(outFile));
3189 while ((data = in.readLine()) != null)
3194 String t = outFile.getAbsolutePath();
3199 warn("Couldn't find entry in Jalview Jar for " + jarEntryName);
3201 } catch (Exception ex)
3203 ex.printStackTrace();
3211 } catch (IOException e)
3225 private class JvAnnotRow
3227 public JvAnnotRow(int i, AlignmentAnnotation jaa)
3234 * persisted version of annotation row from which to take vis properties
3236 public jalview.datamodel.AlignmentAnnotation template;
3239 * original position of the annotation row in the alignment
3245 * Load alignment frame from jalview XML DOM object
3247 * @param jalviewModel
3250 * filename source string
3251 * @param loadTreesAndStructures
3252 * when false only create Viewport
3254 * data source provider
3255 * @return alignment frame created from view stored in DOM
3257 AlignFrame loadFromObject(JalviewModel jalviewModel, String file,
3258 boolean loadTreesAndStructures, jarInputStreamProvider jprovider)
3260 SequenceSet vamsasSet = jalviewModel.getVamsasModel().getSequenceSet().get(0);
3261 List<Sequence> vamsasSeqs = vamsasSet.getSequence();
3263 // JalviewModelSequence jms = object.getJalviewModelSequence();
3265 // Viewport view = (jms.getViewportCount() > 0) ? jms.getViewport(0)
3267 Viewport view = (jalviewModel.getViewport().size() > 0)
3268 ? jalviewModel.getViewport().get(0)
3271 // ////////////////////////////////
3272 // INITIALISE ALIGNMENT SEQUENCESETID AND VIEWID
3275 // If we just load in the same jar file again, the sequenceSetId
3276 // will be the same, and we end up with multiple references
3277 // to the same sequenceSet. We must modify this id on load
3278 // so that each load of the file gives a unique id
3281 * used to resolve correct alignment dataset for alignments with multiple
3284 String uniqueSeqSetId = null;
3285 String viewId = null;
3288 uniqueSeqSetId = view.getSequenceSetId() + uniqueSetSuffix;
3289 viewId = (view.getId() == null ? null
3290 : view.getId() + uniqueSetSuffix);
3293 // ////////////////////////////////
3296 List<SequenceI> hiddenSeqs = null;
3298 List<SequenceI> tmpseqs = new ArrayList<>();
3300 boolean multipleView = false;
3301 SequenceI referenceseqForView = null;
3302 // JSeq[] jseqs = object.getJalviewModelSequence().getJSeq();
3303 List<JSeq> jseqs = jalviewModel.getJSeq();
3304 int vi = 0; // counter in vamsasSeq array
3305 for (int i = 0; i < jseqs.size(); i++)
3307 JSeq jseq = jseqs.get(i);
3308 String seqId = jseq.getId();
3310 SequenceI tmpSeq = seqRefIds.get(seqId);
3313 if (!incompleteSeqs.containsKey(seqId))
3315 // may not need this check, but keep it for at least 2.9,1 release
3316 if (tmpSeq.getStart() != jseq.getStart()
3317 || tmpSeq.getEnd() != jseq.getEnd())
3320 "Warning JAL-2154 regression: updating start/end for sequence "
3321 + tmpSeq.toString() + " to " + jseq);
3326 incompleteSeqs.remove(seqId);
3328 if (vamsasSeqs.size() > vi
3329 && vamsasSeqs.get(vi).getId().equals(seqId))
3331 // most likely we are reading a dataset XML document so
3332 // update from vamsasSeq section of XML for this sequence
3333 tmpSeq.setName(vamsasSeqs.get(vi).getName());
3334 tmpSeq.setDescription(vamsasSeqs.get(vi).getDescription());
3335 tmpSeq.setSequence(vamsasSeqs.get(vi).getSequence());
3340 // reading multiple views, so vamsasSeq set is a subset of JSeq
3341 multipleView = true;
3343 tmpSeq.setStart(jseq.getStart());
3344 tmpSeq.setEnd(jseq.getEnd());
3345 tmpseqs.add(tmpSeq);
3349 Sequence vamsasSeq = vamsasSeqs.get(vi);
3350 tmpSeq = new jalview.datamodel.Sequence(vamsasSeq.getName(),
3351 vamsasSeq.getSequence());
3352 tmpSeq.setDescription(vamsasSeq.getDescription());
3353 tmpSeq.setStart(jseq.getStart());
3354 tmpSeq.setEnd(jseq.getEnd());
3355 tmpSeq.setVamsasId(uniqueSetSuffix + seqId);
3356 seqRefIds.put(vamsasSeq.getId(), tmpSeq);
3357 tmpseqs.add(tmpSeq);
3361 if (safeBoolean(jseq.isViewreference()))
3363 referenceseqForView = tmpseqs.get(tmpseqs.size() - 1);
3366 if (jseq.isHidden() != null && jseq.isHidden().booleanValue())
3368 if (hiddenSeqs == null)
3370 hiddenSeqs = new ArrayList<>();
3373 hiddenSeqs.add(tmpSeq);
3378 // Create the alignment object from the sequence set
3379 // ///////////////////////////////
3380 SequenceI[] orderedSeqs = tmpseqs
3381 .toArray(new SequenceI[tmpseqs.size()]);
3383 AlignmentI al = null;
3384 // so we must create or recover the dataset alignment before going further
3385 // ///////////////////////////////
3386 if (vamsasSet.getDatasetId() == null || vamsasSet.getDatasetId() == "")
3388 // older jalview projects do not have a dataset - so creat alignment and
3390 al = new Alignment(orderedSeqs);
3391 al.setDataset(null);
3395 boolean isdsal = jalviewModel.getViewport().isEmpty();
3398 // we are importing a dataset record, so
3399 // recover reference to an alignment already materialsed as dataset
3400 al = getDatasetFor(vamsasSet.getDatasetId());
3404 // materialse the alignment
3405 al = new Alignment(orderedSeqs);
3409 addDatasetRef(vamsasSet.getDatasetId(), al);
3412 // finally, verify all data in vamsasSet is actually present in al
3413 // passing on flag indicating if it is actually a stored dataset
3414 recoverDatasetFor(vamsasSet, al, isdsal, uniqueSeqSetId);
3417 if (referenceseqForView != null)
3419 al.setSeqrep(referenceseqForView);
3421 // / Add the alignment properties
3422 for (int i = 0; i < vamsasSet.getSequenceSetProperties().size(); i++)
3424 SequenceSetProperties ssp = vamsasSet.getSequenceSetProperties()
3426 al.setProperty(ssp.getKey(), ssp.getValue());
3429 // ///////////////////////////////
3431 Hashtable pdbloaded = new Hashtable(); // TODO nothing writes to this??
3434 // load sequence features, database references and any associated PDB
3435 // structures for the alignment
3437 // prior to 2.10, this part would only be executed the first time a
3438 // sequence was encountered, but not afterwards.
3439 // now, for 2.10 projects, this is also done if the xml doc includes
3440 // dataset sequences not actually present in any particular view.
3442 for (int i = 0; i < vamsasSeqs.size(); i++)
3444 JSeq jseq = jseqs.get(i);
3445 if (jseq.getFeatures().size() > 0)
3447 List<Feature> features = jseq.getFeatures();
3448 for (int f = 0; f < features.size(); f++)
3450 Feature feat = features.get(f);
3451 SequenceFeature sf = new SequenceFeature(feat.getType(),
3452 feat.getDescription(), feat.getBegin(), feat.getEnd(),
3453 safeFloat(feat.getScore()), feat.getFeatureGroup());
3454 sf.setStatus(feat.getStatus());
3457 * load any feature attributes - include map-valued attributes
3459 Map<String, Map<String, String>> mapAttributes = new HashMap<>();
3460 for (int od = 0; od < feat.getOtherData().size(); od++)
3462 OtherData keyValue = feat.getOtherData().get(od);
3463 String attributeName = keyValue.getKey();
3464 String attributeValue = keyValue.getValue();
3465 if (attributeName.startsWith("LINK"))
3467 sf.addLink(attributeValue);
3471 String subAttribute = keyValue.getKey2();
3472 if (subAttribute == null)
3474 // simple string-valued attribute
3475 sf.setValue(attributeName, attributeValue);
3479 // attribute 'key' has sub-attribute 'key2'
3480 if (!mapAttributes.containsKey(attributeName))
3482 mapAttributes.put(attributeName, new HashMap<>());
3484 mapAttributes.get(attributeName).put(subAttribute,
3489 for (Entry<String, Map<String, String>> mapAttribute : mapAttributes
3492 sf.setValue(mapAttribute.getKey(), mapAttribute.getValue());
3495 // adds feature to datasequence's feature set (since Jalview 2.10)
3496 al.getSequenceAt(i).addSequenceFeature(sf);
3499 if (vamsasSeqs.get(i).getDBRef().size() > 0)
3501 // adds dbrefs to datasequence's set (since Jalview 2.10)
3503 al.getSequenceAt(i).getDatasetSequence() == null
3504 ? al.getSequenceAt(i)
3505 : al.getSequenceAt(i).getDatasetSequence(),
3508 if (jseq.getPdbids().size() > 0)
3510 List<Pdbids> ids = jseq.getPdbids();
3511 for (int p = 0; p < ids.size(); p++)
3513 Pdbids pdbid = ids.get(p);
3514 jalview.datamodel.PDBEntry entry = new jalview.datamodel.PDBEntry();
3515 entry.setId(pdbid.getId());
3516 if (pdbid.getType() != null)
3518 if (PDBEntry.Type.getType(pdbid.getType()) != null)
3520 entry.setType(PDBEntry.Type.getType(pdbid.getType()));
3524 entry.setType(PDBEntry.Type.FILE);
3527 // jprovider is null when executing 'New View'
3528 if (pdbid.getFile() != null && jprovider != null)
3530 if (!pdbloaded.containsKey(pdbid.getFile()))
3532 entry.setFile(loadPDBFile(jprovider, pdbid.getId(),
3537 entry.setFile(pdbloaded.get(pdbid.getId()).toString());
3541 if (pdbid.getPdbentryItem() != null)
3543 for (PdbentryItem item : pdbid.getPdbentryItem())
3545 for (Property pr : item.getProperty())
3547 entry.setProperty(pr.getName(), pr.getValue());
3552 for (Property prop : pdbid.getProperty())
3554 entry.setProperty(prop.getName(), prop.getValue());
3556 StructureSelectionManager
3557 .getStructureSelectionManager(Desktop.instance)
3558 .registerPDBEntry(entry);
3559 // adds PDBEntry to datasequence's set (since Jalview 2.10)
3560 if (al.getSequenceAt(i).getDatasetSequence() != null)
3562 al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
3566 al.getSequenceAt(i).addPDBId(entry);
3571 } // end !multipleview
3573 // ///////////////////////////////
3574 // LOAD SEQUENCE MAPPINGS
3576 if (vamsasSet.getAlcodonFrame().size() > 0)
3578 // TODO Potentially this should only be done once for all views of an
3580 List<AlcodonFrame> alc = vamsasSet.getAlcodonFrame();
3581 for (int i = 0; i < alc.size(); i++)
3583 AlignedCodonFrame cf = new AlignedCodonFrame();
3584 if (alc.get(i).getAlcodMap().size() > 0)
3586 List<AlcodMap> maps = alc.get(i).getAlcodMap();
3587 for (int m = 0; m < maps.size(); m++)
3589 AlcodMap map = maps.get(m);
3590 SequenceI dnaseq = seqRefIds.get(map.getDnasq());
3592 jalview.datamodel.Mapping mapping = null;
3593 // attach to dna sequence reference.
3594 if (map.getMapping() != null)
3596 mapping = addMapping(map.getMapping());
3597 if (dnaseq != null && mapping.getTo() != null)
3599 cf.addMap(dnaseq, mapping.getTo(), mapping.getMap());
3605 newAlcodMapRef(map.getDnasq(), cf, mapping));
3609 al.addCodonFrame(cf);
3614 // ////////////////////////////////
3616 List<JvAnnotRow> autoAlan = new ArrayList<>();
3619 * store any annotations which forward reference a group's ID
3621 Map<String, List<AlignmentAnnotation>> groupAnnotRefs = new Hashtable<>();
3623 if (vamsasSet.getAnnotation().size()/*Count()*/ > 0)
3625 List<Annotation> an = vamsasSet.getAnnotation();
3627 for (int i = 0; i < an.size(); i++)
3629 Annotation annotation = an.get(i);
3632 * test if annotation is automatically calculated for this view only
3634 boolean autoForView = false;
3635 if (annotation.getLabel().equals("Quality")
3636 || annotation.getLabel().equals("Conservation")
3637 || annotation.getLabel().equals("Consensus"))
3639 // Kludge for pre 2.5 projects which lacked the autocalculated flag
3641 // JAXB has no has() test; schema defaults value to false
3642 // if (!annotation.hasAutoCalculated())
3644 // annotation.setAutoCalculated(true);
3647 if (autoForView || annotation.isAutoCalculated())
3649 // remove ID - we don't recover annotation from other views for
3650 // view-specific annotation
3651 annotation.setId(null);
3654 // set visibility for other annotation in this view
3655 String annotationId = annotation.getId();
3656 if (annotationId != null && annotationIds.containsKey(annotationId))
3658 AlignmentAnnotation jda = annotationIds.get(annotationId);
3659 // in principle Visible should always be true for annotation displayed
3660 // in multiple views
3661 if (annotation.isVisible() != null)
3663 jda.visible = annotation.isVisible();
3666 al.addAnnotation(jda);
3670 // Construct new annotation from model.
3671 List<AnnotationElement> ae = annotation.getAnnotationElement();
3672 jalview.datamodel.Annotation[] anot = null;
3673 java.awt.Color firstColour = null;
3675 if (!annotation.isScoreOnly())
3677 anot = new jalview.datamodel.Annotation[al.getWidth()];
3678 for (int aa = 0; aa < ae.size() && aa < anot.length; aa++)
3680 AnnotationElement annElement = ae.get(aa);
3681 anpos = annElement.getPosition();
3683 if (anpos >= anot.length)
3688 float value = safeFloat(annElement.getValue());
3689 anot[anpos] = new jalview.datamodel.Annotation(
3690 annElement.getDisplayCharacter(),
3691 annElement.getDescription(),
3692 (annElement.getSecondaryStructure() == null
3693 || annElement.getSecondaryStructure()
3697 .getSecondaryStructure()
3700 anot[anpos].colour = new Color(safeInt(annElement.getColour()));
3701 if (firstColour == null)
3703 firstColour = anot[anpos].colour;
3707 jalview.datamodel.AlignmentAnnotation jaa = null;
3709 if (annotation.isGraph())
3711 float llim = 0, hlim = 0;
3712 // if (autoForView || an[i].isAutoCalculated()) {
3715 jaa = new jalview.datamodel.AlignmentAnnotation(
3716 annotation.getLabel(), annotation.getDescription(), anot,
3717 llim, hlim, safeInt(annotation.getGraphType()));
3719 jaa.graphGroup = safeInt(annotation.getGraphGroup());
3720 jaa._linecolour = firstColour;
3721 if (annotation.getThresholdLine() != null)
3723 jaa.setThreshold(new jalview.datamodel.GraphLine(
3724 safeFloat(annotation.getThresholdLine().getValue()),
3725 annotation.getThresholdLine().getLabel(),
3726 new java.awt.Color(safeInt(
3727 annotation.getThresholdLine().getColour()))));
3729 if (autoForView || annotation.isAutoCalculated())
3731 // Hardwire the symbol display line to ensure that labels for
3732 // histograms are displayed
3738 jaa = new jalview.datamodel.AlignmentAnnotation(
3739 annotation.getLabel(), annotation.getDescription(), anot);
3740 jaa._linecolour = firstColour;
3742 // register new annotation
3743 if (annotation.getId() != null)
3745 annotationIds.put(annotation.getId(), jaa);
3746 jaa.annotationId = annotation.getId();
3748 // recover sequence association
3749 String sequenceRef = annotation.getSequenceRef();
3750 if (sequenceRef != null)
3752 // from 2.9 sequenceRef is to sequence id (JAL-1781)
3753 SequenceI sequence = seqRefIds.get(sequenceRef);
3754 if (sequence == null)
3756 // in pre-2.9 projects sequence ref is to sequence name
3757 sequence = al.findName(sequenceRef);
3759 if (sequence != null)
3761 jaa.createSequenceMapping(sequence, 1, true);
3762 sequence.addAlignmentAnnotation(jaa);
3765 // and make a note of any group association
3766 if (annotation.getGroupRef() != null
3767 && annotation.getGroupRef().length() > 0)
3769 List<jalview.datamodel.AlignmentAnnotation> aal = groupAnnotRefs
3770 .get(annotation.getGroupRef());
3773 aal = new ArrayList<>();
3774 groupAnnotRefs.put(annotation.getGroupRef(), aal);
3779 if (annotation.getScore() != null)
3781 jaa.setScore(annotation.getScore().doubleValue());
3783 if (annotation.isVisible() != null)
3785 jaa.visible = annotation.isVisible().booleanValue();
3788 if (annotation.isCentreColLabels() != null)
3790 jaa.centreColLabels = annotation.isCentreColLabels()
3794 if (annotation.isScaleColLabels() != null)
3796 jaa.scaleColLabel = annotation.isScaleColLabels().booleanValue();
3798 if (annotation.isAutoCalculated())
3800 // newer files have an 'autoCalculated' flag and store calculation
3801 // state in viewport properties
3802 jaa.autoCalculated = true; // means annotation will be marked for
3803 // update at end of load.
3805 if (annotation.getGraphHeight() != null)
3807 jaa.graphHeight = annotation.getGraphHeight().intValue();
3809 jaa.belowAlignment = annotation.isBelowAlignment();
3810 jaa.setCalcId(annotation.getCalcId());
3811 if (annotation.getProperty().size() > 0)
3813 for (Annotation.Property prop : annotation
3816 jaa.setProperty(prop.getName(), prop.getValue());
3819 if (jaa.autoCalculated)
3821 autoAlan.add(new JvAnnotRow(i, jaa));
3824 // if (!autoForView)
3826 // add autocalculated group annotation and any user created annotation
3828 al.addAnnotation(jaa);
3832 // ///////////////////////
3834 // Create alignment markup and styles for this view
3835 if (jalviewModel.getJGroup().size() > 0)
3837 List<JGroup> groups = jalviewModel.getJGroup();
3838 boolean addAnnotSchemeGroup = false;
3839 for (int i = 0; i < groups.size(); i++)
3841 JGroup jGroup = groups.get(i);
3842 ColourSchemeI cs = null;
3843 if (jGroup.getColour() != null)
3845 if (jGroup.getColour().startsWith("ucs"))
3847 cs = getUserColourScheme(jalviewModel, jGroup.getColour());
3849 else if (jGroup.getColour().equals("AnnotationColourGradient")
3850 && jGroup.getAnnotationColours() != null)
3852 addAnnotSchemeGroup = true;
3856 cs = ColourSchemeProperty.getColourScheme(al,
3857 jGroup.getColour());
3860 int pidThreshold = safeInt(jGroup.getPidThreshold());
3862 Vector<SequenceI> seqs = new Vector<>();
3864 for (int s = 0; s < jGroup.getSeq().size(); s++)
3866 String seqId = jGroup.getSeq().get(s);
3867 SequenceI ts = seqRefIds.get(seqId);
3871 seqs.addElement(ts);
3875 if (seqs.size() < 1)
3880 SequenceGroup sg = new SequenceGroup(seqs, jGroup.getName(), cs,
3881 safeBoolean(jGroup.isDisplayBoxes()),
3882 safeBoolean(jGroup.isDisplayText()),
3883 safeBoolean(jGroup.isColourText()),
3884 safeInt(jGroup.getStart()), safeInt(jGroup.getEnd()));
3885 sg.getGroupColourScheme().setThreshold(pidThreshold, true);
3886 sg.getGroupColourScheme()
3887 .setConservationInc(safeInt(jGroup.getConsThreshold()));
3888 sg.setOutlineColour(new Color(safeInt(jGroup.getOutlineColour())));
3890 sg.textColour = new Color(safeInt(jGroup.getTextCol1()));
3891 sg.textColour2 = new Color(safeInt(jGroup.getTextCol2()));
3892 sg.setShowNonconserved(safeBoolean(jGroup.isShowUnconserved()));
3893 sg.thresholdTextColour = safeInt(jGroup.getTextColThreshold());
3894 // attributes with a default in the schema are never null
3895 sg.setShowConsensusHistogram(jGroup.isShowConsensusHistogram());
3896 sg.setshowSequenceLogo(jGroup.isShowSequenceLogo());
3897 sg.setNormaliseSequenceLogo(jGroup.isNormaliseSequenceLogo());
3898 sg.setIgnoreGapsConsensus(jGroup.isIgnoreGapsinConsensus());
3899 if (jGroup.getConsThreshold() != null
3900 && jGroup.getConsThreshold().intValue() != 0)
3902 Conservation c = new Conservation("All", sg.getSequences(null), 0,
3905 c.verdict(false, 25);
3906 sg.cs.setConservation(c);
3909 if (jGroup.getId() != null && groupAnnotRefs.size() > 0)
3911 // re-instate unique group/annotation row reference
3912 List<AlignmentAnnotation> jaal = groupAnnotRefs
3913 .get(jGroup.getId());
3916 for (AlignmentAnnotation jaa : jaal)
3919 if (jaa.autoCalculated)
3921 // match up and try to set group autocalc alignment row for this
3923 if (jaa.label.startsWith("Consensus for "))
3925 sg.setConsensus(jaa);
3927 // match up and try to set group autocalc alignment row for this
3929 if (jaa.label.startsWith("Conservation for "))
3931 sg.setConservationRow(jaa);
3938 if (addAnnotSchemeGroup)
3940 // reconstruct the annotation colourscheme
3941 sg.setColourScheme(constructAnnotationColour(
3942 jGroup.getAnnotationColours(), null, al, jalviewModel, false));
3948 // only dataset in this model, so just return.
3951 // ///////////////////////////////
3954 AlignFrame af = null;
3955 AlignViewport av = null;
3956 // now check to see if we really need to create a new viewport.
3957 if (multipleView && viewportsAdded.size() == 0)
3959 // We recovered an alignment for which a viewport already exists.
3960 // TODO: fix up any settings necessary for overlaying stored state onto
3961 // state recovered from another document. (may not be necessary).
3962 // we may need a binding from a viewport in memory to one recovered from
3964 // and then recover its containing af to allow the settings to be applied.
3965 // TODO: fix for vamsas demo
3967 "About to recover a viewport for existing alignment: Sequence set ID is "
3969 Object seqsetobj = retrieveExistingObj(uniqueSeqSetId);
3970 if (seqsetobj != null)
3972 if (seqsetobj instanceof String)
3974 uniqueSeqSetId = (String) seqsetobj;
3976 "Recovered extant sequence set ID mapping for ID : New Sequence set ID is "
3982 "Warning : Collision between sequence set ID string and existing jalview object mapping.");
3988 * indicate that annotation colours are applied across all groups (pre
3989 * Jalview 2.8.1 behaviour)
3991 boolean doGroupAnnColour = Jalview2XML.isVersionStringLaterThan("2.8.1",
3992 jalviewModel.getVersion());
3994 AlignmentPanel ap = null;
3995 boolean isnewview = true;
3998 // Check to see if this alignment already has a view id == viewId
3999 jalview.gui.AlignmentPanel views[] = Desktop
4000 .getAlignmentPanels(uniqueSeqSetId);
4001 if (views != null && views.length > 0)
4003 for (int v = 0; v < views.length; v++)
4005 if (views[v].av.getViewId().equalsIgnoreCase(viewId))
4007 // recover the existing alignpanel, alignframe, viewport
4008 af = views[v].alignFrame;
4011 // TODO: could even skip resetting view settings if we don't want to
4012 // change the local settings from other jalview processes
4021 af = loadViewport(file, jseqs, hiddenSeqs, al, jalviewModel, view,
4022 uniqueSeqSetId, viewId, autoAlan);
4023 av = af.getViewport();
4028 * Load any trees, PDB structures and viewers
4030 * Not done if flag is false (when this method is used for New View)
4032 if (loadTreesAndStructures)
4034 loadTrees(jalviewModel, view, af, av, ap);
4035 loadPCAViewers(jalviewModel, ap);
4036 loadPDBStructures(jprovider, jseqs, af, ap);
4037 loadRnaViewers(jprovider, jseqs, ap);
4039 // and finally return.
4044 * Instantiate and link any saved RNA (Varna) viewers. The state of the Varna
4045 * panel is restored from separate jar entries, two (gapped and trimmed) per
4046 * sequence and secondary structure.
4048 * Currently each viewer shows just one sequence and structure (gapped and
4049 * trimmed), however this method is designed to support multiple sequences or
4050 * structures in viewers if wanted in future.
4056 private void loadRnaViewers(jarInputStreamProvider jprovider,
4057 List<JSeq> jseqs, AlignmentPanel ap)
4060 * scan the sequences for references to viewers; create each one the first
4061 * time it is referenced, add Rna models to existing viewers
4063 for (JSeq jseq : jseqs)
4065 for (int i = 0; i < jseq.getRnaViewer().size(); i++)
4067 RnaViewer viewer = jseq.getRnaViewer().get(i);
4068 AppVarna appVarna = findOrCreateVarnaViewer(viewer, uniqueSetSuffix,
4071 for (int j = 0; j < viewer.getSecondaryStructure().size(); j++)
4073 SecondaryStructure ss = viewer.getSecondaryStructure().get(j);
4074 SequenceI seq = seqRefIds.get(jseq.getId());
4075 AlignmentAnnotation ann = this.annotationIds
4076 .get(ss.getAnnotationId());
4079 * add the structure to the Varna display (with session state copied
4080 * from the jar to a temporary file)
4082 boolean gapped = safeBoolean(ss.isGapped());
4083 String rnaTitle = ss.getTitle();
4084 String sessionState = ss.getViewerState();
4085 String tempStateFile = copyJarEntry(jprovider, sessionState,
4087 RnaModel rna = new RnaModel(rnaTitle, ann, seq, null, gapped);
4088 appVarna.addModelSession(rna, rnaTitle, tempStateFile);
4090 appVarna.setInitialSelection(safeInt(viewer.getSelectedRna()));
4096 * Locate and return an already instantiated matching AppVarna, or create one
4100 * @param viewIdSuffix
4104 protected AppVarna findOrCreateVarnaViewer(RnaViewer viewer,
4105 String viewIdSuffix, AlignmentPanel ap)
4108 * on each load a suffix is appended to the saved viewId, to avoid conflicts
4109 * if load is repeated
4111 String postLoadId = viewer.getViewId() + viewIdSuffix;
4112 for (JInternalFrame frame : getAllFrames())
4114 if (frame instanceof AppVarna)
4116 AppVarna varna = (AppVarna) frame;
4117 if (postLoadId.equals(varna.getViewId()))
4119 // this viewer is already instantiated
4120 // could in future here add ap as another 'parent' of the
4121 // AppVarna window; currently just 1-to-many
4128 * viewer not found - make it
4130 RnaViewerModel model = new RnaViewerModel(postLoadId, viewer.getTitle(),
4131 safeInt(viewer.getXpos()), safeInt(viewer.getYpos()),
4132 safeInt(viewer.getWidth()), safeInt(viewer.getHeight()),
4133 safeInt(viewer.getDividerLocation()));
4134 AppVarna varna = new AppVarna(model, ap);
4140 * Load any saved trees
4148 protected void loadTrees(JalviewModel jm, Viewport view,
4149 AlignFrame af, AlignViewport av, AlignmentPanel ap)
4151 // TODO result of automated refactoring - are all these parameters needed?
4154 for (int t = 0; t < jm.getTree().size(); t++)
4157 Tree tree = jm.getTree().get(t);
4159 TreePanel tp = (TreePanel) retrieveExistingObj(tree.getId());
4162 tp = af.showNewickTree(new NewickFile(tree.getNewick()),
4163 tree.getTitle(), safeInt(tree.getWidth()),
4164 safeInt(tree.getHeight()), safeInt(tree.getXpos()),
4165 safeInt(tree.getYpos()));
4166 if (tree.getId() != null)
4168 // perhaps bind the tree id to something ?
4173 // update local tree attributes ?
4174 // TODO: should check if tp has been manipulated by user - if so its
4175 // settings shouldn't be modified
4176 tp.setTitle(tree.getTitle());
4177 tp.setBounds(new Rectangle(safeInt(tree.getXpos()),
4178 safeInt(tree.getYpos()), safeInt(tree.getWidth()),
4179 safeInt(tree.getHeight())));
4180 tp.setViewport(av); // af.viewport;
4181 // TODO: verify 'associate with all views' works still
4182 tp.getTreeCanvas().setViewport(av); // af.viewport;
4183 tp.getTreeCanvas().setAssociatedPanel(ap); // af.alignPanel;
4184 // FIXME: should we use safeBoolean here ?
4185 tp.getTreeCanvas().setApplyToAllViews(tree.isLinkToAllViews());
4190 warn("There was a problem recovering stored Newick tree: \n"
4191 + tree.getNewick());
4195 tp.fitToWindow.setState(safeBoolean(tree.isFitToWindow()));
4196 tp.fitToWindow_actionPerformed(null);
4198 if (tree.getFontName() != null)
4201 new Font(tree.getFontName(), safeInt(tree.getFontStyle()),
4202 safeInt(tree.getFontSize())));
4207 new Font(view.getFontName(), safeInt(view.getFontStyle()),
4208 safeInt(view.getFontSize())));
4211 tp.showPlaceholders(safeBoolean(tree.isMarkUnlinked()));
4212 tp.showBootstrap(safeBoolean(tree.isShowBootstrap()));
4213 tp.showDistances(safeBoolean(tree.isShowDistances()));
4215 tp.getTreeCanvas().setThreshold(safeFloat(tree.getThreshold()));
4217 if (safeBoolean(tree.isCurrentTree()))
4219 af.getViewport().setCurrentTree(tp.getTree());
4223 } catch (Exception ex)
4225 ex.printStackTrace();
4230 * Load and link any saved structure viewers.
4237 protected void loadPDBStructures(jarInputStreamProvider jprovider,
4238 List<JSeq> jseqs, AlignFrame af, AlignmentPanel ap)
4241 * Run through all PDB ids on the alignment, and collect mappings between
4242 * distinct view ids and all sequences referring to that view.
4244 Map<String, StructureViewerModel> structureViewers = new LinkedHashMap<>();
4246 for (int i = 0; i < jseqs.size(); i++)
4248 JSeq jseq = jseqs.get(i);
4249 if (jseq.getPdbids().size() > 0)
4251 List<Pdbids> ids = jseq.getPdbids();
4252 for (int p = 0; p < ids.size(); p++)
4254 Pdbids pdbid = ids.get(p);
4255 final int structureStateCount = pdbid.getStructureState().size();
4256 for (int s = 0; s < structureStateCount; s++)
4258 // check to see if we haven't already created this structure view
4259 final StructureState structureState = pdbid
4260 .getStructureState().get(s);
4261 String sviewid = (structureState.getViewId() == null) ? null
4262 : structureState.getViewId() + uniqueSetSuffix;
4263 jalview.datamodel.PDBEntry jpdb = new jalview.datamodel.PDBEntry();
4264 // Originally : pdbid.getFile()
4265 // : TODO: verify external PDB file recovery still works in normal
4266 // jalview project load
4268 loadPDBFile(jprovider, pdbid.getId(), pdbid.getFile()));
4269 jpdb.setId(pdbid.getId());
4271 int x = safeInt(structureState.getXpos());
4272 int y = safeInt(structureState.getYpos());
4273 int width = safeInt(structureState.getWidth());
4274 int height = safeInt(structureState.getHeight());
4276 // Probably don't need to do this anymore...
4277 // Desktop.desktop.getComponentAt(x, y);
4278 // TODO: NOW: check that this recovers the PDB file correctly.
4279 String pdbFile = loadPDBFile(jprovider, pdbid.getId(),
4281 jalview.datamodel.SequenceI seq = seqRefIds
4282 .get(jseq.getId() + "");
4283 if (sviewid == null)
4285 sviewid = "_jalview_pre2_4_" + x + "," + y + "," + width + ","
4288 if (!structureViewers.containsKey(sviewid))
4290 structureViewers.put(sviewid,
4291 new StructureViewerModel(x, y, width, height, false,
4292 false, true, structureState.getViewId(),
4293 structureState.getType()));
4294 // Legacy pre-2.7 conversion JAL-823 :
4295 // do not assume any view has to be linked for colour by
4299 // assemble String[] { pdb files }, String[] { id for each
4300 // file }, orig_fileloc, SequenceI[][] {{ seqs_file 1 }, {
4301 // seqs_file 2}, boolean[] {
4302 // linkAlignPanel,superposeWithAlignpanel}} from hash
4303 StructureViewerModel jmoldat = structureViewers.get(sviewid);
4304 jmoldat.setAlignWithPanel(jmoldat.isAlignWithPanel()
4305 || structureState.isAlignwithAlignPanel());
4308 * Default colour by linked panel to false if not specified (e.g.
4309 * for pre-2.7 projects)
4311 boolean colourWithAlignPanel = jmoldat.isColourWithAlignPanel();
4312 colourWithAlignPanel |= structureState.isColourwithAlignPanel();
4313 jmoldat.setColourWithAlignPanel(colourWithAlignPanel);
4316 * Default colour by viewer to true if not specified (e.g. for
4319 boolean colourByViewer = jmoldat.isColourByViewer();
4320 colourByViewer &= structureState.isColourByJmol();
4321 jmoldat.setColourByViewer(colourByViewer);
4323 if (jmoldat.getStateData().length() < structureState
4324 .getValue()/*Content()*/.length())
4326 jmoldat.setStateData(structureState.getValue());// Content());
4328 if (pdbid.getFile() != null)
4330 File mapkey = new File(pdbid.getFile());
4331 StructureData seqstrmaps = jmoldat.getFileData().get(mapkey);
4332 if (seqstrmaps == null)
4334 jmoldat.getFileData().put(mapkey,
4335 seqstrmaps = jmoldat.new StructureData(pdbFile,
4338 if (!seqstrmaps.getSeqList().contains(seq))
4340 seqstrmaps.getSeqList().add(seq);
4346 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");
4353 // Instantiate the associated structure views
4354 for (Entry<String, StructureViewerModel> entry : structureViewers
4359 createOrLinkStructureViewer(entry, af, ap, jprovider);
4360 } catch (Exception e)
4363 "Error loading structure viewer: " + e.getMessage());
4364 // failed - try the next one
4376 protected void createOrLinkStructureViewer(
4377 Entry<String, StructureViewerModel> viewerData, AlignFrame af,
4378 AlignmentPanel ap, jarInputStreamProvider jprovider)
4380 final StructureViewerModel stateData = viewerData.getValue();
4383 * Search for any viewer windows already open from other alignment views
4384 * that exactly match the stored structure state
4386 StructureViewerBase comp = findMatchingViewer(viewerData);
4390 linkStructureViewer(ap, comp, stateData);
4395 * From 2.9: stateData.type contains JMOL or CHIMERA, data is in jar entry
4396 * "viewer_"+stateData.viewId
4398 if (ViewerType.CHIMERA.toString().equals(stateData.getType()))
4400 createChimeraViewer(viewerData, af, jprovider);
4405 * else Jmol (if pre-2.9, stateData contains JMOL state string)
4407 createJmolViewer(viewerData, af, jprovider);
4412 * Create a new Chimera viewer.
4418 protected void createChimeraViewer(
4419 Entry<String, StructureViewerModel> viewerData, AlignFrame af,
4420 jarInputStreamProvider jprovider)
4422 StructureViewerModel data = viewerData.getValue();
4423 String chimeraSessionFile = data.getStateData();
4426 * Copy Chimera session from jar entry "viewer_"+viewId to a temporary file
4428 * NB this is the 'saved' viewId as in the project file XML, _not_ the
4429 * 'uniquified' sviewid used to reconstruct the viewer here
4431 String viewerJarEntryName = getViewerJarEntryName(data.getViewId());
4432 chimeraSessionFile = copyJarEntry(jprovider, viewerJarEntryName,
4435 Set<Entry<File, StructureData>> fileData = data.getFileData()
4437 List<PDBEntry> pdbs = new ArrayList<>();
4438 List<SequenceI[]> allseqs = new ArrayList<>();
4439 for (Entry<File, StructureData> pdb : fileData)
4441 String filePath = pdb.getValue().getFilePath();
4442 String pdbId = pdb.getValue().getPdbId();
4443 // pdbs.add(new PDBEntry(filePath, pdbId));
4444 pdbs.add(new PDBEntry(pdbId, null, PDBEntry.Type.PDB, filePath));
4445 final List<SequenceI> seqList = pdb.getValue().getSeqList();
4446 SequenceI[] seqs = seqList.toArray(new SequenceI[seqList.size()]);
4450 boolean colourByChimera = data.isColourByViewer();
4451 boolean colourBySequence = data.isColourWithAlignPanel();
4453 // TODO use StructureViewer as a factory here, see JAL-1761
4454 final PDBEntry[] pdbArray = pdbs.toArray(new PDBEntry[pdbs.size()]);
4455 final SequenceI[][] seqsArray = allseqs
4456 .toArray(new SequenceI[allseqs.size()][]);
4457 String newViewId = viewerData.getKey();
4459 ChimeraViewFrame cvf = new ChimeraViewFrame(chimeraSessionFile,
4460 af.alignPanel, pdbArray, seqsArray, colourByChimera,
4461 colourBySequence, newViewId);
4462 cvf.setSize(data.getWidth(), data.getHeight());
4463 cvf.setLocation(data.getX(), data.getY());
4467 * Create a new Jmol window. First parse the Jmol state to translate filenames
4468 * loaded into the view, and record the order in which files are shown in the
4469 * Jmol view, so we can add the sequence mappings in same order.
4475 protected void createJmolViewer(
4476 final Entry<String, StructureViewerModel> viewerData,
4477 AlignFrame af, jarInputStreamProvider jprovider)
4479 final StructureViewerModel svattrib = viewerData.getValue();
4480 String state = svattrib.getStateData();
4483 * Pre-2.9: state element value is the Jmol state string
4485 * 2.9+: @type is "JMOL", state data is in a Jar file member named "viewer_"
4488 if (ViewerType.JMOL.toString().equals(svattrib.getType()))
4490 state = readJarEntry(jprovider,
4491 getViewerJarEntryName(svattrib.getViewId()));
4494 List<String> pdbfilenames = new ArrayList<>();
4495 List<SequenceI[]> seqmaps = new ArrayList<>();
4496 List<String> pdbids = new ArrayList<>();
4497 StringBuilder newFileLoc = new StringBuilder(64);
4498 int cp = 0, ncp, ecp;
4499 Map<File, StructureData> oldFiles = svattrib.getFileData();
4500 while ((ncp = state.indexOf("load ", cp)) > -1)
4504 // look for next filename in load statement
4505 newFileLoc.append(state.substring(cp,
4506 ncp = (state.indexOf("\"", ncp + 1) + 1)));
4507 String oldfilenam = state.substring(ncp,
4508 ecp = state.indexOf("\"", ncp));
4509 // recover the new mapping data for this old filename
4510 // have to normalize filename - since Jmol and jalview do
4512 // translation differently.
4513 StructureData filedat = oldFiles.get(new File(oldfilenam));
4514 if (filedat == null)
4516 String reformatedOldFilename = oldfilenam.replaceAll("/", "\\\\");
4517 filedat = oldFiles.get(new File(reformatedOldFilename));
4519 newFileLoc.append(Platform.escapeString(filedat.getFilePath()));
4520 pdbfilenames.add(filedat.getFilePath());
4521 pdbids.add(filedat.getPdbId());
4522 seqmaps.add(filedat.getSeqList().toArray(new SequenceI[0]));
4523 newFileLoc.append("\"");
4524 cp = ecp + 1; // advance beyond last \" and set cursor so we can
4525 // look for next file statement.
4526 } while ((ncp = state.indexOf("/*file*/", cp)) > -1);
4530 // just append rest of state
4531 newFileLoc.append(state.substring(cp));
4535 System.err.print("Ignoring incomplete Jmol state for PDB ids: ");
4536 newFileLoc = new StringBuilder(state);
4537 newFileLoc.append("; load append ");
4538 for (File id : oldFiles.keySet())
4540 // add this and any other pdb files that should be present in
4542 StructureData filedat = oldFiles.get(id);
4543 newFileLoc.append(filedat.getFilePath());
4544 pdbfilenames.add(filedat.getFilePath());
4545 pdbids.add(filedat.getPdbId());
4546 seqmaps.add(filedat.getSeqList().toArray(new SequenceI[0]));
4547 newFileLoc.append(" \"");
4548 newFileLoc.append(filedat.getFilePath());
4549 newFileLoc.append("\"");
4552 newFileLoc.append(";");
4555 if (newFileLoc.length() == 0)
4559 int histbug = newFileLoc.indexOf("history = ");
4563 * change "history = [true|false];" to "history = [1|0];"
4566 int diff = histbug == -1 ? -1 : newFileLoc.indexOf(";", histbug);
4567 String val = (diff == -1) ? null
4568 : newFileLoc.substring(histbug, diff);
4569 if (val != null && val.length() >= 4)
4571 if (val.contains("e")) // eh? what can it be?
4573 if (val.trim().equals("true"))
4581 newFileLoc.replace(histbug, diff, val);
4586 final String[] pdbf = pdbfilenames
4587 .toArray(new String[pdbfilenames.size()]);
4588 final String[] id = pdbids.toArray(new String[pdbids.size()]);
4589 final SequenceI[][] sq = seqmaps
4590 .toArray(new SequenceI[seqmaps.size()][]);
4591 final String fileloc = newFileLoc.toString();
4592 final String sviewid = viewerData.getKey();
4593 final AlignFrame alf = af;
4594 final Rectangle rect = new Rectangle(svattrib.getX(), svattrib.getY(),
4595 svattrib.getWidth(), svattrib.getHeight());
4598 javax.swing.SwingUtilities.invokeAndWait(new Runnable()
4603 JalviewStructureDisplayI sview = null;
4606 sview = new StructureViewer(
4607 alf.alignPanel.getStructureSelectionManager())
4608 .createView(StructureViewer.ViewerType.JMOL,
4609 pdbf, id, sq, alf.alignPanel, svattrib,
4610 fileloc, rect, sviewid);
4611 addNewStructureViewer(sview);
4612 } catch (OutOfMemoryError ex)
4614 new OOMWarning("restoring structure view for PDB id " + id,
4615 (OutOfMemoryError) ex.getCause());
4616 if (sview != null && sview.isVisible())
4618 sview.closeViewer(false);
4619 sview.setVisible(false);
4625 } catch (InvocationTargetException ex)
4627 warn("Unexpected error when opening Jmol view.", ex);
4629 } catch (InterruptedException e)
4631 // e.printStackTrace();
4637 * Generates a name for the entry in the project jar file to hold state
4638 * information for a structure viewer
4643 protected String getViewerJarEntryName(String viewId)
4645 return VIEWER_PREFIX + viewId;
4649 * Returns any open frame that matches given structure viewer data. The match
4650 * is based on the unique viewId, or (for older project versions) the frame's
4656 protected StructureViewerBase findMatchingViewer(
4657 Entry<String, StructureViewerModel> viewerData)
4659 final String sviewid = viewerData.getKey();
4660 final StructureViewerModel svattrib = viewerData.getValue();
4661 StructureViewerBase comp = null;
4662 JInternalFrame[] frames = getAllFrames();
4663 for (JInternalFrame frame : frames)
4665 if (frame instanceof StructureViewerBase)
4668 * Post jalview 2.4 schema includes structure view id
4670 if (sviewid != null && ((StructureViewerBase) frame).getViewId()
4673 comp = (StructureViewerBase) frame;
4674 break; // break added in 2.9
4677 * Otherwise test for matching position and size of viewer frame
4679 else if (frame.getX() == svattrib.getX()
4680 && frame.getY() == svattrib.getY()
4681 && frame.getHeight() == svattrib.getHeight()
4682 && frame.getWidth() == svattrib.getWidth())
4684 comp = (StructureViewerBase) frame;
4685 // no break in faint hope of an exact match on viewId
4693 * Link an AlignmentPanel to an existing structure viewer.
4698 * @param useinViewerSuperpos
4699 * @param usetoColourbyseq
4700 * @param viewerColouring
4702 protected void linkStructureViewer(AlignmentPanel ap,
4703 StructureViewerBase viewer, StructureViewerModel stateData)
4705 // NOTE: if the jalview project is part of a shared session then
4706 // view synchronization should/could be done here.
4708 final boolean useinViewerSuperpos = stateData.isAlignWithPanel();
4709 final boolean usetoColourbyseq = stateData.isColourWithAlignPanel();
4710 final boolean viewerColouring = stateData.isColourByViewer();
4711 Map<File, StructureData> oldFiles = stateData.getFileData();
4714 * Add mapping for sequences in this view to an already open viewer
4716 final AAStructureBindingModel binding = viewer.getBinding();
4717 for (File id : oldFiles.keySet())
4719 // add this and any other pdb files that should be present in the
4721 StructureData filedat = oldFiles.get(id);
4722 String pdbFile = filedat.getFilePath();
4723 SequenceI[] seq = filedat.getSeqList().toArray(new SequenceI[0]);
4724 binding.getSsm().setMapping(seq, null, pdbFile, DataSourceType.FILE,
4726 binding.addSequenceForStructFile(pdbFile, seq);
4728 // and add the AlignmentPanel's reference to the view panel
4729 viewer.addAlignmentPanel(ap);
4730 if (useinViewerSuperpos)
4732 viewer.useAlignmentPanelForSuperposition(ap);
4736 viewer.excludeAlignmentPanelForSuperposition(ap);
4738 if (usetoColourbyseq)
4740 viewer.useAlignmentPanelForColourbyseq(ap, !viewerColouring);
4744 viewer.excludeAlignmentPanelForColourbyseq(ap);
4749 * Get all frames within the Desktop.
4753 protected JInternalFrame[] getAllFrames()
4755 JInternalFrame[] frames = null;
4756 // TODO is this necessary - is it safe - risk of hanging?
4761 frames = Desktop.desktop.getAllFrames();
4762 } catch (ArrayIndexOutOfBoundsException e)
4764 // occasional No such child exceptions are thrown here...
4768 } catch (InterruptedException f)
4772 } while (frames == null);
4777 * Answers true if 'version' is equal to or later than 'supported', where each
4778 * is formatted as major/minor versions like "2.8.3" or "2.3.4b1" for bugfix
4779 * changes. Development and test values for 'version' are leniently treated
4783 * - minimum version we are comparing against
4785 * - version of data being processsed
4788 public static boolean isVersionStringLaterThan(String supported,
4791 if (supported == null || version == null
4792 || version.equalsIgnoreCase("DEVELOPMENT BUILD")
4793 || version.equalsIgnoreCase("Test")
4794 || version.equalsIgnoreCase("AUTOMATED BUILD"))
4796 System.err.println("Assuming project file with "
4797 + (version == null ? "null" : version)
4798 + " is compatible with Jalview version " + supported);
4803 return StringUtils.compareVersions(version, supported, "b") >= 0;
4807 Vector<JalviewStructureDisplayI> newStructureViewers = null;
4809 protected void addNewStructureViewer(JalviewStructureDisplayI sview)
4811 if (newStructureViewers != null)
4813 sview.getBinding().setFinishedLoadingFromArchive(false);
4814 newStructureViewers.add(sview);
4818 protected void setLoadingFinishedForNewStructureViewers()
4820 if (newStructureViewers != null)
4822 for (JalviewStructureDisplayI sview : newStructureViewers)
4824 sview.getBinding().setFinishedLoadingFromArchive(true);
4826 newStructureViewers.clear();
4827 newStructureViewers = null;
4831 AlignFrame loadViewport(String file, List<JSeq> JSEQ,
4832 List<SequenceI> hiddenSeqs, AlignmentI al,
4833 JalviewModel jm, Viewport view, String uniqueSeqSetId,
4834 String viewId, List<JvAnnotRow> autoAlan)
4836 AlignFrame af = null;
4837 af = new AlignFrame(al, safeInt(view.getWidth()),
4838 safeInt(view.getHeight()), uniqueSeqSetId, viewId);
4840 af.setFileName(file, FileFormat.Jalview);
4842 final AlignViewport viewport = af.getViewport();
4843 for (int i = 0; i < JSEQ.size(); i++)
4845 int colour = safeInt(JSEQ.get(i).getColour());
4846 viewport.setSequenceColour(viewport.getAlignment().getSequenceAt(i),
4852 viewport.setColourByReferenceSeq(true);
4853 viewport.setDisplayReferenceSeq(true);
4856 viewport.setGatherViewsHere(safeBoolean(view.isGatheredViews()));
4858 if (view.getSequenceSetId() != null)
4860 AlignmentViewport av = viewportsAdded.get(uniqueSeqSetId);
4862 viewport.setSequenceSetId(uniqueSeqSetId);
4865 // propagate shared settings to this new view
4866 viewport.setHistoryList(av.getHistoryList());
4867 viewport.setRedoList(av.getRedoList());
4871 viewportsAdded.put(uniqueSeqSetId, viewport);
4873 // TODO: check if this method can be called repeatedly without
4874 // side-effects if alignpanel already registered.
4875 PaintRefresher.Register(af.alignPanel, uniqueSeqSetId);
4877 // apply Hidden regions to view.
4878 if (hiddenSeqs != null)
4880 for (int s = 0; s < JSEQ.size(); s++)
4882 SequenceGroup hidden = new SequenceGroup();
4883 boolean isRepresentative = false;
4884 for (int r = 0; r < JSEQ.get(s).getHiddenSequences().size(); r++)
4886 isRepresentative = true;
4887 SequenceI sequenceToHide = al
4888 .getSequenceAt(JSEQ.get(s).getHiddenSequences().get(r));
4889 hidden.addSequence(sequenceToHide, false);
4890 // remove from hiddenSeqs list so we don't try to hide it twice
4891 hiddenSeqs.remove(sequenceToHide);
4893 if (isRepresentative)
4895 SequenceI representativeSequence = al.getSequenceAt(s);
4896 hidden.addSequence(representativeSequence, false);
4897 viewport.hideRepSequences(representativeSequence, hidden);
4901 SequenceI[] hseqs = hiddenSeqs
4902 .toArray(new SequenceI[hiddenSeqs.size()]);
4903 viewport.hideSequence(hseqs);
4906 // recover view properties and display parameters
4908 viewport.setShowAnnotation(safeBoolean(view.isShowAnnotation()));
4909 viewport.setAbovePIDThreshold(safeBoolean(view.isPidSelected()));
4910 final int pidThreshold = safeInt(view.getPidThreshold());
4911 viewport.setThreshold(pidThreshold);
4913 viewport.setColourText(safeBoolean(view.isShowColourText()));
4916 .setConservationSelected(
4917 safeBoolean(view.isConservationSelected()));
4918 viewport.setIncrement(safeInt(view.getConsThreshold()));
4919 viewport.setShowJVSuffix(safeBoolean(view.isShowFullId()));
4920 viewport.setRightAlignIds(safeBoolean(view.isRightAlignIds()));
4921 viewport.setFont(new Font(view.getFontName(),
4922 safeInt(view.getFontStyle()), safeInt(view.getFontSize())),
4924 ViewStyleI vs = viewport.getViewStyle();
4925 vs.setScaleProteinAsCdna(view.isScaleProteinAsCdna());
4926 viewport.setViewStyle(vs);
4927 // TODO: allow custom charWidth/Heights to be restored by updating them
4928 // after setting font - which means set above to false
4929 viewport.setRenderGaps(safeBoolean(view.isRenderGaps()));
4930 viewport.setWrapAlignment(safeBoolean(view.isWrapAlignment()));
4931 viewport.setShowAnnotation(safeBoolean(view.isShowAnnotation()));
4933 viewport.setShowBoxes(safeBoolean(view.isShowBoxes()));
4935 viewport.setShowText(safeBoolean(view.isShowText()));
4937 viewport.setTextColour(new Color(safeInt(view.getTextCol1())));
4938 viewport.setTextColour2(new Color(safeInt(view.getTextCol2())));
4939 viewport.setThresholdTextColour(safeInt(view.getTextColThreshold()));
4940 viewport.setShowUnconserved(view.isShowUnconserved());
4941 viewport.getRanges().setStartRes(safeInt(view.getStartRes()));
4943 if (view.getViewName() != null)
4945 viewport.setViewName(view.getViewName());
4946 af.setInitialTabVisible();
4948 af.setBounds(safeInt(view.getXpos()), safeInt(view.getYpos()),
4949 safeInt(view.getWidth()), safeInt(view.getHeight()));
4950 // startSeq set in af.alignPanel.updateLayout below
4951 af.alignPanel.updateLayout();
4952 ColourSchemeI cs = null;
4953 // apply colourschemes
4954 if (view.getBgColour() != null)
4956 if (view.getBgColour().startsWith("ucs"))
4958 cs = getUserColourScheme(jm, view.getBgColour());
4960 else if (view.getBgColour().startsWith("Annotation"))
4962 AnnotationColourScheme viewAnnColour = view.getAnnotationColours();
4963 cs = constructAnnotationColour(viewAnnColour, af, al, jm, true);
4970 cs = ColourSchemeProperty.getColourScheme(al, view.getBgColour());
4974 viewport.setGlobalColourScheme(cs);
4975 viewport.getResidueShading().setThreshold(pidThreshold,
4976 view.isIgnoreGapsinConsensus());
4977 viewport.getResidueShading()
4978 .setConsensus(viewport.getSequenceConsensusHash());
4979 viewport.setColourAppliesToAllGroups(false);
4981 if (safeBoolean(view.isConservationSelected()) && cs != null)
4983 viewport.getResidueShading()
4984 .setConservationInc(safeInt(view.getConsThreshold()));
4987 af.changeColour(cs);
4989 viewport.setColourAppliesToAllGroups(true);
4992 .setShowSequenceFeatures(
4993 safeBoolean(view.isShowSequenceFeatures()));
4995 viewport.setCentreColumnLabels(view.isCentreColumnLabels());
4996 viewport.setIgnoreGapsConsensus(view.isIgnoreGapsinConsensus(), null);
4997 viewport.setFollowHighlight(view.isFollowHighlight());
4998 viewport.followSelection = view.isFollowSelection();
4999 viewport.setShowConsensusHistogram(view.isShowConsensusHistogram());
5000 viewport.setShowSequenceLogo(view.isShowSequenceLogo());
5001 viewport.setNormaliseSequenceLogo(view.isNormaliseSequenceLogo());
5002 viewport.setShowDBRefs(safeBoolean(view.isShowDbRefTooltip()));
5003 viewport.setShowNPFeats(safeBoolean(view.isShowNPfeatureTooltip()));
5004 viewport.setShowGroupConsensus(view.isShowGroupConsensus());
5005 viewport.setShowGroupConservation(view.isShowGroupConservation());
5007 // recover feature settings
5008 if (jm.getFeatureSettings() != null)
5010 FeatureRendererModel fr = af.alignPanel.getSeqPanel().seqCanvas
5011 .getFeatureRenderer();
5012 FeaturesDisplayed fdi;
5013 viewport.setFeaturesDisplayed(fdi = new FeaturesDisplayed());
5014 String[] renderOrder = new String[jm.getFeatureSettings()
5015 .getSetting().size()];
5016 Map<String, FeatureColourI> featureColours = new Hashtable<>();
5017 Map<String, Float> featureOrder = new Hashtable<>();
5019 for (int fs = 0; fs < jm.getFeatureSettings()
5020 .getSetting().size(); fs++)
5022 Setting setting = jm.getFeatureSettings().getSetting().get(fs);
5023 String featureType = setting.getType();
5026 * restore feature filters (if any)
5028 jalview.xml.binding.jalview.FeatureMatcherSet filters = setting
5030 if (filters != null)
5032 FeatureMatcherSetI filter = Jalview2XML
5033 .parseFilter(featureType, filters);
5034 if (!filter.isEmpty())
5036 fr.setFeatureFilter(featureType, filter);
5041 * restore feature colour scheme
5043 Color maxColour = new Color(setting.getColour());
5044 if (setting.getMincolour() != null)
5047 * minColour is always set unless a simple colour
5048 * (including for colour by label though it doesn't use it)
5050 Color minColour = new Color(setting.getMincolour().intValue());
5051 Color noValueColour = minColour;
5052 NoValueColour noColour = setting.getNoValueColour();
5053 if (noColour == NoValueColour.NONE)
5055 noValueColour = null;
5057 else if (noColour == NoValueColour.MAX)
5059 noValueColour = maxColour;
5061 float min = safeFloat(safeFloat(setting.getMin()));
5062 float max = setting.getMax() == null ? 1f
5063 : setting.getMax().floatValue();
5064 FeatureColourI gc = new FeatureColour(minColour, maxColour,
5065 noValueColour, min, max);
5066 if (setting.getAttributeName().size() > 0)
5068 gc.setAttributeName(setting.getAttributeName().toArray(
5069 new String[setting.getAttributeName().size()]));
5071 if (setting.getThreshold() != null)
5073 gc.setThreshold(setting.getThreshold().floatValue());
5074 int threshstate = safeInt(setting.getThreshstate());
5075 // -1 = None, 0 = Below, 1 = Above threshold
5076 if (threshstate == 0)
5078 gc.setBelowThreshold(true);
5080 else if (threshstate == 1)
5082 gc.setAboveThreshold(true);
5085 gc.setAutoScaled(true); // default
5086 if (setting.isAutoScale() != null)
5088 gc.setAutoScaled(setting.isAutoScale());
5090 if (setting.isColourByLabel() != null)
5092 gc.setColourByLabel(setting.isColourByLabel());
5094 // and put in the feature colour table.
5095 featureColours.put(featureType, gc);
5099 featureColours.put(featureType,
5100 new FeatureColour(maxColour));
5102 renderOrder[fs] = featureType;
5103 if (setting.getOrder() != null)
5105 featureOrder.put(featureType, setting.getOrder().floatValue());
5109 featureOrder.put(featureType, new Float(
5110 fs / jm.getFeatureSettings().getSetting().size()));
5112 if (safeBoolean(setting.isDisplay()))
5114 fdi.setVisible(featureType);
5117 Map<String, Boolean> fgtable = new Hashtable<>();
5118 for (int gs = 0; gs < jm.getFeatureSettings().getGroup().size(); gs++)
5120 Group grp = jm.getFeatureSettings().getGroup().get(gs);
5121 fgtable.put(grp.getName(), new Boolean(grp.isDisplay()));
5123 // FeatureRendererSettings frs = new FeatureRendererSettings(renderOrder,
5124 // fgtable, featureColours, jms.getFeatureSettings().hasTransparency() ?
5125 // jms.getFeatureSettings().getTransparency() : 0.0, featureOrder);
5126 FeatureRendererSettings frs = new FeatureRendererSettings(renderOrder,
5127 fgtable, featureColours, 1.0f, featureOrder);
5128 fr.transferSettings(frs);
5131 if (view.getHiddenColumns().size() > 0)
5133 for (int c = 0; c < view.getHiddenColumns().size(); c++)
5135 final HiddenColumns hc = view.getHiddenColumns().get(c);
5136 viewport.hideColumns(safeInt(hc.getStart()),
5137 safeInt(hc.getEnd()) /* +1 */);
5140 if (view.getCalcIdParam() != null)
5142 for (CalcIdParam calcIdParam : view.getCalcIdParam())
5144 if (calcIdParam != null)
5146 if (recoverCalcIdParam(calcIdParam, viewport))
5151 warn("Couldn't recover parameters for "
5152 + calcIdParam.getCalcId());
5157 af.setMenusFromViewport(viewport);
5158 af.setTitle(view.getTitle());
5159 // TODO: we don't need to do this if the viewport is aready visible.
5161 * Add the AlignFrame to the desktop (it may be 'gathered' later), unless it
5162 * has a 'cdna/protein complement' view, in which case save it in order to
5163 * populate a SplitFrame once all views have been read in.
5165 String complementaryViewId = view.getComplementId();
5166 if (complementaryViewId == null)
5168 Desktop.addInternalFrame(af, view.getTitle(),
5169 safeInt(view.getWidth()), safeInt(view.getHeight()));
5170 // recompute any autoannotation
5171 af.alignPanel.updateAnnotation(false, true);
5172 reorderAutoannotation(af, al, autoAlan);
5173 af.alignPanel.alignmentChanged();
5177 splitFrameCandidates.put(view, af);
5183 * Reads saved data to restore Colour by Annotation settings
5185 * @param viewAnnColour
5189 * @param checkGroupAnnColour
5192 private ColourSchemeI constructAnnotationColour(
5193 AnnotationColourScheme viewAnnColour, AlignFrame af,
5194 AlignmentI al, JalviewModel model, boolean checkGroupAnnColour)
5196 boolean propagateAnnColour = false;
5197 AlignmentI annAlignment = af != null ? af.getViewport().getAlignment()
5199 if (checkGroupAnnColour && al.getGroups() != null
5200 && al.getGroups().size() > 0)
5202 // pre 2.8.1 behaviour
5203 // check to see if we should transfer annotation colours
5204 propagateAnnColour = true;
5205 for (SequenceGroup sg : al.getGroups())
5207 if (sg.getColourScheme() instanceof AnnotationColourGradient)
5209 propagateAnnColour = false;
5215 * 2.10.2- : saved annotationId is AlignmentAnnotation.annotationId
5217 String annotationId = viewAnnColour.getAnnotation();
5218 AlignmentAnnotation matchedAnnotation = annotationIds.get(annotationId);
5221 * pre 2.10.2: saved annotationId is AlignmentAnnotation.label
5223 if (matchedAnnotation == null
5224 && annAlignment.getAlignmentAnnotation() != null)
5226 for (int i = 0; i < annAlignment.getAlignmentAnnotation().length; i++)
5229 .equals(annAlignment.getAlignmentAnnotation()[i].label))
5231 matchedAnnotation = annAlignment.getAlignmentAnnotation()[i];
5236 if (matchedAnnotation == null)
5238 System.err.println("Failed to match annotation colour scheme for "
5242 if (matchedAnnotation.getThreshold() == null)
5244 matchedAnnotation.setThreshold(
5245 new GraphLine(safeFloat(viewAnnColour.getThreshold()),
5246 "Threshold", Color.black));
5249 AnnotationColourGradient cs = null;
5250 if (viewAnnColour.getColourScheme().equals("None"))
5252 cs = new AnnotationColourGradient(matchedAnnotation,
5253 new Color(safeInt(viewAnnColour.getMinColour())),
5254 new Color(safeInt(viewAnnColour.getMaxColour())),
5255 safeInt(viewAnnColour.getAboveThreshold()));
5257 else if (viewAnnColour.getColourScheme().startsWith("ucs"))
5259 cs = new AnnotationColourGradient(matchedAnnotation,
5260 getUserColourScheme(model, viewAnnColour.getColourScheme()),
5261 safeInt(viewAnnColour.getAboveThreshold()));
5265 cs = new AnnotationColourGradient(matchedAnnotation,
5266 ColourSchemeProperty.getColourScheme(al,
5267 viewAnnColour.getColourScheme()),
5268 safeInt(viewAnnColour.getAboveThreshold()));
5271 boolean perSequenceOnly = safeBoolean(viewAnnColour.isPerSequence());
5272 boolean useOriginalColours = safeBoolean(
5273 viewAnnColour.isPredefinedColours());
5274 cs.setSeqAssociated(perSequenceOnly);
5275 cs.setPredefinedColours(useOriginalColours);
5277 if (propagateAnnColour && al.getGroups() != null)
5279 // Also use these settings for all the groups
5280 for (int g = 0; g < al.getGroups().size(); g++)
5282 SequenceGroup sg = al.getGroups().get(g);
5283 if (sg.getGroupColourScheme() == null)
5288 AnnotationColourGradient groupScheme = new AnnotationColourGradient(
5289 matchedAnnotation, sg.getColourScheme(),
5290 safeInt(viewAnnColour.getAboveThreshold()));
5291 sg.setColourScheme(groupScheme);
5292 groupScheme.setSeqAssociated(perSequenceOnly);
5293 groupScheme.setPredefinedColours(useOriginalColours);
5299 private void reorderAutoannotation(AlignFrame af, AlignmentI al,
5300 List<JvAnnotRow> autoAlan)
5302 // copy over visualization settings for autocalculated annotation in the
5304 if (al.getAlignmentAnnotation() != null)
5307 * Kludge for magic autoannotation names (see JAL-811)
5309 String[] magicNames = new String[] { "Consensus", "Quality",
5311 JvAnnotRow nullAnnot = new JvAnnotRow(-1, null);
5312 Hashtable<String, JvAnnotRow> visan = new Hashtable<>();
5313 for (String nm : magicNames)
5315 visan.put(nm, nullAnnot);
5317 for (JvAnnotRow auan : autoAlan)
5319 visan.put(auan.template.label
5320 + (auan.template.getCalcId() == null ? ""
5321 : "\t" + auan.template.getCalcId()),
5324 int hSize = al.getAlignmentAnnotation().length;
5325 List<JvAnnotRow> reorder = new ArrayList<>();
5326 // work through any autoCalculated annotation already on the view
5327 // removing it if it should be placed in a different location on the
5328 // annotation panel.
5329 List<String> remains = new ArrayList<>(visan.keySet());
5330 for (int h = 0; h < hSize; h++)
5332 jalview.datamodel.AlignmentAnnotation jalan = al
5333 .getAlignmentAnnotation()[h];
5334 if (jalan.autoCalculated)
5337 JvAnnotRow valan = visan.get(k = jalan.label);
5338 if (jalan.getCalcId() != null)
5340 valan = visan.get(k = jalan.label + "\t" + jalan.getCalcId());
5345 // delete the auto calculated row from the alignment
5346 al.deleteAnnotation(jalan, false);
5350 if (valan != nullAnnot)
5352 if (jalan != valan.template)
5354 // newly created autoannotation row instance
5355 // so keep a reference to the visible annotation row
5356 // and copy over all relevant attributes
5357 if (valan.template.graphHeight >= 0)
5360 jalan.graphHeight = valan.template.graphHeight;
5362 jalan.visible = valan.template.visible;
5364 reorder.add(new JvAnnotRow(valan.order, jalan));
5369 // Add any (possibly stale) autocalculated rows that were not appended to
5370 // the view during construction
5371 for (String other : remains)
5373 JvAnnotRow othera = visan.get(other);
5374 if (othera != nullAnnot && othera.template.getCalcId() != null
5375 && othera.template.getCalcId().length() > 0)
5377 reorder.add(othera);
5380 // now put the automatic annotation in its correct place
5381 int s = 0, srt[] = new int[reorder.size()];
5382 JvAnnotRow[] rws = new JvAnnotRow[reorder.size()];
5383 for (JvAnnotRow jvar : reorder)
5386 srt[s++] = jvar.order;
5389 jalview.util.QuickSort.sort(srt, rws);
5390 // and re-insert the annotation at its correct position
5391 for (JvAnnotRow jvar : rws)
5393 al.addAnnotation(jvar.template, jvar.order);
5395 af.alignPanel.adjustAnnotationHeight();
5399 Hashtable skipList = null;
5402 * TODO remove this method
5405 * @return AlignFrame bound to sequenceSetId from view, if one exists. private
5406 * AlignFrame getSkippedFrame(Viewport view) { if (skipList==null) {
5407 * throw new Error("Implementation Error. No skipList defined for this
5408 * Jalview2XML instance."); } return (AlignFrame)
5409 * skipList.get(view.getSequenceSetId()); }
5413 * Check if the Jalview view contained in object should be skipped or not.
5416 * @return true if view's sequenceSetId is a key in skipList
5418 private boolean skipViewport(JalviewModel object)
5420 if (skipList == null)
5424 String id = object.getViewport().get(0).getSequenceSetId();
5425 if (skipList.containsKey(id))
5427 if (Cache.log != null && Cache.log.isDebugEnabled())
5429 Cache.log.debug("Skipping seuqence set id " + id);
5436 public void addToSkipList(AlignFrame af)
5438 if (skipList == null)
5440 skipList = new Hashtable();
5442 skipList.put(af.getViewport().getSequenceSetId(), af);
5445 public void clearSkipList()
5447 if (skipList != null)
5454 private void recoverDatasetFor(SequenceSet vamsasSet, AlignmentI al,
5455 boolean ignoreUnrefed, String uniqueSeqSetId)
5457 jalview.datamodel.AlignmentI ds = getDatasetFor(
5458 vamsasSet.getDatasetId());
5459 AlignmentI xtant_ds = ds;
5460 if (xtant_ds == null)
5462 // good chance we are about to create a new dataset, but check if we've
5463 // seen some of the dataset sequence IDs before.
5464 // TODO: skip this check if we are working with project generated by
5465 // version 2.11 or later
5466 xtant_ds = checkIfHasDataset(vamsasSet.getSequence());
5467 if (xtant_ds != null)
5470 addDatasetRef(vamsasSet.getDatasetId(), ds);
5473 Vector dseqs = null;
5476 // recovering an alignment View
5477 AlignmentI seqSetDS = getDatasetFor(UNIQSEQSETID + uniqueSeqSetId);
5478 if (seqSetDS != null)
5480 if (ds != null && ds != seqSetDS)
5482 warn("JAL-3171 regression: Overwriting a dataset reference for an alignment"
5483 + " - CDS/Protein crossreference data may be lost");
5484 if (xtant_ds != null)
5486 // This can only happen if the unique sequence set ID was bound to a
5487 // dataset that did not contain any of the sequences in the view
5488 // currently being restored.
5489 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.");
5493 addDatasetRef(vamsasSet.getDatasetId(), ds);
5498 // try even harder to restore dataset
5499 AlignmentI xtantDS = checkIfHasDataset(vamsasSet.getSequence());
5500 // create a list of new dataset sequences
5501 dseqs = new Vector();
5503 for (int i = 0, iSize = vamsasSet.getSequence().size(); i < iSize; i++)
5505 Sequence vamsasSeq = vamsasSet.getSequence().get(i);
5506 ensureJalviewDatasetSequence(vamsasSeq, ds, dseqs, ignoreUnrefed, i);
5508 // create a new dataset
5511 SequenceI[] dsseqs = new SequenceI[dseqs.size()];
5512 dseqs.copyInto(dsseqs);
5513 ds = new jalview.datamodel.Alignment(dsseqs);
5514 debug("Created new dataset " + vamsasSet.getDatasetId()
5515 + " for alignment " + System.identityHashCode(al));
5516 addDatasetRef(vamsasSet.getDatasetId(), ds);
5518 // set the dataset for the newly imported alignment.
5519 if (al.getDataset() == null && !ignoreUnrefed)
5522 // register dataset for the alignment's uniqueSeqSetId for legacy projects
5523 addDatasetRef(UNIQSEQSETID + uniqueSeqSetId, ds);
5525 updateSeqDatasetBinding(vamsasSet.getSequence(), ds);
5529 * XML dataset sequence ID to materialised dataset reference
5531 HashMap<String, AlignmentI> seqToDataset = new HashMap<>();
5534 * @return the first materialised dataset reference containing a dataset
5535 * sequence referenced in the given view
5537 * - sequences from the view
5539 AlignmentI checkIfHasDataset(List<Sequence> list)
5541 for (Sequence restoredSeq : list)
5543 AlignmentI datasetFor = seqToDataset.get(restoredSeq.getDsseqid());
5544 if (datasetFor != null)
5553 * Register ds as the containing dataset for the dataset sequences referenced
5554 * by sequences in list
5557 * - sequences in a view
5560 void updateSeqDatasetBinding(List<Sequence> list, AlignmentI ds)
5562 for (Sequence restoredSeq : list)
5564 AlignmentI prevDS = seqToDataset.put(restoredSeq.getDsseqid(), ds);
5565 if (prevDS != null && prevDS != ds)
5567 warn("Dataset sequence appears in many datasets: "
5568 + restoredSeq.getDsseqid());
5569 // TODO: try to merge!
5576 * sequence definition to create/merge dataset sequence for
5580 * vector to add new dataset sequence to
5581 * @param ignoreUnrefed
5582 * - when true, don't create new sequences from vamsasSeq if it's id
5583 * doesn't already have an asssociated Jalview sequence.
5585 * - used to reorder the sequence in the alignment according to the
5586 * vamsasSeq array ordering, to preserve ordering of dataset
5588 private void ensureJalviewDatasetSequence(Sequence vamsasSeq,
5589 AlignmentI ds, Vector dseqs, boolean ignoreUnrefed, int vseqpos)
5591 // JBP TODO: Check this is called for AlCodonFrames to support recovery of
5593 SequenceI sq = seqRefIds.get(vamsasSeq.getId());
5594 boolean reorder = false;
5595 SequenceI dsq = null;
5596 if (sq != null && sq.getDatasetSequence() != null)
5598 dsq = sq.getDatasetSequence();
5604 if (sq == null && ignoreUnrefed)
5608 String sqid = vamsasSeq.getDsseqid();
5611 // need to create or add a new dataset sequence reference to this sequence
5614 dsq = seqRefIds.get(sqid);
5619 // make a new dataset sequence
5620 dsq = sq.createDatasetSequence();
5623 // make up a new dataset reference for this sequence
5624 sqid = seqHash(dsq);
5626 dsq.setVamsasId(uniqueSetSuffix + sqid);
5627 seqRefIds.put(sqid, dsq);
5632 dseqs.addElement(dsq);
5637 ds.addSequence(dsq);
5643 { // make this dataset sequence sq's dataset sequence
5644 sq.setDatasetSequence(dsq);
5645 // and update the current dataset alignment
5650 if (!dseqs.contains(dsq))
5657 if (ds.findIndex(dsq) < 0)
5659 ds.addSequence(dsq);
5666 // TODO: refactor this as a merge dataset sequence function
5667 // now check that sq (the dataset sequence) sequence really is the union of
5668 // all references to it
5669 // boolean pre = sq.getStart() < dsq.getStart();
5670 // boolean post = sq.getEnd() > dsq.getEnd();
5674 // StringBuffer sb = new StringBuffer();
5675 String newres = jalview.analysis.AlignSeq.extractGaps(
5676 jalview.util.Comparison.GapChars, sq.getSequenceAsString());
5677 if (!newres.equalsIgnoreCase(dsq.getSequenceAsString())
5678 && newres.length() > dsq.getLength())
5680 // Update with the longer sequence.
5684 * if (pre) { sb.insert(0, newres .substring(0, dsq.getStart() -
5685 * sq.getStart())); dsq.setStart(sq.getStart()); } if (post) {
5686 * sb.append(newres.substring(newres.length() - sq.getEnd() -
5687 * dsq.getEnd())); dsq.setEnd(sq.getEnd()); }
5689 dsq.setSequence(newres);
5691 // TODO: merges will never happen if we 'know' we have the real dataset
5692 // sequence - this should be detected when id==dssid
5694 "DEBUG Notice: Merged dataset sequence (if you see this often, post at http://issues.jalview.org/browse/JAL-1474)"); // ("
5695 // + (pre ? "prepended" : "") + " "
5696 // + (post ? "appended" : ""));
5701 // sequence refs are identical. We may need to update the existing dataset
5702 // alignment with this one, though.
5703 if (ds != null && dseqs == null)
5705 int opos = ds.findIndex(dsq);
5706 SequenceI tseq = null;
5707 if (opos != -1 && vseqpos != opos)
5709 // remove from old position
5710 ds.deleteSequence(dsq);
5712 if (vseqpos < ds.getHeight())
5714 if (vseqpos != opos)
5716 // save sequence at destination position
5717 tseq = ds.getSequenceAt(vseqpos);
5718 ds.replaceSequenceAt(vseqpos, dsq);
5719 ds.addSequence(tseq);
5724 ds.addSequence(dsq);
5731 * TODO use AlignmentI here and in related methods - needs
5732 * AlignmentI.getDataset() changed to return AlignmentI instead of Alignment
5734 Hashtable<String, AlignmentI> datasetIds = null;
5736 IdentityHashMap<AlignmentI, String> dataset2Ids = null;
5738 private AlignmentI getDatasetFor(String datasetId)
5740 if (datasetIds == null)
5742 datasetIds = new Hashtable<>();
5745 if (datasetIds.containsKey(datasetId))
5747 return datasetIds.get(datasetId);
5752 private void addDatasetRef(String datasetId, AlignmentI dataset)
5754 if (datasetIds == null)
5756 datasetIds = new Hashtable<>();
5758 datasetIds.put(datasetId, dataset);
5762 * make a new dataset ID for this jalview dataset alignment
5767 private String getDatasetIdRef(AlignmentI dataset)
5769 if (dataset.getDataset() != null)
5771 warn("Serious issue! Dataset Object passed to getDatasetIdRef is not a Jalview DATASET alignment...");
5773 String datasetId = makeHashCode(dataset, null);
5774 if (datasetId == null)
5776 // make a new datasetId and record it
5777 if (dataset2Ids == null)
5779 dataset2Ids = new IdentityHashMap<>();
5783 datasetId = dataset2Ids.get(dataset);
5785 if (datasetId == null)
5787 datasetId = "ds" + dataset2Ids.size() + 1;
5788 dataset2Ids.put(dataset, datasetId);
5794 private void addDBRefs(SequenceI datasetSequence, Sequence sequence)
5796 for (int d = 0; d < sequence.getDBRef().size(); d++)
5798 DBRef dr = sequence.getDBRef().get(d);
5799 jalview.datamodel.DBRefEntry entry = new jalview.datamodel.DBRefEntry(
5800 dr.getSource(), dr.getVersion(), dr.getAccessionId());
5801 if (dr.getMapping() != null)
5803 entry.setMap(addMapping(dr.getMapping()));
5805 datasetSequence.addDBRef(entry);
5809 private jalview.datamodel.Mapping addMapping(Mapping m)
5811 SequenceI dsto = null;
5812 // Mapping m = dr.getMapping();
5813 int fr[] = new int[m.getMapListFrom().size() * 2];
5814 Iterator<MapListFrom> from = m.getMapListFrom().iterator();// enumerateMapListFrom();
5815 for (int _i = 0; from.hasNext(); _i += 2)
5817 MapListFrom mf = from.next();
5818 fr[_i] = mf.getStart();
5819 fr[_i + 1] = mf.getEnd();
5821 int fto[] = new int[m.getMapListTo().size() * 2];
5822 Iterator<MapListTo> to = m.getMapListTo().iterator();// enumerateMapListTo();
5823 for (int _i = 0; to.hasNext(); _i += 2)
5825 MapListTo mf = to.next();
5826 fto[_i] = mf.getStart();
5827 fto[_i + 1] = mf.getEnd();
5829 jalview.datamodel.Mapping jmap = new jalview.datamodel.Mapping(dsto, fr,
5830 fto, m.getMapFromUnit().intValue(),
5831 m.getMapToUnit().intValue());
5832 // if (m.getMappingChoice() != null)
5834 // MappingChoice mc = m.getMappingChoice();
5835 if (m.getDseqFor() != null)
5837 String dsfor = m.getDseqFor();
5838 if (seqRefIds.containsKey(dsfor))
5843 jmap.setTo(seqRefIds.get(dsfor));
5847 frefedSequence.add(newMappingRef(dsfor, jmap));
5853 * local sequence definition
5855 Sequence ms = m.getSequence();
5856 SequenceI djs = null;
5857 String sqid = ms.getDsseqid();
5858 if (sqid != null && sqid.length() > 0)
5861 * recover dataset sequence
5863 djs = seqRefIds.get(sqid);
5868 "Warning - making up dataset sequence id for DbRef sequence map reference");
5869 sqid = ((Object) ms).toString(); // make up a new hascode for
5870 // undefined dataset sequence hash
5871 // (unlikely to happen)
5877 * make a new dataset sequence and add it to refIds hash
5879 djs = new jalview.datamodel.Sequence(ms.getName(),
5881 djs.setStart(jmap.getMap().getToLowest());
5882 djs.setEnd(jmap.getMap().getToHighest());
5883 djs.setVamsasId(uniqueSetSuffix + sqid);
5885 incompleteSeqs.put(sqid, djs);
5886 seqRefIds.put(sqid, djs);
5889 jalview.bin.Cache.log.debug("about to recurse on addDBRefs.");
5898 * Provides a 'copy' of an alignment view (on action New View) by 'saving' the
5899 * view as XML (but not to file), and then reloading it
5904 public AlignmentPanel copyAlignPanel(AlignmentPanel ap)
5907 JalviewModel jm = saveState(ap, null, null, null);
5910 jm.getVamsasModel().getSequenceSet().get(0).getDatasetId(),
5911 ap.getAlignment().getDataset());
5913 uniqueSetSuffix = "";
5914 // jm.getJalviewModelSequence().getViewport(0).setId(null);
5915 jm.getViewport().get(0).setId(null);
5916 // we don't overwrite the view we just copied
5918 if (this.frefedSequence == null)
5920 frefedSequence = new Vector<>();
5923 viewportsAdded.clear();
5925 AlignFrame af = loadFromObject(jm, null, false, null);
5926 af.getAlignPanels().clear();
5927 af.closeMenuItem_actionPerformed(true);
5930 * if(ap.av.getAlignment().getAlignmentAnnotation()!=null) { for(int i=0;
5931 * i<ap.av.getAlignment().getAlignmentAnnotation().length; i++) {
5932 * if(!ap.av.getAlignment().getAlignmentAnnotation()[i].autoCalculated) {
5933 * af.alignPanel.av.getAlignment().getAlignmentAnnotation()[i] =
5934 * ap.av.getAlignment().getAlignmentAnnotation()[i]; } } }
5937 return af.alignPanel;
5940 private Hashtable jvids2vobj;
5942 private void warn(String msg)
5947 private void warn(String msg, Exception e)
5949 if (Cache.log != null)
5953 Cache.log.warn(msg, e);
5957 Cache.log.warn(msg);
5962 System.err.println("Warning: " + msg);
5965 e.printStackTrace();
5970 private void debug(String string)
5972 debug(string, null);
5975 private void debug(String msg, Exception e)
5977 if (Cache.log != null)
5981 Cache.log.debug(msg, e);
5985 Cache.log.debug(msg);
5990 System.err.println("Warning: " + msg);
5993 e.printStackTrace();
5999 * set the object to ID mapping tables used to write/recover objects and XML
6000 * ID strings for the jalview project. If external tables are provided then
6001 * finalize and clearSeqRefs will not clear the tables when the Jalview2XML
6002 * object goes out of scope. - also populates the datasetIds hashtable with
6003 * alignment objects containing dataset sequences
6006 * Map from ID strings to jalview datamodel
6008 * Map from jalview datamodel to ID strings
6012 public void setObjectMappingTables(Hashtable vobj2jv,
6013 IdentityHashMap jv2vobj)
6015 this.jv2vobj = jv2vobj;
6016 this.vobj2jv = vobj2jv;
6017 Iterator ds = jv2vobj.keySet().iterator();
6019 while (ds.hasNext())
6021 Object jvobj = ds.next();
6022 id = jv2vobj.get(jvobj).toString();
6023 if (jvobj instanceof jalview.datamodel.Alignment)
6025 if (((jalview.datamodel.Alignment) jvobj).getDataset() == null)
6027 addDatasetRef(id, (jalview.datamodel.Alignment) jvobj);
6030 else if (jvobj instanceof jalview.datamodel.Sequence)
6032 // register sequence object so the XML parser can recover it.
6033 if (seqRefIds == null)
6035 seqRefIds = new HashMap<>();
6037 if (seqsToIds == null)
6039 seqsToIds = new IdentityHashMap<>();
6041 seqRefIds.put(jv2vobj.get(jvobj).toString(), (SequenceI) jvobj);
6042 seqsToIds.put((SequenceI) jvobj, id);
6044 else if (jvobj instanceof jalview.datamodel.AlignmentAnnotation)
6047 AlignmentAnnotation jvann = (AlignmentAnnotation) jvobj;
6048 annotationIds.put(anid = jv2vobj.get(jvobj).toString(), jvann);
6049 if (jvann.annotationId == null)
6051 jvann.annotationId = anid;
6053 if (!jvann.annotationId.equals(anid))
6055 // TODO verify that this is the correct behaviour
6056 this.warn("Overriding Annotation ID for " + anid
6057 + " from different id : " + jvann.annotationId);
6058 jvann.annotationId = anid;
6061 else if (jvobj instanceof String)
6063 if (jvids2vobj == null)
6065 jvids2vobj = new Hashtable();
6066 jvids2vobj.put(jvobj, jv2vobj.get(jvobj).toString());
6071 Cache.log.debug("Ignoring " + jvobj.getClass() + " (ID = " + id);
6077 * set the uniqueSetSuffix used to prefix/suffix object IDs for jalview
6078 * objects created from the project archive. If string is null (default for
6079 * construction) then suffix will be set automatically.
6083 public void setUniqueSetSuffix(String string)
6085 uniqueSetSuffix = string;
6090 * uses skipList2 as the skipList for skipping views on sequence sets
6091 * associated with keys in the skipList
6095 public void setSkipList(Hashtable skipList2)
6097 skipList = skipList2;
6101 * Reads the jar entry of given name and returns its contents, or null if the
6102 * entry is not found.
6105 * @param jarEntryName
6108 protected String readJarEntry(jarInputStreamProvider jprovider,
6109 String jarEntryName)
6111 String result = null;
6112 BufferedReader in = null;
6117 * Reopen the jar input stream and traverse its entries to find a matching
6120 JarInputStream jin = jprovider.getJarInputStream();
6121 JarEntry entry = null;
6124 entry = jin.getNextJarEntry();
6125 } while (entry != null && !entry.getName().equals(jarEntryName));
6129 StringBuilder out = new StringBuilder(256);
6130 in = new BufferedReader(new InputStreamReader(jin, UTF_8));
6133 while ((data = in.readLine()) != null)
6137 result = out.toString();
6141 warn("Couldn't find entry in Jalview Jar for " + jarEntryName);
6143 } catch (Exception ex)
6145 ex.printStackTrace();
6153 } catch (IOException e)
6164 * Returns an incrementing counter (0, 1, 2...)
6168 private synchronized int nextCounter()
6174 * Loads any saved PCA viewers
6179 protected void loadPCAViewers(JalviewModel model, AlignmentPanel ap)
6183 List<PcaViewer> pcaviewers = model.getPcaViewer();
6184 for (PcaViewer viewer : pcaviewers)
6186 String modelName = viewer.getScoreModelName();
6187 SimilarityParamsI params = new SimilarityParams(
6188 viewer.isIncludeGappedColumns(), viewer.isMatchGaps(),
6189 viewer.isIncludeGaps(),
6190 viewer.isDenominateByShortestLength());
6193 * create the panel (without computing the PCA)
6195 PCAPanel panel = new PCAPanel(ap, modelName, params);
6197 panel.setTitle(viewer.getTitle());
6198 panel.setBounds(new Rectangle(viewer.getXpos(), viewer.getYpos(),
6199 viewer.getWidth(), viewer.getHeight()));
6201 boolean showLabels = viewer.isShowLabels();
6202 panel.setShowLabels(showLabels);
6203 panel.getRotatableCanvas().setShowLabels(showLabels);
6204 panel.getRotatableCanvas()
6205 .setBgColour(new Color(viewer.getBgColour()));
6206 panel.getRotatableCanvas()
6207 .setApplyToAllViews(viewer.isLinkToAllViews());
6210 * load PCA output data
6212 ScoreModelI scoreModel = ScoreModels.getInstance()
6213 .getScoreModel(modelName, ap);
6214 PCA pca = new PCA(null, scoreModel, params);
6215 PcaDataType pcaData = viewer.getPcaData();
6217 MatrixI pairwise = loadDoubleMatrix(pcaData.getPairwiseMatrix());
6218 pca.setPairwiseScores(pairwise);
6220 MatrixI triDiag = loadDoubleMatrix(pcaData.getTridiagonalMatrix());
6221 pca.setTridiagonal(triDiag);
6223 MatrixI result = loadDoubleMatrix(pcaData.getEigenMatrix());
6224 pca.setEigenmatrix(result);
6226 panel.getPcaModel().setPCA(pca);
6229 * we haven't saved the input data! (JAL-2647 to do)
6231 panel.setInputData(null);
6234 * add the sequence points for the PCA display
6236 List<jalview.datamodel.SequencePoint> seqPoints = new ArrayList<>();
6237 for (SequencePoint sp : viewer.getSequencePoint())
6239 String seqId = sp.getSequenceRef();
6240 SequenceI seq = seqRefIds.get(seqId);
6243 throw new IllegalStateException(
6244 "Unmatched seqref for PCA: " + seqId);
6246 Point pt = new Point(sp.getXPos(), sp.getYPos(), sp.getZPos());
6247 jalview.datamodel.SequencePoint seqPoint = new jalview.datamodel.SequencePoint(
6249 seqPoints.add(seqPoint);
6251 panel.getRotatableCanvas().setPoints(seqPoints, seqPoints.size());
6254 * set min-max ranges and scale after setPoints (which recomputes them)
6256 panel.getRotatableCanvas().setScaleFactor(viewer.getScaleFactor());
6257 SeqPointMin spMin = viewer.getSeqPointMin();
6258 float[] min = new float[] { spMin.getXPos(), spMin.getYPos(),
6260 SeqPointMax spMax = viewer.getSeqPointMax();
6261 float[] max = new float[] { spMax.getXPos(), spMax.getYPos(),
6263 panel.getRotatableCanvas().setSeqMinMax(min, max);
6265 // todo: hold points list in PCAModel only
6266 panel.getPcaModel().setSequencePoints(seqPoints);
6268 panel.setSelectedDimensionIndex(viewer.getXDim(), X);
6269 panel.setSelectedDimensionIndex(viewer.getYDim(), Y);
6270 panel.setSelectedDimensionIndex(viewer.getZDim(), Z);
6272 // is this duplication needed?
6273 panel.setTop(seqPoints.size() - 1);
6274 panel.getPcaModel().setTop(seqPoints.size() - 1);
6277 * add the axes' end points for the display
6279 for (int i = 0; i < 3; i++)
6281 Axis axis = viewer.getAxis().get(i);
6282 panel.getRotatableCanvas().getAxisEndPoints()[i] = new Point(
6283 axis.getXPos(), axis.getYPos(), axis.getZPos());
6286 Desktop.addInternalFrame(panel, MessageManager.formatMessage(
6287 "label.calc_title", "PCA", modelName), 475, 450);
6289 } catch (Exception ex)
6291 Cache.log.error("Error loading PCA: " + ex.toString());
6296 * Populates an XML model of the feature colour scheme for one feature type
6298 * @param featureType
6302 public static Colour marshalColour(
6303 String featureType, FeatureColourI fcol)
6305 Colour col = new Colour();
6306 if (fcol.isSimpleColour())
6308 col.setRGB(Format.getHexString(fcol.getColour()));
6312 col.setRGB(Format.getHexString(fcol.getMaxColour()));
6313 col.setMin(fcol.getMin());
6314 col.setMax(fcol.getMax());
6315 col.setMinRGB(jalview.util.Format.getHexString(fcol.getMinColour()));
6316 col.setAutoScale(fcol.isAutoScaled());
6317 col.setThreshold(fcol.getThreshold());
6318 col.setColourByLabel(fcol.isColourByLabel());
6319 col.setThreshType(fcol.isAboveThreshold() ? ThresholdType.ABOVE
6320 : (fcol.isBelowThreshold() ? ThresholdType.BELOW
6321 : ThresholdType.NONE));
6322 if (fcol.isColourByAttribute())
6324 final String[] attName = fcol.getAttributeName();
6325 col.getAttributeName().add(attName[0]);
6326 if (attName.length > 1)
6328 col.getAttributeName().add(attName[1]);
6331 Color noColour = fcol.getNoColour();
6332 if (noColour == null)
6334 col.setNoValueColour(NoValueColour.NONE);
6336 else if (noColour == fcol.getMaxColour())
6338 col.setNoValueColour(NoValueColour.MAX);
6342 col.setNoValueColour(NoValueColour.MIN);
6345 col.setName(featureType);
6350 * Populates an XML model of the feature filter(s) for one feature type
6352 * @param firstMatcher
6353 * the first (or only) match condition)
6355 * remaining match conditions (if any)
6357 * if true, conditions are and-ed, else or-ed
6359 public static jalview.xml.binding.jalview.FeatureMatcherSet marshalFilter(
6360 FeatureMatcherI firstMatcher, Iterator<FeatureMatcherI> filters,
6363 jalview.xml.binding.jalview.FeatureMatcherSet result = new jalview.xml.binding.jalview.FeatureMatcherSet();
6365 if (filters.hasNext())
6370 CompoundMatcher compound = new CompoundMatcher();
6371 compound.setAnd(and);
6372 jalview.xml.binding.jalview.FeatureMatcherSet matcher1 = marshalFilter(
6373 firstMatcher, Collections.emptyIterator(), and);
6374 // compound.addMatcherSet(matcher1);
6375 compound.getMatcherSet().add(matcher1);
6376 FeatureMatcherI nextMatcher = filters.next();
6377 jalview.xml.binding.jalview.FeatureMatcherSet matcher2 = marshalFilter(
6378 nextMatcher, filters, and);
6379 // compound.addMatcherSet(matcher2);
6380 compound.getMatcherSet().add(matcher2);
6381 result.setCompoundMatcher(compound);
6386 * single condition matcher
6388 // MatchCondition matcherModel = new MatchCondition();
6389 jalview.xml.binding.jalview.FeatureMatcher matcherModel = new jalview.xml.binding.jalview.FeatureMatcher();
6390 matcherModel.setCondition(
6391 firstMatcher.getMatcher().getCondition().getStableName());
6392 matcherModel.setValue(firstMatcher.getMatcher().getPattern());
6393 if (firstMatcher.isByAttribute())
6395 matcherModel.setBy(FilterBy.BY_ATTRIBUTE);
6396 // matcherModel.setAttributeName(firstMatcher.getAttribute());
6397 String[] attName = firstMatcher.getAttribute();
6398 matcherModel.getAttributeName().add(attName[0]); // attribute
6399 if (attName.length > 1)
6401 matcherModel.getAttributeName().add(attName[1]); // sub-attribute
6404 else if (firstMatcher.isByLabel())
6406 matcherModel.setBy(FilterBy.BY_LABEL);
6408 else if (firstMatcher.isByScore())
6410 matcherModel.setBy(FilterBy.BY_SCORE);
6412 result.setMatchCondition(matcherModel);
6419 * Loads one XML model of a feature filter to a Jalview object
6421 * @param featureType
6422 * @param matcherSetModel
6425 public static FeatureMatcherSetI parseFilter(
6427 jalview.xml.binding.jalview.FeatureMatcherSet matcherSetModel)
6429 FeatureMatcherSetI result = new FeatureMatcherSet();
6432 parseFilterConditions(result, matcherSetModel, true);
6433 } catch (IllegalStateException e)
6435 // mixing AND and OR conditions perhaps
6437 String.format("Error reading filter conditions for '%s': %s",
6438 featureType, e.getMessage()));
6439 // return as much as was parsed up to the error
6446 * Adds feature match conditions to matcherSet as unmarshalled from XML
6447 * (possibly recursively for compound conditions)
6450 * @param matcherSetModel
6452 * if true, multiple conditions are AND-ed, else they are OR-ed
6453 * @throws IllegalStateException
6454 * if AND and OR conditions are mixed
6456 protected static void parseFilterConditions(
6457 FeatureMatcherSetI matcherSet,
6458 jalview.xml.binding.jalview.FeatureMatcherSet matcherSetModel,
6461 jalview.xml.binding.jalview.FeatureMatcher mc = matcherSetModel
6462 .getMatchCondition();
6468 FilterBy filterBy = mc.getBy();
6469 Condition cond = Condition.fromString(mc.getCondition());
6470 String pattern = mc.getValue();
6471 FeatureMatcherI matchCondition = null;
6472 if (filterBy == FilterBy.BY_LABEL)
6474 matchCondition = FeatureMatcher.byLabel(cond, pattern);
6476 else if (filterBy == FilterBy.BY_SCORE)
6478 matchCondition = FeatureMatcher.byScore(cond, pattern);
6481 else if (filterBy == FilterBy.BY_ATTRIBUTE)
6483 final List<String> attributeName = mc.getAttributeName();
6484 String[] attNames = attributeName
6485 .toArray(new String[attributeName.size()]);
6486 matchCondition = FeatureMatcher.byAttribute(cond, pattern,
6491 * note this throws IllegalStateException if AND-ing to a
6492 * previously OR-ed compound condition, or vice versa
6496 matcherSet.and(matchCondition);
6500 matcherSet.or(matchCondition);
6506 * compound condition
6508 List<jalview.xml.binding.jalview.FeatureMatcherSet> matchers = matcherSetModel
6509 .getCompoundMatcher().getMatcherSet();
6510 boolean anded = matcherSetModel.getCompoundMatcher().isAnd();
6511 if (matchers.size() == 2)
6513 parseFilterConditions(matcherSet, matchers.get(0), anded);
6514 parseFilterConditions(matcherSet, matchers.get(1), anded);
6518 System.err.println("Malformed compound filter condition");
6524 * Loads one XML model of a feature colour to a Jalview object
6526 * @param colourModel
6529 public static FeatureColourI parseColour(Colour colourModel)
6531 FeatureColourI colour = null;
6533 if (colourModel.getMax() != null)
6535 Color mincol = null;
6536 Color maxcol = null;
6537 Color noValueColour = null;
6541 mincol = new Color(Integer.parseInt(colourModel.getMinRGB(), 16));
6542 maxcol = new Color(Integer.parseInt(colourModel.getRGB(), 16));
6543 } catch (Exception e)
6545 Cache.log.warn("Couldn't parse out graduated feature color.", e);
6548 NoValueColour noCol = colourModel.getNoValueColour();
6549 if (noCol == NoValueColour.MIN)
6551 noValueColour = mincol;
6553 else if (noCol == NoValueColour.MAX)
6555 noValueColour = maxcol;
6558 colour = new FeatureColour(mincol, maxcol, noValueColour,
6559 safeFloat(colourModel.getMin()),
6560 safeFloat(colourModel.getMax()));
6561 final List<String> attributeName = colourModel.getAttributeName();
6562 String[] attributes = attributeName
6563 .toArray(new String[attributeName.size()]);
6564 if (attributes != null && attributes.length > 0)
6566 colour.setAttributeName(attributes);
6568 if (colourModel.isAutoScale() != null)
6570 colour.setAutoScaled(colourModel.isAutoScale().booleanValue());
6572 if (colourModel.isColourByLabel() != null)
6574 colour.setColourByLabel(
6575 colourModel.isColourByLabel().booleanValue());
6577 if (colourModel.getThreshold() != null)
6579 colour.setThreshold(colourModel.getThreshold().floatValue());
6581 ThresholdType ttyp = colourModel.getThreshType();
6582 if (ttyp == ThresholdType.ABOVE)
6584 colour.setAboveThreshold(true);
6586 else if (ttyp == ThresholdType.BELOW)
6588 colour.setBelowThreshold(true);
6593 Color color = new Color(Integer.parseInt(colourModel.getRGB(), 16));
6594 colour = new FeatureColour(color);