2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 package jalview.project;
23 import static jalview.math.RotatableMatrix.Axis.X;
24 import static jalview.math.RotatableMatrix.Axis.Y;
25 import static jalview.math.RotatableMatrix.Axis.Z;
27 import jalview.analysis.Conservation;
28 import jalview.analysis.PCA;
29 import jalview.analysis.scoremodels.ScoreModels;
30 import jalview.analysis.scoremodels.SimilarityParams;
31 import jalview.api.AlignmentViewPanel;
32 import jalview.api.FeatureColourI;
33 import jalview.api.ViewStyleI;
34 import jalview.api.analysis.ScoreModelI;
35 import jalview.api.analysis.SimilarityParamsI;
36 import jalview.api.structures.JalviewStructureDisplayI;
37 import jalview.bin.Cache;
38 import jalview.datamodel.AlignedCodonFrame;
39 import jalview.datamodel.Alignment;
40 import jalview.datamodel.AlignmentAnnotation;
41 import jalview.datamodel.AlignmentI;
42 import jalview.datamodel.DBRefEntry;
43 import jalview.datamodel.GraphLine;
44 import jalview.datamodel.PDBEntry;
45 import jalview.datamodel.Point;
46 import jalview.datamodel.RnaViewerModel;
47 import jalview.datamodel.SequenceFeature;
48 import jalview.datamodel.SequenceGroup;
49 import jalview.datamodel.SequenceI;
50 import jalview.datamodel.StructureViewerModel;
51 import jalview.datamodel.StructureViewerModel.StructureData;
52 import jalview.datamodel.features.FeatureMatcher;
53 import jalview.datamodel.features.FeatureMatcherI;
54 import jalview.datamodel.features.FeatureMatcherSet;
55 import jalview.datamodel.features.FeatureMatcherSetI;
56 import jalview.ext.varna.RnaModel;
57 import jalview.gui.AlignFrame;
58 import jalview.gui.AlignViewport;
59 import jalview.gui.AlignmentPanel;
60 import jalview.gui.AppVarna;
61 import jalview.gui.ChimeraViewFrame;
62 import jalview.gui.Desktop;
63 import jalview.gui.FeatureRenderer;
64 import jalview.gui.JvOptionPane;
65 import jalview.gui.OOMWarning;
66 import jalview.gui.PCAPanel;
67 import jalview.gui.PaintRefresher;
68 import jalview.gui.SplitFrame;
69 import jalview.gui.StructureViewer;
70 import jalview.gui.StructureViewer.ViewerType;
71 import jalview.gui.StructureViewerBase;
72 import jalview.gui.TreePanel;
73 import jalview.io.BackupFiles;
74 import jalview.io.DataSourceType;
75 import jalview.io.FileFormat;
76 import jalview.io.NewickFile;
77 import jalview.math.Matrix;
78 import jalview.math.MatrixI;
79 import jalview.renderer.ResidueShaderI;
80 import jalview.schemes.AnnotationColourGradient;
81 import jalview.schemes.ColourSchemeI;
82 import jalview.schemes.ColourSchemeProperty;
83 import jalview.schemes.FeatureColour;
84 import jalview.schemes.ResidueProperties;
85 import jalview.schemes.UserColourScheme;
86 import jalview.structures.models.AAStructureBindingModel;
87 import jalview.util.Format;
88 import jalview.util.MessageManager;
89 import jalview.util.Platform;
90 import jalview.util.StringUtils;
91 import jalview.util.jarInputStreamProvider;
92 import jalview.util.matcher.Condition;
93 import jalview.viewmodel.AlignmentViewport;
94 import jalview.viewmodel.PCAModel;
95 import jalview.viewmodel.ViewportRanges;
96 import jalview.viewmodel.seqfeatures.FeatureRendererSettings;
97 import jalview.viewmodel.seqfeatures.FeaturesDisplayed;
98 import jalview.ws.jws2.Jws2Discoverer;
99 import jalview.ws.jws2.dm.AAConSettings;
100 import jalview.ws.jws2.jabaws2.Jws2Instance;
101 import jalview.ws.params.ArgumentI;
102 import jalview.ws.params.AutoCalcSetting;
103 import jalview.ws.params.WsParamSetI;
104 import jalview.xml.binding.jalview.AlcodonFrame;
105 import jalview.xml.binding.jalview.AlcodonFrame.AlcodMap;
106 import jalview.xml.binding.jalview.Annotation;
107 import jalview.xml.binding.jalview.Annotation.ThresholdLine;
108 import jalview.xml.binding.jalview.AnnotationColourScheme;
109 import jalview.xml.binding.jalview.AnnotationElement;
110 import jalview.xml.binding.jalview.DoubleMatrix;
111 import jalview.xml.binding.jalview.DoubleVector;
112 import jalview.xml.binding.jalview.Feature;
113 import jalview.xml.binding.jalview.Feature.OtherData;
114 import jalview.xml.binding.jalview.FeatureMatcherSet.CompoundMatcher;
115 import jalview.xml.binding.jalview.FilterBy;
116 import jalview.xml.binding.jalview.JalviewModel;
117 import jalview.xml.binding.jalview.JalviewModel.FeatureSettings;
118 import jalview.xml.binding.jalview.JalviewModel.FeatureSettings.Group;
119 import jalview.xml.binding.jalview.JalviewModel.FeatureSettings.Setting;
120 import jalview.xml.binding.jalview.JalviewModel.JGroup;
121 import jalview.xml.binding.jalview.JalviewModel.JSeq;
122 import jalview.xml.binding.jalview.JalviewModel.JSeq.Pdbids;
123 import jalview.xml.binding.jalview.JalviewModel.JSeq.Pdbids.StructureState;
124 import jalview.xml.binding.jalview.JalviewModel.JSeq.RnaViewer;
125 import jalview.xml.binding.jalview.JalviewModel.JSeq.RnaViewer.SecondaryStructure;
126 import jalview.xml.binding.jalview.JalviewModel.PcaViewer;
127 import jalview.xml.binding.jalview.JalviewModel.PcaViewer.Axis;
128 import jalview.xml.binding.jalview.JalviewModel.PcaViewer.SeqPointMax;
129 import jalview.xml.binding.jalview.JalviewModel.PcaViewer.SeqPointMin;
130 import jalview.xml.binding.jalview.JalviewModel.PcaViewer.SequencePoint;
131 import jalview.xml.binding.jalview.JalviewModel.Tree;
132 import jalview.xml.binding.jalview.JalviewModel.UserColours;
133 import jalview.xml.binding.jalview.JalviewModel.Viewport;
134 import jalview.xml.binding.jalview.JalviewModel.Viewport.CalcIdParam;
135 import jalview.xml.binding.jalview.JalviewModel.Viewport.HiddenColumns;
136 import jalview.xml.binding.jalview.JalviewUserColours;
137 import jalview.xml.binding.jalview.JalviewUserColours.Colour;
138 import jalview.xml.binding.jalview.MapListType.MapListFrom;
139 import jalview.xml.binding.jalview.MapListType.MapListTo;
140 import jalview.xml.binding.jalview.Mapping;
141 import jalview.xml.binding.jalview.NoValueColour;
142 import jalview.xml.binding.jalview.ObjectFactory;
143 import jalview.xml.binding.jalview.PcaDataType;
144 import jalview.xml.binding.jalview.Pdbentry.Property;
145 import jalview.xml.binding.jalview.Sequence;
146 import jalview.xml.binding.jalview.Sequence.DBRef;
147 import jalview.xml.binding.jalview.SequenceSet;
148 import jalview.xml.binding.jalview.SequenceSet.SequenceSetProperties;
149 import jalview.xml.binding.jalview.ThresholdType;
150 import jalview.xml.binding.jalview.VAMSAS;
152 import java.awt.Color;
153 import java.awt.Dimension;
154 import java.awt.Font;
155 import java.awt.Rectangle;
156 import java.io.BufferedReader;
157 import java.io.ByteArrayInputStream;
158 import java.io.DataInputStream;
159 import java.io.DataOutputStream;
161 import java.io.FileInputStream;
162 import java.io.FileOutputStream;
163 import java.io.IOException;
164 import java.io.InputStream;
165 import java.io.InputStreamReader;
166 import java.io.OutputStreamWriter;
167 import java.io.PrintWriter;
168 import java.math.BigInteger;
169 import java.net.MalformedURLException;
171 import java.util.ArrayList;
172 import java.util.Arrays;
173 import java.util.Collections;
174 import java.util.Enumeration;
175 import java.util.GregorianCalendar;
176 import java.util.HashMap;
177 import java.util.HashSet;
178 import java.util.Hashtable;
179 import java.util.IdentityHashMap;
180 import java.util.Iterator;
181 import java.util.LinkedHashMap;
182 import java.util.List;
183 import java.util.Map;
184 import java.util.Map.Entry;
185 import java.util.Set;
186 import java.util.Vector;
187 import java.util.jar.JarEntry;
188 import java.util.jar.JarInputStream;
189 import java.util.jar.JarOutputStream;
191 import javax.swing.JInternalFrame;
192 import javax.swing.SwingUtilities;
193 import javax.xml.bind.JAXBContext;
194 import javax.xml.bind.JAXBElement;
195 import javax.xml.bind.Marshaller;
196 import javax.xml.datatype.DatatypeConfigurationException;
197 import javax.xml.datatype.DatatypeFactory;
198 import javax.xml.datatype.XMLGregorianCalendar;
199 import javax.xml.stream.XMLInputFactory;
200 import javax.xml.stream.XMLStreamReader;
203 * Write out the current jalview desktop state as a Jalview XML stream.
205 * Note: the vamsas objects referred to here are primitive versions of the
206 * VAMSAS project schema elements - they are not the same and most likely never
210 * @version $Revision: 1.134 $
212 public class Jalview2XML
215 // BH 2018 we add the .jvp binary extension to J2S so that
216 // it will declare that binary when we do the file save from the browser
220 Platform.addJ2SBinaryType(".jvp?");
223 private static final String VIEWER_PREFIX = "viewer_";
225 private static final String RNA_PREFIX = "rna_";
227 private static final String UTF_8 = "UTF-8";
230 * prefix for recovering datasets for alignments with multiple views where
231 * non-existent dataset IDs were written for some views
233 private static final String UNIQSEQSETID = "uniqueSeqSetId.";
235 // use this with nextCounter() to make unique names for entities
236 private int counter = 0;
239 * SequenceI reference -> XML ID string in jalview XML. Populated as XML reps
240 * of sequence objects are created.
242 IdentityHashMap<SequenceI, String> seqsToIds = null;
245 * jalview XML Sequence ID to jalview sequence object reference (both dataset
246 * and alignment sequences. Populated as XML reps of sequence objects are
249 Map<String, SequenceI> seqRefIds = null;
251 Map<String, SequenceI> incompleteSeqs = null;
253 List<SeqFref> frefedSequence = null;
255 boolean raiseGUI = true; // whether errors are raised in dialog boxes or not
258 * Map of reconstructed AlignFrame objects that appear to have come from
259 * SplitFrame objects (have a dna/protein complement view).
261 private Map<Viewport, AlignFrame> splitFrameCandidates = new HashMap<>();
264 * Map from displayed rna structure models to their saved session state jar
267 private Map<RnaModel, String> rnaSessions = new HashMap<>();
270 * contains last error message (if any) encountered by XML loader.
272 String errorMessage = null;
275 * flag to control whether the Jalview2XML_V1 parser should be deferred to if
276 * exceptions are raised during project XML parsing
278 public boolean attemptversion1parse = false;
281 * JalviewJS only -- to allow read file bytes to be saved in the
282 * created AlignFrame, allowing File | Reload of a project file to work
286 private File jarFile;
289 * A helper method for safely using the value of an optional attribute that
290 * may be null if not present in the XML. Answers the boolean value, or false
296 public static boolean safeBoolean(Boolean b)
298 return b == null ? false : b.booleanValue();
302 * A helper method for safely using the value of an optional attribute that
303 * may be null if not present in the XML. Answers the integer value, or zero
309 public static int safeInt(Integer i)
311 return i == null ? 0 : i.intValue();
315 * A helper method for safely using the value of an optional attribute that
316 * may be null if not present in the XML. Answers the float value, or zero if
322 public static float safeFloat(Float f)
324 return f == null ? 0f : f.floatValue();
328 * create/return unique hash string for sq
331 * @return new or existing unique string for sq
333 String seqHash(SequenceI sq)
335 if (seqsToIds == null)
339 if (seqsToIds.containsKey(sq))
341 return seqsToIds.get(sq);
345 // create sequential key
346 String key = "sq" + (seqsToIds.size() + 1);
347 key = makeHashCode(sq, key); // check we don't have an external reference
349 seqsToIds.put(sq, key);
356 if (seqsToIds == null)
358 seqsToIds = new IdentityHashMap<>();
360 if (seqRefIds == null)
362 seqRefIds = new HashMap<>();
364 if (incompleteSeqs == null)
366 incompleteSeqs = new HashMap<>();
368 if (frefedSequence == null)
370 frefedSequence = new ArrayList<>();
378 public Jalview2XML(boolean raiseGUI)
380 this.raiseGUI = raiseGUI;
384 * base class for resolving forward references to sequences by their ID
389 abstract class SeqFref
395 public SeqFref(String _sref, String type)
401 public String getSref()
406 public SequenceI getSrefSeq()
408 return seqRefIds.get(sref);
411 public boolean isResolvable()
413 return seqRefIds.get(sref) != null;
416 public SequenceI getSrefDatasetSeq()
418 SequenceI sq = seqRefIds.get(sref);
421 while (sq.getDatasetSequence() != null)
423 sq = sq.getDatasetSequence();
430 * @return true if the forward reference was fully resolved
432 abstract boolean resolve();
435 public String toString()
437 return type + " reference to " + sref;
442 * create forward reference for a mapping
448 public 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 public 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 public 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 public 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 public JalviewModel saveState(AlignmentPanel ap, String fileName,
893 boolean storeDS, JarOutputStream jout, List<String> viewIds)
897 viewIds = new ArrayList<>();
902 List<UserColourScheme> userColours = new ArrayList<>();
904 AlignViewport av = ap.av;
905 ViewportRanges vpRanges = av.getRanges();
907 final ObjectFactory objectFactory = new ObjectFactory();
908 JalviewModel object = objectFactory.createJalviewModel();
909 object.setVamsasModel(new VAMSAS());
911 // object.setCreationDate(new java.util.Date(System.currentTimeMillis()));
914 GregorianCalendar c = new GregorianCalendar();
915 DatatypeFactory datatypeFactory = DatatypeFactory.newInstance();
916 XMLGregorianCalendar now = datatypeFactory.newXMLGregorianCalendar(c);// gregorianCalendar);
917 object.setCreationDate(now);
918 } catch (DatatypeConfigurationException e)
920 System.err.println("error writing date: " + e.toString());
923 jalview.bin.Cache.getDefault("VERSION", "Development Build"));
926 * rjal is full height alignment, jal is actual alignment with full metadata
927 * but excludes hidden sequences.
929 jalview.datamodel.AlignmentI rjal = av.getAlignment(), jal = rjal;
931 if (av.hasHiddenRows())
933 rjal = jal.getHiddenSequences().getFullAlignment();
936 SequenceSet vamsasSet = new SequenceSet();
938 // JalviewModelSequence jms = new JalviewModelSequence();
940 vamsasSet.setGapChar(jal.getGapCharacter() + "");
942 if (jal.getDataset() != null)
944 // dataset id is the dataset's hashcode
945 vamsasSet.setDatasetId(getDatasetIdRef(jal.getDataset()));
948 // switch jal and the dataset
949 jal = jal.getDataset();
953 if (jal.getProperties() != null)
955 Enumeration en = jal.getProperties().keys();
956 while (en.hasMoreElements())
958 String key = en.nextElement().toString();
959 SequenceSetProperties ssp = new SequenceSetProperties();
961 ssp.setValue(jal.getProperties().get(key).toString());
962 // vamsasSet.addSequenceSetProperties(ssp);
963 vamsasSet.getSequenceSetProperties().add(ssp);
968 Set<String> calcIdSet = new HashSet<>();
969 // record the set of vamsas sequence XML POJO we create.
970 HashMap<String, Sequence> vamsasSetIds = new HashMap<>();
972 for (final SequenceI jds : rjal.getSequences())
974 final SequenceI jdatasq = jds.getDatasetSequence() == null ? jds
975 : jds.getDatasetSequence();
976 String id = seqHash(jds);
977 if (vamsasSetIds.get(id) == null)
979 if (seqRefIds.get(id) != null && !storeDS)
981 // This happens for two reasons: 1. multiple views are being
983 // 2. the hashCode has collided with another sequence's code. This
985 // HAPPEN! (PF00072.15.stk does this)
986 // JBPNote: Uncomment to debug writing out of files that do not read
987 // back in due to ArrayOutOfBoundExceptions.
988 // System.err.println("vamsasSeq backref: "+id+"");
989 // System.err.println(jds.getName()+"
990 // "+jds.getStart()+"-"+jds.getEnd()+" "+jds.getSequenceAsString());
991 // System.err.println("Hashcode: "+seqHash(jds));
992 // SequenceI rsq = (SequenceI) seqRefIds.get(id + "");
993 // System.err.println(rsq.getName()+"
994 // "+rsq.getStart()+"-"+rsq.getEnd()+" "+rsq.getSequenceAsString());
995 // System.err.println("Hashcode: "+seqHash(rsq));
999 vamsasSeq = createVamsasSequence(id, jds);
1000 // vamsasSet.addSequence(vamsasSeq);
1001 vamsasSet.getSequence().add(vamsasSeq);
1002 vamsasSetIds.put(id, vamsasSeq);
1003 seqRefIds.put(id, jds);
1007 jseq.setStart(jds.getStart());
1008 jseq.setEnd(jds.getEnd());
1009 jseq.setColour(av.getSequenceColour(jds).getRGB());
1011 jseq.setId(id); // jseq id should be a string not a number
1014 // Store any sequences this sequence represents
1015 if (av.hasHiddenRows())
1017 // use rjal, contains the full height alignment
1019 av.getAlignment().getHiddenSequences().isHidden(jds));
1021 if (av.isHiddenRepSequence(jds))
1023 jalview.datamodel.SequenceI[] reps = av
1024 .getRepresentedSequences(jds).getSequencesInOrder(rjal);
1026 for (int h = 0; h < reps.length; h++)
1030 // jseq.addHiddenSequences(rjal.findIndex(reps[h]));
1031 jseq.getHiddenSequences().add(rjal.findIndex(reps[h]));
1036 // mark sequence as reference - if it is the reference for this view
1037 if (jal.hasSeqrep())
1039 jseq.setViewreference(jds == jal.getSeqrep());
1043 // TODO: omit sequence features from each alignment view's XML dump if we
1044 // are storing dataset
1045 List<SequenceFeature> sfs = jds.getSequenceFeatures();
1046 for (SequenceFeature sf : sfs)
1048 // Features features = new Features();
1049 Feature features = new Feature();
1051 features.setBegin(sf.getBegin());
1052 features.setEnd(sf.getEnd());
1053 features.setDescription(sf.getDescription());
1054 features.setType(sf.getType());
1055 features.setFeatureGroup(sf.getFeatureGroup());
1056 features.setScore(sf.getScore());
1057 if (sf.links != null)
1059 for (int l = 0; l < sf.links.size(); l++)
1061 OtherData keyValue = new OtherData();
1062 keyValue.setKey("LINK_" + l);
1063 keyValue.setValue(sf.links.elementAt(l).toString());
1064 // features.addOtherData(keyValue);
1065 features.getOtherData().add(keyValue);
1068 if (sf.otherDetails != null)
1071 * save feature attributes, which may be simple strings or
1072 * map valued (have sub-attributes)
1074 for (Entry<String, Object> entry : sf.otherDetails.entrySet())
1076 String key = entry.getKey();
1077 Object value = entry.getValue();
1078 if (value instanceof Map<?, ?>)
1080 for (Entry<String, Object> subAttribute : ((Map<String, Object>) value)
1083 OtherData otherData = new OtherData();
1084 otherData.setKey(key);
1085 otherData.setKey2(subAttribute.getKey());
1086 otherData.setValue(subAttribute.getValue().toString());
1087 // features.addOtherData(otherData);
1088 features.getOtherData().add(otherData);
1093 OtherData otherData = new OtherData();
1094 otherData.setKey(key);
1095 otherData.setValue(value.toString());
1096 // features.addOtherData(otherData);
1097 features.getOtherData().add(otherData);
1102 // jseq.addFeatures(features);
1103 jseq.getFeatures().add(features);
1106 if (jdatasq.getAllPDBEntries() != null)
1108 Enumeration<PDBEntry> en = jdatasq.getAllPDBEntries().elements();
1109 while (en.hasMoreElements())
1111 Pdbids pdb = new Pdbids();
1112 jalview.datamodel.PDBEntry entry = en.nextElement();
1114 String pdbId = entry.getId();
1116 pdb.setType(entry.getType());
1119 * Store any structure views associated with this sequence. This
1120 * section copes with duplicate entries in the project, so a dataset
1121 * only view *should* be coped with sensibly.
1123 // This must have been loaded, is it still visible?
1124 JInternalFrame[] frames = Desktop.getDesktopPane().getAllFrames();
1125 String matchedFile = null;
1126 for (int f = frames.length - 1; f > -1; f--)
1128 if (frames[f] instanceof StructureViewerBase)
1130 StructureViewerBase viewFrame = (StructureViewerBase) frames[f];
1131 matchedFile = saveStructureState(ap, jds, pdb, entry, viewIds,
1132 matchedFile, viewFrame);
1134 * Only store each structure viewer's state once in the project
1135 * jar. First time through only (storeDS==false)
1137 String viewId = viewFrame.getViewId();
1138 if (!storeDS && !viewIds.contains(viewId))
1140 viewIds.add(viewId);
1143 String viewerState = viewFrame.getStateInfo();
1144 writeJarEntry(jout, getViewerJarEntryName(viewId),
1145 viewerState.getBytes());
1146 } catch (IOException e)
1149 "Error saving viewer state: " + e.getMessage());
1155 if (matchedFile != null || entry.getFile() != null)
1157 if (entry.getFile() != null)
1160 matchedFile = entry.getFile();
1162 pdb.setFile(matchedFile); // entry.getFile());
1163 if (pdbfiles == null)
1165 pdbfiles = new ArrayList<>();
1168 if (!pdbfiles.contains(pdbId))
1170 pdbfiles.add(pdbId);
1171 copyFileToJar(jout, matchedFile, pdbId);
1175 Enumeration<String> props = entry.getProperties();
1176 if (props.hasMoreElements())
1178 // PdbentryItem item = new PdbentryItem();
1179 while (props.hasMoreElements())
1181 Property prop = new Property();
1182 String key = props.nextElement();
1184 prop.setValue(entry.getProperty(key).toString());
1185 // item.addProperty(prop);
1186 pdb.getProperty().add(prop);
1188 // pdb.addPdbentryItem(item);
1191 // jseq.addPdbids(pdb);
1192 jseq.getPdbids().add(pdb);
1196 saveRnaViewers(jout, jseq, jds, viewIds, ap, storeDS);
1198 // jms.addJSeq(jseq);
1199 object.getJSeq().add(jseq);
1202 if (!storeDS && av.hasHiddenRows())
1204 jal = av.getAlignment();
1208 if (storeDS && jal.getCodonFrames() != null)
1210 List<AlignedCodonFrame> jac = jal.getCodonFrames();
1211 for (AlignedCodonFrame acf : jac)
1213 AlcodonFrame alc = new AlcodonFrame();
1214 if (acf.getProtMappings() != null
1215 && acf.getProtMappings().length > 0)
1217 boolean hasMap = false;
1218 SequenceI[] dnas = acf.getdnaSeqs();
1219 jalview.datamodel.Mapping[] pmaps = acf.getProtMappings();
1220 for (int m = 0; m < pmaps.length; m++)
1222 AlcodMap alcmap = new AlcodMap();
1223 alcmap.setDnasq(seqHash(dnas[m]));
1225 createVamsasMapping(pmaps[m], dnas[m], null, false));
1226 // alc.addAlcodMap(alcmap);
1227 alc.getAlcodMap().add(alcmap);
1232 // vamsasSet.addAlcodonFrame(alc);
1233 vamsasSet.getAlcodonFrame().add(alc);
1236 // TODO: delete this ? dead code from 2.8.3->2.9 ?
1238 // AlcodonFrame alc = new AlcodonFrame();
1239 // vamsasSet.addAlcodonFrame(alc);
1240 // for (int p = 0; p < acf.aaWidth; p++)
1242 // Alcodon cmap = new Alcodon();
1243 // if (acf.codons[p] != null)
1245 // // Null codons indicate a gapped column in the translated peptide
1247 // cmap.setPos1(acf.codons[p][0]);
1248 // cmap.setPos2(acf.codons[p][1]);
1249 // cmap.setPos3(acf.codons[p][2]);
1251 // alc.addAlcodon(cmap);
1253 // if (acf.getProtMappings() != null
1254 // && acf.getProtMappings().length > 0)
1256 // SequenceI[] dnas = acf.getdnaSeqs();
1257 // jalview.datamodel.Mapping[] pmaps = acf.getProtMappings();
1258 // for (int m = 0; m < pmaps.length; m++)
1260 // AlcodMap alcmap = new AlcodMap();
1261 // alcmap.setDnasq(seqHash(dnas[m]));
1262 // alcmap.setMapping(createVamsasMapping(pmaps[m], dnas[m], null,
1264 // alc.addAlcodMap(alcmap);
1271 // /////////////////////////////////
1272 if (!storeDS && av.getCurrentTree() != null)
1274 // FIND ANY ASSOCIATED TREES
1275 // NOT IMPLEMENTED FOR HEADLESS STATE AT PRESENT
1276 if (Desktop.getDesktopPane() != null)
1278 JInternalFrame[] frames = Desktop.getDesktopPane().getAllFrames();
1280 for (int t = 0; t < frames.length; t++)
1282 if (frames[t] instanceof TreePanel)
1284 TreePanel tp = (TreePanel) frames[t];
1286 if (tp.getTreeCanvas().getViewport().getAlignment() == jal)
1288 JalviewModel.Tree tree = new JalviewModel.Tree();
1289 tree.setTitle(tp.getTitle());
1290 tree.setCurrentTree((av.getCurrentTree() == tp.getTree()));
1291 tree.setNewick(tp.getTree().print());
1292 tree.setThreshold(tp.getTreeCanvas().getThreshold());
1294 tree.setFitToWindow(tp.fitToWindow.getState());
1295 tree.setFontName(tp.getTreeFont().getName());
1296 tree.setFontSize(tp.getTreeFont().getSize());
1297 tree.setFontStyle(tp.getTreeFont().getStyle());
1298 tree.setMarkUnlinked(tp.placeholdersMenu.getState());
1300 tree.setShowBootstrap(tp.bootstrapMenu.getState());
1301 tree.setShowDistances(tp.distanceMenu.getState());
1303 tree.setHeight(tp.getHeight());
1304 tree.setWidth(tp.getWidth());
1305 tree.setXpos(tp.getX());
1306 tree.setYpos(tp.getY());
1307 tree.setId(makeHashCode(tp, null));
1308 tree.setLinkToAllViews(
1309 tp.getTreeCanvas().isApplyToAllViews());
1311 // jms.addTree(tree);
1312 object.getTree().add(tree);
1322 if (!storeDS && Desktop.getDesktopPane() != null)
1324 for (JInternalFrame frame : Desktop.getDesktopPane().getAllFrames())
1326 if (frame instanceof PCAPanel)
1328 PCAPanel panel = (PCAPanel) frame;
1329 if (panel.getAlignViewport().getAlignment() == jal)
1331 savePCA(panel, object);
1339 * store forward refs from an annotationRow to any groups
1341 IdentityHashMap<SequenceGroup, String> groupRefs = new IdentityHashMap<>();
1344 for (SequenceI sq : jal.getSequences())
1346 // Store annotation on dataset sequences only
1347 AlignmentAnnotation[] aa = sq.getAnnotation();
1348 if (aa != null && aa.length > 0)
1350 storeAlignmentAnnotation(aa, groupRefs, av, calcIdSet, storeDS,
1357 if (jal.getAlignmentAnnotation() != null)
1359 // Store the annotation shown on the alignment.
1360 AlignmentAnnotation[] aa = jal.getAlignmentAnnotation();
1361 storeAlignmentAnnotation(aa, groupRefs, av, calcIdSet, storeDS,
1366 if (jal.getGroups() != null)
1368 JGroup[] groups = new JGroup[jal.getGroups().size()];
1370 for (jalview.datamodel.SequenceGroup sg : jal.getGroups())
1372 JGroup jGroup = new JGroup();
1373 groups[++i] = jGroup;
1375 jGroup.setStart(sg.getStartRes());
1376 jGroup.setEnd(sg.getEndRes());
1377 jGroup.setName(sg.getName());
1378 if (groupRefs.containsKey(sg))
1380 // group has references so set its ID field
1381 jGroup.setId(groupRefs.get(sg));
1383 ColourSchemeI colourScheme = sg.getColourScheme();
1384 if (colourScheme != null)
1386 ResidueShaderI groupColourScheme = sg.getGroupColourScheme();
1387 if (groupColourScheme.conservationApplied())
1389 jGroup.setConsThreshold(groupColourScheme.getConservationInc());
1391 if (colourScheme instanceof jalview.schemes.UserColourScheme)
1394 setUserColourScheme(colourScheme, userColours,
1399 jGroup.setColour(colourScheme.getSchemeName());
1402 else if (colourScheme instanceof jalview.schemes.AnnotationColourGradient)
1404 jGroup.setColour("AnnotationColourGradient");
1405 jGroup.setAnnotationColours(constructAnnotationColours(
1406 (jalview.schemes.AnnotationColourGradient) colourScheme,
1407 userColours, object));
1409 else if (colourScheme instanceof jalview.schemes.UserColourScheme)
1412 setUserColourScheme(colourScheme, userColours, object));
1416 jGroup.setColour(colourScheme.getSchemeName());
1419 jGroup.setPidThreshold(groupColourScheme.getThreshold());
1422 jGroup.setOutlineColour(sg.getOutlineColour().getRGB());
1423 jGroup.setDisplayBoxes(sg.getDisplayBoxes());
1424 jGroup.setDisplayText(sg.getDisplayText());
1425 jGroup.setColourText(sg.getColourText());
1426 jGroup.setTextCol1(sg.textColour.getRGB());
1427 jGroup.setTextCol2(sg.textColour2.getRGB());
1428 jGroup.setTextColThreshold(sg.thresholdTextColour);
1429 jGroup.setShowUnconserved(sg.getShowNonconserved());
1430 jGroup.setIgnoreGapsinConsensus(sg.getIgnoreGapsConsensus());
1431 jGroup.setShowConsensusHistogram(sg.isShowConsensusHistogram());
1432 jGroup.setShowSequenceLogo(sg.isShowSequenceLogo());
1433 jGroup.setNormaliseSequenceLogo(sg.isNormaliseSequenceLogo());
1434 for (SequenceI seq : sg.getSequences())
1436 // jGroup.addSeq(seqHash(seq));
1437 jGroup.getSeq().add(seqHash(seq));
1441 //jms.setJGroup(groups);
1443 for (JGroup grp : groups)
1445 object.getJGroup().add(grp);
1450 // /////////SAVE VIEWPORT
1451 Viewport view = new Viewport();
1452 view.setTitle(ap.alignFrame.getTitle());
1453 view.setSequenceSetId(
1454 makeHashCode(av.getSequenceSetId(), av.getSequenceSetId()));
1455 view.setId(av.getViewId());
1456 if (av.getCodingComplement() != null)
1458 view.setComplementId(av.getCodingComplement().getViewId());
1460 view.setViewName(av.getViewName());
1461 view.setGatheredViews(av.isGatherViewsHere());
1463 Rectangle size = ap.av.getExplodedGeometry();
1464 Rectangle position = size;
1467 size = ap.alignFrame.getBounds();
1468 if (av.getCodingComplement() != null)
1470 position = ((SplitFrame) ap.alignFrame.getSplitViewContainer())
1478 view.setXpos(position.x);
1479 view.setYpos(position.y);
1481 view.setWidth(size.width);
1482 view.setHeight(size.height);
1484 view.setStartRes(vpRanges.getStartRes());
1485 view.setStartSeq(vpRanges.getStartSeq());
1487 if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme)
1489 view.setBgColour(setUserColourScheme(av.getGlobalColourScheme(),
1490 userColours, object));
1493 .getGlobalColourScheme() instanceof jalview.schemes.AnnotationColourGradient)
1495 AnnotationColourScheme ac = constructAnnotationColours(
1496 (jalview.schemes.AnnotationColourGradient) av
1497 .getGlobalColourScheme(),
1498 userColours, object);
1500 view.setAnnotationColours(ac);
1501 view.setBgColour("AnnotationColourGradient");
1505 view.setBgColour(ColourSchemeProperty
1506 .getColourName(av.getGlobalColourScheme()));
1509 ResidueShaderI vcs = av.getResidueShading();
1510 ColourSchemeI cs = av.getGlobalColourScheme();
1514 if (vcs.conservationApplied())
1516 view.setConsThreshold(vcs.getConservationInc());
1517 if (cs instanceof jalview.schemes.UserColourScheme)
1519 view.setBgColour(setUserColourScheme(cs, userColours, object));
1522 view.setPidThreshold(vcs.getThreshold());
1525 view.setConservationSelected(av.getConservationSelected());
1526 view.setPidSelected(av.getAbovePIDThreshold());
1527 final Font font = av.getFont();
1528 view.setFontName(font.getName());
1529 view.setFontSize(font.getSize());
1530 view.setFontStyle(font.getStyle());
1531 view.setScaleProteinAsCdna(av.getViewStyle().isScaleProteinAsCdna());
1532 view.setRenderGaps(av.isRenderGaps());
1533 view.setShowAnnotation(av.isShowAnnotation());
1534 view.setShowBoxes(av.getShowBoxes());
1535 view.setShowColourText(av.getColourText());
1536 view.setShowFullId(av.getShowJVSuffix());
1537 view.setRightAlignIds(av.isRightAlignIds());
1538 view.setShowSequenceFeatures(av.isShowSequenceFeatures());
1539 view.setShowText(av.getShowText());
1540 view.setShowUnconserved(av.getShowUnconserved());
1541 view.setWrapAlignment(av.getWrapAlignment());
1542 view.setTextCol1(av.getTextColour().getRGB());
1543 view.setTextCol2(av.getTextColour2().getRGB());
1544 view.setTextColThreshold(av.getThresholdTextColour());
1545 view.setShowConsensusHistogram(av.isShowConsensusHistogram());
1546 view.setShowSequenceLogo(av.isShowSequenceLogo());
1547 view.setNormaliseSequenceLogo(av.isNormaliseSequenceLogo());
1548 view.setShowGroupConsensus(av.isShowGroupConsensus());
1549 view.setShowGroupConservation(av.isShowGroupConservation());
1550 view.setShowNPfeatureTooltip(av.isShowNPFeats());
1551 view.setShowDbRefTooltip(av.isShowDBRefs());
1552 view.setFollowHighlight(av.isFollowHighlight());
1553 view.setFollowSelection(av.followSelection);
1554 view.setIgnoreGapsinConsensus(av.isIgnoreGapsConsensus());
1555 if (av.getFeaturesDisplayed() != null)
1557 FeatureSettings fs = new FeatureSettings();
1559 FeatureRenderer fr = ap.getSeqPanel().seqCanvas
1560 .getFeatureRenderer();
1561 String[] renderOrder = fr.getRenderOrder().toArray(new String[0]);
1563 Vector<String> settingsAdded = new Vector<>();
1564 if (renderOrder != null)
1566 for (String featureType : renderOrder)
1568 FeatureSettings.Setting setting = new FeatureSettings.Setting();
1569 setting.setType(featureType);
1572 * save any filter for the feature type
1574 FeatureMatcherSetI filter = fr.getFeatureFilter(featureType);
1575 if (filter != null) {
1576 Iterator<FeatureMatcherI> filters = filter.getMatchers().iterator();
1577 FeatureMatcherI firstFilter = filters.next();
1578 setting.setMatcherSet(Jalview2XML.marshalFilter(
1579 firstFilter, filters, filter.isAnded()));
1583 * save colour scheme for the feature type
1585 FeatureColourI fcol = fr.getFeatureStyle(featureType);
1586 if (!fcol.isSimpleColour())
1588 setting.setColour(fcol.getMaxColour().getRGB());
1589 setting.setMincolour(fcol.getMinColour().getRGB());
1590 setting.setMin(fcol.getMin());
1591 setting.setMax(fcol.getMax());
1592 setting.setColourByLabel(fcol.isColourByLabel());
1593 if (fcol.isColourByAttribute())
1595 String[] attName = fcol.getAttributeName();
1596 setting.getAttributeName().add(attName[0]);
1597 if (attName.length > 1)
1599 setting.getAttributeName().add(attName[1]);
1602 setting.setAutoScale(fcol.isAutoScaled());
1603 setting.setThreshold(fcol.getThreshold());
1604 Color noColour = fcol.getNoColour();
1605 if (noColour == null)
1607 setting.setNoValueColour(NoValueColour.NONE);
1609 else if (noColour.equals(fcol.getMaxColour()))
1611 setting.setNoValueColour(NoValueColour.MAX);
1615 setting.setNoValueColour(NoValueColour.MIN);
1617 // -1 = No threshold, 0 = Below, 1 = Above
1618 setting.setThreshstate(fcol.isAboveThreshold() ? 1
1619 : (fcol.isBelowThreshold() ? 0 : -1));
1623 setting.setColour(fcol.getColour().getRGB());
1627 av.getFeaturesDisplayed().isVisible(featureType));
1629 .getOrder(featureType);
1632 setting.setOrder(rorder);
1634 /// fs.addSetting(setting);
1635 fs.getSetting().add(setting);
1636 settingsAdded.addElement(featureType);
1640 // is groups actually supposed to be a map here ?
1641 Iterator<String> en = fr.getFeatureGroups().iterator();
1642 Vector<String> groupsAdded = new Vector<>();
1643 while (en.hasNext())
1645 String grp = en.next();
1646 if (groupsAdded.contains(grp))
1650 Group g = new Group();
1652 g.setDisplay(((Boolean) fr.checkGroupVisibility(grp, false))
1655 fs.getGroup().add(g);
1656 groupsAdded.addElement(grp);
1658 // jms.setFeatureSettings(fs);
1659 object.setFeatureSettings(fs);
1662 if (av.hasHiddenColumns())
1664 jalview.datamodel.HiddenColumns hidden = av.getAlignment()
1665 .getHiddenColumns();
1668 warn("REPORT BUG: avoided null columnselection bug (DMAM reported). Please contact Jim about this.");
1672 Iterator<int[]> hiddenRegions = hidden.iterator();
1673 while (hiddenRegions.hasNext())
1675 int[] region = hiddenRegions.next();
1676 HiddenColumns hc = new HiddenColumns();
1677 hc.setStart(region[0]);
1678 hc.setEnd(region[1]);
1679 // view.addHiddenColumns(hc);
1680 view.getHiddenColumns().add(hc);
1684 if (calcIdSet.size() > 0)
1686 for (String calcId : calcIdSet)
1688 if (calcId.trim().length() > 0)
1690 CalcIdParam cidp = createCalcIdParam(calcId, av);
1691 // Some calcIds have no parameters.
1694 // view.addCalcIdParam(cidp);
1695 view.getCalcIdParam().add(cidp);
1701 // jms.addViewport(view);
1702 object.getViewport().add(view);
1704 // object.setJalviewModelSequence(jms);
1705 // object.getVamsasModel().addSequenceSet(vamsasSet);
1706 object.getVamsasModel().getSequenceSet().add(vamsasSet);
1708 if (jout != null && fileName != null)
1710 // We may not want to write the object to disk,
1711 // eg we can copy the alignViewport to a new view object
1712 // using save and then load
1715 fileName = fileName.replace('\\', '/');
1716 System.out.println("Writing jar entry " + fileName);
1717 JarEntry entry = new JarEntry(fileName);
1718 jout.putNextEntry(entry);
1719 PrintWriter pout = new PrintWriter(
1720 new OutputStreamWriter(jout, UTF_8));
1721 JAXBContext jaxbContext = JAXBContext
1722 .newInstance(JalviewModel.class);
1723 Marshaller jaxbMarshaller = jaxbContext.createMarshaller();
1725 // output pretty printed
1726 // jaxbMarshaller.setProperty(Marshaller.JAXB_FORMATTED_OUTPUT, true);
1727 jaxbMarshaller.marshal(
1728 new ObjectFactory().createJalviewModel(object), pout);
1730 // jaxbMarshaller.marshal(object, pout);
1731 // marshaller.marshal(object);
1734 } catch (Exception ex)
1736 // TODO: raise error in GUI if marshalling failed.
1737 System.err.println("Error writing Jalview project");
1738 ex.printStackTrace();
1745 * Writes PCA viewer attributes and computed values to an XML model object and
1746 * adds it to the JalviewModel. Any exceptions are reported by logging.
1748 protected void savePCA(PCAPanel panel, JalviewModel object)
1752 PcaViewer viewer = new PcaViewer();
1753 viewer.setHeight(panel.getHeight());
1754 viewer.setWidth(panel.getWidth());
1755 viewer.setXpos(panel.getX());
1756 viewer.setYpos(panel.getY());
1757 viewer.setTitle(panel.getTitle());
1758 PCAModel pcaModel = panel.getPcaModel();
1759 viewer.setScoreModelName(pcaModel.getScoreModelName());
1760 viewer.setXDim(panel.getSelectedDimensionIndex(X));
1761 viewer.setYDim(panel.getSelectedDimensionIndex(Y));
1762 viewer.setZDim(panel.getSelectedDimensionIndex(Z));
1764 panel.getRotatableCanvas().getBackgroundColour().getRGB());
1765 viewer.setScaleFactor(panel.getRotatableCanvas().getScaleFactor());
1766 float[] spMin = panel.getRotatableCanvas().getSeqMin();
1767 SeqPointMin spmin = new SeqPointMin();
1768 spmin.setXPos(spMin[0]);
1769 spmin.setYPos(spMin[1]);
1770 spmin.setZPos(spMin[2]);
1771 viewer.setSeqPointMin(spmin);
1772 float[] spMax = panel.getRotatableCanvas().getSeqMax();
1773 SeqPointMax spmax = new SeqPointMax();
1774 spmax.setXPos(spMax[0]);
1775 spmax.setYPos(spMax[1]);
1776 spmax.setZPos(spMax[2]);
1777 viewer.setSeqPointMax(spmax);
1778 viewer.setShowLabels(panel.getRotatableCanvas().isShowLabels());
1779 viewer.setLinkToAllViews(
1780 panel.getRotatableCanvas().isApplyToAllViews());
1781 SimilarityParamsI sp = pcaModel.getSimilarityParameters();
1782 viewer.setIncludeGaps(sp.includeGaps());
1783 viewer.setMatchGaps(sp.matchGaps());
1784 viewer.setIncludeGappedColumns(sp.includeGappedColumns());
1785 viewer.setDenominateByShortestLength(sp.denominateByShortestLength());
1788 * sequence points on display
1790 for (jalview.datamodel.SequencePoint spt : pcaModel
1791 .getSequencePoints())
1793 SequencePoint point = new SequencePoint();
1794 point.setSequenceRef(seqHash(spt.getSequence()));
1795 point.setXPos(spt.coord.x);
1796 point.setYPos(spt.coord.y);
1797 point.setZPos(spt.coord.z);
1798 viewer.getSequencePoint().add(point);
1802 * (end points of) axes on display
1804 for (Point p : panel.getRotatableCanvas().getAxisEndPoints())
1807 Axis axis = new Axis();
1811 viewer.getAxis().add(axis);
1815 * raw PCA data (note we are not restoring PCA inputs here -
1816 * alignment view, score model, similarity parameters)
1818 PcaDataType data = new PcaDataType();
1819 viewer.setPcaData(data);
1820 PCA pca = pcaModel.getPcaData();
1822 DoubleMatrix pm = new DoubleMatrix();
1823 saveDoubleMatrix(pca.getPairwiseScores(), pm);
1824 data.setPairwiseMatrix(pm);
1826 DoubleMatrix tm = new DoubleMatrix();
1827 saveDoubleMatrix(pca.getTridiagonal(), tm);
1828 data.setTridiagonalMatrix(tm);
1830 DoubleMatrix eigenMatrix = new DoubleMatrix();
1831 data.setEigenMatrix(eigenMatrix);
1832 saveDoubleMatrix(pca.getEigenmatrix(), eigenMatrix);
1834 object.getPcaViewer().add(viewer);
1835 } catch (Throwable t)
1837 Cache.log.error("Error saving PCA: " + t.getMessage());
1842 * Stores values from a matrix into an XML element, including (if present) the
1847 * @see #loadDoubleMatrix(DoubleMatrix)
1849 protected void saveDoubleMatrix(MatrixI m, DoubleMatrix xmlMatrix)
1851 xmlMatrix.setRows(m.height());
1852 xmlMatrix.setColumns(m.width());
1853 for (int i = 0; i < m.height(); i++)
1855 DoubleVector row = new DoubleVector();
1856 for (int j = 0; j < m.width(); j++)
1858 row.getV().add(m.getValue(i, j));
1860 xmlMatrix.getRow().add(row);
1862 if (m.getD() != null)
1864 DoubleVector dVector = new DoubleVector();
1865 for (double d : m.getD())
1867 dVector.getV().add(d);
1869 xmlMatrix.setD(dVector);
1871 if (m.getE() != null)
1873 DoubleVector eVector = new DoubleVector();
1874 for (double e : m.getE())
1876 eVector.getV().add(e);
1878 xmlMatrix.setE(eVector);
1883 * Loads XML matrix data into a new Matrix object, including the D and/or E
1884 * vectors (if present)
1888 * @see Jalview2XML#saveDoubleMatrix(MatrixI, DoubleMatrix)
1890 protected MatrixI loadDoubleMatrix(DoubleMatrix mData)
1892 int rows = mData.getRows();
1893 double[][] vals = new double[rows][];
1895 for (int i = 0; i < rows; i++)
1897 List<Double> dVector = mData.getRow().get(i).getV();
1898 vals[i] = new double[dVector.size()];
1900 for (Double d : dVector)
1906 MatrixI m = new Matrix(vals);
1908 if (mData.getD() != null)
1910 List<Double> dVector = mData.getD().getV();
1911 double[] vec = new double[dVector.size()];
1913 for (Double d : dVector)
1919 if (mData.getE() != null)
1921 List<Double> dVector = mData.getE().getV();
1922 double[] vec = new double[dVector.size()];
1924 for (Double d : dVector)
1935 * Save any Varna viewers linked to this sequence. Writes an rnaViewer element
1936 * for each viewer, with
1938 * <li>viewer geometry (position, size, split pane divider location)</li>
1939 * <li>index of the selected structure in the viewer (currently shows gapped
1941 * <li>the id of the annotation holding RNA secondary structure</li>
1942 * <li>(currently only one SS is shown per viewer, may be more in future)</li>
1944 * Varna viewer state is also written out (in native Varna XML) to separate
1945 * project jar entries. A separate entry is written for each RNA structure
1946 * displayed, with the naming convention
1948 * <li>rna_viewId_sequenceId_annotationId_[gapped|trimmed]</li>
1956 * @param storeDataset
1958 protected void saveRnaViewers(JarOutputStream jout, JSeq jseq,
1959 final SequenceI jds, List<String> viewIds, AlignmentPanel ap,
1960 boolean storeDataset)
1962 if (Desktop.getDesktopPane() == null)
1966 JInternalFrame[] frames = Desktop.getDesktopPane().getAllFrames();
1967 for (int f = frames.length - 1; f > -1; f--)
1969 if (frames[f] instanceof AppVarna)
1971 AppVarna varna = (AppVarna) frames[f];
1973 * link the sequence to every viewer that is showing it and is linked to
1974 * its alignment panel
1976 if (varna.isListeningFor(jds) && ap == varna.getAlignmentPanel())
1978 String viewId = varna.getViewId();
1979 RnaViewer rna = new RnaViewer();
1980 rna.setViewId(viewId);
1981 rna.setTitle(varna.getTitle());
1982 rna.setXpos(varna.getX());
1983 rna.setYpos(varna.getY());
1984 rna.setWidth(varna.getWidth());
1985 rna.setHeight(varna.getHeight());
1986 rna.setDividerLocation(varna.getDividerLocation());
1987 rna.setSelectedRna(varna.getSelectedIndex());
1988 // jseq.addRnaViewer(rna);
1989 jseq.getRnaViewer().add(rna);
1992 * Store each Varna panel's state once in the project per sequence.
1993 * First time through only (storeDataset==false)
1995 // boolean storeSessions = false;
1996 // String sequenceViewId = viewId + seqsToIds.get(jds);
1997 // if (!storeDataset && !viewIds.contains(sequenceViewId))
1999 // viewIds.add(sequenceViewId);
2000 // storeSessions = true;
2002 for (RnaModel model : varna.getModels())
2004 if (model.seq == jds)
2007 * VARNA saves each view (sequence or alignment secondary
2008 * structure, gapped or trimmed) as a separate XML file
2010 String jarEntryName = rnaSessions.get(model);
2011 if (jarEntryName == null)
2014 String varnaStateFile = varna.getStateInfo(model.rna);
2015 jarEntryName = RNA_PREFIX + viewId + "_" + nextCounter();
2016 copyFileToJar(jout, varnaStateFile, jarEntryName);
2017 rnaSessions.put(model, jarEntryName);
2019 SecondaryStructure ss = new SecondaryStructure();
2020 String annotationId = varna.getAnnotation(jds).annotationId;
2021 ss.setAnnotationId(annotationId);
2022 ss.setViewerState(jarEntryName);
2023 ss.setGapped(model.gapped);
2024 ss.setTitle(model.title);
2025 // rna.addSecondaryStructure(ss);
2026 rna.getSecondaryStructure().add(ss);
2035 * Copy the contents of a file to a new entry added to the output jar
2039 * @param jarEntryName
2041 protected void copyFileToJar(JarOutputStream jout, String infilePath,
2042 String jarEntryName)
2044 DataInputStream dis = null;
2047 File file = new File(infilePath);
2048 if (file.exists() && jout != null)
2050 dis = new DataInputStream(new FileInputStream(file));
2051 byte[] data = new byte[(int) file.length()];
2052 dis.readFully(data);
2053 writeJarEntry(jout, jarEntryName, data);
2055 } catch (Exception ex)
2057 ex.printStackTrace();
2065 } catch (IOException e)
2074 * Write the data to a new entry of given name in the output jar file
2077 * @param jarEntryName
2079 * @throws IOException
2081 protected void writeJarEntry(JarOutputStream jout, String jarEntryName,
2082 byte[] data) throws IOException
2086 jarEntryName = jarEntryName.replace('\\','/');
2087 System.out.println("Writing jar entry " + jarEntryName);
2088 jout.putNextEntry(new JarEntry(jarEntryName));
2089 DataOutputStream dout = new DataOutputStream(jout);
2090 dout.write(data, 0, data.length);
2097 * Save the state of a structure viewer
2102 * the archive XML element under which to save the state
2105 * @param matchedFile
2109 protected String saveStructureState(AlignmentPanel ap, SequenceI jds,
2110 Pdbids pdb, PDBEntry entry, List<String> viewIds,
2111 String matchedFile, StructureViewerBase viewFrame)
2113 final AAStructureBindingModel bindingModel = viewFrame.getBinding();
2116 * Look for any bindings for this viewer to the PDB file of interest
2117 * (including part matches excluding chain id)
2119 for (int peid = 0; peid < bindingModel.getPdbCount(); peid++)
2121 final PDBEntry pdbentry = bindingModel.getPdbEntry(peid);
2122 final String pdbId = pdbentry.getId();
2123 if (!pdbId.equals(entry.getId())
2124 && !(entry.getId().length() > 4 && entry.getId().toLowerCase()
2125 .startsWith(pdbId.toLowerCase())))
2128 * not interested in a binding to a different PDB entry here
2132 if (matchedFile == null)
2134 matchedFile = pdbentry.getFile();
2136 else if (!matchedFile.equals(pdbentry.getFile()))
2139 "Probably lost some PDB-Sequence mappings for this structure file (which apparently has same PDB Entry code): "
2140 + pdbentry.getFile());
2144 // can get at it if the ID
2145 // match is ambiguous (e.g.
2148 for (int smap = 0; smap < viewFrame.getBinding()
2149 .getSequence()[peid].length; smap++)
2151 // if (jal.findIndex(jmol.jmb.sequence[peid][smap]) > -1)
2152 if (jds == viewFrame.getBinding().getSequence()[peid][smap])
2154 StructureState state = new StructureState();
2155 state.setVisible(true);
2156 state.setXpos(viewFrame.getX());
2157 state.setYpos(viewFrame.getY());
2158 state.setWidth(viewFrame.getWidth());
2159 state.setHeight(viewFrame.getHeight());
2160 final String viewId = viewFrame.getViewId();
2161 state.setViewId(viewId);
2162 state.setAlignwithAlignPanel(viewFrame.isUsedforaligment(ap));
2163 state.setColourwithAlignPanel(viewFrame.isUsedforcolourby(ap));
2164 state.setColourByJmol(viewFrame.isColouredByViewer());
2165 state.setType(viewFrame.getViewerType().toString());
2166 // pdb.addStructureState(state);
2167 pdb.getStructureState().add(state);
2175 * Populates the AnnotationColourScheme xml for save. This captures the
2176 * settings of the options in the 'Colour by Annotation' dialog.
2179 * @param userColours
2183 private AnnotationColourScheme constructAnnotationColours(
2184 AnnotationColourGradient acg, List<UserColourScheme> userColours,
2187 AnnotationColourScheme ac = new AnnotationColourScheme();
2188 ac.setAboveThreshold(acg.getAboveThreshold());
2189 ac.setThreshold(acg.getAnnotationThreshold());
2190 // 2.10.2 save annotationId (unique) not annotation label
2191 ac.setAnnotation(acg.getAnnotation().annotationId);
2192 if (acg.getBaseColour() instanceof UserColourScheme)
2195 setUserColourScheme(acg.getBaseColour(), userColours, jm));
2200 ColourSchemeProperty.getColourName(acg.getBaseColour()));
2203 ac.setMaxColour(acg.getMaxColour().getRGB());
2204 ac.setMinColour(acg.getMinColour().getRGB());
2205 ac.setPerSequence(acg.isSeqAssociated());
2206 ac.setPredefinedColours(acg.isPredefinedColours());
2210 private void storeAlignmentAnnotation(AlignmentAnnotation[] aa,
2211 IdentityHashMap<SequenceGroup, String> groupRefs,
2212 AlignmentViewport av, Set<String> calcIdSet, boolean storeDS,
2213 SequenceSet vamsasSet)
2216 for (int i = 0; i < aa.length; i++)
2218 Annotation an = new Annotation();
2220 AlignmentAnnotation annotation = aa[i];
2221 if (annotation.annotationId != null)
2223 annotationIds.put(annotation.annotationId, annotation);
2226 an.setId(annotation.annotationId);
2228 an.setVisible(annotation.visible);
2230 an.setDescription(annotation.description);
2232 if (annotation.sequenceRef != null)
2234 // 2.9 JAL-1781 xref on sequence id rather than name
2235 an.setSequenceRef(seqsToIds.get(annotation.sequenceRef));
2237 if (annotation.groupRef != null)
2239 String groupIdr = groupRefs.get(annotation.groupRef);
2240 if (groupIdr == null)
2242 // make a locally unique String
2243 groupRefs.put(annotation.groupRef,
2244 groupIdr = ("" + System.currentTimeMillis()
2245 + annotation.groupRef.getName()
2246 + groupRefs.size()));
2248 an.setGroupRef(groupIdr.toString());
2251 // store all visualization attributes for annotation
2252 an.setGraphHeight(annotation.graphHeight);
2253 an.setCentreColLabels(annotation.centreColLabels);
2254 an.setScaleColLabels(annotation.scaleColLabel);
2255 an.setShowAllColLabels(annotation.showAllColLabels);
2256 an.setBelowAlignment(annotation.belowAlignment);
2258 if (annotation.graph > 0)
2261 an.setGraphType(annotation.graph);
2262 an.setGraphGroup(annotation.graphGroup);
2263 if (annotation.getThreshold() != null)
2265 ThresholdLine line = new ThresholdLine();
2266 line.setLabel(annotation.getThreshold().label);
2267 line.setValue(annotation.getThreshold().value);
2268 line.setColour(annotation.getThreshold().colour.getRGB());
2269 an.setThresholdLine(line);
2277 an.setLabel(annotation.label);
2279 if (annotation == av.getAlignmentQualityAnnot()
2280 || annotation == av.getAlignmentConservationAnnotation()
2281 || annotation == av.getAlignmentConsensusAnnotation()
2282 || annotation.autoCalculated)
2284 // new way of indicating autocalculated annotation -
2285 an.setAutoCalculated(annotation.autoCalculated);
2287 if (annotation.hasScore())
2289 an.setScore(annotation.getScore());
2292 if (annotation.getCalcId() != null)
2294 calcIdSet.add(annotation.getCalcId());
2295 an.setCalcId(annotation.getCalcId());
2297 if (annotation.hasProperties())
2299 for (String pr : annotation.getProperties())
2301 jalview.xml.binding.jalview.Annotation.Property prop = new jalview.xml.binding.jalview.Annotation.Property();
2303 prop.setValue(annotation.getProperty(pr));
2304 // an.addProperty(prop);
2305 an.getProperty().add(prop);
2309 AnnotationElement ae;
2310 if (annotation.annotations != null)
2312 an.setScoreOnly(false);
2313 for (int a = 0; a < annotation.annotations.length; a++)
2315 if ((annotation == null) || (annotation.annotations[a] == null))
2320 ae = new AnnotationElement();
2321 if (annotation.annotations[a].description != null)
2323 ae.setDescription(annotation.annotations[a].description);
2325 if (annotation.annotations[a].displayCharacter != null)
2327 ae.setDisplayCharacter(
2328 annotation.annotations[a].displayCharacter);
2331 if (!Float.isNaN(annotation.annotations[a].value))
2333 ae.setValue(annotation.annotations[a].value);
2337 if (annotation.annotations[a].secondaryStructure > ' ')
2339 ae.setSecondaryStructure(
2340 annotation.annotations[a].secondaryStructure + "");
2343 if (annotation.annotations[a].colour != null
2344 && annotation.annotations[a].colour != java.awt.Color.black)
2346 ae.setColour(annotation.annotations[a].colour.getRGB());
2349 // an.addAnnotationElement(ae);
2350 an.getAnnotationElement().add(ae);
2351 if (annotation.autoCalculated)
2353 // only write one non-null entry into the annotation row -
2354 // sufficient to get the visualization attributes necessary to
2362 an.setScoreOnly(true);
2364 if (!storeDS || (storeDS && !annotation.autoCalculated))
2366 // skip autocalculated annotation - these are only provided for
2368 // vamsasSet.addAnnotation(an);
2369 vamsasSet.getAnnotation().add(an);
2375 private CalcIdParam createCalcIdParam(String calcId, AlignViewport av)
2377 AutoCalcSetting settings = av.getCalcIdSettingsFor(calcId);
2378 if (settings != null)
2380 CalcIdParam vCalcIdParam = new CalcIdParam();
2381 vCalcIdParam.setCalcId(calcId);
2382 // vCalcIdParam.addServiceURL(settings.getServiceURI());
2383 vCalcIdParam.getServiceURL().add(settings.getServiceURI());
2384 // generic URI allowing a third party to resolve another instance of the
2385 // service used for this calculation
2386 for (String url : settings.getServiceURLs())
2388 // vCalcIdParam.addServiceURL(urls);
2389 vCalcIdParam.getServiceURL().add(url);
2391 vCalcIdParam.setVersion("1.0");
2392 if (settings.getPreset() != null)
2394 WsParamSetI setting = settings.getPreset();
2395 vCalcIdParam.setName(setting.getName());
2396 vCalcIdParam.setDescription(setting.getDescription());
2400 vCalcIdParam.setName("");
2401 vCalcIdParam.setDescription("Last used parameters");
2403 // need to be able to recover 1) settings 2) user-defined presets or
2404 // recreate settings from preset 3) predefined settings provided by
2405 // service - or settings that can be transferred (or discarded)
2406 vCalcIdParam.setParameters(
2407 settings.getWsParamFile().replace("\n", "|\\n|"));
2408 vCalcIdParam.setAutoUpdate(settings.isAutoUpdate());
2409 // todo - decide if updateImmediately is needed for any projects.
2411 return vCalcIdParam;
2416 private boolean recoverCalcIdParam(CalcIdParam calcIdParam,
2419 if (calcIdParam.getVersion().equals("1.0"))
2421 final String[] calcIds = calcIdParam.getServiceURL().toArray(new String[0]);
2422 Jws2Instance service = Jws2Discoverer.getInstance()
2423 .getPreferredServiceFor(calcIds);
2424 if (service != null)
2426 WsParamSetI parmSet = null;
2429 parmSet = service.getParamStore().parseServiceParameterFile(
2430 calcIdParam.getName(), calcIdParam.getDescription(),
2432 calcIdParam.getParameters().replace("|\\n|", "\n"));
2433 } catch (IOException x)
2435 warn("Couldn't parse parameter data for "
2436 + calcIdParam.getCalcId(), x);
2439 List<ArgumentI> argList = null;
2440 if (calcIdParam.getName().length() > 0)
2442 parmSet = service.getParamStore()
2443 .getPreset(calcIdParam.getName());
2444 if (parmSet != null)
2446 // TODO : check we have a good match with settings in AACon -
2447 // otherwise we'll need to create a new preset
2452 argList = parmSet.getArguments();
2455 AAConSettings settings = new AAConSettings(
2456 calcIdParam.isAutoUpdate(), service, parmSet, argList);
2457 av.setCalcIdSettingsFor(calcIdParam.getCalcId(), settings,
2458 calcIdParam.isNeedsUpdate());
2463 warn("Cannot resolve a service for the parameters used in this project. Try configuring a JABAWS server.");
2467 throw new Error(MessageManager.formatMessage(
2468 "error.unsupported_version_calcIdparam", new Object[]
2469 { calcIdParam.toString() }));
2473 * External mapping between jalview objects and objects yielding a valid and
2474 * unique object ID string. This is null for normal Jalview project IO, but
2475 * non-null when a jalview project is being read or written as part of a
2478 IdentityHashMap jv2vobj = null;
2481 * Construct a unique ID for jvobj using either existing bindings or if none
2482 * exist, the result of the hashcode call for the object.
2485 * jalview data object
2486 * @return unique ID for referring to jvobj
2488 private String makeHashCode(Object jvobj, String altCode)
2490 if (jv2vobj != null)
2492 Object id = jv2vobj.get(jvobj);
2495 return id.toString();
2497 // check string ID mappings
2498 if (jvids2vobj != null && jvobj instanceof String)
2500 id = jvids2vobj.get(jvobj);
2504 return id.toString();
2506 // give up and warn that something has gone wrong
2507 warn("Cannot find ID for object in external mapping : " + jvobj);
2513 * return local jalview object mapped to ID, if it exists
2517 * @return null or object bound to idcode
2519 private Object retrieveExistingObj(String idcode)
2521 if (idcode != null && vobj2jv != null)
2523 return vobj2jv.get(idcode);
2529 * binding from ID strings from external mapping table to jalview data model
2532 private Hashtable vobj2jv;
2534 private Sequence createVamsasSequence(String id, SequenceI jds)
2536 return createVamsasSequence(true, id, jds, null);
2539 private Sequence createVamsasSequence(boolean recurse, String id,
2540 SequenceI jds, SequenceI parentseq)
2542 Sequence vamsasSeq = new Sequence();
2543 vamsasSeq.setId(id);
2544 vamsasSeq.setName(jds.getName());
2545 vamsasSeq.setSequence(jds.getSequenceAsString());
2546 vamsasSeq.setDescription(jds.getDescription());
2547 List<DBRefEntry> dbrefs = null;
2548 if (jds.getDatasetSequence() != null)
2550 vamsasSeq.setDsseqid(seqHash(jds.getDatasetSequence()));
2554 // seqId==dsseqid so we can tell which sequences really are
2555 // dataset sequences only
2556 vamsasSeq.setDsseqid(id);
2557 dbrefs = jds.getDBRefs();
2558 if (parentseq == null)
2565 for (int d = 0, nd = dbrefs.size(); d < nd; d++)
2567 DBRef dbref = new DBRef();
2568 DBRefEntry ref = dbrefs.get(d);
2569 dbref.setSource(ref.getSource());
2570 dbref.setVersion(ref.getVersion());
2571 dbref.setAccessionId(ref.getAccessionId());
2574 Mapping mp = createVamsasMapping(ref.getMap(), parentseq,
2576 dbref.setMapping(mp);
2578 // vamsasSeq.addDBRef(dbref);
2579 vamsasSeq.getDBRef().add(dbref);
2585 private Mapping createVamsasMapping(jalview.datamodel.Mapping jmp,
2586 SequenceI parentseq, SequenceI jds, boolean recurse)
2589 if (jmp.getMap() != null)
2593 jalview.util.MapList mlst = jmp.getMap();
2594 List<int[]> r = mlst.getFromRanges();
2595 for (int[] range : r)
2597 MapListFrom mfrom = new MapListFrom();
2598 mfrom.setStart(range[0]);
2599 mfrom.setEnd(range[1]);
2600 // mp.addMapListFrom(mfrom);
2601 mp.getMapListFrom().add(mfrom);
2603 r = mlst.getToRanges();
2604 for (int[] range : r)
2606 MapListTo mto = new MapListTo();
2607 mto.setStart(range[0]);
2608 mto.setEnd(range[1]);
2609 // mp.addMapListTo(mto);
2610 mp.getMapListTo().add(mto);
2612 mp.setMapFromUnit(BigInteger.valueOf(mlst.getFromRatio()));
2613 mp.setMapToUnit(BigInteger.valueOf(mlst.getToRatio()));
2614 if (jmp.getTo() != null)
2616 // MappingChoice mpc = new MappingChoice();
2618 // check/create ID for the sequence referenced by getTo()
2621 SequenceI ps = null;
2622 if (parentseq != jmp.getTo()
2623 && parentseq.getDatasetSequence() != jmp.getTo())
2625 // chaining dbref rather than a handshaking one
2626 jmpid = seqHash(ps = jmp.getTo());
2630 jmpid = seqHash(ps = parentseq);
2632 // mpc.setDseqFor(jmpid);
2633 mp.setDseqFor(jmpid);
2634 if (!seqRefIds.containsKey(jmpid))
2636 jalview.bin.Cache.log.debug("creatign new DseqFor ID");
2637 seqRefIds.put(jmpid, ps);
2641 jalview.bin.Cache.log.debug("reusing DseqFor ID");
2644 // mp.setMappingChoice(mpc);
2650 String setUserColourScheme(jalview.schemes.ColourSchemeI cs,
2651 List<UserColourScheme> userColours, JalviewModel jm)
2654 jalview.schemes.UserColourScheme ucs = (jalview.schemes.UserColourScheme) cs;
2655 boolean newucs = false;
2656 if (!userColours.contains(ucs))
2658 userColours.add(ucs);
2661 id = "ucs" + userColours.indexOf(ucs);
2664 // actually create the scheme's entry in the XML model
2665 java.awt.Color[] colours = ucs.getColours();
2666 UserColours uc = new UserColours();
2667 // UserColourScheme jbucs = new UserColourScheme();
2668 JalviewUserColours jbucs = new JalviewUserColours();
2670 for (int i = 0; i < colours.length; i++)
2672 Colour col = new Colour();
2673 col.setName(ResidueProperties.aa[i]);
2674 col.setRGB(jalview.util.Format.getHexString(colours[i]));
2675 // jbucs.addColour(col);
2676 jbucs.getColour().add(col);
2678 if (ucs.getLowerCaseColours() != null)
2680 colours = ucs.getLowerCaseColours();
2681 for (int i = 0; i < colours.length; i++)
2683 Colour col = new Colour();
2684 col.setName(ResidueProperties.aa[i].toLowerCase());
2685 col.setRGB(jalview.util.Format.getHexString(colours[i]));
2686 // jbucs.addColour(col);
2687 jbucs.getColour().add(col);
2692 uc.setUserColourScheme(jbucs);
2693 // jm.addUserColours(uc);
2694 jm.getUserColours().add(uc);
2700 jalview.schemes.UserColourScheme getUserColourScheme(
2701 JalviewModel jm, String id)
2703 List<UserColours> uc = jm.getUserColours();
2704 UserColours colours = null;
2706 for (int i = 0; i < uc.length; i++)
2708 if (uc[i].getId().equals(id))
2715 for (UserColours c : uc)
2717 if (c.getId().equals(id))
2724 java.awt.Color[] newColours = new java.awt.Color[24];
2726 for (int i = 0; i < 24; i++)
2728 newColours[i] = new java.awt.Color(Integer.parseInt(
2729 // colours.getUserColourScheme().getColour(i).getRGB(), 16));
2730 colours.getUserColourScheme().getColour().get(i).getRGB(),
2734 jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(
2737 if (colours.getUserColourScheme().getColour().size()/*Count()*/ > 24)
2739 newColours = new java.awt.Color[23];
2740 for (int i = 0; i < 23; i++)
2742 newColours[i] = new java.awt.Color(Integer.parseInt(
2743 colours.getUserColourScheme().getColour().get(i + 24)
2747 ucs.setLowerCaseColours(newColours);
2754 * Load a jalview project archive from a jar file
2757 * - HTTP URL or filename
2759 public AlignFrame loadJalviewAlign(final Object file)
2762 jalview.gui.AlignFrame af = null;
2766 // create list to store references for any new Jmol viewers created
2767 newStructureViewers = new Vector<>();
2768 // UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
2769 // Workaround is to make sure caller implements the JarInputStreamProvider
2771 // so we can re-open the jar input stream for each entry.
2773 jarInputStreamProvider jprovider = createjarInputStreamProvider(file);
2774 af = loadJalviewAlign(jprovider);
2777 af.setMenusForViewport();
2779 } catch (MalformedURLException e)
2781 errorMessage = "Invalid URL format for '" + file + "'";
2787 // BH 2019 -- can't wait
2788 SwingUtilities.invokeLater(new Runnable()
2793 setLoadingFinishedForNewStructureViewers();
2796 } catch (Exception x)
2798 System.err.println("Error loading alignment: " + x.getMessage());
2804 @SuppressWarnings("unused")
2805 private jarInputStreamProvider createjarInputStreamProvider(
2806 final Object ofile) throws MalformedURLException
2810 String file = (ofile instanceof File
2811 ? ((File) ofile).getCanonicalPath()
2812 : ofile.toString());
2813 byte[] bytes = Platform.isJS() ? Platform.getFileBytes((File) ofile)
2817 this.jarFile = (File) ofile;
2819 errorMessage = null;
2820 uniqueSetSuffix = null;
2822 viewportsAdded.clear();
2823 frefedSequence = null;
2825 URL url = file.startsWith("http://") ? new URL(file) : null;
2826 return new jarInputStreamProvider()
2829 public JarInputStream getJarInputStream() throws IOException
2831 InputStream is = bytes != null ? new ByteArrayInputStream(bytes)
2832 : (url != null ? url.openStream()
2833 : new FileInputStream(file));
2834 return new JarInputStream(is);
2838 public String getFilename()
2843 } catch (IOException e)
2845 e.printStackTrace();
2851 * Recover jalview session from a jalview project archive. Caller may
2852 * initialise uniqueSetSuffix, seqRefIds, viewportsAdded and frefedSequence
2853 * themselves. Any null fields will be initialised with default values,
2854 * non-null fields are left alone.
2859 public AlignFrame loadJalviewAlign(final jarInputStreamProvider jprovider)
2861 errorMessage = null;
2862 if (uniqueSetSuffix == null)
2864 uniqueSetSuffix = System.currentTimeMillis() % 100000 + "";
2866 if (seqRefIds == null)
2870 AlignFrame af = null, _af = null;
2871 IdentityHashMap<AlignmentI, AlignmentI> importedDatasets = new IdentityHashMap<>();
2872 Map<String, AlignFrame> gatherToThisFrame = new HashMap<>();
2873 final String file = jprovider.getFilename();
2875 List<AlignFrame> alignFrames = new ArrayList<>();
2879 JarInputStream jin = null;
2880 JarEntry jarentry = null;
2884 // Look for all the entry names ending with ".xml"
2885 // This includes all panels and at least one frame.
2886 // Platform.timeCheck(null, Platform.TIME_MARK);
2889 jin = jprovider.getJarInputStream();
2890 for (int i = 0; i < entryCount; i++)
2892 jarentry = jin.getNextJarEntry();
2894 String name = (jarentry == null ? null : jarentry.getName());
2896 // System.out.println("Jalview2XML opening " + name);
2897 if (name != null && name.endsWith(".xml"))
2900 // DataSet for.... is read last.
2903 // The question here is what to do with the two
2904 // .xml files in the jvp file.
2905 // Some number of them, "...Dataset for...", will be the
2906 // Only AlignPanels and will have Viewport.
2907 // One or more will be the source data, with the DBRefs.
2909 // JVP file writing (above) ensures tha the AlignPanels are written
2910 // first, then all relevant datasets (which are
2911 // Jalview.datamodel.Alignment).
2914 // Platform.timeCheck("Jalview2XML JAXB " + name, Platform.TIME_MARK);
2915 JAXBContext jc = JAXBContext
2916 .newInstance("jalview.xml.binding.jalview");
2917 XMLStreamReader streamReader = XMLInputFactory.newInstance()
2918 .createXMLStreamReader(jin);
2919 javax.xml.bind.Unmarshaller um = jc.createUnmarshaller();
2920 JAXBElement<JalviewModel> jbe = um
2921 .unmarshal(streamReader, JalviewModel.class);
2922 JalviewModel model = jbe.getValue();
2924 if (true) // !skipViewport(object))
2926 // Q: Do we have to load from the model, even if it
2927 // does not have a viewport, could we discover that early on?
2928 // Q: Do we need to load this object?
2929 _af = loadFromObject(model, file, true, jprovider);
2930 // Platform.timeCheck("Jalview2XML.loadFromObject",
2931 // Platform.TIME_MARK);
2935 alignFrames.add(_af);
2937 if (_af != null && model.getViewport().size() > 0)
2940 // That is, this is one of the AlignmentPanel models
2943 // store a reference to the first view
2946 if (_af.getViewport().isGatherViewsHere())
2948 // if this is a gathered view, keep its reference since
2949 // after gathering views, only this frame will remain
2951 gatherToThisFrame.put(_af.getViewport().getSequenceSetId(),
2954 // Save dataset to register mappings once all resolved
2955 importedDatasets.put(
2956 af.getViewport().getAlignment().getDataset(),
2957 af.getViewport().getAlignment().getDataset());
2960 // Platform.timeCheck("JAXB " + name, Platform.TIME_MARK);
2963 else if (jarentry != null)
2965 // Some other file here.
2968 } while (jarentry != null);
2969 // Platform.timeCheck("JAXB loop exit", Platform.TIME_MARK);
2970 resolveFrefedSequences();
2971 // Platform.timeCheck("JAXB resolveFrefed", Platform.TIME_MARK);
2973 } catch (IOException ex)
2975 ex.printStackTrace();
2976 errorMessage = "Couldn't locate Jalview XML file : " + file;
2978 "Exception whilst loading jalview XML file : " + ex + "\n");
2979 } catch (Exception ex)
2981 System.err.println("Parsing as Jalview Version 2 file failed.");
2982 ex.printStackTrace(System.err);
2983 if (attemptversion1parse)
2985 // used to attempt to parse as V1 castor-generated xml
2987 if (Desktop.getInstance() != null)
2989 Desktop.getInstance().stopLoading();
2993 System.out.println("Successfully loaded archive file");
2996 ex.printStackTrace();
2999 "Exception whilst loading jalview XML file : " + ex + "\n");
3000 } catch (OutOfMemoryError e)
3002 // Don't use the OOM Window here
3003 errorMessage = "Out of memory loading jalview XML file";
3004 System.err.println("Out of memory whilst loading jalview XML file");
3005 e.printStackTrace();
3008 for (AlignFrame alf : alignFrames)
3010 alf.alignPanel.setHoldRepaint(false);
3016 * Regather multiple views (with the same sequence set id) to the frame (if
3017 * any) that is flagged as the one to gather to, i.e. convert them to tabbed
3018 * views instead of separate frames. Note this doesn't restore a state where
3019 * some expanded views in turn have tabbed views - the last "first tab" read
3020 * in will play the role of gatherer for all.
3022 for (AlignFrame fr : gatherToThisFrame.values())
3024 Desktop.getInstance().gatherViews(fr);
3027 restoreSplitFrames();
3028 for (AlignmentI ds : importedDatasets.keySet())
3030 if (ds.getCodonFrames() != null)
3032 Desktop.getStructureSelectionManager()
3033 .registerMappings(ds.getCodonFrames());
3036 if (errorMessage != null)
3041 if (Desktop.getInstance() != null)
3043 Desktop.getInstance().stopLoading();
3050 * Try to reconstruct and display SplitFrame windows, where each contains
3051 * complementary dna and protein alignments. Done by pairing up AlignFrame
3052 * objects (created earlier) which have complementary viewport ids associated.
3054 protected void restoreSplitFrames()
3056 List<SplitFrame> gatherTo = new ArrayList<>();
3057 List<AlignFrame> addedToSplitFrames = new ArrayList<>();
3058 Map<String, AlignFrame> dna = new HashMap<>();
3061 * Identify the DNA alignments
3063 for (Entry<Viewport, AlignFrame> candidate : splitFrameCandidates
3066 AlignFrame af = candidate.getValue();
3067 if (af.getViewport().getAlignment().isNucleotide())
3069 dna.put(candidate.getKey().getId(), af);
3074 * Try to match up the protein complements
3076 for (Entry<Viewport, AlignFrame> candidate : splitFrameCandidates
3079 AlignFrame af = candidate.getValue();
3080 if (!af.getViewport().getAlignment().isNucleotide())
3082 String complementId = candidate.getKey().getComplementId();
3083 // only non-null complements should be in the Map
3084 if (complementId != null && dna.containsKey(complementId))
3086 final AlignFrame dnaFrame = dna.get(complementId);
3087 SplitFrame sf = createSplitFrame(dnaFrame, af);
3088 addedToSplitFrames.add(dnaFrame);
3089 addedToSplitFrames.add(af);
3090 dnaFrame.setMenusForViewport();
3091 af.setMenusForViewport();
3092 if (af.getViewport().isGatherViewsHere())
3101 * Open any that we failed to pair up (which shouldn't happen!) as
3102 * standalone AlignFrame's.
3104 for (Entry<Viewport, AlignFrame> candidate : splitFrameCandidates
3107 AlignFrame af = candidate.getValue();
3108 if (!addedToSplitFrames.contains(af))
3110 Viewport view = candidate.getKey();
3111 Desktop.addInternalFrame(af, view.getTitle(),
3112 safeInt(view.getWidth()), safeInt(view.getHeight()));
3113 af.setMenusForViewport();
3114 System.err.println("Failed to restore view " + view.getTitle()
3115 + " to split frame");
3120 * Gather back into tabbed views as flagged.
3122 for (SplitFrame sf : gatherTo)
3124 Desktop.getInstance().gatherViews(sf);
3127 splitFrameCandidates.clear();
3131 * Construct and display one SplitFrame holding DNA and protein alignments.
3134 * @param proteinFrame
3137 protected SplitFrame createSplitFrame(AlignFrame dnaFrame,
3138 AlignFrame proteinFrame)
3140 SplitFrame splitFrame = new SplitFrame(dnaFrame, proteinFrame);
3141 String title = MessageManager.getString("label.linked_view_title");
3142 int width = (int) dnaFrame.getBounds().getWidth();
3143 int height = (int) (dnaFrame.getBounds().getHeight()
3144 + proteinFrame.getBounds().getHeight() + 50);
3147 * SplitFrame location is saved to both enclosed frames
3149 splitFrame.setLocation(dnaFrame.getX(), dnaFrame.getY());
3150 Desktop.addInternalFrame(splitFrame, title, width, height);
3153 * And compute cDNA consensus (couldn't do earlier with consensus as
3154 * mappings were not yet present)
3156 proteinFrame.getViewport().alignmentChanged(proteinFrame.alignPanel);
3162 * check errorMessage for a valid error message and raise an error box in the
3163 * GUI or write the current errorMessage to stderr and then clear the error
3166 protected void reportErrors()
3168 reportErrors(false);
3171 protected void reportErrors(final boolean saving)
3173 if (errorMessage != null)
3175 final String finalErrorMessage = errorMessage;
3178 javax.swing.SwingUtilities.invokeLater(new Runnable()
3183 JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(),
3185 "Error " + (saving ? "saving" : "loading")
3187 JvOptionPane.WARNING_MESSAGE);
3193 System.err.println("Problem loading Jalview file: " + errorMessage);
3196 errorMessage = null;
3199 Map<String, String> alreadyLoadedPDB = new HashMap<>();
3202 * when set, local views will be updated from view stored in JalviewXML
3203 * Currently (28th Sep 2008) things will go horribly wrong in vamsas document
3204 * sync if this is set to true.
3206 private final boolean updateLocalViews = false;
3209 * Returns the path to a temporary file holding the PDB file for the given PDB
3210 * id. The first time of asking, searches for a file of that name in the
3211 * Jalview project jar, and copies it to a new temporary file. Any repeat
3212 * requests just return the path to the file previously created.
3218 String loadPDBFile(jarInputStreamProvider jprovider, String pdbId,
3221 if (alreadyLoadedPDB.containsKey(pdbId))
3223 return alreadyLoadedPDB.get(pdbId).toString();
3226 String tempFile = copyJarEntry(jprovider, pdbId, "jalview_pdb",
3228 if (tempFile != null)
3230 alreadyLoadedPDB.put(pdbId, tempFile);
3236 * Copies the jar entry of given name to a new temporary file and returns the
3237 * path to the file, or null if the entry is not found.
3240 * @param jarEntryName
3242 * a prefix for the temporary file name, must be at least three
3245 * null or original file - so new file can be given the same suffix
3249 protected String copyJarEntry(jarInputStreamProvider jprovider,
3250 String jarEntryName, String prefix, String origFile)
3252 BufferedReader in = null;
3253 PrintWriter out = null;
3254 String suffix = ".tmp";
3255 if (origFile == null)
3257 origFile = jarEntryName;
3259 int sfpos = origFile.lastIndexOf(".");
3260 if (sfpos > -1 && sfpos < (origFile.length() - 3))
3262 suffix = "." + origFile.substring(sfpos + 1);
3266 JarInputStream jin = jprovider.getJarInputStream();
3268 * if (jprovider.startsWith("http://")) { jin = new JarInputStream(new
3269 * URL(jprovider).openStream()); } else { jin = new JarInputStream(new
3270 * FileInputStream(jprovider)); }
3273 JarEntry entry = null;
3276 entry = jin.getNextJarEntry();
3277 } while (entry != null && !entry.getName().equals(jarEntryName));
3280 in = new BufferedReader(new InputStreamReader(jin, UTF_8));
3281 File outFile = File.createTempFile(prefix, suffix);
3282 outFile.deleteOnExit();
3283 out = new PrintWriter(new FileOutputStream(outFile));
3286 while ((data = in.readLine()) != null)
3291 String t = outFile.getAbsolutePath();
3296 warn("Couldn't find entry in Jalview Jar for " + jarEntryName);
3298 } catch (Exception ex)
3300 ex.printStackTrace();
3308 } catch (IOException e)
3322 private class JvAnnotRow
3324 public JvAnnotRow(int i, AlignmentAnnotation jaa)
3331 * persisted version of annotation row from which to take vis properties
3333 public jalview.datamodel.AlignmentAnnotation template;
3336 * original position of the annotation row in the alignment
3342 * Load alignment frame from jalview XML DOM object. For a DOM object that
3343 * includes one or more Viewport elements (one with a title that does NOT
3344 * contain "Dataset for"), create the frame.
3346 * @param jalviewModel
3349 * filename source string
3350 * @param loadTreesAndStructures
3351 * when false only create Viewport
3353 * data source provider
3354 * @return alignment frame created from view stored in DOM
3356 AlignFrame loadFromObject(JalviewModel jalviewModel, String file,
3357 boolean loadTreesAndStructures, jarInputStreamProvider jprovider)
3360 // Platform.timeCheck("Jalview2XML.loadFromObject0", Platform.TIME_MARK);
3362 SequenceSet vamsasSet = jalviewModel.getVamsasModel().getSequenceSet().get(0);
3363 List<Sequence> vamsasSeqs = vamsasSet.getSequence();
3366 // JalviewModelSequence jms = object.getJalviewModelSequence();
3368 // Viewport view = (jms.getViewportCount() > 0) ? jms.getViewport(0)
3370 Viewport view = (jalviewModel.getViewport().size() > 0)
3371 ? jalviewModel.getViewport().get(0)
3374 // ////////////////////////////////
3375 // INITIALISE ALIGNMENT SEQUENCESETID AND VIEWID
3378 // If we just load in the same jar file again, the sequenceSetId
3379 // will be the same, and we end up with multiple references
3380 // to the same sequenceSet. We must modify this id on load
3381 // so that each load of the file gives a unique id
3384 * used to resolve correct alignment dataset for alignments with multiple
3387 String uniqueSeqSetId = null;
3388 String viewId = null;
3391 uniqueSeqSetId = view.getSequenceSetId() + uniqueSetSuffix;
3392 viewId = (view.getId() == null ? null
3393 : view.getId() + uniqueSetSuffix);
3396 // Platform.timeCheck("Jalview2XML.loadFromObject1", Platform.TIME_MARK);
3397 // ////////////////////////////////
3400 List<SequenceI> hiddenSeqs = null;
3402 List<SequenceI> tmpseqs = new ArrayList<>();
3404 boolean multipleView = false;
3405 SequenceI referenceseqForView = null;
3406 // JSeq[] jseqs = object.getJalviewModelSequence().getJSeq();
3407 List<JSeq> jseqs = jalviewModel.getJSeq();
3408 int vi = 0; // counter in vamsasSeq array
3409 for (int i = 0; i < jseqs.size(); i++)
3411 JSeq jseq = jseqs.get(i);
3412 String seqId = jseq.getId();
3414 SequenceI tmpSeq = seqRefIds.get(seqId);
3418 if (!incompleteSeqs.containsKey(seqId))
3420 // may not need this check, but keep it for at least 2.9,1 release
3421 if (tmpSeq.getStart() != jseq.getStart()
3422 || tmpSeq.getEnd() != jseq.getEnd())
3425 "Warning JAL-2154 regression: updating start/end for sequence "
3426 + tmpSeq.toString() + " to " + jseq);
3431 incompleteSeqs.remove(seqId);
3433 if (vamsasSeqs.size() > vi
3434 && vamsasSeqs.get(vi).getId().equals(seqId))
3436 // most likely we are reading a dataset XML document so
3437 // update from vamsasSeq section of XML for this sequence
3438 tmpSeq.setName(vamsasSeqs.get(vi).getName());
3439 tmpSeq.setDescription(vamsasSeqs.get(vi).getDescription());
3440 tmpSeq.setSequence(vamsasSeqs.get(vi).getSequence());
3445 // reading multiple views, so vamsasSeq set is a subset of JSeq
3446 multipleView = true;
3448 tmpSeq.setStart(jseq.getStart());
3449 tmpSeq.setEnd(jseq.getEnd());
3450 tmpseqs.add(tmpSeq);
3454 Sequence vamsasSeq = vamsasSeqs.get(vi);
3455 tmpSeq = new jalview.datamodel.Sequence(vamsasSeq.getName(),
3456 vamsasSeq.getSequence());
3457 tmpSeq.setDescription(vamsasSeq.getDescription());
3458 tmpSeq.setStart(jseq.getStart());
3459 tmpSeq.setEnd(jseq.getEnd());
3460 tmpSeq.setVamsasId(uniqueSetSuffix + seqId);
3461 seqRefIds.put(vamsasSeq.getId(), tmpSeq);
3462 tmpseqs.add(tmpSeq);
3466 if (safeBoolean(jseq.isViewreference()))
3468 referenceseqForView = tmpseqs.get(tmpseqs.size() - 1);
3471 if (jseq.isHidden() != null && jseq.isHidden().booleanValue())
3473 if (hiddenSeqs == null)
3475 hiddenSeqs = new ArrayList<>();
3478 hiddenSeqs.add(tmpSeq);
3482 // Platform.timeCheck("Jalview2XML.loadFromObject-seq",
3483 // Platform.TIME_MARK);
3485 // Create the alignment object from the sequence set
3486 // ///////////////////////////////
3487 SequenceI[] orderedSeqs = tmpseqs
3488 .toArray(new SequenceI[tmpseqs.size()]);
3490 AlignmentI al = null;
3491 // so we must create or recover the dataset alignment before going further
3492 // ///////////////////////////////
3493 if (vamsasSet.getDatasetId() == null || vamsasSet.getDatasetId() == "")
3495 // older jalview projects do not have a dataset - so creat alignment and
3497 al = new Alignment(orderedSeqs);
3498 al.setDataset(null);
3502 boolean isdsal = jalviewModel.getViewport().isEmpty();
3505 // we are importing a dataset record, so
3506 // recover reference to an alignment already materialsed as dataset
3507 al = getDatasetFor(vamsasSet.getDatasetId());
3511 // materialse the alignment
3512 al = new Alignment(orderedSeqs);
3516 addDatasetRef(vamsasSet.getDatasetId(), al);
3519 // finally, verify all data in vamsasSet is actually present in al
3520 // passing on flag indicating if it is actually a stored dataset
3521 recoverDatasetFor(vamsasSet, al, isdsal, uniqueSeqSetId);
3524 // Platform.timeCheck("Jalview2XML.loadFromObject-align",
3525 // Platform.TIME_MARK);
3526 if (referenceseqForView != null)
3528 al.setSeqrep(referenceseqForView);
3530 // / Add the alignment properties
3531 for (int i = 0; i < vamsasSet.getSequenceSetProperties().size(); i++)
3533 SequenceSetProperties ssp = vamsasSet.getSequenceSetProperties()
3535 al.setProperty(ssp.getKey(), ssp.getValue());
3538 // Platform.timeCheck("Jalview2XML.loadFromObject-setseqprop",
3539 // Platform.TIME_MARK);
3540 // ///////////////////////////////
3542 Hashtable pdbloaded = new Hashtable(); // TODO nothing writes to this??
3545 // load sequence features, database references and any associated PDB
3546 // structures for the alignment
3548 // prior to 2.10, this part would only be executed the first time a
3549 // sequence was encountered, but not afterwards.
3550 // now, for 2.10 projects, this is also done if the xml doc includes
3551 // dataset sequences not actually present in any particular view.
3553 // Platform.timeCheck("J2XML features0", Platform.TIME_RESET);
3554 for (int i = 0; i < vamsasSeqs.size(); i++)
3556 JSeq jseq = jseqs.get(i);
3557 if (jseq.getFeatures().size() > 0)
3559 List<Feature> features = jseq.getFeatures();
3560 for (int f = 0; f < features.size(); f++)
3562 Feature feat = features.get(f);
3563 SequenceFeature sf = new SequenceFeature(feat.getType(),
3564 feat.getDescription(), feat.getBegin(), feat.getEnd(),
3565 safeFloat(feat.getScore()), feat.getFeatureGroup());
3566 sf.setStatus(feat.getStatus());
3569 * load any feature attributes - include map-valued attributes
3571 Map<String, Map<String, String>> mapAttributes = new HashMap<>();
3572 for (int od = 0; od < feat.getOtherData().size(); od++)
3574 OtherData keyValue = feat.getOtherData().get(od);
3575 String attributeName = keyValue.getKey();
3576 String attributeValue = keyValue.getValue();
3577 if (attributeName.startsWith("LINK"))
3579 sf.addLink(attributeValue);
3583 String subAttribute = keyValue.getKey2();
3584 if (subAttribute == null)
3586 // simple string-valued attribute
3587 sf.setValue(attributeName, attributeValue);
3591 // attribute 'key' has sub-attribute 'key2'
3592 if (!mapAttributes.containsKey(attributeName))
3594 mapAttributes.put(attributeName, new HashMap<>());
3596 mapAttributes.get(attributeName).put(subAttribute,
3601 for (Entry<String, Map<String, String>> mapAttribute : mapAttributes
3604 sf.setValue(mapAttribute.getKey(), mapAttribute.getValue());
3607 // adds feature to datasequence's feature set (since Jalview 2.10)
3608 // Platform.timeCheck(null, Platform.TIME_SET);
3609 al.getSequenceAt(i).addSequenceFeature(sf);
3610 // Platform.timeCheck(null, Platform.TIME_MARK);
3613 if (vamsasSeqs.get(i).getDBRef().size() > 0)
3615 // adds dbrefs to datasequence's set (since Jalview 2.10)
3617 al.getSequenceAt(i).getDatasetSequence() == null
3618 ? al.getSequenceAt(i)
3619 : al.getSequenceAt(i).getDatasetSequence(),
3622 if (jseq.getPdbids().size() > 0)
3624 List<Pdbids> ids = jseq.getPdbids();
3625 for (int p = 0; p < ids.size(); p++)
3627 Pdbids pdbid = ids.get(p);
3628 jalview.datamodel.PDBEntry entry = new jalview.datamodel.PDBEntry();
3629 entry.setId(pdbid.getId());
3630 if (pdbid.getType() != null)
3632 if (PDBEntry.Type.getType(pdbid.getType()) != null)
3634 entry.setType(PDBEntry.Type.getType(pdbid.getType()));
3638 entry.setType(PDBEntry.Type.FILE);
3641 // jprovider is null when executing 'New View'
3642 if (pdbid.getFile() != null && jprovider != null)
3644 if (!pdbloaded.containsKey(pdbid.getFile()))
3646 entry.setFile(loadPDBFile(jprovider, pdbid.getId(),
3651 entry.setFile(pdbloaded.get(pdbid.getId()).toString());
3655 if (pdbid.getPdbentryItem() != null)
3657 for (PdbentryItem item : pdbid.getPdbentryItem())
3659 for (Property pr : item.getProperty())
3661 entry.setProperty(pr.getName(), pr.getValue());
3666 for (Property prop : pdbid.getProperty())
3668 entry.setProperty(prop.getName(), prop.getValue());
3670 Desktop.getStructureSelectionManager()
3671 .registerPDBEntry(entry);
3672 // adds PDBEntry to datasequence's set (since Jalview 2.10)
3673 if (al.getSequenceAt(i).getDatasetSequence() != null)
3675 al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
3679 al.getSequenceAt(i).addPDBId(entry);
3686 // Platform.timeCheck("features done", Platform.TIME_GET);
3687 // Platform.timeCheck("Jalview2XML.loadFromObject-endmultiview",
3688 // Platform.TIME_MARK);
3689 } // end !multipleview
3691 // ///////////////////////////////
3692 // LOAD SEQUENCE MAPPINGS
3694 if (vamsasSet.getAlcodonFrame().size() > 0)
3696 // TODO Potentially this should only be done once for all views of an
3698 List<AlcodonFrame> alc = vamsasSet.getAlcodonFrame();
3699 for (int i = 0; i < alc.size(); i++)
3701 AlignedCodonFrame cf = new AlignedCodonFrame();
3702 if (alc.get(i).getAlcodMap().size() > 0)
3704 List<AlcodMap> maps = alc.get(i).getAlcodMap();
3705 for (int m = 0; m < maps.size(); m++)
3707 AlcodMap map = maps.get(m);
3708 SequenceI dnaseq = seqRefIds.get(map.getDnasq());
3710 jalview.datamodel.Mapping mapping = null;
3711 // attach to dna sequence reference.
3712 if (map.getMapping() != null)
3714 mapping = addMapping(map.getMapping());
3715 if (dnaseq != null && mapping.getTo() != null)
3717 cf.addMap(dnaseq, mapping.getTo(), mapping.getMap());
3723 newAlcodMapRef(map.getDnasq(), cf, mapping));
3727 al.addCodonFrame(cf);
3730 // Platform.timeCheck("Jalview2XML.loadFromObject-seqmap",
3731 // Platform.TIME_MARK);
3734 // ////////////////////////////////
3736 List<JvAnnotRow> autoAlan = new ArrayList<>();
3739 * store any annotations which forward reference a group's ID
3741 Map<String, List<AlignmentAnnotation>> groupAnnotRefs = new Hashtable<>();
3743 if (vamsasSet.getAnnotation().size()/*Count()*/ > 0)
3745 List<Annotation> an = vamsasSet.getAnnotation();
3747 for (int i = 0; i < an.size(); i++)
3749 Annotation annotation = an.get(i);
3752 * test if annotation is automatically calculated for this view only
3754 boolean autoForView = false;
3755 if (annotation.getLabel().equals("Quality")
3756 || annotation.getLabel().equals("Conservation")
3757 || annotation.getLabel().equals("Consensus"))
3759 // Kludge for pre 2.5 projects which lacked the autocalculated flag
3761 // JAXB has no has() test; schema defaults value to false
3762 // if (!annotation.hasAutoCalculated())
3764 // annotation.setAutoCalculated(true);
3767 if (autoForView || annotation.isAutoCalculated())
3769 // remove ID - we don't recover annotation from other views for
3770 // view-specific annotation
3771 annotation.setId(null);
3774 // set visibility for other annotation in this view
3775 String annotationId = annotation.getId();
3776 if (annotationId != null && annotationIds.containsKey(annotationId))
3778 AlignmentAnnotation jda = annotationIds.get(annotationId);
3779 // in principle Visible should always be true for annotation displayed
3780 // in multiple views
3781 if (annotation.isVisible() != null)
3783 jda.visible = annotation.isVisible();
3786 al.addAnnotation(jda);
3790 // Construct new annotation from model.
3791 List<AnnotationElement> ae = annotation.getAnnotationElement();
3792 // System.err.println(
3793 // "Jalview2XML processing " + ae.size() + " annotations");
3795 jalview.datamodel.Annotation[] anot = null;
3796 java.awt.Color firstColour = null;
3798 if (!annotation.isScoreOnly())
3800 anot = new jalview.datamodel.Annotation[al.getWidth()];
3801 for (int aa = 0; aa < ae.size() && aa < anot.length; aa++)
3803 AnnotationElement annElement = ae.get(aa);
3804 anpos = annElement.getPosition();
3806 if (anpos >= anot.length)
3811 float value = safeFloat(annElement.getValue());
3812 anot[anpos] = new jalview.datamodel.Annotation(
3813 annElement.getDisplayCharacter(),
3814 annElement.getDescription(),
3815 (annElement.getSecondaryStructure() == null
3816 || annElement.getSecondaryStructure()
3820 .getSecondaryStructure()
3823 anot[anpos].colour = new Color(safeInt(annElement.getColour()));
3824 if (firstColour == null)
3826 firstColour = anot[anpos].colour;
3830 // create the new AlignmentAnnotation
3831 jalview.datamodel.AlignmentAnnotation jaa = null;
3833 if (annotation.isGraph())
3835 float llim = 0, hlim = 0;
3836 // if (autoForView || an[i].isAutoCalculated()) {
3839 jaa = new jalview.datamodel.AlignmentAnnotation(
3840 annotation.getLabel(), annotation.getDescription(), anot,
3841 llim, hlim, safeInt(annotation.getGraphType()));
3843 jaa.graphGroup = safeInt(annotation.getGraphGroup());
3844 jaa._linecolour = firstColour;
3845 if (annotation.getThresholdLine() != null)
3847 jaa.setThreshold(new jalview.datamodel.GraphLine(
3848 safeFloat(annotation.getThresholdLine().getValue()),
3849 annotation.getThresholdLine().getLabel(),
3850 new java.awt.Color(safeInt(
3851 annotation.getThresholdLine().getColour()))));
3853 if (autoForView || annotation.isAutoCalculated())
3855 // Hardwire the symbol display line to ensure that labels for
3856 // histograms are displayed
3862 jaa = new jalview.datamodel.AlignmentAnnotation(
3863 annotation.getLabel(), annotation.getDescription(), anot);
3864 jaa._linecolour = firstColour;
3866 // register new annotation
3867 // Annotation graphs such as Conservation will not have id.
3868 if (annotation.getId() != null)
3870 annotationIds.put(annotation.getId(), jaa);
3871 jaa.annotationId = annotation.getId();
3873 // recover sequence association
3874 String sequenceRef = annotation.getSequenceRef();
3875 if (sequenceRef != null)
3877 // from 2.9 sequenceRef is to sequence id (JAL-1781)
3878 SequenceI sequence = seqRefIds.get(sequenceRef);
3879 if (sequence == null)
3881 // in pre-2.9 projects sequence ref is to sequence name
3882 sequence = al.findName(sequenceRef);
3884 if (sequence != null)
3886 jaa.createSequenceMapping(sequence, 1, true);
3887 sequence.addAlignmentAnnotation(jaa);
3890 // and make a note of any group association
3891 if (annotation.getGroupRef() != null
3892 && annotation.getGroupRef().length() > 0)
3894 List<jalview.datamodel.AlignmentAnnotation> aal = groupAnnotRefs
3895 .get(annotation.getGroupRef());
3898 aal = new ArrayList<>();
3899 groupAnnotRefs.put(annotation.getGroupRef(), aal);
3904 if (annotation.getScore() != null)
3906 jaa.setScore(annotation.getScore().doubleValue());
3908 if (annotation.isVisible() != null)
3910 jaa.visible = annotation.isVisible().booleanValue();
3913 if (annotation.isCentreColLabels() != null)
3915 jaa.centreColLabels = annotation.isCentreColLabels()
3919 if (annotation.isScaleColLabels() != null)
3921 jaa.scaleColLabel = annotation.isScaleColLabels().booleanValue();
3923 if (annotation.isAutoCalculated())
3925 // newer files have an 'autoCalculated' flag and store calculation
3926 // state in viewport properties
3927 jaa.autoCalculated = true; // means annotation will be marked for
3928 // update at end of load.
3930 if (annotation.getGraphHeight() != null)
3932 jaa.graphHeight = annotation.getGraphHeight().intValue();
3934 jaa.belowAlignment = annotation.isBelowAlignment();
3935 jaa.setCalcId(annotation.getCalcId());
3936 if (annotation.getProperty().size() > 0)
3938 for (Annotation.Property prop : annotation
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
4068 sg.setColourScheme(constructAnnotationColour(
4069 jGroup.getAnnotationColours(), null, al, jalviewModel, false));
4072 // Platform.timeCheck("Jalview2XML.loadFromObject-groups",
4073 // Platform.TIME_MARK);
4077 // only dataset in this model, so just return.
4080 // ///////////////////////////////
4083 // now check to see if we really need to create a new viewport.
4084 if (multipleView && viewportsAdded.size() == 0)
4086 // We recovered an alignment for which a viewport already exists.
4087 // TODO: fix up any settings necessary for overlaying stored state onto
4088 // state recovered from another document. (may not be necessary).
4089 // we may need a binding from a viewport in memory to one recovered from
4091 // and then recover its containing af to allow the settings to be applied.
4092 // TODO: fix for vamsas demo
4094 "About to recover a viewport for existing alignment: Sequence set ID is "
4096 Object seqsetobj = retrieveExistingObj(uniqueSeqSetId);
4097 if (seqsetobj != null)
4099 if (seqsetobj instanceof String)
4101 uniqueSeqSetId = (String) seqsetobj;
4103 "Recovered extant sequence set ID mapping for ID : New Sequence set ID is "
4109 "Warning : Collision between sequence set ID string and existing jalview object mapping.");
4113 // Platform.timeCheck("Jalview2XML.loadFromObject-viewport",
4114 // Platform.TIME_MARK);
4117 * indicate that annotation colours are applied across all groups (pre
4118 * Jalview 2.8.1 behaviour)
4120 boolean doGroupAnnColour = Jalview2XML.isVersionStringLaterThan("2.8.1",
4121 jalviewModel.getVersion());
4123 AlignFrame af = null;
4124 AlignmentPanel ap = null;
4125 AlignViewport av = null;
4128 // Check to see if this alignment already has a view id == viewId
4129 jalview.gui.AlignmentPanel views[] = Desktop
4130 .getAlignmentPanels(uniqueSeqSetId);
4131 if (views != null && views.length > 0)
4133 for (int v = 0; v < views.length; v++)
4137 if (av.getViewId().equalsIgnoreCase(viewId))
4139 // recover the existing alignpanel, alignframe, viewport
4142 // TODO: could even skip resetting view settings if we don't want to
4143 // change the local settings from other jalview processes
4151 af = loadViewport(file, jseqs, hiddenSeqs, al, jalviewModel, view,
4152 uniqueSeqSetId, viewId, autoAlan);
4153 av = af.getViewport();
4154 // note that this only retrieves the most recently accessed
4155 // tab of an AlignFrame.
4160 * Load any trees, PDB structures and viewers
4162 * Not done if flag is false (when this method is used for New View)
4164 final AlignFrame af0 = af;
4165 final AlignViewport av0 = av;
4166 final AlignmentPanel ap0 = ap;
4167 // Platform.timeCheck("Jalview2XML.loadFromObject-beforetree",
4168 // Platform.TIME_MARK);
4169 if (loadTreesAndStructures)
4171 if (!jalviewModel.getTree().isEmpty())
4173 SwingUtilities.invokeLater(new Runnable()
4178 // Platform.timeCheck(null, Platform.TIME_MARK);
4179 loadTrees(jalviewModel, view, af0, av0, ap0);
4180 // Platform.timeCheck("Jalview2XML.loadTrees", Platform.TIME_MARK);
4184 if (!jalviewModel.getPcaViewer().isEmpty())
4186 SwingUtilities.invokeLater(new Runnable()
4191 // Platform.timeCheck(null, Platform.TIME_MARK);
4192 loadPCAViewers(jalviewModel, ap0);
4193 // Platform.timeCheck("Jalview2XML.loadPCA", Platform.TIME_MARK);
4197 SwingUtilities.invokeLater(new Runnable()
4202 // Platform.timeCheck(null, Platform.TIME_MARK);
4203 loadPDBStructures(jprovider, jseqs, af0, ap0);
4204 // Platform.timeCheck("Jalview2XML.loadPDB", Platform.TIME_MARK);
4207 SwingUtilities.invokeLater(new Runnable()
4212 loadRnaViewers(jprovider, jseqs, ap0);
4216 // and finally return.
4217 // but do not set holdRepaint true just yet, because this could be the
4218 // initial frame with just its dataset.
4223 * Instantiate and link any saved RNA (Varna) viewers. The state of the Varna
4224 * panel is restored from separate jar entries, two (gapped and trimmed) per
4225 * sequence and secondary structure.
4227 * Currently each viewer shows just one sequence and structure (gapped and
4228 * trimmed), however this method is designed to support multiple sequences or
4229 * structures in viewers if wanted in future.
4235 protected void loadRnaViewers(jarInputStreamProvider jprovider,
4236 List<JSeq> jseqs, AlignmentPanel ap)
4239 * scan the sequences for references to viewers; create each one the first
4240 * time it is referenced, add Rna models to existing viewers
4242 for (JSeq jseq : jseqs)
4244 for (int i = 0; i < jseq.getRnaViewer().size(); i++)
4246 RnaViewer viewer = jseq.getRnaViewer().get(i);
4247 AppVarna appVarna = findOrCreateVarnaViewer(viewer, uniqueSetSuffix,
4250 for (int j = 0; j < viewer.getSecondaryStructure().size(); j++)
4252 SecondaryStructure ss = viewer.getSecondaryStructure().get(j);
4253 SequenceI seq = seqRefIds.get(jseq.getId());
4254 AlignmentAnnotation ann = this.annotationIds
4255 .get(ss.getAnnotationId());
4258 * add the structure to the Varna display (with session state copied
4259 * from the jar to a temporary file)
4261 boolean gapped = safeBoolean(ss.isGapped());
4262 String rnaTitle = ss.getTitle();
4263 String sessionState = ss.getViewerState();
4264 String tempStateFile = copyJarEntry(jprovider, sessionState,
4266 RnaModel rna = new RnaModel(rnaTitle, ann, seq, null, gapped);
4267 appVarna.addModelSession(rna, rnaTitle, tempStateFile);
4269 appVarna.setInitialSelection(safeInt(viewer.getSelectedRna()));
4275 * Locate and return an already instantiated matching AppVarna, or create one
4279 * @param viewIdSuffix
4283 protected AppVarna findOrCreateVarnaViewer(RnaViewer viewer,
4284 String viewIdSuffix, AlignmentPanel ap)
4287 * on each load a suffix is appended to the saved viewId, to avoid conflicts
4288 * if load is repeated
4290 String postLoadId = viewer.getViewId() + viewIdSuffix;
4291 for (JInternalFrame frame : getAllFrames())
4293 if (frame instanceof AppVarna)
4295 AppVarna varna = (AppVarna) frame;
4296 if (postLoadId.equals(varna.getViewId()))
4298 // this viewer is already instantiated
4299 // could in future here add ap as another 'parent' of the
4300 // AppVarna window; currently just 1-to-many
4307 * viewer not found - make it
4309 RnaViewerModel model = new RnaViewerModel(postLoadId, viewer.getTitle(),
4310 safeInt(viewer.getXpos()), safeInt(viewer.getYpos()),
4311 safeInt(viewer.getWidth()), safeInt(viewer.getHeight()),
4312 safeInt(viewer.getDividerLocation()));
4313 AppVarna varna = new AppVarna(model, ap);
4319 * Load any saved trees
4327 protected void loadTrees(JalviewModel jm, Viewport view,
4328 AlignFrame af, AlignViewport av, AlignmentPanel ap)
4330 // TODO result of automated refactoring - are all these parameters needed?
4333 for (int t = 0; t < jm.getTree().size(); t++)
4336 Tree tree = jm.getTree().get(t);
4338 TreePanel tp = (TreePanel) retrieveExistingObj(tree.getId());
4341 tp = af.showNewickTree(new NewickFile(tree.getNewick()),
4342 tree.getTitle(), safeInt(tree.getWidth()),
4343 safeInt(tree.getHeight()), safeInt(tree.getXpos()),
4344 safeInt(tree.getYpos()));
4345 if (tree.getId() != null)
4347 // perhaps bind the tree id to something ?
4352 // update local tree attributes ?
4353 // TODO: should check if tp has been manipulated by user - if so its
4354 // settings shouldn't be modified
4355 tp.setTitle(tree.getTitle());
4356 tp.setBounds(new Rectangle(safeInt(tree.getXpos()),
4357 safeInt(tree.getYpos()), safeInt(tree.getWidth()),
4358 safeInt(tree.getHeight())));
4359 tp.setViewport(av); // af.viewport;
4360 // TODO: verify 'associate with all views' works still
4361 tp.getTreeCanvas().setViewport(av); // af.viewport;
4362 tp.getTreeCanvas().setAssociatedPanel(ap); // af.alignPanel;
4364 tp.getTreeCanvas().setApplyToAllViews(tree.isLinkToAllViews());
4367 warn("There was a problem recovering stored Newick tree: \n"
4368 + tree.getNewick());
4372 tp.fitToWindow.setState(safeBoolean(tree.isFitToWindow()));
4373 tp.fitToWindow_actionPerformed(null);
4375 if (tree.getFontName() != null)
4378 new Font(tree.getFontName(), safeInt(tree.getFontStyle()),
4379 safeInt(tree.getFontSize())));
4384 new Font(view.getFontName(), safeInt(view.getFontStyle()),
4385 safeInt(view.getFontSize())));
4388 tp.showPlaceholders(safeBoolean(tree.isMarkUnlinked()));
4389 tp.showBootstrap(safeBoolean(tree.isShowBootstrap()));
4390 tp.showDistances(safeBoolean(tree.isShowDistances()));
4392 tp.getTreeCanvas().setThreshold(safeFloat(tree.getThreshold()));
4394 if (safeBoolean(tree.isCurrentTree()))
4396 af.getViewport().setCurrentTree(tp.getTree());
4400 } catch (Exception ex)
4402 ex.printStackTrace();
4407 * Load and link any saved structure viewers.
4414 protected void loadPDBStructures(jarInputStreamProvider jprovider,
4415 List<JSeq> jseqs, AlignFrame af, AlignmentPanel ap)
4418 * Run through all PDB ids on the alignment, and collect mappings between
4419 * distinct view ids and all sequences referring to that view.
4421 Map<String, StructureViewerModel> structureViewers = new LinkedHashMap<>();
4423 for (int i = 0; i < jseqs.size(); i++)
4425 JSeq jseq = jseqs.get(i);
4426 if (jseq.getPdbids().size() > 0)
4428 List<Pdbids> ids = jseq.getPdbids();
4429 for (int p = 0; p < ids.size(); p++)
4431 Pdbids pdbid = ids.get(p);
4432 final int structureStateCount = pdbid.getStructureState().size();
4433 for (int s = 0; s < structureStateCount; s++)
4435 // check to see if we haven't already created this structure view
4436 final StructureState structureState = pdbid
4437 .getStructureState().get(s);
4438 String sviewid = (structureState.getViewId() == null) ? null
4439 : structureState.getViewId() + uniqueSetSuffix;
4440 jalview.datamodel.PDBEntry jpdb = new jalview.datamodel.PDBEntry();
4441 // Originally : pdbid.getFile()
4442 // : TODO: verify external PDB file recovery still works in normal
4443 // jalview project load
4445 loadPDBFile(jprovider, pdbid.getId(), pdbid.getFile()));
4446 jpdb.setId(pdbid.getId());
4448 int x = safeInt(structureState.getXpos());
4449 int y = safeInt(structureState.getYpos());
4450 int width = safeInt(structureState.getWidth());
4451 int height = safeInt(structureState.getHeight());
4453 // Probably don't need to do this anymore...
4454 // Desktop.getDesktop().getComponentAt(x, y);
4455 // TODO: NOW: check that this recovers the PDB file correctly.
4456 String pdbFile = loadPDBFile(jprovider, pdbid.getId(),
4458 jalview.datamodel.SequenceI seq = seqRefIds
4459 .get(jseq.getId() + "");
4460 if (sviewid == null)
4462 sviewid = "_jalview_pre2_4_" + x + "," + y + "," + width + ","
4465 if (!structureViewers.containsKey(sviewid))
4467 structureViewers.put(sviewid,
4468 new StructureViewerModel(x, y, width, height, false,
4469 false, true, structureState.getViewId(),
4470 structureState.getType()));
4471 // Legacy pre-2.7 conversion JAL-823 :
4472 // do not assume any view has to be linked for colour by
4476 // assemble String[] { pdb files }, String[] { id for each
4477 // file }, orig_fileloc, SequenceI[][] {{ seqs_file 1 }, {
4478 // seqs_file 2}, boolean[] {
4479 // linkAlignPanel,superposeWithAlignpanel}} from hash
4480 StructureViewerModel jmoldat = structureViewers.get(sviewid);
4481 jmoldat.setAlignWithPanel(jmoldat.isAlignWithPanel()
4482 || structureState.isAlignwithAlignPanel());
4485 * Default colour by linked panel to false if not specified (e.g.
4486 * for pre-2.7 projects)
4488 boolean colourWithAlignPanel = jmoldat.isColourWithAlignPanel();
4489 colourWithAlignPanel |= structureState.isColourwithAlignPanel();
4490 jmoldat.setColourWithAlignPanel(colourWithAlignPanel);
4493 * Default colour by viewer to true if not specified (e.g. for
4496 boolean colourByViewer = jmoldat.isColourByViewer();
4497 colourByViewer &= structureState.isColourByJmol();
4498 jmoldat.setColourByViewer(colourByViewer);
4500 if (jmoldat.getStateData().length() < structureState
4501 .getValue()/*Content()*/.length())
4503 jmoldat.setStateData(structureState.getValue());// Content());
4505 if (pdbid.getFile() != null)
4507 File mapkey = new File(pdbid.getFile());
4508 StructureData seqstrmaps = jmoldat.getFileData().get(mapkey);
4509 if (seqstrmaps == null)
4511 jmoldat.getFileData().put(mapkey,
4512 seqstrmaps = jmoldat.new StructureData(pdbFile,
4515 if (!seqstrmaps.getSeqList().contains(seq))
4517 seqstrmaps.getSeqList().add(seq);
4523 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");
4530 // Instantiate the associated structure views
4531 for (Entry<String, StructureViewerModel> entry : structureViewers
4536 createOrLinkStructureViewer(entry, af, ap, jprovider);
4537 } catch (Exception e)
4540 "Error loading structure viewer: " + e.getMessage());
4541 // failed - try the next one
4553 protected void createOrLinkStructureViewer(
4554 Entry<String, StructureViewerModel> viewerData, AlignFrame af,
4555 AlignmentPanel ap, jarInputStreamProvider jprovider)
4557 final StructureViewerModel stateData = viewerData.getValue();
4560 * Search for any viewer windows already open from other alignment views
4561 * that exactly match the stored structure state
4563 StructureViewerBase comp = findMatchingViewer(viewerData);
4567 linkStructureViewer(ap, comp, stateData);
4572 * From 2.9: stateData.type contains JMOL or CHIMERA, data is in jar entry
4573 * "viewer_"+stateData.viewId
4575 if (ViewerType.CHIMERA.toString().equals(stateData.getType()))
4577 createChimeraViewer(viewerData, af, jprovider);
4582 * else Jmol (if pre-2.9, stateData contains JMOL state string)
4584 createJmolViewer(viewerData, af, jprovider);
4589 * Create a new Chimera viewer.
4595 protected void createChimeraViewer(
4596 Entry<String, StructureViewerModel> viewerData, AlignFrame af,
4597 jarInputStreamProvider jprovider)
4599 StructureViewerModel data = viewerData.getValue();
4600 String chimeraSessionFile = data.getStateData();
4603 * Copy Chimera session from jar entry "viewer_"+viewId to a temporary file
4605 * NB this is the 'saved' viewId as in the project file XML, _not_ the
4606 * 'uniquified' sviewid used to reconstruct the viewer here
4608 String viewerJarEntryName = getViewerJarEntryName(data.getViewId());
4609 chimeraSessionFile = copyJarEntry(jprovider, viewerJarEntryName,
4612 Set<Entry<File, StructureData>> fileData = data.getFileData()
4614 List<PDBEntry> pdbs = new ArrayList<>();
4615 List<SequenceI[]> allseqs = new ArrayList<>();
4616 for (Entry<File, StructureData> pdb : fileData)
4618 String filePath = pdb.getValue().getFilePath();
4619 String pdbId = pdb.getValue().getPdbId();
4620 // pdbs.add(new PDBEntry(filePath, pdbId));
4621 pdbs.add(new PDBEntry(pdbId, null, PDBEntry.Type.PDB, filePath));
4622 final List<SequenceI> seqList = pdb.getValue().getSeqList();
4623 SequenceI[] seqs = seqList.toArray(new SequenceI[seqList.size()]);
4627 boolean colourByChimera = data.isColourByViewer();
4628 boolean colourBySequence = data.isColourWithAlignPanel();
4630 // TODO use StructureViewer as a factory here, see JAL-1761
4631 final PDBEntry[] pdbArray = pdbs.toArray(new PDBEntry[pdbs.size()]);
4632 final SequenceI[][] seqsArray = allseqs
4633 .toArray(new SequenceI[allseqs.size()][]);
4634 String newViewId = viewerData.getKey();
4636 ChimeraViewFrame cvf = new ChimeraViewFrame(chimeraSessionFile,
4637 af.alignPanel, pdbArray, seqsArray, colourByChimera,
4638 colourBySequence, newViewId);
4639 cvf.setSize(data.getWidth(), data.getHeight());
4640 cvf.setLocation(data.getX(), data.getY());
4644 * Create a new Jmol window. First parse the Jmol state to translate filenames
4645 * loaded into the view, and record the order in which files are shown in the
4646 * Jmol view, so we can add the sequence mappings in same order.
4652 protected void createJmolViewer(
4653 final Entry<String, StructureViewerModel> viewerData,
4654 AlignFrame af, jarInputStreamProvider jprovider)
4656 final StructureViewerModel svattrib = viewerData.getValue();
4657 String state = svattrib.getStateData();
4660 * Pre-2.9: state element value is the Jmol state string
4662 * 2.9+: @type is "JMOL", state data is in a Jar file member named "viewer_"
4665 if (ViewerType.JMOL.toString().equals(svattrib.getType()))
4667 state = readJarEntry(jprovider,
4668 getViewerJarEntryName(svattrib.getViewId()));
4671 List<String> pdbfilenames = new ArrayList<>();
4672 List<SequenceI[]> seqmaps = new ArrayList<>();
4673 List<String> pdbids = new ArrayList<>();
4674 StringBuilder newFileLoc = new StringBuilder(64);
4675 int cp = 0, ncp, ecp;
4676 Map<File, StructureData> oldFiles = svattrib.getFileData();
4677 while ((ncp = state.indexOf("load ", cp)) > -1)
4681 // look for next filename in load statement
4682 newFileLoc.append(state.substring(cp,
4683 ncp = (state.indexOf("\"", ncp + 1) + 1)));
4684 String oldfilenam = state.substring(ncp,
4685 ecp = state.indexOf("\"", ncp));
4686 // recover the new mapping data for this old filename
4687 // have to normalize filename - since Jmol and jalview do
4689 // translation differently.
4690 StructureData filedat = oldFiles.get(new File(oldfilenam));
4691 if (filedat == null)
4693 String reformatedOldFilename = oldfilenam.replaceAll("/", "\\\\");
4694 filedat = oldFiles.get(new File(reformatedOldFilename));
4696 newFileLoc.append(Platform.escapeString(filedat.getFilePath()));
4697 pdbfilenames.add(filedat.getFilePath());
4698 pdbids.add(filedat.getPdbId());
4699 seqmaps.add(filedat.getSeqList().toArray(new SequenceI[0]));
4700 newFileLoc.append("\"");
4701 cp = ecp + 1; // advance beyond last \" and set cursor so we can
4702 // look for next file statement.
4703 } while ((ncp = state.indexOf("/*file*/", cp)) > -1);
4707 // just append rest of state
4708 newFileLoc.append(state.substring(cp));
4712 System.err.print("Ignoring incomplete Jmol state for PDB ids: ");
4713 newFileLoc = new StringBuilder(state);
4714 newFileLoc.append("; load append ");
4715 for (File id : oldFiles.keySet())
4717 // add this and any other pdb files that should be present in
4719 StructureData filedat = oldFiles.get(id);
4720 newFileLoc.append(filedat.getFilePath());
4721 pdbfilenames.add(filedat.getFilePath());
4722 pdbids.add(filedat.getPdbId());
4723 seqmaps.add(filedat.getSeqList().toArray(new SequenceI[0]));
4724 newFileLoc.append(" \"");
4725 newFileLoc.append(filedat.getFilePath());
4726 newFileLoc.append("\"");
4729 newFileLoc.append(";");
4732 if (newFileLoc.length() == 0)
4736 int histbug = newFileLoc.indexOf("history = ");
4740 * change "history = [true|false];" to "history = [1|0];"
4743 int diff = histbug == -1 ? -1 : newFileLoc.indexOf(";", histbug);
4744 String val = (diff == -1) ? null
4745 : newFileLoc.substring(histbug, diff);
4746 if (val != null && val.length() >= 4)
4748 if (val.contains("e")) // eh? what can it be?
4750 if (val.trim().equals("true"))
4758 newFileLoc.replace(histbug, diff, val);
4763 final String[] pdbf = pdbfilenames
4764 .toArray(new String[pdbfilenames.size()]);
4765 final String[] id = pdbids.toArray(new String[pdbids.size()]);
4766 final SequenceI[][] sq = seqmaps
4767 .toArray(new SequenceI[seqmaps.size()][]);
4768 final String fileloc = newFileLoc.toString();
4769 final String sviewid = viewerData.getKey();
4770 final AlignFrame alf = af;
4771 final Rectangle rect = new Rectangle(svattrib.getX(), svattrib.getY(),
4772 svattrib.getWidth(), svattrib.getHeight());
4775 javax.swing.SwingUtilities.invokeLater(new Runnable()
4780 JalviewStructureDisplayI sview = null;
4783 sview = new StructureViewer(
4784 alf.alignPanel.getStructureSelectionManager())
4785 .createView(StructureViewer.ViewerType.JMOL,
4786 pdbf, id, sq, alf.alignPanel, svattrib,
4787 fileloc, rect, sviewid);
4788 addNewStructureViewer(sview);
4789 } catch (OutOfMemoryError ex)
4791 new OOMWarning("restoring structure view for PDB id " + id,
4792 (OutOfMemoryError) ex.getCause());
4793 if (sview != null && sview.isVisible())
4795 sview.closeViewer(false);
4796 sview.setVisible(false);
4802 // } catch (InvocationTargetException ex)
4804 // warn("Unexpected error when opening Jmol view.", ex);
4806 // } catch (InterruptedException e)
4808 // // e.printStackTrace();
4814 * Generates a name for the entry in the project jar file to hold state
4815 * information for a structure viewer
4820 protected String getViewerJarEntryName(String viewId)
4822 return VIEWER_PREFIX + viewId;
4826 * Returns any open frame that matches given structure viewer data. The match
4827 * is based on the unique viewId, or (for older project versions) the frame's
4833 protected StructureViewerBase findMatchingViewer(
4834 Entry<String, StructureViewerModel> viewerData)
4836 final String sviewid = viewerData.getKey();
4837 final StructureViewerModel svattrib = viewerData.getValue();
4838 StructureViewerBase comp = null;
4839 JInternalFrame[] frames = getAllFrames();
4840 for (JInternalFrame frame : frames)
4842 if (frame instanceof StructureViewerBase)
4845 * Post jalview 2.4 schema includes structure view id
4847 if (sviewid != null && ((StructureViewerBase) frame).getViewId()
4850 comp = (StructureViewerBase) frame;
4851 break; // break added in 2.9
4854 * Otherwise test for matching position and size of viewer frame
4856 else if (frame.getX() == svattrib.getX()
4857 && frame.getY() == svattrib.getY()
4858 && frame.getHeight() == svattrib.getHeight()
4859 && frame.getWidth() == svattrib.getWidth())
4861 comp = (StructureViewerBase) frame;
4862 // no break in faint hope of an exact match on viewId
4870 * Link an AlignmentPanel to an existing structure viewer.
4875 * @param useinViewerSuperpos
4876 * @param usetoColourbyseq
4877 * @param viewerColouring
4879 protected void linkStructureViewer(AlignmentPanel ap,
4880 StructureViewerBase viewer, StructureViewerModel stateData)
4882 // NOTE: if the jalview project is part of a shared session then
4883 // view synchronization should/could be done here.
4885 final boolean useinViewerSuperpos = stateData.isAlignWithPanel();
4886 final boolean usetoColourbyseq = stateData.isColourWithAlignPanel();
4887 final boolean viewerColouring = stateData.isColourByViewer();
4888 Map<File, StructureData> oldFiles = stateData.getFileData();
4891 * Add mapping for sequences in this view to an already open viewer
4893 final AAStructureBindingModel binding = viewer.getBinding();
4894 for (File id : oldFiles.keySet())
4896 // add this and any other pdb files that should be present in the
4898 StructureData filedat = oldFiles.get(id);
4899 String pdbFile = filedat.getFilePath();
4900 SequenceI[] seq = filedat.getSeqList().toArray(new SequenceI[0]);
4901 binding.getSsm().setMapping(seq, null, pdbFile, DataSourceType.FILE,
4903 binding.addSequenceForStructFile(pdbFile, seq);
4905 // and add the AlignmentPanel's reference to the view panel
4906 viewer.addAlignmentPanel(ap);
4907 if (useinViewerSuperpos)
4909 viewer.useAlignmentPanelForSuperposition(ap);
4913 viewer.excludeAlignmentPanelForSuperposition(ap);
4915 if (usetoColourbyseq)
4917 viewer.useAlignmentPanelForColourbyseq(ap, !viewerColouring);
4921 viewer.excludeAlignmentPanelForColourbyseq(ap);
4926 * Get all frames within the Desktop.
4930 protected JInternalFrame[] getAllFrames()
4932 JInternalFrame[] frames = null;
4933 // TODO is this necessary - is it safe - risk of hanging?
4938 frames = Desktop.getDesktopPane().getAllFrames();
4939 } catch (ArrayIndexOutOfBoundsException e)
4941 // occasional No such child exceptions are thrown here...
4945 } catch (InterruptedException f)
4949 } while (frames == null);
4954 * Answers true if 'version' is equal to or later than 'supported', where each
4955 * is formatted as major/minor versions like "2.8.3" or "2.3.4b1" for bugfix
4956 * changes. Development and test values for 'version' are leniently treated
4960 * - minimum version we are comparing against
4962 * - version of data being processsed
4965 public static boolean isVersionStringLaterThan(String supported,
4968 if (supported == null || version == null
4969 || version.equalsIgnoreCase("DEVELOPMENT BUILD")
4970 || version.equalsIgnoreCase("Test")
4971 || version.equalsIgnoreCase("AUTOMATED BUILD"))
4973 System.err.println("Assuming project file with "
4974 + (version == null ? "null" : version)
4975 + " is compatible with Jalview version " + supported);
4980 return StringUtils.compareVersions(version, supported, "b") >= 0;
4984 Vector<JalviewStructureDisplayI> newStructureViewers = null;
4986 protected void addNewStructureViewer(JalviewStructureDisplayI sview)
4988 if (newStructureViewers != null)
4990 sview.getBinding().setFinishedLoadingFromArchive(false);
4991 newStructureViewers.add(sview);
4995 protected void setLoadingFinishedForNewStructureViewers()
4997 if (newStructureViewers != null)
4999 for (JalviewStructureDisplayI sview : newStructureViewers)
5001 sview.getBinding().setFinishedLoadingFromArchive(true);
5003 newStructureViewers.clear();
5004 newStructureViewers = null;
5008 AlignFrame loadViewport(String fileName, List<JSeq> JSEQ,
5009 List<SequenceI> hiddenSeqs, AlignmentI al, JalviewModel jm,
5010 Viewport view, String uniqueSeqSetId, String viewId,
5011 List<JvAnnotRow> autoAlan)
5013 AlignFrame af = null;
5014 af = new AlignFrame(al, safeInt(view.getWidth()),
5015 safeInt(view.getHeight()), uniqueSeqSetId, viewId)
5019 // protected void processKeyEvent(java.awt.event.KeyEvent e) {
5020 // System.out.println("Jalview2XML AF " + e);
5021 // super.processKeyEvent(e);
5027 af.alignPanel.setHoldRepaint(true);
5028 af.setFileName(fileName, FileFormat.Jalview);
5029 af.setFileObject(jarFile); // BH 2019 JAL-3436
5031 final AlignViewport viewport = af.getViewport();
5032 for (int i = 0; i < JSEQ.size(); i++)
5034 int colour = safeInt(JSEQ.get(i).getColour());
5035 viewport.setSequenceColour(viewport.getAlignment().getSequenceAt(i),
5041 viewport.setColourByReferenceSeq(true);
5042 viewport.setDisplayReferenceSeq(true);
5045 viewport.setGatherViewsHere(safeBoolean(view.isGatheredViews()));
5047 if (view.getSequenceSetId() != null)
5049 AlignmentViewport av = viewportsAdded.get(uniqueSeqSetId);
5051 viewport.setSequenceSetId(uniqueSeqSetId);
5054 // propagate shared settings to this new view
5055 viewport.setHistoryList(av.getHistoryList());
5056 viewport.setRedoList(av.getRedoList());
5060 viewportsAdded.put(uniqueSeqSetId, viewport);
5062 // TODO: check if this method can be called repeatedly without
5063 // side-effects if alignpanel already registered.
5064 PaintRefresher.Register(af.alignPanel, uniqueSeqSetId);
5066 // apply Hidden regions to view.
5067 if (hiddenSeqs != null)
5069 for (int s = 0; s < JSEQ.size(); s++)
5071 SequenceGroup hidden = new SequenceGroup();
5072 boolean isRepresentative = false;
5073 for (int r = 0; r < JSEQ.get(s).getHiddenSequences().size(); r++)
5075 isRepresentative = true;
5076 SequenceI sequenceToHide = al
5077 .getSequenceAt(JSEQ.get(s).getHiddenSequences().get(r));
5078 hidden.addSequence(sequenceToHide, false);
5079 // remove from hiddenSeqs list so we don't try to hide it twice
5080 hiddenSeqs.remove(sequenceToHide);
5082 if (isRepresentative)
5084 SequenceI representativeSequence = al.getSequenceAt(s);
5085 hidden.addSequence(representativeSequence, false);
5086 viewport.hideRepSequences(representativeSequence, hidden);
5090 SequenceI[] hseqs = hiddenSeqs
5091 .toArray(new SequenceI[hiddenSeqs.size()]);
5092 viewport.hideSequence(hseqs);
5095 // recover view properties and display parameters
5097 viewport.setShowAnnotation(safeBoolean(view.isShowAnnotation()));
5098 viewport.setAbovePIDThreshold(safeBoolean(view.isPidSelected()));
5099 final int pidThreshold = safeInt(view.getPidThreshold());
5100 viewport.setThreshold(pidThreshold);
5102 viewport.setColourText(safeBoolean(view.isShowColourText()));
5104 viewport.setConservationSelected(
5105 safeBoolean(view.isConservationSelected()));
5106 viewport.setIncrement(safeInt(view.getConsThreshold()));
5107 viewport.setShowJVSuffix(safeBoolean(view.isShowFullId()));
5108 viewport.setRightAlignIds(safeBoolean(view.isRightAlignIds()));
5109 viewport.setFont(new Font(view.getFontName(),
5110 safeInt(view.getFontStyle()), safeInt(view.getFontSize())),
5112 ViewStyleI vs = viewport.getViewStyle();
5113 vs.setScaleProteinAsCdna(view.isScaleProteinAsCdna());
5114 viewport.setViewStyle(vs);
5115 // TODO: allow custom charWidth/Heights to be restored by updating them
5116 // after setting font - which means set above to false
5117 viewport.setRenderGaps(safeBoolean(view.isRenderGaps()));
5118 viewport.setWrapAlignment(safeBoolean(view.isWrapAlignment()));
5119 viewport.setShowAnnotation(safeBoolean(view.isShowAnnotation()));
5121 viewport.setShowBoxes(safeBoolean(view.isShowBoxes()));
5123 viewport.setShowText(safeBoolean(view.isShowText()));
5125 viewport.setTextColour(new Color(safeInt(view.getTextCol1())));
5126 viewport.setTextColour2(new Color(safeInt(view.getTextCol2())));
5127 viewport.setThresholdTextColour(safeInt(view.getTextColThreshold()));
5128 viewport.setShowUnconserved(view.isShowUnconserved());
5129 viewport.getRanges().setStartRes(safeInt(view.getStartRes()));
5131 if (view.getViewName() != null)
5133 viewport.setViewName(view.getViewName());
5134 af.setInitialTabVisible();
5136 int x = safeInt(view.getXpos());
5137 int y = safeInt(view.getYpos());
5138 int w = safeInt(view.getWidth());
5139 int h = safeInt(view.getHeight());
5140 // // BH we cannot let the title bar go off the top
5141 // if (Platform.isJS())
5143 // x = Math.max(50 - w, x);
5144 // y = Math.max(0, y);
5147 af.setBounds(x, y, w, h);
5148 // startSeq set in af.alignPanel.updateLayout below
5149 af.alignPanel.updateLayout();
5150 ColourSchemeI cs = null;
5151 // apply colourschemes
5152 if (view.getBgColour() != null)
5154 if (view.getBgColour().startsWith("ucs"))
5156 cs = getUserColourScheme(jm, view.getBgColour());
5158 else if (view.getBgColour().startsWith("Annotation"))
5160 AnnotationColourScheme viewAnnColour = view.getAnnotationColours();
5161 cs = constructAnnotationColour(viewAnnColour, af, al, jm, true);
5168 cs = ColourSchemeProperty.getColourScheme(af.getViewport(), al,
5169 view.getBgColour());
5174 * turn off 'alignment colour applies to all groups'
5175 * while restoring global colour scheme
5177 viewport.setColourAppliesToAllGroups(false);
5178 viewport.setGlobalColourScheme(cs);
5179 viewport.getResidueShading().setThreshold(pidThreshold,
5180 view.isIgnoreGapsinConsensus());
5181 viewport.getResidueShading()
5182 .setConsensus(viewport.getSequenceConsensusHash());
5183 if (safeBoolean(view.isConservationSelected()) && cs != null)
5185 viewport.getResidueShading()
5186 .setConservationInc(safeInt(view.getConsThreshold()));
5188 af.changeColour(cs);
5189 viewport.setColourAppliesToAllGroups(true);
5191 viewport.setShowSequenceFeatures(
5192 safeBoolean(view.isShowSequenceFeatures()));
5194 viewport.setCentreColumnLabels(view.isCentreColumnLabels());
5195 viewport.setIgnoreGapsConsensus(view.isIgnoreGapsinConsensus(), null);
5196 viewport.setFollowHighlight(view.isFollowHighlight());
5197 viewport.followSelection = view.isFollowSelection();
5198 viewport.setShowConsensusHistogram(view.isShowConsensusHistogram());
5199 viewport.setShowSequenceLogo(view.isShowSequenceLogo());
5200 viewport.setNormaliseSequenceLogo(view.isNormaliseSequenceLogo());
5201 viewport.setShowDBRefs(safeBoolean(view.isShowDbRefTooltip()));
5202 viewport.setShowNPFeats(safeBoolean(view.isShowNPfeatureTooltip()));
5203 viewport.setShowGroupConsensus(view.isShowGroupConsensus());
5204 viewport.setShowGroupConservation(view.isShowGroupConservation());
5206 // recover feature settings
5207 if (jm.getFeatureSettings() != null)
5209 FeatureRenderer fr = af.alignPanel.getSeqPanel().seqCanvas
5210 .getFeatureRenderer();
5211 FeaturesDisplayed fdi;
5212 viewport.setFeaturesDisplayed(fdi = new FeaturesDisplayed());
5213 String[] renderOrder = new String[jm.getFeatureSettings().getSetting()
5215 Map<String, FeatureColourI> featureColours = new Hashtable<>();
5216 Map<String, Float> featureOrder = new Hashtable<>();
5218 for (int fs = 0; fs < jm.getFeatureSettings().getSetting()
5221 Setting setting = jm.getFeatureSettings().getSetting().get(fs);
5222 String featureType = setting.getType();
5225 * restore feature filters (if any)
5227 jalview.xml.binding.jalview.FeatureMatcherSet filters = setting
5229 if (filters != null)
5231 FeatureMatcherSetI filter = Jalview2XML.parseFilter(featureType,
5233 if (!filter.isEmpty())
5235 fr.setFeatureFilter(featureType, filter);
5240 * restore feature colour scheme
5242 Color maxColour = new Color(setting.getColour());
5243 if (setting.getMincolour() != null)
5246 * minColour is always set unless a simple colour
5247 * (including for colour by label though it doesn't use it)
5249 Color minColour = new Color(setting.getMincolour().intValue());
5250 Color noValueColour = minColour;
5251 NoValueColour noColour = setting.getNoValueColour();
5252 if (noColour == NoValueColour.NONE)
5254 noValueColour = null;
5256 else if (noColour == NoValueColour.MAX)
5258 noValueColour = maxColour;
5260 float min = safeFloat(safeFloat(setting.getMin()));
5261 float max = setting.getMax() == null ? 1f
5262 : setting.getMax().floatValue();
5263 FeatureColourI gc = new FeatureColour(maxColour, minColour,
5264 maxColour, noValueColour, min, max);
5265 if (setting.getAttributeName().size() > 0)
5267 gc.setAttributeName(setting.getAttributeName().toArray(
5268 new String[setting.getAttributeName().size()]));
5270 if (setting.getThreshold() != null)
5272 gc.setThreshold(setting.getThreshold().floatValue());
5273 int threshstate = safeInt(setting.getThreshstate());
5274 // -1 = None, 0 = Below, 1 = Above threshold
5275 if (threshstate == 0)
5277 gc.setBelowThreshold(true);
5279 else if (threshstate == 1)
5281 gc.setAboveThreshold(true);
5284 gc.setAutoScaled(true); // default
5285 if (setting.isAutoScale() != null)
5287 gc.setAutoScaled(setting.isAutoScale());
5289 if (setting.isColourByLabel() != null)
5291 gc.setColourByLabel(setting.isColourByLabel());
5293 // and put in the feature colour table.
5294 featureColours.put(featureType, gc);
5298 featureColours.put(featureType, new FeatureColour(maxColour));
5300 renderOrder[fs] = featureType;
5301 if (setting.getOrder() != null)
5303 featureOrder.put(featureType, setting.getOrder().floatValue());
5307 featureOrder.put(featureType, new Float(
5308 fs / jm.getFeatureSettings().getSetting().size()));
5310 if (safeBoolean(setting.isDisplay()))
5312 fdi.setVisible(featureType);
5315 Map<String, Boolean> fgtable = new Hashtable<>();
5316 for (int gs = 0; gs < jm.getFeatureSettings().getGroup().size(); gs++)
5318 Group grp = jm.getFeatureSettings().getGroup().get(gs);
5319 fgtable.put(grp.getName(), new Boolean(grp.isDisplay()));
5321 // FeatureRendererSettings frs = new FeatureRendererSettings(renderOrder,
5322 // fgtable, featureColours, jms.getFeatureSettings().hasTransparency() ?
5323 // jms.getFeatureSettings().getTransparency() : 0.0, featureOrder);
5324 FeatureRendererSettings frs = new FeatureRendererSettings(renderOrder,
5325 fgtable, featureColours, 1.0f, featureOrder);
5326 fr.transferSettings(frs);
5329 if (view.getHiddenColumns().size() > 0)
5331 for (int c = 0; c < view.getHiddenColumns().size(); c++)
5333 final HiddenColumns hc = view.getHiddenColumns().get(c);
5334 viewport.hideColumns(safeInt(hc.getStart()),
5335 safeInt(hc.getEnd()) /* +1 */);
5338 if (view.getCalcIdParam() != null)
5340 for (CalcIdParam calcIdParam : view.getCalcIdParam())
5342 if (calcIdParam != null)
5344 if (recoverCalcIdParam(calcIdParam, viewport))
5349 warn("Couldn't recover parameters for "
5350 + calcIdParam.getCalcId());
5355 af.setMenusFromViewport(viewport);
5356 af.setTitle(view.getTitle());
5357 // TODO: we don't need to do this if the viewport is aready visible.
5359 * Add the AlignFrame to the desktop (it may be 'gathered' later), unless it
5360 * has a 'cdna/protein complement' view, in which case save it in order to
5361 * populate a SplitFrame once all views have been read in.
5363 String complementaryViewId = view.getComplementId();
5364 if (complementaryViewId == null)
5366 Dimension dim = Platform.getDimIfEmbedded(af,
5367 safeInt(view.getWidth()), safeInt(view.getHeight()));
5368 Desktop.addInternalFrame(af, view.getTitle(), dim.width, dim.height);
5369 // recompute any autoannotation
5370 af.alignPanel.updateAnnotation(false, true);
5371 reorderAutoannotation(af, al, autoAlan);
5372 af.alignPanel.alignmentChanged();
5376 splitFrameCandidates.put(view, af);
5382 * Reads saved data to restore Colour by Annotation settings
5384 * @param viewAnnColour
5388 * @param checkGroupAnnColour
5391 private ColourSchemeI constructAnnotationColour(
5392 AnnotationColourScheme viewAnnColour, AlignFrame af,
5393 AlignmentI al, JalviewModel model, boolean checkGroupAnnColour)
5395 boolean propagateAnnColour = false;
5396 AlignmentI annAlignment = af != null ? af.getViewport().getAlignment()
5398 if (checkGroupAnnColour && al.getGroups() != null
5399 && al.getGroups().size() > 0)
5401 // pre 2.8.1 behaviour
5402 // check to see if we should transfer annotation colours
5403 propagateAnnColour = true;
5404 for (SequenceGroup sg : al.getGroups())
5406 if (sg.getColourScheme() instanceof AnnotationColourGradient)
5408 propagateAnnColour = false;
5414 * 2.10.2- : saved annotationId is AlignmentAnnotation.annotationId
5416 String annotationId = viewAnnColour.getAnnotation();
5417 AlignmentAnnotation matchedAnnotation = annotationIds.get(annotationId);
5420 * pre 2.10.2: saved annotationId is AlignmentAnnotation.label
5422 if (matchedAnnotation == null
5423 && annAlignment.getAlignmentAnnotation() != null)
5425 for (int i = 0; i < annAlignment.getAlignmentAnnotation().length; i++)
5428 .equals(annAlignment.getAlignmentAnnotation()[i].label))
5430 matchedAnnotation = annAlignment.getAlignmentAnnotation()[i];
5435 if (matchedAnnotation == null)
5437 System.err.println("Failed to match annotation colour scheme for "
5441 if (matchedAnnotation.getThreshold() == null)
5443 matchedAnnotation.setThreshold(
5444 new GraphLine(safeFloat(viewAnnColour.getThreshold()),
5445 "Threshold", Color.black));
5448 AnnotationColourGradient cs = null;
5449 if (viewAnnColour.getColourScheme().equals("None"))
5451 cs = new AnnotationColourGradient(matchedAnnotation,
5452 new Color(safeInt(viewAnnColour.getMinColour())),
5453 new Color(safeInt(viewAnnColour.getMaxColour())),
5454 safeInt(viewAnnColour.getAboveThreshold()));
5456 else if (viewAnnColour.getColourScheme().startsWith("ucs"))
5458 cs = new AnnotationColourGradient(matchedAnnotation,
5459 getUserColourScheme(model, viewAnnColour.getColourScheme()),
5460 safeInt(viewAnnColour.getAboveThreshold()));
5464 cs = new AnnotationColourGradient(matchedAnnotation,
5465 ColourSchemeProperty.getColourScheme(af.getViewport(), al,
5466 viewAnnColour.getColourScheme()),
5467 safeInt(viewAnnColour.getAboveThreshold()));
5470 boolean perSequenceOnly = safeBoolean(viewAnnColour.isPerSequence());
5471 boolean useOriginalColours = safeBoolean(
5472 viewAnnColour.isPredefinedColours());
5473 cs.setSeqAssociated(perSequenceOnly);
5474 cs.setPredefinedColours(useOriginalColours);
5476 if (propagateAnnColour && al.getGroups() != null)
5478 // Also use these settings for all the groups
5479 for (int g = 0; g < al.getGroups().size(); g++)
5481 SequenceGroup sg = al.getGroups().get(g);
5482 if (sg.getGroupColourScheme() == null)
5487 AnnotationColourGradient groupScheme = new AnnotationColourGradient(
5488 matchedAnnotation, sg.getColourScheme(),
5489 safeInt(viewAnnColour.getAboveThreshold()));
5490 sg.setColourScheme(groupScheme);
5491 groupScheme.setSeqAssociated(perSequenceOnly);
5492 groupScheme.setPredefinedColours(useOriginalColours);
5498 private void reorderAutoannotation(AlignFrame af, AlignmentI al,
5499 List<JvAnnotRow> autoAlan)
5501 // copy over visualization settings for autocalculated annotation in the
5503 if (al.getAlignmentAnnotation() != null)
5506 * Kludge for magic autoannotation names (see JAL-811)
5508 String[] magicNames = new String[] { "Consensus", "Quality",
5510 JvAnnotRow nullAnnot = new JvAnnotRow(-1, null);
5511 Hashtable<String, JvAnnotRow> visan = new Hashtable<>();
5512 for (String nm : magicNames)
5514 visan.put(nm, nullAnnot);
5516 for (JvAnnotRow auan : autoAlan)
5518 visan.put(auan.template.label
5519 + (auan.template.getCalcId() == null ? ""
5520 : "\t" + auan.template.getCalcId()),
5523 int hSize = al.getAlignmentAnnotation().length;
5524 List<JvAnnotRow> reorder = new ArrayList<>();
5525 // work through any autoCalculated annotation already on the view
5526 // removing it if it should be placed in a different location on the
5527 // annotation panel.
5528 List<String> remains = new ArrayList<>(visan.keySet());
5529 for (int h = 0; h < hSize; h++)
5531 jalview.datamodel.AlignmentAnnotation jalan = al
5532 .getAlignmentAnnotation()[h];
5533 if (jalan.autoCalculated)
5536 JvAnnotRow valan = visan.get(k = jalan.label);
5537 if (jalan.getCalcId() != null)
5539 valan = visan.get(k = jalan.label + "\t" + jalan.getCalcId());
5544 // delete the auto calculated row from the alignment
5545 al.deleteAnnotation(jalan, false);
5549 if (valan != nullAnnot)
5551 if (jalan != valan.template)
5553 // newly created autoannotation row instance
5554 // so keep a reference to the visible annotation row
5555 // and copy over all relevant attributes
5556 if (valan.template.graphHeight >= 0)
5559 jalan.graphHeight = valan.template.graphHeight;
5561 jalan.visible = valan.template.visible;
5563 reorder.add(new JvAnnotRow(valan.order, jalan));
5568 // Add any (possibly stale) autocalculated rows that were not appended to
5569 // the view during construction
5570 for (String other : remains)
5572 JvAnnotRow othera = visan.get(other);
5573 if (othera != nullAnnot && othera.template.getCalcId() != null
5574 && othera.template.getCalcId().length() > 0)
5576 reorder.add(othera);
5579 // now put the automatic annotation in its correct place
5580 int s = 0, srt[] = new int[reorder.size()];
5581 JvAnnotRow[] rws = new JvAnnotRow[reorder.size()];
5582 for (JvAnnotRow jvar : reorder)
5585 srt[s++] = jvar.order;
5588 jalview.util.QuickSort.sort(srt, rws);
5589 // and re-insert the annotation at its correct position
5590 for (JvAnnotRow jvar : rws)
5592 al.addAnnotation(jvar.template, jvar.order);
5594 af.alignPanel.adjustAnnotationHeight();
5598 Hashtable skipList = null;
5601 * TODO remove this method
5604 * @return AlignFrame bound to sequenceSetId from view, if one exists. private
5605 * AlignFrame getSkippedFrame(Viewport view) { if (skipList==null) {
5606 * throw new Error("Implementation Error. No skipList defined for this
5607 * Jalview2XML instance."); } return (AlignFrame)
5608 * skipList.get(view.getSequenceSetId()); }
5612 * Check if the Jalview view contained in object should be skipped or not.
5615 * @return true if view's sequenceSetId is a key in skipList
5617 private boolean skipViewport(JalviewModel object)
5619 if (skipList == null)
5623 String id = object.getViewport().get(0).getSequenceSetId();
5624 if (skipList.containsKey(id))
5626 if (Cache.log != null && Cache.log.isDebugEnabled())
5628 Cache.log.debug("Skipping seuqence set id " + id);
5635 public void addToSkipList(AlignFrame af)
5637 if (skipList == null)
5639 skipList = new Hashtable();
5641 skipList.put(af.getViewport().getSequenceSetId(), af);
5644 public void clearSkipList()
5646 if (skipList != null)
5653 private void recoverDatasetFor(SequenceSet vamsasSet, AlignmentI al,
5654 boolean ignoreUnrefed, String uniqueSeqSetId)
5656 jalview.datamodel.AlignmentI ds = getDatasetFor(
5657 vamsasSet.getDatasetId());
5658 AlignmentI xtant_ds = ds;
5659 if (xtant_ds == null)
5661 // good chance we are about to create a new dataset, but check if we've
5662 // seen some of the dataset sequence IDs before.
5663 // TODO: skip this check if we are working with project generated by
5664 // version 2.11 or later
5665 xtant_ds = checkIfHasDataset(vamsasSet.getSequence());
5666 if (xtant_ds != null)
5669 addDatasetRef(vamsasSet.getDatasetId(), ds);
5672 Vector dseqs = null;
5675 // recovering an alignment View
5676 AlignmentI seqSetDS = getDatasetFor(UNIQSEQSETID + uniqueSeqSetId);
5677 if (seqSetDS != null)
5679 if (ds != null && ds != seqSetDS)
5681 warn("JAL-3171 regression: Overwriting a dataset reference for an alignment"
5682 + " - CDS/Protein crossreference data may be lost");
5683 if (xtant_ds != null)
5685 // This can only happen if the unique sequence set ID was bound to a
5686 // dataset that did not contain any of the sequences in the view
5687 // currently being restored.
5688 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.");
5692 addDatasetRef(vamsasSet.getDatasetId(), ds);
5697 // try even harder to restore dataset
5698 AlignmentI xtantDS = checkIfHasDataset(vamsasSet.getSequence());
5699 // create a list of new dataset sequences
5700 dseqs = new Vector();
5702 for (int i = 0, iSize = vamsasSet.getSequence().size(); i < iSize; i++)
5704 Sequence vamsasSeq = vamsasSet.getSequence().get(i);
5705 ensureJalviewDatasetSequence(vamsasSeq, ds, dseqs, ignoreUnrefed, i);
5707 // create a new dataset
5710 SequenceI[] dsseqs = new SequenceI[dseqs.size()];
5711 dseqs.copyInto(dsseqs);
5712 ds = new jalview.datamodel.Alignment(dsseqs);
5713 // debug("Jalview2XML Created new dataset " + vamsasSet.getDatasetId()
5714 // + " for alignment " + System.identityHashCode(al));
5715 addDatasetRef(vamsasSet.getDatasetId(), ds);
5717 // set the dataset for the newly imported alignment.
5718 if (al.getDataset() == null && !ignoreUnrefed)
5721 // register dataset for the alignment's uniqueSeqSetId for legacy projects
5722 addDatasetRef(UNIQSEQSETID + uniqueSeqSetId, ds);
5724 updateSeqDatasetBinding(vamsasSet.getSequence(), ds);
5728 * XML dataset sequence ID to materialised dataset reference
5730 HashMap<String, AlignmentI> seqToDataset = new HashMap<>();
5733 * @return the first materialised dataset reference containing a dataset
5734 * sequence referenced in the given view
5736 * - sequences from the view
5738 AlignmentI checkIfHasDataset(List<Sequence> list)
5740 for (Sequence restoredSeq : list)
5742 AlignmentI datasetFor = seqToDataset.get(restoredSeq.getDsseqid());
5743 if (datasetFor != null)
5752 * Register ds as the containing dataset for the dataset sequences referenced
5753 * by sequences in list
5756 * - sequences in a view
5759 void updateSeqDatasetBinding(List<Sequence> list, AlignmentI ds)
5761 for (Sequence restoredSeq : list)
5763 AlignmentI prevDS = seqToDataset.put(restoredSeq.getDsseqid(), ds);
5764 if (prevDS != null && prevDS != ds)
5766 warn("Dataset sequence appears in many datasets: "
5767 + restoredSeq.getDsseqid());
5768 // TODO: try to merge!
5775 * sequence definition to create/merge dataset sequence for
5779 * vector to add new dataset sequence to
5780 * @param ignoreUnrefed
5781 * - when true, don't create new sequences from vamsasSeq if it's id
5782 * doesn't already have an asssociated Jalview sequence.
5784 * - used to reorder the sequence in the alignment according to the
5785 * vamsasSeq array ordering, to preserve ordering of dataset
5787 private void ensureJalviewDatasetSequence(Sequence vamsasSeq,
5788 AlignmentI ds, Vector dseqs, boolean ignoreUnrefed, int vseqpos)
5790 // JBP TODO: Check this is called for AlCodonFrames to support recovery of
5792 SequenceI sq = seqRefIds.get(vamsasSeq.getId());
5793 boolean reorder = false;
5794 SequenceI dsq = null;
5795 if (sq != null && sq.getDatasetSequence() != null)
5797 dsq = sq.getDatasetSequence();
5803 if (sq == null && ignoreUnrefed)
5807 String sqid = vamsasSeq.getDsseqid();
5810 // need to create or add a new dataset sequence reference to this sequence
5813 dsq = seqRefIds.get(sqid);
5818 // make a new dataset sequence
5819 dsq = sq.createDatasetSequence();
5822 // make up a new dataset reference for this sequence
5823 sqid = seqHash(dsq);
5825 dsq.setVamsasId(uniqueSetSuffix + sqid);
5826 seqRefIds.put(sqid, dsq);
5831 dseqs.addElement(dsq);
5836 ds.addSequence(dsq);
5842 { // make this dataset sequence sq's dataset sequence
5843 sq.setDatasetSequence(dsq);
5844 // and update the current dataset alignment
5849 if (!dseqs.contains(dsq))
5856 if (ds.findIndex(dsq) < 0)
5858 ds.addSequence(dsq);
5865 // TODO: refactor this as a merge dataset sequence function
5866 // now check that sq (the dataset sequence) sequence really is the union of
5867 // all references to it
5868 // boolean pre = sq.getStart() < dsq.getStart();
5869 // boolean post = sq.getEnd() > dsq.getEnd();
5873 // StringBuffer sb = new StringBuffer();
5874 String newres = jalview.analysis.AlignSeq.extractGaps(
5875 jalview.util.Comparison.GapChars, sq.getSequenceAsString());
5876 if (!newres.equalsIgnoreCase(dsq.getSequenceAsString())
5877 && newres.length() > dsq.getLength())
5879 // Update with the longer sequence.
5883 * if (pre) { sb.insert(0, newres .substring(0, dsq.getStart() -
5884 * sq.getStart())); dsq.setStart(sq.getStart()); } if (post) {
5885 * sb.append(newres.substring(newres.length() - sq.getEnd() -
5886 * dsq.getEnd())); dsq.setEnd(sq.getEnd()); }
5888 dsq.setSequence(newres);
5890 // TODO: merges will never happen if we 'know' we have the real dataset
5891 // sequence - this should be detected when id==dssid
5893 "DEBUG Notice: Merged dataset sequence (if you see this often, post at http://issues.jalview.org/browse/JAL-1474)"); // ("
5894 // + (pre ? "prepended" : "") + " "
5895 // + (post ? "appended" : ""));
5900 // sequence refs are identical. We may need to update the existing dataset
5901 // alignment with this one, though.
5902 if (ds != null && dseqs == null)
5904 int opos = ds.findIndex(dsq);
5905 SequenceI tseq = null;
5906 if (opos != -1 && vseqpos != opos)
5908 // remove from old position
5909 ds.deleteSequence(dsq);
5911 if (vseqpos < ds.getHeight())
5913 if (vseqpos != opos)
5915 // save sequence at destination position
5916 tseq = ds.getSequenceAt(vseqpos);
5917 ds.replaceSequenceAt(vseqpos, dsq);
5918 ds.addSequence(tseq);
5923 ds.addSequence(dsq);
5930 * TODO use AlignmentI here and in related methods - needs
5931 * AlignmentI.getDataset() changed to return AlignmentI instead of Alignment
5933 Hashtable<String, AlignmentI> datasetIds = null;
5935 IdentityHashMap<AlignmentI, String> dataset2Ids = null;
5937 private AlignmentI getDatasetFor(String datasetId)
5939 if (datasetIds == null)
5941 datasetIds = new Hashtable<>();
5944 if (datasetIds.containsKey(datasetId))
5946 return datasetIds.get(datasetId);
5951 private void addDatasetRef(String datasetId, AlignmentI dataset)
5953 if (datasetIds == null)
5955 datasetIds = new Hashtable<>();
5957 datasetIds.put(datasetId, dataset);
5961 * make a new dataset ID for this jalview dataset alignment
5966 private String getDatasetIdRef(AlignmentI dataset)
5968 if (dataset.getDataset() != null)
5970 warn("Serious issue! Dataset Object passed to getDatasetIdRef is not a Jalview DATASET alignment...");
5972 String datasetId = makeHashCode(dataset, null);
5973 if (datasetId == null)
5975 // make a new datasetId and record it
5976 if (dataset2Ids == null)
5978 dataset2Ids = new IdentityHashMap<>();
5982 datasetId = dataset2Ids.get(dataset);
5984 if (datasetId == null)
5986 datasetId = "ds" + dataset2Ids.size() + 1;
5987 dataset2Ids.put(dataset, datasetId);
5993 private void addDBRefs(SequenceI datasetSequence, Sequence sequence)
5995 for (int d = 0; d < sequence.getDBRef().size(); d++)
5997 DBRef dr = sequence.getDBRef().get(d);
5998 jalview.datamodel.DBRefEntry entry = new jalview.datamodel.DBRefEntry(
5999 dr.getSource(), dr.getVersion(), dr.getAccessionId());
6000 if (dr.getMapping() != null)
6002 entry.setMap(addMapping(dr.getMapping()));
6004 datasetSequence.addDBRef(entry);
6008 private jalview.datamodel.Mapping addMapping(Mapping m)
6010 SequenceI dsto = null;
6011 // Mapping m = dr.getMapping();
6012 int fr[] = new int[m.getMapListFrom().size() * 2];
6013 Iterator<MapListFrom> from = m.getMapListFrom().iterator();// enumerateMapListFrom();
6014 for (int _i = 0; from.hasNext(); _i += 2)
6016 MapListFrom mf = from.next();
6017 fr[_i] = mf.getStart();
6018 fr[_i + 1] = mf.getEnd();
6020 int fto[] = new int[m.getMapListTo().size() * 2];
6021 Iterator<MapListTo> to = m.getMapListTo().iterator();// enumerateMapListTo();
6022 for (int _i = 0; to.hasNext(); _i += 2)
6024 MapListTo mf = to.next();
6025 fto[_i] = mf.getStart();
6026 fto[_i + 1] = mf.getEnd();
6028 jalview.datamodel.Mapping jmap = new jalview.datamodel.Mapping(dsto, fr,
6029 fto, m.getMapFromUnit().intValue(),
6030 m.getMapToUnit().intValue());
6033 * (optional) choice of dseqFor or Sequence
6035 if (m.getDseqFor() != null)
6037 String dsfor = m.getDseqFor();
6038 if (seqRefIds.containsKey(dsfor))
6043 jmap.setTo(seqRefIds.get(dsfor));
6047 frefedSequence.add(newMappingRef(dsfor, jmap));
6050 else if (m.getSequence() != null)
6053 * local sequence definition
6055 Sequence ms = m.getSequence();
6056 SequenceI djs = null;
6057 String sqid = ms.getDsseqid();
6058 if (sqid != null && sqid.length() > 0)
6061 * recover dataset sequence
6063 djs = seqRefIds.get(sqid);
6068 "Warning - making up dataset sequence id for DbRef sequence map reference");
6069 sqid = ((Object) ms).toString(); // make up a new hascode for
6070 // undefined dataset sequence hash
6071 // (unlikely to happen)
6077 * make a new dataset sequence and add it to refIds hash
6079 djs = new jalview.datamodel.Sequence(ms.getName(),
6081 djs.setStart(jmap.getMap().getToLowest());
6082 djs.setEnd(jmap.getMap().getToHighest());
6083 djs.setVamsasId(uniqueSetSuffix + sqid);
6085 incompleteSeqs.put(sqid, djs);
6086 seqRefIds.put(sqid, djs);
6089 jalview.bin.Cache.log.debug("about to recurse on addDBRefs.");
6098 * Provides a 'copy' of an alignment view (on action New View) by 'saving' the
6099 * view as XML (but not to file), and then reloading it
6104 public AlignmentPanel copyAlignPanel(AlignmentPanel ap)
6107 JalviewModel jm = saveState(ap, null, null, null);
6110 jm.getVamsasModel().getSequenceSet().get(0).getDatasetId(),
6111 ap.getAlignment().getDataset());
6113 uniqueSetSuffix = "";
6114 // jm.getJalviewModelSequence().getViewport(0).setId(null);
6115 jm.getViewport().get(0).setId(null);
6116 // we don't overwrite the view we just copied
6118 if (this.frefedSequence == null)
6120 frefedSequence = new Vector<>();
6123 viewportsAdded.clear();
6125 AlignFrame af = loadFromObject(jm, null, false, null);
6126 af.getAlignPanels().clear();
6127 af.closeMenuItem_actionPerformed(true);
6128 af.alignPanel.setHoldRepaint(false);
6130 return af.alignPanel;
6133 private Hashtable jvids2vobj;
6135 private void warn(String msg)
6140 private void warn(String msg, Exception e)
6142 if (Cache.log != null)
6146 Cache.log.warn(msg, e);
6150 Cache.log.warn(msg);
6155 System.err.println("Warning: " + msg);
6158 e.printStackTrace();
6163 private void debug(String string)
6165 debug(string, null);
6168 private void debug(String msg, Exception e)
6170 if (Cache.log != null)
6174 Cache.log.debug(msg, e);
6178 Cache.log.debug(msg);
6183 System.err.println("Warning: " + msg);
6186 e.printStackTrace();
6192 * set the object to ID mapping tables used to write/recover objects and XML
6193 * ID strings for the jalview project. If external tables are provided then
6194 * finalize and clearSeqRefs will not clear the tables when the Jalview2XML
6195 * object goes out of scope. - also populates the datasetIds hashtable with
6196 * alignment objects containing dataset sequences
6199 * Map from ID strings to jalview datamodel
6201 * Map from jalview datamodel to ID strings
6205 public void setObjectMappingTables(Hashtable vobj2jv,
6206 IdentityHashMap jv2vobj)
6208 this.jv2vobj = jv2vobj;
6209 this.vobj2jv = vobj2jv;
6210 Iterator ds = jv2vobj.keySet().iterator();
6212 while (ds.hasNext())
6214 Object jvobj = ds.next();
6215 id = jv2vobj.get(jvobj).toString();
6216 if (jvobj instanceof jalview.datamodel.Alignment)
6218 if (((jalview.datamodel.Alignment) jvobj).getDataset() == null)
6220 addDatasetRef(id, (jalview.datamodel.Alignment) jvobj);
6223 else if (jvobj instanceof jalview.datamodel.Sequence)
6225 // register sequence object so the XML parser can recover it.
6226 if (seqRefIds == null)
6228 seqRefIds = new HashMap<>();
6230 if (seqsToIds == null)
6232 seqsToIds = new IdentityHashMap<>();
6234 seqRefIds.put(jv2vobj.get(jvobj).toString(), (SequenceI) jvobj);
6235 seqsToIds.put((SequenceI) jvobj, id);
6237 else if (jvobj instanceof jalview.datamodel.AlignmentAnnotation)
6240 AlignmentAnnotation jvann = (AlignmentAnnotation) jvobj;
6241 annotationIds.put(anid = jv2vobj.get(jvobj).toString(), jvann);
6242 if (jvann.annotationId == null)
6244 jvann.annotationId = anid;
6246 if (!jvann.annotationId.equals(anid))
6248 // TODO verify that this is the correct behaviour
6249 this.warn("Overriding Annotation ID for " + anid
6250 + " from different id : " + jvann.annotationId);
6251 jvann.annotationId = anid;
6254 else if (jvobj instanceof String)
6256 if (jvids2vobj == null)
6258 jvids2vobj = new Hashtable();
6259 jvids2vobj.put(jvobj, jv2vobj.get(jvobj).toString());
6264 Cache.log.debug("Ignoring " + jvobj.getClass() + " (ID = " + id);
6270 * set the uniqueSetSuffix used to prefix/suffix object IDs for jalview
6271 * objects created from the project archive. If string is null (default for
6272 * construction) then suffix will be set automatically.
6276 public void setUniqueSetSuffix(String string)
6278 uniqueSetSuffix = string;
6283 * uses skipList2 as the skipList for skipping views on sequence sets
6284 * associated with keys in the skipList
6288 public void setSkipList(Hashtable skipList2)
6290 skipList = skipList2;
6294 * Reads the jar entry of given name and returns its contents, or null if the
6295 * entry is not found.
6298 * @param jarEntryName
6301 protected String readJarEntry(jarInputStreamProvider jprovider,
6302 String jarEntryName)
6304 String result = null;
6305 BufferedReader in = null;
6310 * Reopen the jar input stream and traverse its entries to find a matching
6313 JarInputStream jin = jprovider.getJarInputStream();
6314 JarEntry entry = null;
6317 entry = jin.getNextJarEntry();
6318 } while (entry != null && !entry.getName().equals(jarEntryName));
6322 StringBuilder out = new StringBuilder(256);
6323 in = new BufferedReader(new InputStreamReader(jin, UTF_8));
6326 while ((data = in.readLine()) != null)
6330 result = out.toString();
6334 warn("Couldn't find entry in Jalview Jar for " + jarEntryName);
6336 } catch (Exception ex)
6338 ex.printStackTrace();
6346 } catch (IOException e)
6357 * Returns an incrementing counter (0, 1, 2...)
6361 private synchronized int nextCounter()
6367 * Loads any saved PCA viewers
6372 protected void loadPCAViewers(JalviewModel model, AlignmentPanel ap)
6376 List<PcaViewer> pcaviewers = model.getPcaViewer();
6377 for (PcaViewer viewer : pcaviewers)
6379 String modelName = viewer.getScoreModelName();
6380 SimilarityParamsI params = new SimilarityParams(
6381 viewer.isIncludeGappedColumns(), viewer.isMatchGaps(),
6382 viewer.isIncludeGaps(),
6383 viewer.isDenominateByShortestLength());
6386 * create the panel (without computing the PCA)
6388 PCAPanel panel = new PCAPanel(ap, modelName, params);
6390 panel.setTitle(viewer.getTitle());
6391 panel.setBounds(new Rectangle(viewer.getXpos(), viewer.getYpos(),
6392 viewer.getWidth(), viewer.getHeight()));
6394 boolean showLabels = viewer.isShowLabels();
6395 panel.setShowLabels(showLabels);
6396 panel.getRotatableCanvas().setShowLabels(showLabels);
6397 panel.getRotatableCanvas()
6398 .setBgColour(new Color(viewer.getBgColour()));
6399 panel.getRotatableCanvas()
6400 .setApplyToAllViews(viewer.isLinkToAllViews());
6403 * load PCA output data
6405 ScoreModelI scoreModel = ScoreModels.getInstance()
6406 .getScoreModel(modelName, ap);
6407 PCA pca = new PCA(null, scoreModel, params);
6408 PcaDataType pcaData = viewer.getPcaData();
6410 MatrixI pairwise = loadDoubleMatrix(pcaData.getPairwiseMatrix());
6411 pca.setPairwiseScores(pairwise);
6413 MatrixI triDiag = loadDoubleMatrix(pcaData.getTridiagonalMatrix());
6414 pca.setTridiagonal(triDiag);
6416 MatrixI result = loadDoubleMatrix(pcaData.getEigenMatrix());
6417 pca.setEigenmatrix(result);
6419 panel.getPcaModel().setPCA(pca);
6422 * we haven't saved the input data! (JAL-2647 to do)
6424 panel.setInputData(null);
6427 * add the sequence points for the PCA display
6429 List<jalview.datamodel.SequencePoint> seqPoints = new ArrayList<>();
6430 for (SequencePoint sp : viewer.getSequencePoint())
6432 String seqId = sp.getSequenceRef();
6433 SequenceI seq = seqRefIds.get(seqId);
6436 throw new IllegalStateException(
6437 "Unmatched seqref for PCA: " + seqId);
6439 Point pt = new Point(sp.getXPos(), sp.getYPos(), sp.getZPos());
6440 jalview.datamodel.SequencePoint seqPoint = new jalview.datamodel.SequencePoint(
6442 seqPoints.add(seqPoint);
6444 panel.getRotatableCanvas().setPoints(seqPoints, seqPoints.size());
6447 * set min-max ranges and scale after setPoints (which recomputes them)
6449 panel.getRotatableCanvas().setScaleFactor(viewer.getScaleFactor());
6450 SeqPointMin spMin = viewer.getSeqPointMin();
6451 float[] min = new float[] { spMin.getXPos(), spMin.getYPos(),
6453 SeqPointMax spMax = viewer.getSeqPointMax();
6454 float[] max = new float[] { spMax.getXPos(), spMax.getYPos(),
6456 panel.getRotatableCanvas().setSeqMinMax(min, max);
6458 // todo: hold points list in PCAModel only
6459 panel.getPcaModel().setSequencePoints(seqPoints);
6461 panel.setSelectedDimensionIndex(viewer.getXDim(), X);
6462 panel.setSelectedDimensionIndex(viewer.getYDim(), Y);
6463 panel.setSelectedDimensionIndex(viewer.getZDim(), Z);
6465 // is this duplication needed?
6466 panel.setTop(seqPoints.size() - 1);
6467 panel.getPcaModel().setTop(seqPoints.size() - 1);
6470 * add the axes' end points for the display
6472 for (int i = 0; i < 3; i++)
6474 Axis axis = viewer.getAxis().get(i);
6475 panel.getRotatableCanvas().getAxisEndPoints()[i] = new Point(
6476 axis.getXPos(), axis.getYPos(), axis.getZPos());
6479 Dimension dim = Platform.getDimIfEmbedded(panel, 475, 450);
6480 Desktop.addInternalFrame(panel, MessageManager.formatMessage(
6481 "label.calc_title", "PCA", modelName), dim.width,
6484 } catch (Exception ex)
6486 Cache.log.error("Error loading PCA: " + ex.toString());
6491 * Populates an XML model of the feature colour scheme for one feature type
6493 * @param featureType
6497 public static Colour marshalColour(
6498 String featureType, FeatureColourI fcol)
6500 Colour col = new Colour();
6501 if (fcol.isSimpleColour())
6503 col.setRGB(Format.getHexString(fcol.getColour()));
6507 col.setRGB(Format.getHexString(fcol.getMaxColour()));
6508 col.setMin(fcol.getMin());
6509 col.setMax(fcol.getMax());
6510 col.setMinRGB(jalview.util.Format.getHexString(fcol.getMinColour()));
6511 col.setAutoScale(fcol.isAutoScaled());
6512 col.setThreshold(fcol.getThreshold());
6513 col.setColourByLabel(fcol.isColourByLabel());
6514 col.setThreshType(fcol.isAboveThreshold() ? ThresholdType.ABOVE
6515 : (fcol.isBelowThreshold() ? ThresholdType.BELOW
6516 : ThresholdType.NONE));
6517 if (fcol.isColourByAttribute())
6519 final String[] attName = fcol.getAttributeName();
6520 col.getAttributeName().add(attName[0]);
6521 if (attName.length > 1)
6523 col.getAttributeName().add(attName[1]);
6526 Color noColour = fcol.getNoColour();
6527 if (noColour == null)
6529 col.setNoValueColour(NoValueColour.NONE);
6531 else if (noColour == fcol.getMaxColour())
6533 col.setNoValueColour(NoValueColour.MAX);
6537 col.setNoValueColour(NoValueColour.MIN);
6540 col.setName(featureType);
6545 * Populates an XML model of the feature filter(s) for one feature type
6547 * @param firstMatcher
6548 * the first (or only) match condition)
6550 * remaining match conditions (if any)
6552 * if true, conditions are and-ed, else or-ed
6554 public static jalview.xml.binding.jalview.FeatureMatcherSet marshalFilter(
6555 FeatureMatcherI firstMatcher, Iterator<FeatureMatcherI> filters,
6558 jalview.xml.binding.jalview.FeatureMatcherSet result = new jalview.xml.binding.jalview.FeatureMatcherSet();
6560 if (filters.hasNext())
6565 CompoundMatcher compound = new CompoundMatcher();
6566 compound.setAnd(and);
6567 jalview.xml.binding.jalview.FeatureMatcherSet matcher1 = marshalFilter(
6568 firstMatcher, Collections.emptyIterator(), and);
6569 // compound.addMatcherSet(matcher1);
6570 compound.getMatcherSet().add(matcher1);
6571 FeatureMatcherI nextMatcher = filters.next();
6572 jalview.xml.binding.jalview.FeatureMatcherSet matcher2 = marshalFilter(
6573 nextMatcher, filters, and);
6574 // compound.addMatcherSet(matcher2);
6575 compound.getMatcherSet().add(matcher2);
6576 result.setCompoundMatcher(compound);
6581 * single condition matcher
6583 // MatchCondition matcherModel = new MatchCondition();
6584 jalview.xml.binding.jalview.FeatureMatcher matcherModel = new jalview.xml.binding.jalview.FeatureMatcher();
6585 matcherModel.setCondition(
6586 firstMatcher.getMatcher().getCondition().getStableName());
6587 matcherModel.setValue(firstMatcher.getMatcher().getPattern());
6588 if (firstMatcher.isByAttribute())
6590 matcherModel.setBy(FilterBy.BY_ATTRIBUTE);
6591 // matcherModel.setAttributeName(firstMatcher.getAttribute());
6592 String[] attName = firstMatcher.getAttribute();
6593 matcherModel.getAttributeName().add(attName[0]); // attribute
6594 if (attName.length > 1)
6596 matcherModel.getAttributeName().add(attName[1]); // sub-attribute
6599 else if (firstMatcher.isByLabel())
6601 matcherModel.setBy(FilterBy.BY_LABEL);
6603 else if (firstMatcher.isByScore())
6605 matcherModel.setBy(FilterBy.BY_SCORE);
6607 result.setMatchCondition(matcherModel);
6614 * Loads one XML model of a feature filter to a Jalview object
6616 * @param featureType
6617 * @param matcherSetModel
6620 public static FeatureMatcherSetI parseFilter(
6622 jalview.xml.binding.jalview.FeatureMatcherSet matcherSetModel)
6624 FeatureMatcherSetI result = new FeatureMatcherSet();
6627 parseFilterConditions(result, matcherSetModel, true);
6628 } catch (IllegalStateException e)
6630 // mixing AND and OR conditions perhaps
6632 String.format("Error reading filter conditions for '%s': %s",
6633 featureType, e.getMessage()));
6634 // return as much as was parsed up to the error
6641 * Adds feature match conditions to matcherSet as unmarshalled from XML
6642 * (possibly recursively for compound conditions)
6645 * @param matcherSetModel
6647 * if true, multiple conditions are AND-ed, else they are OR-ed
6648 * @throws IllegalStateException
6649 * if AND and OR conditions are mixed
6651 protected static void parseFilterConditions(
6652 FeatureMatcherSetI matcherSet,
6653 jalview.xml.binding.jalview.FeatureMatcherSet matcherSetModel,
6656 jalview.xml.binding.jalview.FeatureMatcher mc = matcherSetModel
6657 .getMatchCondition();
6663 FilterBy filterBy = mc.getBy();
6664 Condition cond = Condition.fromString(mc.getCondition());
6665 String pattern = mc.getValue();
6666 FeatureMatcherI matchCondition = null;
6667 if (filterBy == FilterBy.BY_LABEL)
6669 matchCondition = FeatureMatcher.byLabel(cond, pattern);
6671 else if (filterBy == FilterBy.BY_SCORE)
6673 matchCondition = FeatureMatcher.byScore(cond, pattern);
6676 else if (filterBy == FilterBy.BY_ATTRIBUTE)
6678 final List<String> attributeName = mc.getAttributeName();
6679 String[] attNames = attributeName
6680 .toArray(new String[attributeName.size()]);
6681 matchCondition = FeatureMatcher.byAttribute(cond, pattern,
6686 * note this throws IllegalStateException if AND-ing to a
6687 * previously OR-ed compound condition, or vice versa
6691 matcherSet.and(matchCondition);
6695 matcherSet.or(matchCondition);
6701 * compound condition
6703 List<jalview.xml.binding.jalview.FeatureMatcherSet> matchers = matcherSetModel
6704 .getCompoundMatcher().getMatcherSet();
6705 boolean anded = matcherSetModel.getCompoundMatcher().isAnd();
6706 if (matchers.size() == 2)
6708 parseFilterConditions(matcherSet, matchers.get(0), anded);
6709 parseFilterConditions(matcherSet, matchers.get(1), anded);
6713 System.err.println("Malformed compound filter condition");
6719 * Loads one XML model of a feature colour to a Jalview object
6721 * @param colourModel
6724 public static FeatureColourI parseColour(Colour colourModel)
6726 FeatureColourI colour = null;
6728 if (colourModel.getMax() != null)
6730 Color mincol = null;
6731 Color maxcol = null;
6732 Color noValueColour = null;
6736 mincol = new Color(Integer.parseInt(colourModel.getMinRGB(), 16));
6737 maxcol = new Color(Integer.parseInt(colourModel.getRGB(), 16));
6738 } catch (Exception e)
6740 Cache.log.warn("Couldn't parse out graduated feature color.", e);
6743 NoValueColour noCol = colourModel.getNoValueColour();
6744 if (noCol == NoValueColour.MIN)
6746 noValueColour = mincol;
6748 else if (noCol == NoValueColour.MAX)
6750 noValueColour = maxcol;
6753 colour = new FeatureColour(maxcol, mincol, maxcol, noValueColour,
6754 safeFloat(colourModel.getMin()),
6755 safeFloat(colourModel.getMax()));
6756 final List<String> attributeName = colourModel.getAttributeName();
6757 String[] attributes = attributeName
6758 .toArray(new String[attributeName.size()]);
6759 if (attributes != null && attributes.length > 0)
6761 colour.setAttributeName(attributes);
6763 if (colourModel.isAutoScale() != null)
6765 colour.setAutoScaled(colourModel.isAutoScale().booleanValue());
6767 if (colourModel.isColourByLabel() != null)
6769 colour.setColourByLabel(
6770 colourModel.isColourByLabel().booleanValue());
6772 if (colourModel.getThreshold() != null)
6774 colour.setThreshold(colourModel.getThreshold().floatValue());
6776 ThresholdType ttyp = colourModel.getThreshType();
6777 if (ttyp == ThresholdType.ABOVE)
6779 colour.setAboveThreshold(true);
6781 else if (ttyp == ThresholdType.BELOW)
6783 colour.setBelowThreshold(true);
6788 Color color = new Color(Integer.parseInt(colourModel.getRGB(), 16));
6789 colour = new FeatureColour(color);