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.bin.Jalview;
39 import jalview.datamodel.AlignedCodonFrame;
40 import jalview.datamodel.Alignment;
41 import jalview.datamodel.AlignmentAnnotation;
42 import jalview.datamodel.AlignmentI;
43 import jalview.datamodel.DBRefEntry;
44 import jalview.datamodel.GraphLine;
45 import jalview.datamodel.PDBEntry;
46 import jalview.datamodel.Point;
47 import jalview.datamodel.RnaViewerModel;
48 import jalview.datamodel.SequenceFeature;
49 import jalview.datamodel.SequenceGroup;
50 import jalview.datamodel.SequenceI;
51 import jalview.datamodel.StructureViewerModel;
52 import jalview.datamodel.StructureViewerModel.StructureData;
53 import jalview.datamodel.features.FeatureMatcher;
54 import jalview.datamodel.features.FeatureMatcherI;
55 import jalview.datamodel.features.FeatureMatcherSet;
56 import jalview.datamodel.features.FeatureMatcherSetI;
57 import jalview.ext.varna.RnaModel;
58 import jalview.gui.AlignFrame;
59 import jalview.gui.AlignViewport;
60 import jalview.gui.AlignmentPanel;
61 import jalview.gui.AppVarna;
62 import jalview.gui.ChimeraViewFrame;
63 import jalview.gui.Desktop;
64 import jalview.gui.FeatureRenderer;
65 import jalview.gui.JvOptionPane;
66 import jalview.gui.OOMWarning;
67 import jalview.gui.PCAPanel;
68 import jalview.gui.PaintRefresher;
69 import jalview.gui.SplitFrame;
70 import jalview.gui.StructureViewer;
71 import jalview.gui.StructureViewer.ViewerType;
72 import jalview.gui.StructureViewerBase;
73 import jalview.gui.TreePanel;
74 import jalview.io.BackupFiles;
75 import jalview.io.DataSourceType;
76 import jalview.io.FileFormat;
77 import jalview.io.NewickFile;
78 import jalview.math.Matrix;
79 import jalview.math.MatrixI;
80 import jalview.renderer.ResidueShaderI;
81 import jalview.schemes.AnnotationColourGradient;
82 import jalview.schemes.ColourSchemeI;
83 import jalview.schemes.ColourSchemeProperty;
84 import jalview.schemes.FeatureColour;
85 import jalview.schemes.ResidueProperties;
86 import jalview.schemes.UserColourScheme;
87 import jalview.structures.models.AAStructureBindingModel;
88 import jalview.util.Format;
89 import jalview.util.MessageManager;
90 import jalview.util.Platform;
91 import jalview.util.StringUtils;
92 import jalview.util.jarInputStreamProvider;
93 import jalview.util.matcher.Condition;
94 import jalview.viewmodel.AlignmentViewport;
95 import jalview.viewmodel.PCAModel;
96 import jalview.viewmodel.ViewportRanges;
97 import jalview.viewmodel.seqfeatures.FeatureRendererSettings;
98 import jalview.viewmodel.seqfeatures.FeaturesDisplayed;
99 import jalview.ws.jws2.Jws2Discoverer;
100 import jalview.ws.jws2.dm.AAConSettings;
101 import jalview.ws.jws2.jabaws2.Jws2Instance;
102 import jalview.ws.params.ArgumentI;
103 import jalview.ws.params.AutoCalcSetting;
104 import jalview.ws.params.WsParamSetI;
105 import jalview.xml.binding.jalview.AlcodonFrame;
106 import jalview.xml.binding.jalview.AlcodonFrame.AlcodMap;
107 import jalview.xml.binding.jalview.Annotation;
108 import jalview.xml.binding.jalview.Annotation.ThresholdLine;
109 import jalview.xml.binding.jalview.AnnotationColourScheme;
110 import jalview.xml.binding.jalview.AnnotationElement;
111 import jalview.xml.binding.jalview.DoubleMatrix;
112 import jalview.xml.binding.jalview.DoubleVector;
113 import jalview.xml.binding.jalview.Feature;
114 import jalview.xml.binding.jalview.Feature.OtherData;
115 import jalview.xml.binding.jalview.FeatureMatcherSet.CompoundMatcher;
116 import jalview.xml.binding.jalview.FilterBy;
117 import jalview.xml.binding.jalview.JalviewModel;
118 import jalview.xml.binding.jalview.JalviewModel.FeatureSettings;
119 import jalview.xml.binding.jalview.JalviewModel.FeatureSettings.Group;
120 import jalview.xml.binding.jalview.JalviewModel.FeatureSettings.Setting;
121 import jalview.xml.binding.jalview.JalviewModel.JGroup;
122 import jalview.xml.binding.jalview.JalviewModel.JSeq;
123 import jalview.xml.binding.jalview.JalviewModel.JSeq.Pdbids;
124 import jalview.xml.binding.jalview.JalviewModel.JSeq.Pdbids.StructureState;
125 import jalview.xml.binding.jalview.JalviewModel.JSeq.RnaViewer;
126 import jalview.xml.binding.jalview.JalviewModel.JSeq.RnaViewer.SecondaryStructure;
127 import jalview.xml.binding.jalview.JalviewModel.PcaViewer;
128 import jalview.xml.binding.jalview.JalviewModel.PcaViewer.Axis;
129 import jalview.xml.binding.jalview.JalviewModel.PcaViewer.SeqPointMax;
130 import jalview.xml.binding.jalview.JalviewModel.PcaViewer.SeqPointMin;
131 import jalview.xml.binding.jalview.JalviewModel.PcaViewer.SequencePoint;
132 import jalview.xml.binding.jalview.JalviewModel.Tree;
133 import jalview.xml.binding.jalview.JalviewModel.UserColours;
134 import jalview.xml.binding.jalview.JalviewModel.Viewport;
135 import jalview.xml.binding.jalview.JalviewModel.Viewport.CalcIdParam;
136 import jalview.xml.binding.jalview.JalviewModel.Viewport.HiddenColumns;
137 import jalview.xml.binding.jalview.JalviewUserColours;
138 import jalview.xml.binding.jalview.JalviewUserColours.Colour;
139 import jalview.xml.binding.jalview.MapListType.MapListFrom;
140 import jalview.xml.binding.jalview.MapListType.MapListTo;
141 import jalview.xml.binding.jalview.Mapping;
142 import jalview.xml.binding.jalview.NoValueColour;
143 import jalview.xml.binding.jalview.ObjectFactory;
144 import jalview.xml.binding.jalview.PcaDataType;
145 import jalview.xml.binding.jalview.Pdbentry.Property;
146 import jalview.xml.binding.jalview.Sequence;
147 import jalview.xml.binding.jalview.Sequence.DBRef;
148 import jalview.xml.binding.jalview.SequenceSet;
149 import jalview.xml.binding.jalview.SequenceSet.SequenceSetProperties;
150 import jalview.xml.binding.jalview.ThresholdType;
151 import jalview.xml.binding.jalview.VAMSAS;
153 import java.awt.Color;
154 import java.awt.Dimension;
155 import java.awt.Font;
156 import java.awt.Rectangle;
157 import java.io.BufferedReader;
158 import java.io.ByteArrayInputStream;
159 import java.io.DataInputStream;
160 import java.io.DataOutputStream;
162 import java.io.FileInputStream;
163 import java.io.FileOutputStream;
164 import java.io.IOException;
165 import java.io.InputStream;
166 import java.io.InputStreamReader;
167 import java.io.OutputStreamWriter;
168 import java.io.PrintWriter;
169 import java.math.BigInteger;
170 import java.net.MalformedURLException;
172 import java.util.ArrayList;
173 import java.util.Arrays;
174 import java.util.Collections;
175 import java.util.Enumeration;
176 import java.util.GregorianCalendar;
177 import java.util.HashMap;
178 import java.util.HashSet;
179 import java.util.Hashtable;
180 import java.util.IdentityHashMap;
181 import java.util.Iterator;
182 import java.util.LinkedHashMap;
183 import java.util.List;
184 import java.util.Map;
185 import java.util.Map.Entry;
186 import java.util.Set;
187 import java.util.Vector;
188 import java.util.jar.JarEntry;
189 import java.util.jar.JarInputStream;
190 import java.util.jar.JarOutputStream;
192 import javax.swing.JInternalFrame;
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 + "'";
2788 // BH 2019 -- can't wait
2789 Jalview.execRunnable(new Runnable()
2794 setLoadingFinishedForNewStructureViewers();
2797 } catch (Exception x)
2799 System.err.println("Error loading alignment: " + x.getMessage());
2802 this.jarFile = null;
2806 @SuppressWarnings("unused")
2807 private jarInputStreamProvider createjarInputStreamProvider(
2808 final Object ofile) throws MalformedURLException
2812 String file = (ofile instanceof File
2813 ? ((File) ofile).getCanonicalPath()
2814 : ofile.toString());
2815 byte[] bytes = Platform.isJS() ? Platform.getFileBytes((File) ofile)
2819 this.jarFile = (File) ofile;
2821 errorMessage = null;
2822 uniqueSetSuffix = null;
2824 viewportsAdded.clear();
2825 frefedSequence = null;
2827 URL url = file.startsWith("http://") ? new URL(file) : null;
2828 return new jarInputStreamProvider()
2831 public JarInputStream getJarInputStream() throws IOException
2833 InputStream is = bytes != null ? new ByteArrayInputStream(bytes)
2834 : (url != null ? url.openStream()
2835 : new FileInputStream(file));
2836 return new JarInputStream(is);
2840 public String getFilename()
2845 } catch (IOException e)
2847 e.printStackTrace();
2853 * Recover jalview session from a jalview project archive. Caller may
2854 * initialise uniqueSetSuffix, seqRefIds, viewportsAdded and frefedSequence
2855 * themselves. Any null fields will be initialised with default values,
2856 * non-null fields are left alone.
2861 public AlignFrame loadJalviewAlign(final jarInputStreamProvider jprovider)
2863 errorMessage = null;
2864 if (uniqueSetSuffix == null)
2866 uniqueSetSuffix = System.currentTimeMillis() % 100000 + "";
2868 if (seqRefIds == null)
2872 AlignFrame af = null, _af = null;
2873 IdentityHashMap<AlignmentI, AlignmentI> importedDatasets = new IdentityHashMap<>();
2874 Map<String, AlignFrame> gatherToThisFrame = new HashMap<>();
2875 final String file = jprovider.getFilename();
2877 List<AlignFrame> alignFrames = new ArrayList<>();
2881 JarInputStream jin = null;
2882 JarEntry jarentry = null;
2886 // Look for all the entry names ending with ".xml"
2887 // This includes all panels and at least one frame.
2888 // Platform.timeCheck(null, Platform.TIME_MARK);
2891 jin = jprovider.getJarInputStream();
2892 for (int i = 0; i < entryCount; i++)
2894 jarentry = jin.getNextJarEntry();
2896 String name = (jarentry == null ? null : jarentry.getName());
2898 // System.out.println("Jalview2XML opening " + name);
2899 if (name != null && name.endsWith(".xml"))
2902 // DataSet for.... is read last.
2905 // The question here is what to do with the two
2906 // .xml files in the jvp file.
2907 // Some number of them, "...Dataset for...", will be the
2908 // Only AlignPanels and will have Viewport.
2909 // One or more will be the source data, with the DBRefs.
2911 // JVP file writing (above) ensures tha the AlignPanels are written
2912 // first, then all relevant datasets (which are
2913 // Jalview.datamodel.Alignment).
2916 // Platform.timeCheck("Jalview2XML JAXB " + name, Platform.TIME_MARK);
2917 JAXBContext jc = JAXBContext
2918 .newInstance("jalview.xml.binding.jalview");
2919 XMLStreamReader streamReader = XMLInputFactory.newInstance()
2920 .createXMLStreamReader(jin);
2921 javax.xml.bind.Unmarshaller um = jc.createUnmarshaller();
2922 JAXBElement<JalviewModel> jbe = um
2923 .unmarshal(streamReader, JalviewModel.class);
2924 JalviewModel model = jbe.getValue();
2926 if (true) // !skipViewport(object))
2928 // Q: Do we have to load from the model, even if it
2929 // does not have a viewport, could we discover that early on?
2930 // Q: Do we need to load this object?
2931 _af = loadFromObject(model, file, true, jprovider);
2932 // Platform.timeCheck("Jalview2XML.loadFromObject",
2933 // Platform.TIME_MARK);
2937 alignFrames.add(_af);
2939 if (_af != null && model.getViewport().size() > 0)
2942 // That is, this is one of the AlignmentPanel models
2945 // store a reference to the first view
2948 if (_af.getViewport().isGatherViewsHere())
2950 // if this is a gathered view, keep its reference since
2951 // after gathering views, only this frame will remain
2953 gatherToThisFrame.put(_af.getViewport().getSequenceSetId(),
2956 // Save dataset to register mappings once all resolved
2957 importedDatasets.put(
2958 af.getViewport().getAlignment().getDataset(),
2959 af.getViewport().getAlignment().getDataset());
2962 // Platform.timeCheck("JAXB " + name, Platform.TIME_MARK);
2965 else if (jarentry != null)
2967 // Some other file here.
2970 } while (jarentry != null);
2971 // Platform.timeCheck("JAXB loop exit", Platform.TIME_MARK);
2972 resolveFrefedSequences();
2973 // Platform.timeCheck("JAXB resolveFrefed", Platform.TIME_MARK);
2975 } catch (IOException ex)
2977 ex.printStackTrace();
2978 errorMessage = "Couldn't locate Jalview XML file : " + file;
2980 "Exception whilst loading jalview XML file : " + ex + "\n");
2981 } catch (Exception ex)
2983 System.err.println("Parsing as Jalview Version 2 file failed.");
2984 ex.printStackTrace(System.err);
2985 if (attemptversion1parse)
2987 // used to attempt to parse as V1 castor-generated xml
2989 if (Desktop.getInstance() != null)
2991 Desktop.getInstance().stopLoading();
2995 System.out.println("Successfully loaded archive file");
2998 ex.printStackTrace();
3001 "Exception whilst loading jalview XML file : " + ex + "\n");
3002 } catch (OutOfMemoryError e)
3004 // Don't use the OOM Window here
3005 errorMessage = "Out of memory loading jalview XML file";
3006 System.err.println("Out of memory whilst loading jalview XML file");
3007 e.printStackTrace();
3010 for (AlignFrame alf : alignFrames)
3012 alf.alignPanel.setHoldRepaint(false);
3018 * Regather multiple views (with the same sequence set id) to the frame (if
3019 * any) that is flagged as the one to gather to, i.e. convert them to tabbed
3020 * views instead of separate frames. Note this doesn't restore a state where
3021 * some expanded views in turn have tabbed views - the last "first tab" read
3022 * in will play the role of gatherer for all.
3024 for (AlignFrame fr : gatherToThisFrame.values())
3026 Desktop.getInstance().gatherViews(fr);
3029 restoreSplitFrames();
3030 for (AlignmentI ds : importedDatasets.keySet())
3032 if (ds.getCodonFrames() != null)
3034 Desktop.getStructureSelectionManager()
3035 .registerMappings(ds.getCodonFrames());
3038 if (errorMessage != null)
3043 if (Desktop.getInstance() != null)
3045 Desktop.getInstance().stopLoading();
3052 * Try to reconstruct and display SplitFrame windows, where each contains
3053 * complementary dna and protein alignments. Done by pairing up AlignFrame
3054 * objects (created earlier) which have complementary viewport ids associated.
3056 protected void restoreSplitFrames()
3058 List<SplitFrame> gatherTo = new ArrayList<>();
3059 List<AlignFrame> addedToSplitFrames = new ArrayList<>();
3060 Map<String, AlignFrame> dna = new HashMap<>();
3063 * Identify the DNA alignments
3065 for (Entry<Viewport, AlignFrame> candidate : splitFrameCandidates
3068 AlignFrame af = candidate.getValue();
3069 if (af.getViewport().getAlignment().isNucleotide())
3071 dna.put(candidate.getKey().getId(), af);
3076 * Try to match up the protein complements
3078 for (Entry<Viewport, AlignFrame> candidate : splitFrameCandidates
3081 AlignFrame af = candidate.getValue();
3082 if (!af.getViewport().getAlignment().isNucleotide())
3084 String complementId = candidate.getKey().getComplementId();
3085 // only non-null complements should be in the Map
3086 if (complementId != null && dna.containsKey(complementId))
3088 final AlignFrame dnaFrame = dna.get(complementId);
3089 SplitFrame sf = createSplitFrame(dnaFrame, af);
3090 addedToSplitFrames.add(dnaFrame);
3091 addedToSplitFrames.add(af);
3092 dnaFrame.setMenusForViewport();
3093 af.setMenusForViewport();
3094 if (af.getViewport().isGatherViewsHere())
3103 * Open any that we failed to pair up (which shouldn't happen!) as
3104 * standalone AlignFrame's.
3106 for (Entry<Viewport, AlignFrame> candidate : splitFrameCandidates
3109 AlignFrame af = candidate.getValue();
3110 if (!addedToSplitFrames.contains(af))
3112 Viewport view = candidate.getKey();
3113 Desktop.addInternalFrame(af, view.getTitle(),
3114 safeInt(view.getWidth()), safeInt(view.getHeight()));
3115 af.setMenusForViewport();
3116 System.err.println("Failed to restore view " + view.getTitle()
3117 + " to split frame");
3122 * Gather back into tabbed views as flagged.
3124 for (SplitFrame sf : gatherTo)
3126 Desktop.getInstance().gatherViews(sf);
3129 splitFrameCandidates.clear();
3133 * Construct and display one SplitFrame holding DNA and protein alignments.
3136 * @param proteinFrame
3139 protected SplitFrame createSplitFrame(AlignFrame dnaFrame,
3140 AlignFrame proteinFrame)
3142 SplitFrame splitFrame = new SplitFrame(dnaFrame, proteinFrame);
3143 String title = MessageManager.getString("label.linked_view_title");
3144 int width = (int) dnaFrame.getBounds().getWidth();
3145 int height = (int) (dnaFrame.getBounds().getHeight()
3146 + proteinFrame.getBounds().getHeight() + 50);
3149 * SplitFrame location is saved to both enclosed frames
3151 splitFrame.setLocation(dnaFrame.getX(), dnaFrame.getY());
3152 Desktop.addInternalFrame(splitFrame, title, width, height);
3155 * And compute cDNA consensus (couldn't do earlier with consensus as
3156 * mappings were not yet present)
3158 proteinFrame.getViewport().alignmentChanged(proteinFrame.alignPanel);
3164 * check errorMessage for a valid error message and raise an error box in the
3165 * GUI or write the current errorMessage to stderr and then clear the error
3168 protected void reportErrors()
3170 reportErrors(false);
3173 protected void reportErrors(final boolean saving)
3175 if (errorMessage != null)
3177 final String finalErrorMessage = errorMessage;
3180 javax.swing.SwingUtilities.invokeLater(new Runnable()
3185 JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(),
3187 "Error " + (saving ? "saving" : "loading")
3189 JvOptionPane.WARNING_MESSAGE);
3195 System.err.println("Problem loading Jalview file: " + errorMessage);
3198 errorMessage = null;
3201 Map<String, String> alreadyLoadedPDB = new HashMap<>();
3204 * when set, local views will be updated from view stored in JalviewXML
3205 * Currently (28th Sep 2008) things will go horribly wrong in vamsas document
3206 * sync if this is set to true.
3208 private final boolean updateLocalViews = false;
3211 * Returns the path to a temporary file holding the PDB file for the given PDB
3212 * id. The first time of asking, searches for a file of that name in the
3213 * Jalview project jar, and copies it to a new temporary file. Any repeat
3214 * requests just return the path to the file previously created.
3220 String loadPDBFile(jarInputStreamProvider jprovider, String pdbId,
3223 if (alreadyLoadedPDB.containsKey(pdbId))
3225 return alreadyLoadedPDB.get(pdbId).toString();
3228 String tempFile = copyJarEntry(jprovider, pdbId, "jalview_pdb",
3230 if (tempFile != null)
3232 alreadyLoadedPDB.put(pdbId, tempFile);
3238 * Copies the jar entry of given name to a new temporary file and returns the
3239 * path to the file, or null if the entry is not found.
3242 * @param jarEntryName
3244 * a prefix for the temporary file name, must be at least three
3247 * null or original file - so new file can be given the same suffix
3251 protected String copyJarEntry(jarInputStreamProvider jprovider,
3252 String jarEntryName, String prefix, String origFile)
3254 BufferedReader in = null;
3255 PrintWriter out = null;
3256 String suffix = ".tmp";
3257 if (origFile == null)
3259 origFile = jarEntryName;
3261 int sfpos = origFile.lastIndexOf(".");
3262 if (sfpos > -1 && sfpos < (origFile.length() - 3))
3264 suffix = "." + origFile.substring(sfpos + 1);
3268 JarInputStream jin = jprovider.getJarInputStream();
3270 * if (jprovider.startsWith("http://")) { jin = new JarInputStream(new
3271 * URL(jprovider).openStream()); } else { jin = new JarInputStream(new
3272 * FileInputStream(jprovider)); }
3275 JarEntry entry = null;
3278 entry = jin.getNextJarEntry();
3279 } while (entry != null && !entry.getName().equals(jarEntryName));
3282 in = new BufferedReader(new InputStreamReader(jin, UTF_8));
3283 File outFile = File.createTempFile(prefix, suffix);
3284 outFile.deleteOnExit();
3285 out = new PrintWriter(new FileOutputStream(outFile));
3288 while ((data = in.readLine()) != null)
3293 String t = outFile.getAbsolutePath();
3298 warn("Couldn't find entry in Jalview Jar for " + jarEntryName);
3300 } catch (Exception ex)
3302 ex.printStackTrace();
3310 } catch (IOException e)
3324 private class JvAnnotRow
3326 public JvAnnotRow(int i, AlignmentAnnotation jaa)
3333 * persisted version of annotation row from which to take vis properties
3335 public jalview.datamodel.AlignmentAnnotation template;
3338 * original position of the annotation row in the alignment
3344 * Load alignment frame from jalview XML DOM object. For a DOM object that
3345 * includes one or more Viewport elements (one with a title that does NOT
3346 * contain "Dataset for"), create the frame.
3348 * @param jalviewModel
3351 * filename source string
3352 * @param loadTreesAndStructures
3353 * when false only create Viewport
3355 * data source provider
3356 * @return alignment frame created from view stored in DOM
3358 private AlignFrame loadFromObject(JalviewModel jalviewModel, String file,
3359 boolean loadTreesAndStructures, jarInputStreamProvider jprovider)
3362 // Platform.timeCheck("Jalview2XML.loadFromObject0", Platform.TIME_MARK);
3364 SequenceSet vamsasSet = jalviewModel.getVamsasModel().getSequenceSet()
3366 List<Sequence> vamsasSeqs = vamsasSet.getSequence();
3368 // JalviewModelSequence jms = object.getJalviewModelSequence();
3370 // Viewport view = (jms.getViewportCount() > 0) ? jms.getViewport(0)
3372 Viewport view = (jalviewModel.getViewport().size() > 0)
3373 ? jalviewModel.getViewport().get(0)
3376 // ////////////////////////////////
3377 // INITIALISE ALIGNMENT SEQUENCESETID AND VIEWID
3380 // If we just load in the same jar file again, the sequenceSetId
3381 // will be the same, and we end up with multiple references
3382 // to the same sequenceSet. We must modify this id on load
3383 // so that each load of the file gives a unique id
3386 * used to resolve correct alignment dataset for alignments with multiple
3389 String uniqueSeqSetId = null;
3390 String viewId = null;
3393 uniqueSeqSetId = view.getSequenceSetId() + uniqueSetSuffix;
3394 viewId = (view.getId() == null ? null
3395 : view.getId() + uniqueSetSuffix);
3398 // Platform.timeCheck("Jalview2XML.loadFromObject1", Platform.TIME_MARK);
3399 // ////////////////////////////////
3402 List<SequenceI> hiddenSeqs = null;
3404 List<SequenceI> tmpseqs = new ArrayList<>();
3406 boolean multipleView = false;
3407 SequenceI referenceseqForView = null;
3408 // JSeq[] jseqs = object.getJalviewModelSequence().getJSeq();
3409 List<JSeq> jseqs = jalviewModel.getJSeq();
3410 int vi = 0; // counter in vamsasSeq array
3411 for (int i = 0; i < jseqs.size(); i++)
3413 JSeq jseq = jseqs.get(i);
3414 String seqId = jseq.getId();
3416 SequenceI tmpSeq = seqRefIds.get(seqId);
3420 if (!incompleteSeqs.containsKey(seqId))
3422 // may not need this check, but keep it for at least 2.9,1 release
3423 if (tmpSeq.getStart() != jseq.getStart()
3424 || tmpSeq.getEnd() != jseq.getEnd())
3427 "Warning JAL-2154 regression: updating start/end for sequence "
3428 + tmpSeq.toString() + " to " + jseq);
3433 incompleteSeqs.remove(seqId);
3435 if (vamsasSeqs.size() > vi
3436 && vamsasSeqs.get(vi).getId().equals(seqId))
3438 // most likely we are reading a dataset XML document so
3439 // update from vamsasSeq section of XML for this sequence
3440 tmpSeq.setName(vamsasSeqs.get(vi).getName());
3441 tmpSeq.setDescription(vamsasSeqs.get(vi).getDescription());
3442 tmpSeq.setSequence(vamsasSeqs.get(vi).getSequence());
3447 // reading multiple views, so vamsasSeq set is a subset of JSeq
3448 multipleView = true;
3450 tmpSeq.setStart(jseq.getStart());
3451 tmpSeq.setEnd(jseq.getEnd());
3452 tmpseqs.add(tmpSeq);
3456 Sequence vamsasSeq = vamsasSeqs.get(vi);
3457 tmpSeq = new jalview.datamodel.Sequence(vamsasSeq.getName(),
3458 vamsasSeq.getSequence());
3459 tmpSeq.setDescription(vamsasSeq.getDescription());
3460 tmpSeq.setStart(jseq.getStart());
3461 tmpSeq.setEnd(jseq.getEnd());
3462 tmpSeq.setVamsasId(uniqueSetSuffix + seqId);
3463 seqRefIds.put(vamsasSeq.getId(), tmpSeq);
3464 tmpseqs.add(tmpSeq);
3468 if (safeBoolean(jseq.isViewreference()))
3470 referenceseqForView = tmpseqs.get(tmpseqs.size() - 1);
3473 if (jseq.isHidden() != null && jseq.isHidden().booleanValue())
3475 if (hiddenSeqs == null)
3477 hiddenSeqs = new ArrayList<>();
3480 hiddenSeqs.add(tmpSeq);
3484 // Platform.timeCheck("Jalview2XML.loadFromObject-seq",
3485 // Platform.TIME_MARK);
3487 // Create the alignment object from the sequence set
3488 // ///////////////////////////////
3489 SequenceI[] orderedSeqs = tmpseqs
3490 .toArray(new SequenceI[tmpseqs.size()]);
3492 AlignmentI al = null;
3493 // so we must create or recover the dataset alignment before going further
3494 // ///////////////////////////////
3495 if (vamsasSet.getDatasetId() == null || vamsasSet.getDatasetId() == "")
3497 // older jalview projects do not have a dataset - so creat alignment and
3499 al = new Alignment(orderedSeqs);
3500 al.setDataset(null);
3504 boolean isdsal = jalviewModel.getViewport().isEmpty();
3507 // we are importing a dataset record, so
3508 // recover reference to an alignment already materialsed as dataset
3509 al = getDatasetFor(vamsasSet.getDatasetId());
3513 // materialse the alignment
3514 al = new Alignment(orderedSeqs);
3518 addDatasetRef(vamsasSet.getDatasetId(), al);
3521 // finally, verify all data in vamsasSet is actually present in al
3522 // passing on flag indicating if it is actually a stored dataset
3523 recoverDatasetFor(vamsasSet, al, isdsal, uniqueSeqSetId);
3526 // Platform.timeCheck("Jalview2XML.loadFromObject-align",
3527 // Platform.TIME_MARK);
3528 if (referenceseqForView != null)
3530 al.setSeqrep(referenceseqForView);
3532 // / Add the alignment properties
3533 for (int i = 0; i < vamsasSet.getSequenceSetProperties().size(); i++)
3535 SequenceSetProperties ssp = vamsasSet.getSequenceSetProperties()
3537 al.setProperty(ssp.getKey(), ssp.getValue());
3540 // Platform.timeCheck("Jalview2XML.loadFromObject-setseqprop",
3541 // Platform.TIME_MARK);
3542 // ///////////////////////////////
3544 Hashtable pdbloaded = new Hashtable(); // TODO nothing writes to this??
3547 // load sequence features, database references and any associated PDB
3548 // structures for the alignment
3550 // prior to 2.10, this part would only be executed the first time a
3551 // sequence was encountered, but not afterwards.
3552 // now, for 2.10 projects, this is also done if the xml doc includes
3553 // dataset sequences not actually present in any particular view.
3555 // Platform.timeCheck("J2XML features0", Platform.TIME_RESET);
3556 for (int i = 0; i < vamsasSeqs.size(); i++)
3558 JSeq jseq = jseqs.get(i);
3559 if (jseq.getFeatures().size() > 0)
3561 List<Feature> features = jseq.getFeatures();
3562 for (int f = 0; f < features.size(); f++)
3564 Feature feat = features.get(f);
3565 SequenceFeature sf = new SequenceFeature(feat.getType(),
3566 feat.getDescription(), feat.getBegin(), feat.getEnd(),
3567 safeFloat(feat.getScore()), feat.getFeatureGroup());
3568 sf.setStatus(feat.getStatus());
3571 * load any feature attributes - include map-valued attributes
3573 Map<String, Map<String, String>> mapAttributes = new HashMap<>();
3574 for (int od = 0; od < feat.getOtherData().size(); od++)
3576 OtherData keyValue = feat.getOtherData().get(od);
3577 String attributeName = keyValue.getKey();
3578 String attributeValue = keyValue.getValue();
3579 if (attributeName.startsWith("LINK"))
3581 sf.addLink(attributeValue);
3585 String subAttribute = keyValue.getKey2();
3586 if (subAttribute == null)
3588 // simple string-valued attribute
3589 sf.setValue(attributeName, attributeValue);
3593 // attribute 'key' has sub-attribute 'key2'
3594 if (!mapAttributes.containsKey(attributeName))
3596 mapAttributes.put(attributeName, new HashMap<>());
3598 mapAttributes.get(attributeName).put(subAttribute,
3603 for (Entry<String, Map<String, String>> mapAttribute : mapAttributes
3606 sf.setValue(mapAttribute.getKey(), mapAttribute.getValue());
3609 // adds feature to datasequence's feature set (since Jalview 2.10)
3610 // Platform.timeCheck(null, Platform.TIME_SET);
3611 al.getSequenceAt(i).addSequenceFeature(sf);
3612 // Platform.timeCheck(null, Platform.TIME_MARK);
3615 if (vamsasSeqs.get(i).getDBRef().size() > 0)
3617 // adds dbrefs to datasequence's set (since Jalview 2.10)
3619 al.getSequenceAt(i).getDatasetSequence() == null
3620 ? al.getSequenceAt(i)
3621 : al.getSequenceAt(i).getDatasetSequence(),
3624 if (jseq.getPdbids().size() > 0)
3626 List<Pdbids> ids = jseq.getPdbids();
3627 for (int p = 0; p < ids.size(); p++)
3629 Pdbids pdbid = ids.get(p);
3630 jalview.datamodel.PDBEntry entry = new jalview.datamodel.PDBEntry();
3631 entry.setId(pdbid.getId());
3632 if (pdbid.getType() != null)
3634 if (PDBEntry.Type.getType(pdbid.getType()) != null)
3636 entry.setType(PDBEntry.Type.getType(pdbid.getType()));
3640 entry.setType(PDBEntry.Type.FILE);
3643 // jprovider is null when executing 'New View'
3644 if (pdbid.getFile() != null && jprovider != null)
3646 if (!pdbloaded.containsKey(pdbid.getFile()))
3648 entry.setFile(loadPDBFile(jprovider, pdbid.getId(),
3653 entry.setFile(pdbloaded.get(pdbid.getId()).toString());
3657 if (pdbid.getPdbentryItem() != null)
3659 for (PdbentryItem item : pdbid.getPdbentryItem())
3661 for (Property pr : item.getProperty())
3663 entry.setProperty(pr.getName(), pr.getValue());
3668 for (Property prop : pdbid.getProperty())
3670 entry.setProperty(prop.getName(), prop.getValue());
3672 Desktop.getStructureSelectionManager().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 .add(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.getProperty())
3941 jaa.setProperty(prop.getName(), prop.getValue());
3944 if (jaa.autoCalculated)
3946 autoAlan.add(new JvAnnotRow(i, jaa));
3949 // if (!autoForView)
3951 // add autocalculated group annotation and any user created annotation
3953 al.addAnnotation(jaa);
3956 // Platform.timeCheck("Jalview2XML.loadFromObject-annot",
3957 // Platform.TIME_MARK);
3959 // ///////////////////////
3961 // Create alignment markup and styles for this view
3962 if (jalviewModel.getJGroup().size() > 0)
3964 List<JGroup> groups = jalviewModel.getJGroup();
3965 boolean addAnnotSchemeGroup = false;
3966 for (int i = 0; i < groups.size(); i++)
3968 JGroup jGroup = groups.get(i);
3969 ColourSchemeI cs = null;
3970 if (jGroup.getColour() != null)
3972 if (jGroup.getColour().startsWith("ucs"))
3974 cs = getUserColourScheme(jalviewModel, jGroup.getColour());
3976 else if (jGroup.getColour().equals("AnnotationColourGradient")
3977 && jGroup.getAnnotationColours() != null)
3979 addAnnotSchemeGroup = true;
3983 cs = ColourSchemeProperty.getColourScheme(null, al,
3984 jGroup.getColour());
3987 int pidThreshold = safeInt(jGroup.getPidThreshold());
3989 Vector<SequenceI> seqs = new Vector<>();
3991 for (int s = 0; s < jGroup.getSeq().size(); s++)
3993 String seqId = jGroup.getSeq().get(s);
3994 SequenceI ts = seqRefIds.get(seqId);
3998 seqs.addElement(ts);
4002 if (seqs.size() < 1)
4007 SequenceGroup sg = new SequenceGroup(seqs, jGroup.getName(), cs,
4008 safeBoolean(jGroup.isDisplayBoxes()),
4009 safeBoolean(jGroup.isDisplayText()),
4010 safeBoolean(jGroup.isColourText()),
4011 safeInt(jGroup.getStart()), safeInt(jGroup.getEnd()));
4012 sg.getGroupColourScheme().setThreshold(pidThreshold, true);
4013 sg.getGroupColourScheme()
4014 .setConservationInc(safeInt(jGroup.getConsThreshold()));
4015 sg.setOutlineColour(new Color(safeInt(jGroup.getOutlineColour())));
4017 sg.textColour = new Color(safeInt(jGroup.getTextCol1()));
4018 sg.textColour2 = new Color(safeInt(jGroup.getTextCol2()));
4019 sg.setShowNonconserved(safeBoolean(jGroup.isShowUnconserved()));
4020 sg.thresholdTextColour = safeInt(jGroup.getTextColThreshold());
4021 // attributes with a default in the schema are never null
4022 sg.setShowConsensusHistogram(jGroup.isShowConsensusHistogram());
4023 sg.setshowSequenceLogo(jGroup.isShowSequenceLogo());
4024 sg.setNormaliseSequenceLogo(jGroup.isNormaliseSequenceLogo());
4025 sg.setIgnoreGapsConsensus(jGroup.isIgnoreGapsinConsensus());
4026 if (jGroup.getConsThreshold() != null
4027 && jGroup.getConsThreshold().intValue() != 0)
4029 Conservation c = new Conservation("All", sg.getSequences(null), 0,
4032 c.verdict(false, 25);
4033 sg.cs.setConservation(c);
4036 if (jGroup.getId() != null && groupAnnotRefs.size() > 0)
4038 // re-instate unique group/annotation row reference
4039 List<AlignmentAnnotation> jaal = groupAnnotRefs
4040 .get(jGroup.getId());
4043 for (AlignmentAnnotation jaa : jaal)
4046 if (jaa.autoCalculated)
4048 // match up and try to set group autocalc alignment row for this
4050 if (jaa.label.startsWith("Consensus for "))
4052 sg.setConsensus(jaa);
4054 // match up and try to set group autocalc alignment row for this
4056 if (jaa.label.startsWith("Conservation for "))
4058 sg.setConservationRow(jaa);
4065 if (addAnnotSchemeGroup)
4067 // reconstruct the annotation colourscheme
4069 constructAnnotationColour(jGroup.getAnnotationColours(),
4070 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 Jalview.execRunnable(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 Jalview.execRunnable(new Runnable()
4192 // Platform.timeCheck(null, Platform.TIME_MARK);
4193 loadPCAViewers(jalviewModel, ap0);
4194 // Platform.timeCheck("Jalview2XML.loadPCA", Platform.TIME_MARK);
4198 Jalview.execRunnable(new Runnable()
4203 // Platform.timeCheck(null, Platform.TIME_MARK);
4204 loadPDBStructures(jprovider, jseqs, af0, ap0);
4205 // Platform.timeCheck("Jalview2XML.loadPDB", Platform.TIME_MARK);
4208 Jalview.execRunnable(new Runnable()
4213 loadRnaViewers(jprovider, jseqs, ap0);
4218 // and finally return.
4219 // but do not set holdRepaint true just yet, because this could be the
4220 // initial frame with just its dataset.
4225 * Instantiate and link any saved RNA (Varna) viewers. The state of the Varna
4226 * panel is restored from separate jar entries, two (gapped and trimmed) per
4227 * sequence and secondary structure.
4229 * Currently each viewer shows just one sequence and structure (gapped and
4230 * trimmed), however this method is designed to support multiple sequences or
4231 * structures in viewers if wanted in future.
4237 protected void loadRnaViewers(jarInputStreamProvider jprovider,
4238 List<JSeq> jseqs, AlignmentPanel ap)
4241 * scan the sequences for references to viewers; create each one the first
4242 * time it is referenced, add Rna models to existing viewers
4244 for (JSeq jseq : jseqs)
4246 for (int i = 0; i < jseq.getRnaViewer().size(); i++)
4248 RnaViewer viewer = jseq.getRnaViewer().get(i);
4249 AppVarna appVarna = findOrCreateVarnaViewer(viewer, uniqueSetSuffix,
4252 for (int j = 0; j < viewer.getSecondaryStructure().size(); j++)
4254 SecondaryStructure ss = viewer.getSecondaryStructure().get(j);
4255 SequenceI seq = seqRefIds.get(jseq.getId());
4256 AlignmentAnnotation ann = this.annotationIds
4257 .get(ss.getAnnotationId());
4260 * add the structure to the Varna display (with session state copied
4261 * from the jar to a temporary file)
4263 boolean gapped = safeBoolean(ss.isGapped());
4264 String rnaTitle = ss.getTitle();
4265 String sessionState = ss.getViewerState();
4266 String tempStateFile = copyJarEntry(jprovider, sessionState,
4268 RnaModel rna = new RnaModel(rnaTitle, ann, seq, null, gapped);
4269 appVarna.addModelSession(rna, rnaTitle, tempStateFile);
4271 appVarna.setInitialSelection(safeInt(viewer.getSelectedRna()));
4277 * Locate and return an already instantiated matching AppVarna, or create one
4281 * @param viewIdSuffix
4285 protected AppVarna findOrCreateVarnaViewer(RnaViewer viewer,
4286 String viewIdSuffix, AlignmentPanel ap)
4289 * on each load a suffix is appended to the saved viewId, to avoid conflicts
4290 * if load is repeated
4292 String postLoadId = viewer.getViewId() + viewIdSuffix;
4293 for (JInternalFrame frame : getAllFrames())
4295 if (frame instanceof AppVarna)
4297 AppVarna varna = (AppVarna) frame;
4298 if (postLoadId.equals(varna.getViewId()))
4300 // this viewer is already instantiated
4301 // could in future here add ap as another 'parent' of the
4302 // AppVarna window; currently just 1-to-many
4309 * viewer not found - make it
4311 RnaViewerModel model = new RnaViewerModel(postLoadId, viewer.getTitle(),
4312 safeInt(viewer.getXpos()), safeInt(viewer.getYpos()),
4313 safeInt(viewer.getWidth()), safeInt(viewer.getHeight()),
4314 safeInt(viewer.getDividerLocation()));
4315 AppVarna varna = new AppVarna(model, ap);
4321 * Load any saved trees
4329 protected void loadTrees(JalviewModel jm, Viewport view,
4330 AlignFrame af, AlignViewport av, AlignmentPanel ap)
4332 // TODO result of automated refactoring - are all these parameters needed?
4335 for (int t = 0; t < jm.getTree().size(); t++)
4338 Tree tree = jm.getTree().get(t);
4340 TreePanel tp = (TreePanel) retrieveExistingObj(tree.getId());
4343 tp = af.showNewickTree(new NewickFile(tree.getNewick()),
4344 tree.getTitle(), safeInt(tree.getWidth()),
4345 safeInt(tree.getHeight()), safeInt(tree.getXpos()),
4346 safeInt(tree.getYpos()));
4347 if (tree.getId() != null)
4349 // perhaps bind the tree id to something ?
4354 // update local tree attributes ?
4355 // TODO: should check if tp has been manipulated by user - if so its
4356 // settings shouldn't be modified
4357 tp.setTitle(tree.getTitle());
4358 tp.setBounds(new Rectangle(safeInt(tree.getXpos()),
4359 safeInt(tree.getYpos()), safeInt(tree.getWidth()),
4360 safeInt(tree.getHeight())));
4361 tp.setViewport(av); // af.viewport;
4362 // TODO: verify 'associate with all views' works still
4363 tp.getTreeCanvas().setViewport(av); // af.viewport;
4364 tp.getTreeCanvas().setAssociatedPanel(ap); // af.alignPanel;
4366 tp.getTreeCanvas().setApplyToAllViews(tree.isLinkToAllViews());
4369 warn("There was a problem recovering stored Newick tree: \n"
4370 + tree.getNewick());
4374 tp.fitToWindow.setState(safeBoolean(tree.isFitToWindow()));
4375 tp.fitToWindow_actionPerformed(null);
4377 if (tree.getFontName() != null)
4380 new Font(tree.getFontName(), safeInt(tree.getFontStyle()),
4381 safeInt(tree.getFontSize())));
4386 new Font(view.getFontName(), safeInt(view.getFontStyle()),
4387 safeInt(view.getFontSize())));
4390 tp.showPlaceholders(safeBoolean(tree.isMarkUnlinked()));
4391 tp.showBootstrap(safeBoolean(tree.isShowBootstrap()));
4392 tp.showDistances(safeBoolean(tree.isShowDistances()));
4394 tp.getTreeCanvas().setThreshold(safeFloat(tree.getThreshold()));
4396 if (safeBoolean(tree.isCurrentTree()))
4398 af.getViewport().setCurrentTree(tp.getTree());
4402 } catch (Exception ex)
4404 ex.printStackTrace();
4409 * Load and link any saved structure viewers.
4416 protected void loadPDBStructures(jarInputStreamProvider jprovider,
4417 List<JSeq> jseqs, AlignFrame af, AlignmentPanel ap)
4420 * Run through all PDB ids on the alignment, and collect mappings between
4421 * distinct view ids and all sequences referring to that view.
4423 Map<String, StructureViewerModel> structureViewers = new LinkedHashMap<>();
4425 for (int i = 0; i < jseqs.size(); i++)
4427 JSeq jseq = jseqs.get(i);
4428 if (jseq.getPdbids().size() > 0)
4430 List<Pdbids> ids = jseq.getPdbids();
4431 for (int p = 0; p < ids.size(); p++)
4433 Pdbids pdbid = ids.get(p);
4434 final int structureStateCount = pdbid.getStructureState().size();
4435 for (int s = 0; s < structureStateCount; s++)
4437 // check to see if we haven't already created this structure view
4438 final StructureState structureState = pdbid
4439 .getStructureState().get(s);
4440 String sviewid = (structureState.getViewId() == null) ? null
4441 : structureState.getViewId() + uniqueSetSuffix;
4442 jalview.datamodel.PDBEntry jpdb = new jalview.datamodel.PDBEntry();
4443 // Originally : pdbid.getFile()
4444 // : TODO: verify external PDB file recovery still works in normal
4445 // jalview project load
4447 loadPDBFile(jprovider, pdbid.getId(), pdbid.getFile()));
4448 jpdb.setId(pdbid.getId());
4450 int x = safeInt(structureState.getXpos());
4451 int y = safeInt(structureState.getYpos());
4452 int width = safeInt(structureState.getWidth());
4453 int height = safeInt(structureState.getHeight());
4455 // Probably don't need to do this anymore...
4456 // Desktop.getDesktop().getComponentAt(x, y);
4457 // TODO: NOW: check that this recovers the PDB file correctly.
4458 String pdbFile = loadPDBFile(jprovider, pdbid.getId(),
4460 jalview.datamodel.SequenceI seq = seqRefIds
4461 .get(jseq.getId() + "");
4462 if (sviewid == null)
4464 sviewid = "_jalview_pre2_4_" + x + "," + y + "," + width + ","
4467 if (!structureViewers.containsKey(sviewid))
4469 structureViewers.put(sviewid,
4470 new StructureViewerModel(x, y, width, height, false,
4471 false, true, structureState.getViewId(),
4472 structureState.getType()));
4473 // Legacy pre-2.7 conversion JAL-823 :
4474 // do not assume any view has to be linked for colour by
4478 // assemble String[] { pdb files }, String[] { id for each
4479 // file }, orig_fileloc, SequenceI[][] {{ seqs_file 1 }, {
4480 // seqs_file 2}, boolean[] {
4481 // linkAlignPanel,superposeWithAlignpanel}} from hash
4482 StructureViewerModel jmoldat = structureViewers.get(sviewid);
4483 jmoldat.setAlignWithPanel(jmoldat.isAlignWithPanel()
4484 || structureState.isAlignwithAlignPanel());
4487 * Default colour by linked panel to false if not specified (e.g.
4488 * for pre-2.7 projects)
4490 boolean colourWithAlignPanel = jmoldat.isColourWithAlignPanel();
4491 colourWithAlignPanel |= structureState.isColourwithAlignPanel();
4492 jmoldat.setColourWithAlignPanel(colourWithAlignPanel);
4495 * Default colour by viewer to true if not specified (e.g. for
4498 boolean colourByViewer = jmoldat.isColourByViewer();
4499 colourByViewer &= structureState.isColourByJmol();
4500 jmoldat.setColourByViewer(colourByViewer);
4502 if (jmoldat.getStateData().length() < structureState
4503 .getValue()/*Content()*/.length())
4505 jmoldat.setStateData(structureState.getValue());// Content());
4507 if (pdbid.getFile() != null)
4509 File mapkey = new File(pdbid.getFile());
4510 StructureData seqstrmaps = jmoldat.getFileData().get(mapkey);
4511 if (seqstrmaps == null)
4513 jmoldat.getFileData().put(mapkey,
4514 seqstrmaps = jmoldat.new StructureData(pdbFile,
4517 if (!seqstrmaps.getSeqList().contains(seq))
4519 seqstrmaps.getSeqList().add(seq);
4525 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");
4532 // Instantiate the associated structure views
4533 for (Entry<String, StructureViewerModel> entry : structureViewers
4538 createOrLinkStructureViewer(entry, af, ap, jprovider);
4539 } catch (Exception e)
4542 "Error loading structure viewer: " + e.getMessage());
4543 // failed - try the next one
4555 protected void createOrLinkStructureViewer(
4556 Entry<String, StructureViewerModel> viewerData, AlignFrame af,
4557 AlignmentPanel ap, jarInputStreamProvider jprovider)
4559 final StructureViewerModel stateData = viewerData.getValue();
4562 * Search for any viewer windows already open from other alignment views
4563 * that exactly match the stored structure state
4565 StructureViewerBase comp = findMatchingViewer(viewerData);
4569 linkStructureViewer(ap, comp, stateData);
4574 * From 2.9: stateData.type contains JMOL or CHIMERA, data is in jar entry
4575 * "viewer_"+stateData.viewId
4577 if (ViewerType.CHIMERA.toString().equals(stateData.getType()))
4579 createChimeraViewer(viewerData, af, jprovider);
4584 * else Jmol (if pre-2.9, stateData contains JMOL state string)
4586 createJmolViewer(viewerData, af, jprovider);
4591 * Create a new Chimera viewer.
4597 protected void createChimeraViewer(
4598 Entry<String, StructureViewerModel> viewerData, AlignFrame af,
4599 jarInputStreamProvider jprovider)
4601 StructureViewerModel data = viewerData.getValue();
4602 String chimeraSessionFile = data.getStateData();
4605 * Copy Chimera session from jar entry "viewer_"+viewId to a temporary file
4607 * NB this is the 'saved' viewId as in the project file XML, _not_ the
4608 * 'uniquified' sviewid used to reconstruct the viewer here
4610 String viewerJarEntryName = getViewerJarEntryName(data.getViewId());
4611 chimeraSessionFile = copyJarEntry(jprovider, viewerJarEntryName,
4614 Set<Entry<File, StructureData>> fileData = data.getFileData()
4616 List<PDBEntry> pdbs = new ArrayList<>();
4617 List<SequenceI[]> allseqs = new ArrayList<>();
4618 for (Entry<File, StructureData> pdb : fileData)
4620 String filePath = pdb.getValue().getFilePath();
4621 String pdbId = pdb.getValue().getPdbId();
4622 // pdbs.add(new PDBEntry(filePath, pdbId));
4623 pdbs.add(new PDBEntry(pdbId, null, PDBEntry.Type.PDB, filePath));
4624 final List<SequenceI> seqList = pdb.getValue().getSeqList();
4625 SequenceI[] seqs = seqList.toArray(new SequenceI[seqList.size()]);
4629 boolean colourByChimera = data.isColourByViewer();
4630 boolean colourBySequence = data.isColourWithAlignPanel();
4632 // TODO use StructureViewer as a factory here, see JAL-1761
4633 final PDBEntry[] pdbArray = pdbs.toArray(new PDBEntry[pdbs.size()]);
4634 final SequenceI[][] seqsArray = allseqs
4635 .toArray(new SequenceI[allseqs.size()][]);
4636 String newViewId = viewerData.getKey();
4638 ChimeraViewFrame cvf = new ChimeraViewFrame(chimeraSessionFile,
4639 af.alignPanel, pdbArray, seqsArray, colourByChimera,
4640 colourBySequence, newViewId);
4641 cvf.setSize(data.getWidth(), data.getHeight());
4642 cvf.setLocation(data.getX(), data.getY());
4646 * Create a new Jmol window. First parse the Jmol state to translate filenames
4647 * loaded into the view, and record the order in which files are shown in the
4648 * Jmol view, so we can add the sequence mappings in same order.
4654 protected void createJmolViewer(
4655 final Entry<String, StructureViewerModel> viewerData,
4656 AlignFrame af, jarInputStreamProvider jprovider)
4658 final StructureViewerModel svattrib = viewerData.getValue();
4659 String state = svattrib.getStateData();
4662 * Pre-2.9: state element value is the Jmol state string
4664 * 2.9+: @type is "JMOL", state data is in a Jar file member named "viewer_"
4667 if (ViewerType.JMOL.toString().equals(svattrib.getType()))
4669 state = readJarEntry(jprovider,
4670 getViewerJarEntryName(svattrib.getViewId()));
4673 List<String> pdbfilenames = new ArrayList<>();
4674 List<SequenceI[]> seqmaps = new ArrayList<>();
4675 List<String> pdbids = new ArrayList<>();
4676 StringBuilder newFileLoc = new StringBuilder(64);
4677 int cp = 0, ncp, ecp;
4678 Map<File, StructureData> oldFiles = svattrib.getFileData();
4679 while ((ncp = state.indexOf("load ", cp)) > -1)
4683 // look for next filename in load statement
4684 newFileLoc.append(state.substring(cp,
4685 ncp = (state.indexOf("\"", ncp + 1) + 1)));
4686 String oldfilenam = state.substring(ncp,
4687 ecp = state.indexOf("\"", ncp));
4688 // recover the new mapping data for this old filename
4689 // have to normalize filename - since Jmol and jalview do
4691 // translation differently.
4692 StructureData filedat = oldFiles.get(new File(oldfilenam));
4693 if (filedat == null)
4695 String reformatedOldFilename = oldfilenam.replaceAll("/", "\\\\");
4696 filedat = oldFiles.get(new File(reformatedOldFilename));
4698 newFileLoc.append(Platform.escapeString(filedat.getFilePath()));
4699 pdbfilenames.add(filedat.getFilePath());
4700 pdbids.add(filedat.getPdbId());
4701 seqmaps.add(filedat.getSeqList().toArray(new SequenceI[0]));
4702 newFileLoc.append("\"");
4703 cp = ecp + 1; // advance beyond last \" and set cursor so we can
4704 // look for next file statement.
4705 } while ((ncp = state.indexOf("/*file*/", cp)) > -1);
4709 // just append rest of state
4710 newFileLoc.append(state.substring(cp));
4714 System.err.print("Ignoring incomplete Jmol state for PDB ids: ");
4715 newFileLoc = new StringBuilder(state);
4716 newFileLoc.append("; load append ");
4717 for (File id : oldFiles.keySet())
4719 // add this and any other pdb files that should be present in
4721 StructureData filedat = oldFiles.get(id);
4722 newFileLoc.append(filedat.getFilePath());
4723 pdbfilenames.add(filedat.getFilePath());
4724 pdbids.add(filedat.getPdbId());
4725 seqmaps.add(filedat.getSeqList().toArray(new SequenceI[0]));
4726 newFileLoc.append(" \"");
4727 newFileLoc.append(filedat.getFilePath());
4728 newFileLoc.append("\"");
4731 newFileLoc.append(";");
4734 if (newFileLoc.length() == 0)
4738 int histbug = newFileLoc.indexOf("history = ");
4742 * change "history = [true|false];" to "history = [1|0];"
4745 int diff = histbug == -1 ? -1 : newFileLoc.indexOf(";", histbug);
4746 String val = (diff == -1) ? null
4747 : newFileLoc.substring(histbug, diff);
4748 if (val != null && val.length() >= 4)
4750 if (val.contains("e")) // eh? what can it be?
4752 if (val.trim().equals("true"))
4760 newFileLoc.replace(histbug, diff, val);
4765 final String[] pdbf = pdbfilenames
4766 .toArray(new String[pdbfilenames.size()]);
4767 final String[] id = pdbids.toArray(new String[pdbids.size()]);
4768 final SequenceI[][] sq = seqmaps
4769 .toArray(new SequenceI[seqmaps.size()][]);
4770 final String fileloc = newFileLoc.toString();
4771 final String sviewid = viewerData.getKey();
4772 final AlignFrame alf = af;
4773 final Rectangle rect = new Rectangle(svattrib.getX(), svattrib.getY(),
4774 svattrib.getWidth(), svattrib.getHeight());
4777 Jalview.execRunnable(new Runnable()
4782 JalviewStructureDisplayI sview = null;
4785 sview = new StructureViewer(
4786 alf.alignPanel.getStructureSelectionManager())
4787 .createView(StructureViewer.ViewerType.JMOL,
4788 pdbf, id, sq, alf.alignPanel, svattrib,
4789 fileloc, rect, sviewid);
4790 addNewStructureViewer(sview);
4791 } catch (OutOfMemoryError ex)
4793 new OOMWarning("restoring structure view for PDB id " + id,
4794 (OutOfMemoryError) ex.getCause());
4795 if (sview != null && sview.isVisible())
4797 sview.closeViewer(false);
4798 sview.setVisible(false);
4804 // javax.swing.SwingUtilities.invokeLater(r);
4805 // } catch (InvocationTargetException ex)
4807 // warn("Unexpected error when opening Jmol view.", ex);
4809 // } catch (InterruptedException e)
4811 // // e.printStackTrace();
4817 * Generates a name for the entry in the project jar file to hold state
4818 * information for a structure viewer
4823 protected String getViewerJarEntryName(String viewId)
4825 return VIEWER_PREFIX + viewId;
4829 * Returns any open frame that matches given structure viewer data. The match
4830 * is based on the unique viewId, or (for older project versions) the frame's
4836 protected StructureViewerBase findMatchingViewer(
4837 Entry<String, StructureViewerModel> viewerData)
4839 final String sviewid = viewerData.getKey();
4840 final StructureViewerModel svattrib = viewerData.getValue();
4841 StructureViewerBase comp = null;
4842 JInternalFrame[] frames = getAllFrames();
4843 for (JInternalFrame frame : frames)
4845 if (frame instanceof StructureViewerBase)
4848 * Post jalview 2.4 schema includes structure view id
4850 if (sviewid != null && ((StructureViewerBase) frame).getViewId()
4853 comp = (StructureViewerBase) frame;
4854 break; // break added in 2.9
4857 * Otherwise test for matching position and size of viewer frame
4859 else if (frame.getX() == svattrib.getX()
4860 && frame.getY() == svattrib.getY()
4861 && frame.getHeight() == svattrib.getHeight()
4862 && frame.getWidth() == svattrib.getWidth())
4864 comp = (StructureViewerBase) frame;
4865 // no break in faint hope of an exact match on viewId
4873 * Link an AlignmentPanel to an existing structure viewer.
4878 * @param useinViewerSuperpos
4879 * @param usetoColourbyseq
4880 * @param viewerColouring
4882 protected void linkStructureViewer(AlignmentPanel ap,
4883 StructureViewerBase viewer, StructureViewerModel stateData)
4885 // NOTE: if the jalview project is part of a shared session then
4886 // view synchronization should/could be done here.
4888 final boolean useinViewerSuperpos = stateData.isAlignWithPanel();
4889 final boolean usetoColourbyseq = stateData.isColourWithAlignPanel();
4890 final boolean viewerColouring = stateData.isColourByViewer();
4891 Map<File, StructureData> oldFiles = stateData.getFileData();
4894 * Add mapping for sequences in this view to an already open viewer
4896 final AAStructureBindingModel binding = viewer.getBinding();
4897 for (File id : oldFiles.keySet())
4899 // add this and any other pdb files that should be present in the
4901 StructureData filedat = oldFiles.get(id);
4902 String pdbFile = filedat.getFilePath();
4903 SequenceI[] seq = filedat.getSeqList().toArray(new SequenceI[0]);
4904 binding.getSsm().setMapping(seq, null, pdbFile, DataSourceType.FILE,
4906 binding.addSequenceForStructFile(pdbFile, seq);
4908 // and add the AlignmentPanel's reference to the view panel
4909 viewer.addAlignmentPanel(ap);
4910 if (useinViewerSuperpos)
4912 viewer.useAlignmentPanelForSuperposition(ap);
4916 viewer.excludeAlignmentPanelForSuperposition(ap);
4918 if (usetoColourbyseq)
4920 viewer.useAlignmentPanelForColourbyseq(ap, !viewerColouring);
4924 viewer.excludeAlignmentPanelForColourbyseq(ap);
4929 * Get all frames within the Desktop.
4933 protected JInternalFrame[] getAllFrames()
4935 JInternalFrame[] frames = null;
4936 // TODO is this necessary - is it safe - risk of hanging?
4941 frames = Desktop.getDesktopPane().getAllFrames();
4942 } catch (ArrayIndexOutOfBoundsException e)
4944 // occasional No such child exceptions are thrown here...
4948 } catch (InterruptedException f)
4952 } while (frames == null);
4957 * Answers true if 'version' is equal to or later than 'supported', where each
4958 * is formatted as major/minor versions like "2.8.3" or "2.3.4b1" for bugfix
4959 * changes. Development and test values for 'version' are leniently treated
4963 * - minimum version we are comparing against
4965 * - version of data being processsed
4968 public static boolean isVersionStringLaterThan(String supported,
4971 if (supported == null || version == null
4972 || version.equalsIgnoreCase("DEVELOPMENT BUILD")
4973 || version.equalsIgnoreCase("Test")
4974 || version.equalsIgnoreCase("AUTOMATED BUILD"))
4976 System.err.println("Assuming project file with "
4977 + (version == null ? "null" : version)
4978 + " is compatible with Jalview version " + supported);
4983 return StringUtils.compareVersions(version, supported, "b") >= 0;
4987 Vector<JalviewStructureDisplayI> newStructureViewers = null;
4989 protected void addNewStructureViewer(JalviewStructureDisplayI sview)
4991 if (newStructureViewers != null)
4993 sview.getBinding().setFinishedLoadingFromArchive(false);
4994 newStructureViewers.add(sview);
4998 protected void setLoadingFinishedForNewStructureViewers()
5000 if (newStructureViewers != null)
5002 for (JalviewStructureDisplayI sview : newStructureViewers)
5004 sview.getBinding().setFinishedLoadingFromArchive(true);
5006 newStructureViewers.clear();
5007 newStructureViewers = null;
5011 AlignFrame loadViewport(String fileName, List<JSeq> JSEQ,
5012 List<SequenceI> hiddenSeqs, AlignmentI al, JalviewModel jm,
5013 Viewport view, String uniqueSeqSetId, String viewId,
5014 List<JvAnnotRow> autoAlan)
5016 AlignFrame af = null;
5017 af = new AlignFrame(al, safeInt(view.getWidth()),
5018 safeInt(view.getHeight()), uniqueSeqSetId, viewId)
5022 // protected void processKeyEvent(java.awt.event.KeyEvent e) {
5023 // System.out.println("Jalview2XML AF " + e);
5024 // super.processKeyEvent(e);
5030 af.alignPanel.setHoldRepaint(true);
5031 af.setFileName(fileName, FileFormat.Jalview);
5032 af.setFileObject(jarFile); // BH 2019 JAL-3436
5034 final AlignViewport viewport = af.getViewport();
5035 for (int i = 0; i < JSEQ.size(); i++)
5037 int colour = safeInt(JSEQ.get(i).getColour());
5038 viewport.setSequenceColour(viewport.getAlignment().getSequenceAt(i),
5044 viewport.setColourByReferenceSeq(true);
5045 viewport.setDisplayReferenceSeq(true);
5048 viewport.setGatherViewsHere(safeBoolean(view.isGatheredViews()));
5050 if (view.getSequenceSetId() != null)
5052 AlignmentViewport av = viewportsAdded.get(uniqueSeqSetId);
5054 viewport.setSequenceSetId(uniqueSeqSetId);
5057 // propagate shared settings to this new view
5058 viewport.setHistoryList(av.getHistoryList());
5059 viewport.setRedoList(av.getRedoList());
5063 viewportsAdded.put(uniqueSeqSetId, viewport);
5065 // TODO: check if this method can be called repeatedly without
5066 // side-effects if alignpanel already registered.
5067 PaintRefresher.Register(af.alignPanel, uniqueSeqSetId);
5069 // apply Hidden regions to view.
5070 if (hiddenSeqs != null)
5072 for (int s = 0; s < JSEQ.size(); s++)
5074 SequenceGroup hidden = new SequenceGroup();
5075 boolean isRepresentative = false;
5076 for (int r = 0; r < JSEQ.get(s).getHiddenSequences().size(); r++)
5078 isRepresentative = true;
5079 SequenceI sequenceToHide = al
5080 .getSequenceAt(JSEQ.get(s).getHiddenSequences().get(r));
5081 hidden.addSequence(sequenceToHide, false);
5082 // remove from hiddenSeqs list so we don't try to hide it twice
5083 hiddenSeqs.remove(sequenceToHide);
5085 if (isRepresentative)
5087 SequenceI representativeSequence = al.getSequenceAt(s);
5088 hidden.addSequence(representativeSequence, false);
5089 viewport.hideRepSequences(representativeSequence, hidden);
5093 SequenceI[] hseqs = hiddenSeqs
5094 .toArray(new SequenceI[hiddenSeqs.size()]);
5095 viewport.hideSequence(hseqs);
5098 // recover view properties and display parameters
5100 viewport.setShowAnnotation(safeBoolean(view.isShowAnnotation()));
5101 viewport.setAbovePIDThreshold(safeBoolean(view.isPidSelected()));
5102 final int pidThreshold = safeInt(view.getPidThreshold());
5103 viewport.setThreshold(pidThreshold);
5105 viewport.setColourText(safeBoolean(view.isShowColourText()));
5107 viewport.setConservationSelected(
5108 safeBoolean(view.isConservationSelected()));
5109 viewport.setIncrement(safeInt(view.getConsThreshold()));
5110 viewport.setShowJVSuffix(safeBoolean(view.isShowFullId()));
5111 viewport.setRightAlignIds(safeBoolean(view.isRightAlignIds()));
5112 viewport.setFont(new Font(view.getFontName(),
5113 safeInt(view.getFontStyle()), safeInt(view.getFontSize())),
5115 ViewStyleI vs = viewport.getViewStyle();
5116 vs.setScaleProteinAsCdna(view.isScaleProteinAsCdna());
5117 viewport.setViewStyle(vs);
5118 // TODO: allow custom charWidth/Heights to be restored by updating them
5119 // after setting font - which means set above to false
5120 viewport.setRenderGaps(safeBoolean(view.isRenderGaps()));
5121 viewport.setWrapAlignment(safeBoolean(view.isWrapAlignment()));
5122 viewport.setShowAnnotation(safeBoolean(view.isShowAnnotation()));
5124 viewport.setShowBoxes(safeBoolean(view.isShowBoxes()));
5126 viewport.setShowText(safeBoolean(view.isShowText()));
5128 viewport.setTextColour(new Color(safeInt(view.getTextCol1())));
5129 viewport.setTextColour2(new Color(safeInt(view.getTextCol2())));
5130 viewport.setThresholdTextColour(safeInt(view.getTextColThreshold()));
5131 viewport.setShowUnconserved(view.isShowUnconserved());
5132 viewport.getRanges().setStartRes(safeInt(view.getStartRes()));
5134 if (view.getViewName() != null)
5136 viewport.setViewName(view.getViewName());
5137 af.setInitialTabVisible();
5139 int x = safeInt(view.getXpos());
5140 int y = safeInt(view.getYpos());
5141 int w = safeInt(view.getWidth());
5142 int h = safeInt(view.getHeight());
5143 // // BH we cannot let the title bar go off the top
5144 // if (Platform.isJS())
5146 // x = Math.max(50 - w, x);
5147 // y = Math.max(0, y);
5150 af.setBounds(x, y, w, h);
5151 // startSeq set in af.alignPanel.updateLayout below
5152 af.alignPanel.updateLayout();
5153 ColourSchemeI cs = null;
5154 // apply colourschemes
5155 if (view.getBgColour() != null)
5157 if (view.getBgColour().startsWith("ucs"))
5159 cs = getUserColourScheme(jm, view.getBgColour());
5161 else if (view.getBgColour().startsWith("Annotation"))
5163 AnnotationColourScheme viewAnnColour = view.getAnnotationColours();
5164 cs = constructAnnotationColour(viewAnnColour, af, al, jm, true);
5171 cs = ColourSchemeProperty.getColourScheme(af.getViewport(), al,
5172 view.getBgColour());
5177 * turn off 'alignment colour applies to all groups'
5178 * while restoring global colour scheme
5180 viewport.setColourAppliesToAllGroups(false);
5181 viewport.setGlobalColourScheme(cs);
5182 viewport.getResidueShading().setThreshold(pidThreshold,
5183 view.isIgnoreGapsinConsensus());
5184 viewport.getResidueShading()
5185 .setConsensus(viewport.getSequenceConsensusHash());
5186 if (safeBoolean(view.isConservationSelected()) && cs != null)
5188 viewport.getResidueShading()
5189 .setConservationInc(safeInt(view.getConsThreshold()));
5191 af.changeColour(cs);
5192 viewport.setColourAppliesToAllGroups(true);
5194 viewport.setShowSequenceFeatures(
5195 safeBoolean(view.isShowSequenceFeatures()));
5197 viewport.setCentreColumnLabels(view.isCentreColumnLabels());
5198 viewport.setIgnoreGapsConsensus(view.isIgnoreGapsinConsensus(), null);
5199 viewport.setFollowHighlight(view.isFollowHighlight());
5200 viewport.followSelection = view.isFollowSelection();
5201 viewport.setShowConsensusHistogram(view.isShowConsensusHistogram());
5202 viewport.setShowSequenceLogo(view.isShowSequenceLogo());
5203 viewport.setNormaliseSequenceLogo(view.isNormaliseSequenceLogo());
5204 viewport.setShowDBRefs(safeBoolean(view.isShowDbRefTooltip()));
5205 viewport.setShowNPFeats(safeBoolean(view.isShowNPfeatureTooltip()));
5206 viewport.setShowGroupConsensus(view.isShowGroupConsensus());
5207 viewport.setShowGroupConservation(view.isShowGroupConservation());
5209 // recover feature settings
5210 if (jm.getFeatureSettings() != null)
5212 FeatureRenderer fr = af.alignPanel.getSeqPanel().seqCanvas
5213 .getFeatureRenderer();
5214 FeaturesDisplayed fdi;
5215 viewport.setFeaturesDisplayed(fdi = new FeaturesDisplayed());
5216 String[] renderOrder = new String[jm.getFeatureSettings().getSetting()
5218 Map<String, FeatureColourI> featureColours = new Hashtable<>();
5219 Map<String, Float> featureOrder = new Hashtable<>();
5221 for (int fs = 0; fs < jm.getFeatureSettings().getSetting()
5224 Setting setting = jm.getFeatureSettings().getSetting().get(fs);
5225 String featureType = setting.getType();
5228 * restore feature filters (if any)
5230 jalview.xml.binding.jalview.FeatureMatcherSet filters = setting
5232 if (filters != null)
5234 FeatureMatcherSetI filter = Jalview2XML.parseFilter(featureType,
5236 if (!filter.isEmpty())
5238 fr.setFeatureFilter(featureType, filter);
5243 * restore feature colour scheme
5245 Color maxColour = new Color(setting.getColour());
5246 if (setting.getMincolour() != null)
5249 * minColour is always set unless a simple colour
5250 * (including for colour by label though it doesn't use it)
5252 Color minColour = new Color(setting.getMincolour().intValue());
5253 Color noValueColour = minColour;
5254 NoValueColour noColour = setting.getNoValueColour();
5255 if (noColour == NoValueColour.NONE)
5257 noValueColour = null;
5259 else if (noColour == NoValueColour.MAX)
5261 noValueColour = maxColour;
5263 float min = safeFloat(safeFloat(setting.getMin()));
5264 float max = setting.getMax() == null ? 1f
5265 : setting.getMax().floatValue();
5266 FeatureColourI gc = new FeatureColour(maxColour, minColour,
5267 maxColour, noValueColour, min, max);
5268 if (setting.getAttributeName().size() > 0)
5270 gc.setAttributeName(setting.getAttributeName().toArray(
5271 new String[setting.getAttributeName().size()]));
5273 if (setting.getThreshold() != null)
5275 gc.setThreshold(setting.getThreshold().floatValue());
5276 int threshstate = safeInt(setting.getThreshstate());
5277 // -1 = None, 0 = Below, 1 = Above threshold
5278 if (threshstate == 0)
5280 gc.setBelowThreshold(true);
5282 else if (threshstate == 1)
5284 gc.setAboveThreshold(true);
5287 gc.setAutoScaled(true); // default
5288 if (setting.isAutoScale() != null)
5290 gc.setAutoScaled(setting.isAutoScale());
5292 if (setting.isColourByLabel() != null)
5294 gc.setColourByLabel(setting.isColourByLabel());
5296 // and put in the feature colour table.
5297 featureColours.put(featureType, gc);
5301 featureColours.put(featureType, new FeatureColour(maxColour));
5303 renderOrder[fs] = featureType;
5304 if (setting.getOrder() != null)
5306 featureOrder.put(featureType, setting.getOrder().floatValue());
5310 featureOrder.put(featureType, new Float(
5311 fs / jm.getFeatureSettings().getSetting().size()));
5313 if (safeBoolean(setting.isDisplay()))
5315 fdi.setVisible(featureType);
5318 Map<String, Boolean> fgtable = new Hashtable<>();
5319 for (int gs = 0; gs < jm.getFeatureSettings().getGroup().size(); gs++)
5321 Group grp = jm.getFeatureSettings().getGroup().get(gs);
5322 fgtable.put(grp.getName(), new Boolean(grp.isDisplay()));
5324 // FeatureRendererSettings frs = new FeatureRendererSettings(renderOrder,
5325 // fgtable, featureColours, jms.getFeatureSettings().hasTransparency() ?
5326 // jms.getFeatureSettings().getTransparency() : 0.0, featureOrder);
5327 FeatureRendererSettings frs = new FeatureRendererSettings(renderOrder,
5328 fgtable, featureColours, 1.0f, featureOrder);
5329 fr.transferSettings(frs);
5332 if (view.getHiddenColumns().size() > 0)
5334 for (int c = 0; c < view.getHiddenColumns().size(); c++)
5336 final HiddenColumns hc = view.getHiddenColumns().get(c);
5337 viewport.hideColumns(safeInt(hc.getStart()),
5338 safeInt(hc.getEnd()) /* +1 */);
5341 if (view.getCalcIdParam() != null)
5343 for (CalcIdParam calcIdParam : view.getCalcIdParam())
5345 if (calcIdParam != null)
5347 if (recoverCalcIdParam(calcIdParam, viewport))
5352 warn("Couldn't recover parameters for "
5353 + calcIdParam.getCalcId());
5358 af.setMenusFromViewport(viewport);
5359 af.setTitle(view.getTitle());
5360 // TODO: we don't need to do this if the viewport is aready visible.
5362 * Add the AlignFrame to the desktop (it may be 'gathered' later), unless it
5363 * has a 'cdna/protein complement' view, in which case save it in order to
5364 * populate a SplitFrame once all views have been read in.
5366 String complementaryViewId = view.getComplementId();
5367 if (complementaryViewId == null)
5369 Dimension dim = Platform.getDimIfEmbedded(af,
5370 safeInt(view.getWidth()), safeInt(view.getHeight()));
5371 Desktop.addInternalFrame(af, view.getTitle(), dim.width, dim.height);
5372 // recompute any autoannotation
5373 af.alignPanel.updateAnnotation(false, true);
5374 reorderAutoannotation(af, al, autoAlan);
5375 af.alignPanel.alignmentChanged();
5379 splitFrameCandidates.put(view, af);
5385 * Reads saved data to restore Colour by Annotation settings
5387 * @param viewAnnColour
5391 * @param checkGroupAnnColour
5394 private ColourSchemeI constructAnnotationColour(
5395 AnnotationColourScheme viewAnnColour, AlignFrame af,
5396 AlignmentI al, JalviewModel model, boolean checkGroupAnnColour)
5398 boolean propagateAnnColour = false;
5399 AlignmentI annAlignment = af != null ? af.getViewport().getAlignment()
5401 if (checkGroupAnnColour && al.getGroups() != null
5402 && al.getGroups().size() > 0)
5404 // pre 2.8.1 behaviour
5405 // check to see if we should transfer annotation colours
5406 propagateAnnColour = true;
5407 for (SequenceGroup sg : al.getGroups())
5409 if (sg.getColourScheme() instanceof AnnotationColourGradient)
5411 propagateAnnColour = false;
5417 * 2.10.2- : saved annotationId is AlignmentAnnotation.annotationId
5419 String annotationId = viewAnnColour.getAnnotation();
5420 AlignmentAnnotation matchedAnnotation = annotationIds.get(annotationId);
5423 * pre 2.10.2: saved annotationId is AlignmentAnnotation.label
5425 if (matchedAnnotation == null
5426 && annAlignment.getAlignmentAnnotation() != null)
5428 for (int i = 0; i < annAlignment.getAlignmentAnnotation().length; i++)
5431 .equals(annAlignment.getAlignmentAnnotation()[i].label))
5433 matchedAnnotation = annAlignment.getAlignmentAnnotation()[i];
5438 if (matchedAnnotation == null)
5440 System.err.println("Failed to match annotation colour scheme for "
5444 if (matchedAnnotation.getThreshold() == null)
5446 matchedAnnotation.setThreshold(
5447 new GraphLine(safeFloat(viewAnnColour.getThreshold()),
5448 "Threshold", Color.black));
5451 AnnotationColourGradient cs = null;
5452 if (viewAnnColour.getColourScheme().equals("None"))
5454 cs = new AnnotationColourGradient(matchedAnnotation,
5455 new Color(safeInt(viewAnnColour.getMinColour())),
5456 new Color(safeInt(viewAnnColour.getMaxColour())),
5457 safeInt(viewAnnColour.getAboveThreshold()));
5459 else if (viewAnnColour.getColourScheme().startsWith("ucs"))
5461 cs = new AnnotationColourGradient(matchedAnnotation,
5462 getUserColourScheme(model, viewAnnColour.getColourScheme()),
5463 safeInt(viewAnnColour.getAboveThreshold()));
5467 cs = new AnnotationColourGradient(matchedAnnotation,
5468 ColourSchemeProperty.getColourScheme(af.getViewport(), al,
5469 viewAnnColour.getColourScheme()),
5470 safeInt(viewAnnColour.getAboveThreshold()));
5473 boolean perSequenceOnly = safeBoolean(viewAnnColour.isPerSequence());
5474 boolean useOriginalColours = safeBoolean(
5475 viewAnnColour.isPredefinedColours());
5476 cs.setSeqAssociated(perSequenceOnly);
5477 cs.setPredefinedColours(useOriginalColours);
5479 if (propagateAnnColour && al.getGroups() != null)
5481 // Also use these settings for all the groups
5482 for (int g = 0; g < al.getGroups().size(); g++)
5484 SequenceGroup sg = al.getGroups().get(g);
5485 if (sg.getGroupColourScheme() == null)
5490 AnnotationColourGradient groupScheme = new AnnotationColourGradient(
5491 matchedAnnotation, sg.getColourScheme(),
5492 safeInt(viewAnnColour.getAboveThreshold()));
5493 sg.setColourScheme(groupScheme);
5494 groupScheme.setSeqAssociated(perSequenceOnly);
5495 groupScheme.setPredefinedColours(useOriginalColours);
5501 private void reorderAutoannotation(AlignFrame af, AlignmentI al,
5502 List<JvAnnotRow> autoAlan)
5504 // copy over visualization settings for autocalculated annotation in the
5506 if (al.getAlignmentAnnotation() != null)
5509 * Kludge for magic autoannotation names (see JAL-811)
5511 String[] magicNames = new String[] { "Consensus", "Quality",
5513 JvAnnotRow nullAnnot = new JvAnnotRow(-1, null);
5514 Hashtable<String, JvAnnotRow> visan = new Hashtable<>();
5515 for (String nm : magicNames)
5517 visan.put(nm, nullAnnot);
5519 for (JvAnnotRow auan : autoAlan)
5521 visan.put(auan.template.label
5522 + (auan.template.getCalcId() == null ? ""
5523 : "\t" + auan.template.getCalcId()),
5526 int hSize = al.getAlignmentAnnotation().length;
5527 List<JvAnnotRow> reorder = new ArrayList<>();
5528 // work through any autoCalculated annotation already on the view
5529 // removing it if it should be placed in a different location on the
5530 // annotation panel.
5531 List<String> remains = new ArrayList<>(visan.keySet());
5532 for (int h = 0; h < hSize; h++)
5534 jalview.datamodel.AlignmentAnnotation jalan = al
5535 .getAlignmentAnnotation()[h];
5536 if (jalan.autoCalculated)
5539 JvAnnotRow valan = visan.get(k = jalan.label);
5540 if (jalan.getCalcId() != null)
5542 valan = visan.get(k = jalan.label + "\t" + jalan.getCalcId());
5547 // delete the auto calculated row from the alignment
5548 al.deleteAnnotation(jalan, false);
5552 if (valan != nullAnnot)
5554 if (jalan != valan.template)
5556 // newly created autoannotation row instance
5557 // so keep a reference to the visible annotation row
5558 // and copy over all relevant attributes
5559 if (valan.template.graphHeight >= 0)
5562 jalan.graphHeight = valan.template.graphHeight;
5564 jalan.visible = valan.template.visible;
5566 reorder.add(new JvAnnotRow(valan.order, jalan));
5571 // Add any (possibly stale) autocalculated rows that were not appended to
5572 // the view during construction
5573 for (String other : remains)
5575 JvAnnotRow othera = visan.get(other);
5576 if (othera != nullAnnot && othera.template.getCalcId() != null
5577 && othera.template.getCalcId().length() > 0)
5579 reorder.add(othera);
5582 // now put the automatic annotation in its correct place
5583 int s = 0, srt[] = new int[reorder.size()];
5584 JvAnnotRow[] rws = new JvAnnotRow[reorder.size()];
5585 for (JvAnnotRow jvar : reorder)
5588 srt[s++] = jvar.order;
5591 jalview.util.QuickSort.sort(srt, rws);
5592 // and re-insert the annotation at its correct position
5593 for (JvAnnotRow jvar : rws)
5595 al.addAnnotation(jvar.template, jvar.order);
5597 af.alignPanel.adjustAnnotationHeight();
5601 Hashtable skipList = null;
5604 * TODO remove this method
5607 * @return AlignFrame bound to sequenceSetId from view, if one exists. private
5608 * AlignFrame getSkippedFrame(Viewport view) { if (skipList==null) {
5609 * throw new Error("Implementation Error. No skipList defined for this
5610 * Jalview2XML instance."); } return (AlignFrame)
5611 * skipList.get(view.getSequenceSetId()); }
5615 * Check if the Jalview view contained in object should be skipped or not.
5618 * @return true if view's sequenceSetId is a key in skipList
5620 private boolean skipViewport(JalviewModel object)
5622 if (skipList == null)
5626 String id = object.getViewport().get(0).getSequenceSetId();
5627 if (skipList.containsKey(id))
5629 if (Cache.log != null && Cache.log.isDebugEnabled())
5631 Cache.log.debug("Skipping seuqence set id " + id);
5638 protected void addToSkipList(AlignFrame af)
5640 if (skipList == null)
5642 skipList = new Hashtable();
5644 skipList.put(af.getViewport().getSequenceSetId(), af);
5647 protected void clearSkipList()
5649 if (skipList != null)
5656 private void recoverDatasetFor(SequenceSet vamsasSet, AlignmentI al,
5657 boolean ignoreUnrefed, String uniqueSeqSetId)
5659 jalview.datamodel.AlignmentI ds = getDatasetFor(
5660 vamsasSet.getDatasetId());
5661 AlignmentI xtant_ds = ds;
5662 if (xtant_ds == null)
5664 // good chance we are about to create a new dataset, but check if we've
5665 // seen some of the dataset sequence IDs before.
5666 // TODO: skip this check if we are working with project generated by
5667 // version 2.11 or later
5668 xtant_ds = checkIfHasDataset(vamsasSet.getSequence());
5669 if (xtant_ds != null)
5672 addDatasetRef(vamsasSet.getDatasetId(), ds);
5675 Vector dseqs = null;
5678 // recovering an alignment View
5679 AlignmentI seqSetDS = getDatasetFor(UNIQSEQSETID + uniqueSeqSetId);
5680 if (seqSetDS != null)
5682 if (ds != null && ds != seqSetDS)
5684 warn("JAL-3171 regression: Overwriting a dataset reference for an alignment"
5685 + " - CDS/Protein crossreference data may be lost");
5686 if (xtant_ds != null)
5688 // This can only happen if the unique sequence set ID was bound to a
5689 // dataset that did not contain any of the sequences in the view
5690 // currently being restored.
5691 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.");
5695 addDatasetRef(vamsasSet.getDatasetId(), ds);
5700 // try even harder to restore dataset
5701 AlignmentI xtantDS = checkIfHasDataset(vamsasSet.getSequence());
5702 // create a list of new dataset sequences
5703 dseqs = new Vector();
5705 for (int i = 0, iSize = vamsasSet.getSequence().size(); i < iSize; i++)
5707 Sequence vamsasSeq = vamsasSet.getSequence().get(i);
5708 ensureJalviewDatasetSequence(vamsasSeq, ds, dseqs, ignoreUnrefed, i);
5710 // create a new dataset
5713 SequenceI[] dsseqs = new SequenceI[dseqs.size()];
5714 dseqs.copyInto(dsseqs);
5715 ds = new jalview.datamodel.Alignment(dsseqs);
5716 // debug("Jalview2XML Created new dataset " + vamsasSet.getDatasetId()
5717 // + " for alignment " + System.identityHashCode(al));
5718 addDatasetRef(vamsasSet.getDatasetId(), ds);
5720 // set the dataset for the newly imported alignment.
5721 if (al.getDataset() == null && !ignoreUnrefed)
5724 // register dataset for the alignment's uniqueSeqSetId for legacy projects
5725 addDatasetRef(UNIQSEQSETID + uniqueSeqSetId, ds);
5727 updateSeqDatasetBinding(vamsasSet.getSequence(), ds);
5731 * XML dataset sequence ID to materialised dataset reference
5733 HashMap<String, AlignmentI> seqToDataset = new HashMap<>();
5736 * @return the first materialised dataset reference containing a dataset
5737 * sequence referenced in the given view
5739 * - sequences from the view
5741 AlignmentI checkIfHasDataset(List<Sequence> list)
5743 for (Sequence restoredSeq : list)
5745 AlignmentI datasetFor = seqToDataset.get(restoredSeq.getDsseqid());
5746 if (datasetFor != null)
5755 * Register ds as the containing dataset for the dataset sequences referenced
5756 * by sequences in list
5759 * - sequences in a view
5762 void updateSeqDatasetBinding(List<Sequence> list, AlignmentI ds)
5764 for (Sequence restoredSeq : list)
5766 AlignmentI prevDS = seqToDataset.put(restoredSeq.getDsseqid(), ds);
5767 if (prevDS != null && prevDS != ds)
5769 warn("Dataset sequence appears in many datasets: "
5770 + restoredSeq.getDsseqid());
5771 // TODO: try to merge!
5778 * sequence definition to create/merge dataset sequence for
5782 * vector to add new dataset sequence to
5783 * @param ignoreUnrefed
5784 * - when true, don't create new sequences from vamsasSeq if it's id
5785 * doesn't already have an asssociated Jalview sequence.
5787 * - used to reorder the sequence in the alignment according to the
5788 * vamsasSeq array ordering, to preserve ordering of dataset
5790 private void ensureJalviewDatasetSequence(Sequence vamsasSeq,
5791 AlignmentI ds, Vector dseqs, boolean ignoreUnrefed, int vseqpos)
5793 // JBP TODO: Check this is called for AlCodonFrames to support recovery of
5795 SequenceI sq = seqRefIds.get(vamsasSeq.getId());
5796 boolean reorder = false;
5797 SequenceI dsq = null;
5798 if (sq != null && sq.getDatasetSequence() != null)
5800 dsq = sq.getDatasetSequence();
5806 if (sq == null && ignoreUnrefed)
5810 String sqid = vamsasSeq.getDsseqid();
5813 // need to create or add a new dataset sequence reference to this sequence
5816 dsq = seqRefIds.get(sqid);
5821 // make a new dataset sequence
5822 dsq = sq.createDatasetSequence();
5825 // make up a new dataset reference for this sequence
5826 sqid = seqHash(dsq);
5828 dsq.setVamsasId(uniqueSetSuffix + sqid);
5829 seqRefIds.put(sqid, dsq);
5834 dseqs.addElement(dsq);
5839 ds.addSequence(dsq);
5845 { // make this dataset sequence sq's dataset sequence
5846 sq.setDatasetSequence(dsq);
5847 // and update the current dataset alignment
5852 if (!dseqs.contains(dsq))
5859 if (ds.findIndex(dsq) < 0)
5861 ds.addSequence(dsq);
5868 // TODO: refactor this as a merge dataset sequence function
5869 // now check that sq (the dataset sequence) sequence really is the union of
5870 // all references to it
5871 // boolean pre = sq.getStart() < dsq.getStart();
5872 // boolean post = sq.getEnd() > dsq.getEnd();
5876 // StringBuffer sb = new StringBuffer();
5877 String newres = jalview.analysis.AlignSeq.extractGaps(
5878 jalview.util.Comparison.GapChars, sq.getSequenceAsString());
5879 if (!newres.equalsIgnoreCase(dsq.getSequenceAsString())
5880 && newres.length() > dsq.getLength())
5882 // Update with the longer sequence.
5886 * if (pre) { sb.insert(0, newres .substring(0, dsq.getStart() -
5887 * sq.getStart())); dsq.setStart(sq.getStart()); } if (post) {
5888 * sb.append(newres.substring(newres.length() - sq.getEnd() -
5889 * dsq.getEnd())); dsq.setEnd(sq.getEnd()); }
5891 dsq.setSequence(newres);
5893 // TODO: merges will never happen if we 'know' we have the real dataset
5894 // sequence - this should be detected when id==dssid
5896 "DEBUG Notice: Merged dataset sequence (if you see this often, post at http://issues.jalview.org/browse/JAL-1474)"); // ("
5897 // + (pre ? "prepended" : "") + " "
5898 // + (post ? "appended" : ""));
5903 // sequence refs are identical. We may need to update the existing dataset
5904 // alignment with this one, though.
5905 if (ds != null && dseqs == null)
5907 int opos = ds.findIndex(dsq);
5908 SequenceI tseq = null;
5909 if (opos != -1 && vseqpos != opos)
5911 // remove from old position
5912 ds.deleteSequence(dsq);
5914 if (vseqpos < ds.getHeight())
5916 if (vseqpos != opos)
5918 // save sequence at destination position
5919 tseq = ds.getSequenceAt(vseqpos);
5920 ds.replaceSequenceAt(vseqpos, dsq);
5921 ds.addSequence(tseq);
5926 ds.addSequence(dsq);
5933 * TODO use AlignmentI here and in related methods - needs
5934 * AlignmentI.getDataset() changed to return AlignmentI instead of Alignment
5936 Hashtable<String, AlignmentI> datasetIds = null;
5938 IdentityHashMap<AlignmentI, String> dataset2Ids = null;
5940 private AlignmentI getDatasetFor(String datasetId)
5942 if (datasetIds == null)
5944 datasetIds = new Hashtable<>();
5947 if (datasetIds.containsKey(datasetId))
5949 return datasetIds.get(datasetId);
5954 private void addDatasetRef(String datasetId, AlignmentI dataset)
5956 if (datasetIds == null)
5958 datasetIds = new Hashtable<>();
5960 datasetIds.put(datasetId, dataset);
5964 * make a new dataset ID for this jalview dataset alignment
5969 private String getDatasetIdRef(AlignmentI dataset)
5971 if (dataset.getDataset() != null)
5973 warn("Serious issue! Dataset Object passed to getDatasetIdRef is not a Jalview DATASET alignment...");
5975 String datasetId = makeHashCode(dataset, null);
5976 if (datasetId == null)
5978 // make a new datasetId and record it
5979 if (dataset2Ids == null)
5981 dataset2Ids = new IdentityHashMap<>();
5985 datasetId = dataset2Ids.get(dataset);
5987 if (datasetId == null)
5989 datasetId = "ds" + dataset2Ids.size() + 1;
5990 dataset2Ids.put(dataset, datasetId);
5996 private void addDBRefs(SequenceI datasetSequence, Sequence sequence)
5998 for (int d = 0; d < sequence.getDBRef().size(); d++)
6000 DBRef dr = sequence.getDBRef().get(d);
6001 jalview.datamodel.DBRefEntry entry = new jalview.datamodel.DBRefEntry(
6002 dr.getSource(), dr.getVersion(), dr.getAccessionId());
6003 if (dr.getMapping() != null)
6005 entry.setMap(addMapping(dr.getMapping()));
6007 datasetSequence.addDBRef(entry);
6011 private jalview.datamodel.Mapping addMapping(Mapping m)
6013 SequenceI dsto = null;
6014 // Mapping m = dr.getMapping();
6015 int fr[] = new int[m.getMapListFrom().size() * 2];
6016 Iterator<MapListFrom> from = m.getMapListFrom().iterator();// enumerateMapListFrom();
6017 for (int _i = 0; from.hasNext(); _i += 2)
6019 MapListFrom mf = from.next();
6020 fr[_i] = mf.getStart();
6021 fr[_i + 1] = mf.getEnd();
6023 int fto[] = new int[m.getMapListTo().size() * 2];
6024 Iterator<MapListTo> to = m.getMapListTo().iterator();// enumerateMapListTo();
6025 for (int _i = 0; to.hasNext(); _i += 2)
6027 MapListTo mf = to.next();
6028 fto[_i] = mf.getStart();
6029 fto[_i + 1] = mf.getEnd();
6031 jalview.datamodel.Mapping jmap = new jalview.datamodel.Mapping(dsto, fr,
6032 fto, m.getMapFromUnit().intValue(),
6033 m.getMapToUnit().intValue());
6036 * (optional) choice of dseqFor or Sequence
6038 if (m.getDseqFor() != null)
6040 String dsfor = m.getDseqFor();
6041 if (seqRefIds.containsKey(dsfor))
6046 jmap.setTo(seqRefIds.get(dsfor));
6050 frefedSequence.add(newMappingRef(dsfor, jmap));
6053 else if (m.getSequence() != null)
6056 * local sequence definition
6058 Sequence ms = m.getSequence();
6059 SequenceI djs = null;
6060 String sqid = ms.getDsseqid();
6061 if (sqid != null && sqid.length() > 0)
6064 * recover dataset sequence
6066 djs = seqRefIds.get(sqid);
6071 "Warning - making up dataset sequence id for DbRef sequence map reference");
6072 sqid = ((Object) ms).toString(); // make up a new hascode for
6073 // undefined dataset sequence hash
6074 // (unlikely to happen)
6080 * make a new dataset sequence and add it to refIds hash
6082 djs = new jalview.datamodel.Sequence(ms.getName(),
6084 djs.setStart(jmap.getMap().getToLowest());
6085 djs.setEnd(jmap.getMap().getToHighest());
6086 djs.setVamsasId(uniqueSetSuffix + sqid);
6088 incompleteSeqs.put(sqid, djs);
6089 seqRefIds.put(sqid, djs);
6092 jalview.bin.Cache.log.debug("about to recurse on addDBRefs.");
6101 * Provides a 'copy' of an alignment view (on action New View) by 'saving' the
6102 * view as XML (but not to file), and then reloading it
6107 public AlignmentPanel copyAlignPanel(AlignmentPanel ap)
6110 JalviewModel jm = saveState(ap, null, null, null);
6113 jm.getVamsasModel().getSequenceSet().get(0).getDatasetId(),
6114 ap.getAlignment().getDataset());
6116 uniqueSetSuffix = "";
6117 // jm.getJalviewModelSequence().getViewport(0).setId(null);
6118 jm.getViewport().get(0).setId(null);
6119 // we don't overwrite the view we just copied
6121 if (this.frefedSequence == null)
6123 frefedSequence = new Vector<>();
6126 viewportsAdded.clear();
6128 AlignFrame af = loadFromObject(jm, null, false, null);
6129 af.getAlignPanels().clear();
6130 af.closeMenuItem_actionPerformed(true);
6131 af.alignPanel.setHoldRepaint(false);
6132 this.jarFile = null;
6134 return af.alignPanel;
6137 private Hashtable jvids2vobj;
6139 private void warn(String msg)
6144 private void warn(String msg, Exception e)
6146 if (Cache.log != null)
6150 Cache.log.warn(msg, e);
6154 Cache.log.warn(msg);
6159 System.err.println("Warning: " + msg);
6162 e.printStackTrace();
6167 private void debug(String string)
6169 debug(string, null);
6172 private void debug(String msg, Exception e)
6174 if (Cache.log != null)
6178 Cache.log.debug(msg, e);
6182 Cache.log.debug(msg);
6187 System.err.println("Warning: " + msg);
6190 e.printStackTrace();
6196 * set the object to ID mapping tables used to write/recover objects and XML
6197 * ID strings for the jalview project. If external tables are provided then
6198 * finalize and clearSeqRefs will not clear the tables when the Jalview2XML
6199 * object goes out of scope. - also populates the datasetIds hashtable with
6200 * alignment objects containing dataset sequences
6203 * Map from ID strings to jalview datamodel
6205 * Map from jalview datamodel to ID strings
6209 public void setObjectMappingTables(Hashtable vobj2jv,
6210 IdentityHashMap jv2vobj)
6212 this.jv2vobj = jv2vobj;
6213 this.vobj2jv = vobj2jv;
6214 Iterator ds = jv2vobj.keySet().iterator();
6216 while (ds.hasNext())
6218 Object jvobj = ds.next();
6219 id = jv2vobj.get(jvobj).toString();
6220 if (jvobj instanceof jalview.datamodel.Alignment)
6222 if (((jalview.datamodel.Alignment) jvobj).getDataset() == null)
6224 addDatasetRef(id, (jalview.datamodel.Alignment) jvobj);
6227 else if (jvobj instanceof jalview.datamodel.Sequence)
6229 // register sequence object so the XML parser can recover it.
6230 if (seqRefIds == null)
6232 seqRefIds = new HashMap<>();
6234 if (seqsToIds == null)
6236 seqsToIds = new IdentityHashMap<>();
6238 seqRefIds.put(jv2vobj.get(jvobj).toString(), (SequenceI) jvobj);
6239 seqsToIds.put((SequenceI) jvobj, id);
6241 else if (jvobj instanceof jalview.datamodel.AlignmentAnnotation)
6244 AlignmentAnnotation jvann = (AlignmentAnnotation) jvobj;
6245 annotationIds.put(anid = jv2vobj.get(jvobj).toString(), jvann);
6246 if (jvann.annotationId == null)
6248 jvann.annotationId = anid;
6250 if (!jvann.annotationId.equals(anid))
6252 // TODO verify that this is the correct behaviour
6253 this.warn("Overriding Annotation ID for " + anid
6254 + " from different id : " + jvann.annotationId);
6255 jvann.annotationId = anid;
6258 else if (jvobj instanceof String)
6260 if (jvids2vobj == null)
6262 jvids2vobj = new Hashtable();
6263 jvids2vobj.put(jvobj, jv2vobj.get(jvobj).toString());
6268 Cache.log.debug("Ignoring " + jvobj.getClass() + " (ID = " + id);
6274 * set the uniqueSetSuffix used to prefix/suffix object IDs for jalview
6275 * objects created from the project archive. If string is null (default for
6276 * construction) then suffix will be set automatically.
6280 public void setUniqueSetSuffix(String string)
6282 uniqueSetSuffix = string;
6287 * uses skipList2 as the skipList for skipping views on sequence sets
6288 * associated with keys in the skipList
6292 public void setSkipList(Hashtable skipList2)
6294 skipList = skipList2;
6298 * Reads the jar entry of given name and returns its contents, or null if the
6299 * entry is not found.
6302 * @param jarEntryName
6305 protected String readJarEntry(jarInputStreamProvider jprovider,
6306 String jarEntryName)
6308 String result = null;
6309 BufferedReader in = null;
6314 * Reopen the jar input stream and traverse its entries to find a matching
6317 JarInputStream jin = jprovider.getJarInputStream();
6318 JarEntry entry = null;
6321 entry = jin.getNextJarEntry();
6322 } while (entry != null && !entry.getName().equals(jarEntryName));
6326 StringBuilder out = new StringBuilder(256);
6327 in = new BufferedReader(new InputStreamReader(jin, UTF_8));
6330 while ((data = in.readLine()) != null)
6334 result = out.toString();
6338 warn("Couldn't find entry in Jalview Jar for " + jarEntryName);
6340 } catch (Exception ex)
6342 ex.printStackTrace();
6350 } catch (IOException e)
6361 * Returns an incrementing counter (0, 1, 2...)
6365 private synchronized int nextCounter()
6371 * Loads any saved PCA viewers
6376 protected void loadPCAViewers(JalviewModel model, AlignmentPanel ap)
6380 List<PcaViewer> pcaviewers = model.getPcaViewer();
6381 for (PcaViewer viewer : pcaviewers)
6383 String modelName = viewer.getScoreModelName();
6384 SimilarityParamsI params = new SimilarityParams(
6385 viewer.isIncludeGappedColumns(), viewer.isMatchGaps(),
6386 viewer.isIncludeGaps(),
6387 viewer.isDenominateByShortestLength());
6390 * create the panel (without computing the PCA)
6392 PCAPanel panel = new PCAPanel(ap, modelName, params);
6394 panel.setTitle(viewer.getTitle());
6395 panel.setBounds(new Rectangle(viewer.getXpos(), viewer.getYpos(),
6396 viewer.getWidth(), viewer.getHeight()));
6398 boolean showLabels = viewer.isShowLabels();
6399 panel.setShowLabels(showLabels);
6400 panel.getRotatableCanvas().setShowLabels(showLabels);
6401 panel.getRotatableCanvas()
6402 .setBgColour(new Color(viewer.getBgColour()));
6403 panel.getRotatableCanvas()
6404 .setApplyToAllViews(viewer.isLinkToAllViews());
6407 * load PCA output data
6409 ScoreModelI scoreModel = ScoreModels.getInstance()
6410 .getScoreModel(modelName, ap);
6411 PCA pca = new PCA(null, scoreModel, params);
6412 PcaDataType pcaData = viewer.getPcaData();
6414 MatrixI pairwise = loadDoubleMatrix(pcaData.getPairwiseMatrix());
6415 pca.setPairwiseScores(pairwise);
6417 MatrixI triDiag = loadDoubleMatrix(pcaData.getTridiagonalMatrix());
6418 pca.setTridiagonal(triDiag);
6420 MatrixI result = loadDoubleMatrix(pcaData.getEigenMatrix());
6421 pca.setEigenmatrix(result);
6423 panel.getPcaModel().setPCA(pca);
6426 * we haven't saved the input data! (JAL-2647 to do)
6428 panel.setInputData(null);
6431 * add the sequence points for the PCA display
6433 List<jalview.datamodel.SequencePoint> seqPoints = new ArrayList<>();
6434 for (SequencePoint sp : viewer.getSequencePoint())
6436 String seqId = sp.getSequenceRef();
6437 SequenceI seq = seqRefIds.get(seqId);
6440 throw new IllegalStateException(
6441 "Unmatched seqref for PCA: " + seqId);
6443 Point pt = new Point(sp.getXPos(), sp.getYPos(), sp.getZPos());
6444 jalview.datamodel.SequencePoint seqPoint = new jalview.datamodel.SequencePoint(
6446 seqPoints.add(seqPoint);
6448 panel.getRotatableCanvas().setPoints(seqPoints, seqPoints.size());
6451 * set min-max ranges and scale after setPoints (which recomputes them)
6453 panel.getRotatableCanvas().setScaleFactor(viewer.getScaleFactor());
6454 SeqPointMin spMin = viewer.getSeqPointMin();
6455 float[] min = new float[] { spMin.getXPos(), spMin.getYPos(),
6457 SeqPointMax spMax = viewer.getSeqPointMax();
6458 float[] max = new float[] { spMax.getXPos(), spMax.getYPos(),
6460 panel.getRotatableCanvas().setSeqMinMax(min, max);
6462 // todo: hold points list in PCAModel only
6463 panel.getPcaModel().setSequencePoints(seqPoints);
6465 panel.setSelectedDimensionIndex(viewer.getXDim(), X);
6466 panel.setSelectedDimensionIndex(viewer.getYDim(), Y);
6467 panel.setSelectedDimensionIndex(viewer.getZDim(), Z);
6469 // is this duplication needed?
6470 panel.setTop(seqPoints.size() - 1);
6471 panel.getPcaModel().setTop(seqPoints.size() - 1);
6474 * add the axes' end points for the display
6476 for (int i = 0; i < 3; i++)
6478 Axis axis = viewer.getAxis().get(i);
6479 panel.getRotatableCanvas().getAxisEndPoints()[i] = new Point(
6480 axis.getXPos(), axis.getYPos(), axis.getZPos());
6483 Dimension dim = Platform.getDimIfEmbedded(panel, 475, 450);
6484 Desktop.addInternalFrame(panel, MessageManager.formatMessage(
6485 "label.calc_title", "PCA", modelName), dim.width,
6488 } catch (Exception ex)
6490 Cache.log.error("Error loading PCA: " + ex.toString());
6495 * Populates an XML model of the feature colour scheme for one feature type
6497 * @param featureType
6501 public static Colour marshalColour(
6502 String featureType, FeatureColourI fcol)
6504 Colour col = new Colour();
6505 if (fcol.isSimpleColour())
6507 col.setRGB(Format.getHexString(fcol.getColour()));
6511 col.setRGB(Format.getHexString(fcol.getMaxColour()));
6512 col.setMin(fcol.getMin());
6513 col.setMax(fcol.getMax());
6514 col.setMinRGB(jalview.util.Format.getHexString(fcol.getMinColour()));
6515 col.setAutoScale(fcol.isAutoScaled());
6516 col.setThreshold(fcol.getThreshold());
6517 col.setColourByLabel(fcol.isColourByLabel());
6518 col.setThreshType(fcol.isAboveThreshold() ? ThresholdType.ABOVE
6519 : (fcol.isBelowThreshold() ? ThresholdType.BELOW
6520 : ThresholdType.NONE));
6521 if (fcol.isColourByAttribute())
6523 final String[] attName = fcol.getAttributeName();
6524 col.getAttributeName().add(attName[0]);
6525 if (attName.length > 1)
6527 col.getAttributeName().add(attName[1]);
6530 Color noColour = fcol.getNoColour();
6531 if (noColour == null)
6533 col.setNoValueColour(NoValueColour.NONE);
6535 else if (noColour == fcol.getMaxColour())
6537 col.setNoValueColour(NoValueColour.MAX);
6541 col.setNoValueColour(NoValueColour.MIN);
6544 col.setName(featureType);
6549 * Populates an XML model of the feature filter(s) for one feature type
6551 * @param firstMatcher
6552 * the first (or only) match condition)
6554 * remaining match conditions (if any)
6556 * if true, conditions are and-ed, else or-ed
6558 public static jalview.xml.binding.jalview.FeatureMatcherSet marshalFilter(
6559 FeatureMatcherI firstMatcher, Iterator<FeatureMatcherI> filters,
6562 jalview.xml.binding.jalview.FeatureMatcherSet result = new jalview.xml.binding.jalview.FeatureMatcherSet();
6564 if (filters.hasNext())
6569 CompoundMatcher compound = new CompoundMatcher();
6570 compound.setAnd(and);
6571 jalview.xml.binding.jalview.FeatureMatcherSet matcher1 = marshalFilter(
6572 firstMatcher, Collections.emptyIterator(), and);
6573 // compound.addMatcherSet(matcher1);
6574 compound.getMatcherSet().add(matcher1);
6575 FeatureMatcherI nextMatcher = filters.next();
6576 jalview.xml.binding.jalview.FeatureMatcherSet matcher2 = marshalFilter(
6577 nextMatcher, filters, and);
6578 // compound.addMatcherSet(matcher2);
6579 compound.getMatcherSet().add(matcher2);
6580 result.setCompoundMatcher(compound);
6585 * single condition matcher
6587 // MatchCondition matcherModel = new MatchCondition();
6588 jalview.xml.binding.jalview.FeatureMatcher matcherModel = new jalview.xml.binding.jalview.FeatureMatcher();
6589 matcherModel.setCondition(
6590 firstMatcher.getMatcher().getCondition().getStableName());
6591 matcherModel.setValue(firstMatcher.getMatcher().getPattern());
6592 if (firstMatcher.isByAttribute())
6594 matcherModel.setBy(FilterBy.BY_ATTRIBUTE);
6595 // matcherModel.setAttributeName(firstMatcher.getAttribute());
6596 String[] attName = firstMatcher.getAttribute();
6597 matcherModel.getAttributeName().add(attName[0]); // attribute
6598 if (attName.length > 1)
6600 matcherModel.getAttributeName().add(attName[1]); // sub-attribute
6603 else if (firstMatcher.isByLabel())
6605 matcherModel.setBy(FilterBy.BY_LABEL);
6607 else if (firstMatcher.isByScore())
6609 matcherModel.setBy(FilterBy.BY_SCORE);
6611 result.setMatchCondition(matcherModel);
6618 * Loads one XML model of a feature filter to a Jalview object
6620 * @param featureType
6621 * @param matcherSetModel
6624 public static FeatureMatcherSetI parseFilter(
6626 jalview.xml.binding.jalview.FeatureMatcherSet matcherSetModel)
6628 FeatureMatcherSetI result = new FeatureMatcherSet();
6631 parseFilterConditions(result, matcherSetModel, true);
6632 } catch (IllegalStateException e)
6634 // mixing AND and OR conditions perhaps
6636 String.format("Error reading filter conditions for '%s': %s",
6637 featureType, e.getMessage()));
6638 // return as much as was parsed up to the error
6645 * Adds feature match conditions to matcherSet as unmarshalled from XML
6646 * (possibly recursively for compound conditions)
6649 * @param matcherSetModel
6651 * if true, multiple conditions are AND-ed, else they are OR-ed
6652 * @throws IllegalStateException
6653 * if AND and OR conditions are mixed
6655 protected static void parseFilterConditions(
6656 FeatureMatcherSetI matcherSet,
6657 jalview.xml.binding.jalview.FeatureMatcherSet matcherSetModel,
6660 jalview.xml.binding.jalview.FeatureMatcher mc = matcherSetModel
6661 .getMatchCondition();
6667 FilterBy filterBy = mc.getBy();
6668 Condition cond = Condition.fromString(mc.getCondition());
6669 String pattern = mc.getValue();
6670 FeatureMatcherI matchCondition = null;
6671 if (filterBy == FilterBy.BY_LABEL)
6673 matchCondition = FeatureMatcher.byLabel(cond, pattern);
6675 else if (filterBy == FilterBy.BY_SCORE)
6677 matchCondition = FeatureMatcher.byScore(cond, pattern);
6680 else if (filterBy == FilterBy.BY_ATTRIBUTE)
6682 final List<String> attributeName = mc.getAttributeName();
6683 String[] attNames = attributeName
6684 .toArray(new String[attributeName.size()]);
6685 matchCondition = FeatureMatcher.byAttribute(cond, pattern,
6690 * note this throws IllegalStateException if AND-ing to a
6691 * previously OR-ed compound condition, or vice versa
6695 matcherSet.and(matchCondition);
6699 matcherSet.or(matchCondition);
6705 * compound condition
6707 List<jalview.xml.binding.jalview.FeatureMatcherSet> matchers = matcherSetModel
6708 .getCompoundMatcher().getMatcherSet();
6709 boolean anded = matcherSetModel.getCompoundMatcher().isAnd();
6710 if (matchers.size() == 2)
6712 parseFilterConditions(matcherSet, matchers.get(0), anded);
6713 parseFilterConditions(matcherSet, matchers.get(1), anded);
6717 System.err.println("Malformed compound filter condition");
6723 * Loads one XML model of a feature colour to a Jalview object
6725 * @param colourModel
6728 public static FeatureColourI parseColour(Colour colourModel)
6730 FeatureColourI colour = null;
6732 if (colourModel.getMax() != null)
6734 Color mincol = null;
6735 Color maxcol = null;
6736 Color noValueColour = null;
6740 mincol = new Color(Integer.parseInt(colourModel.getMinRGB(), 16));
6741 maxcol = new Color(Integer.parseInt(colourModel.getRGB(), 16));
6742 } catch (Exception e)
6744 Cache.log.warn("Couldn't parse out graduated feature color.", e);
6747 NoValueColour noCol = colourModel.getNoValueColour();
6748 if (noCol == NoValueColour.MIN)
6750 noValueColour = mincol;
6752 else if (noCol == NoValueColour.MAX)
6754 noValueColour = maxcol;
6757 colour = new FeatureColour(maxcol, mincol, maxcol, noValueColour,
6758 safeFloat(colourModel.getMin()),
6759 safeFloat(colourModel.getMax()));
6760 final List<String> attributeName = colourModel.getAttributeName();
6761 String[] attributes = attributeName
6762 .toArray(new String[attributeName.size()]);
6763 if (attributes != null && attributes.length > 0)
6765 colour.setAttributeName(attributes);
6767 if (colourModel.isAutoScale() != null)
6769 colour.setAutoScaled(colourModel.isAutoScale().booleanValue());
6771 if (colourModel.isColourByLabel() != null)
6773 colour.setColourByLabel(
6774 colourModel.isColourByLabel().booleanValue());
6776 if (colourModel.getThreshold() != null)
6778 colour.setThreshold(colourModel.getThreshold().floatValue());
6780 ThresholdType ttyp = colourModel.getThreshType();
6781 if (ttyp == ThresholdType.ABOVE)
6783 colour.setAboveThreshold(true);
6785 else if (ttyp == ThresholdType.BELOW)
6787 colour.setBelowThreshold(true);
6792 Color color = new Color(Integer.parseInt(colourModel.getRGB(), 16));
6793 colour = new FeatureColour(color);