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.AlignmentViewPanel;
32 import jalview.api.FeatureColourI;
33 import jalview.api.ViewStyleI;
34 import jalview.api.analysis.ScoreModelI;
35 import jalview.api.analysis.SimilarityParamsI;
36 import jalview.api.structures.JalviewStructureDisplayI;
37 import jalview.bin.Cache;
38 import jalview.datamodel.AlignedCodonFrame;
39 import jalview.datamodel.Alignment;
40 import jalview.datamodel.AlignmentAnnotation;
41 import jalview.datamodel.AlignmentI;
42 import jalview.datamodel.DBRefEntry;
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.structures.models.AAStructureBindingModel;
87 import jalview.util.Format;
88 import jalview.util.MessageManager;
89 import jalview.util.Platform;
90 import jalview.util.StringUtils;
91 import jalview.util.jarInputStreamProvider;
92 import jalview.util.matcher.Condition;
93 import jalview.viewmodel.AlignmentViewport;
94 import jalview.viewmodel.PCAModel;
95 import jalview.viewmodel.ViewportRanges;
96 import jalview.viewmodel.seqfeatures.FeatureRendererSettings;
97 import jalview.viewmodel.seqfeatures.FeaturesDisplayed;
98 import jalview.ws.jws2.Jws2Discoverer;
99 import jalview.ws.jws2.dm.AAConSettings;
100 import jalview.ws.jws2.jabaws2.Jws2Instance;
101 import jalview.ws.params.ArgumentI;
102 import jalview.ws.params.AutoCalcSetting;
103 import jalview.ws.params.WsParamSetI;
104 import jalview.xml.binding.jalview.AlcodonFrame;
105 import jalview.xml.binding.jalview.AlcodonFrame.AlcodMap;
106 import jalview.xml.binding.jalview.Annotation;
107 import jalview.xml.binding.jalview.Annotation.ThresholdLine;
108 import jalview.xml.binding.jalview.AnnotationColourScheme;
109 import jalview.xml.binding.jalview.AnnotationElement;
110 import jalview.xml.binding.jalview.DoubleMatrix;
111 import jalview.xml.binding.jalview.DoubleVector;
112 import jalview.xml.binding.jalview.Feature;
113 import jalview.xml.binding.jalview.Feature.OtherData;
114 import jalview.xml.binding.jalview.FeatureMatcherSet.CompoundMatcher;
115 import jalview.xml.binding.jalview.FilterBy;
116 import jalview.xml.binding.jalview.JalviewModel;
117 import jalview.xml.binding.jalview.JalviewModel.FeatureSettings;
118 import jalview.xml.binding.jalview.JalviewModel.FeatureSettings.Group;
119 import jalview.xml.binding.jalview.JalviewModel.FeatureSettings.Setting;
120 import jalview.xml.binding.jalview.JalviewModel.JGroup;
121 import jalview.xml.binding.jalview.JalviewModel.JSeq;
122 import jalview.xml.binding.jalview.JalviewModel.JSeq.Pdbids;
123 import jalview.xml.binding.jalview.JalviewModel.JSeq.Pdbids.StructureState;
124 import jalview.xml.binding.jalview.JalviewModel.JSeq.RnaViewer;
125 import jalview.xml.binding.jalview.JalviewModel.JSeq.RnaViewer.SecondaryStructure;
126 import jalview.xml.binding.jalview.JalviewModel.PcaViewer;
127 import jalview.xml.binding.jalview.JalviewModel.PcaViewer.Axis;
128 import jalview.xml.binding.jalview.JalviewModel.PcaViewer.SeqPointMax;
129 import jalview.xml.binding.jalview.JalviewModel.PcaViewer.SeqPointMin;
130 import jalview.xml.binding.jalview.JalviewModel.PcaViewer.SequencePoint;
131 import jalview.xml.binding.jalview.JalviewModel.Tree;
132 import jalview.xml.binding.jalview.JalviewModel.UserColours;
133 import jalview.xml.binding.jalview.JalviewModel.Viewport;
134 import jalview.xml.binding.jalview.JalviewModel.Viewport.CalcIdParam;
135 import jalview.xml.binding.jalview.JalviewModel.Viewport.HiddenColumns;
136 import jalview.xml.binding.jalview.JalviewUserColours;
137 import jalview.xml.binding.jalview.JalviewUserColours.Colour;
138 import jalview.xml.binding.jalview.MapListType.MapListFrom;
139 import jalview.xml.binding.jalview.MapListType.MapListTo;
140 import jalview.xml.binding.jalview.Mapping;
141 import jalview.xml.binding.jalview.NoValueColour;
142 import jalview.xml.binding.jalview.ObjectFactory;
143 import jalview.xml.binding.jalview.PcaDataType;
144 import jalview.xml.binding.jalview.Pdbentry.Property;
145 import jalview.xml.binding.jalview.Sequence;
146 import jalview.xml.binding.jalview.Sequence.DBRef;
147 import jalview.xml.binding.jalview.SequenceSet;
148 import jalview.xml.binding.jalview.SequenceSet.SequenceSetProperties;
149 import jalview.xml.binding.jalview.ThresholdType;
150 import jalview.xml.binding.jalview.VAMSAS;
152 import java.awt.Color;
153 import java.awt.Dimension;
154 import java.awt.Font;
155 import java.awt.Rectangle;
156 import java.io.BufferedReader;
157 import java.io.ByteArrayInputStream;
158 import java.io.DataInputStream;
159 import java.io.DataOutputStream;
161 import java.io.FileInputStream;
162 import java.io.FileOutputStream;
163 import java.io.IOException;
164 import java.io.InputStream;
165 import java.io.InputStreamReader;
166 import java.io.OutputStreamWriter;
167 import java.io.PrintWriter;
168 import java.math.BigInteger;
169 import java.net.MalformedURLException;
171 import java.util.ArrayList;
172 import java.util.Arrays;
173 import java.util.Collections;
174 import java.util.Enumeration;
175 import java.util.GregorianCalendar;
176 import java.util.HashMap;
177 import java.util.HashSet;
178 import java.util.Hashtable;
179 import java.util.IdentityHashMap;
180 import java.util.Iterator;
181 import java.util.LinkedHashMap;
182 import java.util.List;
183 import java.util.Map;
184 import java.util.Map.Entry;
185 import java.util.Set;
186 import java.util.Vector;
187 import java.util.jar.JarEntry;
188 import java.util.jar.JarInputStream;
189 import java.util.jar.JarOutputStream;
191 import javax.swing.JInternalFrame;
192 import javax.swing.SwingUtilities;
193 import javax.xml.bind.JAXBContext;
194 import javax.xml.bind.JAXBElement;
195 import javax.xml.bind.Marshaller;
196 import javax.xml.datatype.DatatypeConfigurationException;
197 import javax.xml.datatype.DatatypeFactory;
198 import javax.xml.datatype.XMLGregorianCalendar;
199 import javax.xml.stream.XMLInputFactory;
200 import javax.xml.stream.XMLStreamReader;
203 * Write out the current jalview desktop state as a Jalview XML stream.
205 * Note: the vamsas objects referred to here are primitive versions of the
206 * VAMSAS project schema elements - they are not the same and most likely never
210 * @version $Revision: 1.134 $
212 public class Jalview2XML
215 // BH 2018 we add the .jvp binary extension to J2S so that
216 // it will declare that binary when we do the file save from the browser
220 Platform.addJ2SBinaryType(".jvp?");
223 private static final String VIEWER_PREFIX = "viewer_";
225 private static final String RNA_PREFIX = "rna_";
227 private static final String UTF_8 = "UTF-8";
230 * prefix for recovering datasets for alignments with multiple views where
231 * non-existent dataset IDs were written for some views
233 private static final String UNIQSEQSETID = "uniqueSeqSetId.";
235 // use this with nextCounter() to make unique names for entities
236 private int counter = 0;
239 * SequenceI reference -> XML ID string in jalview XML. Populated as XML reps
240 * of sequence objects are created.
242 IdentityHashMap<SequenceI, String> seqsToIds = null;
245 * jalview XML Sequence ID to jalview sequence object reference (both dataset
246 * and alignment sequences. Populated as XML reps of sequence objects are
249 Map<String, SequenceI> seqRefIds = null;
251 Map<String, SequenceI> incompleteSeqs = null;
253 List<SeqFref> frefedSequence = null;
255 boolean raiseGUI = true; // whether errors are raised in dialog boxes or not
258 * Map of reconstructed AlignFrame objects that appear to have come from
259 * SplitFrame objects (have a dna/protein complement view).
261 private Map<Viewport, AlignFrame> splitFrameCandidates = new HashMap<>();
264 * Map from displayed rna structure models to their saved session state jar
267 private Map<RnaModel, String> rnaSessions = new HashMap<>();
270 * contains last error message (if any) encountered by XML loader.
272 String errorMessage = null;
275 * flag to control whether the Jalview2XML_V1 parser should be deferred to if
276 * exceptions are raised during project XML parsing
278 public boolean attemptversion1parse = false;
281 * JalviewJS only -- to allow read file bytes to be saved in the
282 * created AlignFrame, allowing File | Reload of a project file to work
286 private File jarFile;
289 * A helper method for safely using the value of an optional attribute that
290 * may be null if not present in the XML. Answers the boolean value, or false
296 public static boolean safeBoolean(Boolean b)
298 return b == null ? false : b.booleanValue();
302 * A helper method for safely using the value of an optional attribute that
303 * may be null if not present in the XML. Answers the integer value, or zero
309 public static int safeInt(Integer i)
311 return i == null ? 0 : i.intValue();
315 * A helper method for safely using the value of an optional attribute that
316 * may be null if not present in the XML. Answers the float value, or zero if
322 public static float safeFloat(Float f)
324 return f == null ? 0f : f.floatValue();
328 * create/return unique hash string for sq
331 * @return new or existing unique string for sq
333 String seqHash(SequenceI sq)
335 if (seqsToIds == null)
339 if (seqsToIds.containsKey(sq))
341 return seqsToIds.get(sq);
345 // create sequential key
346 String key = "sq" + (seqsToIds.size() + 1);
347 key = makeHashCode(sq, key); // check we don't have an external reference
349 seqsToIds.put(sq, key);
356 if (seqsToIds == null)
358 seqsToIds = new IdentityHashMap<>();
360 if (seqRefIds == null)
362 seqRefIds = new HashMap<>();
364 if (incompleteSeqs == null)
366 incompleteSeqs = new HashMap<>();
368 if (frefedSequence == null)
370 frefedSequence = new ArrayList<>();
378 public Jalview2XML(boolean raiseGUI)
380 this.raiseGUI = raiseGUI;
384 * base class for resolving forward references to sequences by their ID
389 abstract class SeqFref
395 public SeqFref(String _sref, String type)
401 public String getSref()
406 public SequenceI getSrefSeq()
408 return seqRefIds.get(sref);
411 public boolean isResolvable()
413 return seqRefIds.get(sref) != null;
416 public SequenceI getSrefDatasetSeq()
418 SequenceI sq = seqRefIds.get(sref);
421 while (sq.getDatasetSequence() != null)
423 sq = sq.getDatasetSequence();
430 * @return true if the forward reference was fully resolved
432 abstract boolean resolve();
435 public String toString()
437 return type + " reference to " + sref;
442 * create forward reference for a mapping
448 protected SeqFref newMappingRef(final String sref,
449 final jalview.datamodel.Mapping _jmap)
451 SeqFref fref = new SeqFref(sref, "Mapping")
453 public jalview.datamodel.Mapping jmap = _jmap;
458 SequenceI seq = getSrefDatasetSeq();
470 protected SeqFref newAlcodMapRef(final String sref,
471 final AlignedCodonFrame _cf,
472 final jalview.datamodel.Mapping _jmap)
475 SeqFref fref = new SeqFref(sref, "Codon Frame")
477 AlignedCodonFrame cf = _cf;
479 public jalview.datamodel.Mapping mp = _jmap;
482 public boolean isResolvable()
484 return super.isResolvable() && mp.getTo() != null;
490 SequenceI seq = getSrefDatasetSeq();
495 cf.addMap(seq, mp.getTo(), mp.getMap());
502 protected void resolveFrefedSequences()
504 Iterator<SeqFref> nextFref = frefedSequence.iterator();
505 int toresolve = frefedSequence.size();
506 int unresolved = 0, failedtoresolve = 0;
507 while (nextFref.hasNext())
509 SeqFref ref = nextFref.next();
510 if (ref.isResolvable())
522 } catch (Exception x)
525 "IMPLEMENTATION ERROR: Failed to resolve forward reference for sequence "
538 System.err.println("Jalview Project Import: There were " + unresolved
539 + " forward references left unresolved on the stack.");
541 if (failedtoresolve > 0)
543 System.err.println("SERIOUS! " + failedtoresolve
544 + " resolvable forward references failed to resolve.");
546 if (incompleteSeqs != null && incompleteSeqs.size() > 0)
549 "Jalview Project Import: There are " + incompleteSeqs.size()
550 + " sequences which may have incomplete metadata.");
551 if (incompleteSeqs.size() < 10)
553 for (SequenceI s : incompleteSeqs.values())
555 System.err.println(s.toString());
561 "Too many to report. Skipping output of incomplete sequences.");
567 * This maintains a map of viewports, the key being the seqSetId. Important to
568 * set historyItem and redoList for multiple views
570 Map<String, AlignViewport> viewportsAdded = new HashMap<>();
572 Map<String, AlignmentAnnotation> annotationIds = new HashMap<>();
574 String uniqueSetSuffix = "";
577 * List of pdbfiles added to Jar
579 List<String> pdbfiles = null;
581 // SAVES SEVERAL ALIGNMENT WINDOWS TO SAME JARFILE
582 public void saveState(File statefile)
584 FileOutputStream fos = null;
589 fos = new FileOutputStream(statefile);
591 JarOutputStream jout = new JarOutputStream(fos);
595 } catch (Exception e)
597 Cache.log.error("Couln't write Jalview state to " + statefile, e);
598 // TODO: inform user of the problem - they need to know if their data was
600 if (errorMessage == null)
602 errorMessage = "Did't write Jalview Archive to output file '"
603 + statefile + "' - See console error log for details";
607 errorMessage += "(Didn't write Jalview Archive to output file '"
618 } catch (IOException e)
628 * Writes a jalview project archive to the given Jar output stream.
632 public void saveState(JarOutputStream jout)
634 AlignFrame[] frames = Desktop.getAlignFrames();
640 saveAllFrames(Arrays.asList(frames), jout);
644 * core method for storing state for a set of AlignFrames.
647 * - frames involving all data to be exported (including those
648 * contained in splitframes, though not the split frames themselves)
650 * - project output stream
652 private void saveAllFrames(List<AlignFrame> frames, JarOutputStream jout)
655 Hashtable<String, AlignFrame> dsses = new Hashtable<>();
658 * ensure cached data is clear before starting
660 // todo tidy up seqRefIds, seqsToIds initialisation / reset
662 splitFrameCandidates.clear();
667 // NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS
668 // //////////////////////////////////////////////////
670 List<String> shortNames = new ArrayList<>();
671 List<String> viewIds = new ArrayList<>();
674 for (int i = frames.size() - 1; i > -1; i--)
676 AlignFrame af = frames.get(i);
677 AlignViewport vp = af.getViewport();
679 if (skipList != null && skipList
680 .containsKey(vp.getSequenceSetId()))
685 String shortName = makeFilename(af, shortNames);
687 AlignmentI alignment = vp.getAlignment();
688 List<? extends AlignmentViewPanel> panels = af.getAlignPanels();
689 int apSize = panels.size();
690 for (int ap = 0; ap < apSize; ap++)
692 AlignmentPanel apanel = (AlignmentPanel) panels.get(ap);
693 String fileName = apSize == 1 ? shortName : ap + shortName;
694 if (!fileName.endsWith(".xml"))
696 fileName = fileName + ".xml";
699 saveState(apanel, fileName, jout, viewIds);
703 // BH moved next bit out of inner loop, not that it really matters.
704 // so we are testing to make sure we actually have an alignment,
706 String dssid = getDatasetIdRef(alignment.getDataset());
707 if (!dsses.containsKey(dssid))
709 // We have not already covered this data by reference from another
711 dsses.put(dssid, af);
716 writeDatasetFor(dsses, "" + jout.hashCode() + " " + uniqueSetSuffix,
722 } catch (Exception foo)
726 } catch (Exception ex)
728 // TODO: inform user of the problem - they need to know if their data was
730 if (errorMessage == null)
732 errorMessage = "Couldn't write Jalview Archive - see error output for details";
734 ex.printStackTrace();
739 * Generates a distinct file name, based on the title of the AlignFrame, by
740 * appending _n for increasing n until an unused name is generated. The new
741 * name (without its extension) is added to the list.
745 * @return the generated name, with .xml extension
747 protected String makeFilename(AlignFrame af, List<String> namesUsed)
749 String shortName = af.getTitle();
751 if (shortName.indexOf(File.separatorChar) > -1)
753 shortName = shortName
754 .substring(shortName.lastIndexOf(File.separatorChar) + 1);
759 while (namesUsed.contains(shortName))
761 if (shortName.endsWith("_" + (count - 1)))
763 shortName = shortName.substring(0, shortName.lastIndexOf("_"));
766 shortName = shortName.concat("_" + count);
770 namesUsed.add(shortName);
772 if (!shortName.endsWith(".xml"))
774 shortName = shortName + ".xml";
779 // USE THIS METHOD TO SAVE A SINGLE ALIGNMENT WINDOW
780 public boolean saveAlignment(AlignFrame af, String jarFile,
785 // create backupfiles object and get new temp filename destination
786 boolean doBackup = BackupFiles.getEnabled();
787 BackupFiles backupfiles = doBackup ? new BackupFiles(jarFile) : null;
788 FileOutputStream fos = new FileOutputStream(doBackup ?
789 backupfiles.getTempFilePath() : jarFile);
791 JarOutputStream jout = new JarOutputStream(fos);
792 List<AlignFrame> frames = new ArrayList<>();
794 // resolve splitframes
795 if (af.getViewport().getCodingComplement() != null)
797 frames = ((SplitFrame) af.getSplitViewContainer()).getAlignFrames();
803 saveAllFrames(frames, jout);
807 } catch (Exception foo)
811 boolean success = true;
815 backupfiles.setWriteSuccess(success);
816 success = backupfiles.rollBackupsAndRenameTempFile();
820 } catch (Exception ex)
822 errorMessage = "Couldn't Write alignment view to Jalview Archive - see error output for details";
823 ex.printStackTrace();
829 * Each AlignFrame has a single data set associated with it. Note that none of
830 * these frames are split frames, because Desktop.getAlignFrames() collects
831 * top and bottom separately here.
837 private void writeDatasetFor(Hashtable<String, AlignFrame> dsses,
838 String fileName, JarOutputStream jout)
841 // Note that in saveAllFrames we have associated each specific dataset to
842 // ONE of its associated frames.
844 for (String dssids : dsses.keySet())
846 AlignFrame _af = dsses.get(dssids);
847 String jfileName = fileName + " Dataset for " + _af.getTitle();
848 if (!jfileName.endsWith(".xml"))
850 jfileName = jfileName + ".xml";
852 saveState(_af.alignPanel, jfileName, true, jout, null);
857 * create a JalviewModel from an alignment view and marshall it to a
861 * panel to create jalview model for
863 * name of alignment panel written to output stream
870 protected JalviewModel saveState(AlignmentPanel ap, String fileName,
871 JarOutputStream jout, List<String> viewIds)
873 return saveState(ap, fileName, false, jout, viewIds);
877 * create a JalviewModel from an alignment view and marshall it to a
881 * panel to create jalview model for
883 * name of alignment panel written to output stream
885 * when true, only write the dataset for the alignment, not the data
886 * associated with the view.
892 protected JalviewModel saveState(AlignmentPanel ap, String fileName,
893 boolean storeDS, JarOutputStream jout, List<String> viewIds)
897 viewIds = new ArrayList<>();
902 List<UserColourScheme> userColours = new ArrayList<>();
904 AlignViewport av = ap.av;
905 ViewportRanges vpRanges = av.getRanges();
907 final ObjectFactory objectFactory = new ObjectFactory();
908 JalviewModel object = objectFactory.createJalviewModel();
909 object.setVamsasModel(new VAMSAS());
911 // object.setCreationDate(new java.util.Date(System.currentTimeMillis()));
914 GregorianCalendar c = new GregorianCalendar();
915 DatatypeFactory datatypeFactory = DatatypeFactory.newInstance();
916 XMLGregorianCalendar now = datatypeFactory.newXMLGregorianCalendar(c);// gregorianCalendar);
917 object.setCreationDate(now);
918 } catch (DatatypeConfigurationException e)
920 System.err.println("error writing date: " + e.toString());
923 jalview.bin.Cache.getDefault("VERSION", "Development Build"));
926 * rjal is full height alignment, jal is actual alignment with full metadata
927 * but excludes hidden sequences.
929 jalview.datamodel.AlignmentI rjal = av.getAlignment(), jal = rjal;
931 if (av.hasHiddenRows())
933 rjal = jal.getHiddenSequences().getFullAlignment();
936 SequenceSet vamsasSet = new SequenceSet();
938 // JalviewModelSequence jms = new JalviewModelSequence();
940 vamsasSet.setGapChar(jal.getGapCharacter() + "");
942 if (jal.getDataset() != null)
944 // dataset id is the dataset's hashcode
945 vamsasSet.setDatasetId(getDatasetIdRef(jal.getDataset()));
948 // switch jal and the dataset
949 jal = jal.getDataset();
953 if (jal.getProperties() != null)
955 Enumeration en = jal.getProperties().keys();
956 while (en.hasMoreElements())
958 String key = en.nextElement().toString();
959 SequenceSetProperties ssp = new SequenceSetProperties();
961 ssp.setValue(jal.getProperties().get(key).toString());
962 // vamsasSet.addSequenceSetProperties(ssp);
963 vamsasSet.getSequenceSetProperties().add(ssp);
968 Set<String> calcIdSet = new HashSet<>();
969 // record the set of vamsas sequence XML POJO we create.
970 HashMap<String, Sequence> vamsasSetIds = new HashMap<>();
972 for (final SequenceI jds : rjal.getSequences())
974 final SequenceI jdatasq = jds.getDatasetSequence() == null ? jds
975 : jds.getDatasetSequence();
976 String id = seqHash(jds);
977 if (vamsasSetIds.get(id) == null)
979 if (seqRefIds.get(id) != null && !storeDS)
981 // This happens for two reasons: 1. multiple views are being
983 // 2. the hashCode has collided with another sequence's code. This
985 // HAPPEN! (PF00072.15.stk does this)
986 // JBPNote: Uncomment to debug writing out of files that do not read
987 // back in due to ArrayOutOfBoundExceptions.
988 // System.err.println("vamsasSeq backref: "+id+"");
989 // System.err.println(jds.getName()+"
990 // "+jds.getStart()+"-"+jds.getEnd()+" "+jds.getSequenceAsString());
991 // System.err.println("Hashcode: "+seqHash(jds));
992 // SequenceI rsq = (SequenceI) seqRefIds.get(id + "");
993 // System.err.println(rsq.getName()+"
994 // "+rsq.getStart()+"-"+rsq.getEnd()+" "+rsq.getSequenceAsString());
995 // System.err.println("Hashcode: "+seqHash(rsq));
999 vamsasSeq = createVamsasSequence(id, jds);
1000 // vamsasSet.addSequence(vamsasSeq);
1001 vamsasSet.getSequence().add(vamsasSeq);
1002 vamsasSetIds.put(id, vamsasSeq);
1003 seqRefIds.put(id, jds);
1007 jseq.setStart(jds.getStart());
1008 jseq.setEnd(jds.getEnd());
1009 jseq.setColour(av.getSequenceColour(jds).getRGB());
1011 jseq.setId(id); // jseq id should be a string not a number
1014 // Store any sequences this sequence represents
1015 if (av.hasHiddenRows())
1017 // use rjal, contains the full height alignment
1019 av.getAlignment().getHiddenSequences().isHidden(jds));
1021 if (av.isHiddenRepSequence(jds))
1023 jalview.datamodel.SequenceI[] reps = av
1024 .getRepresentedSequences(jds).getSequencesInOrder(rjal);
1026 for (int h = 0; h < reps.length; h++)
1030 // jseq.addHiddenSequences(rjal.findIndex(reps[h]));
1031 jseq.getHiddenSequences().add(rjal.findIndex(reps[h]));
1036 // mark sequence as reference - if it is the reference for this view
1037 if (jal.hasSeqrep())
1039 jseq.setViewreference(jds == jal.getSeqrep());
1043 // TODO: omit sequence features from each alignment view's XML dump if we
1044 // are storing dataset
1045 List<SequenceFeature> sfs = jds.getSequenceFeatures();
1046 for (SequenceFeature sf : sfs)
1048 // Features features = new Features();
1049 Feature features = new Feature();
1051 features.setBegin(sf.getBegin());
1052 features.setEnd(sf.getEnd());
1053 features.setDescription(sf.getDescription());
1054 features.setType(sf.getType());
1055 features.setFeatureGroup(sf.getFeatureGroup());
1056 features.setScore(sf.getScore());
1057 if (sf.links != null)
1059 for (int l = 0; l < sf.links.size(); l++)
1061 OtherData keyValue = new OtherData();
1062 keyValue.setKey("LINK_" + l);
1063 keyValue.setValue(sf.links.elementAt(l).toString());
1064 // features.addOtherData(keyValue);
1065 features.getOtherData().add(keyValue);
1068 if (sf.otherDetails != null)
1071 * save feature attributes, which may be simple strings or
1072 * map valued (have sub-attributes)
1074 for (Entry<String, Object> entry : sf.otherDetails.entrySet())
1076 String key = entry.getKey();
1077 Object value = entry.getValue();
1078 if (value instanceof Map<?, ?>)
1080 for (Entry<String, Object> subAttribute : ((Map<String, Object>) value)
1083 OtherData otherData = new OtherData();
1084 otherData.setKey(key);
1085 otherData.setKey2(subAttribute.getKey());
1086 otherData.setValue(subAttribute.getValue().toString());
1087 // features.addOtherData(otherData);
1088 features.getOtherData().add(otherData);
1093 OtherData otherData = new OtherData();
1094 otherData.setKey(key);
1095 otherData.setValue(value.toString());
1096 // features.addOtherData(otherData);
1097 features.getOtherData().add(otherData);
1102 // jseq.addFeatures(features);
1103 jseq.getFeatures().add(features);
1106 if (jdatasq.getAllPDBEntries() != null)
1108 Enumeration<PDBEntry> en = jdatasq.getAllPDBEntries().elements();
1109 while (en.hasMoreElements())
1111 Pdbids pdb = new Pdbids();
1112 jalview.datamodel.PDBEntry entry = en.nextElement();
1114 String pdbId = entry.getId();
1116 pdb.setType(entry.getType());
1119 * Store any structure views associated with this sequence. This
1120 * section copes with duplicate entries in the project, so a dataset
1121 * only view *should* be coped with sensibly.
1123 // This must have been loaded, is it still visible?
1124 JInternalFrame[] frames = Desktop.getDesktopPane().getAllFrames();
1125 String matchedFile = null;
1126 for (int f = frames.length - 1; f > -1; f--)
1128 if (frames[f] instanceof StructureViewerBase)
1130 StructureViewerBase viewFrame = (StructureViewerBase) frames[f];
1131 matchedFile = saveStructureState(ap, jds, pdb, entry, viewIds,
1132 matchedFile, viewFrame);
1134 * Only store each structure viewer's state once in the project
1135 * jar. First time through only (storeDS==false)
1137 String viewId = viewFrame.getViewId();
1138 if (!storeDS && !viewIds.contains(viewId))
1140 viewIds.add(viewId);
1143 String viewerState = viewFrame.getStateInfo();
1144 writeJarEntry(jout, getViewerJarEntryName(viewId),
1145 viewerState.getBytes());
1146 } catch (IOException e)
1149 "Error saving viewer state: " + e.getMessage());
1155 if (matchedFile != null || entry.getFile() != null)
1157 if (entry.getFile() != null)
1160 matchedFile = entry.getFile();
1162 pdb.setFile(matchedFile); // entry.getFile());
1163 if (pdbfiles == null)
1165 pdbfiles = new ArrayList<>();
1168 if (!pdbfiles.contains(pdbId))
1170 pdbfiles.add(pdbId);
1171 copyFileToJar(jout, matchedFile, pdbId);
1175 Enumeration<String> props = entry.getProperties();
1176 if (props.hasMoreElements())
1178 // PdbentryItem item = new PdbentryItem();
1179 while (props.hasMoreElements())
1181 Property prop = new Property();
1182 String key = props.nextElement();
1184 prop.setValue(entry.getProperty(key).toString());
1185 // item.addProperty(prop);
1186 pdb.getProperty().add(prop);
1188 // pdb.addPdbentryItem(item);
1191 // jseq.addPdbids(pdb);
1192 jseq.getPdbids().add(pdb);
1196 saveRnaViewers(jout, jseq, jds, viewIds, ap, storeDS);
1198 // jms.addJSeq(jseq);
1199 object.getJSeq().add(jseq);
1202 if (!storeDS && av.hasHiddenRows())
1204 jal = av.getAlignment();
1208 if (storeDS && jal.getCodonFrames() != null)
1210 List<AlignedCodonFrame> jac = jal.getCodonFrames();
1211 for (AlignedCodonFrame acf : jac)
1213 AlcodonFrame alc = new AlcodonFrame();
1214 if (acf.getProtMappings() != null
1215 && acf.getProtMappings().length > 0)
1217 boolean hasMap = false;
1218 SequenceI[] dnas = acf.getdnaSeqs();
1219 jalview.datamodel.Mapping[] pmaps = acf.getProtMappings();
1220 for (int m = 0; m < pmaps.length; m++)
1222 AlcodMap alcmap = new AlcodMap();
1223 alcmap.setDnasq(seqHash(dnas[m]));
1225 createVamsasMapping(pmaps[m], dnas[m], null, false));
1226 // alc.addAlcodMap(alcmap);
1227 alc.getAlcodMap().add(alcmap);
1232 // vamsasSet.addAlcodonFrame(alc);
1233 vamsasSet.getAlcodonFrame().add(alc);
1236 // TODO: delete this ? dead code from 2.8.3->2.9 ?
1238 // AlcodonFrame alc = new AlcodonFrame();
1239 // vamsasSet.addAlcodonFrame(alc);
1240 // for (int p = 0; p < acf.aaWidth; p++)
1242 // Alcodon cmap = new Alcodon();
1243 // if (acf.codons[p] != null)
1245 // // Null codons indicate a gapped column in the translated peptide
1247 // cmap.setPos1(acf.codons[p][0]);
1248 // cmap.setPos2(acf.codons[p][1]);
1249 // cmap.setPos3(acf.codons[p][2]);
1251 // alc.addAlcodon(cmap);
1253 // if (acf.getProtMappings() != null
1254 // && acf.getProtMappings().length > 0)
1256 // SequenceI[] dnas = acf.getdnaSeqs();
1257 // jalview.datamodel.Mapping[] pmaps = acf.getProtMappings();
1258 // for (int m = 0; m < pmaps.length; m++)
1260 // AlcodMap alcmap = new AlcodMap();
1261 // alcmap.setDnasq(seqHash(dnas[m]));
1262 // alcmap.setMapping(createVamsasMapping(pmaps[m], dnas[m], null,
1264 // alc.addAlcodMap(alcmap);
1271 // /////////////////////////////////
1272 if (!storeDS && av.getCurrentTree() != null)
1274 // FIND ANY ASSOCIATED TREES
1275 // NOT IMPLEMENTED FOR HEADLESS STATE AT PRESENT
1276 if (Desktop.getDesktopPane() != null)
1278 JInternalFrame[] frames = Desktop.getDesktopPane().getAllFrames();
1280 for (int t = 0; t < frames.length; t++)
1282 if (frames[t] instanceof TreePanel)
1284 TreePanel tp = (TreePanel) frames[t];
1286 if (tp.getTreeCanvas().getViewport().getAlignment() == jal)
1288 JalviewModel.Tree tree = new JalviewModel.Tree();
1289 tree.setTitle(tp.getTitle());
1290 tree.setCurrentTree((av.getCurrentTree() == tp.getTree()));
1291 tree.setNewick(tp.getTree().print());
1292 tree.setThreshold(tp.getTreeCanvas().getThreshold());
1294 tree.setFitToWindow(tp.fitToWindow.getState());
1295 tree.setFontName(tp.getTreeFont().getName());
1296 tree.setFontSize(tp.getTreeFont().getSize());
1297 tree.setFontStyle(tp.getTreeFont().getStyle());
1298 tree.setMarkUnlinked(tp.placeholdersMenu.getState());
1300 tree.setShowBootstrap(tp.bootstrapMenu.getState());
1301 tree.setShowDistances(tp.distanceMenu.getState());
1303 tree.setHeight(tp.getHeight());
1304 tree.setWidth(tp.getWidth());
1305 tree.setXpos(tp.getX());
1306 tree.setYpos(tp.getY());
1307 tree.setId(makeHashCode(tp, null));
1308 tree.setLinkToAllViews(
1309 tp.getTreeCanvas().isApplyToAllViews());
1311 // jms.addTree(tree);
1312 object.getTree().add(tree);
1322 if (!storeDS && Desktop.getDesktopPane() != null)
1324 for (JInternalFrame frame : Desktop.getDesktopPane().getAllFrames())
1326 if (frame instanceof PCAPanel)
1328 PCAPanel panel = (PCAPanel) frame;
1329 if (panel.getAlignViewport().getAlignment() == jal)
1331 savePCA(panel, object);
1339 * store forward refs from an annotationRow to any groups
1341 IdentityHashMap<SequenceGroup, String> groupRefs = new IdentityHashMap<>();
1344 for (SequenceI sq : jal.getSequences())
1346 // Store annotation on dataset sequences only
1347 AlignmentAnnotation[] aa = sq.getAnnotation();
1348 if (aa != null && aa.length > 0)
1350 storeAlignmentAnnotation(aa, groupRefs, av, calcIdSet, storeDS,
1357 if (jal.getAlignmentAnnotation() != null)
1359 // Store the annotation shown on the alignment.
1360 AlignmentAnnotation[] aa = jal.getAlignmentAnnotation();
1361 storeAlignmentAnnotation(aa, groupRefs, av, calcIdSet, storeDS,
1366 if (jal.getGroups() != null)
1368 JGroup[] groups = new JGroup[jal.getGroups().size()];
1370 for (jalview.datamodel.SequenceGroup sg : jal.getGroups())
1372 JGroup jGroup = new JGroup();
1373 groups[++i] = jGroup;
1375 jGroup.setStart(sg.getStartRes());
1376 jGroup.setEnd(sg.getEndRes());
1377 jGroup.setName(sg.getName());
1378 if (groupRefs.containsKey(sg))
1380 // group has references so set its ID field
1381 jGroup.setId(groupRefs.get(sg));
1383 ColourSchemeI colourScheme = sg.getColourScheme();
1384 if (colourScheme != null)
1386 ResidueShaderI groupColourScheme = sg.getGroupColourScheme();
1387 if (groupColourScheme.conservationApplied())
1389 jGroup.setConsThreshold(groupColourScheme.getConservationInc());
1391 if (colourScheme instanceof jalview.schemes.UserColourScheme)
1394 setUserColourScheme(colourScheme, userColours,
1399 jGroup.setColour(colourScheme.getSchemeName());
1402 else if (colourScheme instanceof jalview.schemes.AnnotationColourGradient)
1404 jGroup.setColour("AnnotationColourGradient");
1405 jGroup.setAnnotationColours(constructAnnotationColours(
1406 (jalview.schemes.AnnotationColourGradient) colourScheme,
1407 userColours, object));
1409 else if (colourScheme instanceof jalview.schemes.UserColourScheme)
1412 setUserColourScheme(colourScheme, userColours, object));
1416 jGroup.setColour(colourScheme.getSchemeName());
1419 jGroup.setPidThreshold(groupColourScheme.getThreshold());
1422 jGroup.setOutlineColour(sg.getOutlineColour().getRGB());
1423 jGroup.setDisplayBoxes(sg.getDisplayBoxes());
1424 jGroup.setDisplayText(sg.getDisplayText());
1425 jGroup.setColourText(sg.getColourText());
1426 jGroup.setTextCol1(sg.textColour.getRGB());
1427 jGroup.setTextCol2(sg.textColour2.getRGB());
1428 jGroup.setTextColThreshold(sg.thresholdTextColour);
1429 jGroup.setShowUnconserved(sg.getShowNonconserved());
1430 jGroup.setIgnoreGapsinConsensus(sg.getIgnoreGapsConsensus());
1431 jGroup.setShowConsensusHistogram(sg.isShowConsensusHistogram());
1432 jGroup.setShowSequenceLogo(sg.isShowSequenceLogo());
1433 jGroup.setNormaliseSequenceLogo(sg.isNormaliseSequenceLogo());
1434 for (SequenceI seq : sg.getSequences())
1436 // jGroup.addSeq(seqHash(seq));
1437 jGroup.getSeq().add(seqHash(seq));
1441 //jms.setJGroup(groups);
1443 for (JGroup grp : groups)
1445 object.getJGroup().add(grp);
1450 // /////////SAVE VIEWPORT
1451 Viewport view = new Viewport();
1452 view.setTitle(ap.alignFrame.getTitle());
1453 view.setSequenceSetId(
1454 makeHashCode(av.getSequenceSetId(), av.getSequenceSetId()));
1455 view.setId(av.getViewId());
1456 if (av.getCodingComplement() != null)
1458 view.setComplementId(av.getCodingComplement().getViewId());
1460 view.setViewName(av.getViewName());
1461 view.setGatheredViews(av.isGatherViewsHere());
1463 Rectangle size = ap.av.getExplodedGeometry();
1464 Rectangle position = size;
1467 size = ap.alignFrame.getBounds();
1468 if (av.getCodingComplement() != null)
1470 position = ((SplitFrame) ap.alignFrame.getSplitViewContainer())
1478 view.setXpos(position.x);
1479 view.setYpos(position.y);
1481 view.setWidth(size.width);
1482 view.setHeight(size.height);
1484 view.setStartRes(vpRanges.getStartRes());
1485 view.setStartSeq(vpRanges.getStartSeq());
1487 if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme)
1489 view.setBgColour(setUserColourScheme(av.getGlobalColourScheme(),
1490 userColours, object));
1493 .getGlobalColourScheme() instanceof jalview.schemes.AnnotationColourGradient)
1495 AnnotationColourScheme ac = constructAnnotationColours(
1496 (jalview.schemes.AnnotationColourGradient) av
1497 .getGlobalColourScheme(),
1498 userColours, object);
1500 view.setAnnotationColours(ac);
1501 view.setBgColour("AnnotationColourGradient");
1505 view.setBgColour(ColourSchemeProperty
1506 .getColourName(av.getGlobalColourScheme()));
1509 ResidueShaderI vcs = av.getResidueShading();
1510 ColourSchemeI cs = av.getGlobalColourScheme();
1514 if (vcs.conservationApplied())
1516 view.setConsThreshold(vcs.getConservationInc());
1517 if (cs instanceof jalview.schemes.UserColourScheme)
1519 view.setBgColour(setUserColourScheme(cs, userColours, object));
1522 view.setPidThreshold(vcs.getThreshold());
1525 view.setConservationSelected(av.getConservationSelected());
1526 view.setPidSelected(av.getAbovePIDThreshold());
1527 final Font font = av.getFont();
1528 view.setFontName(font.getName());
1529 view.setFontSize(font.getSize());
1530 view.setFontStyle(font.getStyle());
1531 view.setScaleProteinAsCdna(av.getViewStyle().isScaleProteinAsCdna());
1532 view.setRenderGaps(av.isRenderGaps());
1533 view.setShowAnnotation(av.isShowAnnotation());
1534 view.setShowBoxes(av.getShowBoxes());
1535 view.setShowColourText(av.getColourText());
1536 view.setShowFullId(av.getShowJVSuffix());
1537 view.setRightAlignIds(av.isRightAlignIds());
1538 view.setShowSequenceFeatures(av.isShowSequenceFeatures());
1539 view.setShowText(av.getShowText());
1540 view.setShowUnconserved(av.getShowUnconserved());
1541 view.setWrapAlignment(av.getWrapAlignment());
1542 view.setTextCol1(av.getTextColour().getRGB());
1543 view.setTextCol2(av.getTextColour2().getRGB());
1544 view.setTextColThreshold(av.getThresholdTextColour());
1545 view.setShowConsensusHistogram(av.isShowConsensusHistogram());
1546 view.setShowSequenceLogo(av.isShowSequenceLogo());
1547 view.setNormaliseSequenceLogo(av.isNormaliseSequenceLogo());
1548 view.setShowGroupConsensus(av.isShowGroupConsensus());
1549 view.setShowGroupConservation(av.isShowGroupConservation());
1550 view.setShowNPfeatureTooltip(av.isShowNPFeats());
1551 view.setShowDbRefTooltip(av.isShowDBRefs());
1552 view.setFollowHighlight(av.isFollowHighlight());
1553 view.setFollowSelection(av.followSelection);
1554 view.setIgnoreGapsinConsensus(av.isIgnoreGapsConsensus());
1555 if (av.getFeaturesDisplayed() != null)
1557 FeatureSettings fs = new FeatureSettings();
1559 FeatureRenderer fr = ap.getSeqPanel().seqCanvas
1560 .getFeatureRenderer();
1561 String[] renderOrder = fr.getRenderOrder().toArray(new String[0]);
1563 Vector<String> settingsAdded = new Vector<>();
1564 if (renderOrder != null)
1566 for (String featureType : renderOrder)
1568 FeatureSettings.Setting setting = new FeatureSettings.Setting();
1569 setting.setType(featureType);
1572 * save any filter for the feature type
1574 FeatureMatcherSetI filter = fr.getFeatureFilter(featureType);
1575 if (filter != null) {
1576 Iterator<FeatureMatcherI> filters = filter.getMatchers().iterator();
1577 FeatureMatcherI firstFilter = filters.next();
1578 setting.setMatcherSet(Jalview2XML.marshalFilter(
1579 firstFilter, filters, filter.isAnded()));
1583 * save colour scheme for the feature type
1585 FeatureColourI fcol = fr.getFeatureStyle(featureType);
1586 if (!fcol.isSimpleColour())
1588 setting.setColour(fcol.getMaxColour().getRGB());
1589 setting.setMincolour(fcol.getMinColour().getRGB());
1590 setting.setMin(fcol.getMin());
1591 setting.setMax(fcol.getMax());
1592 setting.setColourByLabel(fcol.isColourByLabel());
1593 if (fcol.isColourByAttribute())
1595 String[] attName = fcol.getAttributeName();
1596 setting.getAttributeName().add(attName[0]);
1597 if (attName.length > 1)
1599 setting.getAttributeName().add(attName[1]);
1602 setting.setAutoScale(fcol.isAutoScaled());
1603 setting.setThreshold(fcol.getThreshold());
1604 Color noColour = fcol.getNoColour();
1605 if (noColour == null)
1607 setting.setNoValueColour(NoValueColour.NONE);
1609 else if (noColour.equals(fcol.getMaxColour()))
1611 setting.setNoValueColour(NoValueColour.MAX);
1615 setting.setNoValueColour(NoValueColour.MIN);
1617 // -1 = No threshold, 0 = Below, 1 = Above
1618 setting.setThreshstate(fcol.isAboveThreshold() ? 1
1619 : (fcol.isBelowThreshold() ? 0 : -1));
1623 setting.setColour(fcol.getColour().getRGB());
1627 av.getFeaturesDisplayed().isVisible(featureType));
1629 .getOrder(featureType);
1632 setting.setOrder(rorder);
1634 /// fs.addSetting(setting);
1635 fs.getSetting().add(setting);
1636 settingsAdded.addElement(featureType);
1640 // is groups actually supposed to be a map here ?
1641 Iterator<String> en = fr.getFeatureGroups().iterator();
1642 Vector<String> groupsAdded = new Vector<>();
1643 while (en.hasNext())
1645 String grp = en.next();
1646 if (groupsAdded.contains(grp))
1650 Group g = new Group();
1652 g.setDisplay(((Boolean) fr.checkGroupVisibility(grp, false))
1655 fs.getGroup().add(g);
1656 groupsAdded.addElement(grp);
1658 // jms.setFeatureSettings(fs);
1659 object.setFeatureSettings(fs);
1662 if (av.hasHiddenColumns())
1664 jalview.datamodel.HiddenColumns hidden = av.getAlignment()
1665 .getHiddenColumns();
1668 warn("REPORT BUG: avoided null columnselection bug (DMAM reported). Please contact Jim about this.");
1672 Iterator<int[]> hiddenRegions = hidden.iterator();
1673 while (hiddenRegions.hasNext())
1675 int[] region = hiddenRegions.next();
1676 HiddenColumns hc = new HiddenColumns();
1677 hc.setStart(region[0]);
1678 hc.setEnd(region[1]);
1679 // view.addHiddenColumns(hc);
1680 view.getHiddenColumns().add(hc);
1684 if (calcIdSet.size() > 0)
1686 for (String calcId : calcIdSet)
1688 if (calcId.trim().length() > 0)
1690 CalcIdParam cidp = createCalcIdParam(calcId, av);
1691 // Some calcIds have no parameters.
1694 // view.addCalcIdParam(cidp);
1695 view.getCalcIdParam().add(cidp);
1701 // jms.addViewport(view);
1702 object.getViewport().add(view);
1704 // object.setJalviewModelSequence(jms);
1705 // object.getVamsasModel().addSequenceSet(vamsasSet);
1706 object.getVamsasModel().getSequenceSet().add(vamsasSet);
1708 if (jout != null && fileName != null)
1710 // We may not want to write the object to disk,
1711 // eg we can copy the alignViewport to a new view object
1712 // using save and then load
1715 fileName = fileName.replace('\\', '/');
1716 System.out.println("Writing jar entry " + fileName);
1717 JarEntry entry = new JarEntry(fileName);
1718 jout.putNextEntry(entry);
1719 PrintWriter pout = new PrintWriter(
1720 new OutputStreamWriter(jout, UTF_8));
1721 JAXBContext jaxbContext = JAXBContext
1722 .newInstance(JalviewModel.class);
1723 Marshaller jaxbMarshaller = jaxbContext.createMarshaller();
1725 // output pretty printed
1726 // jaxbMarshaller.setProperty(Marshaller.JAXB_FORMATTED_OUTPUT, true);
1727 jaxbMarshaller.marshal(
1728 new ObjectFactory().createJalviewModel(object), pout);
1730 // jaxbMarshaller.marshal(object, pout);
1731 // marshaller.marshal(object);
1734 } catch (Exception ex)
1736 // TODO: raise error in GUI if marshalling failed.
1737 System.err.println("Error writing Jalview project");
1738 ex.printStackTrace();
1745 * Writes PCA viewer attributes and computed values to an XML model object and
1746 * adds it to the JalviewModel. Any exceptions are reported by logging.
1748 protected void savePCA(PCAPanel panel, JalviewModel object)
1752 PcaViewer viewer = new PcaViewer();
1753 viewer.setHeight(panel.getHeight());
1754 viewer.setWidth(panel.getWidth());
1755 viewer.setXpos(panel.getX());
1756 viewer.setYpos(panel.getY());
1757 viewer.setTitle(panel.getTitle());
1758 PCAModel pcaModel = panel.getPcaModel();
1759 viewer.setScoreModelName(pcaModel.getScoreModelName());
1760 viewer.setXDim(panel.getSelectedDimensionIndex(X));
1761 viewer.setYDim(panel.getSelectedDimensionIndex(Y));
1762 viewer.setZDim(panel.getSelectedDimensionIndex(Z));
1764 panel.getRotatableCanvas().getBackgroundColour().getRGB());
1765 viewer.setScaleFactor(panel.getRotatableCanvas().getScaleFactor());
1766 float[] spMin = panel.getRotatableCanvas().getSeqMin();
1767 SeqPointMin spmin = new SeqPointMin();
1768 spmin.setXPos(spMin[0]);
1769 spmin.setYPos(spMin[1]);
1770 spmin.setZPos(spMin[2]);
1771 viewer.setSeqPointMin(spmin);
1772 float[] spMax = panel.getRotatableCanvas().getSeqMax();
1773 SeqPointMax spmax = new SeqPointMax();
1774 spmax.setXPos(spMax[0]);
1775 spmax.setYPos(spMax[1]);
1776 spmax.setZPos(spMax[2]);
1777 viewer.setSeqPointMax(spmax);
1778 viewer.setShowLabels(panel.getRotatableCanvas().isShowLabels());
1779 viewer.setLinkToAllViews(
1780 panel.getRotatableCanvas().isApplyToAllViews());
1781 SimilarityParamsI sp = pcaModel.getSimilarityParameters();
1782 viewer.setIncludeGaps(sp.includeGaps());
1783 viewer.setMatchGaps(sp.matchGaps());
1784 viewer.setIncludeGappedColumns(sp.includeGappedColumns());
1785 viewer.setDenominateByShortestLength(sp.denominateByShortestLength());
1788 * sequence points on display
1790 for (jalview.datamodel.SequencePoint spt : pcaModel
1791 .getSequencePoints())
1793 SequencePoint point = new SequencePoint();
1794 point.setSequenceRef(seqHash(spt.getSequence()));
1795 point.setXPos(spt.coord.x);
1796 point.setYPos(spt.coord.y);
1797 point.setZPos(spt.coord.z);
1798 viewer.getSequencePoint().add(point);
1802 * (end points of) axes on display
1804 for (Point p : panel.getRotatableCanvas().getAxisEndPoints())
1807 Axis axis = new Axis();
1811 viewer.getAxis().add(axis);
1815 * raw PCA data (note we are not restoring PCA inputs here -
1816 * alignment view, score model, similarity parameters)
1818 PcaDataType data = new PcaDataType();
1819 viewer.setPcaData(data);
1820 PCA pca = pcaModel.getPcaData();
1822 DoubleMatrix pm = new DoubleMatrix();
1823 saveDoubleMatrix(pca.getPairwiseScores(), pm);
1824 data.setPairwiseMatrix(pm);
1826 DoubleMatrix tm = new DoubleMatrix();
1827 saveDoubleMatrix(pca.getTridiagonal(), tm);
1828 data.setTridiagonalMatrix(tm);
1830 DoubleMatrix eigenMatrix = new DoubleMatrix();
1831 data.setEigenMatrix(eigenMatrix);
1832 saveDoubleMatrix(pca.getEigenmatrix(), eigenMatrix);
1834 object.getPcaViewer().add(viewer);
1835 } catch (Throwable t)
1837 Cache.log.error("Error saving PCA: " + t.getMessage());
1842 * Stores values from a matrix into an XML element, including (if present) the
1847 * @see #loadDoubleMatrix(DoubleMatrix)
1849 protected void saveDoubleMatrix(MatrixI m, DoubleMatrix xmlMatrix)
1851 xmlMatrix.setRows(m.height());
1852 xmlMatrix.setColumns(m.width());
1853 for (int i = 0; i < m.height(); i++)
1855 DoubleVector row = new DoubleVector();
1856 for (int j = 0; j < m.width(); j++)
1858 row.getV().add(m.getValue(i, j));
1860 xmlMatrix.getRow().add(row);
1862 if (m.getD() != null)
1864 DoubleVector dVector = new DoubleVector();
1865 for (double d : m.getD())
1867 dVector.getV().add(d);
1869 xmlMatrix.setD(dVector);
1871 if (m.getE() != null)
1873 DoubleVector eVector = new DoubleVector();
1874 for (double e : m.getE())
1876 eVector.getV().add(e);
1878 xmlMatrix.setE(eVector);
1883 * Loads XML matrix data into a new Matrix object, including the D and/or E
1884 * vectors (if present)
1888 * @see Jalview2XML#saveDoubleMatrix(MatrixI, DoubleMatrix)
1890 protected MatrixI loadDoubleMatrix(DoubleMatrix mData)
1892 int rows = mData.getRows();
1893 double[][] vals = new double[rows][];
1895 for (int i = 0; i < rows; i++)
1897 List<Double> dVector = mData.getRow().get(i).getV();
1898 vals[i] = new double[dVector.size()];
1900 for (Double d : dVector)
1906 MatrixI m = new Matrix(vals);
1908 if (mData.getD() != null)
1910 List<Double> dVector = mData.getD().getV();
1911 double[] vec = new double[dVector.size()];
1913 for (Double d : dVector)
1919 if (mData.getE() != null)
1921 List<Double> dVector = mData.getE().getV();
1922 double[] vec = new double[dVector.size()];
1924 for (Double d : dVector)
1935 * Save any Varna viewers linked to this sequence. Writes an rnaViewer element
1936 * for each viewer, with
1938 * <li>viewer geometry (position, size, split pane divider location)</li>
1939 * <li>index of the selected structure in the viewer (currently shows gapped
1941 * <li>the id of the annotation holding RNA secondary structure</li>
1942 * <li>(currently only one SS is shown per viewer, may be more in future)</li>
1944 * Varna viewer state is also written out (in native Varna XML) to separate
1945 * project jar entries. A separate entry is written for each RNA structure
1946 * displayed, with the naming convention
1948 * <li>rna_viewId_sequenceId_annotationId_[gapped|trimmed]</li>
1956 * @param storeDataset
1958 protected void saveRnaViewers(JarOutputStream jout, JSeq jseq,
1959 final SequenceI jds, List<String> viewIds, AlignmentPanel ap,
1960 boolean storeDataset)
1962 if (Desktop.getDesktopPane() == null)
1966 JInternalFrame[] frames = Desktop.getDesktopPane().getAllFrames();
1967 for (int f = frames.length - 1; f > -1; f--)
1969 if (frames[f] instanceof AppVarna)
1971 AppVarna varna = (AppVarna) frames[f];
1973 * link the sequence to every viewer that is showing it and is linked to
1974 * its alignment panel
1976 if (varna.isListeningFor(jds) && ap == varna.getAlignmentPanel())
1978 String viewId = varna.getViewId();
1979 RnaViewer rna = new RnaViewer();
1980 rna.setViewId(viewId);
1981 rna.setTitle(varna.getTitle());
1982 rna.setXpos(varna.getX());
1983 rna.setYpos(varna.getY());
1984 rna.setWidth(varna.getWidth());
1985 rna.setHeight(varna.getHeight());
1986 rna.setDividerLocation(varna.getDividerLocation());
1987 rna.setSelectedRna(varna.getSelectedIndex());
1988 // jseq.addRnaViewer(rna);
1989 jseq.getRnaViewer().add(rna);
1992 * Store each Varna panel's state once in the project per sequence.
1993 * First time through only (storeDataset==false)
1995 // boolean storeSessions = false;
1996 // String sequenceViewId = viewId + seqsToIds.get(jds);
1997 // if (!storeDataset && !viewIds.contains(sequenceViewId))
1999 // viewIds.add(sequenceViewId);
2000 // storeSessions = true;
2002 for (RnaModel model : varna.getModels())
2004 if (model.seq == jds)
2007 * VARNA saves each view (sequence or alignment secondary
2008 * structure, gapped or trimmed) as a separate XML file
2010 String jarEntryName = rnaSessions.get(model);
2011 if (jarEntryName == null)
2014 String varnaStateFile = varna.getStateInfo(model.rna);
2015 jarEntryName = RNA_PREFIX + viewId + "_" + nextCounter();
2016 copyFileToJar(jout, varnaStateFile, jarEntryName);
2017 rnaSessions.put(model, jarEntryName);
2019 SecondaryStructure ss = new SecondaryStructure();
2020 String annotationId = varna.getAnnotation(jds).annotationId;
2021 ss.setAnnotationId(annotationId);
2022 ss.setViewerState(jarEntryName);
2023 ss.setGapped(model.gapped);
2024 ss.setTitle(model.title);
2025 // rna.addSecondaryStructure(ss);
2026 rna.getSecondaryStructure().add(ss);
2035 * Copy the contents of a file to a new entry added to the output jar
2039 * @param jarEntryName
2041 protected void copyFileToJar(JarOutputStream jout, String infilePath,
2042 String jarEntryName)
2044 DataInputStream dis = null;
2047 File file = new File(infilePath);
2048 if (file.exists() && jout != null)
2050 dis = new DataInputStream(new FileInputStream(file));
2051 byte[] data = new byte[(int) file.length()];
2052 dis.readFully(data);
2053 writeJarEntry(jout, jarEntryName, data);
2055 } catch (Exception ex)
2057 ex.printStackTrace();
2065 } catch (IOException e)
2074 * Write the data to a new entry of given name in the output jar file
2077 * @param jarEntryName
2079 * @throws IOException
2081 protected void writeJarEntry(JarOutputStream jout, String jarEntryName,
2082 byte[] data) throws IOException
2086 jarEntryName = jarEntryName.replace('\\','/');
2087 System.out.println("Writing jar entry " + jarEntryName);
2088 jout.putNextEntry(new JarEntry(jarEntryName));
2089 DataOutputStream dout = new DataOutputStream(jout);
2090 dout.write(data, 0, data.length);
2097 * Save the state of a structure viewer
2102 * the archive XML element under which to save the state
2105 * @param matchedFile
2109 protected String saveStructureState(AlignmentPanel ap, SequenceI jds,
2110 Pdbids pdb, PDBEntry entry, List<String> viewIds,
2111 String matchedFile, StructureViewerBase viewFrame)
2113 final AAStructureBindingModel bindingModel = viewFrame.getBinding();
2116 * Look for any bindings for this viewer to the PDB file of interest
2117 * (including part matches excluding chain id)
2119 for (int peid = 0; peid < bindingModel.getPdbCount(); peid++)
2121 final PDBEntry pdbentry = bindingModel.getPdbEntry(peid);
2122 final String pdbId = pdbentry.getId();
2123 if (!pdbId.equals(entry.getId())
2124 && !(entry.getId().length() > 4 && entry.getId().toLowerCase()
2125 .startsWith(pdbId.toLowerCase())))
2128 * not interested in a binding to a different PDB entry here
2132 if (matchedFile == null)
2134 matchedFile = pdbentry.getFile();
2136 else if (!matchedFile.equals(pdbentry.getFile()))
2139 "Probably lost some PDB-Sequence mappings for this structure file (which apparently has same PDB Entry code): "
2140 + pdbentry.getFile());
2144 // can get at it if the ID
2145 // match is ambiguous (e.g.
2148 for (int smap = 0; smap < viewFrame.getBinding()
2149 .getSequence()[peid].length; smap++)
2151 // if (jal.findIndex(jmol.jmb.sequence[peid][smap]) > -1)
2152 if (jds == viewFrame.getBinding().getSequence()[peid][smap])
2154 StructureState state = new StructureState();
2155 state.setVisible(true);
2156 state.setXpos(viewFrame.getX());
2157 state.setYpos(viewFrame.getY());
2158 state.setWidth(viewFrame.getWidth());
2159 state.setHeight(viewFrame.getHeight());
2160 final String viewId = viewFrame.getViewId();
2161 state.setViewId(viewId);
2162 state.setAlignwithAlignPanel(viewFrame.isUsedforaligment(ap));
2163 state.setColourwithAlignPanel(viewFrame.isUsedforcolourby(ap));
2164 state.setColourByJmol(viewFrame.isColouredByViewer());
2165 state.setType(viewFrame.getViewerType().toString());
2166 // pdb.addStructureState(state);
2167 pdb.getStructureState().add(state);
2175 * Populates the AnnotationColourScheme xml for save. This captures the
2176 * settings of the options in the 'Colour by Annotation' dialog.
2179 * @param userColours
2183 private AnnotationColourScheme constructAnnotationColours(
2184 AnnotationColourGradient acg, List<UserColourScheme> userColours,
2187 AnnotationColourScheme ac = new AnnotationColourScheme();
2188 ac.setAboveThreshold(acg.getAboveThreshold());
2189 ac.setThreshold(acg.getAnnotationThreshold());
2190 // 2.10.2 save annotationId (unique) not annotation label
2191 ac.setAnnotation(acg.getAnnotation().annotationId);
2192 if (acg.getBaseColour() instanceof UserColourScheme)
2195 setUserColourScheme(acg.getBaseColour(), userColours, jm));
2200 ColourSchemeProperty.getColourName(acg.getBaseColour()));
2203 ac.setMaxColour(acg.getMaxColour().getRGB());
2204 ac.setMinColour(acg.getMinColour().getRGB());
2205 ac.setPerSequence(acg.isSeqAssociated());
2206 ac.setPredefinedColours(acg.isPredefinedColours());
2210 private void storeAlignmentAnnotation(AlignmentAnnotation[] aa,
2211 IdentityHashMap<SequenceGroup, String> groupRefs,
2212 AlignmentViewport av, Set<String> calcIdSet, boolean storeDS,
2213 SequenceSet vamsasSet)
2216 for (int i = 0; i < aa.length; i++)
2218 Annotation an = new Annotation();
2220 AlignmentAnnotation annotation = aa[i];
2221 if (annotation.annotationId != null)
2223 annotationIds.put(annotation.annotationId, annotation);
2226 an.setId(annotation.annotationId);
2228 an.setVisible(annotation.visible);
2230 an.setDescription(annotation.description);
2232 if (annotation.sequenceRef != null)
2234 // 2.9 JAL-1781 xref on sequence id rather than name
2235 an.setSequenceRef(seqsToIds.get(annotation.sequenceRef));
2237 if (annotation.groupRef != null)
2239 String groupIdr = groupRefs.get(annotation.groupRef);
2240 if (groupIdr == null)
2242 // make a locally unique String
2243 groupRefs.put(annotation.groupRef,
2244 groupIdr = ("" + System.currentTimeMillis()
2245 + annotation.groupRef.getName()
2246 + groupRefs.size()));
2248 an.setGroupRef(groupIdr.toString());
2251 // store all visualization attributes for annotation
2252 an.setGraphHeight(annotation.graphHeight);
2253 an.setCentreColLabels(annotation.centreColLabels);
2254 an.setScaleColLabels(annotation.scaleColLabel);
2255 an.setShowAllColLabels(annotation.showAllColLabels);
2256 an.setBelowAlignment(annotation.belowAlignment);
2258 if (annotation.graph > 0)
2261 an.setGraphType(annotation.graph);
2262 an.setGraphGroup(annotation.graphGroup);
2263 if (annotation.getThreshold() != null)
2265 ThresholdLine line = new ThresholdLine();
2266 line.setLabel(annotation.getThreshold().label);
2267 line.setValue(annotation.getThreshold().value);
2268 line.setColour(annotation.getThreshold().colour.getRGB());
2269 an.setThresholdLine(line);
2277 an.setLabel(annotation.label);
2279 if (annotation == av.getAlignmentQualityAnnot()
2280 || annotation == av.getAlignmentConservationAnnotation()
2281 || annotation == av.getAlignmentConsensusAnnotation()
2282 || annotation.autoCalculated)
2284 // new way of indicating autocalculated annotation -
2285 an.setAutoCalculated(annotation.autoCalculated);
2287 if (annotation.hasScore())
2289 an.setScore(annotation.getScore());
2292 if (annotation.getCalcId() != null)
2294 calcIdSet.add(annotation.getCalcId());
2295 an.setCalcId(annotation.getCalcId());
2297 if (annotation.hasProperties())
2299 for (String pr : annotation.getProperties())
2301 jalview.xml.binding.jalview.Annotation.Property prop = new jalview.xml.binding.jalview.Annotation.Property();
2303 prop.setValue(annotation.getProperty(pr));
2304 // an.addProperty(prop);
2305 an.getProperty().add(prop);
2309 AnnotationElement ae;
2310 if (annotation.annotations != null)
2312 an.setScoreOnly(false);
2313 for (int a = 0; a < annotation.annotations.length; a++)
2315 if ((annotation == null) || (annotation.annotations[a] == null))
2320 ae = new AnnotationElement();
2321 if (annotation.annotations[a].description != null)
2323 ae.setDescription(annotation.annotations[a].description);
2325 if (annotation.annotations[a].displayCharacter != null)
2327 ae.setDisplayCharacter(
2328 annotation.annotations[a].displayCharacter);
2331 if (!Float.isNaN(annotation.annotations[a].value))
2333 ae.setValue(annotation.annotations[a].value);
2337 if (annotation.annotations[a].secondaryStructure > ' ')
2339 ae.setSecondaryStructure(
2340 annotation.annotations[a].secondaryStructure + "");
2343 if (annotation.annotations[a].colour != null
2344 && annotation.annotations[a].colour != java.awt.Color.black)
2346 ae.setColour(annotation.annotations[a].colour.getRGB());
2349 // an.addAnnotationElement(ae);
2350 an.getAnnotationElement().add(ae);
2351 if (annotation.autoCalculated)
2353 // only write one non-null entry into the annotation row -
2354 // sufficient to get the visualization attributes necessary to
2362 an.setScoreOnly(true);
2364 if (!storeDS || (storeDS && !annotation.autoCalculated))
2366 // skip autocalculated annotation - these are only provided for
2368 // vamsasSet.addAnnotation(an);
2369 vamsasSet.getAnnotation().add(an);
2375 private CalcIdParam createCalcIdParam(String calcId, AlignViewport av)
2377 AutoCalcSetting settings = av.getCalcIdSettingsFor(calcId);
2378 if (settings != null)
2380 CalcIdParam vCalcIdParam = new CalcIdParam();
2381 vCalcIdParam.setCalcId(calcId);
2382 // vCalcIdParam.addServiceURL(settings.getServiceURI());
2383 vCalcIdParam.getServiceURL().add(settings.getServiceURI());
2384 // generic URI allowing a third party to resolve another instance of the
2385 // service used for this calculation
2386 for (String url : settings.getServiceURLs())
2388 // vCalcIdParam.addServiceURL(urls);
2389 vCalcIdParam.getServiceURL().add(url);
2391 vCalcIdParam.setVersion("1.0");
2392 if (settings.getPreset() != null)
2394 WsParamSetI setting = settings.getPreset();
2395 vCalcIdParam.setName(setting.getName());
2396 vCalcIdParam.setDescription(setting.getDescription());
2400 vCalcIdParam.setName("");
2401 vCalcIdParam.setDescription("Last used parameters");
2403 // need to be able to recover 1) settings 2) user-defined presets or
2404 // recreate settings from preset 3) predefined settings provided by
2405 // service - or settings that can be transferred (or discarded)
2406 vCalcIdParam.setParameters(
2407 settings.getWsParamFile().replace("\n", "|\\n|"));
2408 vCalcIdParam.setAutoUpdate(settings.isAutoUpdate());
2409 // todo - decide if updateImmediately is needed for any projects.
2411 return vCalcIdParam;
2416 private boolean recoverCalcIdParam(CalcIdParam calcIdParam,
2419 if (calcIdParam.getVersion().equals("1.0"))
2421 final String[] calcIds = calcIdParam.getServiceURL().toArray(new String[0]);
2422 Jws2Instance service = Jws2Discoverer.getInstance()
2423 .getPreferredServiceFor(calcIds);
2424 if (service != null)
2426 WsParamSetI parmSet = null;
2429 parmSet = service.getParamStore().parseServiceParameterFile(
2430 calcIdParam.getName(), calcIdParam.getDescription(),
2432 calcIdParam.getParameters().replace("|\\n|", "\n"));
2433 } catch (IOException x)
2435 warn("Couldn't parse parameter data for "
2436 + calcIdParam.getCalcId(), x);
2439 List<ArgumentI> argList = null;
2440 if (calcIdParam.getName().length() > 0)
2442 parmSet = service.getParamStore()
2443 .getPreset(calcIdParam.getName());
2444 if (parmSet != null)
2446 // TODO : check we have a good match with settings in AACon -
2447 // otherwise we'll need to create a new preset
2452 argList = parmSet.getArguments();
2455 AAConSettings settings = new AAConSettings(
2456 calcIdParam.isAutoUpdate(), service, parmSet, argList);
2457 av.setCalcIdSettingsFor(calcIdParam.getCalcId(), settings,
2458 calcIdParam.isNeedsUpdate());
2463 warn("Cannot resolve a service for the parameters used in this project. Try configuring a JABAWS server.");
2467 throw new Error(MessageManager.formatMessage(
2468 "error.unsupported_version_calcIdparam", new Object[]
2469 { calcIdParam.toString() }));
2473 * External mapping between jalview objects and objects yielding a valid and
2474 * unique object ID string. This is null for normal Jalview project IO, but
2475 * non-null when a jalview project is being read or written as part of a
2478 IdentityHashMap jv2vobj = null;
2481 * Construct a unique ID for jvobj using either existing bindings or if none
2482 * exist, the result of the hashcode call for the object.
2485 * jalview data object
2486 * @return unique ID for referring to jvobj
2488 private String makeHashCode(Object jvobj, String altCode)
2490 if (jv2vobj != null)
2492 Object id = jv2vobj.get(jvobj);
2495 return id.toString();
2497 // check string ID mappings
2498 if (jvids2vobj != null && jvobj instanceof String)
2500 id = jvids2vobj.get(jvobj);
2504 return id.toString();
2506 // give up and warn that something has gone wrong
2507 warn("Cannot find ID for object in external mapping : " + jvobj);
2513 * return local jalview object mapped to ID, if it exists
2517 * @return null or object bound to idcode
2519 private Object retrieveExistingObj(String idcode)
2521 if (idcode != null && vobj2jv != null)
2523 return vobj2jv.get(idcode);
2529 * binding from ID strings from external mapping table to jalview data model
2532 private Hashtable vobj2jv;
2534 private Sequence createVamsasSequence(String id, SequenceI jds)
2536 return createVamsasSequence(true, id, jds, null);
2539 private Sequence createVamsasSequence(boolean recurse, String id,
2540 SequenceI jds, SequenceI parentseq)
2542 Sequence vamsasSeq = new Sequence();
2543 vamsasSeq.setId(id);
2544 vamsasSeq.setName(jds.getName());
2545 vamsasSeq.setSequence(jds.getSequenceAsString());
2546 vamsasSeq.setDescription(jds.getDescription());
2547 List<DBRefEntry> dbrefs = null;
2548 if (jds.getDatasetSequence() != null)
2550 vamsasSeq.setDsseqid(seqHash(jds.getDatasetSequence()));
2554 // seqId==dsseqid so we can tell which sequences really are
2555 // dataset sequences only
2556 vamsasSeq.setDsseqid(id);
2557 dbrefs = jds.getDBRefs();
2558 if (parentseq == null)
2565 for (int d = 0, nd = dbrefs.size(); d < nd; d++)
2567 DBRef dbref = new DBRef();
2568 DBRefEntry ref = dbrefs.get(d);
2569 dbref.setSource(ref.getSource());
2570 dbref.setVersion(ref.getVersion());
2571 dbref.setAccessionId(ref.getAccessionId());
2574 Mapping mp = createVamsasMapping(ref.getMap(), parentseq,
2576 dbref.setMapping(mp);
2578 // vamsasSeq.addDBRef(dbref);
2579 vamsasSeq.getDBRef().add(dbref);
2585 private Mapping createVamsasMapping(jalview.datamodel.Mapping jmp,
2586 SequenceI parentseq, SequenceI jds, boolean recurse)
2589 if (jmp.getMap() != null)
2593 jalview.util.MapList mlst = jmp.getMap();
2594 List<int[]> r = mlst.getFromRanges();
2595 for (int[] range : r)
2597 MapListFrom mfrom = new MapListFrom();
2598 mfrom.setStart(range[0]);
2599 mfrom.setEnd(range[1]);
2600 // mp.addMapListFrom(mfrom);
2601 mp.getMapListFrom().add(mfrom);
2603 r = mlst.getToRanges();
2604 for (int[] range : r)
2606 MapListTo mto = new MapListTo();
2607 mto.setStart(range[0]);
2608 mto.setEnd(range[1]);
2609 // mp.addMapListTo(mto);
2610 mp.getMapListTo().add(mto);
2612 mp.setMapFromUnit(BigInteger.valueOf(mlst.getFromRatio()));
2613 mp.setMapToUnit(BigInteger.valueOf(mlst.getToRatio()));
2614 if (jmp.getTo() != null)
2616 // MappingChoice mpc = new MappingChoice();
2618 // check/create ID for the sequence referenced by getTo()
2621 SequenceI ps = null;
2622 if (parentseq != jmp.getTo()
2623 && parentseq.getDatasetSequence() != jmp.getTo())
2625 // chaining dbref rather than a handshaking one
2626 jmpid = seqHash(ps = jmp.getTo());
2630 jmpid = seqHash(ps = parentseq);
2632 // mpc.setDseqFor(jmpid);
2633 mp.setDseqFor(jmpid);
2634 if (!seqRefIds.containsKey(jmpid))
2636 jalview.bin.Cache.log.debug("creatign new DseqFor ID");
2637 seqRefIds.put(jmpid, ps);
2641 jalview.bin.Cache.log.debug("reusing DseqFor ID");
2644 // mp.setMappingChoice(mpc);
2650 String setUserColourScheme(jalview.schemes.ColourSchemeI cs,
2651 List<UserColourScheme> userColours, JalviewModel jm)
2654 jalview.schemes.UserColourScheme ucs = (jalview.schemes.UserColourScheme) cs;
2655 boolean newucs = false;
2656 if (!userColours.contains(ucs))
2658 userColours.add(ucs);
2661 id = "ucs" + userColours.indexOf(ucs);
2664 // actually create the scheme's entry in the XML model
2665 java.awt.Color[] colours = ucs.getColours();
2666 UserColours uc = new UserColours();
2667 // UserColourScheme jbucs = new UserColourScheme();
2668 JalviewUserColours jbucs = new JalviewUserColours();
2670 for (int i = 0; i < colours.length; i++)
2672 Colour col = new Colour();
2673 col.setName(ResidueProperties.aa[i]);
2674 col.setRGB(jalview.util.Format.getHexString(colours[i]));
2675 // jbucs.addColour(col);
2676 jbucs.getColour().add(col);
2678 if (ucs.getLowerCaseColours() != null)
2680 colours = ucs.getLowerCaseColours();
2681 for (int i = 0; i < colours.length; i++)
2683 Colour col = new Colour();
2684 col.setName(ResidueProperties.aa[i].toLowerCase());
2685 col.setRGB(jalview.util.Format.getHexString(colours[i]));
2686 // jbucs.addColour(col);
2687 jbucs.getColour().add(col);
2692 uc.setUserColourScheme(jbucs);
2693 // jm.addUserColours(uc);
2694 jm.getUserColours().add(uc);
2700 jalview.schemes.UserColourScheme getUserColourScheme(
2701 JalviewModel jm, String id)
2703 List<UserColours> uc = jm.getUserColours();
2704 UserColours colours = null;
2706 for (int i = 0; i < uc.length; i++)
2708 if (uc[i].getId().equals(id))
2715 for (UserColours c : uc)
2717 if (c.getId().equals(id))
2724 java.awt.Color[] newColours = new java.awt.Color[24];
2726 for (int i = 0; i < 24; i++)
2728 newColours[i] = new java.awt.Color(Integer.parseInt(
2729 // colours.getUserColourScheme().getColour(i).getRGB(), 16));
2730 colours.getUserColourScheme().getColour().get(i).getRGB(),
2734 jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(
2737 if (colours.getUserColourScheme().getColour().size()/*Count()*/ > 24)
2739 newColours = new java.awt.Color[23];
2740 for (int i = 0; i < 23; i++)
2742 newColours[i] = new java.awt.Color(Integer.parseInt(
2743 colours.getUserColourScheme().getColour().get(i + 24)
2747 ucs.setLowerCaseColours(newColours);
2754 * Load a jalview project archive from a jar file
2757 * - HTTP URL or filename
2759 public AlignFrame loadJalviewAlign(final Object file)
2762 jalview.gui.AlignFrame af = null;
2766 // create list to store references for any new Jmol viewers created
2767 newStructureViewers = new Vector<>();
2768 // UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
2769 // Workaround is to make sure caller implements the JarInputStreamProvider
2771 // so we can re-open the jar input stream for each entry.
2773 jarInputStreamProvider jprovider = createjarInputStreamProvider(file);
2774 af = loadJalviewAlign(jprovider);
2777 af.setMenusForViewport();
2779 } catch (MalformedURLException e)
2781 errorMessage = "Invalid URL format for '" + file + "'";
2787 // BH 2019 -- can't wait
2788 SwingUtilities.invokeLater(new Runnable()
2793 setLoadingFinishedForNewStructureViewers();
2796 } catch (Exception x)
2798 System.err.println("Error loading alignment: " + x.getMessage());
2801 this.jarFile = null;
2805 @SuppressWarnings("unused")
2806 private jarInputStreamProvider createjarInputStreamProvider(
2807 final Object ofile) throws MalformedURLException
2811 String file = (ofile instanceof File
2812 ? ((File) ofile).getCanonicalPath()
2813 : ofile.toString());
2814 byte[] bytes = Platform.isJS() ? Platform.getFileBytes((File) ofile)
2818 this.jarFile = (File) ofile;
2820 errorMessage = null;
2821 uniqueSetSuffix = null;
2823 viewportsAdded.clear();
2824 frefedSequence = null;
2826 URL url = file.startsWith("http://") ? new URL(file) : null;
2827 return new jarInputStreamProvider()
2830 public JarInputStream getJarInputStream() throws IOException
2832 InputStream is = bytes != null ? new ByteArrayInputStream(bytes)
2833 : (url != null ? url.openStream()
2834 : new FileInputStream(file));
2835 return new JarInputStream(is);
2839 public String getFilename()
2844 } catch (IOException e)
2846 e.printStackTrace();
2852 * Recover jalview session from a jalview project archive. Caller may
2853 * initialise uniqueSetSuffix, seqRefIds, viewportsAdded and frefedSequence
2854 * themselves. Any null fields will be initialised with default values,
2855 * non-null fields are left alone.
2860 public AlignFrame loadJalviewAlign(final jarInputStreamProvider jprovider)
2862 errorMessage = null;
2863 if (uniqueSetSuffix == null)
2865 uniqueSetSuffix = System.currentTimeMillis() % 100000 + "";
2867 if (seqRefIds == null)
2871 AlignFrame af = null, _af = null;
2872 IdentityHashMap<AlignmentI, AlignmentI> importedDatasets = new IdentityHashMap<>();
2873 Map<String, AlignFrame> gatherToThisFrame = new HashMap<>();
2874 final String file = jprovider.getFilename();
2876 List<AlignFrame> alignFrames = new ArrayList<>();
2880 JarInputStream jin = null;
2881 JarEntry jarentry = null;
2885 // Look for all the entry names ending with ".xml"
2886 // This includes all panels and at least one frame.
2887 // Platform.timeCheck(null, Platform.TIME_MARK);
2890 jin = jprovider.getJarInputStream();
2891 for (int i = 0; i < entryCount; i++)
2893 jarentry = jin.getNextJarEntry();
2895 String name = (jarentry == null ? null : jarentry.getName());
2897 // System.out.println("Jalview2XML opening " + name);
2898 if (name != null && name.endsWith(".xml"))
2901 // DataSet for.... is read last.
2904 // The question here is what to do with the two
2905 // .xml files in the jvp file.
2906 // Some number of them, "...Dataset for...", will be the
2907 // Only AlignPanels and will have Viewport.
2908 // One or more will be the source data, with the DBRefs.
2910 // JVP file writing (above) ensures tha the AlignPanels are written
2911 // first, then all relevant datasets (which are
2912 // Jalview.datamodel.Alignment).
2915 // Platform.timeCheck("Jalview2XML JAXB " + name, Platform.TIME_MARK);
2916 JAXBContext jc = JAXBContext
2917 .newInstance("jalview.xml.binding.jalview");
2918 XMLStreamReader streamReader = XMLInputFactory.newInstance()
2919 .createXMLStreamReader(jin);
2920 javax.xml.bind.Unmarshaller um = jc.createUnmarshaller();
2921 JAXBElement<JalviewModel> jbe = um
2922 .unmarshal(streamReader, JalviewModel.class);
2923 JalviewModel model = jbe.getValue();
2925 if (true) // !skipViewport(object))
2927 // Q: Do we have to load from the model, even if it
2928 // does not have a viewport, could we discover that early on?
2929 // Q: Do we need to load this object?
2930 _af = loadFromObject(model, file, true, jprovider);
2931 // Platform.timeCheck("Jalview2XML.loadFromObject",
2932 // Platform.TIME_MARK);
2936 alignFrames.add(_af);
2938 if (_af != null && model.getViewport().size() > 0)
2941 // That is, this is one of the AlignmentPanel models
2944 // store a reference to the first view
2947 if (_af.getViewport().isGatherViewsHere())
2949 // if this is a gathered view, keep its reference since
2950 // after gathering views, only this frame will remain
2952 gatherToThisFrame.put(_af.getViewport().getSequenceSetId(),
2955 // Save dataset to register mappings once all resolved
2956 importedDatasets.put(
2957 af.getViewport().getAlignment().getDataset(),
2958 af.getViewport().getAlignment().getDataset());
2961 // Platform.timeCheck("JAXB " + name, Platform.TIME_MARK);
2964 else if (jarentry != null)
2966 // Some other file here.
2969 } while (jarentry != null);
2970 // Platform.timeCheck("JAXB loop exit", Platform.TIME_MARK);
2971 resolveFrefedSequences();
2972 // Platform.timeCheck("JAXB resolveFrefed", Platform.TIME_MARK);
2974 } catch (IOException ex)
2976 ex.printStackTrace();
2977 errorMessage = "Couldn't locate Jalview XML file : " + file;
2979 "Exception whilst loading jalview XML file : " + ex + "\n");
2980 } catch (Exception ex)
2982 System.err.println("Parsing as Jalview Version 2 file failed.");
2983 ex.printStackTrace(System.err);
2984 if (attemptversion1parse)
2986 // used to attempt to parse as V1 castor-generated xml
2988 if (Desktop.getInstance() != null)
2990 Desktop.getInstance().stopLoading();
2994 System.out.println("Successfully loaded archive file");
2997 ex.printStackTrace();
3000 "Exception whilst loading jalview XML file : " + ex + "\n");
3001 } catch (OutOfMemoryError e)
3003 // Don't use the OOM Window here
3004 errorMessage = "Out of memory loading jalview XML file";
3005 System.err.println("Out of memory whilst loading jalview XML file");
3006 e.printStackTrace();
3009 for (AlignFrame alf : alignFrames)
3011 alf.alignPanel.setHoldRepaint(false);
3017 * Regather multiple views (with the same sequence set id) to the frame (if
3018 * any) that is flagged as the one to gather to, i.e. convert them to tabbed
3019 * views instead of separate frames. Note this doesn't restore a state where
3020 * some expanded views in turn have tabbed views - the last "first tab" read
3021 * in will play the role of gatherer for all.
3023 for (AlignFrame fr : gatherToThisFrame.values())
3025 Desktop.getInstance().gatherViews(fr);
3028 restoreSplitFrames();
3029 for (AlignmentI ds : importedDatasets.keySet())
3031 if (ds.getCodonFrames() != null)
3033 Desktop.getStructureSelectionManager()
3034 .registerMappings(ds.getCodonFrames());
3037 if (errorMessage != null)
3042 if (Desktop.getInstance() != null)
3044 Desktop.getInstance().stopLoading();
3051 * Try to reconstruct and display SplitFrame windows, where each contains
3052 * complementary dna and protein alignments. Done by pairing up AlignFrame
3053 * objects (created earlier) which have complementary viewport ids associated.
3055 protected void restoreSplitFrames()
3057 List<SplitFrame> gatherTo = new ArrayList<>();
3058 List<AlignFrame> addedToSplitFrames = new ArrayList<>();
3059 Map<String, AlignFrame> dna = new HashMap<>();
3062 * Identify the DNA alignments
3064 for (Entry<Viewport, AlignFrame> candidate : splitFrameCandidates
3067 AlignFrame af = candidate.getValue();
3068 if (af.getViewport().getAlignment().isNucleotide())
3070 dna.put(candidate.getKey().getId(), af);
3075 * Try to match up the protein complements
3077 for (Entry<Viewport, AlignFrame> candidate : splitFrameCandidates
3080 AlignFrame af = candidate.getValue();
3081 if (!af.getViewport().getAlignment().isNucleotide())
3083 String complementId = candidate.getKey().getComplementId();
3084 // only non-null complements should be in the Map
3085 if (complementId != null && dna.containsKey(complementId))
3087 final AlignFrame dnaFrame = dna.get(complementId);
3088 SplitFrame sf = createSplitFrame(dnaFrame, af);
3089 addedToSplitFrames.add(dnaFrame);
3090 addedToSplitFrames.add(af);
3091 dnaFrame.setMenusForViewport();
3092 af.setMenusForViewport();
3093 if (af.getViewport().isGatherViewsHere())
3102 * Open any that we failed to pair up (which shouldn't happen!) as
3103 * standalone AlignFrame's.
3105 for (Entry<Viewport, AlignFrame> candidate : splitFrameCandidates
3108 AlignFrame af = candidate.getValue();
3109 if (!addedToSplitFrames.contains(af))
3111 Viewport view = candidate.getKey();
3112 Desktop.addInternalFrame(af, view.getTitle(),
3113 safeInt(view.getWidth()), safeInt(view.getHeight()));
3114 af.setMenusForViewport();
3115 System.err.println("Failed to restore view " + view.getTitle()
3116 + " to split frame");
3121 * Gather back into tabbed views as flagged.
3123 for (SplitFrame sf : gatherTo)
3125 Desktop.getInstance().gatherViews(sf);
3128 splitFrameCandidates.clear();
3132 * Construct and display one SplitFrame holding DNA and protein alignments.
3135 * @param proteinFrame
3138 protected SplitFrame createSplitFrame(AlignFrame dnaFrame,
3139 AlignFrame proteinFrame)
3141 SplitFrame splitFrame = new SplitFrame(dnaFrame, proteinFrame);
3142 String title = MessageManager.getString("label.linked_view_title");
3143 int width = (int) dnaFrame.getBounds().getWidth();
3144 int height = (int) (dnaFrame.getBounds().getHeight()
3145 + proteinFrame.getBounds().getHeight() + 50);
3148 * SplitFrame location is saved to both enclosed frames
3150 splitFrame.setLocation(dnaFrame.getX(), dnaFrame.getY());
3151 Desktop.addInternalFrame(splitFrame, title, width, height);
3154 * And compute cDNA consensus (couldn't do earlier with consensus as
3155 * mappings were not yet present)
3157 proteinFrame.getViewport().alignmentChanged(proteinFrame.alignPanel);
3163 * check errorMessage for a valid error message and raise an error box in the
3164 * GUI or write the current errorMessage to stderr and then clear the error
3167 protected void reportErrors()
3169 reportErrors(false);
3172 protected void reportErrors(final boolean saving)
3174 if (errorMessage != null)
3176 final String finalErrorMessage = errorMessage;
3179 javax.swing.SwingUtilities.invokeLater(new Runnable()
3184 JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(),
3186 "Error " + (saving ? "saving" : "loading")
3188 JvOptionPane.WARNING_MESSAGE);
3194 System.err.println("Problem loading Jalview file: " + errorMessage);
3197 errorMessage = null;
3200 Map<String, String> alreadyLoadedPDB = new HashMap<>();
3203 * when set, local views will be updated from view stored in JalviewXML
3204 * Currently (28th Sep 2008) things will go horribly wrong in vamsas document
3205 * sync if this is set to true.
3207 private final boolean updateLocalViews = false;
3210 * Returns the path to a temporary file holding the PDB file for the given PDB
3211 * id. The first time of asking, searches for a file of that name in the
3212 * Jalview project jar, and copies it to a new temporary file. Any repeat
3213 * requests just return the path to the file previously created.
3219 String loadPDBFile(jarInputStreamProvider jprovider, String pdbId,
3222 if (alreadyLoadedPDB.containsKey(pdbId))
3224 return alreadyLoadedPDB.get(pdbId).toString();
3227 String tempFile = copyJarEntry(jprovider, pdbId, "jalview_pdb",
3229 if (tempFile != null)
3231 alreadyLoadedPDB.put(pdbId, tempFile);
3237 * Copies the jar entry of given name to a new temporary file and returns the
3238 * path to the file, or null if the entry is not found.
3241 * @param jarEntryName
3243 * a prefix for the temporary file name, must be at least three
3246 * null or original file - so new file can be given the same suffix
3250 protected String copyJarEntry(jarInputStreamProvider jprovider,
3251 String jarEntryName, String prefix, String origFile)
3253 BufferedReader in = null;
3254 PrintWriter out = null;
3255 String suffix = ".tmp";
3256 if (origFile == null)
3258 origFile = jarEntryName;
3260 int sfpos = origFile.lastIndexOf(".");
3261 if (sfpos > -1 && sfpos < (origFile.length() - 3))
3263 suffix = "." + origFile.substring(sfpos + 1);
3267 JarInputStream jin = jprovider.getJarInputStream();
3269 * if (jprovider.startsWith("http://")) { jin = new JarInputStream(new
3270 * URL(jprovider).openStream()); } else { jin = new JarInputStream(new
3271 * FileInputStream(jprovider)); }
3274 JarEntry entry = null;
3277 entry = jin.getNextJarEntry();
3278 } while (entry != null && !entry.getName().equals(jarEntryName));
3281 in = new BufferedReader(new InputStreamReader(jin, UTF_8));
3282 File outFile = File.createTempFile(prefix, suffix);
3283 outFile.deleteOnExit();
3284 out = new PrintWriter(new FileOutputStream(outFile));
3287 while ((data = in.readLine()) != null)
3292 String t = outFile.getAbsolutePath();
3297 warn("Couldn't find entry in Jalview Jar for " + jarEntryName);
3299 } catch (Exception ex)
3301 ex.printStackTrace();
3309 } catch (IOException e)
3323 private class JvAnnotRow
3325 public JvAnnotRow(int i, AlignmentAnnotation jaa)
3332 * persisted version of annotation row from which to take vis properties
3334 public jalview.datamodel.AlignmentAnnotation template;
3337 * original position of the annotation row in the alignment
3343 * Load alignment frame from jalview XML DOM object. For a DOM object that
3344 * includes one or more Viewport elements (one with a title that does NOT
3345 * contain "Dataset for"), create the frame.
3347 * @param jalviewModel
3350 * filename source string
3351 * @param loadTreesAndStructures
3352 * when false only create Viewport
3354 * data source provider
3355 * @return alignment frame created from view stored in DOM
3357 AlignFrame loadFromObject(JalviewModel jalviewModel, String file,
3358 boolean loadTreesAndStructures, jarInputStreamProvider jprovider)
3361 // Platform.timeCheck("Jalview2XML.loadFromObject0", Platform.TIME_MARK);
3363 SequenceSet vamsasSet = jalviewModel.getVamsasModel().getSequenceSet().get(0);
3364 List<Sequence> vamsasSeqs = vamsasSet.getSequence();
3367 // JalviewModelSequence jms = object.getJalviewModelSequence();
3369 // Viewport view = (jms.getViewportCount() > 0) ? jms.getViewport(0)
3371 Viewport view = (jalviewModel.getViewport().size() > 0)
3372 ? jalviewModel.getViewport().get(0)
3375 // ////////////////////////////////
3376 // INITIALISE ALIGNMENT SEQUENCESETID AND VIEWID
3379 // If we just load in the same jar file again, the sequenceSetId
3380 // will be the same, and we end up with multiple references
3381 // to the same sequenceSet. We must modify this id on load
3382 // so that each load of the file gives a unique id
3385 * used to resolve correct alignment dataset for alignments with multiple
3388 String uniqueSeqSetId = null;
3389 String viewId = null;
3392 uniqueSeqSetId = view.getSequenceSetId() + uniqueSetSuffix;
3393 viewId = (view.getId() == null ? null
3394 : view.getId() + uniqueSetSuffix);
3397 // Platform.timeCheck("Jalview2XML.loadFromObject1", Platform.TIME_MARK);
3398 // ////////////////////////////////
3401 List<SequenceI> hiddenSeqs = null;
3403 List<SequenceI> tmpseqs = new ArrayList<>();
3405 boolean multipleView = false;
3406 SequenceI referenceseqForView = null;
3407 // JSeq[] jseqs = object.getJalviewModelSequence().getJSeq();
3408 List<JSeq> jseqs = jalviewModel.getJSeq();
3409 int vi = 0; // counter in vamsasSeq array
3410 for (int i = 0; i < jseqs.size(); i++)
3412 JSeq jseq = jseqs.get(i);
3413 String seqId = jseq.getId();
3415 SequenceI tmpSeq = seqRefIds.get(seqId);
3419 if (!incompleteSeqs.containsKey(seqId))
3421 // may not need this check, but keep it for at least 2.9,1 release
3422 if (tmpSeq.getStart() != jseq.getStart()
3423 || tmpSeq.getEnd() != jseq.getEnd())
3426 "Warning JAL-2154 regression: updating start/end for sequence "
3427 + tmpSeq.toString() + " to " + jseq);
3432 incompleteSeqs.remove(seqId);
3434 if (vamsasSeqs.size() > vi
3435 && vamsasSeqs.get(vi).getId().equals(seqId))
3437 // most likely we are reading a dataset XML document so
3438 // update from vamsasSeq section of XML for this sequence
3439 tmpSeq.setName(vamsasSeqs.get(vi).getName());
3440 tmpSeq.setDescription(vamsasSeqs.get(vi).getDescription());
3441 tmpSeq.setSequence(vamsasSeqs.get(vi).getSequence());
3446 // reading multiple views, so vamsasSeq set is a subset of JSeq
3447 multipleView = true;
3449 tmpSeq.setStart(jseq.getStart());
3450 tmpSeq.setEnd(jseq.getEnd());
3451 tmpseqs.add(tmpSeq);
3455 Sequence vamsasSeq = vamsasSeqs.get(vi);
3456 tmpSeq = new jalview.datamodel.Sequence(vamsasSeq.getName(),
3457 vamsasSeq.getSequence());
3458 tmpSeq.setDescription(vamsasSeq.getDescription());
3459 tmpSeq.setStart(jseq.getStart());
3460 tmpSeq.setEnd(jseq.getEnd());
3461 tmpSeq.setVamsasId(uniqueSetSuffix + seqId);
3462 seqRefIds.put(vamsasSeq.getId(), tmpSeq);
3463 tmpseqs.add(tmpSeq);
3467 if (safeBoolean(jseq.isViewreference()))
3469 referenceseqForView = tmpseqs.get(tmpseqs.size() - 1);
3472 if (jseq.isHidden() != null && jseq.isHidden().booleanValue())
3474 if (hiddenSeqs == null)
3476 hiddenSeqs = new ArrayList<>();
3479 hiddenSeqs.add(tmpSeq);
3483 // Platform.timeCheck("Jalview2XML.loadFromObject-seq",
3484 // Platform.TIME_MARK);
3486 // Create the alignment object from the sequence set
3487 // ///////////////////////////////
3488 SequenceI[] orderedSeqs = tmpseqs
3489 .toArray(new SequenceI[tmpseqs.size()]);
3491 AlignmentI al = null;
3492 // so we must create or recover the dataset alignment before going further
3493 // ///////////////////////////////
3494 if (vamsasSet.getDatasetId() == null || vamsasSet.getDatasetId() == "")
3496 // older jalview projects do not have a dataset - so creat alignment and
3498 al = new Alignment(orderedSeqs);
3499 al.setDataset(null);
3503 boolean isdsal = jalviewModel.getViewport().isEmpty();
3506 // we are importing a dataset record, so
3507 // recover reference to an alignment already materialsed as dataset
3508 al = getDatasetFor(vamsasSet.getDatasetId());
3512 // materialse the alignment
3513 al = new Alignment(orderedSeqs);
3517 addDatasetRef(vamsasSet.getDatasetId(), al);
3520 // finally, verify all data in vamsasSet is actually present in al
3521 // passing on flag indicating if it is actually a stored dataset
3522 recoverDatasetFor(vamsasSet, al, isdsal, uniqueSeqSetId);
3525 // Platform.timeCheck("Jalview2XML.loadFromObject-align",
3526 // Platform.TIME_MARK);
3527 if (referenceseqForView != null)
3529 al.setSeqrep(referenceseqForView);
3531 // / Add the alignment properties
3532 for (int i = 0; i < vamsasSet.getSequenceSetProperties().size(); i++)
3534 SequenceSetProperties ssp = vamsasSet.getSequenceSetProperties()
3536 al.setProperty(ssp.getKey(), ssp.getValue());
3539 // Platform.timeCheck("Jalview2XML.loadFromObject-setseqprop",
3540 // Platform.TIME_MARK);
3541 // ///////////////////////////////
3543 Hashtable pdbloaded = new Hashtable(); // TODO nothing writes to this??
3546 // load sequence features, database references and any associated PDB
3547 // structures for the alignment
3549 // prior to 2.10, this part would only be executed the first time a
3550 // sequence was encountered, but not afterwards.
3551 // now, for 2.10 projects, this is also done if the xml doc includes
3552 // dataset sequences not actually present in any particular view.
3554 // Platform.timeCheck("J2XML features0", Platform.TIME_RESET);
3555 for (int i = 0; i < vamsasSeqs.size(); i++)
3557 JSeq jseq = jseqs.get(i);
3558 if (jseq.getFeatures().size() > 0)
3560 List<Feature> features = jseq.getFeatures();
3561 for (int f = 0; f < features.size(); f++)
3563 Feature feat = features.get(f);
3564 SequenceFeature sf = new SequenceFeature(feat.getType(),
3565 feat.getDescription(), feat.getBegin(), feat.getEnd(),
3566 safeFloat(feat.getScore()), feat.getFeatureGroup());
3567 sf.setStatus(feat.getStatus());
3570 * load any feature attributes - include map-valued attributes
3572 Map<String, Map<String, String>> mapAttributes = new HashMap<>();
3573 for (int od = 0; od < feat.getOtherData().size(); od++)
3575 OtherData keyValue = feat.getOtherData().get(od);
3576 String attributeName = keyValue.getKey();
3577 String attributeValue = keyValue.getValue();
3578 if (attributeName.startsWith("LINK"))
3580 sf.addLink(attributeValue);
3584 String subAttribute = keyValue.getKey2();
3585 if (subAttribute == null)
3587 // simple string-valued attribute
3588 sf.setValue(attributeName, attributeValue);
3592 // attribute 'key' has sub-attribute 'key2'
3593 if (!mapAttributes.containsKey(attributeName))
3595 mapAttributes.put(attributeName, new HashMap<>());
3597 mapAttributes.get(attributeName).put(subAttribute,
3602 for (Entry<String, Map<String, String>> mapAttribute : mapAttributes
3605 sf.setValue(mapAttribute.getKey(), mapAttribute.getValue());
3608 // adds feature to datasequence's feature set (since Jalview 2.10)
3609 // Platform.timeCheck(null, Platform.TIME_SET);
3610 al.getSequenceAt(i).addSequenceFeature(sf);
3611 // Platform.timeCheck(null, Platform.TIME_MARK);
3614 if (vamsasSeqs.get(i).getDBRef().size() > 0)
3616 // adds dbrefs to datasequence's set (since Jalview 2.10)
3618 al.getSequenceAt(i).getDatasetSequence() == null
3619 ? al.getSequenceAt(i)
3620 : al.getSequenceAt(i).getDatasetSequence(),
3623 if (jseq.getPdbids().size() > 0)
3625 List<Pdbids> ids = jseq.getPdbids();
3626 for (int p = 0; p < ids.size(); p++)
3628 Pdbids pdbid = ids.get(p);
3629 jalview.datamodel.PDBEntry entry = new jalview.datamodel.PDBEntry();
3630 entry.setId(pdbid.getId());
3631 if (pdbid.getType() != null)
3633 if (PDBEntry.Type.getType(pdbid.getType()) != null)
3635 entry.setType(PDBEntry.Type.getType(pdbid.getType()));
3639 entry.setType(PDBEntry.Type.FILE);
3642 // jprovider is null when executing 'New View'
3643 if (pdbid.getFile() != null && jprovider != null)
3645 if (!pdbloaded.containsKey(pdbid.getFile()))
3647 entry.setFile(loadPDBFile(jprovider, pdbid.getId(),
3652 entry.setFile(pdbloaded.get(pdbid.getId()).toString());
3656 if (pdbid.getPdbentryItem() != null)
3658 for (PdbentryItem item : pdbid.getPdbentryItem())
3660 for (Property pr : item.getProperty())
3662 entry.setProperty(pr.getName(), pr.getValue());
3667 for (Property prop : pdbid.getProperty())
3669 entry.setProperty(prop.getName(), prop.getValue());
3671 Desktop.getStructureSelectionManager()
3672 .registerPDBEntry(entry);
3673 // adds PDBEntry to datasequence's set (since Jalview 2.10)
3674 if (al.getSequenceAt(i).getDatasetSequence() != null)
3676 al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
3680 al.getSequenceAt(i).addPDBId(entry);
3687 // Platform.timeCheck("features done", Platform.TIME_GET);
3688 // Platform.timeCheck("Jalview2XML.loadFromObject-endmultiview",
3689 // Platform.TIME_MARK);
3690 } // end !multipleview
3692 // ///////////////////////////////
3693 // LOAD SEQUENCE MAPPINGS
3695 if (vamsasSet.getAlcodonFrame().size() > 0)
3697 // TODO Potentially this should only be done once for all views of an
3699 List<AlcodonFrame> alc = vamsasSet.getAlcodonFrame();
3700 for (int i = 0; i < alc.size(); i++)
3702 AlignedCodonFrame cf = new AlignedCodonFrame();
3703 if (alc.get(i).getAlcodMap().size() > 0)
3705 List<AlcodMap> maps = alc.get(i).getAlcodMap();
3706 for (int m = 0; m < maps.size(); m++)
3708 AlcodMap map = maps.get(m);
3709 SequenceI dnaseq = seqRefIds.get(map.getDnasq());
3711 jalview.datamodel.Mapping mapping = null;
3712 // attach to dna sequence reference.
3713 if (map.getMapping() != null)
3715 mapping = addMapping(map.getMapping());
3716 if (dnaseq != null && mapping.getTo() != null)
3718 cf.addMap(dnaseq, mapping.getTo(), mapping.getMap());
3724 newAlcodMapRef(map.getDnasq(), cf, mapping));
3728 al.addCodonFrame(cf);
3731 // Platform.timeCheck("Jalview2XML.loadFromObject-seqmap",
3732 // Platform.TIME_MARK);
3735 // ////////////////////////////////
3737 List<JvAnnotRow> autoAlan = new ArrayList<>();
3740 * store any annotations which forward reference a group's ID
3742 Map<String, List<AlignmentAnnotation>> groupAnnotRefs = new Hashtable<>();
3744 if (vamsasSet.getAnnotation().size()/*Count()*/ > 0)
3746 List<Annotation> an = vamsasSet.getAnnotation();
3748 for (int i = 0; i < an.size(); i++)
3750 Annotation annotation = an.get(i);
3753 * test if annotation is automatically calculated for this view only
3755 boolean autoForView = false;
3756 if (annotation.getLabel().equals("Quality")
3757 || annotation.getLabel().equals("Conservation")
3758 || annotation.getLabel().equals("Consensus"))
3760 // Kludge for pre 2.5 projects which lacked the autocalculated flag
3762 // JAXB has no has() test; schema defaults value to false
3763 // if (!annotation.hasAutoCalculated())
3765 // annotation.setAutoCalculated(true);
3768 if (autoForView || annotation.isAutoCalculated())
3770 // remove ID - we don't recover annotation from other views for
3771 // view-specific annotation
3772 annotation.setId(null);
3775 // set visibility for other annotation in this view
3776 String annotationId = annotation.getId();
3777 if (annotationId != null && annotationIds.containsKey(annotationId))
3779 AlignmentAnnotation jda = annotationIds.get(annotationId);
3780 // in principle Visible should always be true for annotation displayed
3781 // in multiple views
3782 if (annotation.isVisible() != null)
3784 jda.visible = annotation.isVisible();
3787 al.addAnnotation(jda);
3791 // Construct new annotation from model.
3792 List<AnnotationElement> ae = annotation.getAnnotationElement();
3793 // System.err.println(
3794 // "Jalview2XML processing " + ae.size() + " annotations");
3796 jalview.datamodel.Annotation[] anot = null;
3797 java.awt.Color firstColour = null;
3799 if (!annotation.isScoreOnly())
3801 anot = new jalview.datamodel.Annotation[al.getWidth()];
3802 for (int aa = 0; aa < ae.size() && aa < anot.length; aa++)
3804 AnnotationElement annElement = ae.get(aa);
3805 anpos = annElement.getPosition();
3807 if (anpos >= anot.length)
3812 float value = safeFloat(annElement.getValue());
3813 anot[anpos] = new jalview.datamodel.Annotation(
3814 annElement.getDisplayCharacter(),
3815 annElement.getDescription(),
3816 (annElement.getSecondaryStructure() == null
3817 || annElement.getSecondaryStructure()
3821 .getSecondaryStructure()
3824 anot[anpos].colour = new Color(safeInt(annElement.getColour()));
3825 if (firstColour == null)
3827 firstColour = anot[anpos].colour;
3831 // create the new AlignmentAnnotation
3832 jalview.datamodel.AlignmentAnnotation jaa = null;
3834 if (annotation.isGraph())
3836 float llim = 0, hlim = 0;
3837 // if (autoForView || an[i].isAutoCalculated()) {
3840 jaa = new jalview.datamodel.AlignmentAnnotation(
3841 annotation.getLabel(), annotation.getDescription(), anot,
3842 llim, hlim, safeInt(annotation.getGraphType()));
3844 jaa.graphGroup = safeInt(annotation.getGraphGroup());
3845 jaa._linecolour = firstColour;
3846 if (annotation.getThresholdLine() != null)
3848 jaa.setThreshold(new jalview.datamodel.GraphLine(
3849 safeFloat(annotation.getThresholdLine().getValue()),
3850 annotation.getThresholdLine().getLabel(),
3851 new java.awt.Color(safeInt(
3852 annotation.getThresholdLine().getColour()))));
3854 if (autoForView || annotation.isAutoCalculated())
3856 // Hardwire the symbol display line to ensure that labels for
3857 // histograms are displayed
3863 jaa = new jalview.datamodel.AlignmentAnnotation(
3864 annotation.getLabel(), annotation.getDescription(), anot);
3865 jaa._linecolour = firstColour;
3867 // register new annotation
3868 // Annotation graphs such as Conservation will not have id.
3869 if (annotation.getId() != null)
3871 annotationIds.put(annotation.getId(), jaa);
3872 jaa.annotationId = annotation.getId();
3874 // recover sequence association
3875 String sequenceRef = annotation.getSequenceRef();
3876 if (sequenceRef != null)
3878 // from 2.9 sequenceRef is to sequence id (JAL-1781)
3879 SequenceI sequence = seqRefIds.get(sequenceRef);
3880 if (sequence == null)
3882 // in pre-2.9 projects sequence ref is to sequence name
3883 sequence = al.findName(sequenceRef);
3885 if (sequence != null)
3887 jaa.createSequenceMapping(sequence, 1, true);
3888 sequence.addAlignmentAnnotation(jaa);
3891 // and make a note of any group association
3892 if (annotation.getGroupRef() != null
3893 && annotation.getGroupRef().length() > 0)
3895 List<jalview.datamodel.AlignmentAnnotation> aal = groupAnnotRefs
3896 .get(annotation.getGroupRef());
3899 aal = new ArrayList<>();
3900 groupAnnotRefs.put(annotation.getGroupRef(), aal);
3905 if (annotation.getScore() != null)
3907 jaa.setScore(annotation.getScore().doubleValue());
3909 if (annotation.isVisible() != null)
3911 jaa.visible = annotation.isVisible().booleanValue();
3914 if (annotation.isCentreColLabels() != null)
3916 jaa.centreColLabels = annotation.isCentreColLabels()
3920 if (annotation.isScaleColLabels() != null)
3922 jaa.scaleColLabel = annotation.isScaleColLabels().booleanValue();
3924 if (annotation.isAutoCalculated())
3926 // newer files have an 'autoCalculated' flag and store calculation
3927 // state in viewport properties
3928 jaa.autoCalculated = true; // means annotation will be marked for
3929 // update at end of load.
3931 if (annotation.getGraphHeight() != null)
3933 jaa.graphHeight = annotation.getGraphHeight().intValue();
3935 jaa.belowAlignment = annotation.isBelowAlignment();
3936 jaa.setCalcId(annotation.getCalcId());
3937 if (annotation.getProperty().size() > 0)
3939 for (Annotation.Property prop : annotation
3942 jaa.setProperty(prop.getName(), prop.getValue());
3945 if (jaa.autoCalculated)
3947 autoAlan.add(new JvAnnotRow(i, jaa));
3950 // if (!autoForView)
3952 // add autocalculated group annotation and any user created annotation
3954 al.addAnnotation(jaa);
3957 // Platform.timeCheck("Jalview2XML.loadFromObject-annot",
3958 // Platform.TIME_MARK);
3960 // ///////////////////////
3962 // Create alignment markup and styles for this view
3963 if (jalviewModel.getJGroup().size() > 0)
3965 List<JGroup> groups = jalviewModel.getJGroup();
3966 boolean addAnnotSchemeGroup = false;
3967 for (int i = 0; i < groups.size(); i++)
3969 JGroup jGroup = groups.get(i);
3970 ColourSchemeI cs = null;
3971 if (jGroup.getColour() != null)
3973 if (jGroup.getColour().startsWith("ucs"))
3975 cs = getUserColourScheme(jalviewModel, jGroup.getColour());
3977 else if (jGroup.getColour().equals("AnnotationColourGradient")
3978 && jGroup.getAnnotationColours() != null)
3980 addAnnotSchemeGroup = true;
3984 cs = ColourSchemeProperty.getColourScheme(null, al,
3985 jGroup.getColour());
3988 int pidThreshold = safeInt(jGroup.getPidThreshold());
3990 Vector<SequenceI> seqs = new Vector<>();
3992 for (int s = 0; s < jGroup.getSeq().size(); s++)
3994 String seqId = jGroup.getSeq().get(s);
3995 SequenceI ts = seqRefIds.get(seqId);
3999 seqs.addElement(ts);
4003 if (seqs.size() < 1)
4008 SequenceGroup sg = new SequenceGroup(seqs, jGroup.getName(), cs,
4009 safeBoolean(jGroup.isDisplayBoxes()),
4010 safeBoolean(jGroup.isDisplayText()),
4011 safeBoolean(jGroup.isColourText()),
4012 safeInt(jGroup.getStart()), safeInt(jGroup.getEnd()));
4013 sg.getGroupColourScheme().setThreshold(pidThreshold, true);
4014 sg.getGroupColourScheme()
4015 .setConservationInc(safeInt(jGroup.getConsThreshold()));
4016 sg.setOutlineColour(new Color(safeInt(jGroup.getOutlineColour())));
4018 sg.textColour = new Color(safeInt(jGroup.getTextCol1()));
4019 sg.textColour2 = new Color(safeInt(jGroup.getTextCol2()));
4020 sg.setShowNonconserved(safeBoolean(jGroup.isShowUnconserved()));
4021 sg.thresholdTextColour = safeInt(jGroup.getTextColThreshold());
4022 // attributes with a default in the schema are never null
4023 sg.setShowConsensusHistogram(jGroup.isShowConsensusHistogram());
4024 sg.setshowSequenceLogo(jGroup.isShowSequenceLogo());
4025 sg.setNormaliseSequenceLogo(jGroup.isNormaliseSequenceLogo());
4026 sg.setIgnoreGapsConsensus(jGroup.isIgnoreGapsinConsensus());
4027 if (jGroup.getConsThreshold() != null
4028 && jGroup.getConsThreshold().intValue() != 0)
4030 Conservation c = new Conservation("All", sg.getSequences(null), 0,
4033 c.verdict(false, 25);
4034 sg.cs.setConservation(c);
4037 if (jGroup.getId() != null && groupAnnotRefs.size() > 0)
4039 // re-instate unique group/annotation row reference
4040 List<AlignmentAnnotation> jaal = groupAnnotRefs
4041 .get(jGroup.getId());
4044 for (AlignmentAnnotation jaa : jaal)
4047 if (jaa.autoCalculated)
4049 // match up and try to set group autocalc alignment row for this
4051 if (jaa.label.startsWith("Consensus for "))
4053 sg.setConsensus(jaa);
4055 // match up and try to set group autocalc alignment row for this
4057 if (jaa.label.startsWith("Conservation for "))
4059 sg.setConservationRow(jaa);
4066 if (addAnnotSchemeGroup)
4068 // reconstruct the annotation colourscheme
4069 sg.setColourScheme(constructAnnotationColour(
4070 jGroup.getAnnotationColours(), null, al, jalviewModel, false));
4073 // Platform.timeCheck("Jalview2XML.loadFromObject-groups",
4074 // Platform.TIME_MARK);
4078 // only dataset in this model, so just return.
4081 // ///////////////////////////////
4084 // now check to see if we really need to create a new viewport.
4085 if (multipleView && viewportsAdded.size() == 0)
4087 // We recovered an alignment for which a viewport already exists.
4088 // TODO: fix up any settings necessary for overlaying stored state onto
4089 // state recovered from another document. (may not be necessary).
4090 // we may need a binding from a viewport in memory to one recovered from
4092 // and then recover its containing af to allow the settings to be applied.
4093 // TODO: fix for vamsas demo
4095 "About to recover a viewport for existing alignment: Sequence set ID is "
4097 Object seqsetobj = retrieveExistingObj(uniqueSeqSetId);
4098 if (seqsetobj != null)
4100 if (seqsetobj instanceof String)
4102 uniqueSeqSetId = (String) seqsetobj;
4104 "Recovered extant sequence set ID mapping for ID : New Sequence set ID is "
4110 "Warning : Collision between sequence set ID string and existing jalview object mapping.");
4114 // Platform.timeCheck("Jalview2XML.loadFromObject-viewport",
4115 // Platform.TIME_MARK);
4118 * indicate that annotation colours are applied across all groups (pre
4119 * Jalview 2.8.1 behaviour)
4121 boolean doGroupAnnColour = Jalview2XML.isVersionStringLaterThan("2.8.1",
4122 jalviewModel.getVersion());
4124 AlignFrame af = null;
4125 AlignmentPanel ap = null;
4126 AlignViewport av = null;
4129 // Check to see if this alignment already has a view id == viewId
4130 jalview.gui.AlignmentPanel views[] = Desktop
4131 .getAlignmentPanels(uniqueSeqSetId);
4132 if (views != null && views.length > 0)
4134 for (int v = 0; v < views.length; v++)
4138 if (av.getViewId().equalsIgnoreCase(viewId))
4140 // recover the existing alignpanel, alignframe, viewport
4143 // TODO: could even skip resetting view settings if we don't want to
4144 // change the local settings from other jalview processes
4152 af = loadViewport(file, jseqs, hiddenSeqs, al, jalviewModel, view,
4153 uniqueSeqSetId, viewId, autoAlan);
4154 av = af.getViewport();
4155 // note that this only retrieves the most recently accessed
4156 // tab of an AlignFrame.
4161 * Load any trees, PDB structures and viewers
4163 * Not done if flag is false (when this method is used for New View)
4165 final AlignFrame af0 = af;
4166 final AlignViewport av0 = av;
4167 final AlignmentPanel ap0 = ap;
4168 // Platform.timeCheck("Jalview2XML.loadFromObject-beforetree",
4169 // Platform.TIME_MARK);
4170 if (loadTreesAndStructures)
4172 if (!jalviewModel.getTree().isEmpty())
4174 SwingUtilities.invokeLater(new Runnable()
4179 // Platform.timeCheck(null, Platform.TIME_MARK);
4180 loadTrees(jalviewModel, view, af0, av0, ap0);
4181 // Platform.timeCheck("Jalview2XML.loadTrees", Platform.TIME_MARK);
4185 if (!jalviewModel.getPcaViewer().isEmpty())
4187 SwingUtilities.invokeLater(new Runnable()
4192 // Platform.timeCheck(null, Platform.TIME_MARK);
4193 loadPCAViewers(jalviewModel, ap0);
4194 // Platform.timeCheck("Jalview2XML.loadPCA", Platform.TIME_MARK);
4198 SwingUtilities.invokeLater(new Runnable()
4203 // Platform.timeCheck(null, Platform.TIME_MARK);
4204 loadPDBStructures(jprovider, jseqs, af0, ap0);
4205 // Platform.timeCheck("Jalview2XML.loadPDB", Platform.TIME_MARK);
4208 SwingUtilities.invokeLater(new Runnable()
4213 loadRnaViewers(jprovider, jseqs, ap0);
4217 // and finally return.
4218 // but do not set holdRepaint true just yet, because this could be the
4219 // initial frame with just its dataset.
4224 * Instantiate and link any saved RNA (Varna) viewers. The state of the Varna
4225 * panel is restored from separate jar entries, two (gapped and trimmed) per
4226 * sequence and secondary structure.
4228 * Currently each viewer shows just one sequence and structure (gapped and
4229 * trimmed), however this method is designed to support multiple sequences or
4230 * structures in viewers if wanted in future.
4236 protected void loadRnaViewers(jarInputStreamProvider jprovider,
4237 List<JSeq> jseqs, AlignmentPanel ap)
4240 * scan the sequences for references to viewers; create each one the first
4241 * time it is referenced, add Rna models to existing viewers
4243 for (JSeq jseq : jseqs)
4245 for (int i = 0; i < jseq.getRnaViewer().size(); i++)
4247 RnaViewer viewer = jseq.getRnaViewer().get(i);
4248 AppVarna appVarna = findOrCreateVarnaViewer(viewer, uniqueSetSuffix,
4251 for (int j = 0; j < viewer.getSecondaryStructure().size(); j++)
4253 SecondaryStructure ss = viewer.getSecondaryStructure().get(j);
4254 SequenceI seq = seqRefIds.get(jseq.getId());
4255 AlignmentAnnotation ann = this.annotationIds
4256 .get(ss.getAnnotationId());
4259 * add the structure to the Varna display (with session state copied
4260 * from the jar to a temporary file)
4262 boolean gapped = safeBoolean(ss.isGapped());
4263 String rnaTitle = ss.getTitle();
4264 String sessionState = ss.getViewerState();
4265 String tempStateFile = copyJarEntry(jprovider, sessionState,
4267 RnaModel rna = new RnaModel(rnaTitle, ann, seq, null, gapped);
4268 appVarna.addModelSession(rna, rnaTitle, tempStateFile);
4270 appVarna.setInitialSelection(safeInt(viewer.getSelectedRna()));
4276 * Locate and return an already instantiated matching AppVarna, or create one
4280 * @param viewIdSuffix
4284 protected AppVarna findOrCreateVarnaViewer(RnaViewer viewer,
4285 String viewIdSuffix, AlignmentPanel ap)
4288 * on each load a suffix is appended to the saved viewId, to avoid conflicts
4289 * if load is repeated
4291 String postLoadId = viewer.getViewId() + viewIdSuffix;
4292 for (JInternalFrame frame : getAllFrames())
4294 if (frame instanceof AppVarna)
4296 AppVarna varna = (AppVarna) frame;
4297 if (postLoadId.equals(varna.getViewId()))
4299 // this viewer is already instantiated
4300 // could in future here add ap as another 'parent' of the
4301 // AppVarna window; currently just 1-to-many
4308 * viewer not found - make it
4310 RnaViewerModel model = new RnaViewerModel(postLoadId, viewer.getTitle(),
4311 safeInt(viewer.getXpos()), safeInt(viewer.getYpos()),
4312 safeInt(viewer.getWidth()), safeInt(viewer.getHeight()),
4313 safeInt(viewer.getDividerLocation()));
4314 AppVarna varna = new AppVarna(model, ap);
4320 * Load any saved trees
4328 protected void loadTrees(JalviewModel jm, Viewport view,
4329 AlignFrame af, AlignViewport av, AlignmentPanel ap)
4331 // TODO result of automated refactoring - are all these parameters needed?
4334 for (int t = 0; t < jm.getTree().size(); t++)
4337 Tree tree = jm.getTree().get(t);
4339 TreePanel tp = (TreePanel) retrieveExistingObj(tree.getId());
4342 tp = af.showNewickTree(new NewickFile(tree.getNewick()),
4343 tree.getTitle(), safeInt(tree.getWidth()),
4344 safeInt(tree.getHeight()), safeInt(tree.getXpos()),
4345 safeInt(tree.getYpos()));
4346 if (tree.getId() != null)
4348 // perhaps bind the tree id to something ?
4353 // update local tree attributes ?
4354 // TODO: should check if tp has been manipulated by user - if so its
4355 // settings shouldn't be modified
4356 tp.setTitle(tree.getTitle());
4357 tp.setBounds(new Rectangle(safeInt(tree.getXpos()),
4358 safeInt(tree.getYpos()), safeInt(tree.getWidth()),
4359 safeInt(tree.getHeight())));
4360 tp.setViewport(av); // af.viewport;
4361 // TODO: verify 'associate with all views' works still
4362 tp.getTreeCanvas().setViewport(av); // af.viewport;
4363 tp.getTreeCanvas().setAssociatedPanel(ap); // af.alignPanel;
4365 tp.getTreeCanvas().setApplyToAllViews(tree.isLinkToAllViews());
4368 warn("There was a problem recovering stored Newick tree: \n"
4369 + tree.getNewick());
4373 tp.fitToWindow.setState(safeBoolean(tree.isFitToWindow()));
4374 tp.fitToWindow_actionPerformed(null);
4376 if (tree.getFontName() != null)
4379 new Font(tree.getFontName(), safeInt(tree.getFontStyle()),
4380 safeInt(tree.getFontSize())));
4385 new Font(view.getFontName(), safeInt(view.getFontStyle()),
4386 safeInt(view.getFontSize())));
4389 tp.showPlaceholders(safeBoolean(tree.isMarkUnlinked()));
4390 tp.showBootstrap(safeBoolean(tree.isShowBootstrap()));
4391 tp.showDistances(safeBoolean(tree.isShowDistances()));
4393 tp.getTreeCanvas().setThreshold(safeFloat(tree.getThreshold()));
4395 if (safeBoolean(tree.isCurrentTree()))
4397 af.getViewport().setCurrentTree(tp.getTree());
4401 } catch (Exception ex)
4403 ex.printStackTrace();
4408 * Load and link any saved structure viewers.
4415 protected void loadPDBStructures(jarInputStreamProvider jprovider,
4416 List<JSeq> jseqs, AlignFrame af, AlignmentPanel ap)
4419 * Run through all PDB ids on the alignment, and collect mappings between
4420 * distinct view ids and all sequences referring to that view.
4422 Map<String, StructureViewerModel> structureViewers = new LinkedHashMap<>();
4424 for (int i = 0; i < jseqs.size(); i++)
4426 JSeq jseq = jseqs.get(i);
4427 if (jseq.getPdbids().size() > 0)
4429 List<Pdbids> ids = jseq.getPdbids();
4430 for (int p = 0; p < ids.size(); p++)
4432 Pdbids pdbid = ids.get(p);
4433 final int structureStateCount = pdbid.getStructureState().size();
4434 for (int s = 0; s < structureStateCount; s++)
4436 // check to see if we haven't already created this structure view
4437 final StructureState structureState = pdbid
4438 .getStructureState().get(s);
4439 String sviewid = (structureState.getViewId() == null) ? null
4440 : structureState.getViewId() + uniqueSetSuffix;
4441 jalview.datamodel.PDBEntry jpdb = new jalview.datamodel.PDBEntry();
4442 // Originally : pdbid.getFile()
4443 // : TODO: verify external PDB file recovery still works in normal
4444 // jalview project load
4446 loadPDBFile(jprovider, pdbid.getId(), pdbid.getFile()));
4447 jpdb.setId(pdbid.getId());
4449 int x = safeInt(structureState.getXpos());
4450 int y = safeInt(structureState.getYpos());
4451 int width = safeInt(structureState.getWidth());
4452 int height = safeInt(structureState.getHeight());
4454 // Probably don't need to do this anymore...
4455 // Desktop.getDesktop().getComponentAt(x, y);
4456 // TODO: NOW: check that this recovers the PDB file correctly.
4457 String pdbFile = loadPDBFile(jprovider, pdbid.getId(),
4459 jalview.datamodel.SequenceI seq = seqRefIds
4460 .get(jseq.getId() + "");
4461 if (sviewid == null)
4463 sviewid = "_jalview_pre2_4_" + x + "," + y + "," + width + ","
4466 if (!structureViewers.containsKey(sviewid))
4468 structureViewers.put(sviewid,
4469 new StructureViewerModel(x, y, width, height, false,
4470 false, true, structureState.getViewId(),
4471 structureState.getType()));
4472 // Legacy pre-2.7 conversion JAL-823 :
4473 // do not assume any view has to be linked for colour by
4477 // assemble String[] { pdb files }, String[] { id for each
4478 // file }, orig_fileloc, SequenceI[][] {{ seqs_file 1 }, {
4479 // seqs_file 2}, boolean[] {
4480 // linkAlignPanel,superposeWithAlignpanel}} from hash
4481 StructureViewerModel jmoldat = structureViewers.get(sviewid);
4482 jmoldat.setAlignWithPanel(jmoldat.isAlignWithPanel()
4483 || structureState.isAlignwithAlignPanel());
4486 * Default colour by linked panel to false if not specified (e.g.
4487 * for pre-2.7 projects)
4489 boolean colourWithAlignPanel = jmoldat.isColourWithAlignPanel();
4490 colourWithAlignPanel |= structureState.isColourwithAlignPanel();
4491 jmoldat.setColourWithAlignPanel(colourWithAlignPanel);
4494 * Default colour by viewer to true if not specified (e.g. for
4497 boolean colourByViewer = jmoldat.isColourByViewer();
4498 colourByViewer &= structureState.isColourByJmol();
4499 jmoldat.setColourByViewer(colourByViewer);
4501 if (jmoldat.getStateData().length() < structureState
4502 .getValue()/*Content()*/.length())
4504 jmoldat.setStateData(structureState.getValue());// Content());
4506 if (pdbid.getFile() != null)
4508 File mapkey = new File(pdbid.getFile());
4509 StructureData seqstrmaps = jmoldat.getFileData().get(mapkey);
4510 if (seqstrmaps == null)
4512 jmoldat.getFileData().put(mapkey,
4513 seqstrmaps = jmoldat.new StructureData(pdbFile,
4516 if (!seqstrmaps.getSeqList().contains(seq))
4518 seqstrmaps.getSeqList().add(seq);
4524 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");
4531 // Instantiate the associated structure views
4532 for (Entry<String, StructureViewerModel> entry : structureViewers
4537 createOrLinkStructureViewer(entry, af, ap, jprovider);
4538 } catch (Exception e)
4541 "Error loading structure viewer: " + e.getMessage());
4542 // failed - try the next one
4554 protected void createOrLinkStructureViewer(
4555 Entry<String, StructureViewerModel> viewerData, AlignFrame af,
4556 AlignmentPanel ap, jarInputStreamProvider jprovider)
4558 final StructureViewerModel stateData = viewerData.getValue();
4561 * Search for any viewer windows already open from other alignment views
4562 * that exactly match the stored structure state
4564 StructureViewerBase comp = findMatchingViewer(viewerData);
4568 linkStructureViewer(ap, comp, stateData);
4573 * From 2.9: stateData.type contains JMOL or CHIMERA, data is in jar entry
4574 * "viewer_"+stateData.viewId
4576 if (ViewerType.CHIMERA.toString().equals(stateData.getType()))
4578 createChimeraViewer(viewerData, af, jprovider);
4583 * else Jmol (if pre-2.9, stateData contains JMOL state string)
4585 createJmolViewer(viewerData, af, jprovider);
4590 * Create a new Chimera viewer.
4596 protected void createChimeraViewer(
4597 Entry<String, StructureViewerModel> viewerData, AlignFrame af,
4598 jarInputStreamProvider jprovider)
4600 StructureViewerModel data = viewerData.getValue();
4601 String chimeraSessionFile = data.getStateData();
4604 * Copy Chimera session from jar entry "viewer_"+viewId to a temporary file
4606 * NB this is the 'saved' viewId as in the project file XML, _not_ the
4607 * 'uniquified' sviewid used to reconstruct the viewer here
4609 String viewerJarEntryName = getViewerJarEntryName(data.getViewId());
4610 chimeraSessionFile = copyJarEntry(jprovider, viewerJarEntryName,
4613 Set<Entry<File, StructureData>> fileData = data.getFileData()
4615 List<PDBEntry> pdbs = new ArrayList<>();
4616 List<SequenceI[]> allseqs = new ArrayList<>();
4617 for (Entry<File, StructureData> pdb : fileData)
4619 String filePath = pdb.getValue().getFilePath();
4620 String pdbId = pdb.getValue().getPdbId();
4621 // pdbs.add(new PDBEntry(filePath, pdbId));
4622 pdbs.add(new PDBEntry(pdbId, null, PDBEntry.Type.PDB, filePath));
4623 final List<SequenceI> seqList = pdb.getValue().getSeqList();
4624 SequenceI[] seqs = seqList.toArray(new SequenceI[seqList.size()]);
4628 boolean colourByChimera = data.isColourByViewer();
4629 boolean colourBySequence = data.isColourWithAlignPanel();
4631 // TODO use StructureViewer as a factory here, see JAL-1761
4632 final PDBEntry[] pdbArray = pdbs.toArray(new PDBEntry[pdbs.size()]);
4633 final SequenceI[][] seqsArray = allseqs
4634 .toArray(new SequenceI[allseqs.size()][]);
4635 String newViewId = viewerData.getKey();
4637 ChimeraViewFrame cvf = new ChimeraViewFrame(chimeraSessionFile,
4638 af.alignPanel, pdbArray, seqsArray, colourByChimera,
4639 colourBySequence, newViewId);
4640 cvf.setSize(data.getWidth(), data.getHeight());
4641 cvf.setLocation(data.getX(), data.getY());
4645 * Create a new Jmol window. First parse the Jmol state to translate filenames
4646 * loaded into the view, and record the order in which files are shown in the
4647 * Jmol view, so we can add the sequence mappings in same order.
4653 protected void createJmolViewer(
4654 final Entry<String, StructureViewerModel> viewerData,
4655 AlignFrame af, jarInputStreamProvider jprovider)
4657 final StructureViewerModel svattrib = viewerData.getValue();
4658 String state = svattrib.getStateData();
4661 * Pre-2.9: state element value is the Jmol state string
4663 * 2.9+: @type is "JMOL", state data is in a Jar file member named "viewer_"
4666 if (ViewerType.JMOL.toString().equals(svattrib.getType()))
4668 state = readJarEntry(jprovider,
4669 getViewerJarEntryName(svattrib.getViewId()));
4672 List<String> pdbfilenames = new ArrayList<>();
4673 List<SequenceI[]> seqmaps = new ArrayList<>();
4674 List<String> pdbids = new ArrayList<>();
4675 StringBuilder newFileLoc = new StringBuilder(64);
4676 int cp = 0, ncp, ecp;
4677 Map<File, StructureData> oldFiles = svattrib.getFileData();
4678 while ((ncp = state.indexOf("load ", cp)) > -1)
4682 // look for next filename in load statement
4683 newFileLoc.append(state.substring(cp,
4684 ncp = (state.indexOf("\"", ncp + 1) + 1)));
4685 String oldfilenam = state.substring(ncp,
4686 ecp = state.indexOf("\"", ncp));
4687 // recover the new mapping data for this old filename
4688 // have to normalize filename - since Jmol and jalview do
4690 // translation differently.
4691 StructureData filedat = oldFiles.get(new File(oldfilenam));
4692 if (filedat == null)
4694 String reformatedOldFilename = oldfilenam.replaceAll("/", "\\\\");
4695 filedat = oldFiles.get(new File(reformatedOldFilename));
4697 newFileLoc.append(Platform.escapeString(filedat.getFilePath()));
4698 pdbfilenames.add(filedat.getFilePath());
4699 pdbids.add(filedat.getPdbId());
4700 seqmaps.add(filedat.getSeqList().toArray(new SequenceI[0]));
4701 newFileLoc.append("\"");
4702 cp = ecp + 1; // advance beyond last \" and set cursor so we can
4703 // look for next file statement.
4704 } while ((ncp = state.indexOf("/*file*/", cp)) > -1);
4708 // just append rest of state
4709 newFileLoc.append(state.substring(cp));
4713 System.err.print("Ignoring incomplete Jmol state for PDB ids: ");
4714 newFileLoc = new StringBuilder(state);
4715 newFileLoc.append("; load append ");
4716 for (File id : oldFiles.keySet())
4718 // add this and any other pdb files that should be present in
4720 StructureData filedat = oldFiles.get(id);
4721 newFileLoc.append(filedat.getFilePath());
4722 pdbfilenames.add(filedat.getFilePath());
4723 pdbids.add(filedat.getPdbId());
4724 seqmaps.add(filedat.getSeqList().toArray(new SequenceI[0]));
4725 newFileLoc.append(" \"");
4726 newFileLoc.append(filedat.getFilePath());
4727 newFileLoc.append("\"");
4730 newFileLoc.append(";");
4733 if (newFileLoc.length() == 0)
4737 int histbug = newFileLoc.indexOf("history = ");
4741 * change "history = [true|false];" to "history = [1|0];"
4744 int diff = histbug == -1 ? -1 : newFileLoc.indexOf(";", histbug);
4745 String val = (diff == -1) ? null
4746 : newFileLoc.substring(histbug, diff);
4747 if (val != null && val.length() >= 4)
4749 if (val.contains("e")) // eh? what can it be?
4751 if (val.trim().equals("true"))
4759 newFileLoc.replace(histbug, diff, val);
4764 final String[] pdbf = pdbfilenames
4765 .toArray(new String[pdbfilenames.size()]);
4766 final String[] id = pdbids.toArray(new String[pdbids.size()]);
4767 final SequenceI[][] sq = seqmaps
4768 .toArray(new SequenceI[seqmaps.size()][]);
4769 final String fileloc = newFileLoc.toString();
4770 final String sviewid = viewerData.getKey();
4771 final AlignFrame alf = af;
4772 final Rectangle rect = new Rectangle(svattrib.getX(), svattrib.getY(),
4773 svattrib.getWidth(), svattrib.getHeight());
4776 javax.swing.SwingUtilities.invokeLater(new Runnable()
4781 JalviewStructureDisplayI sview = null;
4784 sview = new StructureViewer(
4785 alf.alignPanel.getStructureSelectionManager())
4786 .createView(StructureViewer.ViewerType.JMOL,
4787 pdbf, id, sq, alf.alignPanel, svattrib,
4788 fileloc, rect, sviewid);
4789 addNewStructureViewer(sview);
4790 } catch (OutOfMemoryError ex)
4792 new OOMWarning("restoring structure view for PDB id " + id,
4793 (OutOfMemoryError) ex.getCause());
4794 if (sview != null && sview.isVisible())
4796 sview.closeViewer(false);
4797 sview.setVisible(false);
4803 // } catch (InvocationTargetException ex)
4805 // warn("Unexpected error when opening Jmol view.", ex);
4807 // } catch (InterruptedException e)
4809 // // e.printStackTrace();
4815 * Generates a name for the entry in the project jar file to hold state
4816 * information for a structure viewer
4821 protected String getViewerJarEntryName(String viewId)
4823 return VIEWER_PREFIX + viewId;
4827 * Returns any open frame that matches given structure viewer data. The match
4828 * is based on the unique viewId, or (for older project versions) the frame's
4834 protected StructureViewerBase findMatchingViewer(
4835 Entry<String, StructureViewerModel> viewerData)
4837 final String sviewid = viewerData.getKey();
4838 final StructureViewerModel svattrib = viewerData.getValue();
4839 StructureViewerBase comp = null;
4840 JInternalFrame[] frames = getAllFrames();
4841 for (JInternalFrame frame : frames)
4843 if (frame instanceof StructureViewerBase)
4846 * Post jalview 2.4 schema includes structure view id
4848 if (sviewid != null && ((StructureViewerBase) frame).getViewId()
4851 comp = (StructureViewerBase) frame;
4852 break; // break added in 2.9
4855 * Otherwise test for matching position and size of viewer frame
4857 else if (frame.getX() == svattrib.getX()
4858 && frame.getY() == svattrib.getY()
4859 && frame.getHeight() == svattrib.getHeight()
4860 && frame.getWidth() == svattrib.getWidth())
4862 comp = (StructureViewerBase) frame;
4863 // no break in faint hope of an exact match on viewId
4871 * Link an AlignmentPanel to an existing structure viewer.
4876 * @param useinViewerSuperpos
4877 * @param usetoColourbyseq
4878 * @param viewerColouring
4880 protected void linkStructureViewer(AlignmentPanel ap,
4881 StructureViewerBase viewer, StructureViewerModel stateData)
4883 // NOTE: if the jalview project is part of a shared session then
4884 // view synchronization should/could be done here.
4886 final boolean useinViewerSuperpos = stateData.isAlignWithPanel();
4887 final boolean usetoColourbyseq = stateData.isColourWithAlignPanel();
4888 final boolean viewerColouring = stateData.isColourByViewer();
4889 Map<File, StructureData> oldFiles = stateData.getFileData();
4892 * Add mapping for sequences in this view to an already open viewer
4894 final AAStructureBindingModel binding = viewer.getBinding();
4895 for (File id : oldFiles.keySet())
4897 // add this and any other pdb files that should be present in the
4899 StructureData filedat = oldFiles.get(id);
4900 String pdbFile = filedat.getFilePath();
4901 SequenceI[] seq = filedat.getSeqList().toArray(new SequenceI[0]);
4902 binding.getSsm().setMapping(seq, null, pdbFile, DataSourceType.FILE,
4904 binding.addSequenceForStructFile(pdbFile, seq);
4906 // and add the AlignmentPanel's reference to the view panel
4907 viewer.addAlignmentPanel(ap);
4908 if (useinViewerSuperpos)
4910 viewer.useAlignmentPanelForSuperposition(ap);
4914 viewer.excludeAlignmentPanelForSuperposition(ap);
4916 if (usetoColourbyseq)
4918 viewer.useAlignmentPanelForColourbyseq(ap, !viewerColouring);
4922 viewer.excludeAlignmentPanelForColourbyseq(ap);
4927 * Get all frames within the Desktop.
4931 protected JInternalFrame[] getAllFrames()
4933 JInternalFrame[] frames = null;
4934 // TODO is this necessary - is it safe - risk of hanging?
4939 frames = Desktop.getDesktopPane().getAllFrames();
4940 } catch (ArrayIndexOutOfBoundsException e)
4942 // occasional No such child exceptions are thrown here...
4946 } catch (InterruptedException f)
4950 } while (frames == null);
4955 * Answers true if 'version' is equal to or later than 'supported', where each
4956 * is formatted as major/minor versions like "2.8.3" or "2.3.4b1" for bugfix
4957 * changes. Development and test values for 'version' are leniently treated
4961 * - minimum version we are comparing against
4963 * - version of data being processsed
4966 public static boolean isVersionStringLaterThan(String supported,
4969 if (supported == null || version == null
4970 || version.equalsIgnoreCase("DEVELOPMENT BUILD")
4971 || version.equalsIgnoreCase("Test")
4972 || version.equalsIgnoreCase("AUTOMATED BUILD"))
4974 System.err.println("Assuming project file with "
4975 + (version == null ? "null" : version)
4976 + " is compatible with Jalview version " + supported);
4981 return StringUtils.compareVersions(version, supported, "b") >= 0;
4985 Vector<JalviewStructureDisplayI> newStructureViewers = null;
4987 protected void addNewStructureViewer(JalviewStructureDisplayI sview)
4989 if (newStructureViewers != null)
4991 sview.getBinding().setFinishedLoadingFromArchive(false);
4992 newStructureViewers.add(sview);
4996 protected void setLoadingFinishedForNewStructureViewers()
4998 if (newStructureViewers != null)
5000 for (JalviewStructureDisplayI sview : newStructureViewers)
5002 sview.getBinding().setFinishedLoadingFromArchive(true);
5004 newStructureViewers.clear();
5005 newStructureViewers = null;
5009 AlignFrame loadViewport(String fileName, List<JSeq> JSEQ,
5010 List<SequenceI> hiddenSeqs, AlignmentI al, JalviewModel jm,
5011 Viewport view, String uniqueSeqSetId, String viewId,
5012 List<JvAnnotRow> autoAlan)
5014 AlignFrame af = null;
5015 af = new AlignFrame(al, safeInt(view.getWidth()),
5016 safeInt(view.getHeight()), uniqueSeqSetId, viewId)
5020 // protected void processKeyEvent(java.awt.event.KeyEvent e) {
5021 // System.out.println("Jalview2XML AF " + e);
5022 // super.processKeyEvent(e);
5028 af.alignPanel.setHoldRepaint(true);
5029 af.setFileName(fileName, FileFormat.Jalview);
5030 af.setFileObject(jarFile); // BH 2019 JAL-3436
5032 final AlignViewport viewport = af.getViewport();
5033 for (int i = 0; i < JSEQ.size(); i++)
5035 int colour = safeInt(JSEQ.get(i).getColour());
5036 viewport.setSequenceColour(viewport.getAlignment().getSequenceAt(i),
5042 viewport.setColourByReferenceSeq(true);
5043 viewport.setDisplayReferenceSeq(true);
5046 viewport.setGatherViewsHere(safeBoolean(view.isGatheredViews()));
5048 if (view.getSequenceSetId() != null)
5050 AlignmentViewport av = viewportsAdded.get(uniqueSeqSetId);
5052 viewport.setSequenceSetId(uniqueSeqSetId);
5055 // propagate shared settings to this new view
5056 viewport.setHistoryList(av.getHistoryList());
5057 viewport.setRedoList(av.getRedoList());
5061 viewportsAdded.put(uniqueSeqSetId, viewport);
5063 // TODO: check if this method can be called repeatedly without
5064 // side-effects if alignpanel already registered.
5065 PaintRefresher.Register(af.alignPanel, uniqueSeqSetId);
5067 // apply Hidden regions to view.
5068 if (hiddenSeqs != null)
5070 for (int s = 0; s < JSEQ.size(); s++)
5072 SequenceGroup hidden = new SequenceGroup();
5073 boolean isRepresentative = false;
5074 for (int r = 0; r < JSEQ.get(s).getHiddenSequences().size(); r++)
5076 isRepresentative = true;
5077 SequenceI sequenceToHide = al
5078 .getSequenceAt(JSEQ.get(s).getHiddenSequences().get(r));
5079 hidden.addSequence(sequenceToHide, false);
5080 // remove from hiddenSeqs list so we don't try to hide it twice
5081 hiddenSeqs.remove(sequenceToHide);
5083 if (isRepresentative)
5085 SequenceI representativeSequence = al.getSequenceAt(s);
5086 hidden.addSequence(representativeSequence, false);
5087 viewport.hideRepSequences(representativeSequence, hidden);
5091 SequenceI[] hseqs = hiddenSeqs
5092 .toArray(new SequenceI[hiddenSeqs.size()]);
5093 viewport.hideSequence(hseqs);
5096 // recover view properties and display parameters
5098 viewport.setShowAnnotation(safeBoolean(view.isShowAnnotation()));
5099 viewport.setAbovePIDThreshold(safeBoolean(view.isPidSelected()));
5100 final int pidThreshold = safeInt(view.getPidThreshold());
5101 viewport.setThreshold(pidThreshold);
5103 viewport.setColourText(safeBoolean(view.isShowColourText()));
5105 viewport.setConservationSelected(
5106 safeBoolean(view.isConservationSelected()));
5107 viewport.setIncrement(safeInt(view.getConsThreshold()));
5108 viewport.setShowJVSuffix(safeBoolean(view.isShowFullId()));
5109 viewport.setRightAlignIds(safeBoolean(view.isRightAlignIds()));
5110 viewport.setFont(new Font(view.getFontName(),
5111 safeInt(view.getFontStyle()), safeInt(view.getFontSize())),
5113 ViewStyleI vs = viewport.getViewStyle();
5114 vs.setScaleProteinAsCdna(view.isScaleProteinAsCdna());
5115 viewport.setViewStyle(vs);
5116 // TODO: allow custom charWidth/Heights to be restored by updating them
5117 // after setting font - which means set above to false
5118 viewport.setRenderGaps(safeBoolean(view.isRenderGaps()));
5119 viewport.setWrapAlignment(safeBoolean(view.isWrapAlignment()));
5120 viewport.setShowAnnotation(safeBoolean(view.isShowAnnotation()));
5122 viewport.setShowBoxes(safeBoolean(view.isShowBoxes()));
5124 viewport.setShowText(safeBoolean(view.isShowText()));
5126 viewport.setTextColour(new Color(safeInt(view.getTextCol1())));
5127 viewport.setTextColour2(new Color(safeInt(view.getTextCol2())));
5128 viewport.setThresholdTextColour(safeInt(view.getTextColThreshold()));
5129 viewport.setShowUnconserved(view.isShowUnconserved());
5130 viewport.getRanges().setStartRes(safeInt(view.getStartRes()));
5132 if (view.getViewName() != null)
5134 viewport.setViewName(view.getViewName());
5135 af.setInitialTabVisible();
5137 int x = safeInt(view.getXpos());
5138 int y = safeInt(view.getYpos());
5139 int w = safeInt(view.getWidth());
5140 int h = safeInt(view.getHeight());
5141 // // BH we cannot let the title bar go off the top
5142 // if (Platform.isJS())
5144 // x = Math.max(50 - w, x);
5145 // y = Math.max(0, y);
5148 af.setBounds(x, y, w, h);
5149 // startSeq set in af.alignPanel.updateLayout below
5150 af.alignPanel.updateLayout();
5151 ColourSchemeI cs = null;
5152 // apply colourschemes
5153 if (view.getBgColour() != null)
5155 if (view.getBgColour().startsWith("ucs"))
5157 cs = getUserColourScheme(jm, view.getBgColour());
5159 else if (view.getBgColour().startsWith("Annotation"))
5161 AnnotationColourScheme viewAnnColour = view.getAnnotationColours();
5162 cs = constructAnnotationColour(viewAnnColour, af, al, jm, true);
5169 cs = ColourSchemeProperty.getColourScheme(af.getViewport(), al,
5170 view.getBgColour());
5175 * turn off 'alignment colour applies to all groups'
5176 * while restoring global colour scheme
5178 viewport.setColourAppliesToAllGroups(false);
5179 viewport.setGlobalColourScheme(cs);
5180 viewport.getResidueShading().setThreshold(pidThreshold,
5181 view.isIgnoreGapsinConsensus());
5182 viewport.getResidueShading()
5183 .setConsensus(viewport.getSequenceConsensusHash());
5184 if (safeBoolean(view.isConservationSelected()) && cs != null)
5186 viewport.getResidueShading()
5187 .setConservationInc(safeInt(view.getConsThreshold()));
5189 af.changeColour(cs);
5190 viewport.setColourAppliesToAllGroups(true);
5192 viewport.setShowSequenceFeatures(
5193 safeBoolean(view.isShowSequenceFeatures()));
5195 viewport.setCentreColumnLabels(view.isCentreColumnLabels());
5196 viewport.setIgnoreGapsConsensus(view.isIgnoreGapsinConsensus(), null);
5197 viewport.setFollowHighlight(view.isFollowHighlight());
5198 viewport.followSelection = view.isFollowSelection();
5199 viewport.setShowConsensusHistogram(view.isShowConsensusHistogram());
5200 viewport.setShowSequenceLogo(view.isShowSequenceLogo());
5201 viewport.setNormaliseSequenceLogo(view.isNormaliseSequenceLogo());
5202 viewport.setShowDBRefs(safeBoolean(view.isShowDbRefTooltip()));
5203 viewport.setShowNPFeats(safeBoolean(view.isShowNPfeatureTooltip()));
5204 viewport.setShowGroupConsensus(view.isShowGroupConsensus());
5205 viewport.setShowGroupConservation(view.isShowGroupConservation());
5207 // recover feature settings
5208 if (jm.getFeatureSettings() != null)
5210 FeatureRenderer fr = af.alignPanel.getSeqPanel().seqCanvas
5211 .getFeatureRenderer();
5212 FeaturesDisplayed fdi;
5213 viewport.setFeaturesDisplayed(fdi = new FeaturesDisplayed());
5214 String[] renderOrder = new String[jm.getFeatureSettings().getSetting()
5216 Map<String, FeatureColourI> featureColours = new Hashtable<>();
5217 Map<String, Float> featureOrder = new Hashtable<>();
5219 for (int fs = 0; fs < jm.getFeatureSettings().getSetting()
5222 Setting setting = jm.getFeatureSettings().getSetting().get(fs);
5223 String featureType = setting.getType();
5226 * restore feature filters (if any)
5228 jalview.xml.binding.jalview.FeatureMatcherSet filters = setting
5230 if (filters != null)
5232 FeatureMatcherSetI filter = Jalview2XML.parseFilter(featureType,
5234 if (!filter.isEmpty())
5236 fr.setFeatureFilter(featureType, filter);
5241 * restore feature colour scheme
5243 Color maxColour = new Color(setting.getColour());
5244 if (setting.getMincolour() != null)
5247 * minColour is always set unless a simple colour
5248 * (including for colour by label though it doesn't use it)
5250 Color minColour = new Color(setting.getMincolour().intValue());
5251 Color noValueColour = minColour;
5252 NoValueColour noColour = setting.getNoValueColour();
5253 if (noColour == NoValueColour.NONE)
5255 noValueColour = null;
5257 else if (noColour == NoValueColour.MAX)
5259 noValueColour = maxColour;
5261 float min = safeFloat(safeFloat(setting.getMin()));
5262 float max = setting.getMax() == null ? 1f
5263 : setting.getMax().floatValue();
5264 FeatureColourI gc = new FeatureColour(maxColour, minColour,
5265 maxColour, noValueColour, min, max);
5266 if (setting.getAttributeName().size() > 0)
5268 gc.setAttributeName(setting.getAttributeName().toArray(
5269 new String[setting.getAttributeName().size()]));
5271 if (setting.getThreshold() != null)
5273 gc.setThreshold(setting.getThreshold().floatValue());
5274 int threshstate = safeInt(setting.getThreshstate());
5275 // -1 = None, 0 = Below, 1 = Above threshold
5276 if (threshstate == 0)
5278 gc.setBelowThreshold(true);
5280 else if (threshstate == 1)
5282 gc.setAboveThreshold(true);
5285 gc.setAutoScaled(true); // default
5286 if (setting.isAutoScale() != null)
5288 gc.setAutoScaled(setting.isAutoScale());
5290 if (setting.isColourByLabel() != null)
5292 gc.setColourByLabel(setting.isColourByLabel());
5294 // and put in the feature colour table.
5295 featureColours.put(featureType, gc);
5299 featureColours.put(featureType, new FeatureColour(maxColour));
5301 renderOrder[fs] = featureType;
5302 if (setting.getOrder() != null)
5304 featureOrder.put(featureType, setting.getOrder().floatValue());
5308 featureOrder.put(featureType, new Float(
5309 fs / jm.getFeatureSettings().getSetting().size()));
5311 if (safeBoolean(setting.isDisplay()))
5313 fdi.setVisible(featureType);
5316 Map<String, Boolean> fgtable = new Hashtable<>();
5317 for (int gs = 0; gs < jm.getFeatureSettings().getGroup().size(); gs++)
5319 Group grp = jm.getFeatureSettings().getGroup().get(gs);
5320 fgtable.put(grp.getName(), new Boolean(grp.isDisplay()));
5322 // FeatureRendererSettings frs = new FeatureRendererSettings(renderOrder,
5323 // fgtable, featureColours, jms.getFeatureSettings().hasTransparency() ?
5324 // jms.getFeatureSettings().getTransparency() : 0.0, featureOrder);
5325 FeatureRendererSettings frs = new FeatureRendererSettings(renderOrder,
5326 fgtable, featureColours, 1.0f, featureOrder);
5327 fr.transferSettings(frs);
5330 if (view.getHiddenColumns().size() > 0)
5332 for (int c = 0; c < view.getHiddenColumns().size(); c++)
5334 final HiddenColumns hc = view.getHiddenColumns().get(c);
5335 viewport.hideColumns(safeInt(hc.getStart()),
5336 safeInt(hc.getEnd()) /* +1 */);
5339 if (view.getCalcIdParam() != null)
5341 for (CalcIdParam calcIdParam : view.getCalcIdParam())
5343 if (calcIdParam != null)
5345 if (recoverCalcIdParam(calcIdParam, viewport))
5350 warn("Couldn't recover parameters for "
5351 + calcIdParam.getCalcId());
5356 af.setMenusFromViewport(viewport);
5357 af.setTitle(view.getTitle());
5358 // TODO: we don't need to do this if the viewport is aready visible.
5360 * Add the AlignFrame to the desktop (it may be 'gathered' later), unless it
5361 * has a 'cdna/protein complement' view, in which case save it in order to
5362 * populate a SplitFrame once all views have been read in.
5364 String complementaryViewId = view.getComplementId();
5365 if (complementaryViewId == null)
5367 Dimension dim = Platform.getDimIfEmbedded(af,
5368 safeInt(view.getWidth()), safeInt(view.getHeight()));
5369 Desktop.addInternalFrame(af, view.getTitle(), dim.width, dim.height);
5370 // recompute any autoannotation
5371 af.alignPanel.updateAnnotation(false, true);
5372 reorderAutoannotation(af, al, autoAlan);
5373 af.alignPanel.alignmentChanged();
5377 splitFrameCandidates.put(view, af);
5383 * Reads saved data to restore Colour by Annotation settings
5385 * @param viewAnnColour
5389 * @param checkGroupAnnColour
5392 private ColourSchemeI constructAnnotationColour(
5393 AnnotationColourScheme viewAnnColour, AlignFrame af,
5394 AlignmentI al, JalviewModel model, boolean checkGroupAnnColour)
5396 boolean propagateAnnColour = false;
5397 AlignmentI annAlignment = af != null ? af.getViewport().getAlignment()
5399 if (checkGroupAnnColour && al.getGroups() != null
5400 && al.getGroups().size() > 0)
5402 // pre 2.8.1 behaviour
5403 // check to see if we should transfer annotation colours
5404 propagateAnnColour = true;
5405 for (SequenceGroup sg : al.getGroups())
5407 if (sg.getColourScheme() instanceof AnnotationColourGradient)
5409 propagateAnnColour = false;
5415 * 2.10.2- : saved annotationId is AlignmentAnnotation.annotationId
5417 String annotationId = viewAnnColour.getAnnotation();
5418 AlignmentAnnotation matchedAnnotation = annotationIds.get(annotationId);
5421 * pre 2.10.2: saved annotationId is AlignmentAnnotation.label
5423 if (matchedAnnotation == null
5424 && annAlignment.getAlignmentAnnotation() != null)
5426 for (int i = 0; i < annAlignment.getAlignmentAnnotation().length; i++)
5429 .equals(annAlignment.getAlignmentAnnotation()[i].label))
5431 matchedAnnotation = annAlignment.getAlignmentAnnotation()[i];
5436 if (matchedAnnotation == null)
5438 System.err.println("Failed to match annotation colour scheme for "
5442 if (matchedAnnotation.getThreshold() == null)
5444 matchedAnnotation.setThreshold(
5445 new GraphLine(safeFloat(viewAnnColour.getThreshold()),
5446 "Threshold", Color.black));
5449 AnnotationColourGradient cs = null;
5450 if (viewAnnColour.getColourScheme().equals("None"))
5452 cs = new AnnotationColourGradient(matchedAnnotation,
5453 new Color(safeInt(viewAnnColour.getMinColour())),
5454 new Color(safeInt(viewAnnColour.getMaxColour())),
5455 safeInt(viewAnnColour.getAboveThreshold()));
5457 else if (viewAnnColour.getColourScheme().startsWith("ucs"))
5459 cs = new AnnotationColourGradient(matchedAnnotation,
5460 getUserColourScheme(model, viewAnnColour.getColourScheme()),
5461 safeInt(viewAnnColour.getAboveThreshold()));
5465 cs = new AnnotationColourGradient(matchedAnnotation,
5466 ColourSchemeProperty.getColourScheme(af.getViewport(), al,
5467 viewAnnColour.getColourScheme()),
5468 safeInt(viewAnnColour.getAboveThreshold()));
5471 boolean perSequenceOnly = safeBoolean(viewAnnColour.isPerSequence());
5472 boolean useOriginalColours = safeBoolean(
5473 viewAnnColour.isPredefinedColours());
5474 cs.setSeqAssociated(perSequenceOnly);
5475 cs.setPredefinedColours(useOriginalColours);
5477 if (propagateAnnColour && al.getGroups() != null)
5479 // Also use these settings for all the groups
5480 for (int g = 0; g < al.getGroups().size(); g++)
5482 SequenceGroup sg = al.getGroups().get(g);
5483 if (sg.getGroupColourScheme() == null)
5488 AnnotationColourGradient groupScheme = new AnnotationColourGradient(
5489 matchedAnnotation, sg.getColourScheme(),
5490 safeInt(viewAnnColour.getAboveThreshold()));
5491 sg.setColourScheme(groupScheme);
5492 groupScheme.setSeqAssociated(perSequenceOnly);
5493 groupScheme.setPredefinedColours(useOriginalColours);
5499 private void reorderAutoannotation(AlignFrame af, AlignmentI al,
5500 List<JvAnnotRow> autoAlan)
5502 // copy over visualization settings for autocalculated annotation in the
5504 if (al.getAlignmentAnnotation() != null)
5507 * Kludge for magic autoannotation names (see JAL-811)
5509 String[] magicNames = new String[] { "Consensus", "Quality",
5511 JvAnnotRow nullAnnot = new JvAnnotRow(-1, null);
5512 Hashtable<String, JvAnnotRow> visan = new Hashtable<>();
5513 for (String nm : magicNames)
5515 visan.put(nm, nullAnnot);
5517 for (JvAnnotRow auan : autoAlan)
5519 visan.put(auan.template.label
5520 + (auan.template.getCalcId() == null ? ""
5521 : "\t" + auan.template.getCalcId()),
5524 int hSize = al.getAlignmentAnnotation().length;
5525 List<JvAnnotRow> reorder = new ArrayList<>();
5526 // work through any autoCalculated annotation already on the view
5527 // removing it if it should be placed in a different location on the
5528 // annotation panel.
5529 List<String> remains = new ArrayList<>(visan.keySet());
5530 for (int h = 0; h < hSize; h++)
5532 jalview.datamodel.AlignmentAnnotation jalan = al
5533 .getAlignmentAnnotation()[h];
5534 if (jalan.autoCalculated)
5537 JvAnnotRow valan = visan.get(k = jalan.label);
5538 if (jalan.getCalcId() != null)
5540 valan = visan.get(k = jalan.label + "\t" + jalan.getCalcId());
5545 // delete the auto calculated row from the alignment
5546 al.deleteAnnotation(jalan, false);
5550 if (valan != nullAnnot)
5552 if (jalan != valan.template)
5554 // newly created autoannotation row instance
5555 // so keep a reference to the visible annotation row
5556 // and copy over all relevant attributes
5557 if (valan.template.graphHeight >= 0)
5560 jalan.graphHeight = valan.template.graphHeight;
5562 jalan.visible = valan.template.visible;
5564 reorder.add(new JvAnnotRow(valan.order, jalan));
5569 // Add any (possibly stale) autocalculated rows that were not appended to
5570 // the view during construction
5571 for (String other : remains)
5573 JvAnnotRow othera = visan.get(other);
5574 if (othera != nullAnnot && othera.template.getCalcId() != null
5575 && othera.template.getCalcId().length() > 0)
5577 reorder.add(othera);
5580 // now put the automatic annotation in its correct place
5581 int s = 0, srt[] = new int[reorder.size()];
5582 JvAnnotRow[] rws = new JvAnnotRow[reorder.size()];
5583 for (JvAnnotRow jvar : reorder)
5586 srt[s++] = jvar.order;
5589 jalview.util.QuickSort.sort(srt, rws);
5590 // and re-insert the annotation at its correct position
5591 for (JvAnnotRow jvar : rws)
5593 al.addAnnotation(jvar.template, jvar.order);
5595 af.alignPanel.adjustAnnotationHeight();
5599 Hashtable skipList = null;
5602 * TODO remove this method
5605 * @return AlignFrame bound to sequenceSetId from view, if one exists. private
5606 * AlignFrame getSkippedFrame(Viewport view) { if (skipList==null) {
5607 * throw new Error("Implementation Error. No skipList defined for this
5608 * Jalview2XML instance."); } return (AlignFrame)
5609 * skipList.get(view.getSequenceSetId()); }
5613 * Check if the Jalview view contained in object should be skipped or not.
5616 * @return true if view's sequenceSetId is a key in skipList
5618 private boolean skipViewport(JalviewModel object)
5620 if (skipList == null)
5624 String id = object.getViewport().get(0).getSequenceSetId();
5625 if (skipList.containsKey(id))
5627 if (Cache.log != null && Cache.log.isDebugEnabled())
5629 Cache.log.debug("Skipping seuqence set id " + id);
5636 protected void addToSkipList(AlignFrame af)
5638 if (skipList == null)
5640 skipList = new Hashtable();
5642 skipList.put(af.getViewport().getSequenceSetId(), af);
5645 protected void clearSkipList()
5647 if (skipList != null)
5654 private void recoverDatasetFor(SequenceSet vamsasSet, AlignmentI al,
5655 boolean ignoreUnrefed, String uniqueSeqSetId)
5657 jalview.datamodel.AlignmentI ds = getDatasetFor(
5658 vamsasSet.getDatasetId());
5659 AlignmentI xtant_ds = ds;
5660 if (xtant_ds == null)
5662 // good chance we are about to create a new dataset, but check if we've
5663 // seen some of the dataset sequence IDs before.
5664 // TODO: skip this check if we are working with project generated by
5665 // version 2.11 or later
5666 xtant_ds = checkIfHasDataset(vamsasSet.getSequence());
5667 if (xtant_ds != null)
5670 addDatasetRef(vamsasSet.getDatasetId(), ds);
5673 Vector dseqs = null;
5676 // recovering an alignment View
5677 AlignmentI seqSetDS = getDatasetFor(UNIQSEQSETID + uniqueSeqSetId);
5678 if (seqSetDS != null)
5680 if (ds != null && ds != seqSetDS)
5682 warn("JAL-3171 regression: Overwriting a dataset reference for an alignment"
5683 + " - CDS/Protein crossreference data may be lost");
5684 if (xtant_ds != null)
5686 // This can only happen if the unique sequence set ID was bound to a
5687 // dataset that did not contain any of the sequences in the view
5688 // currently being restored.
5689 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.");
5693 addDatasetRef(vamsasSet.getDatasetId(), ds);
5698 // try even harder to restore dataset
5699 AlignmentI xtantDS = checkIfHasDataset(vamsasSet.getSequence());
5700 // create a list of new dataset sequences
5701 dseqs = new Vector();
5703 for (int i = 0, iSize = vamsasSet.getSequence().size(); i < iSize; i++)
5705 Sequence vamsasSeq = vamsasSet.getSequence().get(i);
5706 ensureJalviewDatasetSequence(vamsasSeq, ds, dseqs, ignoreUnrefed, i);
5708 // create a new dataset
5711 SequenceI[] dsseqs = new SequenceI[dseqs.size()];
5712 dseqs.copyInto(dsseqs);
5713 ds = new jalview.datamodel.Alignment(dsseqs);
5714 // debug("Jalview2XML Created new dataset " + vamsasSet.getDatasetId()
5715 // + " for alignment " + System.identityHashCode(al));
5716 addDatasetRef(vamsasSet.getDatasetId(), ds);
5718 // set the dataset for the newly imported alignment.
5719 if (al.getDataset() == null && !ignoreUnrefed)
5722 // register dataset for the alignment's uniqueSeqSetId for legacy projects
5723 addDatasetRef(UNIQSEQSETID + uniqueSeqSetId, ds);
5725 updateSeqDatasetBinding(vamsasSet.getSequence(), ds);
5729 * XML dataset sequence ID to materialised dataset reference
5731 HashMap<String, AlignmentI> seqToDataset = new HashMap<>();
5734 * @return the first materialised dataset reference containing a dataset
5735 * sequence referenced in the given view
5737 * - sequences from the view
5739 AlignmentI checkIfHasDataset(List<Sequence> list)
5741 for (Sequence restoredSeq : list)
5743 AlignmentI datasetFor = seqToDataset.get(restoredSeq.getDsseqid());
5744 if (datasetFor != null)
5753 * Register ds as the containing dataset for the dataset sequences referenced
5754 * by sequences in list
5757 * - sequences in a view
5760 void updateSeqDatasetBinding(List<Sequence> list, AlignmentI ds)
5762 for (Sequence restoredSeq : list)
5764 AlignmentI prevDS = seqToDataset.put(restoredSeq.getDsseqid(), ds);
5765 if (prevDS != null && prevDS != ds)
5767 warn("Dataset sequence appears in many datasets: "
5768 + restoredSeq.getDsseqid());
5769 // TODO: try to merge!
5776 * sequence definition to create/merge dataset sequence for
5780 * vector to add new dataset sequence to
5781 * @param ignoreUnrefed
5782 * - when true, don't create new sequences from vamsasSeq if it's id
5783 * doesn't already have an asssociated Jalview sequence.
5785 * - used to reorder the sequence in the alignment according to the
5786 * vamsasSeq array ordering, to preserve ordering of dataset
5788 private void ensureJalviewDatasetSequence(Sequence vamsasSeq,
5789 AlignmentI ds, Vector dseqs, boolean ignoreUnrefed, int vseqpos)
5791 // JBP TODO: Check this is called for AlCodonFrames to support recovery of
5793 SequenceI sq = seqRefIds.get(vamsasSeq.getId());
5794 boolean reorder = false;
5795 SequenceI dsq = null;
5796 if (sq != null && sq.getDatasetSequence() != null)
5798 dsq = sq.getDatasetSequence();
5804 if (sq == null && ignoreUnrefed)
5808 String sqid = vamsasSeq.getDsseqid();
5811 // need to create or add a new dataset sequence reference to this sequence
5814 dsq = seqRefIds.get(sqid);
5819 // make a new dataset sequence
5820 dsq = sq.createDatasetSequence();
5823 // make up a new dataset reference for this sequence
5824 sqid = seqHash(dsq);
5826 dsq.setVamsasId(uniqueSetSuffix + sqid);
5827 seqRefIds.put(sqid, dsq);
5832 dseqs.addElement(dsq);
5837 ds.addSequence(dsq);
5843 { // make this dataset sequence sq's dataset sequence
5844 sq.setDatasetSequence(dsq);
5845 // and update the current dataset alignment
5850 if (!dseqs.contains(dsq))
5857 if (ds.findIndex(dsq) < 0)
5859 ds.addSequence(dsq);
5866 // TODO: refactor this as a merge dataset sequence function
5867 // now check that sq (the dataset sequence) sequence really is the union of
5868 // all references to it
5869 // boolean pre = sq.getStart() < dsq.getStart();
5870 // boolean post = sq.getEnd() > dsq.getEnd();
5874 // StringBuffer sb = new StringBuffer();
5875 String newres = jalview.analysis.AlignSeq.extractGaps(
5876 jalview.util.Comparison.GapChars, sq.getSequenceAsString());
5877 if (!newres.equalsIgnoreCase(dsq.getSequenceAsString())
5878 && newres.length() > dsq.getLength())
5880 // Update with the longer sequence.
5884 * if (pre) { sb.insert(0, newres .substring(0, dsq.getStart() -
5885 * sq.getStart())); dsq.setStart(sq.getStart()); } if (post) {
5886 * sb.append(newres.substring(newres.length() - sq.getEnd() -
5887 * dsq.getEnd())); dsq.setEnd(sq.getEnd()); }
5889 dsq.setSequence(newres);
5891 // TODO: merges will never happen if we 'know' we have the real dataset
5892 // sequence - this should be detected when id==dssid
5894 "DEBUG Notice: Merged dataset sequence (if you see this often, post at http://issues.jalview.org/browse/JAL-1474)"); // ("
5895 // + (pre ? "prepended" : "") + " "
5896 // + (post ? "appended" : ""));
5901 // sequence refs are identical. We may need to update the existing dataset
5902 // alignment with this one, though.
5903 if (ds != null && dseqs == null)
5905 int opos = ds.findIndex(dsq);
5906 SequenceI tseq = null;
5907 if (opos != -1 && vseqpos != opos)
5909 // remove from old position
5910 ds.deleteSequence(dsq);
5912 if (vseqpos < ds.getHeight())
5914 if (vseqpos != opos)
5916 // save sequence at destination position
5917 tseq = ds.getSequenceAt(vseqpos);
5918 ds.replaceSequenceAt(vseqpos, dsq);
5919 ds.addSequence(tseq);
5924 ds.addSequence(dsq);
5931 * TODO use AlignmentI here and in related methods - needs
5932 * AlignmentI.getDataset() changed to return AlignmentI instead of Alignment
5934 Hashtable<String, AlignmentI> datasetIds = null;
5936 IdentityHashMap<AlignmentI, String> dataset2Ids = null;
5938 private AlignmentI getDatasetFor(String datasetId)
5940 if (datasetIds == null)
5942 datasetIds = new Hashtable<>();
5945 if (datasetIds.containsKey(datasetId))
5947 return datasetIds.get(datasetId);
5952 private void addDatasetRef(String datasetId, AlignmentI dataset)
5954 if (datasetIds == null)
5956 datasetIds = new Hashtable<>();
5958 datasetIds.put(datasetId, dataset);
5962 * make a new dataset ID for this jalview dataset alignment
5967 private String getDatasetIdRef(AlignmentI dataset)
5969 if (dataset.getDataset() != null)
5971 warn("Serious issue! Dataset Object passed to getDatasetIdRef is not a Jalview DATASET alignment...");
5973 String datasetId = makeHashCode(dataset, null);
5974 if (datasetId == null)
5976 // make a new datasetId and record it
5977 if (dataset2Ids == null)
5979 dataset2Ids = new IdentityHashMap<>();
5983 datasetId = dataset2Ids.get(dataset);
5985 if (datasetId == null)
5987 datasetId = "ds" + dataset2Ids.size() + 1;
5988 dataset2Ids.put(dataset, datasetId);
5994 private void addDBRefs(SequenceI datasetSequence, Sequence sequence)
5996 for (int d = 0; d < sequence.getDBRef().size(); d++)
5998 DBRef dr = sequence.getDBRef().get(d);
5999 jalview.datamodel.DBRefEntry entry = new jalview.datamodel.DBRefEntry(
6000 dr.getSource(), dr.getVersion(), dr.getAccessionId());
6001 if (dr.getMapping() != null)
6003 entry.setMap(addMapping(dr.getMapping()));
6005 datasetSequence.addDBRef(entry);
6009 private jalview.datamodel.Mapping addMapping(Mapping m)
6011 SequenceI dsto = null;
6012 // Mapping m = dr.getMapping();
6013 int fr[] = new int[m.getMapListFrom().size() * 2];
6014 Iterator<MapListFrom> from = m.getMapListFrom().iterator();// enumerateMapListFrom();
6015 for (int _i = 0; from.hasNext(); _i += 2)
6017 MapListFrom mf = from.next();
6018 fr[_i] = mf.getStart();
6019 fr[_i + 1] = mf.getEnd();
6021 int fto[] = new int[m.getMapListTo().size() * 2];
6022 Iterator<MapListTo> to = m.getMapListTo().iterator();// enumerateMapListTo();
6023 for (int _i = 0; to.hasNext(); _i += 2)
6025 MapListTo mf = to.next();
6026 fto[_i] = mf.getStart();
6027 fto[_i + 1] = mf.getEnd();
6029 jalview.datamodel.Mapping jmap = new jalview.datamodel.Mapping(dsto, fr,
6030 fto, m.getMapFromUnit().intValue(),
6031 m.getMapToUnit().intValue());
6034 * (optional) choice of dseqFor or Sequence
6036 if (m.getDseqFor() != null)
6038 String dsfor = m.getDseqFor();
6039 if (seqRefIds.containsKey(dsfor))
6044 jmap.setTo(seqRefIds.get(dsfor));
6048 frefedSequence.add(newMappingRef(dsfor, jmap));
6051 else if (m.getSequence() != null)
6054 * local sequence definition
6056 Sequence ms = m.getSequence();
6057 SequenceI djs = null;
6058 String sqid = ms.getDsseqid();
6059 if (sqid != null && sqid.length() > 0)
6062 * recover dataset sequence
6064 djs = seqRefIds.get(sqid);
6069 "Warning - making up dataset sequence id for DbRef sequence map reference");
6070 sqid = ((Object) ms).toString(); // make up a new hascode for
6071 // undefined dataset sequence hash
6072 // (unlikely to happen)
6078 * make a new dataset sequence and add it to refIds hash
6080 djs = new jalview.datamodel.Sequence(ms.getName(),
6082 djs.setStart(jmap.getMap().getToLowest());
6083 djs.setEnd(jmap.getMap().getToHighest());
6084 djs.setVamsasId(uniqueSetSuffix + sqid);
6086 incompleteSeqs.put(sqid, djs);
6087 seqRefIds.put(sqid, djs);
6090 jalview.bin.Cache.log.debug("about to recurse on addDBRefs.");
6099 * Provides a 'copy' of an alignment view (on action New View) by 'saving' the
6100 * view as XML (but not to file), and then reloading it
6105 public AlignmentPanel copyAlignPanel(AlignmentPanel ap)
6108 JalviewModel jm = saveState(ap, null, null, null);
6111 jm.getVamsasModel().getSequenceSet().get(0).getDatasetId(),
6112 ap.getAlignment().getDataset());
6114 uniqueSetSuffix = "";
6115 // jm.getJalviewModelSequence().getViewport(0).setId(null);
6116 jm.getViewport().get(0).setId(null);
6117 // we don't overwrite the view we just copied
6119 if (this.frefedSequence == null)
6121 frefedSequence = new Vector<>();
6124 viewportsAdded.clear();
6126 AlignFrame af = loadFromObject(jm, null, false, null);
6127 af.getAlignPanels().clear();
6128 af.closeMenuItem_actionPerformed(true);
6129 af.alignPanel.setHoldRepaint(false);
6130 this.jarFile = null;
6132 return af.alignPanel;
6135 private Hashtable jvids2vobj;
6137 private void warn(String msg)
6142 private void warn(String msg, Exception e)
6144 if (Cache.log != null)
6148 Cache.log.warn(msg, e);
6152 Cache.log.warn(msg);
6157 System.err.println("Warning: " + msg);
6160 e.printStackTrace();
6165 private void debug(String string)
6167 debug(string, null);
6170 private void debug(String msg, Exception e)
6172 if (Cache.log != null)
6176 Cache.log.debug(msg, e);
6180 Cache.log.debug(msg);
6185 System.err.println("Warning: " + msg);
6188 e.printStackTrace();
6194 * set the object to ID mapping tables used to write/recover objects and XML
6195 * ID strings for the jalview project. If external tables are provided then
6196 * finalize and clearSeqRefs will not clear the tables when the Jalview2XML
6197 * object goes out of scope. - also populates the datasetIds hashtable with
6198 * alignment objects containing dataset sequences
6201 * Map from ID strings to jalview datamodel
6203 * Map from jalview datamodel to ID strings
6207 public void setObjectMappingTables(Hashtable vobj2jv,
6208 IdentityHashMap jv2vobj)
6210 this.jv2vobj = jv2vobj;
6211 this.vobj2jv = vobj2jv;
6212 Iterator ds = jv2vobj.keySet().iterator();
6214 while (ds.hasNext())
6216 Object jvobj = ds.next();
6217 id = jv2vobj.get(jvobj).toString();
6218 if (jvobj instanceof jalview.datamodel.Alignment)
6220 if (((jalview.datamodel.Alignment) jvobj).getDataset() == null)
6222 addDatasetRef(id, (jalview.datamodel.Alignment) jvobj);
6225 else if (jvobj instanceof jalview.datamodel.Sequence)
6227 // register sequence object so the XML parser can recover it.
6228 if (seqRefIds == null)
6230 seqRefIds = new HashMap<>();
6232 if (seqsToIds == null)
6234 seqsToIds = new IdentityHashMap<>();
6236 seqRefIds.put(jv2vobj.get(jvobj).toString(), (SequenceI) jvobj);
6237 seqsToIds.put((SequenceI) jvobj, id);
6239 else if (jvobj instanceof jalview.datamodel.AlignmentAnnotation)
6242 AlignmentAnnotation jvann = (AlignmentAnnotation) jvobj;
6243 annotationIds.put(anid = jv2vobj.get(jvobj).toString(), jvann);
6244 if (jvann.annotationId == null)
6246 jvann.annotationId = anid;
6248 if (!jvann.annotationId.equals(anid))
6250 // TODO verify that this is the correct behaviour
6251 this.warn("Overriding Annotation ID for " + anid
6252 + " from different id : " + jvann.annotationId);
6253 jvann.annotationId = anid;
6256 else if (jvobj instanceof String)
6258 if (jvids2vobj == null)
6260 jvids2vobj = new Hashtable();
6261 jvids2vobj.put(jvobj, jv2vobj.get(jvobj).toString());
6266 Cache.log.debug("Ignoring " + jvobj.getClass() + " (ID = " + id);
6272 * set the uniqueSetSuffix used to prefix/suffix object IDs for jalview
6273 * objects created from the project archive. If string is null (default for
6274 * construction) then suffix will be set automatically.
6278 public void setUniqueSetSuffix(String string)
6280 uniqueSetSuffix = string;
6285 * uses skipList2 as the skipList for skipping views on sequence sets
6286 * associated with keys in the skipList
6290 public void setSkipList(Hashtable skipList2)
6292 skipList = skipList2;
6296 * Reads the jar entry of given name and returns its contents, or null if the
6297 * entry is not found.
6300 * @param jarEntryName
6303 protected String readJarEntry(jarInputStreamProvider jprovider,
6304 String jarEntryName)
6306 String result = null;
6307 BufferedReader in = null;
6312 * Reopen the jar input stream and traverse its entries to find a matching
6315 JarInputStream jin = jprovider.getJarInputStream();
6316 JarEntry entry = null;
6319 entry = jin.getNextJarEntry();
6320 } while (entry != null && !entry.getName().equals(jarEntryName));
6324 StringBuilder out = new StringBuilder(256);
6325 in = new BufferedReader(new InputStreamReader(jin, UTF_8));
6328 while ((data = in.readLine()) != null)
6332 result = out.toString();
6336 warn("Couldn't find entry in Jalview Jar for " + jarEntryName);
6338 } catch (Exception ex)
6340 ex.printStackTrace();
6348 } catch (IOException e)
6359 * Returns an incrementing counter (0, 1, 2...)
6363 private synchronized int nextCounter()
6369 * Loads any saved PCA viewers
6374 protected void loadPCAViewers(JalviewModel model, AlignmentPanel ap)
6378 List<PcaViewer> pcaviewers = model.getPcaViewer();
6379 for (PcaViewer viewer : pcaviewers)
6381 String modelName = viewer.getScoreModelName();
6382 SimilarityParamsI params = new SimilarityParams(
6383 viewer.isIncludeGappedColumns(), viewer.isMatchGaps(),
6384 viewer.isIncludeGaps(),
6385 viewer.isDenominateByShortestLength());
6388 * create the panel (without computing the PCA)
6390 PCAPanel panel = new PCAPanel(ap, modelName, params);
6392 panel.setTitle(viewer.getTitle());
6393 panel.setBounds(new Rectangle(viewer.getXpos(), viewer.getYpos(),
6394 viewer.getWidth(), viewer.getHeight()));
6396 boolean showLabels = viewer.isShowLabels();
6397 panel.setShowLabels(showLabels);
6398 panel.getRotatableCanvas().setShowLabels(showLabels);
6399 panel.getRotatableCanvas()
6400 .setBgColour(new Color(viewer.getBgColour()));
6401 panel.getRotatableCanvas()
6402 .setApplyToAllViews(viewer.isLinkToAllViews());
6405 * load PCA output data
6407 ScoreModelI scoreModel = ScoreModels.getInstance()
6408 .getScoreModel(modelName, ap);
6409 PCA pca = new PCA(null, scoreModel, params);
6410 PcaDataType pcaData = viewer.getPcaData();
6412 MatrixI pairwise = loadDoubleMatrix(pcaData.getPairwiseMatrix());
6413 pca.setPairwiseScores(pairwise);
6415 MatrixI triDiag = loadDoubleMatrix(pcaData.getTridiagonalMatrix());
6416 pca.setTridiagonal(triDiag);
6418 MatrixI result = loadDoubleMatrix(pcaData.getEigenMatrix());
6419 pca.setEigenmatrix(result);
6421 panel.getPcaModel().setPCA(pca);
6424 * we haven't saved the input data! (JAL-2647 to do)
6426 panel.setInputData(null);
6429 * add the sequence points for the PCA display
6431 List<jalview.datamodel.SequencePoint> seqPoints = new ArrayList<>();
6432 for (SequencePoint sp : viewer.getSequencePoint())
6434 String seqId = sp.getSequenceRef();
6435 SequenceI seq = seqRefIds.get(seqId);
6438 throw new IllegalStateException(
6439 "Unmatched seqref for PCA: " + seqId);
6441 Point pt = new Point(sp.getXPos(), sp.getYPos(), sp.getZPos());
6442 jalview.datamodel.SequencePoint seqPoint = new jalview.datamodel.SequencePoint(
6444 seqPoints.add(seqPoint);
6446 panel.getRotatableCanvas().setPoints(seqPoints, seqPoints.size());
6449 * set min-max ranges and scale after setPoints (which recomputes them)
6451 panel.getRotatableCanvas().setScaleFactor(viewer.getScaleFactor());
6452 SeqPointMin spMin = viewer.getSeqPointMin();
6453 float[] min = new float[] { spMin.getXPos(), spMin.getYPos(),
6455 SeqPointMax spMax = viewer.getSeqPointMax();
6456 float[] max = new float[] { spMax.getXPos(), spMax.getYPos(),
6458 panel.getRotatableCanvas().setSeqMinMax(min, max);
6460 // todo: hold points list in PCAModel only
6461 panel.getPcaModel().setSequencePoints(seqPoints);
6463 panel.setSelectedDimensionIndex(viewer.getXDim(), X);
6464 panel.setSelectedDimensionIndex(viewer.getYDim(), Y);
6465 panel.setSelectedDimensionIndex(viewer.getZDim(), Z);
6467 // is this duplication needed?
6468 panel.setTop(seqPoints.size() - 1);
6469 panel.getPcaModel().setTop(seqPoints.size() - 1);
6472 * add the axes' end points for the display
6474 for (int i = 0; i < 3; i++)
6476 Axis axis = viewer.getAxis().get(i);
6477 panel.getRotatableCanvas().getAxisEndPoints()[i] = new Point(
6478 axis.getXPos(), axis.getYPos(), axis.getZPos());
6481 Dimension dim = Platform.getDimIfEmbedded(panel, 475, 450);
6482 Desktop.addInternalFrame(panel, MessageManager.formatMessage(
6483 "label.calc_title", "PCA", modelName), dim.width,
6486 } catch (Exception ex)
6488 Cache.log.error("Error loading PCA: " + ex.toString());
6493 * Populates an XML model of the feature colour scheme for one feature type
6495 * @param featureType
6499 public static Colour marshalColour(
6500 String featureType, FeatureColourI fcol)
6502 Colour col = new Colour();
6503 if (fcol.isSimpleColour())
6505 col.setRGB(Format.getHexString(fcol.getColour()));
6509 col.setRGB(Format.getHexString(fcol.getMaxColour()));
6510 col.setMin(fcol.getMin());
6511 col.setMax(fcol.getMax());
6512 col.setMinRGB(jalview.util.Format.getHexString(fcol.getMinColour()));
6513 col.setAutoScale(fcol.isAutoScaled());
6514 col.setThreshold(fcol.getThreshold());
6515 col.setColourByLabel(fcol.isColourByLabel());
6516 col.setThreshType(fcol.isAboveThreshold() ? ThresholdType.ABOVE
6517 : (fcol.isBelowThreshold() ? ThresholdType.BELOW
6518 : ThresholdType.NONE));
6519 if (fcol.isColourByAttribute())
6521 final String[] attName = fcol.getAttributeName();
6522 col.getAttributeName().add(attName[0]);
6523 if (attName.length > 1)
6525 col.getAttributeName().add(attName[1]);
6528 Color noColour = fcol.getNoColour();
6529 if (noColour == null)
6531 col.setNoValueColour(NoValueColour.NONE);
6533 else if (noColour == fcol.getMaxColour())
6535 col.setNoValueColour(NoValueColour.MAX);
6539 col.setNoValueColour(NoValueColour.MIN);
6542 col.setName(featureType);
6547 * Populates an XML model of the feature filter(s) for one feature type
6549 * @param firstMatcher
6550 * the first (or only) match condition)
6552 * remaining match conditions (if any)
6554 * if true, conditions are and-ed, else or-ed
6556 public static jalview.xml.binding.jalview.FeatureMatcherSet marshalFilter(
6557 FeatureMatcherI firstMatcher, Iterator<FeatureMatcherI> filters,
6560 jalview.xml.binding.jalview.FeatureMatcherSet result = new jalview.xml.binding.jalview.FeatureMatcherSet();
6562 if (filters.hasNext())
6567 CompoundMatcher compound = new CompoundMatcher();
6568 compound.setAnd(and);
6569 jalview.xml.binding.jalview.FeatureMatcherSet matcher1 = marshalFilter(
6570 firstMatcher, Collections.emptyIterator(), and);
6571 // compound.addMatcherSet(matcher1);
6572 compound.getMatcherSet().add(matcher1);
6573 FeatureMatcherI nextMatcher = filters.next();
6574 jalview.xml.binding.jalview.FeatureMatcherSet matcher2 = marshalFilter(
6575 nextMatcher, filters, and);
6576 // compound.addMatcherSet(matcher2);
6577 compound.getMatcherSet().add(matcher2);
6578 result.setCompoundMatcher(compound);
6583 * single condition matcher
6585 // MatchCondition matcherModel = new MatchCondition();
6586 jalview.xml.binding.jalview.FeatureMatcher matcherModel = new jalview.xml.binding.jalview.FeatureMatcher();
6587 matcherModel.setCondition(
6588 firstMatcher.getMatcher().getCondition().getStableName());
6589 matcherModel.setValue(firstMatcher.getMatcher().getPattern());
6590 if (firstMatcher.isByAttribute())
6592 matcherModel.setBy(FilterBy.BY_ATTRIBUTE);
6593 // matcherModel.setAttributeName(firstMatcher.getAttribute());
6594 String[] attName = firstMatcher.getAttribute();
6595 matcherModel.getAttributeName().add(attName[0]); // attribute
6596 if (attName.length > 1)
6598 matcherModel.getAttributeName().add(attName[1]); // sub-attribute
6601 else if (firstMatcher.isByLabel())
6603 matcherModel.setBy(FilterBy.BY_LABEL);
6605 else if (firstMatcher.isByScore())
6607 matcherModel.setBy(FilterBy.BY_SCORE);
6609 result.setMatchCondition(matcherModel);
6616 * Loads one XML model of a feature filter to a Jalview object
6618 * @param featureType
6619 * @param matcherSetModel
6622 public static FeatureMatcherSetI parseFilter(
6624 jalview.xml.binding.jalview.FeatureMatcherSet matcherSetModel)
6626 FeatureMatcherSetI result = new FeatureMatcherSet();
6629 parseFilterConditions(result, matcherSetModel, true);
6630 } catch (IllegalStateException e)
6632 // mixing AND and OR conditions perhaps
6634 String.format("Error reading filter conditions for '%s': %s",
6635 featureType, e.getMessage()));
6636 // return as much as was parsed up to the error
6643 * Adds feature match conditions to matcherSet as unmarshalled from XML
6644 * (possibly recursively for compound conditions)
6647 * @param matcherSetModel
6649 * if true, multiple conditions are AND-ed, else they are OR-ed
6650 * @throws IllegalStateException
6651 * if AND and OR conditions are mixed
6653 protected static void parseFilterConditions(
6654 FeatureMatcherSetI matcherSet,
6655 jalview.xml.binding.jalview.FeatureMatcherSet matcherSetModel,
6658 jalview.xml.binding.jalview.FeatureMatcher mc = matcherSetModel
6659 .getMatchCondition();
6665 FilterBy filterBy = mc.getBy();
6666 Condition cond = Condition.fromString(mc.getCondition());
6667 String pattern = mc.getValue();
6668 FeatureMatcherI matchCondition = null;
6669 if (filterBy == FilterBy.BY_LABEL)
6671 matchCondition = FeatureMatcher.byLabel(cond, pattern);
6673 else if (filterBy == FilterBy.BY_SCORE)
6675 matchCondition = FeatureMatcher.byScore(cond, pattern);
6678 else if (filterBy == FilterBy.BY_ATTRIBUTE)
6680 final List<String> attributeName = mc.getAttributeName();
6681 String[] attNames = attributeName
6682 .toArray(new String[attributeName.size()]);
6683 matchCondition = FeatureMatcher.byAttribute(cond, pattern,
6688 * note this throws IllegalStateException if AND-ing to a
6689 * previously OR-ed compound condition, or vice versa
6693 matcherSet.and(matchCondition);
6697 matcherSet.or(matchCondition);
6703 * compound condition
6705 List<jalview.xml.binding.jalview.FeatureMatcherSet> matchers = matcherSetModel
6706 .getCompoundMatcher().getMatcherSet();
6707 boolean anded = matcherSetModel.getCompoundMatcher().isAnd();
6708 if (matchers.size() == 2)
6710 parseFilterConditions(matcherSet, matchers.get(0), anded);
6711 parseFilterConditions(matcherSet, matchers.get(1), anded);
6715 System.err.println("Malformed compound filter condition");
6721 * Loads one XML model of a feature colour to a Jalview object
6723 * @param colourModel
6726 public static FeatureColourI parseColour(Colour colourModel)
6728 FeatureColourI colour = null;
6730 if (colourModel.getMax() != null)
6732 Color mincol = null;
6733 Color maxcol = null;
6734 Color noValueColour = null;
6738 mincol = new Color(Integer.parseInt(colourModel.getMinRGB(), 16));
6739 maxcol = new Color(Integer.parseInt(colourModel.getRGB(), 16));
6740 } catch (Exception e)
6742 Cache.log.warn("Couldn't parse out graduated feature color.", e);
6745 NoValueColour noCol = colourModel.getNoValueColour();
6746 if (noCol == NoValueColour.MIN)
6748 noValueColour = mincol;
6750 else if (noCol == NoValueColour.MAX)
6752 noValueColour = maxcol;
6755 colour = new FeatureColour(maxcol, mincol, maxcol, noValueColour,
6756 safeFloat(colourModel.getMin()),
6757 safeFloat(colourModel.getMax()));
6758 final List<String> attributeName = colourModel.getAttributeName();
6759 String[] attributes = attributeName
6760 .toArray(new String[attributeName.size()]);
6761 if (attributes != null && attributes.length > 0)
6763 colour.setAttributeName(attributes);
6765 if (colourModel.isAutoScale() != null)
6767 colour.setAutoScaled(colourModel.isAutoScale().booleanValue());
6769 if (colourModel.isColourByLabel() != null)
6771 colour.setColourByLabel(
6772 colourModel.isColourByLabel().booleanValue());
6774 if (colourModel.getThreshold() != null)
6776 colour.setThreshold(colourModel.getThreshold().floatValue());
6778 ThresholdType ttyp = colourModel.getThreshType();
6779 if (ttyp == ThresholdType.ABOVE)
6781 colour.setAboveThreshold(true);
6783 else if (ttyp == ThresholdType.BELOW)
6785 colour.setBelowThreshold(true);
6790 Color color = new Color(Integer.parseInt(colourModel.getRGB(), 16));
6791 colour = new FeatureColour(color);