2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 package jalview.project;
23 import static jalview.math.RotatableMatrix.Axis.X;
24 import static jalview.math.RotatableMatrix.Axis.Y;
25 import static jalview.math.RotatableMatrix.Axis.Z;
27 import jalview.analysis.Conservation;
28 import jalview.analysis.PCA;
29 import jalview.analysis.scoremodels.ScoreModels;
30 import jalview.analysis.scoremodels.SimilarityParams;
31 import jalview.api.FeatureColourI;
32 import jalview.api.ViewStyleI;
33 import jalview.api.analysis.ScoreModelI;
34 import jalview.api.analysis.SimilarityParamsI;
35 import jalview.api.structures.JalviewStructureDisplayI;
36 import jalview.bin.Cache;
37 import jalview.datamodel.AlignedCodonFrame;
38 import jalview.datamodel.Alignment;
39 import jalview.datamodel.AlignmentAnnotation;
40 import jalview.datamodel.AlignmentI;
41 import jalview.datamodel.DBRefEntry;
42 import jalview.datamodel.GeneLocus;
43 import jalview.datamodel.GraphLine;
44 import jalview.datamodel.PDBEntry;
45 import jalview.datamodel.Point;
46 import jalview.datamodel.RnaViewerModel;
47 import jalview.datamodel.SequenceFeature;
48 import jalview.datamodel.SequenceGroup;
49 import jalview.datamodel.SequenceI;
50 import jalview.datamodel.StructureViewerModel;
51 import jalview.datamodel.StructureViewerModel.StructureData;
52 import jalview.datamodel.features.FeatureMatcher;
53 import jalview.datamodel.features.FeatureMatcherI;
54 import jalview.datamodel.features.FeatureMatcherSet;
55 import jalview.datamodel.features.FeatureMatcherSetI;
56 import jalview.ext.varna.RnaModel;
57 import jalview.gui.AlignFrame;
58 import jalview.gui.AlignViewport;
59 import jalview.gui.AlignmentPanel;
60 import jalview.gui.AppVarna;
61 import jalview.gui.ChimeraViewFrame;
62 import jalview.gui.Desktop;
63 import jalview.gui.FeatureRenderer;
64 import jalview.gui.JvOptionPane;
65 import jalview.gui.OOMWarning;
66 import jalview.gui.PCAPanel;
67 import jalview.gui.PaintRefresher;
68 import jalview.gui.SplitFrame;
69 import jalview.gui.StructureViewer;
70 import jalview.gui.StructureViewer.ViewerType;
71 import jalview.gui.StructureViewerBase;
72 import jalview.gui.TreePanel;
73 import jalview.io.BackupFiles;
74 import jalview.io.DataSourceType;
75 import jalview.io.FileFormat;
76 import jalview.io.NewickFile;
77 import jalview.math.Matrix;
78 import jalview.math.MatrixI;
79 import jalview.renderer.ResidueShaderI;
80 import jalview.schemes.AnnotationColourGradient;
81 import jalview.schemes.ColourSchemeI;
82 import jalview.schemes.ColourSchemeProperty;
83 import jalview.schemes.FeatureColour;
84 import jalview.schemes.ResidueProperties;
85 import jalview.schemes.UserColourScheme;
86 import jalview.structure.StructureSelectionManager;
87 import jalview.structures.models.AAStructureBindingModel;
88 import jalview.util.Format;
89 import jalview.util.MessageManager;
90 import jalview.util.Platform;
91 import jalview.util.StringUtils;
92 import jalview.util.jarInputStreamProvider;
93 import jalview.util.matcher.Condition;
94 import jalview.viewmodel.AlignmentViewport;
95 import jalview.viewmodel.PCAModel;
96 import jalview.viewmodel.ViewportRanges;
97 import jalview.viewmodel.seqfeatures.FeatureRendererSettings;
98 import jalview.viewmodel.seqfeatures.FeaturesDisplayed;
99 import jalview.ws.jws2.Jws2Discoverer;
100 import jalview.ws.jws2.dm.AAConSettings;
101 import jalview.ws.jws2.jabaws2.Jws2Instance;
102 import jalview.ws.params.ArgumentI;
103 import jalview.ws.params.AutoCalcSetting;
104 import jalview.ws.params.WsParamSetI;
105 import jalview.xml.binding.jalview.AlcodonFrame;
106 import jalview.xml.binding.jalview.AlcodonFrame.AlcodMap;
107 import jalview.xml.binding.jalview.Annotation;
108 import jalview.xml.binding.jalview.Annotation.ThresholdLine;
109 import jalview.xml.binding.jalview.AnnotationColourScheme;
110 import jalview.xml.binding.jalview.AnnotationElement;
111 import jalview.xml.binding.jalview.DoubleMatrix;
112 import jalview.xml.binding.jalview.DoubleVector;
113 import jalview.xml.binding.jalview.Feature;
114 import jalview.xml.binding.jalview.Feature.OtherData;
115 import jalview.xml.binding.jalview.FeatureMatcherSet.CompoundMatcher;
116 import jalview.xml.binding.jalview.FilterBy;
117 import jalview.xml.binding.jalview.JalviewModel;
118 import jalview.xml.binding.jalview.JalviewModel.FeatureSettings;
119 import jalview.xml.binding.jalview.JalviewModel.FeatureSettings.Group;
120 import jalview.xml.binding.jalview.JalviewModel.FeatureSettings.Setting;
121 import jalview.xml.binding.jalview.JalviewModel.JGroup;
122 import jalview.xml.binding.jalview.JalviewModel.JSeq;
123 import jalview.xml.binding.jalview.JalviewModel.JSeq.Pdbids;
124 import jalview.xml.binding.jalview.JalviewModel.JSeq.Pdbids.StructureState;
125 import jalview.xml.binding.jalview.JalviewModel.JSeq.RnaViewer;
126 import jalview.xml.binding.jalview.JalviewModel.JSeq.RnaViewer.SecondaryStructure;
127 import jalview.xml.binding.jalview.JalviewModel.PcaViewer;
128 import jalview.xml.binding.jalview.JalviewModel.PcaViewer.Axis;
129 import jalview.xml.binding.jalview.JalviewModel.PcaViewer.SeqPointMax;
130 import jalview.xml.binding.jalview.JalviewModel.PcaViewer.SeqPointMin;
131 import jalview.xml.binding.jalview.JalviewModel.PcaViewer.SequencePoint;
132 import jalview.xml.binding.jalview.JalviewModel.Tree;
133 import jalview.xml.binding.jalview.JalviewModel.UserColours;
134 import jalview.xml.binding.jalview.JalviewModel.Viewport;
135 import jalview.xml.binding.jalview.JalviewModel.Viewport.CalcIdParam;
136 import jalview.xml.binding.jalview.JalviewModel.Viewport.HiddenColumns;
137 import jalview.xml.binding.jalview.JalviewUserColours;
138 import jalview.xml.binding.jalview.JalviewUserColours.Colour;
139 import jalview.xml.binding.jalview.MapListType.MapListFrom;
140 import jalview.xml.binding.jalview.MapListType.MapListTo;
141 import jalview.xml.binding.jalview.Mapping;
142 import jalview.xml.binding.jalview.NoValueColour;
143 import jalview.xml.binding.jalview.ObjectFactory;
144 import jalview.xml.binding.jalview.PcaDataType;
145 import jalview.xml.binding.jalview.Pdbentry.Property;
146 import jalview.xml.binding.jalview.Sequence;
147 import jalview.xml.binding.jalview.Sequence.DBRef;
148 import jalview.xml.binding.jalview.SequenceSet;
149 import jalview.xml.binding.jalview.SequenceSet.SequenceSetProperties;
150 import jalview.xml.binding.jalview.ThresholdType;
151 import jalview.xml.binding.jalview.VAMSAS;
153 import java.awt.Color;
154 import java.awt.Font;
155 import java.awt.Rectangle;
156 import java.io.BufferedReader;
157 import java.io.DataInputStream;
158 import java.io.DataOutputStream;
160 import java.io.FileInputStream;
161 import java.io.FileOutputStream;
162 import java.io.IOException;
163 import java.io.InputStreamReader;
164 import java.io.OutputStreamWriter;
165 import java.io.PrintWriter;
166 import java.lang.reflect.InvocationTargetException;
167 import java.math.BigInteger;
168 import java.net.MalformedURLException;
170 import java.util.ArrayList;
171 import java.util.Arrays;
172 import java.util.Collections;
173 import java.util.Enumeration;
174 import java.util.GregorianCalendar;
175 import java.util.HashMap;
176 import java.util.HashSet;
177 import java.util.Hashtable;
178 import java.util.IdentityHashMap;
179 import java.util.Iterator;
180 import java.util.LinkedHashMap;
181 import java.util.List;
182 import java.util.Map;
183 import java.util.Map.Entry;
184 import java.util.Set;
185 import java.util.Vector;
186 import java.util.jar.JarEntry;
187 import java.util.jar.JarInputStream;
188 import java.util.jar.JarOutputStream;
190 import javax.swing.JInternalFrame;
191 import javax.swing.SwingUtilities;
192 import javax.xml.bind.JAXBContext;
193 import javax.xml.bind.JAXBElement;
194 import javax.xml.bind.Marshaller;
195 import javax.xml.datatype.DatatypeConfigurationException;
196 import javax.xml.datatype.DatatypeFactory;
197 import javax.xml.datatype.XMLGregorianCalendar;
198 import javax.xml.stream.XMLInputFactory;
199 import javax.xml.stream.XMLStreamReader;
202 * Write out the current jalview desktop state as a Jalview XML stream.
204 * Note: the vamsas objects referred to here are primitive versions of the
205 * VAMSAS project schema elements - they are not the same and most likely never
209 * @version $Revision: 1.134 $
211 public class Jalview2XML
213 private static final String VIEWER_PREFIX = "viewer_";
215 private static final String RNA_PREFIX = "rna_";
217 private static final String UTF_8 = "UTF-8";
220 * prefix for recovering datasets for alignments with multiple views where
221 * non-existent dataset IDs were written for some views
223 private static final String UNIQSEQSETID = "uniqueSeqSetId.";
225 // use this with nextCounter() to make unique names for entities
226 private int counter = 0;
229 * SequenceI reference -> XML ID string in jalview XML. Populated as XML reps
230 * of sequence objects are created.
232 IdentityHashMap<SequenceI, String> seqsToIds = null;
235 * jalview XML Sequence ID to jalview sequence object reference (both dataset
236 * and alignment sequences. Populated as XML reps of sequence objects are
239 Map<String, SequenceI> seqRefIds = null;
241 Map<String, SequenceI> incompleteSeqs = null;
243 List<SeqFref> frefedSequence = null;
245 boolean raiseGUI = true; // whether errors are raised in dialog boxes or not
248 * Map of reconstructed AlignFrame objects that appear to have come from
249 * SplitFrame objects (have a dna/protein complement view).
251 private Map<Viewport, AlignFrame> splitFrameCandidates = new HashMap<>();
254 * Map from displayed rna structure models to their saved session state jar
257 private Map<RnaModel, String> rnaSessions = new HashMap<>();
260 * A helper method for safely using the value of an optional attribute that
261 * may be null if not present in the XML. Answers the boolean value, or false
267 public static boolean safeBoolean(Boolean b)
269 return b == null ? false : b.booleanValue();
273 * A helper method for safely using the value of an optional attribute that
274 * may be null if not present in the XML. Answers the integer value, or zero
280 public static int safeInt(Integer i)
282 return i == null ? 0 : i.intValue();
286 * A helper method for safely using the value of an optional attribute that
287 * may be null if not present in the XML. Answers the float value, or zero if
293 public static float safeFloat(Float f)
295 return f == null ? 0f : f.floatValue();
299 * create/return unique hash string for sq
302 * @return new or existing unique string for sq
304 String seqHash(SequenceI sq)
306 if (seqsToIds == null)
310 if (seqsToIds.containsKey(sq))
312 return seqsToIds.get(sq);
316 // create sequential key
317 String key = "sq" + (seqsToIds.size() + 1);
318 key = makeHashCode(sq, key); // check we don't have an external reference
320 seqsToIds.put(sq, key);
327 if (seqsToIds == null)
329 seqsToIds = new IdentityHashMap<>();
331 if (seqRefIds == null)
333 seqRefIds = new HashMap<>();
335 if (incompleteSeqs == null)
337 incompleteSeqs = new HashMap<>();
339 if (frefedSequence == null)
341 frefedSequence = new ArrayList<>();
349 public Jalview2XML(boolean raiseGUI)
351 this.raiseGUI = raiseGUI;
355 * base class for resolving forward references to sequences by their ID
360 abstract class SeqFref
366 public SeqFref(String _sref, String type)
372 public String getSref()
377 public SequenceI getSrefSeq()
379 return seqRefIds.get(sref);
382 public boolean isResolvable()
384 return seqRefIds.get(sref) != null;
387 public SequenceI getSrefDatasetSeq()
389 SequenceI sq = seqRefIds.get(sref);
392 while (sq.getDatasetSequence() != null)
394 sq = sq.getDatasetSequence();
401 * @return true if the forward reference was fully resolved
403 abstract boolean resolve();
406 public String toString()
408 return type + " reference to " + sref;
413 * create forward reference for a mapping
419 public SeqFref newMappingRef(final String sref,
420 final jalview.datamodel.Mapping _jmap)
422 SeqFref fref = new SeqFref(sref, "Mapping")
424 public jalview.datamodel.Mapping jmap = _jmap;
429 SequenceI seq = getSrefDatasetSeq();
441 public SeqFref newAlcodMapRef(final String sref,
442 final AlignedCodonFrame _cf,
443 final jalview.datamodel.Mapping _jmap)
446 SeqFref fref = new SeqFref(sref, "Codon Frame")
448 AlignedCodonFrame cf = _cf;
450 public jalview.datamodel.Mapping mp = _jmap;
453 public boolean isResolvable()
455 return super.isResolvable() && mp.getTo() != null;
461 SequenceI seq = getSrefDatasetSeq();
466 cf.addMap(seq, mp.getTo(), mp.getMap());
473 public void resolveFrefedSequences()
475 Iterator<SeqFref> nextFref = frefedSequence.iterator();
476 int toresolve = frefedSequence.size();
477 int unresolved = 0, failedtoresolve = 0;
478 while (nextFref.hasNext())
480 SeqFref ref = nextFref.next();
481 if (ref.isResolvable())
493 } catch (Exception x)
496 "IMPLEMENTATION ERROR: Failed to resolve forward reference for sequence "
509 System.err.println("Jalview Project Import: There were " + unresolved
510 + " forward references left unresolved on the stack.");
512 if (failedtoresolve > 0)
514 System.err.println("SERIOUS! " + failedtoresolve
515 + " resolvable forward references failed to resolve.");
517 if (incompleteSeqs != null && incompleteSeqs.size() > 0)
520 "Jalview Project Import: There are " + incompleteSeqs.size()
521 + " sequences which may have incomplete metadata.");
522 if (incompleteSeqs.size() < 10)
524 for (SequenceI s : incompleteSeqs.values())
526 System.err.println(s.toString());
532 "Too many to report. Skipping output of incomplete sequences.");
538 * This maintains a map of viewports, the key being the seqSetId. Important to
539 * set historyItem and redoList for multiple views
541 Map<String, AlignViewport> viewportsAdded = new HashMap<>();
543 Map<String, AlignmentAnnotation> annotationIds = new HashMap<>();
545 String uniqueSetSuffix = "";
548 * List of pdbfiles added to Jar
550 List<String> pdbfiles = null;
552 // SAVES SEVERAL ALIGNMENT WINDOWS TO SAME JARFILE
553 public void saveState(File statefile)
555 FileOutputStream fos = null;
560 fos = new FileOutputStream(statefile);
562 JarOutputStream jout = new JarOutputStream(fos);
566 } catch (Exception e)
568 Cache.log.error("Couln't write Jalview state to " + statefile, e);
569 // TODO: inform user of the problem - they need to know if their data was
571 if (errorMessage == null)
573 errorMessage = "Did't write Jalview Archive to output file '"
574 + statefile + "' - See console error log for details";
578 errorMessage += "(Didn't write Jalview Archive to output file '"
589 } catch (IOException e)
599 * Writes a jalview project archive to the given Jar output stream.
603 public void saveState(JarOutputStream jout)
605 AlignFrame[] frames = Desktop.getAlignFrames();
611 saveAllFrames(Arrays.asList(frames), jout);
615 * core method for storing state for a set of AlignFrames.
618 * - frames involving all data to be exported (including containing
621 * - project output stream
623 private void saveAllFrames(List<AlignFrame> frames, JarOutputStream jout)
625 Hashtable<String, AlignFrame> dsses = new Hashtable<>();
628 * ensure cached data is clear before starting
630 // todo tidy up seqRefIds, seqsToIds initialisation / reset
632 splitFrameCandidates.clear();
637 // NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS
638 // //////////////////////////////////////////////////
640 List<String> shortNames = new ArrayList<>();
641 List<String> viewIds = new ArrayList<>();
644 for (int i = frames.size() - 1; i > -1; i--)
646 AlignFrame af = frames.get(i);
648 if (skipList != null && skipList
649 .containsKey(af.getViewport().getSequenceSetId()))
654 String shortName = makeFilename(af, shortNames);
656 int apSize = af.getAlignPanels().size();
658 for (int ap = 0; ap < apSize; ap++)
660 AlignmentPanel apanel = (AlignmentPanel) af.getAlignPanels()
662 String fileName = apSize == 1 ? shortName : ap + shortName;
663 if (!fileName.endsWith(".xml"))
665 fileName = fileName + ".xml";
668 saveState(apanel, fileName, jout, viewIds);
670 String dssid = getDatasetIdRef(
671 af.getViewport().getAlignment().getDataset());
672 if (!dsses.containsKey(dssid))
674 dsses.put(dssid, af);
679 writeDatasetFor(dsses, "" + jout.hashCode() + " " + uniqueSetSuffix,
685 } catch (Exception foo)
690 } catch (Exception ex)
692 // TODO: inform user of the problem - they need to know if their data was
694 if (errorMessage == null)
696 errorMessage = "Couldn't write Jalview Archive - see error output for details";
698 ex.printStackTrace();
703 * Generates a distinct file name, based on the title of the AlignFrame, by
704 * appending _n for increasing n until an unused name is generated. The new
705 * name (without its extension) is added to the list.
709 * @return the generated name, with .xml extension
711 protected String makeFilename(AlignFrame af, List<String> namesUsed)
713 String shortName = af.getTitle();
715 if (shortName.indexOf(File.separatorChar) > -1)
717 shortName = shortName
718 .substring(shortName.lastIndexOf(File.separatorChar) + 1);
723 while (namesUsed.contains(shortName))
725 if (shortName.endsWith("_" + (count - 1)))
727 shortName = shortName.substring(0, shortName.lastIndexOf("_"));
730 shortName = shortName.concat("_" + count);
734 namesUsed.add(shortName);
736 if (!shortName.endsWith(".xml"))
738 shortName = shortName + ".xml";
743 // USE THIS METHOD TO SAVE A SINGLE ALIGNMENT WINDOW
744 public boolean saveAlignment(AlignFrame af, String jarFile,
749 // create backupfiles object and get new temp filename destination
750 BackupFiles backupfiles = new BackupFiles(jarFile);
751 FileOutputStream fos = new FileOutputStream(
752 backupfiles.getTempFilePath());
754 JarOutputStream jout = new JarOutputStream(fos);
755 List<AlignFrame> frames = new ArrayList<>();
757 // resolve splitframes
758 if (af.getViewport().getCodingComplement() != null)
760 frames = ((SplitFrame) af.getSplitViewContainer()).getAlignFrames();
766 saveAllFrames(frames, jout);
770 } catch (Exception foo)
775 boolean success = true;
777 backupfiles.setWriteSuccess(success);
778 success = backupfiles.rollBackupsAndRenameTempFile();
781 } catch (Exception ex)
783 errorMessage = "Couldn't Write alignment view to Jalview Archive - see error output for details";
784 ex.printStackTrace();
789 private void writeDatasetFor(Hashtable<String, AlignFrame> dsses,
790 String fileName, JarOutputStream jout)
793 for (String dssids : dsses.keySet())
795 AlignFrame _af = dsses.get(dssids);
796 String jfileName = fileName + " Dataset for " + _af.getTitle();
797 if (!jfileName.endsWith(".xml"))
799 jfileName = jfileName + ".xml";
801 saveState(_af.alignPanel, jfileName, true, jout, null);
806 * create a JalviewModel from an alignment view and marshall it to a
810 * panel to create jalview model for
812 * name of alignment panel written to output stream
819 public JalviewModel saveState(AlignmentPanel ap, String fileName,
820 JarOutputStream jout, List<String> viewIds)
822 return saveState(ap, fileName, false, jout, viewIds);
826 * create a JalviewModel from an alignment view and marshall it to a
830 * panel to create jalview model for
832 * name of alignment panel written to output stream
834 * when true, only write the dataset for the alignment, not the data
835 * associated with the view.
841 public JalviewModel saveState(AlignmentPanel ap, String fileName,
842 boolean storeDS, JarOutputStream jout, List<String> viewIds)
846 viewIds = new ArrayList<>();
851 List<UserColourScheme> userColours = new ArrayList<>();
853 AlignViewport av = ap.av;
854 ViewportRanges vpRanges = av.getRanges();
856 final ObjectFactory objectFactory = new ObjectFactory();
857 JalviewModel object = objectFactory.createJalviewModel();
858 object.setVamsasModel(new VAMSAS());
860 // object.setCreationDate(new java.util.Date(System.currentTimeMillis()));
863 GregorianCalendar c = new GregorianCalendar();
864 DatatypeFactory datatypeFactory = DatatypeFactory.newInstance();
865 XMLGregorianCalendar now = datatypeFactory.newXMLGregorianCalendar(c);// gregorianCalendar);
866 object.setCreationDate(now);
867 } catch (DatatypeConfigurationException e)
869 System.err.println("error writing date: " + e.toString());
872 jalview.bin.Cache.getDefault("VERSION", "Development Build"));
875 * rjal is full height alignment, jal is actual alignment with full metadata
876 * but excludes hidden sequences.
878 jalview.datamodel.AlignmentI rjal = av.getAlignment(), jal = rjal;
880 if (av.hasHiddenRows())
882 rjal = jal.getHiddenSequences().getFullAlignment();
885 SequenceSet vamsasSet = new SequenceSet();
887 // JalviewModelSequence jms = new JalviewModelSequence();
889 vamsasSet.setGapChar(jal.getGapCharacter() + "");
891 if (jal.getDataset() != null)
893 // dataset id is the dataset's hashcode
894 vamsasSet.setDatasetId(getDatasetIdRef(jal.getDataset()));
897 // switch jal and the dataset
898 jal = jal.getDataset();
902 if (jal.getProperties() != null)
904 Enumeration en = jal.getProperties().keys();
905 while (en.hasMoreElements())
907 String key = en.nextElement().toString();
908 SequenceSetProperties ssp = new SequenceSetProperties();
910 ssp.setValue(jal.getProperties().get(key).toString());
911 // vamsasSet.addSequenceSetProperties(ssp);
912 vamsasSet.getSequenceSetProperties().add(ssp);
917 Set<String> calcIdSet = new HashSet<>();
918 // record the set of vamsas sequence XML POJO we create.
919 HashMap<String, Sequence> vamsasSetIds = new HashMap<>();
921 for (final SequenceI jds : rjal.getSequences())
923 final SequenceI jdatasq = jds.getDatasetSequence() == null ? jds
924 : jds.getDatasetSequence();
925 String id = seqHash(jds);
926 if (vamsasSetIds.get(id) == null)
928 if (seqRefIds.get(id) != null && !storeDS)
930 // This happens for two reasons: 1. multiple views are being
932 // 2. the hashCode has collided with another sequence's code. This
934 // HAPPEN! (PF00072.15.stk does this)
935 // JBPNote: Uncomment to debug writing out of files that do not read
936 // back in due to ArrayOutOfBoundExceptions.
937 // System.err.println("vamsasSeq backref: "+id+"");
938 // System.err.println(jds.getName()+"
939 // "+jds.getStart()+"-"+jds.getEnd()+" "+jds.getSequenceAsString());
940 // System.err.println("Hashcode: "+seqHash(jds));
941 // SequenceI rsq = (SequenceI) seqRefIds.get(id + "");
942 // System.err.println(rsq.getName()+"
943 // "+rsq.getStart()+"-"+rsq.getEnd()+" "+rsq.getSequenceAsString());
944 // System.err.println("Hashcode: "+seqHash(rsq));
948 vamsasSeq = createVamsasSequence(id, jds);
949 // vamsasSet.addSequence(vamsasSeq);
950 vamsasSet.getSequence().add(vamsasSeq);
951 vamsasSetIds.put(id, vamsasSeq);
952 seqRefIds.put(id, jds);
956 jseq.setStart(jds.getStart());
957 jseq.setEnd(jds.getEnd());
958 jseq.setColour(av.getSequenceColour(jds).getRGB());
960 jseq.setId(id); // jseq id should be a string not a number
963 // Store any sequences this sequence represents
964 if (av.hasHiddenRows())
966 // use rjal, contains the full height alignment
968 av.getAlignment().getHiddenSequences().isHidden(jds));
970 if (av.isHiddenRepSequence(jds))
972 jalview.datamodel.SequenceI[] reps = av
973 .getRepresentedSequences(jds).getSequencesInOrder(rjal);
975 for (int h = 0; h < reps.length; h++)
979 // jseq.addHiddenSequences(rjal.findIndex(reps[h]));
980 jseq.getHiddenSequences().add(rjal.findIndex(reps[h]));
985 // mark sequence as reference - if it is the reference for this view
988 jseq.setViewreference(jds == jal.getSeqrep());
992 // TODO: omit sequence features from each alignment view's XML dump if we
993 // are storing dataset
994 List<SequenceFeature> sfs = jds.getSequenceFeatures();
995 for (SequenceFeature sf : sfs)
997 // Features features = new Features();
998 Feature features = new Feature();
1000 features.setBegin(sf.getBegin());
1001 features.setEnd(sf.getEnd());
1002 features.setDescription(sf.getDescription());
1003 features.setType(sf.getType());
1004 features.setFeatureGroup(sf.getFeatureGroup());
1005 features.setScore(sf.getScore());
1006 if (sf.links != null)
1008 for (int l = 0; l < sf.links.size(); l++)
1010 OtherData keyValue = new OtherData();
1011 keyValue.setKey("LINK_" + l);
1012 keyValue.setValue(sf.links.elementAt(l).toString());
1013 // features.addOtherData(keyValue);
1014 features.getOtherData().add(keyValue);
1017 if (sf.otherDetails != null)
1020 * save feature attributes, which may be simple strings or
1021 * map valued (have sub-attributes)
1023 for (Entry<String, Object> entry : sf.otherDetails.entrySet())
1025 String key = entry.getKey();
1026 Object value = entry.getValue();
1027 if (value instanceof Map<?, ?>)
1029 for (Entry<String, Object> subAttribute : ((Map<String, Object>) value)
1032 OtherData otherData = new OtherData();
1033 otherData.setKey(key);
1034 otherData.setKey2(subAttribute.getKey());
1035 otherData.setValue(subAttribute.getValue().toString());
1036 // features.addOtherData(otherData);
1037 features.getOtherData().add(otherData);
1042 OtherData otherData = new OtherData();
1043 otherData.setKey(key);
1044 otherData.setValue(value.toString());
1045 // features.addOtherData(otherData);
1046 features.getOtherData().add(otherData);
1051 // jseq.addFeatures(features);
1052 jseq.getFeatures().add(features);
1055 if (jdatasq.getAllPDBEntries() != null)
1057 Enumeration<PDBEntry> en = jdatasq.getAllPDBEntries().elements();
1058 while (en.hasMoreElements())
1060 Pdbids pdb = new Pdbids();
1061 jalview.datamodel.PDBEntry entry = en.nextElement();
1063 String pdbId = entry.getId();
1065 pdb.setType(entry.getType());
1068 * Store any structure views associated with this sequence. This
1069 * section copes with duplicate entries in the project, so a dataset
1070 * only view *should* be coped with sensibly.
1072 // This must have been loaded, is it still visible?
1073 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1074 String matchedFile = null;
1075 for (int f = frames.length - 1; f > -1; f--)
1077 if (frames[f] instanceof StructureViewerBase)
1079 StructureViewerBase viewFrame = (StructureViewerBase) frames[f];
1080 matchedFile = saveStructureState(ap, jds, pdb, entry, viewIds,
1081 matchedFile, viewFrame);
1083 * Only store each structure viewer's state once in the project
1084 * jar. First time through only (storeDS==false)
1086 String viewId = viewFrame.getViewId();
1087 if (!storeDS && !viewIds.contains(viewId))
1089 viewIds.add(viewId);
1092 String viewerState = viewFrame.getStateInfo();
1093 writeJarEntry(jout, getViewerJarEntryName(viewId),
1094 viewerState.getBytes());
1095 } catch (IOException e)
1098 "Error saving viewer state: " + e.getMessage());
1104 if (matchedFile != null || entry.getFile() != null)
1106 if (entry.getFile() != null)
1109 matchedFile = entry.getFile();
1111 pdb.setFile(matchedFile); // entry.getFile());
1112 if (pdbfiles == null)
1114 pdbfiles = new ArrayList<>();
1117 if (!pdbfiles.contains(pdbId))
1119 pdbfiles.add(pdbId);
1120 copyFileToJar(jout, matchedFile, pdbId);
1124 Enumeration<String> props = entry.getProperties();
1125 if (props.hasMoreElements())
1127 // PdbentryItem item = new PdbentryItem();
1128 while (props.hasMoreElements())
1130 Property prop = new Property();
1131 String key = props.nextElement();
1133 prop.setValue(entry.getProperty(key).toString());
1134 // item.addProperty(prop);
1135 pdb.getProperty().add(prop);
1137 // pdb.addPdbentryItem(item);
1140 // jseq.addPdbids(pdb);
1141 jseq.getPdbids().add(pdb);
1145 saveRnaViewers(jout, jseq, jds, viewIds, ap, storeDS);
1147 // jms.addJSeq(jseq);
1148 object.getJSeq().add(jseq);
1151 if (!storeDS && av.hasHiddenRows())
1153 jal = av.getAlignment();
1157 if (storeDS && jal.getCodonFrames() != null)
1159 List<AlignedCodonFrame> jac = jal.getCodonFrames();
1160 for (AlignedCodonFrame acf : jac)
1162 AlcodonFrame alc = new AlcodonFrame();
1163 if (acf.getProtMappings() != null
1164 && acf.getProtMappings().length > 0)
1166 boolean hasMap = false;
1167 SequenceI[] dnas = acf.getdnaSeqs();
1168 jalview.datamodel.Mapping[] pmaps = acf.getProtMappings();
1169 for (int m = 0; m < pmaps.length; m++)
1171 AlcodMap alcmap = new AlcodMap();
1172 alcmap.setDnasq(seqHash(dnas[m]));
1174 createVamsasMapping(pmaps[m], dnas[m], null, false));
1175 // alc.addAlcodMap(alcmap);
1176 alc.getAlcodMap().add(alcmap);
1181 // vamsasSet.addAlcodonFrame(alc);
1182 vamsasSet.getAlcodonFrame().add(alc);
1185 // TODO: delete this ? dead code from 2.8.3->2.9 ?
1187 // AlcodonFrame alc = new AlcodonFrame();
1188 // vamsasSet.addAlcodonFrame(alc);
1189 // for (int p = 0; p < acf.aaWidth; p++)
1191 // Alcodon cmap = new Alcodon();
1192 // if (acf.codons[p] != null)
1194 // // Null codons indicate a gapped column in the translated peptide
1196 // cmap.setPos1(acf.codons[p][0]);
1197 // cmap.setPos2(acf.codons[p][1]);
1198 // cmap.setPos3(acf.codons[p][2]);
1200 // alc.addAlcodon(cmap);
1202 // if (acf.getProtMappings() != null
1203 // && acf.getProtMappings().length > 0)
1205 // SequenceI[] dnas = acf.getdnaSeqs();
1206 // jalview.datamodel.Mapping[] pmaps = acf.getProtMappings();
1207 // for (int m = 0; m < pmaps.length; m++)
1209 // AlcodMap alcmap = new AlcodMap();
1210 // alcmap.setDnasq(seqHash(dnas[m]));
1211 // alcmap.setMapping(createVamsasMapping(pmaps[m], dnas[m], null,
1213 // alc.addAlcodMap(alcmap);
1220 // /////////////////////////////////
1221 if (!storeDS && av.getCurrentTree() != null)
1223 // FIND ANY ASSOCIATED TREES
1224 // NOT IMPLEMENTED FOR HEADLESS STATE AT PRESENT
1225 if (Desktop.desktop != null)
1227 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1229 for (int t = 0; t < frames.length; t++)
1231 if (frames[t] instanceof TreePanel)
1233 TreePanel tp = (TreePanel) frames[t];
1235 if (tp.getTreeCanvas().getViewport().getAlignment() == jal)
1237 JalviewModel.Tree tree = new JalviewModel.Tree();
1238 tree.setTitle(tp.getTitle());
1239 tree.setCurrentTree((av.getCurrentTree() == tp.getTree()));
1240 tree.setNewick(tp.getTree().print());
1241 tree.setThreshold(tp.getTreeCanvas().getThreshold());
1243 tree.setFitToWindow(tp.fitToWindow.getState());
1244 tree.setFontName(tp.getTreeFont().getName());
1245 tree.setFontSize(tp.getTreeFont().getSize());
1246 tree.setFontStyle(tp.getTreeFont().getStyle());
1247 tree.setMarkUnlinked(tp.placeholdersMenu.getState());
1249 tree.setShowBootstrap(tp.bootstrapMenu.getState());
1250 tree.setShowDistances(tp.distanceMenu.getState());
1252 tree.setHeight(tp.getHeight());
1253 tree.setWidth(tp.getWidth());
1254 tree.setXpos(tp.getX());
1255 tree.setYpos(tp.getY());
1256 tree.setId(makeHashCode(tp, null));
1257 tree.setLinkToAllViews(
1258 tp.getTreeCanvas().isApplyToAllViews());
1260 // jms.addTree(tree);
1261 object.getTree().add(tree);
1271 if (!storeDS && Desktop.desktop != null)
1273 for (JInternalFrame frame : Desktop.desktop.getAllFrames())
1275 if (frame instanceof PCAPanel)
1277 PCAPanel panel = (PCAPanel) frame;
1278 if (panel.getAlignViewport().getAlignment() == jal)
1280 savePCA(panel, object);
1288 * store forward refs from an annotationRow to any groups
1290 IdentityHashMap<SequenceGroup, String> groupRefs = new IdentityHashMap<>();
1293 for (SequenceI sq : jal.getSequences())
1295 // Store annotation on dataset sequences only
1296 AlignmentAnnotation[] aa = sq.getAnnotation();
1297 if (aa != null && aa.length > 0)
1299 storeAlignmentAnnotation(aa, groupRefs, av, calcIdSet, storeDS,
1306 if (jal.getAlignmentAnnotation() != null)
1308 // Store the annotation shown on the alignment.
1309 AlignmentAnnotation[] aa = jal.getAlignmentAnnotation();
1310 storeAlignmentAnnotation(aa, groupRefs, av, calcIdSet, storeDS,
1315 if (jal.getGroups() != null)
1317 JGroup[] groups = new JGroup[jal.getGroups().size()];
1319 for (jalview.datamodel.SequenceGroup sg : jal.getGroups())
1321 JGroup jGroup = new JGroup();
1322 groups[++i] = jGroup;
1324 jGroup.setStart(sg.getStartRes());
1325 jGroup.setEnd(sg.getEndRes());
1326 jGroup.setName(sg.getName());
1327 if (groupRefs.containsKey(sg))
1329 // group has references so set its ID field
1330 jGroup.setId(groupRefs.get(sg));
1332 ColourSchemeI colourScheme = sg.getColourScheme();
1333 if (colourScheme != null)
1335 ResidueShaderI groupColourScheme = sg.getGroupColourScheme();
1336 if (groupColourScheme.conservationApplied())
1338 jGroup.setConsThreshold(groupColourScheme.getConservationInc());
1340 if (colourScheme instanceof jalview.schemes.UserColourScheme)
1343 setUserColourScheme(colourScheme, userColours,
1348 jGroup.setColour(colourScheme.getSchemeName());
1351 else if (colourScheme instanceof jalview.schemes.AnnotationColourGradient)
1353 jGroup.setColour("AnnotationColourGradient");
1354 jGroup.setAnnotationColours(constructAnnotationColours(
1355 (jalview.schemes.AnnotationColourGradient) colourScheme,
1356 userColours, object));
1358 else if (colourScheme instanceof jalview.schemes.UserColourScheme)
1361 setUserColourScheme(colourScheme, userColours, object));
1365 jGroup.setColour(colourScheme.getSchemeName());
1368 jGroup.setPidThreshold(groupColourScheme.getThreshold());
1371 jGroup.setOutlineColour(sg.getOutlineColour().getRGB());
1372 jGroup.setDisplayBoxes(sg.getDisplayBoxes());
1373 jGroup.setDisplayText(sg.getDisplayText());
1374 jGroup.setColourText(sg.getColourText());
1375 jGroup.setTextCol1(sg.textColour.getRGB());
1376 jGroup.setTextCol2(sg.textColour2.getRGB());
1377 jGroup.setTextColThreshold(sg.thresholdTextColour);
1378 jGroup.setShowUnconserved(sg.getShowNonconserved());
1379 jGroup.setIgnoreGapsinConsensus(sg.getIgnoreGapsConsensus());
1380 jGroup.setShowConsensusHistogram(sg.isShowConsensusHistogram());
1381 jGroup.setShowSequenceLogo(sg.isShowSequenceLogo());
1382 jGroup.setNormaliseSequenceLogo(sg.isNormaliseSequenceLogo());
1383 for (SequenceI seq : sg.getSequences())
1385 // jGroup.addSeq(seqHash(seq));
1386 jGroup.getSeq().add(seqHash(seq));
1390 //jms.setJGroup(groups);
1392 for (JGroup grp : groups)
1394 object.getJGroup().add(grp);
1399 // /////////SAVE VIEWPORT
1400 Viewport view = new Viewport();
1401 view.setTitle(ap.alignFrame.getTitle());
1402 view.setSequenceSetId(
1403 makeHashCode(av.getSequenceSetId(), av.getSequenceSetId()));
1404 view.setId(av.getViewId());
1405 if (av.getCodingComplement() != null)
1407 view.setComplementId(av.getCodingComplement().getViewId());
1409 view.setViewName(av.getViewName());
1410 view.setGatheredViews(av.isGatherViewsHere());
1412 Rectangle size = ap.av.getExplodedGeometry();
1413 Rectangle position = size;
1416 size = ap.alignFrame.getBounds();
1417 if (av.getCodingComplement() != null)
1419 position = ((SplitFrame) ap.alignFrame.getSplitViewContainer())
1427 view.setXpos(position.x);
1428 view.setYpos(position.y);
1430 view.setWidth(size.width);
1431 view.setHeight(size.height);
1433 view.setStartRes(vpRanges.getStartRes());
1434 view.setStartSeq(vpRanges.getStartSeq());
1436 if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme)
1438 view.setBgColour(setUserColourScheme(av.getGlobalColourScheme(),
1439 userColours, object));
1442 .getGlobalColourScheme() instanceof jalview.schemes.AnnotationColourGradient)
1444 AnnotationColourScheme ac = constructAnnotationColours(
1445 (jalview.schemes.AnnotationColourGradient) av
1446 .getGlobalColourScheme(),
1447 userColours, object);
1449 view.setAnnotationColours(ac);
1450 view.setBgColour("AnnotationColourGradient");
1454 view.setBgColour(ColourSchemeProperty
1455 .getColourName(av.getGlobalColourScheme()));
1458 ResidueShaderI vcs = av.getResidueShading();
1459 ColourSchemeI cs = av.getGlobalColourScheme();
1463 if (vcs.conservationApplied())
1465 view.setConsThreshold(vcs.getConservationInc());
1466 if (cs instanceof jalview.schemes.UserColourScheme)
1468 view.setBgColour(setUserColourScheme(cs, userColours, object));
1471 view.setPidThreshold(vcs.getThreshold());
1474 view.setConservationSelected(av.getConservationSelected());
1475 view.setPidSelected(av.getAbovePIDThreshold());
1476 final Font font = av.getFont();
1477 view.setFontName(font.getName());
1478 view.setFontSize(font.getSize());
1479 view.setFontStyle(font.getStyle());
1480 view.setScaleProteinAsCdna(av.getViewStyle().isScaleProteinAsCdna());
1481 view.setRenderGaps(av.isRenderGaps());
1482 view.setShowAnnotation(av.isShowAnnotation());
1483 view.setShowBoxes(av.getShowBoxes());
1484 view.setShowColourText(av.getColourText());
1485 view.setShowFullId(av.getShowJVSuffix());
1486 view.setRightAlignIds(av.isRightAlignIds());
1487 view.setShowSequenceFeatures(av.isShowSequenceFeatures());
1488 view.setShowText(av.getShowText());
1489 view.setShowUnconserved(av.getShowUnconserved());
1490 view.setWrapAlignment(av.getWrapAlignment());
1491 view.setTextCol1(av.getTextColour().getRGB());
1492 view.setTextCol2(av.getTextColour2().getRGB());
1493 view.setTextColThreshold(av.getThresholdTextColour());
1494 view.setShowConsensusHistogram(av.isShowConsensusHistogram());
1495 view.setShowSequenceLogo(av.isShowSequenceLogo());
1496 view.setNormaliseSequenceLogo(av.isNormaliseSequenceLogo());
1497 view.setShowGroupConsensus(av.isShowGroupConsensus());
1498 view.setShowGroupConservation(av.isShowGroupConservation());
1499 view.setShowNPfeatureTooltip(av.isShowNPFeats());
1500 view.setShowDbRefTooltip(av.isShowDBRefs());
1501 view.setFollowHighlight(av.isFollowHighlight());
1502 view.setFollowSelection(av.followSelection);
1503 view.setIgnoreGapsinConsensus(av.isIgnoreGapsConsensus());
1504 if (av.getFeaturesDisplayed() != null)
1506 FeatureSettings fs = new FeatureSettings();
1508 FeatureRenderer fr = ap.getSeqPanel().seqCanvas
1509 .getFeatureRenderer();
1510 String[] renderOrder = fr.getRenderOrder().toArray(new String[0]);
1512 Vector<String> settingsAdded = new Vector<>();
1513 if (renderOrder != null)
1515 for (String featureType : renderOrder)
1517 FeatureSettings.Setting setting = new FeatureSettings.Setting();
1518 setting.setType(featureType);
1521 * save any filter for the feature type
1523 FeatureMatcherSetI filter = fr.getFeatureFilter(featureType);
1524 if (filter != null) {
1525 Iterator<FeatureMatcherI> filters = filter.getMatchers().iterator();
1526 FeatureMatcherI firstFilter = filters.next();
1527 setting.setMatcherSet(Jalview2XML.marshalFilter(
1528 firstFilter, filters, filter.isAnded()));
1532 * save colour scheme for the feature type
1534 FeatureColourI fcol = fr.getFeatureStyle(featureType);
1535 if (!fcol.isSimpleColour())
1537 setting.setColour(fcol.getMaxColour().getRGB());
1538 setting.setMincolour(fcol.getMinColour().getRGB());
1539 setting.setMin(fcol.getMin());
1540 setting.setMax(fcol.getMax());
1541 setting.setColourByLabel(fcol.isColourByLabel());
1542 if (fcol.isColourByAttribute())
1544 String[] attName = fcol.getAttributeName();
1545 setting.getAttributeName().add(attName[0]);
1546 if (attName.length > 1)
1548 setting.getAttributeName().add(attName[1]);
1551 setting.setAutoScale(fcol.isAutoScaled());
1552 setting.setThreshold(fcol.getThreshold());
1553 Color noColour = fcol.getNoColour();
1554 if (noColour == null)
1556 setting.setNoValueColour(NoValueColour.NONE);
1558 else if (noColour.equals(fcol.getMaxColour()))
1560 setting.setNoValueColour(NoValueColour.MAX);
1564 setting.setNoValueColour(NoValueColour.MIN);
1566 // -1 = No threshold, 0 = Below, 1 = Above
1567 setting.setThreshstate(fcol.isAboveThreshold() ? 1
1568 : (fcol.isBelowThreshold() ? 0 : -1));
1572 setting.setColour(fcol.getColour().getRGB());
1576 av.getFeaturesDisplayed().isVisible(featureType));
1578 .getOrder(featureType);
1581 setting.setOrder(rorder);
1583 /// fs.addSetting(setting);
1584 fs.getSetting().add(setting);
1585 settingsAdded.addElement(featureType);
1589 // is groups actually supposed to be a map here ?
1590 Iterator<String> en = fr.getFeatureGroups().iterator();
1591 Vector<String> groupsAdded = new Vector<>();
1592 while (en.hasNext())
1594 String grp = en.next();
1595 if (groupsAdded.contains(grp))
1599 Group g = new Group();
1601 g.setDisplay(((Boolean) fr.checkGroupVisibility(grp, false))
1604 fs.getGroup().add(g);
1605 groupsAdded.addElement(grp);
1607 // jms.setFeatureSettings(fs);
1608 object.setFeatureSettings(fs);
1611 if (av.hasHiddenColumns())
1613 jalview.datamodel.HiddenColumns hidden = av.getAlignment()
1614 .getHiddenColumns();
1617 warn("REPORT BUG: avoided null columnselection bug (DMAM reported). Please contact Jim about this.");
1621 Iterator<int[]> hiddenRegions = hidden.iterator();
1622 while (hiddenRegions.hasNext())
1624 int[] region = hiddenRegions.next();
1625 HiddenColumns hc = new HiddenColumns();
1626 hc.setStart(region[0]);
1627 hc.setEnd(region[1]);
1628 // view.addHiddenColumns(hc);
1629 view.getHiddenColumns().add(hc);
1633 if (calcIdSet.size() > 0)
1635 for (String calcId : calcIdSet)
1637 if (calcId.trim().length() > 0)
1639 CalcIdParam cidp = createCalcIdParam(calcId, av);
1640 // Some calcIds have no parameters.
1643 // view.addCalcIdParam(cidp);
1644 view.getCalcIdParam().add(cidp);
1650 // jms.addViewport(view);
1651 object.getViewport().add(view);
1653 // object.setJalviewModelSequence(jms);
1654 // object.getVamsasModel().addSequenceSet(vamsasSet);
1655 object.getVamsasModel().getSequenceSet().add(vamsasSet);
1657 if (jout != null && fileName != null)
1659 // We may not want to write the object to disk,
1660 // eg we can copy the alignViewport to a new view object
1661 // using save and then load
1664 System.out.println("Writing jar entry " + fileName);
1665 JarEntry entry = new JarEntry(fileName);
1666 jout.putNextEntry(entry);
1667 PrintWriter pout = new PrintWriter(
1668 new OutputStreamWriter(jout, UTF_8));
1669 JAXBContext jaxbContext = JAXBContext
1670 .newInstance(JalviewModel.class);
1671 Marshaller jaxbMarshaller = jaxbContext.createMarshaller();
1673 // output pretty printed
1674 // jaxbMarshaller.setProperty(Marshaller.JAXB_FORMATTED_OUTPUT, true);
1675 jaxbMarshaller.marshal(
1676 new ObjectFactory().createJalviewModel(object), pout);
1678 // jaxbMarshaller.marshal(object, pout);
1679 // marshaller.marshal(object);
1682 } catch (Exception ex)
1684 // TODO: raise error in GUI if marshalling failed.
1685 System.err.println("Error writing Jalview project");
1686 ex.printStackTrace();
1693 * Writes PCA viewer attributes and computed values to an XML model object and
1694 * adds it to the JalviewModel. Any exceptions are reported by logging.
1696 protected void savePCA(PCAPanel panel, JalviewModel object)
1700 PcaViewer viewer = new PcaViewer();
1701 viewer.setHeight(panel.getHeight());
1702 viewer.setWidth(panel.getWidth());
1703 viewer.setXpos(panel.getX());
1704 viewer.setYpos(panel.getY());
1705 viewer.setTitle(panel.getTitle());
1706 PCAModel pcaModel = panel.getPcaModel();
1707 viewer.setScoreModelName(pcaModel.getScoreModelName());
1708 viewer.setXDim(panel.getSelectedDimensionIndex(X));
1709 viewer.setYDim(panel.getSelectedDimensionIndex(Y));
1710 viewer.setZDim(panel.getSelectedDimensionIndex(Z));
1712 panel.getRotatableCanvas().getBackgroundColour().getRGB());
1713 viewer.setScaleFactor(panel.getRotatableCanvas().getScaleFactor());
1714 float[] spMin = panel.getRotatableCanvas().getSeqMin();
1715 SeqPointMin spmin = new SeqPointMin();
1716 spmin.setXPos(spMin[0]);
1717 spmin.setYPos(spMin[1]);
1718 spmin.setZPos(spMin[2]);
1719 viewer.setSeqPointMin(spmin);
1720 float[] spMax = panel.getRotatableCanvas().getSeqMax();
1721 SeqPointMax spmax = new SeqPointMax();
1722 spmax.setXPos(spMax[0]);
1723 spmax.setYPos(spMax[1]);
1724 spmax.setZPos(spMax[2]);
1725 viewer.setSeqPointMax(spmax);
1726 viewer.setShowLabels(panel.getRotatableCanvas().isShowLabels());
1727 viewer.setLinkToAllViews(
1728 panel.getRotatableCanvas().isApplyToAllViews());
1729 SimilarityParamsI sp = pcaModel.getSimilarityParameters();
1730 viewer.setIncludeGaps(sp.includeGaps());
1731 viewer.setMatchGaps(sp.matchGaps());
1732 viewer.setIncludeGappedColumns(sp.includeGappedColumns());
1733 viewer.setDenominateByShortestLength(sp.denominateByShortestLength());
1736 * sequence points on display
1738 for (jalview.datamodel.SequencePoint spt : pcaModel
1739 .getSequencePoints())
1741 SequencePoint point = new SequencePoint();
1742 point.setSequenceRef(seqHash(spt.getSequence()));
1743 point.setXPos(spt.coord.x);
1744 point.setYPos(spt.coord.y);
1745 point.setZPos(spt.coord.z);
1746 viewer.getSequencePoint().add(point);
1750 * (end points of) axes on display
1752 for (Point p : panel.getRotatableCanvas().getAxisEndPoints())
1755 Axis axis = new Axis();
1759 viewer.getAxis().add(axis);
1763 * raw PCA data (note we are not restoring PCA inputs here -
1764 * alignment view, score model, similarity parameters)
1766 PcaDataType data = new PcaDataType();
1767 viewer.setPcaData(data);
1768 PCA pca = pcaModel.getPcaData();
1770 DoubleMatrix pm = new DoubleMatrix();
1771 saveDoubleMatrix(pca.getPairwiseScores(), pm);
1772 data.setPairwiseMatrix(pm);
1774 DoubleMatrix tm = new DoubleMatrix();
1775 saveDoubleMatrix(pca.getTridiagonal(), tm);
1776 data.setTridiagonalMatrix(tm);
1778 DoubleMatrix eigenMatrix = new DoubleMatrix();
1779 data.setEigenMatrix(eigenMatrix);
1780 saveDoubleMatrix(pca.getEigenmatrix(), eigenMatrix);
1782 object.getPcaViewer().add(viewer);
1783 } catch (Throwable t)
1785 Cache.log.error("Error saving PCA: " + t.getMessage());
1790 * Stores values from a matrix into an XML element, including (if present) the
1795 * @see #loadDoubleMatrix(DoubleMatrix)
1797 protected void saveDoubleMatrix(MatrixI m, DoubleMatrix xmlMatrix)
1799 xmlMatrix.setRows(m.height());
1800 xmlMatrix.setColumns(m.width());
1801 for (int i = 0; i < m.height(); i++)
1803 DoubleVector row = new DoubleVector();
1804 for (int j = 0; j < m.width(); j++)
1806 row.getV().add(m.getValue(i, j));
1808 xmlMatrix.getRow().add(row);
1810 if (m.getD() != null)
1812 DoubleVector dVector = new DoubleVector();
1813 for (double d : m.getD())
1815 dVector.getV().add(d);
1817 xmlMatrix.setD(dVector);
1819 if (m.getE() != null)
1821 DoubleVector eVector = new DoubleVector();
1822 for (double e : m.getE())
1824 eVector.getV().add(e);
1826 xmlMatrix.setE(eVector);
1831 * Loads XML matrix data into a new Matrix object, including the D and/or E
1832 * vectors (if present)
1836 * @see Jalview2XML#saveDoubleMatrix(MatrixI, DoubleMatrix)
1838 protected MatrixI loadDoubleMatrix(DoubleMatrix mData)
1840 int rows = mData.getRows();
1841 double[][] vals = new double[rows][];
1843 for (int i = 0; i < rows; i++)
1845 List<Double> dVector = mData.getRow().get(i).getV();
1846 vals[i] = new double[dVector.size()];
1848 for (Double d : dVector)
1854 MatrixI m = new Matrix(vals);
1856 if (mData.getD() != null)
1858 List<Double> dVector = mData.getD().getV();
1859 double[] vec = new double[dVector.size()];
1861 for (Double d : dVector)
1867 if (mData.getE() != null)
1869 List<Double> dVector = mData.getE().getV();
1870 double[] vec = new double[dVector.size()];
1872 for (Double d : dVector)
1883 * Save any Varna viewers linked to this sequence. Writes an rnaViewer element
1884 * for each viewer, with
1886 * <li>viewer geometry (position, size, split pane divider location)</li>
1887 * <li>index of the selected structure in the viewer (currently shows gapped
1889 * <li>the id of the annotation holding RNA secondary structure</li>
1890 * <li>(currently only one SS is shown per viewer, may be more in future)</li>
1892 * Varna viewer state is also written out (in native Varna XML) to separate
1893 * project jar entries. A separate entry is written for each RNA structure
1894 * displayed, with the naming convention
1896 * <li>rna_viewId_sequenceId_annotationId_[gapped|trimmed]</li>
1904 * @param storeDataset
1906 protected void saveRnaViewers(JarOutputStream jout, JSeq jseq,
1907 final SequenceI jds, List<String> viewIds, AlignmentPanel ap,
1908 boolean storeDataset)
1910 if (Desktop.desktop == null)
1914 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1915 for (int f = frames.length - 1; f > -1; f--)
1917 if (frames[f] instanceof AppVarna)
1919 AppVarna varna = (AppVarna) frames[f];
1921 * link the sequence to every viewer that is showing it and is linked to
1922 * its alignment panel
1924 if (varna.isListeningFor(jds) && ap == varna.getAlignmentPanel())
1926 String viewId = varna.getViewId();
1927 RnaViewer rna = new RnaViewer();
1928 rna.setViewId(viewId);
1929 rna.setTitle(varna.getTitle());
1930 rna.setXpos(varna.getX());
1931 rna.setYpos(varna.getY());
1932 rna.setWidth(varna.getWidth());
1933 rna.setHeight(varna.getHeight());
1934 rna.setDividerLocation(varna.getDividerLocation());
1935 rna.setSelectedRna(varna.getSelectedIndex());
1936 // jseq.addRnaViewer(rna);
1937 jseq.getRnaViewer().add(rna);
1940 * Store each Varna panel's state once in the project per sequence.
1941 * First time through only (storeDataset==false)
1943 // boolean storeSessions = false;
1944 // String sequenceViewId = viewId + seqsToIds.get(jds);
1945 // if (!storeDataset && !viewIds.contains(sequenceViewId))
1947 // viewIds.add(sequenceViewId);
1948 // storeSessions = true;
1950 for (RnaModel model : varna.getModels())
1952 if (model.seq == jds)
1955 * VARNA saves each view (sequence or alignment secondary
1956 * structure, gapped or trimmed) as a separate XML file
1958 String jarEntryName = rnaSessions.get(model);
1959 if (jarEntryName == null)
1962 String varnaStateFile = varna.getStateInfo(model.rna);
1963 jarEntryName = RNA_PREFIX + viewId + "_" + nextCounter();
1964 copyFileToJar(jout, varnaStateFile, jarEntryName);
1965 rnaSessions.put(model, jarEntryName);
1967 SecondaryStructure ss = new SecondaryStructure();
1968 String annotationId = varna.getAnnotation(jds).annotationId;
1969 ss.setAnnotationId(annotationId);
1970 ss.setViewerState(jarEntryName);
1971 ss.setGapped(model.gapped);
1972 ss.setTitle(model.title);
1973 // rna.addSecondaryStructure(ss);
1974 rna.getSecondaryStructure().add(ss);
1983 * Copy the contents of a file to a new entry added to the output jar
1987 * @param jarEntryName
1989 protected void copyFileToJar(JarOutputStream jout, String infilePath,
1990 String jarEntryName)
1992 DataInputStream dis = null;
1995 File file = new File(infilePath);
1996 if (file.exists() && jout != null)
1998 dis = new DataInputStream(new FileInputStream(file));
1999 byte[] data = new byte[(int) file.length()];
2000 dis.readFully(data);
2001 writeJarEntry(jout, jarEntryName, data);
2003 } catch (Exception ex)
2005 ex.printStackTrace();
2013 } catch (IOException e)
2022 * Write the data to a new entry of given name in the output jar file
2025 * @param jarEntryName
2027 * @throws IOException
2029 protected void writeJarEntry(JarOutputStream jout, String jarEntryName,
2030 byte[] data) throws IOException
2034 System.out.println("Writing jar entry " + jarEntryName);
2035 jout.putNextEntry(new JarEntry(jarEntryName));
2036 DataOutputStream dout = new DataOutputStream(jout);
2037 dout.write(data, 0, data.length);
2044 * Save the state of a structure viewer
2049 * the archive XML element under which to save the state
2052 * @param matchedFile
2056 protected String saveStructureState(AlignmentPanel ap, SequenceI jds,
2057 Pdbids pdb, PDBEntry entry, List<String> viewIds,
2058 String matchedFile, StructureViewerBase viewFrame)
2060 final AAStructureBindingModel bindingModel = viewFrame.getBinding();
2063 * Look for any bindings for this viewer to the PDB file of interest
2064 * (including part matches excluding chain id)
2066 for (int peid = 0; peid < bindingModel.getPdbCount(); peid++)
2068 final PDBEntry pdbentry = bindingModel.getPdbEntry(peid);
2069 final String pdbId = pdbentry.getId();
2070 if (!pdbId.equals(entry.getId())
2071 && !(entry.getId().length() > 4 && entry.getId().toLowerCase()
2072 .startsWith(pdbId.toLowerCase())))
2075 * not interested in a binding to a different PDB entry here
2079 if (matchedFile == null)
2081 matchedFile = pdbentry.getFile();
2083 else if (!matchedFile.equals(pdbentry.getFile()))
2086 "Probably lost some PDB-Sequence mappings for this structure file (which apparently has same PDB Entry code): "
2087 + pdbentry.getFile());
2091 // can get at it if the ID
2092 // match is ambiguous (e.g.
2095 for (int smap = 0; smap < viewFrame.getBinding()
2096 .getSequence()[peid].length; smap++)
2098 // if (jal.findIndex(jmol.jmb.sequence[peid][smap]) > -1)
2099 if (jds == viewFrame.getBinding().getSequence()[peid][smap])
2101 StructureState state = new StructureState();
2102 state.setVisible(true);
2103 state.setXpos(viewFrame.getX());
2104 state.setYpos(viewFrame.getY());
2105 state.setWidth(viewFrame.getWidth());
2106 state.setHeight(viewFrame.getHeight());
2107 final String viewId = viewFrame.getViewId();
2108 state.setViewId(viewId);
2109 state.setAlignwithAlignPanel(viewFrame.isUsedforaligment(ap));
2110 state.setColourwithAlignPanel(viewFrame.isUsedforcolourby(ap));
2111 state.setColourByJmol(viewFrame.isColouredByViewer());
2112 state.setType(viewFrame.getViewerType().toString());
2113 // pdb.addStructureState(state);
2114 pdb.getStructureState().add(state);
2122 * Populates the AnnotationColourScheme xml for save. This captures the
2123 * settings of the options in the 'Colour by Annotation' dialog.
2126 * @param userColours
2130 private AnnotationColourScheme constructAnnotationColours(
2131 AnnotationColourGradient acg, List<UserColourScheme> userColours,
2134 AnnotationColourScheme ac = new AnnotationColourScheme();
2135 ac.setAboveThreshold(acg.getAboveThreshold());
2136 ac.setThreshold(acg.getAnnotationThreshold());
2137 // 2.10.2 save annotationId (unique) not annotation label
2138 ac.setAnnotation(acg.getAnnotation().annotationId);
2139 if (acg.getBaseColour() instanceof UserColourScheme)
2142 setUserColourScheme(acg.getBaseColour(), userColours, jm));
2147 ColourSchemeProperty.getColourName(acg.getBaseColour()));
2150 ac.setMaxColour(acg.getMaxColour().getRGB());
2151 ac.setMinColour(acg.getMinColour().getRGB());
2152 ac.setPerSequence(acg.isSeqAssociated());
2153 ac.setPredefinedColours(acg.isPredefinedColours());
2157 private void storeAlignmentAnnotation(AlignmentAnnotation[] aa,
2158 IdentityHashMap<SequenceGroup, String> groupRefs,
2159 AlignmentViewport av, Set<String> calcIdSet, boolean storeDS,
2160 SequenceSet vamsasSet)
2163 for (int i = 0; i < aa.length; i++)
2165 Annotation an = new Annotation();
2167 AlignmentAnnotation annotation = aa[i];
2168 if (annotation.annotationId != null)
2170 annotationIds.put(annotation.annotationId, annotation);
2173 an.setId(annotation.annotationId);
2175 an.setVisible(annotation.visible);
2177 an.setDescription(annotation.description);
2179 if (annotation.sequenceRef != null)
2181 // 2.9 JAL-1781 xref on sequence id rather than name
2182 an.setSequenceRef(seqsToIds.get(annotation.sequenceRef));
2184 if (annotation.groupRef != null)
2186 String groupIdr = groupRefs.get(annotation.groupRef);
2187 if (groupIdr == null)
2189 // make a locally unique String
2190 groupRefs.put(annotation.groupRef,
2191 groupIdr = ("" + System.currentTimeMillis()
2192 + annotation.groupRef.getName()
2193 + groupRefs.size()));
2195 an.setGroupRef(groupIdr.toString());
2198 // store all visualization attributes for annotation
2199 an.setGraphHeight(annotation.graphHeight);
2200 an.setCentreColLabels(annotation.centreColLabels);
2201 an.setScaleColLabels(annotation.scaleColLabel);
2202 an.setShowAllColLabels(annotation.showAllColLabels);
2203 an.setBelowAlignment(annotation.belowAlignment);
2205 if (annotation.graph > 0)
2208 an.setGraphType(annotation.graph);
2209 an.setGraphGroup(annotation.graphGroup);
2210 if (annotation.getThreshold() != null)
2212 ThresholdLine line = new ThresholdLine();
2213 line.setLabel(annotation.getThreshold().label);
2214 line.setValue(annotation.getThreshold().value);
2215 line.setColour(annotation.getThreshold().colour.getRGB());
2216 an.setThresholdLine(line);
2224 an.setLabel(annotation.label);
2226 if (annotation == av.getAlignmentQualityAnnot()
2227 || annotation == av.getAlignmentConservationAnnotation()
2228 || annotation == av.getAlignmentConsensusAnnotation()
2229 || annotation.autoCalculated)
2231 // new way of indicating autocalculated annotation -
2232 an.setAutoCalculated(annotation.autoCalculated);
2234 if (annotation.hasScore())
2236 an.setScore(annotation.getScore());
2239 if (annotation.getCalcId() != null)
2241 calcIdSet.add(annotation.getCalcId());
2242 an.setCalcId(annotation.getCalcId());
2244 if (annotation.hasProperties())
2246 for (String pr : annotation.getProperties())
2248 jalview.xml.binding.jalview.Annotation.Property prop = new jalview.xml.binding.jalview.Annotation.Property();
2250 prop.setValue(annotation.getProperty(pr));
2251 // an.addProperty(prop);
2252 an.getProperty().add(prop);
2256 AnnotationElement ae;
2257 if (annotation.annotations != null)
2259 an.setScoreOnly(false);
2260 for (int a = 0; a < annotation.annotations.length; a++)
2262 if ((annotation == null) || (annotation.annotations[a] == null))
2267 ae = new AnnotationElement();
2268 if (annotation.annotations[a].description != null)
2270 ae.setDescription(annotation.annotations[a].description);
2272 if (annotation.annotations[a].displayCharacter != null)
2274 ae.setDisplayCharacter(
2275 annotation.annotations[a].displayCharacter);
2278 if (!Float.isNaN(annotation.annotations[a].value))
2280 ae.setValue(annotation.annotations[a].value);
2284 if (annotation.annotations[a].secondaryStructure > ' ')
2286 ae.setSecondaryStructure(
2287 annotation.annotations[a].secondaryStructure + "");
2290 if (annotation.annotations[a].colour != null
2291 && annotation.annotations[a].colour != java.awt.Color.black)
2293 ae.setColour(annotation.annotations[a].colour.getRGB());
2296 // an.addAnnotationElement(ae);
2297 an.getAnnotationElement().add(ae);
2298 if (annotation.autoCalculated)
2300 // only write one non-null entry into the annotation row -
2301 // sufficient to get the visualization attributes necessary to
2309 an.setScoreOnly(true);
2311 if (!storeDS || (storeDS && !annotation.autoCalculated))
2313 // skip autocalculated annotation - these are only provided for
2315 // vamsasSet.addAnnotation(an);
2316 vamsasSet.getAnnotation().add(an);
2322 private CalcIdParam createCalcIdParam(String calcId, AlignViewport av)
2324 AutoCalcSetting settings = av.getCalcIdSettingsFor(calcId);
2325 if (settings != null)
2327 CalcIdParam vCalcIdParam = new CalcIdParam();
2328 vCalcIdParam.setCalcId(calcId);
2329 // vCalcIdParam.addServiceURL(settings.getServiceURI());
2330 vCalcIdParam.getServiceURL().add(settings.getServiceURI());
2331 // generic URI allowing a third party to resolve another instance of the
2332 // service used for this calculation
2333 for (String url : settings.getServiceURLs())
2335 // vCalcIdParam.addServiceURL(urls);
2336 vCalcIdParam.getServiceURL().add(url);
2338 vCalcIdParam.setVersion("1.0");
2339 if (settings.getPreset() != null)
2341 WsParamSetI setting = settings.getPreset();
2342 vCalcIdParam.setName(setting.getName());
2343 vCalcIdParam.setDescription(setting.getDescription());
2347 vCalcIdParam.setName("");
2348 vCalcIdParam.setDescription("Last used parameters");
2350 // need to be able to recover 1) settings 2) user-defined presets or
2351 // recreate settings from preset 3) predefined settings provided by
2352 // service - or settings that can be transferred (or discarded)
2353 vCalcIdParam.setParameters(
2354 settings.getWsParamFile().replace("\n", "|\\n|"));
2355 vCalcIdParam.setAutoUpdate(settings.isAutoUpdate());
2356 // todo - decide if updateImmediately is needed for any projects.
2358 return vCalcIdParam;
2363 private boolean recoverCalcIdParam(CalcIdParam calcIdParam,
2366 if (calcIdParam.getVersion().equals("1.0"))
2368 final String[] calcIds = calcIdParam.getServiceURL().toArray(new String[0]);
2369 Jws2Instance service = Jws2Discoverer.getDiscoverer()
2370 .getPreferredServiceFor(calcIds);
2371 if (service != null)
2373 WsParamSetI parmSet = null;
2376 parmSet = service.getParamStore().parseServiceParameterFile(
2377 calcIdParam.getName(), calcIdParam.getDescription(),
2379 calcIdParam.getParameters().replace("|\\n|", "\n"));
2380 } catch (IOException x)
2382 warn("Couldn't parse parameter data for "
2383 + calcIdParam.getCalcId(), x);
2386 List<ArgumentI> argList = null;
2387 if (calcIdParam.getName().length() > 0)
2389 parmSet = service.getParamStore()
2390 .getPreset(calcIdParam.getName());
2391 if (parmSet != null)
2393 // TODO : check we have a good match with settings in AACon -
2394 // otherwise we'll need to create a new preset
2399 argList = parmSet.getArguments();
2402 AAConSettings settings = new AAConSettings(
2403 calcIdParam.isAutoUpdate(), service, parmSet, argList);
2404 av.setCalcIdSettingsFor(calcIdParam.getCalcId(), settings,
2405 calcIdParam.isNeedsUpdate());
2410 warn("Cannot resolve a service for the parameters used in this project. Try configuring a JABAWS server.");
2414 throw new Error(MessageManager.formatMessage(
2415 "error.unsupported_version_calcIdparam", new Object[]
2416 { calcIdParam.toString() }));
2420 * External mapping between jalview objects and objects yielding a valid and
2421 * unique object ID string. This is null for normal Jalview project IO, but
2422 * non-null when a jalview project is being read or written as part of a
2425 IdentityHashMap jv2vobj = null;
2428 * Construct a unique ID for jvobj using either existing bindings or if none
2429 * exist, the result of the hashcode call for the object.
2432 * jalview data object
2433 * @return unique ID for referring to jvobj
2435 private String makeHashCode(Object jvobj, String altCode)
2437 if (jv2vobj != null)
2439 Object id = jv2vobj.get(jvobj);
2442 return id.toString();
2444 // check string ID mappings
2445 if (jvids2vobj != null && jvobj instanceof String)
2447 id = jvids2vobj.get(jvobj);
2451 return id.toString();
2453 // give up and warn that something has gone wrong
2454 warn("Cannot find ID for object in external mapping : " + jvobj);
2460 * return local jalview object mapped to ID, if it exists
2464 * @return null or object bound to idcode
2466 private Object retrieveExistingObj(String idcode)
2468 if (idcode != null && vobj2jv != null)
2470 return vobj2jv.get(idcode);
2476 * binding from ID strings from external mapping table to jalview data model
2479 private Hashtable vobj2jv;
2481 private Sequence createVamsasSequence(String id, SequenceI jds)
2483 return createVamsasSequence(true, id, jds, null);
2486 private Sequence createVamsasSequence(boolean recurse, String id,
2487 SequenceI jds, SequenceI parentseq)
2489 Sequence vamsasSeq = new Sequence();
2490 vamsasSeq.setId(id);
2491 vamsasSeq.setName(jds.getName());
2492 vamsasSeq.setSequence(jds.getSequenceAsString());
2493 vamsasSeq.setDescription(jds.getDescription());
2494 jalview.datamodel.DBRefEntry[] dbrefs = null;
2495 if (jds.getDatasetSequence() != null)
2497 vamsasSeq.setDsseqid(seqHash(jds.getDatasetSequence()));
2501 // seqId==dsseqid so we can tell which sequences really are
2502 // dataset sequences only
2503 vamsasSeq.setDsseqid(id);
2504 dbrefs = jds.getDBRefs();
2505 if (parentseq == null)
2512 * save any dbrefs; special subclass GeneLocus is flagged as 'locus'
2516 for (int d = 0; d < dbrefs.length; d++)
2518 DBRef dbref = new DBRef();
2519 DBRefEntry dbRefEntry = dbrefs[d];
2520 dbref.setSource(dbRefEntry.getSource());
2521 dbref.setVersion(dbRefEntry.getVersion());
2522 dbref.setAccessionId(dbRefEntry.getAccessionId());
2523 if (dbRefEntry instanceof GeneLocus)
2525 dbref.setLocus(true);
2527 if (dbRefEntry.hasMap())
2529 Mapping mp = createVamsasMapping(dbRefEntry.getMap(), parentseq,
2531 dbref.setMapping(mp);
2533 vamsasSeq.getDBRef().add(dbref);
2539 private Mapping createVamsasMapping(jalview.datamodel.Mapping jmp,
2540 SequenceI parentseq, SequenceI jds, boolean recurse)
2543 if (jmp.getMap() != null)
2547 jalview.util.MapList mlst = jmp.getMap();
2548 List<int[]> r = mlst.getFromRanges();
2549 for (int[] range : r)
2551 MapListFrom mfrom = new MapListFrom();
2552 mfrom.setStart(range[0]);
2553 mfrom.setEnd(range[1]);
2554 // mp.addMapListFrom(mfrom);
2555 mp.getMapListFrom().add(mfrom);
2557 r = mlst.getToRanges();
2558 for (int[] range : r)
2560 MapListTo mto = new MapListTo();
2561 mto.setStart(range[0]);
2562 mto.setEnd(range[1]);
2563 // mp.addMapListTo(mto);
2564 mp.getMapListTo().add(mto);
2566 mp.setMapFromUnit(BigInteger.valueOf(mlst.getFromRatio()));
2567 mp.setMapToUnit(BigInteger.valueOf(mlst.getToRatio()));
2568 if (jmp.getTo() != null)
2570 // MappingChoice mpc = new MappingChoice();
2572 // check/create ID for the sequence referenced by getTo()
2575 SequenceI ps = null;
2576 if (parentseq != jmp.getTo()
2577 && parentseq.getDatasetSequence() != jmp.getTo())
2579 // chaining dbref rather than a handshaking one
2580 jmpid = seqHash(ps = jmp.getTo());
2584 jmpid = seqHash(ps = parentseq);
2586 // mpc.setDseqFor(jmpid);
2587 mp.setDseqFor(jmpid);
2588 if (!seqRefIds.containsKey(jmpid))
2590 jalview.bin.Cache.log.debug("creatign new DseqFor ID");
2591 seqRefIds.put(jmpid, ps);
2595 jalview.bin.Cache.log.debug("reusing DseqFor ID");
2598 // mp.setMappingChoice(mpc);
2604 String setUserColourScheme(jalview.schemes.ColourSchemeI cs,
2605 List<UserColourScheme> userColours, JalviewModel jm)
2608 jalview.schemes.UserColourScheme ucs = (jalview.schemes.UserColourScheme) cs;
2609 boolean newucs = false;
2610 if (!userColours.contains(ucs))
2612 userColours.add(ucs);
2615 id = "ucs" + userColours.indexOf(ucs);
2618 // actually create the scheme's entry in the XML model
2619 java.awt.Color[] colours = ucs.getColours();
2620 UserColours uc = new UserColours();
2621 // UserColourScheme jbucs = new UserColourScheme();
2622 JalviewUserColours jbucs = new JalviewUserColours();
2624 for (int i = 0; i < colours.length; i++)
2626 Colour col = new Colour();
2627 col.setName(ResidueProperties.aa[i]);
2628 col.setRGB(jalview.util.Format.getHexString(colours[i]));
2629 // jbucs.addColour(col);
2630 jbucs.getColour().add(col);
2632 if (ucs.getLowerCaseColours() != null)
2634 colours = ucs.getLowerCaseColours();
2635 for (int i = 0; i < colours.length; i++)
2637 Colour col = new Colour();
2638 col.setName(ResidueProperties.aa[i].toLowerCase());
2639 col.setRGB(jalview.util.Format.getHexString(colours[i]));
2640 // jbucs.addColour(col);
2641 jbucs.getColour().add(col);
2646 uc.setUserColourScheme(jbucs);
2647 // jm.addUserColours(uc);
2648 jm.getUserColours().add(uc);
2654 jalview.schemes.UserColourScheme getUserColourScheme(
2655 JalviewModel jm, String id)
2657 List<UserColours> uc = jm.getUserColours();
2658 UserColours colours = null;
2660 for (int i = 0; i < uc.length; i++)
2662 if (uc[i].getId().equals(id))
2669 for (UserColours c : uc)
2671 if (c.getId().equals(id))
2678 java.awt.Color[] newColours = new java.awt.Color[24];
2680 for (int i = 0; i < 24; i++)
2682 newColours[i] = new java.awt.Color(Integer.parseInt(
2683 // colours.getUserColourScheme().getColour(i).getRGB(), 16));
2684 colours.getUserColourScheme().getColour().get(i).getRGB(),
2688 jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(
2691 if (colours.getUserColourScheme().getColour().size()/*Count()*/ > 24)
2693 newColours = new java.awt.Color[23];
2694 for (int i = 0; i < 23; i++)
2696 newColours[i] = new java.awt.Color(Integer.parseInt(
2697 colours.getUserColourScheme().getColour().get(i + 24)
2701 ucs.setLowerCaseColours(newColours);
2708 * contains last error message (if any) encountered by XML loader.
2710 String errorMessage = null;
2713 * flag to control whether the Jalview2XML_V1 parser should be deferred to if
2714 * exceptions are raised during project XML parsing
2716 public boolean attemptversion1parse = false;
2719 * Load a jalview project archive from a jar file
2722 * - HTTP URL or filename
2724 public AlignFrame loadJalviewAlign(final String file)
2727 jalview.gui.AlignFrame af = null;
2731 // create list to store references for any new Jmol viewers created
2732 newStructureViewers = new Vector<>();
2733 // UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
2734 // Workaround is to make sure caller implements the JarInputStreamProvider
2736 // so we can re-open the jar input stream for each entry.
2738 jarInputStreamProvider jprovider = createjarInputStreamProvider(file);
2739 af = loadJalviewAlign(jprovider);
2742 af.setMenusForViewport();
2744 } catch (MalformedURLException e)
2746 errorMessage = "Invalid URL format for '" + file + "'";
2752 SwingUtilities.invokeAndWait(new Runnable()
2757 setLoadingFinishedForNewStructureViewers();
2760 } catch (Exception x)
2762 System.err.println("Error loading alignment: " + x.getMessage());
2768 private jarInputStreamProvider createjarInputStreamProvider(
2769 final String file) throws MalformedURLException
2772 errorMessage = null;
2773 uniqueSetSuffix = null;
2775 viewportsAdded.clear();
2776 frefedSequence = null;
2778 if (file.startsWith("http://"))
2780 url = new URL(file);
2782 final URL _url = url;
2783 return new jarInputStreamProvider()
2787 public JarInputStream getJarInputStream() throws IOException
2791 return new JarInputStream(_url.openStream());
2795 return new JarInputStream(new FileInputStream(file));
2800 public String getFilename()
2808 * Recover jalview session from a jalview project archive. Caller may
2809 * initialise uniqueSetSuffix, seqRefIds, viewportsAdded and frefedSequence
2810 * themselves. Any null fields will be initialised with default values,
2811 * non-null fields are left alone.
2816 public AlignFrame loadJalviewAlign(final jarInputStreamProvider jprovider)
2818 errorMessage = null;
2819 if (uniqueSetSuffix == null)
2821 uniqueSetSuffix = System.currentTimeMillis() % 100000 + "";
2823 if (seqRefIds == null)
2827 AlignFrame af = null, _af = null;
2828 IdentityHashMap<AlignmentI, AlignmentI> importedDatasets = new IdentityHashMap<>();
2829 Map<String, AlignFrame> gatherToThisFrame = new HashMap<>();
2830 final String file = jprovider.getFilename();
2833 JarInputStream jin = null;
2834 JarEntry jarentry = null;
2839 jin = jprovider.getJarInputStream();
2840 for (int i = 0; i < entryCount; i++)
2842 jarentry = jin.getNextJarEntry();
2845 if (jarentry != null && jarentry.getName().endsWith(".xml"))
2847 InputStreamReader in = new InputStreamReader(jin, UTF_8);
2848 // JalviewModel object = new JalviewModel();
2850 JAXBContext jc = JAXBContext
2851 .newInstance("jalview.xml.binding.jalview");
2852 XMLStreamReader streamReader = XMLInputFactory.newInstance()
2853 .createXMLStreamReader(jin);
2854 javax.xml.bind.Unmarshaller um = jc.createUnmarshaller();
2855 JAXBElement<JalviewModel> jbe = um
2856 .unmarshal(streamReader, JalviewModel.class);
2857 JalviewModel object = jbe.getValue();
2860 Unmarshaller unmar = new Unmarshaller(object);
2861 unmar.setValidation(false);
2862 object = (JalviewModel) unmar.unmarshal(in);
2864 if (true) // !skipViewport(object))
2866 _af = loadFromObject(object, file, true, jprovider);
2867 if (_af != null && object.getViewport().size() > 0)
2868 // getJalviewModelSequence().getViewportCount() > 0)
2872 // store a reference to the first view
2875 if (_af.getViewport().isGatherViewsHere())
2877 // if this is a gathered view, keep its reference since
2878 // after gathering views, only this frame will remain
2880 gatherToThisFrame.put(_af.getViewport().getSequenceSetId(),
2883 // Save dataset to register mappings once all resolved
2884 importedDatasets.put(
2885 af.getViewport().getAlignment().getDataset(),
2886 af.getViewport().getAlignment().getDataset());
2891 else if (jarentry != null)
2893 // Some other file here.
2896 } while (jarentry != null);
2897 resolveFrefedSequences();
2898 } catch (IOException ex)
2900 ex.printStackTrace();
2901 errorMessage = "Couldn't locate Jalview XML file : " + file;
2903 "Exception whilst loading jalview XML file : " + ex + "\n");
2904 } catch (Exception ex)
2906 System.err.println("Parsing as Jalview Version 2 file failed.");
2907 ex.printStackTrace(System.err);
2908 if (attemptversion1parse)
2910 // used to attempt to parse as V1 castor-generated xml
2912 if (Desktop.instance != null)
2914 Desktop.instance.stopLoading();
2918 System.out.println("Successfully loaded archive file");
2921 ex.printStackTrace();
2924 "Exception whilst loading jalview XML file : " + ex + "\n");
2925 } catch (OutOfMemoryError e)
2927 // Don't use the OOM Window here
2928 errorMessage = "Out of memory loading jalview XML file";
2929 System.err.println("Out of memory whilst loading jalview XML file");
2930 e.printStackTrace();
2934 * Regather multiple views (with the same sequence set id) to the frame (if
2935 * any) that is flagged as the one to gather to, i.e. convert them to tabbed
2936 * views instead of separate frames. Note this doesn't restore a state where
2937 * some expanded views in turn have tabbed views - the last "first tab" read
2938 * in will play the role of gatherer for all.
2940 for (AlignFrame fr : gatherToThisFrame.values())
2942 Desktop.instance.gatherViews(fr);
2945 restoreSplitFrames();
2946 for (AlignmentI ds : importedDatasets.keySet())
2948 if (ds.getCodonFrames() != null)
2950 StructureSelectionManager
2951 .getStructureSelectionManager(Desktop.instance)
2952 .registerMappings(ds.getCodonFrames());
2955 if (errorMessage != null)
2960 if (Desktop.instance != null)
2962 Desktop.instance.stopLoading();
2969 * Try to reconstruct and display SplitFrame windows, where each contains
2970 * complementary dna and protein alignments. Done by pairing up AlignFrame
2971 * objects (created earlier) which have complementary viewport ids associated.
2973 protected void restoreSplitFrames()
2975 List<SplitFrame> gatherTo = new ArrayList<>();
2976 List<AlignFrame> addedToSplitFrames = new ArrayList<>();
2977 Map<String, AlignFrame> dna = new HashMap<>();
2980 * Identify the DNA alignments
2982 for (Entry<Viewport, AlignFrame> candidate : splitFrameCandidates
2985 AlignFrame af = candidate.getValue();
2986 if (af.getViewport().getAlignment().isNucleotide())
2988 dna.put(candidate.getKey().getId(), af);
2993 * Try to match up the protein complements
2995 for (Entry<Viewport, AlignFrame> candidate : splitFrameCandidates
2998 AlignFrame af = candidate.getValue();
2999 if (!af.getViewport().getAlignment().isNucleotide())
3001 String complementId = candidate.getKey().getComplementId();
3002 // only non-null complements should be in the Map
3003 if (complementId != null && dna.containsKey(complementId))
3005 final AlignFrame dnaFrame = dna.get(complementId);
3006 SplitFrame sf = createSplitFrame(dnaFrame, af);
3007 addedToSplitFrames.add(dnaFrame);
3008 addedToSplitFrames.add(af);
3009 dnaFrame.setMenusForViewport();
3010 af.setMenusForViewport();
3011 if (af.getViewport().isGatherViewsHere())
3020 * Open any that we failed to pair up (which shouldn't happen!) as
3021 * standalone AlignFrame's.
3023 for (Entry<Viewport, AlignFrame> candidate : splitFrameCandidates
3026 AlignFrame af = candidate.getValue();
3027 if (!addedToSplitFrames.contains(af))
3029 Viewport view = candidate.getKey();
3030 Desktop.addInternalFrame(af, view.getTitle(),
3031 safeInt(view.getWidth()), safeInt(view.getHeight()));
3032 af.setMenusForViewport();
3033 System.err.println("Failed to restore view " + view.getTitle()
3034 + " to split frame");
3039 * Gather back into tabbed views as flagged.
3041 for (SplitFrame sf : gatherTo)
3043 Desktop.instance.gatherViews(sf);
3046 splitFrameCandidates.clear();
3050 * Construct and display one SplitFrame holding DNA and protein alignments.
3053 * @param proteinFrame
3056 protected SplitFrame createSplitFrame(AlignFrame dnaFrame,
3057 AlignFrame proteinFrame)
3059 SplitFrame splitFrame = new SplitFrame(dnaFrame, proteinFrame);
3060 String title = MessageManager.getString("label.linked_view_title");
3061 int width = (int) dnaFrame.getBounds().getWidth();
3062 int height = (int) (dnaFrame.getBounds().getHeight()
3063 + proteinFrame.getBounds().getHeight() + 50);
3066 * SplitFrame location is saved to both enclosed frames
3068 splitFrame.setLocation(dnaFrame.getX(), dnaFrame.getY());
3069 Desktop.addInternalFrame(splitFrame, title, width, height);
3072 * And compute cDNA consensus (couldn't do earlier with consensus as
3073 * mappings were not yet present)
3075 proteinFrame.getViewport().alignmentChanged(proteinFrame.alignPanel);
3081 * check errorMessage for a valid error message and raise an error box in the
3082 * GUI or write the current errorMessage to stderr and then clear the error
3085 protected void reportErrors()
3087 reportErrors(false);
3090 protected void reportErrors(final boolean saving)
3092 if (errorMessage != null)
3094 final String finalErrorMessage = errorMessage;
3097 javax.swing.SwingUtilities.invokeLater(new Runnable()
3102 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
3104 "Error " + (saving ? "saving" : "loading")
3106 JvOptionPane.WARNING_MESSAGE);
3112 System.err.println("Problem loading Jalview file: " + errorMessage);
3115 errorMessage = null;
3118 Map<String, String> alreadyLoadedPDB = new HashMap<>();
3121 * when set, local views will be updated from view stored in JalviewXML
3122 * Currently (28th Sep 2008) things will go horribly wrong in vamsas document
3123 * sync if this is set to true.
3125 private final boolean updateLocalViews = false;
3128 * Returns the path to a temporary file holding the PDB file for the given PDB
3129 * id. The first time of asking, searches for a file of that name in the
3130 * Jalview project jar, and copies it to a new temporary file. Any repeat
3131 * requests just return the path to the file previously created.
3137 String loadPDBFile(jarInputStreamProvider jprovider, String pdbId,
3140 if (alreadyLoadedPDB.containsKey(pdbId))
3142 return alreadyLoadedPDB.get(pdbId).toString();
3145 String tempFile = copyJarEntry(jprovider, pdbId, "jalview_pdb",
3147 if (tempFile != null)
3149 alreadyLoadedPDB.put(pdbId, tempFile);
3155 * Copies the jar entry of given name to a new temporary file and returns the
3156 * path to the file, or null if the entry is not found.
3159 * @param jarEntryName
3161 * a prefix for the temporary file name, must be at least three
3164 * null or original file - so new file can be given the same suffix
3168 protected String copyJarEntry(jarInputStreamProvider jprovider,
3169 String jarEntryName, String prefix, String origFile)
3171 BufferedReader in = null;
3172 PrintWriter out = null;
3173 String suffix = ".tmp";
3174 if (origFile == null)
3176 origFile = jarEntryName;
3178 int sfpos = origFile.lastIndexOf(".");
3179 if (sfpos > -1 && sfpos < (origFile.length() - 3))
3181 suffix = "." + origFile.substring(sfpos + 1);
3185 JarInputStream jin = jprovider.getJarInputStream();
3187 * if (jprovider.startsWith("http://")) { jin = new JarInputStream(new
3188 * URL(jprovider).openStream()); } else { jin = new JarInputStream(new
3189 * FileInputStream(jprovider)); }
3192 JarEntry entry = null;
3195 entry = jin.getNextJarEntry();
3196 } while (entry != null && !entry.getName().equals(jarEntryName));
3199 in = new BufferedReader(new InputStreamReader(jin, UTF_8));
3200 File outFile = File.createTempFile(prefix, suffix);
3201 outFile.deleteOnExit();
3202 out = new PrintWriter(new FileOutputStream(outFile));
3205 while ((data = in.readLine()) != null)
3210 String t = outFile.getAbsolutePath();
3215 warn("Couldn't find entry in Jalview Jar for " + jarEntryName);
3217 } catch (Exception ex)
3219 ex.printStackTrace();
3227 } catch (IOException e)
3241 private class JvAnnotRow
3243 public JvAnnotRow(int i, AlignmentAnnotation jaa)
3250 * persisted version of annotation row from which to take vis properties
3252 public jalview.datamodel.AlignmentAnnotation template;
3255 * original position of the annotation row in the alignment
3261 * Load alignment frame from jalview XML DOM object
3263 * @param jalviewModel
3266 * filename source string
3267 * @param loadTreesAndStructures
3268 * when false only create Viewport
3270 * data source provider
3271 * @return alignment frame created from view stored in DOM
3273 AlignFrame loadFromObject(JalviewModel jalviewModel, String file,
3274 boolean loadTreesAndStructures, jarInputStreamProvider jprovider)
3276 SequenceSet vamsasSet = jalviewModel.getVamsasModel().getSequenceSet().get(0);
3277 List<Sequence> vamsasSeqs = vamsasSet.getSequence();
3279 // JalviewModelSequence jms = object.getJalviewModelSequence();
3281 // Viewport view = (jms.getViewportCount() > 0) ? jms.getViewport(0)
3283 Viewport view = (jalviewModel.getViewport().size() > 0)
3284 ? jalviewModel.getViewport().get(0)
3287 // ////////////////////////////////
3288 // INITIALISE ALIGNMENT SEQUENCESETID AND VIEWID
3291 // If we just load in the same jar file again, the sequenceSetId
3292 // will be the same, and we end up with multiple references
3293 // to the same sequenceSet. We must modify this id on load
3294 // so that each load of the file gives a unique id
3297 * used to resolve correct alignment dataset for alignments with multiple
3300 String uniqueSeqSetId = null;
3301 String viewId = null;
3304 uniqueSeqSetId = view.getSequenceSetId() + uniqueSetSuffix;
3305 viewId = (view.getId() == null ? null
3306 : view.getId() + uniqueSetSuffix);
3309 // ////////////////////////////////
3312 List<SequenceI> hiddenSeqs = null;
3314 List<SequenceI> tmpseqs = new ArrayList<>();
3316 boolean multipleView = false;
3317 SequenceI referenceseqForView = null;
3318 // JSeq[] jseqs = object.getJalviewModelSequence().getJSeq();
3319 List<JSeq> jseqs = jalviewModel.getJSeq();
3320 int vi = 0; // counter in vamsasSeq array
3321 for (int i = 0; i < jseqs.size(); i++)
3323 JSeq jseq = jseqs.get(i);
3324 String seqId = jseq.getId();
3326 SequenceI tmpSeq = seqRefIds.get(seqId);
3329 if (!incompleteSeqs.containsKey(seqId))
3331 // may not need this check, but keep it for at least 2.9,1 release
3332 if (tmpSeq.getStart() != jseq.getStart()
3333 || tmpSeq.getEnd() != jseq.getEnd())
3336 "Warning JAL-2154 regression: updating start/end for sequence "
3337 + tmpSeq.toString() + " to " + jseq);
3342 incompleteSeqs.remove(seqId);
3344 if (vamsasSeqs.size() > vi
3345 && vamsasSeqs.get(vi).getId().equals(seqId))
3347 // most likely we are reading a dataset XML document so
3348 // update from vamsasSeq section of XML for this sequence
3349 tmpSeq.setName(vamsasSeqs.get(vi).getName());
3350 tmpSeq.setDescription(vamsasSeqs.get(vi).getDescription());
3351 tmpSeq.setSequence(vamsasSeqs.get(vi).getSequence());
3356 // reading multiple views, so vamsasSeq set is a subset of JSeq
3357 multipleView = true;
3359 tmpSeq.setStart(jseq.getStart());
3360 tmpSeq.setEnd(jseq.getEnd());
3361 tmpseqs.add(tmpSeq);
3365 Sequence vamsasSeq = vamsasSeqs.get(vi);
3366 tmpSeq = new jalview.datamodel.Sequence(vamsasSeq.getName(),
3367 vamsasSeq.getSequence());
3368 tmpSeq.setDescription(vamsasSeq.getDescription());
3369 tmpSeq.setStart(jseq.getStart());
3370 tmpSeq.setEnd(jseq.getEnd());
3371 tmpSeq.setVamsasId(uniqueSetSuffix + seqId);
3372 seqRefIds.put(vamsasSeq.getId(), tmpSeq);
3373 tmpseqs.add(tmpSeq);
3377 if (safeBoolean(jseq.isViewreference()))
3379 referenceseqForView = tmpseqs.get(tmpseqs.size() - 1);
3382 if (jseq.isHidden() != null && jseq.isHidden().booleanValue())
3384 if (hiddenSeqs == null)
3386 hiddenSeqs = new ArrayList<>();
3389 hiddenSeqs.add(tmpSeq);
3394 // Create the alignment object from the sequence set
3395 // ///////////////////////////////
3396 SequenceI[] orderedSeqs = tmpseqs
3397 .toArray(new SequenceI[tmpseqs.size()]);
3399 AlignmentI al = null;
3400 // so we must create or recover the dataset alignment before going further
3401 // ///////////////////////////////
3402 if (vamsasSet.getDatasetId() == null || vamsasSet.getDatasetId() == "")
3404 // older jalview projects do not have a dataset - so creat alignment and
3406 al = new Alignment(orderedSeqs);
3407 al.setDataset(null);
3411 boolean isdsal = jalviewModel.getViewport().isEmpty();
3414 // we are importing a dataset record, so
3415 // recover reference to an alignment already materialsed as dataset
3416 al = getDatasetFor(vamsasSet.getDatasetId());
3420 // materialse the alignment
3421 al = new Alignment(orderedSeqs);
3425 addDatasetRef(vamsasSet.getDatasetId(), al);
3428 // finally, verify all data in vamsasSet is actually present in al
3429 // passing on flag indicating if it is actually a stored dataset
3430 recoverDatasetFor(vamsasSet, al, isdsal, uniqueSeqSetId);
3433 if (referenceseqForView != null)
3435 al.setSeqrep(referenceseqForView);
3437 // / Add the alignment properties
3438 for (int i = 0; i < vamsasSet.getSequenceSetProperties().size(); i++)
3440 SequenceSetProperties ssp = vamsasSet.getSequenceSetProperties()
3442 al.setProperty(ssp.getKey(), ssp.getValue());
3445 // ///////////////////////////////
3447 Hashtable pdbloaded = new Hashtable(); // TODO nothing writes to this??
3450 // load sequence features, database references and any associated PDB
3451 // structures for the alignment
3453 // prior to 2.10, this part would only be executed the first time a
3454 // sequence was encountered, but not afterwards.
3455 // now, for 2.10 projects, this is also done if the xml doc includes
3456 // dataset sequences not actually present in any particular view.
3458 for (int i = 0; i < vamsasSeqs.size(); i++)
3460 JSeq jseq = jseqs.get(i);
3461 if (jseq.getFeatures().size() > 0)
3463 List<Feature> features = jseq.getFeatures();
3464 for (int f = 0; f < features.size(); f++)
3466 Feature feat = features.get(f);
3467 SequenceFeature sf = new SequenceFeature(feat.getType(),
3468 feat.getDescription(), feat.getBegin(), feat.getEnd(),
3469 safeFloat(feat.getScore()), feat.getFeatureGroup());
3470 sf.setStatus(feat.getStatus());
3473 * load any feature attributes - include map-valued attributes
3475 Map<String, Map<String, String>> mapAttributes = new HashMap<>();
3476 for (int od = 0; od < feat.getOtherData().size(); od++)
3478 OtherData keyValue = feat.getOtherData().get(od);
3479 String attributeName = keyValue.getKey();
3480 String attributeValue = keyValue.getValue();
3481 if (attributeName.startsWith("LINK"))
3483 sf.addLink(attributeValue);
3487 String subAttribute = keyValue.getKey2();
3488 if (subAttribute == null)
3490 // simple string-valued attribute
3491 sf.setValue(attributeName, attributeValue);
3495 // attribute 'key' has sub-attribute 'key2'
3496 if (!mapAttributes.containsKey(attributeName))
3498 mapAttributes.put(attributeName, new HashMap<>());
3500 mapAttributes.get(attributeName).put(subAttribute,
3505 for (Entry<String, Map<String, String>> mapAttribute : mapAttributes
3508 sf.setValue(mapAttribute.getKey(), mapAttribute.getValue());
3511 // adds feature to datasequence's feature set (since Jalview 2.10)
3512 al.getSequenceAt(i).addSequenceFeature(sf);
3515 if (vamsasSeqs.get(i).getDBRef().size() > 0)
3517 // adds dbrefs to datasequence's set (since Jalview 2.10)
3519 al.getSequenceAt(i).getDatasetSequence() == null
3520 ? al.getSequenceAt(i)
3521 : al.getSequenceAt(i).getDatasetSequence(),
3524 if (jseq.getPdbids().size() > 0)
3526 List<Pdbids> ids = jseq.getPdbids();
3527 for (int p = 0; p < ids.size(); p++)
3529 Pdbids pdbid = ids.get(p);
3530 jalview.datamodel.PDBEntry entry = new jalview.datamodel.PDBEntry();
3531 entry.setId(pdbid.getId());
3532 if (pdbid.getType() != null)
3534 if (PDBEntry.Type.getType(pdbid.getType()) != null)
3536 entry.setType(PDBEntry.Type.getType(pdbid.getType()));
3540 entry.setType(PDBEntry.Type.FILE);
3543 // jprovider is null when executing 'New View'
3544 if (pdbid.getFile() != null && jprovider != null)
3546 if (!pdbloaded.containsKey(pdbid.getFile()))
3548 entry.setFile(loadPDBFile(jprovider, pdbid.getId(),
3553 entry.setFile(pdbloaded.get(pdbid.getId()).toString());
3557 if (pdbid.getPdbentryItem() != null)
3559 for (PdbentryItem item : pdbid.getPdbentryItem())
3561 for (Property pr : item.getProperty())
3563 entry.setProperty(pr.getName(), pr.getValue());
3568 for (Property prop : pdbid.getProperty())
3570 entry.setProperty(prop.getName(), prop.getValue());
3572 StructureSelectionManager
3573 .getStructureSelectionManager(Desktop.instance)
3574 .registerPDBEntry(entry);
3575 // adds PDBEntry to datasequence's set (since Jalview 2.10)
3576 if (al.getSequenceAt(i).getDatasetSequence() != null)
3578 al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
3582 al.getSequenceAt(i).addPDBId(entry);
3587 } // end !multipleview
3589 // ///////////////////////////////
3590 // LOAD SEQUENCE MAPPINGS
3592 if (vamsasSet.getAlcodonFrame().size() > 0)
3594 // TODO Potentially this should only be done once for all views of an
3596 List<AlcodonFrame> alc = vamsasSet.getAlcodonFrame();
3597 for (int i = 0; i < alc.size(); i++)
3599 AlignedCodonFrame cf = new AlignedCodonFrame();
3600 if (alc.get(i).getAlcodMap().size() > 0)
3602 List<AlcodMap> maps = alc.get(i).getAlcodMap();
3603 for (int m = 0; m < maps.size(); m++)
3605 AlcodMap map = maps.get(m);
3606 SequenceI dnaseq = seqRefIds.get(map.getDnasq());
3608 jalview.datamodel.Mapping mapping = null;
3609 // attach to dna sequence reference.
3610 if (map.getMapping() != null)
3612 mapping = addMapping(map.getMapping());
3613 if (dnaseq != null && mapping.getTo() != null)
3615 cf.addMap(dnaseq, mapping.getTo(), mapping.getMap());
3621 newAlcodMapRef(map.getDnasq(), cf, mapping));
3625 al.addCodonFrame(cf);
3630 // ////////////////////////////////
3632 List<JvAnnotRow> autoAlan = new ArrayList<>();
3635 * store any annotations which forward reference a group's ID
3637 Map<String, List<AlignmentAnnotation>> groupAnnotRefs = new Hashtable<>();
3639 if (vamsasSet.getAnnotation().size()/*Count()*/ > 0)
3641 List<Annotation> an = vamsasSet.getAnnotation();
3643 for (int i = 0; i < an.size(); i++)
3645 Annotation annotation = an.get(i);
3648 * test if annotation is automatically calculated for this view only
3650 boolean autoForView = false;
3651 if (annotation.getLabel().equals("Quality")
3652 || annotation.getLabel().equals("Conservation")
3653 || annotation.getLabel().equals("Consensus"))
3655 // Kludge for pre 2.5 projects which lacked the autocalculated flag
3657 // JAXB has no has() test; schema defaults value to false
3658 // if (!annotation.hasAutoCalculated())
3660 // annotation.setAutoCalculated(true);
3663 if (autoForView || annotation.isAutoCalculated())
3665 // remove ID - we don't recover annotation from other views for
3666 // view-specific annotation
3667 annotation.setId(null);
3670 // set visibility for other annotation in this view
3671 String annotationId = annotation.getId();
3672 if (annotationId != null && annotationIds.containsKey(annotationId))
3674 AlignmentAnnotation jda = annotationIds.get(annotationId);
3675 // in principle Visible should always be true for annotation displayed
3676 // in multiple views
3677 if (annotation.isVisible() != null)
3679 jda.visible = annotation.isVisible();
3682 al.addAnnotation(jda);
3686 // Construct new annotation from model.
3687 List<AnnotationElement> ae = annotation.getAnnotationElement();
3688 jalview.datamodel.Annotation[] anot = null;
3689 java.awt.Color firstColour = null;
3691 if (!annotation.isScoreOnly())
3693 anot = new jalview.datamodel.Annotation[al.getWidth()];
3694 for (int aa = 0; aa < ae.size() && aa < anot.length; aa++)
3696 AnnotationElement annElement = ae.get(aa);
3697 anpos = annElement.getPosition();
3699 if (anpos >= anot.length)
3704 float value = safeFloat(annElement.getValue());
3705 anot[anpos] = new jalview.datamodel.Annotation(
3706 annElement.getDisplayCharacter(),
3707 annElement.getDescription(),
3708 (annElement.getSecondaryStructure() == null
3709 || annElement.getSecondaryStructure()
3713 .getSecondaryStructure()
3716 anot[anpos].colour = new Color(safeInt(annElement.getColour()));
3717 if (firstColour == null)
3719 firstColour = anot[anpos].colour;
3723 jalview.datamodel.AlignmentAnnotation jaa = null;
3725 if (annotation.isGraph())
3727 float llim = 0, hlim = 0;
3728 // if (autoForView || an[i].isAutoCalculated()) {
3731 jaa = new jalview.datamodel.AlignmentAnnotation(
3732 annotation.getLabel(), annotation.getDescription(), anot,
3733 llim, hlim, safeInt(annotation.getGraphType()));
3735 jaa.graphGroup = safeInt(annotation.getGraphGroup());
3736 jaa._linecolour = firstColour;
3737 if (annotation.getThresholdLine() != null)
3739 jaa.setThreshold(new jalview.datamodel.GraphLine(
3740 safeFloat(annotation.getThresholdLine().getValue()),
3741 annotation.getThresholdLine().getLabel(),
3742 new java.awt.Color(safeInt(
3743 annotation.getThresholdLine().getColour()))));
3745 if (autoForView || annotation.isAutoCalculated())
3747 // Hardwire the symbol display line to ensure that labels for
3748 // histograms are displayed
3754 jaa = new jalview.datamodel.AlignmentAnnotation(
3755 annotation.getLabel(), annotation.getDescription(), anot);
3756 jaa._linecolour = firstColour;
3758 // register new annotation
3759 if (annotation.getId() != null)
3761 annotationIds.put(annotation.getId(), jaa);
3762 jaa.annotationId = annotation.getId();
3764 // recover sequence association
3765 String sequenceRef = annotation.getSequenceRef();
3766 if (sequenceRef != null)
3768 // from 2.9 sequenceRef is to sequence id (JAL-1781)
3769 SequenceI sequence = seqRefIds.get(sequenceRef);
3770 if (sequence == null)
3772 // in pre-2.9 projects sequence ref is to sequence name
3773 sequence = al.findName(sequenceRef);
3775 if (sequence != null)
3777 jaa.createSequenceMapping(sequence, 1, true);
3778 sequence.addAlignmentAnnotation(jaa);
3781 // and make a note of any group association
3782 if (annotation.getGroupRef() != null
3783 && annotation.getGroupRef().length() > 0)
3785 List<jalview.datamodel.AlignmentAnnotation> aal = groupAnnotRefs
3786 .get(annotation.getGroupRef());
3789 aal = new ArrayList<>();
3790 groupAnnotRefs.put(annotation.getGroupRef(), aal);
3795 if (annotation.getScore() != null)
3797 jaa.setScore(annotation.getScore().doubleValue());
3799 if (annotation.isVisible() != null)
3801 jaa.visible = annotation.isVisible().booleanValue();
3804 if (annotation.isCentreColLabels() != null)
3806 jaa.centreColLabels = annotation.isCentreColLabels()
3810 if (annotation.isScaleColLabels() != null)
3812 jaa.scaleColLabel = annotation.isScaleColLabels().booleanValue();
3814 if (annotation.isAutoCalculated())
3816 // newer files have an 'autoCalculated' flag and store calculation
3817 // state in viewport properties
3818 jaa.autoCalculated = true; // means annotation will be marked for
3819 // update at end of load.
3821 if (annotation.getGraphHeight() != null)
3823 jaa.graphHeight = annotation.getGraphHeight().intValue();
3825 jaa.belowAlignment = annotation.isBelowAlignment();
3826 jaa.setCalcId(annotation.getCalcId());
3827 if (annotation.getProperty().size() > 0)
3829 for (Annotation.Property prop : annotation
3832 jaa.setProperty(prop.getName(), prop.getValue());
3835 if (jaa.autoCalculated)
3837 autoAlan.add(new JvAnnotRow(i, jaa));
3840 // if (!autoForView)
3842 // add autocalculated group annotation and any user created annotation
3844 al.addAnnotation(jaa);
3848 // ///////////////////////
3850 // Create alignment markup and styles for this view
3851 if (jalviewModel.getJGroup().size() > 0)
3853 List<JGroup> groups = jalviewModel.getJGroup();
3854 boolean addAnnotSchemeGroup = false;
3855 for (int i = 0; i < groups.size(); i++)
3857 JGroup jGroup = groups.get(i);
3858 ColourSchemeI cs = null;
3859 if (jGroup.getColour() != null)
3861 if (jGroup.getColour().startsWith("ucs"))
3863 cs = getUserColourScheme(jalviewModel, jGroup.getColour());
3865 else if (jGroup.getColour().equals("AnnotationColourGradient")
3866 && jGroup.getAnnotationColours() != null)
3868 addAnnotSchemeGroup = true;
3872 cs = ColourSchemeProperty.getColourScheme(null, al,
3873 jGroup.getColour());
3876 int pidThreshold = safeInt(jGroup.getPidThreshold());
3878 Vector<SequenceI> seqs = new Vector<>();
3880 for (int s = 0; s < jGroup.getSeq().size(); s++)
3882 String seqId = jGroup.getSeq().get(s);
3883 SequenceI ts = seqRefIds.get(seqId);
3887 seqs.addElement(ts);
3891 if (seqs.size() < 1)
3896 SequenceGroup sg = new SequenceGroup(seqs, jGroup.getName(), cs,
3897 safeBoolean(jGroup.isDisplayBoxes()),
3898 safeBoolean(jGroup.isDisplayText()),
3899 safeBoolean(jGroup.isColourText()),
3900 safeInt(jGroup.getStart()), safeInt(jGroup.getEnd()));
3901 sg.getGroupColourScheme().setThreshold(pidThreshold, true);
3902 sg.getGroupColourScheme()
3903 .setConservationInc(safeInt(jGroup.getConsThreshold()));
3904 sg.setOutlineColour(new Color(safeInt(jGroup.getOutlineColour())));
3906 sg.textColour = new Color(safeInt(jGroup.getTextCol1()));
3907 sg.textColour2 = new Color(safeInt(jGroup.getTextCol2()));
3908 sg.setShowNonconserved(safeBoolean(jGroup.isShowUnconserved()));
3909 sg.thresholdTextColour = safeInt(jGroup.getTextColThreshold());
3910 // attributes with a default in the schema are never null
3911 sg.setShowConsensusHistogram(jGroup.isShowConsensusHistogram());
3912 sg.setshowSequenceLogo(jGroup.isShowSequenceLogo());
3913 sg.setNormaliseSequenceLogo(jGroup.isNormaliseSequenceLogo());
3914 sg.setIgnoreGapsConsensus(jGroup.isIgnoreGapsinConsensus());
3915 if (jGroup.getConsThreshold() != null
3916 && jGroup.getConsThreshold().intValue() != 0)
3918 Conservation c = new Conservation("All", sg.getSequences(null), 0,
3921 c.verdict(false, 25);
3922 sg.cs.setConservation(c);
3925 if (jGroup.getId() != null && groupAnnotRefs.size() > 0)
3927 // re-instate unique group/annotation row reference
3928 List<AlignmentAnnotation> jaal = groupAnnotRefs
3929 .get(jGroup.getId());
3932 for (AlignmentAnnotation jaa : jaal)
3935 if (jaa.autoCalculated)
3937 // match up and try to set group autocalc alignment row for this
3939 if (jaa.label.startsWith("Consensus for "))
3941 sg.setConsensus(jaa);
3943 // match up and try to set group autocalc alignment row for this
3945 if (jaa.label.startsWith("Conservation for "))
3947 sg.setConservationRow(jaa);
3954 if (addAnnotSchemeGroup)
3956 // reconstruct the annotation colourscheme
3957 sg.setColourScheme(constructAnnotationColour(
3958 jGroup.getAnnotationColours(), null, al, jalviewModel, false));
3964 // only dataset in this model, so just return.
3967 // ///////////////////////////////
3970 AlignFrame af = null;
3971 AlignViewport av = null;
3972 // now check to see if we really need to create a new viewport.
3973 if (multipleView && viewportsAdded.size() == 0)
3975 // We recovered an alignment for which a viewport already exists.
3976 // TODO: fix up any settings necessary for overlaying stored state onto
3977 // state recovered from another document. (may not be necessary).
3978 // we may need a binding from a viewport in memory to one recovered from
3980 // and then recover its containing af to allow the settings to be applied.
3981 // TODO: fix for vamsas demo
3983 "About to recover a viewport for existing alignment: Sequence set ID is "
3985 Object seqsetobj = retrieveExistingObj(uniqueSeqSetId);
3986 if (seqsetobj != null)
3988 if (seqsetobj instanceof String)
3990 uniqueSeqSetId = (String) seqsetobj;
3992 "Recovered extant sequence set ID mapping for ID : New Sequence set ID is "
3998 "Warning : Collision between sequence set ID string and existing jalview object mapping.");
4004 * indicate that annotation colours are applied across all groups (pre
4005 * Jalview 2.8.1 behaviour)
4007 boolean doGroupAnnColour = Jalview2XML.isVersionStringLaterThan("2.8.1",
4008 jalviewModel.getVersion());
4010 AlignmentPanel ap = null;
4011 boolean isnewview = true;
4014 // Check to see if this alignment already has a view id == viewId
4015 jalview.gui.AlignmentPanel views[] = Desktop
4016 .getAlignmentPanels(uniqueSeqSetId);
4017 if (views != null && views.length > 0)
4019 for (int v = 0; v < views.length; v++)
4021 if (views[v].av.getViewId().equalsIgnoreCase(viewId))
4023 // recover the existing alignpanel, alignframe, viewport
4024 af = views[v].alignFrame;
4027 // TODO: could even skip resetting view settings if we don't want to
4028 // change the local settings from other jalview processes
4037 af = loadViewport(file, jseqs, hiddenSeqs, al, jalviewModel, view,
4038 uniqueSeqSetId, viewId, autoAlan);
4039 av = af.getViewport();
4044 * Load any trees, PDB structures and viewers
4046 * Not done if flag is false (when this method is used for New View)
4048 if (loadTreesAndStructures)
4050 loadTrees(jalviewModel, view, af, av, ap);
4051 loadPCAViewers(jalviewModel, ap);
4052 loadPDBStructures(jprovider, jseqs, af, ap);
4053 loadRnaViewers(jprovider, jseqs, ap);
4055 // and finally return.
4060 * Instantiate and link any saved RNA (Varna) viewers. The state of the Varna
4061 * panel is restored from separate jar entries, two (gapped and trimmed) per
4062 * sequence and secondary structure.
4064 * Currently each viewer shows just one sequence and structure (gapped and
4065 * trimmed), however this method is designed to support multiple sequences or
4066 * structures in viewers if wanted in future.
4072 private void loadRnaViewers(jarInputStreamProvider jprovider,
4073 List<JSeq> jseqs, AlignmentPanel ap)
4076 * scan the sequences for references to viewers; create each one the first
4077 * time it is referenced, add Rna models to existing viewers
4079 for (JSeq jseq : jseqs)
4081 for (int i = 0; i < jseq.getRnaViewer().size(); i++)
4083 RnaViewer viewer = jseq.getRnaViewer().get(i);
4084 AppVarna appVarna = findOrCreateVarnaViewer(viewer, uniqueSetSuffix,
4087 for (int j = 0; j < viewer.getSecondaryStructure().size(); j++)
4089 SecondaryStructure ss = viewer.getSecondaryStructure().get(j);
4090 SequenceI seq = seqRefIds.get(jseq.getId());
4091 AlignmentAnnotation ann = this.annotationIds
4092 .get(ss.getAnnotationId());
4095 * add the structure to the Varna display (with session state copied
4096 * from the jar to a temporary file)
4098 boolean gapped = safeBoolean(ss.isGapped());
4099 String rnaTitle = ss.getTitle();
4100 String sessionState = ss.getViewerState();
4101 String tempStateFile = copyJarEntry(jprovider, sessionState,
4103 RnaModel rna = new RnaModel(rnaTitle, ann, seq, null, gapped);
4104 appVarna.addModelSession(rna, rnaTitle, tempStateFile);
4106 appVarna.setInitialSelection(safeInt(viewer.getSelectedRna()));
4112 * Locate and return an already instantiated matching AppVarna, or create one
4116 * @param viewIdSuffix
4120 protected AppVarna findOrCreateVarnaViewer(RnaViewer viewer,
4121 String viewIdSuffix, AlignmentPanel ap)
4124 * on each load a suffix is appended to the saved viewId, to avoid conflicts
4125 * if load is repeated
4127 String postLoadId = viewer.getViewId() + viewIdSuffix;
4128 for (JInternalFrame frame : getAllFrames())
4130 if (frame instanceof AppVarna)
4132 AppVarna varna = (AppVarna) frame;
4133 if (postLoadId.equals(varna.getViewId()))
4135 // this viewer is already instantiated
4136 // could in future here add ap as another 'parent' of the
4137 // AppVarna window; currently just 1-to-many
4144 * viewer not found - make it
4146 RnaViewerModel model = new RnaViewerModel(postLoadId, viewer.getTitle(),
4147 safeInt(viewer.getXpos()), safeInt(viewer.getYpos()),
4148 safeInt(viewer.getWidth()), safeInt(viewer.getHeight()),
4149 safeInt(viewer.getDividerLocation()));
4150 AppVarna varna = new AppVarna(model, ap);
4156 * Load any saved trees
4164 protected void loadTrees(JalviewModel jm, Viewport view,
4165 AlignFrame af, AlignViewport av, AlignmentPanel ap)
4167 // TODO result of automated refactoring - are all these parameters needed?
4170 for (int t = 0; t < jm.getTree().size(); t++)
4173 Tree tree = jm.getTree().get(t);
4175 TreePanel tp = (TreePanel) retrieveExistingObj(tree.getId());
4178 tp = af.showNewickTree(new NewickFile(tree.getNewick()),
4179 tree.getTitle(), safeInt(tree.getWidth()),
4180 safeInt(tree.getHeight()), safeInt(tree.getXpos()),
4181 safeInt(tree.getYpos()));
4182 if (tree.getId() != null)
4184 // perhaps bind the tree id to something ?
4189 // update local tree attributes ?
4190 // TODO: should check if tp has been manipulated by user - if so its
4191 // settings shouldn't be modified
4192 tp.setTitle(tree.getTitle());
4193 tp.setBounds(new Rectangle(safeInt(tree.getXpos()),
4194 safeInt(tree.getYpos()), safeInt(tree.getWidth()),
4195 safeInt(tree.getHeight())));
4196 tp.setViewport(av); // af.viewport;
4197 // TODO: verify 'associate with all views' works still
4198 tp.getTreeCanvas().setViewport(av); // af.viewport;
4199 tp.getTreeCanvas().setAssociatedPanel(ap); // af.alignPanel;
4201 tp.getTreeCanvas().setApplyToAllViews(tree.isLinkToAllViews());
4204 warn("There was a problem recovering stored Newick tree: \n"
4205 + tree.getNewick());
4209 tp.fitToWindow.setState(safeBoolean(tree.isFitToWindow()));
4210 tp.fitToWindow_actionPerformed(null);
4212 if (tree.getFontName() != null)
4215 new Font(tree.getFontName(), safeInt(tree.getFontStyle()),
4216 safeInt(tree.getFontSize())));
4221 new Font(view.getFontName(), safeInt(view.getFontStyle()),
4222 safeInt(view.getFontSize())));
4225 tp.showPlaceholders(safeBoolean(tree.isMarkUnlinked()));
4226 tp.showBootstrap(safeBoolean(tree.isShowBootstrap()));
4227 tp.showDistances(safeBoolean(tree.isShowDistances()));
4229 tp.getTreeCanvas().setThreshold(safeFloat(tree.getThreshold()));
4231 if (safeBoolean(tree.isCurrentTree()))
4233 af.getViewport().setCurrentTree(tp.getTree());
4237 } catch (Exception ex)
4239 ex.printStackTrace();
4244 * Load and link any saved structure viewers.
4251 protected void loadPDBStructures(jarInputStreamProvider jprovider,
4252 List<JSeq> jseqs, AlignFrame af, AlignmentPanel ap)
4255 * Run through all PDB ids on the alignment, and collect mappings between
4256 * distinct view ids and all sequences referring to that view.
4258 Map<String, StructureViewerModel> structureViewers = new LinkedHashMap<>();
4260 for (int i = 0; i < jseqs.size(); i++)
4262 JSeq jseq = jseqs.get(i);
4263 if (jseq.getPdbids().size() > 0)
4265 List<Pdbids> ids = jseq.getPdbids();
4266 for (int p = 0; p < ids.size(); p++)
4268 Pdbids pdbid = ids.get(p);
4269 final int structureStateCount = pdbid.getStructureState().size();
4270 for (int s = 0; s < structureStateCount; s++)
4272 // check to see if we haven't already created this structure view
4273 final StructureState structureState = pdbid
4274 .getStructureState().get(s);
4275 String sviewid = (structureState.getViewId() == null) ? null
4276 : structureState.getViewId() + uniqueSetSuffix;
4277 jalview.datamodel.PDBEntry jpdb = new jalview.datamodel.PDBEntry();
4278 // Originally : pdbid.getFile()
4279 // : TODO: verify external PDB file recovery still works in normal
4280 // jalview project load
4282 loadPDBFile(jprovider, pdbid.getId(), pdbid.getFile()));
4283 jpdb.setId(pdbid.getId());
4285 int x = safeInt(structureState.getXpos());
4286 int y = safeInt(structureState.getYpos());
4287 int width = safeInt(structureState.getWidth());
4288 int height = safeInt(structureState.getHeight());
4290 // Probably don't need to do this anymore...
4291 // Desktop.desktop.getComponentAt(x, y);
4292 // TODO: NOW: check that this recovers the PDB file correctly.
4293 String pdbFile = loadPDBFile(jprovider, pdbid.getId(),
4295 jalview.datamodel.SequenceI seq = seqRefIds
4296 .get(jseq.getId() + "");
4297 if (sviewid == null)
4299 sviewid = "_jalview_pre2_4_" + x + "," + y + "," + width + ","
4302 if (!structureViewers.containsKey(sviewid))
4304 structureViewers.put(sviewid,
4305 new StructureViewerModel(x, y, width, height, false,
4306 false, true, structureState.getViewId(),
4307 structureState.getType()));
4308 // Legacy pre-2.7 conversion JAL-823 :
4309 // do not assume any view has to be linked for colour by
4313 // assemble String[] { pdb files }, String[] { id for each
4314 // file }, orig_fileloc, SequenceI[][] {{ seqs_file 1 }, {
4315 // seqs_file 2}, boolean[] {
4316 // linkAlignPanel,superposeWithAlignpanel}} from hash
4317 StructureViewerModel jmoldat = structureViewers.get(sviewid);
4318 jmoldat.setAlignWithPanel(jmoldat.isAlignWithPanel()
4319 || structureState.isAlignwithAlignPanel());
4322 * Default colour by linked panel to false if not specified (e.g.
4323 * for pre-2.7 projects)
4325 boolean colourWithAlignPanel = jmoldat.isColourWithAlignPanel();
4326 colourWithAlignPanel |= structureState.isColourwithAlignPanel();
4327 jmoldat.setColourWithAlignPanel(colourWithAlignPanel);
4330 * Default colour by viewer to true if not specified (e.g. for
4333 boolean colourByViewer = jmoldat.isColourByViewer();
4334 colourByViewer &= structureState.isColourByJmol();
4335 jmoldat.setColourByViewer(colourByViewer);
4337 if (jmoldat.getStateData().length() < structureState
4338 .getValue()/*Content()*/.length())
4340 jmoldat.setStateData(structureState.getValue());// Content());
4342 if (pdbid.getFile() != null)
4344 File mapkey = new File(pdbid.getFile());
4345 StructureData seqstrmaps = jmoldat.getFileData().get(mapkey);
4346 if (seqstrmaps == null)
4348 jmoldat.getFileData().put(mapkey,
4349 seqstrmaps = jmoldat.new StructureData(pdbFile,
4352 if (!seqstrmaps.getSeqList().contains(seq))
4354 seqstrmaps.getSeqList().add(seq);
4360 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");
4367 // Instantiate the associated structure views
4368 for (Entry<String, StructureViewerModel> entry : structureViewers
4373 createOrLinkStructureViewer(entry, af, ap, jprovider);
4374 } catch (Exception e)
4377 "Error loading structure viewer: " + e.getMessage());
4378 // failed - try the next one
4390 protected void createOrLinkStructureViewer(
4391 Entry<String, StructureViewerModel> viewerData, AlignFrame af,
4392 AlignmentPanel ap, jarInputStreamProvider jprovider)
4394 final StructureViewerModel stateData = viewerData.getValue();
4397 * Search for any viewer windows already open from other alignment views
4398 * that exactly match the stored structure state
4400 StructureViewerBase comp = findMatchingViewer(viewerData);
4404 linkStructureViewer(ap, comp, stateData);
4409 * From 2.9: stateData.type contains JMOL or CHIMERA, data is in jar entry
4410 * "viewer_"+stateData.viewId
4412 if (ViewerType.CHIMERA.toString().equals(stateData.getType()))
4414 createChimeraViewer(viewerData, af, jprovider);
4419 * else Jmol (if pre-2.9, stateData contains JMOL state string)
4421 createJmolViewer(viewerData, af, jprovider);
4426 * Create a new Chimera viewer.
4432 protected void createChimeraViewer(
4433 Entry<String, StructureViewerModel> viewerData, AlignFrame af,
4434 jarInputStreamProvider jprovider)
4436 StructureViewerModel data = viewerData.getValue();
4437 String chimeraSessionFile = data.getStateData();
4440 * Copy Chimera session from jar entry "viewer_"+viewId to a temporary file
4442 * NB this is the 'saved' viewId as in the project file XML, _not_ the
4443 * 'uniquified' sviewid used to reconstruct the viewer here
4445 String viewerJarEntryName = getViewerJarEntryName(data.getViewId());
4446 chimeraSessionFile = copyJarEntry(jprovider, viewerJarEntryName,
4449 Set<Entry<File, StructureData>> fileData = data.getFileData()
4451 List<PDBEntry> pdbs = new ArrayList<>();
4452 List<SequenceI[]> allseqs = new ArrayList<>();
4453 for (Entry<File, StructureData> pdb : fileData)
4455 String filePath = pdb.getValue().getFilePath();
4456 String pdbId = pdb.getValue().getPdbId();
4457 // pdbs.add(new PDBEntry(filePath, pdbId));
4458 pdbs.add(new PDBEntry(pdbId, null, PDBEntry.Type.PDB, filePath));
4459 final List<SequenceI> seqList = pdb.getValue().getSeqList();
4460 SequenceI[] seqs = seqList.toArray(new SequenceI[seqList.size()]);
4464 boolean colourByChimera = data.isColourByViewer();
4465 boolean colourBySequence = data.isColourWithAlignPanel();
4467 // TODO use StructureViewer as a factory here, see JAL-1761
4468 final PDBEntry[] pdbArray = pdbs.toArray(new PDBEntry[pdbs.size()]);
4469 final SequenceI[][] seqsArray = allseqs
4470 .toArray(new SequenceI[allseqs.size()][]);
4471 String newViewId = viewerData.getKey();
4473 ChimeraViewFrame cvf = new ChimeraViewFrame(chimeraSessionFile,
4474 af.alignPanel, pdbArray, seqsArray, colourByChimera,
4475 colourBySequence, newViewId);
4476 cvf.setSize(data.getWidth(), data.getHeight());
4477 cvf.setLocation(data.getX(), data.getY());
4481 * Create a new Jmol window. First parse the Jmol state to translate filenames
4482 * loaded into the view, and record the order in which files are shown in the
4483 * Jmol view, so we can add the sequence mappings in same order.
4489 protected void createJmolViewer(
4490 final Entry<String, StructureViewerModel> viewerData,
4491 AlignFrame af, jarInputStreamProvider jprovider)
4493 final StructureViewerModel svattrib = viewerData.getValue();
4494 String state = svattrib.getStateData();
4497 * Pre-2.9: state element value is the Jmol state string
4499 * 2.9+: @type is "JMOL", state data is in a Jar file member named "viewer_"
4502 if (ViewerType.JMOL.toString().equals(svattrib.getType()))
4504 state = readJarEntry(jprovider,
4505 getViewerJarEntryName(svattrib.getViewId()));
4508 List<String> pdbfilenames = new ArrayList<>();
4509 List<SequenceI[]> seqmaps = new ArrayList<>();
4510 List<String> pdbids = new ArrayList<>();
4511 StringBuilder newFileLoc = new StringBuilder(64);
4512 int cp = 0, ncp, ecp;
4513 Map<File, StructureData> oldFiles = svattrib.getFileData();
4514 while ((ncp = state.indexOf("load ", cp)) > -1)
4518 // look for next filename in load statement
4519 newFileLoc.append(state.substring(cp,
4520 ncp = (state.indexOf("\"", ncp + 1) + 1)));
4521 String oldfilenam = state.substring(ncp,
4522 ecp = state.indexOf("\"", ncp));
4523 // recover the new mapping data for this old filename
4524 // have to normalize filename - since Jmol and jalview do
4526 // translation differently.
4527 StructureData filedat = oldFiles.get(new File(oldfilenam));
4528 if (filedat == null)
4530 String reformatedOldFilename = oldfilenam.replaceAll("/", "\\\\");
4531 filedat = oldFiles.get(new File(reformatedOldFilename));
4533 newFileLoc.append(Platform.escapeBackslashes(filedat.getFilePath()));
4534 pdbfilenames.add(filedat.getFilePath());
4535 pdbids.add(filedat.getPdbId());
4536 seqmaps.add(filedat.getSeqList().toArray(new SequenceI[0]));
4537 newFileLoc.append("\"");
4538 cp = ecp + 1; // advance beyond last \" and set cursor so we can
4539 // look for next file statement.
4540 } while ((ncp = state.indexOf("/*file*/", cp)) > -1);
4544 // just append rest of state
4545 newFileLoc.append(state.substring(cp));
4549 System.err.print("Ignoring incomplete Jmol state for PDB ids: ");
4550 newFileLoc = new StringBuilder(state);
4551 newFileLoc.append("; load append ");
4552 for (File id : oldFiles.keySet())
4554 // add this and any other pdb files that should be present in
4556 StructureData filedat = oldFiles.get(id);
4557 newFileLoc.append(filedat.getFilePath());
4558 pdbfilenames.add(filedat.getFilePath());
4559 pdbids.add(filedat.getPdbId());
4560 seqmaps.add(filedat.getSeqList().toArray(new SequenceI[0]));
4561 newFileLoc.append(" \"");
4562 newFileLoc.append(filedat.getFilePath());
4563 newFileLoc.append("\"");
4566 newFileLoc.append(";");
4569 if (newFileLoc.length() == 0)
4573 int histbug = newFileLoc.indexOf("history = ");
4577 * change "history = [true|false];" to "history = [1|0];"
4580 int diff = histbug == -1 ? -1 : newFileLoc.indexOf(";", histbug);
4581 String val = (diff == -1) ? null
4582 : newFileLoc.substring(histbug, diff);
4583 if (val != null && val.length() >= 4)
4585 if (val.contains("e")) // eh? what can it be?
4587 if (val.trim().equals("true"))
4595 newFileLoc.replace(histbug, diff, val);
4600 final String[] pdbf = pdbfilenames
4601 .toArray(new String[pdbfilenames.size()]);
4602 final String[] id = pdbids.toArray(new String[pdbids.size()]);
4603 final SequenceI[][] sq = seqmaps
4604 .toArray(new SequenceI[seqmaps.size()][]);
4605 final String fileloc = newFileLoc.toString();
4606 final String sviewid = viewerData.getKey();
4607 final AlignFrame alf = af;
4608 final Rectangle rect = new Rectangle(svattrib.getX(), svattrib.getY(),
4609 svattrib.getWidth(), svattrib.getHeight());
4612 javax.swing.SwingUtilities.invokeAndWait(new Runnable()
4617 JalviewStructureDisplayI sview = null;
4620 sview = new StructureViewer(
4621 alf.alignPanel.getStructureSelectionManager())
4622 .createView(StructureViewer.ViewerType.JMOL,
4623 pdbf, id, sq, alf.alignPanel, svattrib,
4624 fileloc, rect, sviewid);
4625 addNewStructureViewer(sview);
4626 } catch (OutOfMemoryError ex)
4628 new OOMWarning("restoring structure view for PDB id " + id,
4629 (OutOfMemoryError) ex.getCause());
4630 if (sview != null && sview.isVisible())
4632 sview.closeViewer(false);
4633 sview.setVisible(false);
4639 } catch (InvocationTargetException ex)
4641 warn("Unexpected error when opening Jmol view.", ex);
4643 } catch (InterruptedException e)
4645 // e.printStackTrace();
4651 * Generates a name for the entry in the project jar file to hold state
4652 * information for a structure viewer
4657 protected String getViewerJarEntryName(String viewId)
4659 return VIEWER_PREFIX + viewId;
4663 * Returns any open frame that matches given structure viewer data. The match
4664 * is based on the unique viewId, or (for older project versions) the frame's
4670 protected StructureViewerBase findMatchingViewer(
4671 Entry<String, StructureViewerModel> viewerData)
4673 final String sviewid = viewerData.getKey();
4674 final StructureViewerModel svattrib = viewerData.getValue();
4675 StructureViewerBase comp = null;
4676 JInternalFrame[] frames = getAllFrames();
4677 for (JInternalFrame frame : frames)
4679 if (frame instanceof StructureViewerBase)
4682 * Post jalview 2.4 schema includes structure view id
4684 if (sviewid != null && ((StructureViewerBase) frame).getViewId()
4687 comp = (StructureViewerBase) frame;
4688 break; // break added in 2.9
4691 * Otherwise test for matching position and size of viewer frame
4693 else if (frame.getX() == svattrib.getX()
4694 && frame.getY() == svattrib.getY()
4695 && frame.getHeight() == svattrib.getHeight()
4696 && frame.getWidth() == svattrib.getWidth())
4698 comp = (StructureViewerBase) frame;
4699 // no break in faint hope of an exact match on viewId
4707 * Link an AlignmentPanel to an existing structure viewer.
4712 * @param useinViewerSuperpos
4713 * @param usetoColourbyseq
4714 * @param viewerColouring
4716 protected void linkStructureViewer(AlignmentPanel ap,
4717 StructureViewerBase viewer, StructureViewerModel stateData)
4719 // NOTE: if the jalview project is part of a shared session then
4720 // view synchronization should/could be done here.
4722 final boolean useinViewerSuperpos = stateData.isAlignWithPanel();
4723 final boolean usetoColourbyseq = stateData.isColourWithAlignPanel();
4724 final boolean viewerColouring = stateData.isColourByViewer();
4725 Map<File, StructureData> oldFiles = stateData.getFileData();
4728 * Add mapping for sequences in this view to an already open viewer
4730 final AAStructureBindingModel binding = viewer.getBinding();
4731 for (File id : oldFiles.keySet())
4733 // add this and any other pdb files that should be present in the
4735 StructureData filedat = oldFiles.get(id);
4736 String pdbFile = filedat.getFilePath();
4737 SequenceI[] seq = filedat.getSeqList().toArray(new SequenceI[0]);
4738 binding.getSsm().setMapping(seq, null, pdbFile, DataSourceType.FILE,
4740 binding.addSequenceForStructFile(pdbFile, seq);
4742 // and add the AlignmentPanel's reference to the view panel
4743 viewer.addAlignmentPanel(ap);
4744 if (useinViewerSuperpos)
4746 viewer.useAlignmentPanelForSuperposition(ap);
4750 viewer.excludeAlignmentPanelForSuperposition(ap);
4752 if (usetoColourbyseq)
4754 viewer.useAlignmentPanelForColourbyseq(ap, !viewerColouring);
4758 viewer.excludeAlignmentPanelForColourbyseq(ap);
4763 * Get all frames within the Desktop.
4767 protected JInternalFrame[] getAllFrames()
4769 JInternalFrame[] frames = null;
4770 // TODO is this necessary - is it safe - risk of hanging?
4775 frames = Desktop.desktop.getAllFrames();
4776 } catch (ArrayIndexOutOfBoundsException e)
4778 // occasional No such child exceptions are thrown here...
4782 } catch (InterruptedException f)
4786 } while (frames == null);
4791 * Answers true if 'version' is equal to or later than 'supported', where each
4792 * is formatted as major/minor versions like "2.8.3" or "2.3.4b1" for bugfix
4793 * changes. Development and test values for 'version' are leniently treated
4797 * - minimum version we are comparing against
4799 * - version of data being processsed
4802 public static boolean isVersionStringLaterThan(String supported,
4805 if (supported == null || version == null
4806 || version.equalsIgnoreCase("DEVELOPMENT BUILD")
4807 || version.equalsIgnoreCase("Test")
4808 || version.equalsIgnoreCase("AUTOMATED BUILD"))
4810 System.err.println("Assuming project file with "
4811 + (version == null ? "null" : version)
4812 + " is compatible with Jalview version " + supported);
4817 return StringUtils.compareVersions(version, supported, "b") >= 0;
4821 Vector<JalviewStructureDisplayI> newStructureViewers = null;
4823 protected void addNewStructureViewer(JalviewStructureDisplayI sview)
4825 if (newStructureViewers != null)
4827 sview.getBinding().setFinishedLoadingFromArchive(false);
4828 newStructureViewers.add(sview);
4832 protected void setLoadingFinishedForNewStructureViewers()
4834 if (newStructureViewers != null)
4836 for (JalviewStructureDisplayI sview : newStructureViewers)
4838 sview.getBinding().setFinishedLoadingFromArchive(true);
4840 newStructureViewers.clear();
4841 newStructureViewers = null;
4845 AlignFrame loadViewport(String file, List<JSeq> JSEQ,
4846 List<SequenceI> hiddenSeqs, AlignmentI al,
4847 JalviewModel jm, Viewport view, String uniqueSeqSetId,
4848 String viewId, List<JvAnnotRow> autoAlan)
4850 AlignFrame af = null;
4851 af = new AlignFrame(al, safeInt(view.getWidth()),
4852 safeInt(view.getHeight()), uniqueSeqSetId, viewId);
4854 af.setFileName(file, FileFormat.Jalview);
4856 final AlignViewport viewport = af.getViewport();
4857 for (int i = 0; i < JSEQ.size(); i++)
4859 int colour = safeInt(JSEQ.get(i).getColour());
4860 viewport.setSequenceColour(viewport.getAlignment().getSequenceAt(i),
4866 viewport.setColourByReferenceSeq(true);
4867 viewport.setDisplayReferenceSeq(true);
4870 viewport.setGatherViewsHere(safeBoolean(view.isGatheredViews()));
4872 if (view.getSequenceSetId() != null)
4874 AlignmentViewport av = viewportsAdded.get(uniqueSeqSetId);
4876 viewport.setSequenceSetId(uniqueSeqSetId);
4879 // propagate shared settings to this new view
4880 viewport.setHistoryList(av.getHistoryList());
4881 viewport.setRedoList(av.getRedoList());
4885 viewportsAdded.put(uniqueSeqSetId, viewport);
4887 // TODO: check if this method can be called repeatedly without
4888 // side-effects if alignpanel already registered.
4889 PaintRefresher.Register(af.alignPanel, uniqueSeqSetId);
4891 // apply Hidden regions to view.
4892 if (hiddenSeqs != null)
4894 for (int s = 0; s < JSEQ.size(); s++)
4896 SequenceGroup hidden = new SequenceGroup();
4897 boolean isRepresentative = false;
4898 for (int r = 0; r < JSEQ.get(s).getHiddenSequences().size(); r++)
4900 isRepresentative = true;
4901 SequenceI sequenceToHide = al
4902 .getSequenceAt(JSEQ.get(s).getHiddenSequences().get(r));
4903 hidden.addSequence(sequenceToHide, false);
4904 // remove from hiddenSeqs list so we don't try to hide it twice
4905 hiddenSeqs.remove(sequenceToHide);
4907 if (isRepresentative)
4909 SequenceI representativeSequence = al.getSequenceAt(s);
4910 hidden.addSequence(representativeSequence, false);
4911 viewport.hideRepSequences(representativeSequence, hidden);
4915 SequenceI[] hseqs = hiddenSeqs
4916 .toArray(new SequenceI[hiddenSeqs.size()]);
4917 viewport.hideSequence(hseqs);
4920 // recover view properties and display parameters
4922 viewport.setShowAnnotation(safeBoolean(view.isShowAnnotation()));
4923 viewport.setAbovePIDThreshold(safeBoolean(view.isPidSelected()));
4924 final int pidThreshold = safeInt(view.getPidThreshold());
4925 viewport.setThreshold(pidThreshold);
4927 viewport.setColourText(safeBoolean(view.isShowColourText()));
4930 .setConservationSelected(
4931 safeBoolean(view.isConservationSelected()));
4932 viewport.setIncrement(safeInt(view.getConsThreshold()));
4933 viewport.setShowJVSuffix(safeBoolean(view.isShowFullId()));
4934 viewport.setRightAlignIds(safeBoolean(view.isRightAlignIds()));
4935 viewport.setFont(new Font(view.getFontName(),
4936 safeInt(view.getFontStyle()), safeInt(view.getFontSize())),
4938 ViewStyleI vs = viewport.getViewStyle();
4939 vs.setScaleProteinAsCdna(view.isScaleProteinAsCdna());
4940 viewport.setViewStyle(vs);
4941 // TODO: allow custom charWidth/Heights to be restored by updating them
4942 // after setting font - which means set above to false
4943 viewport.setRenderGaps(safeBoolean(view.isRenderGaps()));
4944 viewport.setWrapAlignment(safeBoolean(view.isWrapAlignment()));
4945 viewport.setShowAnnotation(safeBoolean(view.isShowAnnotation()));
4947 viewport.setShowBoxes(safeBoolean(view.isShowBoxes()));
4949 viewport.setShowText(safeBoolean(view.isShowText()));
4951 viewport.setTextColour(new Color(safeInt(view.getTextCol1())));
4952 viewport.setTextColour2(new Color(safeInt(view.getTextCol2())));
4953 viewport.setThresholdTextColour(safeInt(view.getTextColThreshold()));
4954 viewport.setShowUnconserved(view.isShowUnconserved());
4955 viewport.getRanges().setStartRes(safeInt(view.getStartRes()));
4957 if (view.getViewName() != null)
4959 viewport.setViewName(view.getViewName());
4960 af.setInitialTabVisible();
4962 af.setBounds(safeInt(view.getXpos()), safeInt(view.getYpos()),
4963 safeInt(view.getWidth()), safeInt(view.getHeight()));
4964 // startSeq set in af.alignPanel.updateLayout below
4965 af.alignPanel.updateLayout();
4966 ColourSchemeI cs = null;
4967 // apply colourschemes
4968 if (view.getBgColour() != null)
4970 if (view.getBgColour().startsWith("ucs"))
4972 cs = getUserColourScheme(jm, view.getBgColour());
4974 else if (view.getBgColour().startsWith("Annotation"))
4976 AnnotationColourScheme viewAnnColour = view.getAnnotationColours();
4977 cs = constructAnnotationColour(viewAnnColour, af, al, jm, true);
4984 cs = ColourSchemeProperty.getColourScheme(af.getViewport(), al,
4985 view.getBgColour());
4990 * turn off 'alignment colour applies to all groups'
4991 * while restoring global colour scheme
4993 viewport.setColourAppliesToAllGroups(false);
4994 viewport.setGlobalColourScheme(cs);
4995 viewport.getResidueShading().setThreshold(pidThreshold,
4996 view.isIgnoreGapsinConsensus());
4997 viewport.getResidueShading()
4998 .setConsensus(viewport.getSequenceConsensusHash());
4999 if (safeBoolean(view.isConservationSelected()) && cs != null)
5001 viewport.getResidueShading()
5002 .setConservationInc(safeInt(view.getConsThreshold()));
5004 af.changeColour(cs);
5005 viewport.setColourAppliesToAllGroups(true);
5008 .setShowSequenceFeatures(
5009 safeBoolean(view.isShowSequenceFeatures()));
5011 viewport.setCentreColumnLabels(view.isCentreColumnLabels());
5012 viewport.setIgnoreGapsConsensus(view.isIgnoreGapsinConsensus(), null);
5013 viewport.setFollowHighlight(view.isFollowHighlight());
5014 viewport.followSelection = view.isFollowSelection();
5015 viewport.setShowConsensusHistogram(view.isShowConsensusHistogram());
5016 viewport.setShowSequenceLogo(view.isShowSequenceLogo());
5017 viewport.setNormaliseSequenceLogo(view.isNormaliseSequenceLogo());
5018 viewport.setShowDBRefs(safeBoolean(view.isShowDbRefTooltip()));
5019 viewport.setShowNPFeats(safeBoolean(view.isShowNPfeatureTooltip()));
5020 viewport.setShowGroupConsensus(view.isShowGroupConsensus());
5021 viewport.setShowGroupConservation(view.isShowGroupConservation());
5023 // recover feature settings
5024 if (jm.getFeatureSettings() != null)
5026 FeatureRenderer fr = af.alignPanel.getSeqPanel().seqCanvas
5027 .getFeatureRenderer();
5028 FeaturesDisplayed fdi;
5029 viewport.setFeaturesDisplayed(fdi = new FeaturesDisplayed());
5030 String[] renderOrder = new String[jm.getFeatureSettings()
5031 .getSetting().size()];
5032 Map<String, FeatureColourI> featureColours = new Hashtable<>();
5033 Map<String, Float> featureOrder = new Hashtable<>();
5035 for (int fs = 0; fs < jm.getFeatureSettings()
5036 .getSetting().size(); fs++)
5038 Setting setting = jm.getFeatureSettings().getSetting().get(fs);
5039 String featureType = setting.getType();
5042 * restore feature filters (if any)
5044 jalview.xml.binding.jalview.FeatureMatcherSet filters = setting
5046 if (filters != null)
5048 FeatureMatcherSetI filter = Jalview2XML
5049 .parseFilter(featureType, filters);
5050 if (!filter.isEmpty())
5052 fr.setFeatureFilter(featureType, filter);
5057 * restore feature colour scheme
5059 Color maxColour = new Color(setting.getColour());
5060 if (setting.getMincolour() != null)
5063 * minColour is always set unless a simple colour
5064 * (including for colour by label though it doesn't use it)
5066 Color minColour = new Color(setting.getMincolour().intValue());
5067 Color noValueColour = minColour;
5068 NoValueColour noColour = setting.getNoValueColour();
5069 if (noColour == NoValueColour.NONE)
5071 noValueColour = null;
5073 else if (noColour == NoValueColour.MAX)
5075 noValueColour = maxColour;
5077 float min = safeFloat(safeFloat(setting.getMin()));
5078 float max = setting.getMax() == null ? 1f
5079 : setting.getMax().floatValue();
5080 FeatureColourI gc = new FeatureColour(maxColour, minColour,
5082 noValueColour, min, max);
5083 if (setting.getAttributeName().size() > 0)
5085 gc.setAttributeName(setting.getAttributeName().toArray(
5086 new String[setting.getAttributeName().size()]));
5088 if (setting.getThreshold() != null)
5090 gc.setThreshold(setting.getThreshold().floatValue());
5091 int threshstate = safeInt(setting.getThreshstate());
5092 // -1 = None, 0 = Below, 1 = Above threshold
5093 if (threshstate == 0)
5095 gc.setBelowThreshold(true);
5097 else if (threshstate == 1)
5099 gc.setAboveThreshold(true);
5102 gc.setAutoScaled(true); // default
5103 if (setting.isAutoScale() != null)
5105 gc.setAutoScaled(setting.isAutoScale());
5107 if (setting.isColourByLabel() != null)
5109 gc.setColourByLabel(setting.isColourByLabel());
5111 // and put in the feature colour table.
5112 featureColours.put(featureType, gc);
5116 featureColours.put(featureType,
5117 new FeatureColour(maxColour));
5119 renderOrder[fs] = featureType;
5120 if (setting.getOrder() != null)
5122 featureOrder.put(featureType, setting.getOrder().floatValue());
5126 featureOrder.put(featureType, Float.valueOf(
5127 fs / jm.getFeatureSettings().getSetting().size()));
5129 if (safeBoolean(setting.isDisplay()))
5131 fdi.setVisible(featureType);
5134 Map<String, Boolean> fgtable = new Hashtable<>();
5135 for (int gs = 0; gs < jm.getFeatureSettings().getGroup().size(); gs++)
5137 Group grp = jm.getFeatureSettings().getGroup().get(gs);
5138 fgtable.put(grp.getName(), Boolean.valueOf(grp.isDisplay()));
5140 // FeatureRendererSettings frs = new FeatureRendererSettings(renderOrder,
5141 // fgtable, featureColours, jms.getFeatureSettings().hasTransparency() ?
5142 // jms.getFeatureSettings().getTransparency() : 0.0, featureOrder);
5143 FeatureRendererSettings frs = new FeatureRendererSettings(renderOrder,
5144 fgtable, featureColours, 1.0f, featureOrder);
5145 fr.transferSettings(frs);
5148 if (view.getHiddenColumns().size() > 0)
5150 for (int c = 0; c < view.getHiddenColumns().size(); c++)
5152 final HiddenColumns hc = view.getHiddenColumns().get(c);
5153 viewport.hideColumns(safeInt(hc.getStart()),
5154 safeInt(hc.getEnd()) /* +1 */);
5157 if (view.getCalcIdParam() != null)
5159 for (CalcIdParam calcIdParam : view.getCalcIdParam())
5161 if (calcIdParam != null)
5163 if (recoverCalcIdParam(calcIdParam, viewport))
5168 warn("Couldn't recover parameters for "
5169 + calcIdParam.getCalcId());
5174 af.setMenusFromViewport(viewport);
5175 af.setTitle(view.getTitle());
5176 // TODO: we don't need to do this if the viewport is aready visible.
5178 * Add the AlignFrame to the desktop (it may be 'gathered' later), unless it
5179 * has a 'cdna/protein complement' view, in which case save it in order to
5180 * populate a SplitFrame once all views have been read in.
5182 String complementaryViewId = view.getComplementId();
5183 if (complementaryViewId == null)
5185 Desktop.addInternalFrame(af, view.getTitle(),
5186 safeInt(view.getWidth()), safeInt(view.getHeight()));
5187 // recompute any autoannotation
5188 af.alignPanel.updateAnnotation(false, true);
5189 reorderAutoannotation(af, al, autoAlan);
5190 af.alignPanel.alignmentChanged();
5194 splitFrameCandidates.put(view, af);
5200 * Reads saved data to restore Colour by Annotation settings
5202 * @param viewAnnColour
5206 * @param checkGroupAnnColour
5209 private ColourSchemeI constructAnnotationColour(
5210 AnnotationColourScheme viewAnnColour, AlignFrame af,
5211 AlignmentI al, JalviewModel model, boolean checkGroupAnnColour)
5213 boolean propagateAnnColour = false;
5214 AlignmentI annAlignment = af != null ? af.getViewport().getAlignment()
5216 if (checkGroupAnnColour && al.getGroups() != null
5217 && al.getGroups().size() > 0)
5219 // pre 2.8.1 behaviour
5220 // check to see if we should transfer annotation colours
5221 propagateAnnColour = true;
5222 for (SequenceGroup sg : al.getGroups())
5224 if (sg.getColourScheme() instanceof AnnotationColourGradient)
5226 propagateAnnColour = false;
5232 * 2.10.2- : saved annotationId is AlignmentAnnotation.annotationId
5234 String annotationId = viewAnnColour.getAnnotation();
5235 AlignmentAnnotation matchedAnnotation = annotationIds.get(annotationId);
5238 * pre 2.10.2: saved annotationId is AlignmentAnnotation.label
5240 if (matchedAnnotation == null
5241 && annAlignment.getAlignmentAnnotation() != null)
5243 for (int i = 0; i < annAlignment.getAlignmentAnnotation().length; i++)
5246 .equals(annAlignment.getAlignmentAnnotation()[i].label))
5248 matchedAnnotation = annAlignment.getAlignmentAnnotation()[i];
5253 if (matchedAnnotation == null)
5255 System.err.println("Failed to match annotation colour scheme for "
5259 if (matchedAnnotation.getThreshold() == null)
5261 matchedAnnotation.setThreshold(
5262 new GraphLine(safeFloat(viewAnnColour.getThreshold()),
5263 "Threshold", Color.black));
5266 AnnotationColourGradient cs = null;
5267 if (viewAnnColour.getColourScheme().equals("None"))
5269 cs = new AnnotationColourGradient(matchedAnnotation,
5270 new Color(safeInt(viewAnnColour.getMinColour())),
5271 new Color(safeInt(viewAnnColour.getMaxColour())),
5272 safeInt(viewAnnColour.getAboveThreshold()));
5274 else if (viewAnnColour.getColourScheme().startsWith("ucs"))
5276 cs = new AnnotationColourGradient(matchedAnnotation,
5277 getUserColourScheme(model, viewAnnColour.getColourScheme()),
5278 safeInt(viewAnnColour.getAboveThreshold()));
5282 cs = new AnnotationColourGradient(matchedAnnotation,
5283 ColourSchemeProperty.getColourScheme(af.getViewport(), al,
5284 viewAnnColour.getColourScheme()),
5285 safeInt(viewAnnColour.getAboveThreshold()));
5288 boolean perSequenceOnly = safeBoolean(viewAnnColour.isPerSequence());
5289 boolean useOriginalColours = safeBoolean(
5290 viewAnnColour.isPredefinedColours());
5291 cs.setSeqAssociated(perSequenceOnly);
5292 cs.setPredefinedColours(useOriginalColours);
5294 if (propagateAnnColour && al.getGroups() != null)
5296 // Also use these settings for all the groups
5297 for (int g = 0; g < al.getGroups().size(); g++)
5299 SequenceGroup sg = al.getGroups().get(g);
5300 if (sg.getGroupColourScheme() == null)
5305 AnnotationColourGradient groupScheme = new AnnotationColourGradient(
5306 matchedAnnotation, sg.getColourScheme(),
5307 safeInt(viewAnnColour.getAboveThreshold()));
5308 sg.setColourScheme(groupScheme);
5309 groupScheme.setSeqAssociated(perSequenceOnly);
5310 groupScheme.setPredefinedColours(useOriginalColours);
5316 private void reorderAutoannotation(AlignFrame af, AlignmentI al,
5317 List<JvAnnotRow> autoAlan)
5319 // copy over visualization settings for autocalculated annotation in the
5321 if (al.getAlignmentAnnotation() != null)
5324 * Kludge for magic autoannotation names (see JAL-811)
5326 String[] magicNames = new String[] { "Consensus", "Quality",
5328 JvAnnotRow nullAnnot = new JvAnnotRow(-1, null);
5329 Hashtable<String, JvAnnotRow> visan = new Hashtable<>();
5330 for (String nm : magicNames)
5332 visan.put(nm, nullAnnot);
5334 for (JvAnnotRow auan : autoAlan)
5336 visan.put(auan.template.label
5337 + (auan.template.getCalcId() == null ? ""
5338 : "\t" + auan.template.getCalcId()),
5341 int hSize = al.getAlignmentAnnotation().length;
5342 List<JvAnnotRow> reorder = new ArrayList<>();
5343 // work through any autoCalculated annotation already on the view
5344 // removing it if it should be placed in a different location on the
5345 // annotation panel.
5346 List<String> remains = new ArrayList<>(visan.keySet());
5347 for (int h = 0; h < hSize; h++)
5349 jalview.datamodel.AlignmentAnnotation jalan = al
5350 .getAlignmentAnnotation()[h];
5351 if (jalan.autoCalculated)
5354 JvAnnotRow valan = visan.get(k = jalan.label);
5355 if (jalan.getCalcId() != null)
5357 valan = visan.get(k = jalan.label + "\t" + jalan.getCalcId());
5362 // delete the auto calculated row from the alignment
5363 al.deleteAnnotation(jalan, false);
5367 if (valan != nullAnnot)
5369 if (jalan != valan.template)
5371 // newly created autoannotation row instance
5372 // so keep a reference to the visible annotation row
5373 // and copy over all relevant attributes
5374 if (valan.template.graphHeight >= 0)
5377 jalan.graphHeight = valan.template.graphHeight;
5379 jalan.visible = valan.template.visible;
5381 reorder.add(new JvAnnotRow(valan.order, jalan));
5386 // Add any (possibly stale) autocalculated rows that were not appended to
5387 // the view during construction
5388 for (String other : remains)
5390 JvAnnotRow othera = visan.get(other);
5391 if (othera != nullAnnot && othera.template.getCalcId() != null
5392 && othera.template.getCalcId().length() > 0)
5394 reorder.add(othera);
5397 // now put the automatic annotation in its correct place
5398 int s = 0, srt[] = new int[reorder.size()];
5399 JvAnnotRow[] rws = new JvAnnotRow[reorder.size()];
5400 for (JvAnnotRow jvar : reorder)
5403 srt[s++] = jvar.order;
5406 jalview.util.QuickSort.sort(srt, rws);
5407 // and re-insert the annotation at its correct position
5408 for (JvAnnotRow jvar : rws)
5410 al.addAnnotation(jvar.template, jvar.order);
5412 af.alignPanel.adjustAnnotationHeight();
5416 Hashtable skipList = null;
5419 * TODO remove this method
5422 * @return AlignFrame bound to sequenceSetId from view, if one exists. private
5423 * AlignFrame getSkippedFrame(Viewport view) { if (skipList==null) {
5424 * throw new Error("Implementation Error. No skipList defined for this
5425 * Jalview2XML instance."); } return (AlignFrame)
5426 * skipList.get(view.getSequenceSetId()); }
5430 * Check if the Jalview view contained in object should be skipped or not.
5433 * @return true if view's sequenceSetId is a key in skipList
5435 private boolean skipViewport(JalviewModel object)
5437 if (skipList == null)
5441 String id = object.getViewport().get(0).getSequenceSetId();
5442 if (skipList.containsKey(id))
5444 if (Cache.log != null && Cache.log.isDebugEnabled())
5446 Cache.log.debug("Skipping seuqence set id " + id);
5453 public void addToSkipList(AlignFrame af)
5455 if (skipList == null)
5457 skipList = new Hashtable();
5459 skipList.put(af.getViewport().getSequenceSetId(), af);
5462 public void clearSkipList()
5464 if (skipList != null)
5471 private void recoverDatasetFor(SequenceSet vamsasSet, AlignmentI al,
5472 boolean ignoreUnrefed, String uniqueSeqSetId)
5474 jalview.datamodel.AlignmentI ds = getDatasetFor(
5475 vamsasSet.getDatasetId());
5476 AlignmentI xtant_ds = ds;
5477 if (xtant_ds == null)
5479 // good chance we are about to create a new dataset, but check if we've
5480 // seen some of the dataset sequence IDs before.
5481 // TODO: skip this check if we are working with project generated by
5482 // version 2.11 or later
5483 xtant_ds = checkIfHasDataset(vamsasSet.getSequence());
5484 if (xtant_ds != null)
5487 addDatasetRef(vamsasSet.getDatasetId(), ds);
5490 Vector dseqs = null;
5493 // recovering an alignment View
5494 AlignmentI seqSetDS = getDatasetFor(UNIQSEQSETID + uniqueSeqSetId);
5495 if (seqSetDS != null)
5497 if (ds != null && ds != seqSetDS)
5499 warn("JAL-3171 regression: Overwriting a dataset reference for an alignment"
5500 + " - CDS/Protein crossreference data may be lost");
5501 if (xtant_ds != null)
5503 // This can only happen if the unique sequence set ID was bound to a
5504 // dataset that did not contain any of the sequences in the view
5505 // currently being restored.
5506 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.");
5510 addDatasetRef(vamsasSet.getDatasetId(), ds);
5515 // try even harder to restore dataset
5516 AlignmentI xtantDS = checkIfHasDataset(vamsasSet.getSequence());
5517 // create a list of new dataset sequences
5518 dseqs = new Vector();
5520 for (int i = 0, iSize = vamsasSet.getSequence().size(); i < iSize; i++)
5522 Sequence vamsasSeq = vamsasSet.getSequence().get(i);
5523 ensureJalviewDatasetSequence(vamsasSeq, ds, dseqs, ignoreUnrefed, i);
5525 // create a new dataset
5528 SequenceI[] dsseqs = new SequenceI[dseqs.size()];
5529 dseqs.copyInto(dsseqs);
5530 ds = new jalview.datamodel.Alignment(dsseqs);
5531 debug("Created new dataset " + vamsasSet.getDatasetId()
5532 + " for alignment " + System.identityHashCode(al));
5533 addDatasetRef(vamsasSet.getDatasetId(), ds);
5535 // set the dataset for the newly imported alignment.
5536 if (al.getDataset() == null && !ignoreUnrefed)
5539 // register dataset for the alignment's uniqueSeqSetId for legacy projects
5540 addDatasetRef(UNIQSEQSETID + uniqueSeqSetId, ds);
5542 updateSeqDatasetBinding(vamsasSet.getSequence(), ds);
5546 * XML dataset sequence ID to materialised dataset reference
5548 HashMap<String, AlignmentI> seqToDataset = new HashMap<>();
5551 * @return the first materialised dataset reference containing a dataset
5552 * sequence referenced in the given view
5554 * - sequences from the view
5556 AlignmentI checkIfHasDataset(List<Sequence> list)
5558 for (Sequence restoredSeq : list)
5560 AlignmentI datasetFor = seqToDataset.get(restoredSeq.getDsseqid());
5561 if (datasetFor != null)
5570 * Register ds as the containing dataset for the dataset sequences referenced
5571 * by sequences in list
5574 * - sequences in a view
5577 void updateSeqDatasetBinding(List<Sequence> list, AlignmentI ds)
5579 for (Sequence restoredSeq : list)
5581 AlignmentI prevDS = seqToDataset.put(restoredSeq.getDsseqid(), ds);
5582 if (prevDS != null && prevDS != ds)
5584 warn("Dataset sequence appears in many datasets: "
5585 + restoredSeq.getDsseqid());
5586 // TODO: try to merge!
5593 * sequence definition to create/merge dataset sequence for
5597 * vector to add new dataset sequence to
5598 * @param ignoreUnrefed
5599 * - when true, don't create new sequences from vamsasSeq if it's id
5600 * doesn't already have an asssociated Jalview sequence.
5602 * - used to reorder the sequence in the alignment according to the
5603 * vamsasSeq array ordering, to preserve ordering of dataset
5605 private void ensureJalviewDatasetSequence(Sequence vamsasSeq,
5606 AlignmentI ds, Vector dseqs, boolean ignoreUnrefed, int vseqpos)
5608 // JBP TODO: Check this is called for AlCodonFrames to support recovery of
5610 SequenceI sq = seqRefIds.get(vamsasSeq.getId());
5611 boolean reorder = false;
5612 SequenceI dsq = null;
5613 if (sq != null && sq.getDatasetSequence() != null)
5615 dsq = sq.getDatasetSequence();
5621 if (sq == null && ignoreUnrefed)
5625 String sqid = vamsasSeq.getDsseqid();
5628 // need to create or add a new dataset sequence reference to this sequence
5631 dsq = seqRefIds.get(sqid);
5636 // make a new dataset sequence
5637 dsq = sq.createDatasetSequence();
5640 // make up a new dataset reference for this sequence
5641 sqid = seqHash(dsq);
5643 dsq.setVamsasId(uniqueSetSuffix + sqid);
5644 seqRefIds.put(sqid, dsq);
5649 dseqs.addElement(dsq);
5654 ds.addSequence(dsq);
5660 { // make this dataset sequence sq's dataset sequence
5661 sq.setDatasetSequence(dsq);
5662 // and update the current dataset alignment
5667 if (!dseqs.contains(dsq))
5674 if (ds.findIndex(dsq) < 0)
5676 ds.addSequence(dsq);
5683 // TODO: refactor this as a merge dataset sequence function
5684 // now check that sq (the dataset sequence) sequence really is the union of
5685 // all references to it
5686 // boolean pre = sq.getStart() < dsq.getStart();
5687 // boolean post = sq.getEnd() > dsq.getEnd();
5691 // StringBuffer sb = new StringBuffer();
5692 String newres = jalview.analysis.AlignSeq.extractGaps(
5693 jalview.util.Comparison.GapChars, sq.getSequenceAsString());
5694 if (!newres.equalsIgnoreCase(dsq.getSequenceAsString())
5695 && newres.length() > dsq.getLength())
5697 // Update with the longer sequence.
5701 * if (pre) { sb.insert(0, newres .substring(0, dsq.getStart() -
5702 * sq.getStart())); dsq.setStart(sq.getStart()); } if (post) {
5703 * sb.append(newres.substring(newres.length() - sq.getEnd() -
5704 * dsq.getEnd())); dsq.setEnd(sq.getEnd()); }
5706 dsq.setSequence(newres);
5708 // TODO: merges will never happen if we 'know' we have the real dataset
5709 // sequence - this should be detected when id==dssid
5711 "DEBUG Notice: Merged dataset sequence (if you see this often, post at http://issues.jalview.org/browse/JAL-1474)"); // ("
5712 // + (pre ? "prepended" : "") + " "
5713 // + (post ? "appended" : ""));
5718 // sequence refs are identical. We may need to update the existing dataset
5719 // alignment with this one, though.
5720 if (ds != null && dseqs == null)
5722 int opos = ds.findIndex(dsq);
5723 SequenceI tseq = null;
5724 if (opos != -1 && vseqpos != opos)
5726 // remove from old position
5727 ds.deleteSequence(dsq);
5729 if (vseqpos < ds.getHeight())
5731 if (vseqpos != opos)
5733 // save sequence at destination position
5734 tseq = ds.getSequenceAt(vseqpos);
5735 ds.replaceSequenceAt(vseqpos, dsq);
5736 ds.addSequence(tseq);
5741 ds.addSequence(dsq);
5748 * TODO use AlignmentI here and in related methods - needs
5749 * AlignmentI.getDataset() changed to return AlignmentI instead of Alignment
5751 Hashtable<String, AlignmentI> datasetIds = null;
5753 IdentityHashMap<AlignmentI, String> dataset2Ids = null;
5755 private AlignmentI getDatasetFor(String datasetId)
5757 if (datasetIds == null)
5759 datasetIds = new Hashtable<>();
5762 if (datasetIds.containsKey(datasetId))
5764 return datasetIds.get(datasetId);
5769 private void addDatasetRef(String datasetId, AlignmentI dataset)
5771 if (datasetIds == null)
5773 datasetIds = new Hashtable<>();
5775 datasetIds.put(datasetId, dataset);
5779 * make a new dataset ID for this jalview dataset alignment
5784 private String getDatasetIdRef(AlignmentI dataset)
5786 if (dataset.getDataset() != null)
5788 warn("Serious issue! Dataset Object passed to getDatasetIdRef is not a Jalview DATASET alignment...");
5790 String datasetId = makeHashCode(dataset, null);
5791 if (datasetId == null)
5793 // make a new datasetId and record it
5794 if (dataset2Ids == null)
5796 dataset2Ids = new IdentityHashMap<>();
5800 datasetId = dataset2Ids.get(dataset);
5802 if (datasetId == null)
5804 datasetId = "ds" + dataset2Ids.size() + 1;
5805 dataset2Ids.put(dataset, datasetId);
5812 * Add any saved DBRefEntry's to the sequence. An entry flagged as 'locus' is
5813 * constructed as a special subclass GeneLocus.
5815 * @param datasetSequence
5818 private void addDBRefs(SequenceI datasetSequence, Sequence sequence)
5820 for (int d = 0; d < sequence.getDBRef().size(); d++)
5822 DBRef dr = sequence.getDBRef().get(d);
5826 entry = new GeneLocus(dr.getSource(), dr.getVersion(),
5827 dr.getAccessionId());
5831 entry = new DBRefEntry(dr.getSource(), dr.getVersion(),
5832 dr.getAccessionId());
5834 if (dr.getMapping() != null)
5836 entry.setMap(addMapping(dr.getMapping()));
5838 datasetSequence.addDBRef(entry);
5842 private jalview.datamodel.Mapping addMapping(Mapping m)
5844 SequenceI dsto = null;
5845 // Mapping m = dr.getMapping();
5846 int fr[] = new int[m.getMapListFrom().size() * 2];
5847 Iterator<MapListFrom> from = m.getMapListFrom().iterator();// enumerateMapListFrom();
5848 for (int _i = 0; from.hasNext(); _i += 2)
5850 MapListFrom mf = from.next();
5851 fr[_i] = mf.getStart();
5852 fr[_i + 1] = mf.getEnd();
5854 int fto[] = new int[m.getMapListTo().size() * 2];
5855 Iterator<MapListTo> to = m.getMapListTo().iterator();// enumerateMapListTo();
5856 for (int _i = 0; to.hasNext(); _i += 2)
5858 MapListTo mf = to.next();
5859 fto[_i] = mf.getStart();
5860 fto[_i + 1] = mf.getEnd();
5862 jalview.datamodel.Mapping jmap = new jalview.datamodel.Mapping(dsto, fr,
5863 fto, m.getMapFromUnit().intValue(),
5864 m.getMapToUnit().intValue());
5867 * (optional) choice of dseqFor or Sequence
5869 if (m.getDseqFor() != null)
5871 String dsfor = m.getDseqFor();
5872 if (seqRefIds.containsKey(dsfor))
5877 jmap.setTo(seqRefIds.get(dsfor));
5881 frefedSequence.add(newMappingRef(dsfor, jmap));
5884 else if (m.getSequence() != null)
5887 * local sequence definition
5889 Sequence ms = m.getSequence();
5890 SequenceI djs = null;
5891 String sqid = ms.getDsseqid();
5892 if (sqid != null && sqid.length() > 0)
5895 * recover dataset sequence
5897 djs = seqRefIds.get(sqid);
5902 "Warning - making up dataset sequence id for DbRef sequence map reference");
5903 sqid = ((Object) ms).toString(); // make up a new hascode for
5904 // undefined dataset sequence hash
5905 // (unlikely to happen)
5911 * make a new dataset sequence and add it to refIds hash
5913 djs = new jalview.datamodel.Sequence(ms.getName(),
5915 djs.setStart(jmap.getMap().getToLowest());
5916 djs.setEnd(jmap.getMap().getToHighest());
5917 djs.setVamsasId(uniqueSetSuffix + sqid);
5919 incompleteSeqs.put(sqid, djs);
5920 seqRefIds.put(sqid, djs);
5923 jalview.bin.Cache.log.debug("about to recurse on addDBRefs.");
5932 * Provides a 'copy' of an alignment view (on action New View) by 'saving' the
5933 * view as XML (but not to file), and then reloading it
5938 public AlignmentPanel copyAlignPanel(AlignmentPanel ap)
5941 JalviewModel jm = saveState(ap, null, null, null);
5944 jm.getVamsasModel().getSequenceSet().get(0).getDatasetId(),
5945 ap.getAlignment().getDataset());
5947 uniqueSetSuffix = "";
5948 // jm.getJalviewModelSequence().getViewport(0).setId(null);
5949 jm.getViewport().get(0).setId(null);
5950 // we don't overwrite the view we just copied
5952 if (this.frefedSequence == null)
5954 frefedSequence = new Vector<>();
5957 viewportsAdded.clear();
5959 AlignFrame af = loadFromObject(jm, null, false, null);
5960 af.getAlignPanels().clear();
5961 af.closeMenuItem_actionPerformed(true);
5964 * if(ap.av.getAlignment().getAlignmentAnnotation()!=null) { for(int i=0;
5965 * i<ap.av.getAlignment().getAlignmentAnnotation().length; i++) {
5966 * if(!ap.av.getAlignment().getAlignmentAnnotation()[i].autoCalculated) {
5967 * af.alignPanel.av.getAlignment().getAlignmentAnnotation()[i] =
5968 * ap.av.getAlignment().getAlignmentAnnotation()[i]; } } }
5971 return af.alignPanel;
5974 private Hashtable jvids2vobj;
5976 private void warn(String msg)
5981 private void warn(String msg, Exception e)
5983 if (Cache.log != null)
5987 Cache.log.warn(msg, e);
5991 Cache.log.warn(msg);
5996 System.err.println("Warning: " + msg);
5999 e.printStackTrace();
6004 private void debug(String string)
6006 debug(string, null);
6009 private void debug(String msg, Exception e)
6011 if (Cache.log != null)
6015 Cache.log.debug(msg, e);
6019 Cache.log.debug(msg);
6024 System.err.println("Warning: " + msg);
6027 e.printStackTrace();
6033 * set the object to ID mapping tables used to write/recover objects and XML
6034 * ID strings for the jalview project. If external tables are provided then
6035 * finalize and clearSeqRefs will not clear the tables when the Jalview2XML
6036 * object goes out of scope. - also populates the datasetIds hashtable with
6037 * alignment objects containing dataset sequences
6040 * Map from ID strings to jalview datamodel
6042 * Map from jalview datamodel to ID strings
6046 public void setObjectMappingTables(Hashtable vobj2jv,
6047 IdentityHashMap jv2vobj)
6049 this.jv2vobj = jv2vobj;
6050 this.vobj2jv = vobj2jv;
6051 Iterator ds = jv2vobj.keySet().iterator();
6053 while (ds.hasNext())
6055 Object jvobj = ds.next();
6056 id = jv2vobj.get(jvobj).toString();
6057 if (jvobj instanceof jalview.datamodel.Alignment)
6059 if (((jalview.datamodel.Alignment) jvobj).getDataset() == null)
6061 addDatasetRef(id, (jalview.datamodel.Alignment) jvobj);
6064 else if (jvobj instanceof jalview.datamodel.Sequence)
6066 // register sequence object so the XML parser can recover it.
6067 if (seqRefIds == null)
6069 seqRefIds = new HashMap<>();
6071 if (seqsToIds == null)
6073 seqsToIds = new IdentityHashMap<>();
6075 seqRefIds.put(jv2vobj.get(jvobj).toString(), (SequenceI) jvobj);
6076 seqsToIds.put((SequenceI) jvobj, id);
6078 else if (jvobj instanceof jalview.datamodel.AlignmentAnnotation)
6081 AlignmentAnnotation jvann = (AlignmentAnnotation) jvobj;
6082 annotationIds.put(anid = jv2vobj.get(jvobj).toString(), jvann);
6083 if (jvann.annotationId == null)
6085 jvann.annotationId = anid;
6087 if (!jvann.annotationId.equals(anid))
6089 // TODO verify that this is the correct behaviour
6090 this.warn("Overriding Annotation ID for " + anid
6091 + " from different id : " + jvann.annotationId);
6092 jvann.annotationId = anid;
6095 else if (jvobj instanceof String)
6097 if (jvids2vobj == null)
6099 jvids2vobj = new Hashtable();
6100 jvids2vobj.put(jvobj, jv2vobj.get(jvobj).toString());
6105 Cache.log.debug("Ignoring " + jvobj.getClass() + " (ID = " + id);
6111 * set the uniqueSetSuffix used to prefix/suffix object IDs for jalview
6112 * objects created from the project archive. If string is null (default for
6113 * construction) then suffix will be set automatically.
6117 public void setUniqueSetSuffix(String string)
6119 uniqueSetSuffix = string;
6124 * uses skipList2 as the skipList for skipping views on sequence sets
6125 * associated with keys in the skipList
6129 public void setSkipList(Hashtable skipList2)
6131 skipList = skipList2;
6135 * Reads the jar entry of given name and returns its contents, or null if the
6136 * entry is not found.
6139 * @param jarEntryName
6142 protected String readJarEntry(jarInputStreamProvider jprovider,
6143 String jarEntryName)
6145 String result = null;
6146 BufferedReader in = null;
6151 * Reopen the jar input stream and traverse its entries to find a matching
6154 JarInputStream jin = jprovider.getJarInputStream();
6155 JarEntry entry = null;
6158 entry = jin.getNextJarEntry();
6159 } while (entry != null && !entry.getName().equals(jarEntryName));
6163 StringBuilder out = new StringBuilder(256);
6164 in = new BufferedReader(new InputStreamReader(jin, UTF_8));
6167 while ((data = in.readLine()) != null)
6171 result = out.toString();
6175 warn("Couldn't find entry in Jalview Jar for " + jarEntryName);
6177 } catch (Exception ex)
6179 ex.printStackTrace();
6187 } catch (IOException e)
6198 * Returns an incrementing counter (0, 1, 2...)
6202 private synchronized int nextCounter()
6208 * Loads any saved PCA viewers
6213 protected void loadPCAViewers(JalviewModel model, AlignmentPanel ap)
6217 List<PcaViewer> pcaviewers = model.getPcaViewer();
6218 for (PcaViewer viewer : pcaviewers)
6220 String modelName = viewer.getScoreModelName();
6221 SimilarityParamsI params = new SimilarityParams(
6222 viewer.isIncludeGappedColumns(), viewer.isMatchGaps(),
6223 viewer.isIncludeGaps(),
6224 viewer.isDenominateByShortestLength());
6227 * create the panel (without computing the PCA)
6229 PCAPanel panel = new PCAPanel(ap, modelName, params);
6231 panel.setTitle(viewer.getTitle());
6232 panel.setBounds(new Rectangle(viewer.getXpos(), viewer.getYpos(),
6233 viewer.getWidth(), viewer.getHeight()));
6235 boolean showLabels = viewer.isShowLabels();
6236 panel.setShowLabels(showLabels);
6237 panel.getRotatableCanvas().setShowLabels(showLabels);
6238 panel.getRotatableCanvas()
6239 .setBgColour(new Color(viewer.getBgColour()));
6240 panel.getRotatableCanvas()
6241 .setApplyToAllViews(viewer.isLinkToAllViews());
6244 * load PCA output data
6246 ScoreModelI scoreModel = ScoreModels.getInstance()
6247 .getScoreModel(modelName, ap);
6248 PCA pca = new PCA(null, scoreModel, params);
6249 PcaDataType pcaData = viewer.getPcaData();
6251 MatrixI pairwise = loadDoubleMatrix(pcaData.getPairwiseMatrix());
6252 pca.setPairwiseScores(pairwise);
6254 MatrixI triDiag = loadDoubleMatrix(pcaData.getTridiagonalMatrix());
6255 pca.setTridiagonal(triDiag);
6257 MatrixI result = loadDoubleMatrix(pcaData.getEigenMatrix());
6258 pca.setEigenmatrix(result);
6260 panel.getPcaModel().setPCA(pca);
6263 * we haven't saved the input data! (JAL-2647 to do)
6265 panel.setInputData(null);
6268 * add the sequence points for the PCA display
6270 List<jalview.datamodel.SequencePoint> seqPoints = new ArrayList<>();
6271 for (SequencePoint sp : viewer.getSequencePoint())
6273 String seqId = sp.getSequenceRef();
6274 SequenceI seq = seqRefIds.get(seqId);
6277 throw new IllegalStateException(
6278 "Unmatched seqref for PCA: " + seqId);
6280 Point pt = new Point(sp.getXPos(), sp.getYPos(), sp.getZPos());
6281 jalview.datamodel.SequencePoint seqPoint = new jalview.datamodel.SequencePoint(
6283 seqPoints.add(seqPoint);
6285 panel.getRotatableCanvas().setPoints(seqPoints, seqPoints.size());
6288 * set min-max ranges and scale after setPoints (which recomputes them)
6290 panel.getRotatableCanvas().setScaleFactor(viewer.getScaleFactor());
6291 SeqPointMin spMin = viewer.getSeqPointMin();
6292 float[] min = new float[] { spMin.getXPos(), spMin.getYPos(),
6294 SeqPointMax spMax = viewer.getSeqPointMax();
6295 float[] max = new float[] { spMax.getXPos(), spMax.getYPos(),
6297 panel.getRotatableCanvas().setSeqMinMax(min, max);
6299 // todo: hold points list in PCAModel only
6300 panel.getPcaModel().setSequencePoints(seqPoints);
6302 panel.setSelectedDimensionIndex(viewer.getXDim(), X);
6303 panel.setSelectedDimensionIndex(viewer.getYDim(), Y);
6304 panel.setSelectedDimensionIndex(viewer.getZDim(), Z);
6306 // is this duplication needed?
6307 panel.setTop(seqPoints.size() - 1);
6308 panel.getPcaModel().setTop(seqPoints.size() - 1);
6311 * add the axes' end points for the display
6313 for (int i = 0; i < 3; i++)
6315 Axis axis = viewer.getAxis().get(i);
6316 panel.getRotatableCanvas().getAxisEndPoints()[i] = new Point(
6317 axis.getXPos(), axis.getYPos(), axis.getZPos());
6320 Desktop.addInternalFrame(panel, MessageManager.formatMessage(
6321 "label.calc_title", "PCA", modelName), 475, 450);
6323 } catch (Exception ex)
6325 Cache.log.error("Error loading PCA: " + ex.toString());
6330 * Populates an XML model of the feature colour scheme for one feature type
6332 * @param featureType
6336 public static Colour marshalColour(
6337 String featureType, FeatureColourI fcol)
6339 Colour col = new Colour();
6340 if (fcol.isSimpleColour())
6342 col.setRGB(Format.getHexString(fcol.getColour()));
6346 col.setRGB(Format.getHexString(fcol.getMaxColour()));
6347 col.setMin(fcol.getMin());
6348 col.setMax(fcol.getMax());
6349 col.setMinRGB(jalview.util.Format.getHexString(fcol.getMinColour()));
6350 col.setAutoScale(fcol.isAutoScaled());
6351 col.setThreshold(fcol.getThreshold());
6352 col.setColourByLabel(fcol.isColourByLabel());
6353 col.setThreshType(fcol.isAboveThreshold() ? ThresholdType.ABOVE
6354 : (fcol.isBelowThreshold() ? ThresholdType.BELOW
6355 : ThresholdType.NONE));
6356 if (fcol.isColourByAttribute())
6358 final String[] attName = fcol.getAttributeName();
6359 col.getAttributeName().add(attName[0]);
6360 if (attName.length > 1)
6362 col.getAttributeName().add(attName[1]);
6365 Color noColour = fcol.getNoColour();
6366 if (noColour == null)
6368 col.setNoValueColour(NoValueColour.NONE);
6370 else if (noColour == fcol.getMaxColour())
6372 col.setNoValueColour(NoValueColour.MAX);
6376 col.setNoValueColour(NoValueColour.MIN);
6379 col.setName(featureType);
6384 * Populates an XML model of the feature filter(s) for one feature type
6386 * @param firstMatcher
6387 * the first (or only) match condition)
6389 * remaining match conditions (if any)
6391 * if true, conditions are and-ed, else or-ed
6393 public static jalview.xml.binding.jalview.FeatureMatcherSet marshalFilter(
6394 FeatureMatcherI firstMatcher, Iterator<FeatureMatcherI> filters,
6397 jalview.xml.binding.jalview.FeatureMatcherSet result = new jalview.xml.binding.jalview.FeatureMatcherSet();
6399 if (filters.hasNext())
6404 CompoundMatcher compound = new CompoundMatcher();
6405 compound.setAnd(and);
6406 jalview.xml.binding.jalview.FeatureMatcherSet matcher1 = marshalFilter(
6407 firstMatcher, Collections.emptyIterator(), and);
6408 // compound.addMatcherSet(matcher1);
6409 compound.getMatcherSet().add(matcher1);
6410 FeatureMatcherI nextMatcher = filters.next();
6411 jalview.xml.binding.jalview.FeatureMatcherSet matcher2 = marshalFilter(
6412 nextMatcher, filters, and);
6413 // compound.addMatcherSet(matcher2);
6414 compound.getMatcherSet().add(matcher2);
6415 result.setCompoundMatcher(compound);
6420 * single condition matcher
6422 // MatchCondition matcherModel = new MatchCondition();
6423 jalview.xml.binding.jalview.FeatureMatcher matcherModel = new jalview.xml.binding.jalview.FeatureMatcher();
6424 matcherModel.setCondition(
6425 firstMatcher.getMatcher().getCondition().getStableName());
6426 matcherModel.setValue(firstMatcher.getMatcher().getPattern());
6427 if (firstMatcher.isByAttribute())
6429 matcherModel.setBy(FilterBy.BY_ATTRIBUTE);
6430 // matcherModel.setAttributeName(firstMatcher.getAttribute());
6431 String[] attName = firstMatcher.getAttribute();
6432 matcherModel.getAttributeName().add(attName[0]); // attribute
6433 if (attName.length > 1)
6435 matcherModel.getAttributeName().add(attName[1]); // sub-attribute
6438 else if (firstMatcher.isByLabel())
6440 matcherModel.setBy(FilterBy.BY_LABEL);
6442 else if (firstMatcher.isByScore())
6444 matcherModel.setBy(FilterBy.BY_SCORE);
6446 result.setMatchCondition(matcherModel);
6453 * Loads one XML model of a feature filter to a Jalview object
6455 * @param featureType
6456 * @param matcherSetModel
6459 public static FeatureMatcherSetI parseFilter(
6461 jalview.xml.binding.jalview.FeatureMatcherSet matcherSetModel)
6463 FeatureMatcherSetI result = new FeatureMatcherSet();
6466 parseFilterConditions(result, matcherSetModel, true);
6467 } catch (IllegalStateException e)
6469 // mixing AND and OR conditions perhaps
6471 String.format("Error reading filter conditions for '%s': %s",
6472 featureType, e.getMessage()));
6473 // return as much as was parsed up to the error
6480 * Adds feature match conditions to matcherSet as unmarshalled from XML
6481 * (possibly recursively for compound conditions)
6484 * @param matcherSetModel
6486 * if true, multiple conditions are AND-ed, else they are OR-ed
6487 * @throws IllegalStateException
6488 * if AND and OR conditions are mixed
6490 protected static void parseFilterConditions(
6491 FeatureMatcherSetI matcherSet,
6492 jalview.xml.binding.jalview.FeatureMatcherSet matcherSetModel,
6495 jalview.xml.binding.jalview.FeatureMatcher mc = matcherSetModel
6496 .getMatchCondition();
6502 FilterBy filterBy = mc.getBy();
6503 Condition cond = Condition.fromString(mc.getCondition());
6504 String pattern = mc.getValue();
6505 FeatureMatcherI matchCondition = null;
6506 if (filterBy == FilterBy.BY_LABEL)
6508 matchCondition = FeatureMatcher.byLabel(cond, pattern);
6510 else if (filterBy == FilterBy.BY_SCORE)
6512 matchCondition = FeatureMatcher.byScore(cond, pattern);
6515 else if (filterBy == FilterBy.BY_ATTRIBUTE)
6517 final List<String> attributeName = mc.getAttributeName();
6518 String[] attNames = attributeName
6519 .toArray(new String[attributeName.size()]);
6520 matchCondition = FeatureMatcher.byAttribute(cond, pattern,
6525 * note this throws IllegalStateException if AND-ing to a
6526 * previously OR-ed compound condition, or vice versa
6530 matcherSet.and(matchCondition);
6534 matcherSet.or(matchCondition);
6540 * compound condition
6542 List<jalview.xml.binding.jalview.FeatureMatcherSet> matchers = matcherSetModel
6543 .getCompoundMatcher().getMatcherSet();
6544 boolean anded = matcherSetModel.getCompoundMatcher().isAnd();
6545 if (matchers.size() == 2)
6547 parseFilterConditions(matcherSet, matchers.get(0), anded);
6548 parseFilterConditions(matcherSet, matchers.get(1), anded);
6552 System.err.println("Malformed compound filter condition");
6558 * Loads one XML model of a feature colour to a Jalview object
6560 * @param colourModel
6563 public static FeatureColourI parseColour(Colour colourModel)
6565 FeatureColourI colour = null;
6567 if (colourModel.getMax() != null)
6569 Color mincol = null;
6570 Color maxcol = null;
6571 Color noValueColour = null;
6575 mincol = new Color(Integer.parseInt(colourModel.getMinRGB(), 16));
6576 maxcol = new Color(Integer.parseInt(colourModel.getRGB(), 16));
6577 } catch (Exception e)
6579 Cache.log.warn("Couldn't parse out graduated feature color.", e);
6582 NoValueColour noCol = colourModel.getNoValueColour();
6583 if (noCol == NoValueColour.MIN)
6585 noValueColour = mincol;
6587 else if (noCol == NoValueColour.MAX)
6589 noValueColour = maxcol;
6592 colour = new FeatureColour(maxcol, mincol, maxcol, noValueColour,
6593 safeFloat(colourModel.getMin()),
6594 safeFloat(colourModel.getMax()));
6595 final List<String> attributeName = colourModel.getAttributeName();
6596 String[] attributes = attributeName
6597 .toArray(new String[attributeName.size()]);
6598 if (attributes != null && attributes.length > 0)
6600 colour.setAttributeName(attributes);
6602 if (colourModel.isAutoScale() != null)
6604 colour.setAutoScaled(colourModel.isAutoScale().booleanValue());
6606 if (colourModel.isColourByLabel() != null)
6608 colour.setColourByLabel(
6609 colourModel.isColourByLabel().booleanValue());
6611 if (colourModel.getThreshold() != null)
6613 colour.setThreshold(colourModel.getThreshold().floatValue());
6615 ThresholdType ttyp = colourModel.getThreshType();
6616 if (ttyp == ThresholdType.ABOVE)
6618 colour.setAboveThreshold(true);
6620 else if (ttyp == ThresholdType.BELOW)
6622 colour.setBelowThreshold(true);
6627 Color color = new Color(Integer.parseInt(colourModel.getRGB(), 16));
6628 colour = new FeatureColour(color);