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 jalview.analysis.Conservation;
24 import jalview.api.FeatureColourI;
25 import jalview.api.ViewStyleI;
26 import jalview.api.structures.JalviewStructureDisplayI;
27 import jalview.bin.Cache;
28 import jalview.datamodel.AlignedCodonFrame;
29 import jalview.datamodel.Alignment;
30 import jalview.datamodel.AlignmentAnnotation;
31 import jalview.datamodel.AlignmentI;
32 import jalview.datamodel.GraphLine;
33 import jalview.datamodel.PDBEntry;
34 import jalview.datamodel.RnaViewerModel;
35 import jalview.datamodel.SequenceFeature;
36 import jalview.datamodel.SequenceGroup;
37 import jalview.datamodel.SequenceI;
38 import jalview.datamodel.StructureViewerModel;
39 import jalview.datamodel.StructureViewerModel.StructureData;
40 import jalview.datamodel.features.FeatureMatcher;
41 import jalview.datamodel.features.FeatureMatcherI;
42 import jalview.datamodel.features.FeatureMatcherSet;
43 import jalview.datamodel.features.FeatureMatcherSetI;
44 import jalview.ext.varna.RnaModel;
45 import jalview.gui.AlignFrame;
46 import jalview.gui.AlignViewport;
47 import jalview.gui.AlignmentPanel;
48 import jalview.gui.AppVarna;
49 import jalview.gui.ChimeraViewFrame;
50 import jalview.gui.Desktop;
51 import jalview.gui.FeatureRenderer;
52 import jalview.gui.Jalview2XML_V1;
53 import jalview.gui.JvOptionPane;
54 import jalview.gui.OOMWarning;
55 import jalview.gui.PaintRefresher;
56 import jalview.gui.SplitFrame;
57 import jalview.gui.StructureViewer;
58 import jalview.gui.StructureViewer.ViewerType;
59 import jalview.gui.StructureViewerBase;
60 import jalview.gui.TreePanel;
61 import jalview.io.DataSourceType;
62 import jalview.io.FileFormat;
63 import jalview.io.NewickFile;
64 import jalview.renderer.ResidueShaderI;
65 import jalview.schemes.AnnotationColourGradient;
66 import jalview.schemes.ColourSchemeI;
67 import jalview.schemes.ColourSchemeProperty;
68 import jalview.schemes.FeatureColour;
69 import jalview.schemes.ResidueProperties;
70 import jalview.schemes.UserColourScheme;
71 import jalview.structure.StructureSelectionManager;
72 import jalview.structures.models.AAStructureBindingModel;
73 import jalview.util.Format;
74 import jalview.util.MessageManager;
75 import jalview.util.Platform;
76 import jalview.util.StringUtils;
77 import jalview.util.jarInputStreamProvider;
78 import jalview.util.matcher.Condition;
79 import jalview.viewmodel.AlignmentViewport;
80 import jalview.viewmodel.ViewportRanges;
81 import jalview.viewmodel.seqfeatures.FeatureRendererSettings;
82 import jalview.viewmodel.seqfeatures.FeaturesDisplayed;
83 import jalview.ws.jws2.Jws2Discoverer;
84 import jalview.ws.jws2.dm.AAConSettings;
85 import jalview.ws.jws2.jabaws2.Jws2Instance;
86 import jalview.ws.params.ArgumentI;
87 import jalview.ws.params.AutoCalcSetting;
88 import jalview.ws.params.WsParamSetI;
89 import jalview.xml.binding.jalview.AlcodonFrame;
90 import jalview.xml.binding.jalview.AlcodonFrame.AlcodMap;
91 import jalview.xml.binding.jalview.Annotation;
92 import jalview.xml.binding.jalview.Annotation.ThresholdLine;
93 import jalview.xml.binding.jalview.AnnotationColourScheme;
94 import jalview.xml.binding.jalview.AnnotationElement;
95 import jalview.xml.binding.jalview.Feature;
96 import jalview.xml.binding.jalview.Feature.OtherData;
97 import jalview.xml.binding.jalview.FeatureMatcherSet.CompoundMatcher;
98 import jalview.xml.binding.jalview.FilterBy;
99 import jalview.xml.binding.jalview.JalviewModel;
100 import jalview.xml.binding.jalview.JalviewModel.FeatureSettings;
101 import jalview.xml.binding.jalview.JalviewModel.FeatureSettings.Group;
102 import jalview.xml.binding.jalview.JalviewModel.FeatureSettings.Setting;
103 import jalview.xml.binding.jalview.JalviewModel.JGroup;
104 import jalview.xml.binding.jalview.JalviewModel.JSeq;
105 import jalview.xml.binding.jalview.JalviewModel.JSeq.Pdbids;
106 import jalview.xml.binding.jalview.JalviewModel.JSeq.Pdbids.StructureState;
107 import jalview.xml.binding.jalview.JalviewModel.JSeq.RnaViewer;
108 import jalview.xml.binding.jalview.JalviewModel.JSeq.RnaViewer.SecondaryStructure;
109 import jalview.xml.binding.jalview.JalviewModel.Tree;
110 import jalview.xml.binding.jalview.JalviewModel.UserColours;
111 import jalview.xml.binding.jalview.JalviewModel.Viewport;
112 import jalview.xml.binding.jalview.JalviewModel.Viewport.CalcIdParam;
113 import jalview.xml.binding.jalview.JalviewModel.Viewport.HiddenColumns;
114 import jalview.xml.binding.jalview.JalviewUserColours;
115 import jalview.xml.binding.jalview.JalviewUserColours.Colour;
116 import jalview.xml.binding.jalview.MapListType.MapListFrom;
117 import jalview.xml.binding.jalview.MapListType.MapListTo;
118 import jalview.xml.binding.jalview.Mapping;
119 import jalview.xml.binding.jalview.NoValueColour;
120 import jalview.xml.binding.jalview.ObjectFactory;
121 import jalview.xml.binding.jalview.Pdbentry.Property;
122 import jalview.xml.binding.jalview.Sequence;
123 import jalview.xml.binding.jalview.Sequence.DBRef;
124 import jalview.xml.binding.jalview.SequenceSet;
125 import jalview.xml.binding.jalview.SequenceSet.SequenceSetProperties;
126 import jalview.xml.binding.jalview.ThresholdType;
127 import jalview.xml.binding.jalview.VAMSAS;
129 import java.awt.Color;
130 import java.awt.Font;
131 import java.awt.Rectangle;
132 import java.io.BufferedReader;
133 import java.io.ByteArrayInputStream;
134 import java.io.DataInputStream;
135 import java.io.DataOutputStream;
137 import java.io.FileInputStream;
138 import java.io.FileOutputStream;
139 import java.io.IOException;
140 import java.io.InputStreamReader;
141 import java.io.OutputStreamWriter;
142 import java.io.PrintWriter;
143 import java.lang.reflect.InvocationTargetException;
144 import java.math.BigInteger;
145 import java.net.MalformedURLException;
147 import java.util.ArrayList;
148 import java.util.Arrays;
149 import java.util.Collections;
150 import java.util.Enumeration;
151 import java.util.GregorianCalendar;
152 import java.util.HashMap;
153 import java.util.HashSet;
154 import java.util.Hashtable;
155 import java.util.IdentityHashMap;
156 import java.util.Iterator;
157 import java.util.LinkedHashMap;
158 import java.util.List;
159 import java.util.Map;
160 import java.util.Map.Entry;
161 import java.util.Set;
162 import java.util.Vector;
163 import java.util.jar.JarEntry;
164 import java.util.jar.JarInputStream;
165 import java.util.jar.JarOutputStream;
167 import javax.swing.JInternalFrame;
168 import javax.swing.SwingUtilities;
169 import javax.xml.bind.JAXBContext;
170 import javax.xml.bind.JAXBElement;
171 import javax.xml.bind.Marshaller;
172 import javax.xml.datatype.DatatypeConfigurationException;
173 import javax.xml.datatype.DatatypeFactory;
174 import javax.xml.datatype.XMLGregorianCalendar;
175 import javax.xml.stream.XMLInputFactory;
176 import javax.xml.stream.XMLStreamReader;
179 * Write out the current jalview desktop state as a Jalview XML stream.
181 * Note: the vamsas objects referred to here are primitive versions of the
182 * VAMSAS project schema elements - they are not the same and most likely never
186 * @version $Revision: 1.134 $
188 public class Jalview2XML
191 // BH 2018 we add the .jvp binary extension to J2S so that
192 // it will declare that binary when we do the file save from the browser
194 private static void addJ2SBinaryType(String ext)
196 ext = "." + ext + "?";
201 * J2S._binaryTypes.push(ext);
208 addJ2SBinaryType(".jvp?");
211 private static final String VIEWER_PREFIX = "viewer_";
213 private static final String RNA_PREFIX = "rna_";
215 private static final String UTF_8 = "UTF-8";
217 // use this with nextCounter() to make unique names for entities
218 private int counter = 0;
221 * SequenceI reference -> XML ID string in jalview XML. Populated as XML reps
222 * of sequence objects are created.
224 IdentityHashMap<SequenceI, String> seqsToIds = null;
227 * jalview XML Sequence ID to jalview sequence object reference (both dataset
228 * and alignment sequences. Populated as XML reps of sequence objects are
231 Map<String, SequenceI> seqRefIds = null;
233 Map<String, SequenceI> incompleteSeqs = null;
235 List<SeqFref> frefedSequence = null;
237 boolean raiseGUI = true; // whether errors are raised in dialog boxes or not
240 * Map of reconstructed AlignFrame objects that appear to have come from
241 * SplitFrame objects (have a dna/protein complement view).
243 private Map<Viewport, AlignFrame> splitFrameCandidates = new HashMap<>();
246 * Map from displayed rna structure models to their saved session state jar
249 private Map<RnaModel, String> rnaSessions = new HashMap<>();
252 * A helper method for safely using the value of an optional attribute that
253 * may be null if not present in the XML. Answers the boolean value, or false
259 public static boolean safeBoolean(Boolean b)
261 return b == null ? false : b.booleanValue();
265 * A helper method for safely using the value of an optional attribute that
266 * may be null if not present in the XML. Answers the integer value, or zero
272 public static int safeInt(Integer i)
274 return i == null ? 0 : i.intValue();
278 * A helper method for safely using the value of an optional attribute that
279 * may be null if not present in the XML. Answers the float value, or zero if
285 public static float safeFloat(Float f)
287 return f == null ? 0f : f.floatValue();
291 * create/return unique hash string for sq
294 * @return new or existing unique string for sq
296 String seqHash(SequenceI sq)
298 if (seqsToIds == null)
302 if (seqsToIds.containsKey(sq))
304 return seqsToIds.get(sq);
308 // create sequential key
309 String key = "sq" + (seqsToIds.size() + 1);
310 key = makeHashCode(sq, key); // check we don't have an external reference
312 seqsToIds.put(sq, key);
319 if (seqsToIds == null)
321 seqsToIds = new IdentityHashMap<>();
323 if (seqRefIds == null)
325 seqRefIds = new HashMap<>();
327 if (incompleteSeqs == null)
329 incompleteSeqs = new HashMap<>();
331 if (frefedSequence == null)
333 frefedSequence = new ArrayList<>();
341 public Jalview2XML(boolean raiseGUI)
343 this.raiseGUI = raiseGUI;
347 * base class for resolving forward references to sequences by their ID
352 abstract class SeqFref
358 public SeqFref(String _sref, String type)
364 public String getSref()
369 public SequenceI getSrefSeq()
371 return seqRefIds.get(sref);
374 public boolean isResolvable()
376 return seqRefIds.get(sref) != null;
379 public SequenceI getSrefDatasetSeq()
381 SequenceI sq = seqRefIds.get(sref);
384 while (sq.getDatasetSequence() != null)
386 sq = sq.getDatasetSequence();
393 * @return true if the forward reference was fully resolved
395 abstract boolean resolve();
398 public String toString()
400 return type + " reference to " + sref;
405 * create forward reference for a mapping
411 public SeqFref newMappingRef(final String sref,
412 final jalview.datamodel.Mapping _jmap)
414 SeqFref fref = new SeqFref(sref, "Mapping")
416 public jalview.datamodel.Mapping jmap = _jmap;
421 SequenceI seq = getSrefDatasetSeq();
433 public SeqFref newAlcodMapRef(final String sref,
434 final AlignedCodonFrame _cf,
435 final jalview.datamodel.Mapping _jmap)
438 SeqFref fref = new SeqFref(sref, "Codon Frame")
440 AlignedCodonFrame cf = _cf;
442 public jalview.datamodel.Mapping mp = _jmap;
445 public boolean isResolvable()
447 return super.isResolvable() && mp.getTo() != null;
453 SequenceI seq = getSrefDatasetSeq();
458 cf.addMap(seq, mp.getTo(), mp.getMap());
465 public void resolveFrefedSequences()
467 Iterator<SeqFref> nextFref = frefedSequence.iterator();
468 int toresolve = frefedSequence.size();
469 int unresolved = 0, failedtoresolve = 0;
470 while (nextFref.hasNext())
472 SeqFref ref = nextFref.next();
473 if (ref.isResolvable())
485 } catch (Exception x)
488 "IMPLEMENTATION ERROR: Failed to resolve forward reference for sequence "
501 System.err.println("Jalview Project Import: There were " + unresolved
502 + " forward references left unresolved on the stack.");
504 if (failedtoresolve > 0)
506 System.err.println("SERIOUS! " + failedtoresolve
507 + " resolvable forward references failed to resolve.");
509 if (incompleteSeqs != null && incompleteSeqs.size() > 0)
512 "Jalview Project Import: There are " + incompleteSeqs.size()
513 + " sequences which may have incomplete metadata.");
514 if (incompleteSeqs.size() < 10)
516 for (SequenceI s : incompleteSeqs.values())
518 System.err.println(s.toString());
524 "Too many to report. Skipping output of incomplete sequences.");
530 * This maintains a map of viewports, the key being the seqSetId. Important to
531 * set historyItem and redoList for multiple views
533 Map<String, AlignViewport> viewportsAdded = new HashMap<>();
535 Map<String, AlignmentAnnotation> annotationIds = new HashMap<>();
537 String uniqueSetSuffix = "";
540 * List of pdbfiles added to Jar
542 List<String> pdbfiles = null;
544 // SAVES SEVERAL ALIGNMENT WINDOWS TO SAME JARFILE
545 public void saveState(File statefile)
547 FileOutputStream fos = null;
550 fos = new FileOutputStream(statefile);
551 JarOutputStream jout = new JarOutputStream(fos);
554 } catch (Exception e)
556 // TODO: inform user of the problem - they need to know if their data was
558 if (errorMessage == null)
560 errorMessage = "Couldn't write Jalview Archive to output file '"
561 + statefile + "' - See console error log for details";
565 errorMessage += "(output file was '" + statefile + "')";
575 } catch (IOException e)
585 * Writes a jalview project archive to the given Jar output stream.
589 public void saveState(JarOutputStream jout)
591 AlignFrame[] frames = Desktop.getAlignFrames();
597 saveAllFrames(Arrays.asList(frames), jout);
601 * core method for storing state for a set of AlignFrames.
604 * - frames involving all data to be exported (including containing
607 * - project output stream
609 private void saveAllFrames(List<AlignFrame> frames, JarOutputStream jout)
611 Hashtable<String, AlignFrame> dsses = new Hashtable<>();
614 * ensure cached data is clear before starting
616 // todo tidy up seqRefIds, seqsToIds initialisation / reset
618 splitFrameCandidates.clear();
623 // NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS
624 // //////////////////////////////////////////////////
626 List<String> shortNames = new ArrayList<>();
627 List<String> viewIds = new ArrayList<>();
630 for (int i = frames.size() - 1; i > -1; i--)
632 AlignFrame af = frames.get(i);
634 if (skipList != null && skipList
635 .containsKey(af.getViewport().getSequenceSetId()))
640 String shortName = makeFilename(af, shortNames);
642 int apSize = af.getAlignPanels().size();
644 for (int ap = 0; ap < apSize; ap++)
646 AlignmentPanel apanel = (AlignmentPanel) af.getAlignPanels()
648 String fileName = apSize == 1 ? shortName : ap + shortName;
649 if (!fileName.endsWith(".xml"))
651 fileName = fileName + ".xml";
654 saveState(apanel, fileName, jout, viewIds);
656 String dssid = getDatasetIdRef(
657 af.getViewport().getAlignment().getDataset());
658 if (!dsses.containsKey(dssid))
660 dsses.put(dssid, af);
665 writeDatasetFor(dsses, "" + jout.hashCode() + " " + uniqueSetSuffix,
671 } catch (Exception foo)
676 } catch (Exception ex)
678 // TODO: inform user of the problem - they need to know if their data was
680 if (errorMessage == null)
682 errorMessage = "Couldn't write Jalview Archive - see error output for details";
684 ex.printStackTrace();
689 * Generates a distinct file name, based on the title of the AlignFrame, by
690 * appending _n for increasing n until an unused name is generated. The new
691 * name (without its extension) is added to the list.
695 * @return the generated name, with .xml extension
697 protected String makeFilename(AlignFrame af, List<String> namesUsed)
699 String shortName = af.getTitle();
701 if (shortName.indexOf(File.separatorChar) > -1)
703 shortName = shortName
704 .substring(shortName.lastIndexOf(File.separatorChar) + 1);
709 while (namesUsed.contains(shortName))
711 if (shortName.endsWith("_" + (count - 1)))
713 shortName = shortName.substring(0, shortName.lastIndexOf("_"));
716 shortName = shortName.concat("_" + count);
720 namesUsed.add(shortName);
722 if (!shortName.endsWith(".xml"))
724 shortName = shortName + ".xml";
729 // USE THIS METHOD TO SAVE A SINGLE ALIGNMENT WINDOW
730 public boolean saveAlignment(AlignFrame af, String jarFile,
735 FileOutputStream fos = new FileOutputStream(jarFile);
736 JarOutputStream jout = new JarOutputStream(fos);
737 List<AlignFrame> frames = new ArrayList<>();
739 // resolve splitframes
740 if (af.getViewport().getCodingComplement() != null)
742 frames = ((SplitFrame) af.getSplitViewContainer()).getAlignFrames();
748 saveAllFrames(frames, jout);
752 } catch (Exception foo)
758 } catch (Exception ex)
760 errorMessage = "Couldn't Write alignment view to Jalview Archive - see error output for details";
761 ex.printStackTrace();
766 private void writeDatasetFor(Hashtable<String, AlignFrame> dsses,
767 String fileName, JarOutputStream jout)
770 for (String dssids : dsses.keySet())
772 AlignFrame _af = dsses.get(dssids);
773 String jfileName = fileName + " Dataset for " + _af.getTitle();
774 if (!jfileName.endsWith(".xml"))
776 jfileName = jfileName + ".xml";
778 saveState(_af.alignPanel, jfileName, true, jout, null);
783 * create a JalviewModel from an alignment view and marshall it to a
787 * panel to create jalview model for
789 * name of alignment panel written to output stream
796 public JalviewModel saveState(AlignmentPanel ap, String fileName,
797 JarOutputStream jout, List<String> viewIds)
799 return saveState(ap, fileName, false, jout, viewIds);
803 * create a JalviewModel from an alignment view and marshall it to a
807 * panel to create jalview model for
809 * name of alignment panel written to output stream
811 * when true, only write the dataset for the alignment, not the data
812 * associated with the view.
818 public JalviewModel saveState(AlignmentPanel ap, String fileName,
819 boolean storeDS, JarOutputStream jout, List<String> viewIds)
823 viewIds = new ArrayList<>();
828 List<UserColourScheme> userColours = new ArrayList<>();
830 AlignViewport av = ap.av;
831 ViewportRanges vpRanges = av.getRanges();
833 final ObjectFactory objectFactory = new ObjectFactory();
834 JalviewModel object = objectFactory.createJalviewModel();
835 object.setVamsasModel(new VAMSAS());
837 // object.setCreationDate(new java.util.Date(System.currentTimeMillis()));
840 GregorianCalendar c = new GregorianCalendar();
841 DatatypeFactory datatypeFactory = DatatypeFactory.newInstance();
842 XMLGregorianCalendar now = datatypeFactory.newXMLGregorianCalendar(c);// gregorianCalendar);
843 object.setCreationDate(now);
844 } catch (DatatypeConfigurationException e)
846 System.err.println("error writing date: " + e.toString());
849 jalview.bin.Cache.getDefault("VERSION", "Development Build"));
852 * rjal is full height alignment, jal is actual alignment with full metadata
853 * but excludes hidden sequences.
855 jalview.datamodel.AlignmentI rjal = av.getAlignment(), jal = rjal;
857 if (av.hasHiddenRows())
859 rjal = jal.getHiddenSequences().getFullAlignment();
862 SequenceSet vamsasSet = new SequenceSet();
864 // JalviewModelSequence jms = new JalviewModelSequence();
866 vamsasSet.setGapChar(jal.getGapCharacter() + "");
868 if (jal.getDataset() != null)
870 // dataset id is the dataset's hashcode
871 vamsasSet.setDatasetId(getDatasetIdRef(jal.getDataset()));
874 // switch jal and the dataset
875 jal = jal.getDataset();
879 if (jal.getProperties() != null)
881 Enumeration en = jal.getProperties().keys();
882 while (en.hasMoreElements())
884 String key = en.nextElement().toString();
885 SequenceSetProperties ssp = new SequenceSetProperties();
887 ssp.setValue(jal.getProperties().get(key).toString());
888 // vamsasSet.addSequenceSetProperties(ssp);
889 vamsasSet.getSequenceSetProperties().add(ssp);
894 Set<String> calcIdSet = new HashSet<>();
895 // record the set of vamsas sequence XML POJO we create.
896 HashMap<String, Sequence> vamsasSetIds = new HashMap<>();
898 for (final SequenceI jds : rjal.getSequences())
900 final SequenceI jdatasq = jds.getDatasetSequence() == null ? jds
901 : jds.getDatasetSequence();
902 String id = seqHash(jds);
903 if (vamsasSetIds.get(id) == null)
905 if (seqRefIds.get(id) != null && !storeDS)
907 // This happens for two reasons: 1. multiple views are being
909 // 2. the hashCode has collided with another sequence's code. This
911 // HAPPEN! (PF00072.15.stk does this)
912 // JBPNote: Uncomment to debug writing out of files that do not read
913 // back in due to ArrayOutOfBoundExceptions.
914 // System.err.println("vamsasSeq backref: "+id+"");
915 // System.err.println(jds.getName()+"
916 // "+jds.getStart()+"-"+jds.getEnd()+" "+jds.getSequenceAsString());
917 // System.err.println("Hashcode: "+seqHash(jds));
918 // SequenceI rsq = (SequenceI) seqRefIds.get(id + "");
919 // System.err.println(rsq.getName()+"
920 // "+rsq.getStart()+"-"+rsq.getEnd()+" "+rsq.getSequenceAsString());
921 // System.err.println("Hashcode: "+seqHash(rsq));
925 vamsasSeq = createVamsasSequence(id, jds);
926 // vamsasSet.addSequence(vamsasSeq);
927 vamsasSet.getSequence().add(vamsasSeq);
928 vamsasSetIds.put(id, vamsasSeq);
929 seqRefIds.put(id, jds);
933 jseq.setStart(jds.getStart());
934 jseq.setEnd(jds.getEnd());
935 jseq.setColour(av.getSequenceColour(jds).getRGB());
937 jseq.setId(id); // jseq id should be a string not a number
940 // Store any sequences this sequence represents
941 if (av.hasHiddenRows())
943 // use rjal, contains the full height alignment
945 av.getAlignment().getHiddenSequences().isHidden(jds));
947 if (av.isHiddenRepSequence(jds))
949 jalview.datamodel.SequenceI[] reps = av
950 .getRepresentedSequences(jds).getSequencesInOrder(rjal);
952 for (int h = 0; h < reps.length; h++)
956 // jseq.addHiddenSequences(rjal.findIndex(reps[h]));
957 jseq.getHiddenSequences().add(rjal.findIndex(reps[h]));
962 // mark sequence as reference - if it is the reference for this view
965 jseq.setViewreference(jds == jal.getSeqrep());
969 // TODO: omit sequence features from each alignment view's XML dump if we
970 // are storing dataset
971 List<SequenceFeature> sfs = jds.getSequenceFeatures();
972 for (SequenceFeature sf : sfs)
974 // Features features = new Features();
975 Feature features = new Feature();
977 features.setBegin(sf.getBegin());
978 features.setEnd(sf.getEnd());
979 features.setDescription(sf.getDescription());
980 features.setType(sf.getType());
981 features.setFeatureGroup(sf.getFeatureGroup());
982 features.setScore(sf.getScore());
983 if (sf.links != null)
985 for (int l = 0; l < sf.links.size(); l++)
987 OtherData keyValue = new OtherData();
988 keyValue.setKey("LINK_" + l);
989 keyValue.setValue(sf.links.elementAt(l).toString());
990 // features.addOtherData(keyValue);
991 features.getOtherData().add(keyValue);
994 if (sf.otherDetails != null)
997 * save feature attributes, which may be simple strings or
998 * map valued (have sub-attributes)
1000 for (Entry<String, Object> entry : sf.otherDetails.entrySet())
1002 String key = entry.getKey();
1003 Object value = entry.getValue();
1004 if (value instanceof Map<?, ?>)
1006 for (Entry<String, Object> subAttribute : ((Map<String, Object>) value)
1009 OtherData otherData = new OtherData();
1010 otherData.setKey(key);
1011 otherData.setKey2(subAttribute.getKey());
1012 otherData.setValue(subAttribute.getValue().toString());
1013 // features.addOtherData(otherData);
1014 features.getOtherData().add(otherData);
1019 OtherData otherData = new OtherData();
1020 otherData.setKey(key);
1021 otherData.setValue(value.toString());
1022 // features.addOtherData(otherData);
1023 features.getOtherData().add(otherData);
1028 // jseq.addFeatures(features);
1029 jseq.getFeatures().add(features);
1032 if (jdatasq.getAllPDBEntries() != null)
1034 Enumeration<PDBEntry> en = jdatasq.getAllPDBEntries().elements();
1035 while (en.hasMoreElements())
1037 Pdbids pdb = new Pdbids();
1038 jalview.datamodel.PDBEntry entry = en.nextElement();
1040 String pdbId = entry.getId();
1042 pdb.setType(entry.getType());
1045 * Store any structure views associated with this sequence. This
1046 * section copes with duplicate entries in the project, so a dataset
1047 * only view *should* be coped with sensibly.
1049 // This must have been loaded, is it still visible?
1050 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1051 String matchedFile = null;
1052 for (int f = frames.length - 1; f > -1; f--)
1054 if (frames[f] instanceof StructureViewerBase)
1056 StructureViewerBase viewFrame = (StructureViewerBase) frames[f];
1057 matchedFile = saveStructureState(ap, jds, pdb, entry, viewIds,
1058 matchedFile, viewFrame);
1060 * Only store each structure viewer's state once in the project
1061 * jar. First time through only (storeDS==false)
1063 String viewId = viewFrame.getViewId();
1064 if (!storeDS && !viewIds.contains(viewId))
1066 viewIds.add(viewId);
1069 String viewerState = viewFrame.getStateInfo();
1070 writeJarEntry(jout, getViewerJarEntryName(viewId),
1071 viewerState.getBytes());
1072 } catch (IOException e)
1075 "Error saving viewer state: " + e.getMessage());
1081 if (matchedFile != null || entry.getFile() != null)
1083 if (entry.getFile() != null)
1086 matchedFile = entry.getFile();
1088 pdb.setFile(matchedFile); // entry.getFile());
1089 if (pdbfiles == null)
1091 pdbfiles = new ArrayList<>();
1094 if (!pdbfiles.contains(pdbId))
1096 pdbfiles.add(pdbId);
1097 copyFileToJar(jout, matchedFile, pdbId);
1101 Enumeration<String> props = entry.getProperties();
1102 if (props.hasMoreElements())
1104 // PdbentryItem item = new PdbentryItem();
1105 while (props.hasMoreElements())
1107 Property prop = new Property();
1108 String key = props.nextElement();
1110 prop.setValue(entry.getProperty(key).toString());
1111 // item.addProperty(prop);
1112 pdb.getProperty().add(prop);
1114 // pdb.addPdbentryItem(item);
1117 // jseq.addPdbids(pdb);
1118 jseq.getPdbids().add(pdb);
1122 saveRnaViewers(jout, jseq, jds, viewIds, ap, storeDS);
1124 // jms.addJSeq(jseq);
1125 object.getJSeq().add(jseq);
1128 if (!storeDS && av.hasHiddenRows())
1130 jal = av.getAlignment();
1134 if (storeDS && jal.getCodonFrames() != null)
1136 List<AlignedCodonFrame> jac = jal.getCodonFrames();
1137 for (AlignedCodonFrame acf : jac)
1139 AlcodonFrame alc = new AlcodonFrame();
1140 if (acf.getProtMappings() != null
1141 && acf.getProtMappings().length > 0)
1143 boolean hasMap = false;
1144 SequenceI[] dnas = acf.getdnaSeqs();
1145 jalview.datamodel.Mapping[] pmaps = acf.getProtMappings();
1146 for (int m = 0; m < pmaps.length; m++)
1148 AlcodMap alcmap = new AlcodMap();
1149 alcmap.setDnasq(seqHash(dnas[m]));
1151 createVamsasMapping(pmaps[m], dnas[m], null, false));
1152 // alc.addAlcodMap(alcmap);
1153 alc.getAlcodMap().add(alcmap);
1158 // vamsasSet.addAlcodonFrame(alc);
1159 vamsasSet.getAlcodonFrame().add(alc);
1162 // TODO: delete this ? dead code from 2.8.3->2.9 ?
1164 // AlcodonFrame alc = new AlcodonFrame();
1165 // vamsasSet.addAlcodonFrame(alc);
1166 // for (int p = 0; p < acf.aaWidth; p++)
1168 // Alcodon cmap = new Alcodon();
1169 // if (acf.codons[p] != null)
1171 // // Null codons indicate a gapped column in the translated peptide
1173 // cmap.setPos1(acf.codons[p][0]);
1174 // cmap.setPos2(acf.codons[p][1]);
1175 // cmap.setPos3(acf.codons[p][2]);
1177 // alc.addAlcodon(cmap);
1179 // if (acf.getProtMappings() != null
1180 // && acf.getProtMappings().length > 0)
1182 // SequenceI[] dnas = acf.getdnaSeqs();
1183 // jalview.datamodel.Mapping[] pmaps = acf.getProtMappings();
1184 // for (int m = 0; m < pmaps.length; m++)
1186 // AlcodMap alcmap = new AlcodMap();
1187 // alcmap.setDnasq(seqHash(dnas[m]));
1188 // alcmap.setMapping(createVamsasMapping(pmaps[m], dnas[m], null,
1190 // alc.addAlcodMap(alcmap);
1197 // /////////////////////////////////
1198 if (!storeDS && av.getCurrentTree() != null)
1200 // FIND ANY ASSOCIATED TREES
1201 // NOT IMPLEMENTED FOR HEADLESS STATE AT PRESENT
1202 if (Desktop.desktop != null)
1204 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1206 for (int t = 0; t < frames.length; t++)
1208 if (frames[t] instanceof TreePanel)
1210 TreePanel tp = (TreePanel) frames[t];
1212 if (tp.getTreeCanvas().getViewport().getAlignment() == jal)
1214 JalviewModel.Tree tree = new JalviewModel.Tree();
1215 tree.setTitle(tp.getTitle());
1216 tree.setCurrentTree((av.getCurrentTree() == tp.getTree()));
1217 tree.setNewick(tp.getTree().print());
1218 tree.setThreshold(tp.getTreeCanvas().getThreshold());
1220 tree.setFitToWindow(tp.fitToWindow.getState());
1221 tree.setFontName(tp.getTreeFont().getName());
1222 tree.setFontSize(tp.getTreeFont().getSize());
1223 tree.setFontStyle(tp.getTreeFont().getStyle());
1224 tree.setMarkUnlinked(tp.placeholdersMenu.getState());
1226 tree.setShowBootstrap(tp.bootstrapMenu.getState());
1227 tree.setShowDistances(tp.distanceMenu.getState());
1229 tree.setHeight(tp.getHeight());
1230 tree.setWidth(tp.getWidth());
1231 tree.setXpos(tp.getX());
1232 tree.setYpos(tp.getY());
1233 tree.setId(makeHashCode(tp, null));
1234 // jms.addTree(tree);
1235 object.getTree().add(tree);
1244 * store forward refs from an annotationRow to any groups
1246 IdentityHashMap<SequenceGroup, String> groupRefs = new IdentityHashMap<>();
1249 for (SequenceI sq : jal.getSequences())
1251 // Store annotation on dataset sequences only
1252 AlignmentAnnotation[] aa = sq.getAnnotation();
1253 if (aa != null && aa.length > 0)
1255 storeAlignmentAnnotation(aa, groupRefs, av, calcIdSet, storeDS,
1262 if (jal.getAlignmentAnnotation() != null)
1264 // Store the annotation shown on the alignment.
1265 AlignmentAnnotation[] aa = jal.getAlignmentAnnotation();
1266 storeAlignmentAnnotation(aa, groupRefs, av, calcIdSet, storeDS,
1271 if (jal.getGroups() != null)
1273 JGroup[] groups = new JGroup[jal.getGroups().size()];
1275 for (jalview.datamodel.SequenceGroup sg : jal.getGroups())
1277 JGroup jGroup = new JGroup();
1278 groups[++i] = jGroup;
1280 jGroup.setStart(sg.getStartRes());
1281 jGroup.setEnd(sg.getEndRes());
1282 jGroup.setName(sg.getName());
1283 if (groupRefs.containsKey(sg))
1285 // group has references so set its ID field
1286 jGroup.setId(groupRefs.get(sg));
1288 ColourSchemeI colourScheme = sg.getColourScheme();
1289 if (colourScheme != null)
1291 ResidueShaderI groupColourScheme = sg.getGroupColourScheme();
1292 if (groupColourScheme.conservationApplied())
1294 jGroup.setConsThreshold(groupColourScheme.getConservationInc());
1296 if (colourScheme instanceof jalview.schemes.UserColourScheme)
1299 setUserColourScheme(colourScheme, userColours,
1304 jGroup.setColour(colourScheme.getSchemeName());
1307 else if (colourScheme instanceof jalview.schemes.AnnotationColourGradient)
1309 jGroup.setColour("AnnotationColourGradient");
1310 jGroup.setAnnotationColours(constructAnnotationColours(
1311 (jalview.schemes.AnnotationColourGradient) colourScheme,
1312 userColours, object));
1314 else if (colourScheme instanceof jalview.schemes.UserColourScheme)
1317 setUserColourScheme(colourScheme, userColours, object));
1321 jGroup.setColour(colourScheme.getSchemeName());
1324 jGroup.setPidThreshold(groupColourScheme.getThreshold());
1327 jGroup.setOutlineColour(sg.getOutlineColour().getRGB());
1328 jGroup.setDisplayBoxes(sg.getDisplayBoxes());
1329 jGroup.setDisplayText(sg.getDisplayText());
1330 jGroup.setColourText(sg.getColourText());
1331 jGroup.setTextCol1(sg.textColour.getRGB());
1332 jGroup.setTextCol2(sg.textColour2.getRGB());
1333 jGroup.setTextColThreshold(sg.thresholdTextColour);
1334 jGroup.setShowUnconserved(sg.getShowNonconserved());
1335 jGroup.setIgnoreGapsinConsensus(sg.getIgnoreGapsConsensus());
1336 jGroup.setShowConsensusHistogram(sg.isShowConsensusHistogram());
1337 jGroup.setShowSequenceLogo(sg.isShowSequenceLogo());
1338 jGroup.setNormaliseSequenceLogo(sg.isNormaliseSequenceLogo());
1339 for (SequenceI seq : sg.getSequences())
1341 // jGroup.addSeq(seqHash(seq));
1342 jGroup.getSeq().add(seqHash(seq));
1346 //jms.setJGroup(groups);
1348 for (JGroup grp : groups)
1350 object.getJGroup().add(grp);
1355 // /////////SAVE VIEWPORT
1356 Viewport view = new Viewport();
1357 view.setTitle(ap.alignFrame.getTitle());
1358 view.setSequenceSetId(
1359 makeHashCode(av.getSequenceSetId(), av.getSequenceSetId()));
1360 view.setId(av.getViewId());
1361 if (av.getCodingComplement() != null)
1363 view.setComplementId(av.getCodingComplement().getViewId());
1365 view.setViewName(av.getViewName());
1366 view.setGatheredViews(av.isGatherViewsHere());
1368 Rectangle size = ap.av.getExplodedGeometry();
1369 Rectangle position = size;
1372 size = ap.alignFrame.getBounds();
1373 if (av.getCodingComplement() != null)
1375 position = ((SplitFrame) ap.alignFrame.getSplitViewContainer())
1383 view.setXpos(position.x);
1384 view.setYpos(position.y);
1386 view.setWidth(size.width);
1387 view.setHeight(size.height);
1389 view.setStartRes(vpRanges.getStartRes());
1390 view.setStartSeq(vpRanges.getStartSeq());
1392 if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme)
1394 view.setBgColour(setUserColourScheme(av.getGlobalColourScheme(),
1395 userColours, object));
1398 .getGlobalColourScheme() instanceof jalview.schemes.AnnotationColourGradient)
1400 AnnotationColourScheme ac = constructAnnotationColours(
1401 (jalview.schemes.AnnotationColourGradient) av
1402 .getGlobalColourScheme(),
1403 userColours, object);
1405 view.setAnnotationColours(ac);
1406 view.setBgColour("AnnotationColourGradient");
1410 view.setBgColour(ColourSchemeProperty
1411 .getColourName(av.getGlobalColourScheme()));
1414 ResidueShaderI vcs = av.getResidueShading();
1415 ColourSchemeI cs = av.getGlobalColourScheme();
1419 if (vcs.conservationApplied())
1421 view.setConsThreshold(vcs.getConservationInc());
1422 if (cs instanceof jalview.schemes.UserColourScheme)
1424 view.setBgColour(setUserColourScheme(cs, userColours, object));
1427 view.setPidThreshold(vcs.getThreshold());
1430 view.setConservationSelected(av.getConservationSelected());
1431 view.setPidSelected(av.getAbovePIDThreshold());
1432 final Font font = av.getFont();
1433 view.setFontName(font.getName());
1434 view.setFontSize(font.getSize());
1435 view.setFontStyle(font.getStyle());
1436 view.setScaleProteinAsCdna(av.getViewStyle().isScaleProteinAsCdna());
1437 view.setRenderGaps(av.isRenderGaps());
1438 view.setShowAnnotation(av.isShowAnnotation());
1439 view.setShowBoxes(av.getShowBoxes());
1440 view.setShowColourText(av.getColourText());
1441 view.setShowFullId(av.getShowJVSuffix());
1442 view.setRightAlignIds(av.isRightAlignIds());
1443 view.setShowSequenceFeatures(av.isShowSequenceFeatures());
1444 view.setShowText(av.getShowText());
1445 view.setShowUnconserved(av.getShowUnconserved());
1446 view.setWrapAlignment(av.getWrapAlignment());
1447 view.setTextCol1(av.getTextColour().getRGB());
1448 view.setTextCol2(av.getTextColour2().getRGB());
1449 view.setTextColThreshold(av.getThresholdTextColour());
1450 view.setShowConsensusHistogram(av.isShowConsensusHistogram());
1451 view.setShowSequenceLogo(av.isShowSequenceLogo());
1452 view.setNormaliseSequenceLogo(av.isNormaliseSequenceLogo());
1453 view.setShowGroupConsensus(av.isShowGroupConsensus());
1454 view.setShowGroupConservation(av.isShowGroupConservation());
1455 view.setShowNPfeatureTooltip(av.isShowNPFeats());
1456 view.setShowDbRefTooltip(av.isShowDBRefs());
1457 view.setFollowHighlight(av.isFollowHighlight());
1458 view.setFollowSelection(av.followSelection);
1459 view.setIgnoreGapsinConsensus(av.isIgnoreGapsConsensus());
1460 if (av.getFeaturesDisplayed() != null)
1462 FeatureSettings fs = new FeatureSettings();
1464 FeatureRenderer fr = ap.getSeqPanel().seqCanvas
1465 .getFeatureRenderer();
1466 String[] renderOrder = fr.getRenderOrder().toArray(new String[0]);
1468 Vector<String> settingsAdded = new Vector<>();
1469 if (renderOrder != null)
1471 for (String featureType : renderOrder)
1473 FeatureSettings.Setting setting = new FeatureSettings.Setting();
1474 setting.setType(featureType);
1477 * save any filter for the feature type
1479 FeatureMatcherSetI filter = fr.getFeatureFilter(featureType);
1480 if (filter != null) {
1481 Iterator<FeatureMatcherI> filters = filter.getMatchers().iterator();
1482 FeatureMatcherI firstFilter = filters.next();
1483 setting.setMatcherSet(Jalview2XML.marshalFilter(
1484 firstFilter, filters, filter.isAnded()));
1488 * save colour scheme for the feature type
1490 FeatureColourI fcol = fr.getFeatureStyle(featureType);
1491 if (!fcol.isSimpleColour())
1493 setting.setColour(fcol.getMaxColour().getRGB());
1494 setting.setMincolour(fcol.getMinColour().getRGB());
1495 setting.setMin(fcol.getMin());
1496 setting.setMax(fcol.getMax());
1497 setting.setColourByLabel(fcol.isColourByLabel());
1498 if (fcol.isColourByAttribute())
1500 String[] attName = fcol.getAttributeName();
1501 setting.getAttributeName().add(attName[0]);
1502 if (attName.length > 1)
1504 setting.getAttributeName().add(attName[1]);
1507 setting.setAutoScale(fcol.isAutoScaled());
1508 setting.setThreshold(fcol.getThreshold());
1509 Color noColour = fcol.getNoColour();
1510 if (noColour == null)
1512 setting.setNoValueColour(NoValueColour.NONE);
1514 else if (noColour.equals(fcol.getMaxColour()))
1516 setting.setNoValueColour(NoValueColour.MAX);
1520 setting.setNoValueColour(NoValueColour.MIN);
1522 // -1 = No threshold, 0 = Below, 1 = Above
1523 setting.setThreshstate(fcol.isAboveThreshold() ? 1
1524 : (fcol.isBelowThreshold() ? 0 : -1));
1528 setting.setColour(fcol.getColour().getRGB());
1532 av.getFeaturesDisplayed().isVisible(featureType));
1534 .getOrder(featureType);
1537 setting.setOrder(rorder);
1539 /// fs.addSetting(setting);
1540 fs.getSetting().add(setting);
1541 settingsAdded.addElement(featureType);
1545 // is groups actually supposed to be a map here ?
1546 Iterator<String> en = fr.getFeatureGroups().iterator();
1547 Vector<String> groupsAdded = new Vector<>();
1548 while (en.hasNext())
1550 String grp = en.next();
1551 if (groupsAdded.contains(grp))
1555 Group g = new Group();
1557 g.setDisplay(((Boolean) fr.checkGroupVisibility(grp, false))
1560 fs.getGroup().add(g);
1561 groupsAdded.addElement(grp);
1563 // jms.setFeatureSettings(fs);
1564 object.setFeatureSettings(fs);
1567 if (av.hasHiddenColumns())
1569 jalview.datamodel.HiddenColumns hidden = av.getAlignment()
1570 .getHiddenColumns();
1573 warn("REPORT BUG: avoided null columnselection bug (DMAM reported). Please contact Jim about this.");
1577 Iterator<int[]> hiddenRegions = hidden.iterator();
1578 while (hiddenRegions.hasNext())
1580 int[] region = hiddenRegions.next();
1581 HiddenColumns hc = new HiddenColumns();
1582 hc.setStart(region[0]);
1583 hc.setEnd(region[1]);
1584 // view.addHiddenColumns(hc);
1585 view.getHiddenColumns().add(hc);
1589 if (calcIdSet.size() > 0)
1591 for (String calcId : calcIdSet)
1593 if (calcId.trim().length() > 0)
1595 CalcIdParam cidp = createCalcIdParam(calcId, av);
1596 // Some calcIds have no parameters.
1599 // view.addCalcIdParam(cidp);
1600 view.getCalcIdParam().add(cidp);
1606 // jms.addViewport(view);
1607 object.getViewport().add(view);
1609 // object.setJalviewModelSequence(jms);
1610 // object.getVamsasModel().addSequenceSet(vamsasSet);
1611 object.getVamsasModel().getSequenceSet().add(vamsasSet);
1613 if (jout != null && fileName != null)
1615 // We may not want to write the object to disk,
1616 // eg we can copy the alignViewport to a new view object
1617 // using save and then load
1620 fileName = fileName.replace('\\', '/');
1621 System.out.println("Writing jar entry " + fileName);
1622 JarEntry entry = new JarEntry(fileName);
1623 jout.putNextEntry(entry);
1624 PrintWriter pout = new PrintWriter(
1625 new OutputStreamWriter(jout, UTF_8));
1626 JAXBContext jaxbContext = JAXBContext
1627 .newInstance(JalviewModel.class);
1628 Marshaller jaxbMarshaller = jaxbContext.createMarshaller();
1630 // output pretty printed
1631 // jaxbMarshaller.setProperty(Marshaller.JAXB_FORMATTED_OUTPUT, true);
1632 jaxbMarshaller.marshal(
1633 new ObjectFactory().createJalviewModel(object), pout);
1635 // jaxbMarshaller.marshal(object, pout);
1636 // marshaller.marshal(object);
1639 } catch (Exception ex)
1641 // TODO: raise error in GUI if marshalling failed.
1642 System.err.println("Error writing Jalview project");
1643 ex.printStackTrace();
1650 * Save any Varna viewers linked to this sequence. Writes an rnaViewer element
1651 * for each viewer, with
1653 * <li>viewer geometry (position, size, split pane divider location)</li>
1654 * <li>index of the selected structure in the viewer (currently shows gapped
1656 * <li>the id of the annotation holding RNA secondary structure</li>
1657 * <li>(currently only one SS is shown per viewer, may be more in future)</li>
1659 * Varna viewer state is also written out (in native Varna XML) to separate
1660 * project jar entries. A separate entry is written for each RNA structure
1661 * displayed, with the naming convention
1663 * <li>rna_viewId_sequenceId_annotationId_[gapped|trimmed]</li>
1671 * @param storeDataset
1673 protected void saveRnaViewers(JarOutputStream jout, JSeq jseq,
1674 final SequenceI jds, List<String> viewIds, AlignmentPanel ap,
1675 boolean storeDataset)
1677 if (Desktop.desktop == null)
1681 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1682 for (int f = frames.length - 1; f > -1; f--)
1684 if (frames[f] instanceof AppVarna)
1686 AppVarna varna = (AppVarna) frames[f];
1688 * link the sequence to every viewer that is showing it and is linked to
1689 * its alignment panel
1691 if (varna.isListeningFor(jds) && ap == varna.getAlignmentPanel())
1693 String viewId = varna.getViewId();
1694 RnaViewer rna = new RnaViewer();
1695 rna.setViewId(viewId);
1696 rna.setTitle(varna.getTitle());
1697 rna.setXpos(varna.getX());
1698 rna.setYpos(varna.getY());
1699 rna.setWidth(varna.getWidth());
1700 rna.setHeight(varna.getHeight());
1701 rna.setDividerLocation(varna.getDividerLocation());
1702 rna.setSelectedRna(varna.getSelectedIndex());
1703 // jseq.addRnaViewer(rna);
1704 jseq.getRnaViewer().add(rna);
1707 * Store each Varna panel's state once in the project per sequence.
1708 * First time through only (storeDataset==false)
1710 // boolean storeSessions = false;
1711 // String sequenceViewId = viewId + seqsToIds.get(jds);
1712 // if (!storeDataset && !viewIds.contains(sequenceViewId))
1714 // viewIds.add(sequenceViewId);
1715 // storeSessions = true;
1717 for (RnaModel model : varna.getModels())
1719 if (model.seq == jds)
1722 * VARNA saves each view (sequence or alignment secondary
1723 * structure, gapped or trimmed) as a separate XML file
1725 String jarEntryName = rnaSessions.get(model);
1726 if (jarEntryName == null)
1729 String varnaStateFile = varna.getStateInfo(model.rna);
1730 jarEntryName = RNA_PREFIX + viewId + "_" + nextCounter();
1731 copyFileToJar(jout, varnaStateFile, jarEntryName);
1732 rnaSessions.put(model, jarEntryName);
1734 SecondaryStructure ss = new SecondaryStructure();
1735 String annotationId = varna.getAnnotation(jds).annotationId;
1736 ss.setAnnotationId(annotationId);
1737 ss.setViewerState(jarEntryName);
1738 ss.setGapped(model.gapped);
1739 ss.setTitle(model.title);
1740 // rna.addSecondaryStructure(ss);
1741 rna.getSecondaryStructure().add(ss);
1750 * Copy the contents of a file to a new entry added to the output jar
1754 * @param jarEntryName
1756 protected void copyFileToJar(JarOutputStream jout, String infilePath,
1757 String jarEntryName)
1759 DataInputStream dis = null;
1762 File file = new File(infilePath);
1763 if (file.exists() && jout != null)
1765 dis = new DataInputStream(new FileInputStream(file));
1766 byte[] data = new byte[(int) file.length()];
1767 dis.readFully(data);
1768 writeJarEntry(jout, jarEntryName, data);
1770 } catch (Exception ex)
1772 ex.printStackTrace();
1780 } catch (IOException e)
1789 * Write the data to a new entry of given name in the output jar file
1792 * @param jarEntryName
1794 * @throws IOException
1796 protected void writeJarEntry(JarOutputStream jout, String jarEntryName,
1797 byte[] data) throws IOException
1801 jarEntryName = jarEntryName.replace('\\','/');
1802 System.out.println("Writing jar entry " + jarEntryName);
1803 jout.putNextEntry(new JarEntry(jarEntryName));
1804 DataOutputStream dout = new DataOutputStream(jout);
1805 dout.write(data, 0, data.length);
1812 * Save the state of a structure viewer
1817 * the archive XML element under which to save the state
1820 * @param matchedFile
1824 protected String saveStructureState(AlignmentPanel ap, SequenceI jds,
1825 Pdbids pdb, PDBEntry entry, List<String> viewIds,
1826 String matchedFile, StructureViewerBase viewFrame)
1828 final AAStructureBindingModel bindingModel = viewFrame.getBinding();
1831 * Look for any bindings for this viewer to the PDB file of interest
1832 * (including part matches excluding chain id)
1834 for (int peid = 0; peid < bindingModel.getPdbCount(); peid++)
1836 final PDBEntry pdbentry = bindingModel.getPdbEntry(peid);
1837 final String pdbId = pdbentry.getId();
1838 if (!pdbId.equals(entry.getId())
1839 && !(entry.getId().length() > 4 && entry.getId().toLowerCase()
1840 .startsWith(pdbId.toLowerCase())))
1843 * not interested in a binding to a different PDB entry here
1847 if (matchedFile == null)
1849 matchedFile = pdbentry.getFile();
1851 else if (!matchedFile.equals(pdbentry.getFile()))
1854 "Probably lost some PDB-Sequence mappings for this structure file (which apparently has same PDB Entry code): "
1855 + pdbentry.getFile());
1859 // can get at it if the ID
1860 // match is ambiguous (e.g.
1863 for (int smap = 0; smap < viewFrame.getBinding()
1864 .getSequence()[peid].length; smap++)
1866 // if (jal.findIndex(jmol.jmb.sequence[peid][smap]) > -1)
1867 if (jds == viewFrame.getBinding().getSequence()[peid][smap])
1869 StructureState state = new StructureState();
1870 state.setVisible(true);
1871 state.setXpos(viewFrame.getX());
1872 state.setYpos(viewFrame.getY());
1873 state.setWidth(viewFrame.getWidth());
1874 state.setHeight(viewFrame.getHeight());
1875 final String viewId = viewFrame.getViewId();
1876 state.setViewId(viewId);
1877 state.setAlignwithAlignPanel(viewFrame.isUsedforaligment(ap));
1878 state.setColourwithAlignPanel(viewFrame.isUsedforcolourby(ap));
1879 state.setColourByJmol(viewFrame.isColouredByViewer());
1880 state.setType(viewFrame.getViewerType().toString());
1881 // pdb.addStructureState(state);
1882 pdb.getStructureState().add(state);
1890 * Populates the AnnotationColourScheme xml for save. This captures the
1891 * settings of the options in the 'Colour by Annotation' dialog.
1894 * @param userColours
1898 private AnnotationColourScheme constructAnnotationColours(
1899 AnnotationColourGradient acg, List<UserColourScheme> userColours,
1902 AnnotationColourScheme ac = new AnnotationColourScheme();
1903 ac.setAboveThreshold(acg.getAboveThreshold());
1904 ac.setThreshold(acg.getAnnotationThreshold());
1905 // 2.10.2 save annotationId (unique) not annotation label
1906 ac.setAnnotation(acg.getAnnotation().annotationId);
1907 if (acg.getBaseColour() instanceof UserColourScheme)
1910 setUserColourScheme(acg.getBaseColour(), userColours, jm));
1915 ColourSchemeProperty.getColourName(acg.getBaseColour()));
1918 ac.setMaxColour(acg.getMaxColour().getRGB());
1919 ac.setMinColour(acg.getMinColour().getRGB());
1920 ac.setPerSequence(acg.isSeqAssociated());
1921 ac.setPredefinedColours(acg.isPredefinedColours());
1925 private void storeAlignmentAnnotation(AlignmentAnnotation[] aa,
1926 IdentityHashMap<SequenceGroup, String> groupRefs,
1927 AlignmentViewport av, Set<String> calcIdSet, boolean storeDS,
1928 SequenceSet vamsasSet)
1931 for (int i = 0; i < aa.length; i++)
1933 Annotation an = new Annotation();
1935 AlignmentAnnotation annotation = aa[i];
1936 if (annotation.annotationId != null)
1938 annotationIds.put(annotation.annotationId, annotation);
1941 an.setId(annotation.annotationId);
1943 an.setVisible(annotation.visible);
1945 an.setDescription(annotation.description);
1947 if (annotation.sequenceRef != null)
1949 // 2.9 JAL-1781 xref on sequence id rather than name
1950 an.setSequenceRef(seqsToIds.get(annotation.sequenceRef));
1952 if (annotation.groupRef != null)
1954 String groupIdr = groupRefs.get(annotation.groupRef);
1955 if (groupIdr == null)
1957 // make a locally unique String
1958 groupRefs.put(annotation.groupRef,
1959 groupIdr = ("" + System.currentTimeMillis()
1960 + annotation.groupRef.getName()
1961 + groupRefs.size()));
1963 an.setGroupRef(groupIdr.toString());
1966 // store all visualization attributes for annotation
1967 an.setGraphHeight(annotation.graphHeight);
1968 an.setCentreColLabels(annotation.centreColLabels);
1969 an.setScaleColLabels(annotation.scaleColLabel);
1970 an.setShowAllColLabels(annotation.showAllColLabels);
1971 an.setBelowAlignment(annotation.belowAlignment);
1973 if (annotation.graph > 0)
1976 an.setGraphType(annotation.graph);
1977 an.setGraphGroup(annotation.graphGroup);
1978 if (annotation.getThreshold() != null)
1980 ThresholdLine line = new ThresholdLine();
1981 line.setLabel(annotation.getThreshold().label);
1982 line.setValue(annotation.getThreshold().value);
1983 line.setColour(annotation.getThreshold().colour.getRGB());
1984 an.setThresholdLine(line);
1992 an.setLabel(annotation.label);
1994 if (annotation == av.getAlignmentQualityAnnot()
1995 || annotation == av.getAlignmentConservationAnnotation()
1996 || annotation == av.getAlignmentConsensusAnnotation()
1997 || annotation.autoCalculated)
1999 // new way of indicating autocalculated annotation -
2000 an.setAutoCalculated(annotation.autoCalculated);
2002 if (annotation.hasScore())
2004 an.setScore(annotation.getScore());
2007 if (annotation.getCalcId() != null)
2009 calcIdSet.add(annotation.getCalcId());
2010 an.setCalcId(annotation.getCalcId());
2012 if (annotation.hasProperties())
2014 for (String pr : annotation.getProperties())
2016 jalview.xml.binding.jalview.Annotation.Property prop = new jalview.xml.binding.jalview.Annotation.Property();
2018 prop.setValue(annotation.getProperty(pr));
2019 // an.addProperty(prop);
2020 an.getProperty().add(prop);
2024 AnnotationElement ae;
2025 if (annotation.annotations != null)
2027 an.setScoreOnly(false);
2028 for (int a = 0; a < annotation.annotations.length; a++)
2030 if ((annotation == null) || (annotation.annotations[a] == null))
2035 ae = new AnnotationElement();
2036 if (annotation.annotations[a].description != null)
2038 ae.setDescription(annotation.annotations[a].description);
2040 if (annotation.annotations[a].displayCharacter != null)
2042 ae.setDisplayCharacter(
2043 annotation.annotations[a].displayCharacter);
2046 if (!Float.isNaN(annotation.annotations[a].value))
2048 ae.setValue(annotation.annotations[a].value);
2052 if (annotation.annotations[a].secondaryStructure > ' ')
2054 ae.setSecondaryStructure(
2055 annotation.annotations[a].secondaryStructure + "");
2058 if (annotation.annotations[a].colour != null
2059 && annotation.annotations[a].colour != java.awt.Color.black)
2061 ae.setColour(annotation.annotations[a].colour.getRGB());
2064 // an.addAnnotationElement(ae);
2065 an.getAnnotationElement().add(ae);
2066 if (annotation.autoCalculated)
2068 // only write one non-null entry into the annotation row -
2069 // sufficient to get the visualization attributes necessary to
2077 an.setScoreOnly(true);
2079 if (!storeDS || (storeDS && !annotation.autoCalculated))
2081 // skip autocalculated annotation - these are only provided for
2083 // vamsasSet.addAnnotation(an);
2084 vamsasSet.getAnnotation().add(an);
2090 private CalcIdParam createCalcIdParam(String calcId, AlignViewport av)
2092 AutoCalcSetting settings = av.getCalcIdSettingsFor(calcId);
2093 if (settings != null)
2095 CalcIdParam vCalcIdParam = new CalcIdParam();
2096 vCalcIdParam.setCalcId(calcId);
2097 // vCalcIdParam.addServiceURL(settings.getServiceURI());
2098 vCalcIdParam.getServiceURL().add(settings.getServiceURI());
2099 // generic URI allowing a third party to resolve another instance of the
2100 // service used for this calculation
2101 for (String url : settings.getServiceURLs())
2103 // vCalcIdParam.addServiceURL(urls);
2104 vCalcIdParam.getServiceURL().add(url);
2106 vCalcIdParam.setVersion("1.0");
2107 if (settings.getPreset() != null)
2109 WsParamSetI setting = settings.getPreset();
2110 vCalcIdParam.setName(setting.getName());
2111 vCalcIdParam.setDescription(setting.getDescription());
2115 vCalcIdParam.setName("");
2116 vCalcIdParam.setDescription("Last used parameters");
2118 // need to be able to recover 1) settings 2) user-defined presets or
2119 // recreate settings from preset 3) predefined settings provided by
2120 // service - or settings that can be transferred (or discarded)
2121 vCalcIdParam.setParameters(
2122 settings.getWsParamFile().replace("\n", "|\\n|"));
2123 vCalcIdParam.setAutoUpdate(settings.isAutoUpdate());
2124 // todo - decide if updateImmediately is needed for any projects.
2126 return vCalcIdParam;
2131 private boolean recoverCalcIdParam(CalcIdParam calcIdParam,
2134 if (calcIdParam.getVersion().equals("1.0"))
2136 final String[] calcIds = calcIdParam.getServiceURL().toArray(new String[0]);
2137 Jws2Instance service = Jws2Discoverer.getDiscoverer()
2138 .getPreferredServiceFor(calcIds);
2139 if (service != null)
2141 WsParamSetI parmSet = null;
2144 parmSet = service.getParamStore().parseServiceParameterFile(
2145 calcIdParam.getName(), calcIdParam.getDescription(),
2147 calcIdParam.getParameters().replace("|\\n|", "\n"));
2148 } catch (IOException x)
2150 warn("Couldn't parse parameter data for "
2151 + calcIdParam.getCalcId(), x);
2154 List<ArgumentI> argList = null;
2155 if (calcIdParam.getName().length() > 0)
2157 parmSet = service.getParamStore()
2158 .getPreset(calcIdParam.getName());
2159 if (parmSet != null)
2161 // TODO : check we have a good match with settings in AACon -
2162 // otherwise we'll need to create a new preset
2167 argList = parmSet.getArguments();
2170 AAConSettings settings = new AAConSettings(
2171 calcIdParam.isAutoUpdate(), service, parmSet, argList);
2172 av.setCalcIdSettingsFor(calcIdParam.getCalcId(), settings,
2173 calcIdParam.isNeedsUpdate());
2178 warn("Cannot resolve a service for the parameters used in this project. Try configuring a JABAWS server.");
2182 throw new Error(MessageManager.formatMessage(
2183 "error.unsupported_version_calcIdparam", new Object[]
2184 { calcIdParam.toString() }));
2188 * External mapping between jalview objects and objects yielding a valid and
2189 * unique object ID string. This is null for normal Jalview project IO, but
2190 * non-null when a jalview project is being read or written as part of a
2193 IdentityHashMap jv2vobj = null;
2196 * Construct a unique ID for jvobj using either existing bindings or if none
2197 * exist, the result of the hashcode call for the object.
2200 * jalview data object
2201 * @return unique ID for referring to jvobj
2203 private String makeHashCode(Object jvobj, String altCode)
2205 if (jv2vobj != null)
2207 Object id = jv2vobj.get(jvobj);
2210 return id.toString();
2212 // check string ID mappings
2213 if (jvids2vobj != null && jvobj instanceof String)
2215 id = jvids2vobj.get(jvobj);
2219 return id.toString();
2221 // give up and warn that something has gone wrong
2222 warn("Cannot find ID for object in external mapping : " + jvobj);
2228 * return local jalview object mapped to ID, if it exists
2232 * @return null or object bound to idcode
2234 private Object retrieveExistingObj(String idcode)
2236 if (idcode != null && vobj2jv != null)
2238 return vobj2jv.get(idcode);
2244 * binding from ID strings from external mapping table to jalview data model
2247 private Hashtable vobj2jv;
2249 private Sequence createVamsasSequence(String id, SequenceI jds)
2251 return createVamsasSequence(true, id, jds, null);
2254 private Sequence createVamsasSequence(boolean recurse, String id,
2255 SequenceI jds, SequenceI parentseq)
2257 Sequence vamsasSeq = new Sequence();
2258 vamsasSeq.setId(id);
2259 vamsasSeq.setName(jds.getName());
2260 vamsasSeq.setSequence(jds.getSequenceAsString());
2261 vamsasSeq.setDescription(jds.getDescription());
2262 jalview.datamodel.DBRefEntry[] dbrefs = null;
2263 if (jds.getDatasetSequence() != null)
2265 vamsasSeq.setDsseqid(seqHash(jds.getDatasetSequence()));
2269 // seqId==dsseqid so we can tell which sequences really are
2270 // dataset sequences only
2271 vamsasSeq.setDsseqid(id);
2272 dbrefs = jds.getDBRefs();
2273 if (parentseq == null)
2280 for (int d = 0; d < dbrefs.length; d++)
2282 DBRef dbref = new DBRef();
2283 dbref.setSource(dbrefs[d].getSource());
2284 dbref.setVersion(dbrefs[d].getVersion());
2285 dbref.setAccessionId(dbrefs[d].getAccessionId());
2286 if (dbrefs[d].hasMap())
2288 Mapping mp = createVamsasMapping(dbrefs[d].getMap(), parentseq,
2290 dbref.setMapping(mp);
2292 // vamsasSeq.addDBRef(dbref);
2293 vamsasSeq.getDBRef().add(dbref);
2299 private Mapping createVamsasMapping(jalview.datamodel.Mapping jmp,
2300 SequenceI parentseq, SequenceI jds, boolean recurse)
2303 if (jmp.getMap() != null)
2307 jalview.util.MapList mlst = jmp.getMap();
2308 List<int[]> r = mlst.getFromRanges();
2309 for (int[] range : r)
2311 MapListFrom mfrom = new MapListFrom();
2312 mfrom.setStart(range[0]);
2313 mfrom.setEnd(range[1]);
2314 // mp.addMapListFrom(mfrom);
2315 mp.getMapListFrom().add(mfrom);
2317 r = mlst.getToRanges();
2318 for (int[] range : r)
2320 MapListTo mto = new MapListTo();
2321 mto.setStart(range[0]);
2322 mto.setEnd(range[1]);
2323 // mp.addMapListTo(mto);
2324 mp.getMapListTo().add(mto);
2326 mp.setMapFromUnit(BigInteger.valueOf(mlst.getFromRatio()));
2327 mp.setMapToUnit(BigInteger.valueOf(mlst.getToRatio()));
2328 if (jmp.getTo() != null)
2330 // MappingChoice mpc = new MappingChoice();
2332 // check/create ID for the sequence referenced by getTo()
2335 SequenceI ps = null;
2336 if (parentseq != jmp.getTo()
2337 && parentseq.getDatasetSequence() != jmp.getTo())
2339 // chaining dbref rather than a handshaking one
2340 jmpid = seqHash(ps = jmp.getTo());
2344 jmpid = seqHash(ps = parentseq);
2346 // mpc.setDseqFor(jmpid);
2347 mp.setDseqFor(jmpid);
2348 if (!seqRefIds.containsKey(jmpid))
2350 jalview.bin.Cache.log.debug("creatign new DseqFor ID");
2351 seqRefIds.put(jmpid, ps);
2355 jalview.bin.Cache.log.debug("reusing DseqFor ID");
2358 // mp.setMappingChoice(mpc);
2364 String setUserColourScheme(jalview.schemes.ColourSchemeI cs,
2365 List<UserColourScheme> userColours, JalviewModel jm)
2368 jalview.schemes.UserColourScheme ucs = (jalview.schemes.UserColourScheme) cs;
2369 boolean newucs = false;
2370 if (!userColours.contains(ucs))
2372 userColours.add(ucs);
2375 id = "ucs" + userColours.indexOf(ucs);
2378 // actually create the scheme's entry in the XML model
2379 java.awt.Color[] colours = ucs.getColours();
2380 UserColours uc = new UserColours();
2381 // UserColourScheme jbucs = new UserColourScheme();
2382 JalviewUserColours jbucs = new JalviewUserColours();
2384 for (int i = 0; i < colours.length; i++)
2386 Colour col = new Colour();
2387 col.setName(ResidueProperties.aa[i]);
2388 col.setRGB(jalview.util.Format.getHexString(colours[i]));
2389 // jbucs.addColour(col);
2390 jbucs.getColour().add(col);
2392 if (ucs.getLowerCaseColours() != null)
2394 colours = ucs.getLowerCaseColours();
2395 for (int i = 0; i < colours.length; i++)
2397 Colour col = new Colour();
2398 col.setName(ResidueProperties.aa[i].toLowerCase());
2399 col.setRGB(jalview.util.Format.getHexString(colours[i]));
2400 // jbucs.addColour(col);
2401 jbucs.getColour().add(col);
2406 uc.setUserColourScheme(jbucs);
2407 // jm.addUserColours(uc);
2408 jm.getUserColours().add(uc);
2414 jalview.schemes.UserColourScheme getUserColourScheme(
2415 JalviewModel jm, String id)
2417 List<UserColours> uc = jm.getUserColours();
2418 UserColours colours = null;
2420 for (int i = 0; i < uc.length; i++)
2422 if (uc[i].getId().equals(id))
2429 for (UserColours c : uc)
2431 if (c.getId().equals(id))
2438 java.awt.Color[] newColours = new java.awt.Color[24];
2440 for (int i = 0; i < 24; i++)
2442 newColours[i] = new java.awt.Color(Integer.parseInt(
2443 // colours.getUserColourScheme().getColour(i).getRGB(), 16));
2444 colours.getUserColourScheme().getColour().get(i).getRGB(),
2448 jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(
2451 if (colours.getUserColourScheme().getColour().size()/*Count()*/ > 24)
2453 newColours = new java.awt.Color[23];
2454 for (int i = 0; i < 23; i++)
2456 newColours[i] = new java.awt.Color(Integer.parseInt(
2457 colours.getUserColourScheme().getColour().get(i + 24)
2461 ucs.setLowerCaseColours(newColours);
2468 * contains last error message (if any) encountered by XML loader.
2470 String errorMessage = null;
2473 * flag to control whether the Jalview2XML_V1 parser should be deferred to if
2474 * exceptions are raised during project XML parsing
2476 public boolean attemptversion1parse = false;
2479 * Load a jalview project archive from a jar file
2482 * - HTTP URL or filename
2484 public AlignFrame loadJalviewAlign(final Object file)
2487 jalview.gui.AlignFrame af = null;
2491 // create list to store references for any new Jmol viewers created
2492 newStructureViewers = new Vector<>();
2493 // UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
2494 // Workaround is to make sure caller implements the JarInputStreamProvider
2496 // so we can re-open the jar input stream for each entry.
2498 jarInputStreamProvider jprovider = createjarInputStreamProvider(file);
2499 af = loadJalviewAlign(jprovider);
2502 af.setMenusForViewport();
2504 } catch (MalformedURLException e)
2506 errorMessage = "Invalid URL format for '" + file + "'";
2512 SwingUtilities.invokeAndWait(new Runnable()
2517 setLoadingFinishedForNewStructureViewers();
2520 } catch (Exception x)
2522 System.err.println("Error loading alignment: " + x.getMessage());
2528 @SuppressWarnings("unused")
2529 private jarInputStreamProvider createjarInputStreamProvider(final Object ofile) throws MalformedURLException {
2531 // BH 2018 allow for bytes already attached to File object
2533 String file = (ofile instanceof File ? ((File) ofile).getCanonicalPath() : ofile.toString());
2534 byte[] bytes = /** @j2sNative ofile._bytes || */
2537 errorMessage = null;
2538 uniqueSetSuffix = null;
2540 viewportsAdded.clear();
2541 frefedSequence = null;
2543 if (file.startsWith("http://")) {
2544 url = new URL(file);
2546 final URL _url = url;
2547 return new jarInputStreamProvider() {
2550 public JarInputStream getJarInputStream() throws IOException {
2551 if (bytes != null) {
2552 System.out.println("Jalview2XML: opening byte jarInputStream for bytes.length=" + bytes.length);
2553 return new JarInputStream(new ByteArrayInputStream(bytes));
2556 System.out.println("Jalview2XML: opening url jarInputStream for " + _url);
2557 return new JarInputStream(_url.openStream());
2559 System.out.println("Jalview2XML: opening file jarInputStream for " + file);
2560 return new JarInputStream(new FileInputStream(file));
2565 public String getFilename() {
2569 } catch (IOException e) {
2570 e.printStackTrace();
2576 * Recover jalview session from a jalview project archive. Caller may
2577 * initialise uniqueSetSuffix, seqRefIds, viewportsAdded and frefedSequence
2578 * themselves. Any null fields will be initialised with default values,
2579 * non-null fields are left alone.
2584 public AlignFrame loadJalviewAlign(final jarInputStreamProvider jprovider)
2586 errorMessage = null;
2587 if (uniqueSetSuffix == null)
2589 uniqueSetSuffix = System.currentTimeMillis() % 100000 + "";
2591 if (seqRefIds == null)
2595 AlignFrame af = null, _af = null;
2596 IdentityHashMap<AlignmentI, AlignmentI> importedDatasets = new IdentityHashMap<>();
2597 Map<String, AlignFrame> gatherToThisFrame = new HashMap<>();
2598 final String file = jprovider.getFilename();
2601 JarInputStream jin = null;
2602 JarEntry jarentry = null;
2607 jin = jprovider.getJarInputStream();
2608 for (int i = 0; i < entryCount; i++)
2610 jarentry = jin.getNextJarEntry();
2611 System.out.println("Jalview2XML#loadJalviewAlign: jarentry=" + (jarentry == null ? null : jarentry.getName()));
2614 if (jarentry != null && jarentry.getName().endsWith(".xml"))
2616 InputStreamReader in = new InputStreamReader(jin, UTF_8);
2617 // JalviewModel object = new JalviewModel();
2619 JAXBContext jc = JAXBContext
2620 .newInstance("jalview.xml.binding.jalview");
2621 XMLStreamReader streamReader = XMLInputFactory.newInstance()
2622 .createXMLStreamReader(jin);
2623 javax.xml.bind.Unmarshaller um = jc.createUnmarshaller();
2624 JAXBElement<JalviewModel> jbe = um
2625 .unmarshal(streamReader, JalviewModel.class);
2626 JalviewModel object = jbe.getValue();
2627 System.out.println("processing JalviewModel object=" + object);
2629 Unmarshaller unmar = new Unmarshaller(object);
2630 unmar.setValidation(false);
2631 object = (JalviewModel) unmar.unmarshal(in);
2633 if (true) // !skipViewport(object))
2635 _af = loadFromObject(object, file, true, jprovider);
2636 if (_af != null && object.getViewport().size() > 0)
2637 // getJalviewModelSequence().getViewportCount() > 0)
2641 // store a reference to the first view
2644 if (_af.getViewport().isGatherViewsHere())
2646 // if this is a gathered view, keep its reference since
2647 // after gathering views, only this frame will remain
2649 gatherToThisFrame.put(_af.getViewport().getSequenceSetId(),
2652 // Save dataset to register mappings once all resolved
2653 importedDatasets.put(
2654 af.getViewport().getAlignment().getDataset(),
2655 af.getViewport().getAlignment().getDataset());
2660 else if (jarentry != null)
2662 // Some other file here.
2665 } while (jarentry != null);
2666 resolveFrefedSequences();
2667 } catch (IOException ex)
2669 ex.printStackTrace();
2670 errorMessage = "Couldn't locate Jalview XML file : " + file;
2672 "Exception whilst loading jalview XML file : " + ex + "\n");
2673 } catch (Exception ex)
2675 System.err.println("Parsing as Jalview Version 2 file failed.");
2676 ex.printStackTrace(System.err);
2677 if (attemptversion1parse)
2679 // Is Version 1 Jar file?
2682 af = new Jalview2XML_V1(raiseGUI).LoadJalviewAlign(jprovider);
2683 } catch (Exception ex2)
2685 System.err.println("Exception whilst loading as jalviewXMLV1:");
2686 ex2.printStackTrace();
2690 if (Desktop.instance != null)
2692 Desktop.instance.stopLoading();
2696 System.out.println("Successfully loaded archive file");
2699 ex.printStackTrace();
2702 "Exception whilst loading jalview XML file : " + ex + "\n");
2703 } catch (OutOfMemoryError e)
2705 // Don't use the OOM Window here
2706 errorMessage = "Out of memory loading jalview XML file";
2707 System.err.println("Out of memory whilst loading jalview XML file");
2708 e.printStackTrace();
2712 * Regather multiple views (with the same sequence set id) to the frame (if
2713 * any) that is flagged as the one to gather to, i.e. convert them to tabbed
2714 * views instead of separate frames. Note this doesn't restore a state where
2715 * some expanded views in turn have tabbed views - the last "first tab" read
2716 * in will play the role of gatherer for all.
2718 for (AlignFrame fr : gatherToThisFrame.values())
2720 Desktop.instance.gatherViews(fr);
2723 restoreSplitFrames();
2724 for (AlignmentI ds : importedDatasets.keySet())
2726 if (ds.getCodonFrames() != null)
2728 StructureSelectionManager
2729 .getStructureSelectionManager(Desktop.instance)
2730 .registerMappings(ds.getCodonFrames());
2733 if (errorMessage != null)
2738 if (Desktop.instance != null)
2740 Desktop.instance.stopLoading();
2747 * Try to reconstruct and display SplitFrame windows, where each contains
2748 * complementary dna and protein alignments. Done by pairing up AlignFrame
2749 * objects (created earlier) which have complementary viewport ids associated.
2751 protected void restoreSplitFrames()
2753 List<SplitFrame> gatherTo = new ArrayList<>();
2754 List<AlignFrame> addedToSplitFrames = new ArrayList<>();
2755 Map<String, AlignFrame> dna = new HashMap<>();
2758 * Identify the DNA alignments
2760 for (Entry<Viewport, AlignFrame> candidate : splitFrameCandidates
2763 AlignFrame af = candidate.getValue();
2764 if (af.getViewport().getAlignment().isNucleotide())
2766 dna.put(candidate.getKey().getId(), af);
2771 * Try to match up the protein complements
2773 for (Entry<Viewport, AlignFrame> candidate : splitFrameCandidates
2776 AlignFrame af = candidate.getValue();
2777 if (!af.getViewport().getAlignment().isNucleotide())
2779 String complementId = candidate.getKey().getComplementId();
2780 // only non-null complements should be in the Map
2781 if (complementId != null && dna.containsKey(complementId))
2783 final AlignFrame dnaFrame = dna.get(complementId);
2784 SplitFrame sf = createSplitFrame(dnaFrame, af);
2785 addedToSplitFrames.add(dnaFrame);
2786 addedToSplitFrames.add(af);
2787 dnaFrame.setMenusForViewport();
2788 af.setMenusForViewport();
2789 if (af.getViewport().isGatherViewsHere())
2798 * Open any that we failed to pair up (which shouldn't happen!) as
2799 * standalone AlignFrame's.
2801 for (Entry<Viewport, AlignFrame> candidate : splitFrameCandidates
2804 AlignFrame af = candidate.getValue();
2805 if (!addedToSplitFrames.contains(af))
2807 Viewport view = candidate.getKey();
2808 Desktop.addInternalFrame(af, view.getTitle(),
2809 safeInt(view.getWidth()), safeInt(view.getHeight()));
2810 af.setMenusForViewport();
2811 System.err.println("Failed to restore view " + view.getTitle()
2812 + " to split frame");
2817 * Gather back into tabbed views as flagged.
2819 for (SplitFrame sf : gatherTo)
2821 Desktop.instance.gatherViews(sf);
2824 splitFrameCandidates.clear();
2828 * Construct and display one SplitFrame holding DNA and protein alignments.
2831 * @param proteinFrame
2834 protected SplitFrame createSplitFrame(AlignFrame dnaFrame,
2835 AlignFrame proteinFrame)
2837 SplitFrame splitFrame = new SplitFrame(dnaFrame, proteinFrame);
2838 String title = MessageManager.getString("label.linked_view_title");
2839 int width = (int) dnaFrame.getBounds().getWidth();
2840 int height = (int) (dnaFrame.getBounds().getHeight()
2841 + proteinFrame.getBounds().getHeight() + 50);
2844 * SplitFrame location is saved to both enclosed frames
2846 splitFrame.setLocation(dnaFrame.getX(), dnaFrame.getY());
2847 Desktop.addInternalFrame(splitFrame, title, width, height);
2850 * And compute cDNA consensus (couldn't do earlier with consensus as
2851 * mappings were not yet present)
2853 proteinFrame.getViewport().alignmentChanged(proteinFrame.alignPanel);
2859 * check errorMessage for a valid error message and raise an error box in the
2860 * GUI or write the current errorMessage to stderr and then clear the error
2863 protected void reportErrors()
2865 reportErrors(false);
2868 protected void reportErrors(final boolean saving)
2870 if (errorMessage != null)
2872 final String finalErrorMessage = errorMessage;
2875 javax.swing.SwingUtilities.invokeLater(new Runnable()
2880 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
2882 "Error " + (saving ? "saving" : "loading")
2884 JvOptionPane.WARNING_MESSAGE);
2890 System.err.println("Problem loading Jalview file: " + errorMessage);
2893 errorMessage = null;
2896 Map<String, String> alreadyLoadedPDB = new HashMap<>();
2899 * when set, local views will be updated from view stored in JalviewXML
2900 * Currently (28th Sep 2008) things will go horribly wrong in vamsas document
2901 * sync if this is set to true.
2903 private final boolean updateLocalViews = false;
2906 * Returns the path to a temporary file holding the PDB file for the given PDB
2907 * id. The first time of asking, searches for a file of that name in the
2908 * Jalview project jar, and copies it to a new temporary file. Any repeat
2909 * requests just return the path to the file previously created.
2915 String loadPDBFile(jarInputStreamProvider jprovider, String pdbId,
2918 if (alreadyLoadedPDB.containsKey(pdbId))
2920 return alreadyLoadedPDB.get(pdbId).toString();
2923 String tempFile = copyJarEntry(jprovider, pdbId, "jalview_pdb",
2925 if (tempFile != null)
2927 alreadyLoadedPDB.put(pdbId, tempFile);
2933 * Copies the jar entry of given name to a new temporary file and returns the
2934 * path to the file, or null if the entry is not found.
2937 * @param jarEntryName
2939 * a prefix for the temporary file name, must be at least three
2942 * null or original file - so new file can be given the same suffix
2946 protected String copyJarEntry(jarInputStreamProvider jprovider,
2947 String jarEntryName, String prefix, String origFile)
2949 BufferedReader in = null;
2950 PrintWriter out = null;
2951 String suffix = ".tmp";
2952 if (origFile == null)
2954 origFile = jarEntryName;
2956 int sfpos = origFile.lastIndexOf(".");
2957 if (sfpos > -1 && sfpos < (origFile.length() - 3))
2959 suffix = "." + origFile.substring(sfpos + 1);
2963 JarInputStream jin = jprovider.getJarInputStream();
2965 * if (jprovider.startsWith("http://")) { jin = new JarInputStream(new
2966 * URL(jprovider).openStream()); } else { jin = new JarInputStream(new
2967 * FileInputStream(jprovider)); }
2970 JarEntry entry = null;
2973 entry = jin.getNextJarEntry();
2974 System.out.println("Jalview2XML#copyJarEntry: jarentry=" + (entry == null ? null : entry.getName()));
2975 } while (entry != null && !entry.getName().equals(jarEntryName));
2978 in = new BufferedReader(new InputStreamReader(jin, UTF_8));
2979 File outFile = File.createTempFile(prefix, suffix);
2980 outFile.deleteOnExit();
2981 out = new PrintWriter(new FileOutputStream(outFile));
2984 while ((data = in.readLine()) != null)
2989 String t = outFile.getAbsolutePath();
2994 warn("Couldn't find entry in Jalview Jar for " + jarEntryName);
2996 } catch (Exception ex)
2998 ex.printStackTrace();
3006 } catch (IOException e)
3020 private class JvAnnotRow
3022 public JvAnnotRow(int i, AlignmentAnnotation jaa)
3029 * persisted version of annotation row from which to take vis properties
3031 public jalview.datamodel.AlignmentAnnotation template;
3034 * original position of the annotation row in the alignment
3040 * Load alignment frame from jalview XML DOM object
3042 * @param jalviewModel
3045 * filename source string
3046 * @param loadTreesAndStructures
3047 * when false only create Viewport
3049 * data source provider
3050 * @return alignment frame created from view stored in DOM
3052 AlignFrame loadFromObject(JalviewModel jalviewModel, String file,
3053 boolean loadTreesAndStructures, jarInputStreamProvider jprovider)
3055 SequenceSet vamsasSet = jalviewModel.getVamsasModel().getSequenceSet().get(0);
3056 List<Sequence> vamsasSeqs = vamsasSet.getSequence();
3058 // JalviewModelSequence jms = object.getJalviewModelSequence();
3060 // Viewport view = (jms.getViewportCount() > 0) ? jms.getViewport(0)
3062 Viewport view = (jalviewModel.getViewport().size() > 0)
3063 ? jalviewModel.getViewport().get(0)
3066 // ////////////////////////////////
3069 List<SequenceI> hiddenSeqs = null;
3071 List<SequenceI> tmpseqs = new ArrayList<>();
3073 boolean multipleView = false;
3074 SequenceI referenceseqForView = null;
3075 // JSeq[] jseqs = object.getJalviewModelSequence().getJSeq();
3076 List<JSeq> jseqs = jalviewModel.getJSeq();
3077 int vi = 0; // counter in vamsasSeq array
3078 for (int i = 0; i < jseqs.size(); i++)
3080 JSeq jseq = jseqs.get(i);
3081 String seqId = jseq.getId();
3083 SequenceI tmpSeq = seqRefIds.get(seqId);
3086 if (!incompleteSeqs.containsKey(seqId))
3088 // may not need this check, but keep it for at least 2.9,1 release
3089 if (tmpSeq.getStart() != jseq.getStart()
3090 || tmpSeq.getEnd() != jseq.getEnd())
3093 "Warning JAL-2154 regression: updating start/end for sequence "
3094 + tmpSeq.toString() + " to " + jseq);
3099 incompleteSeqs.remove(seqId);
3101 if (vamsasSeqs.size() > vi
3102 && vamsasSeqs.get(vi).getId().equals(seqId))
3104 // most likely we are reading a dataset XML document so
3105 // update from vamsasSeq section of XML for this sequence
3106 tmpSeq.setName(vamsasSeqs.get(vi).getName());
3107 tmpSeq.setDescription(vamsasSeqs.get(vi).getDescription());
3108 tmpSeq.setSequence(vamsasSeqs.get(vi).getSequence());
3113 // reading multiple views, so vamsasSeq set is a subset of JSeq
3114 multipleView = true;
3116 tmpSeq.setStart(jseq.getStart());
3117 tmpSeq.setEnd(jseq.getEnd());
3118 tmpseqs.add(tmpSeq);
3122 Sequence vamsasSeq = vamsasSeqs.get(vi);
3123 tmpSeq = new jalview.datamodel.Sequence(vamsasSeq.getName(),
3124 vamsasSeq.getSequence());
3125 tmpSeq.setDescription(vamsasSeq.getDescription());
3126 tmpSeq.setStart(jseq.getStart());
3127 tmpSeq.setEnd(jseq.getEnd());
3128 tmpSeq.setVamsasId(uniqueSetSuffix + seqId);
3129 seqRefIds.put(vamsasSeq.getId(), tmpSeq);
3130 tmpseqs.add(tmpSeq);
3134 if (safeBoolean(jseq.isViewreference()))
3136 referenceseqForView = tmpseqs.get(tmpseqs.size() - 1);
3139 if (jseq.isHidden() != null && jseq.isHidden().booleanValue())
3141 if (hiddenSeqs == null)
3143 hiddenSeqs = new ArrayList<>();
3146 hiddenSeqs.add(tmpSeq);
3151 // Create the alignment object from the sequence set
3152 // ///////////////////////////////
3153 SequenceI[] orderedSeqs = tmpseqs
3154 .toArray(new SequenceI[tmpseqs.size()]);
3156 AlignmentI al = null;
3157 // so we must create or recover the dataset alignment before going further
3158 // ///////////////////////////////
3159 if (vamsasSet.getDatasetId() == null || vamsasSet.getDatasetId() == "")
3161 // older jalview projects do not have a dataset - so creat alignment and
3163 al = new Alignment(orderedSeqs);
3164 al.setDataset(null);
3168 boolean isdsal = jalviewModel.getViewport().isEmpty();
3171 // we are importing a dataset record, so
3172 // recover reference to an alignment already materialsed as dataset
3173 al = getDatasetFor(vamsasSet.getDatasetId());
3177 // materialse the alignment
3178 al = new Alignment(orderedSeqs);
3182 addDatasetRef(vamsasSet.getDatasetId(), al);
3185 // finally, verify all data in vamsasSet is actually present in al
3186 // passing on flag indicating if it is actually a stored dataset
3187 recoverDatasetFor(vamsasSet, al, isdsal);
3190 if (referenceseqForView != null)
3192 al.setSeqrep(referenceseqForView);
3194 // / Add the alignment properties
3195 for (int i = 0; i < vamsasSet.getSequenceSetProperties().size(); i++)
3197 SequenceSetProperties ssp = vamsasSet.getSequenceSetProperties()
3199 al.setProperty(ssp.getKey(), ssp.getValue());
3202 // ///////////////////////////////
3204 Hashtable pdbloaded = new Hashtable(); // TODO nothing writes to this??
3207 // load sequence features, database references and any associated PDB
3208 // structures for the alignment
3210 // prior to 2.10, this part would only be executed the first time a
3211 // sequence was encountered, but not afterwards.
3212 // now, for 2.10 projects, this is also done if the xml doc includes
3213 // dataset sequences not actually present in any particular view.
3215 for (int i = 0; i < vamsasSeqs.size(); i++)
3217 JSeq jseq = jseqs.get(i);
3218 if (jseq.getFeatures().size() > 0)
3220 List<Feature> features = jseq.getFeatures();
3221 for (int f = 0; f < features.size(); f++)
3223 Feature feat = features.get(f);
3224 SequenceFeature sf = new SequenceFeature(feat.getType(),
3225 feat.getDescription(), feat.getBegin(), feat.getEnd(),
3226 safeFloat(feat.getScore()), feat.getFeatureGroup());
3227 sf.setStatus(feat.getStatus());
3230 * load any feature attributes - include map-valued attributes
3232 Map<String, Map<String, String>> mapAttributes = new HashMap<>();
3233 for (int od = 0; od < feat.getOtherData().size(); od++)
3235 OtherData keyValue = feat.getOtherData().get(od);
3236 String attributeName = keyValue.getKey();
3237 String attributeValue = keyValue.getValue();
3238 if (attributeName.startsWith("LINK"))
3240 sf.addLink(attributeValue);
3244 String subAttribute = keyValue.getKey2();
3245 if (subAttribute == null)
3247 // simple string-valued attribute
3248 sf.setValue(attributeName, attributeValue);
3252 // attribute 'key' has sub-attribute 'key2'
3253 if (!mapAttributes.containsKey(attributeName))
3255 mapAttributes.put(attributeName, new HashMap<>());
3257 mapAttributes.get(attributeName).put(subAttribute,
3262 for (Entry<String, Map<String, String>> mapAttribute : mapAttributes
3265 sf.setValue(mapAttribute.getKey(), mapAttribute.getValue());
3268 // adds feature to datasequence's feature set (since Jalview 2.10)
3269 al.getSequenceAt(i).addSequenceFeature(sf);
3272 if (vamsasSeqs.get(i).getDBRef().size() > 0)
3274 // adds dbrefs to datasequence's set (since Jalview 2.10)
3276 al.getSequenceAt(i).getDatasetSequence() == null
3277 ? al.getSequenceAt(i)
3278 : al.getSequenceAt(i).getDatasetSequence(),
3281 if (jseq.getPdbids().size() > 0)
3283 List<Pdbids> ids = jseq.getPdbids();
3284 for (int p = 0; p < ids.size(); p++)
3286 Pdbids pdbid = ids.get(p);
3287 jalview.datamodel.PDBEntry entry = new jalview.datamodel.PDBEntry();
3288 entry.setId(pdbid.getId());
3289 if (pdbid.getType() != null)
3291 if (PDBEntry.Type.getType(pdbid.getType()) != null)
3293 entry.setType(PDBEntry.Type.getType(pdbid.getType()));
3297 entry.setType(PDBEntry.Type.FILE);
3300 // jprovider is null when executing 'New View'
3301 if (pdbid.getFile() != null && jprovider != null)
3303 if (!pdbloaded.containsKey(pdbid.getFile()))
3305 entry.setFile(loadPDBFile(jprovider, pdbid.getId(),
3310 entry.setFile(pdbloaded.get(pdbid.getId()).toString());
3314 if (pdbid.getPdbentryItem() != null)
3316 for (PdbentryItem item : pdbid.getPdbentryItem())
3318 for (Property pr : item.getProperty())
3320 entry.setProperty(pr.getName(), pr.getValue());
3325 for (Property prop : pdbid.getProperty())
3327 entry.setProperty(prop.getName(), prop.getValue());
3329 StructureSelectionManager
3330 .getStructureSelectionManager(Desktop.instance)
3331 .registerPDBEntry(entry);
3332 // adds PDBEntry to datasequence's set (since Jalview 2.10)
3333 if (al.getSequenceAt(i).getDatasetSequence() != null)
3335 al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
3339 al.getSequenceAt(i).addPDBId(entry);
3344 } // end !multipleview
3346 // ///////////////////////////////
3347 // LOAD SEQUENCE MAPPINGS
3349 if (vamsasSet.getAlcodonFrame().size() > 0)
3351 // TODO Potentially this should only be done once for all views of an
3353 List<AlcodonFrame> alc = vamsasSet.getAlcodonFrame();
3354 for (int i = 0; i < alc.size(); i++)
3356 AlignedCodonFrame cf = new AlignedCodonFrame();
3357 if (alc.get(i).getAlcodMap().size() > 0)
3359 List<AlcodMap> maps = alc.get(i).getAlcodMap();
3360 for (int m = 0; m < maps.size(); m++)
3362 AlcodMap map = maps.get(m);
3363 SequenceI dnaseq = seqRefIds.get(map.getDnasq());
3365 jalview.datamodel.Mapping mapping = null;
3366 // attach to dna sequence reference.
3367 if (map.getMapping() != null)
3369 mapping = addMapping(map.getMapping());
3370 if (dnaseq != null && mapping.getTo() != null)
3372 cf.addMap(dnaseq, mapping.getTo(), mapping.getMap());
3378 newAlcodMapRef(map.getDnasq(), cf, mapping));
3382 al.addCodonFrame(cf);
3387 // ////////////////////////////////
3389 List<JvAnnotRow> autoAlan = new ArrayList<>();
3392 * store any annotations which forward reference a group's ID
3394 Map<String, List<AlignmentAnnotation>> groupAnnotRefs = new Hashtable<>();
3396 if (vamsasSet.getAnnotation().size()/*Count()*/ > 0)
3398 List<Annotation> an = vamsasSet.getAnnotation();
3400 for (int i = 0; i < an.size(); i++)
3402 Annotation annotation = an.get(i);
3405 * test if annotation is automatically calculated for this view only
3407 boolean autoForView = false;
3408 if (annotation.getLabel().equals("Quality")
3409 || annotation.getLabel().equals("Conservation")
3410 || annotation.getLabel().equals("Consensus"))
3412 // Kludge for pre 2.5 projects which lacked the autocalculated flag
3414 // JAXB has no has() test; schema defaults value to false
3415 // if (!annotation.hasAutoCalculated())
3417 // annotation.setAutoCalculated(true);
3420 if (autoForView || annotation.isAutoCalculated())
3422 // remove ID - we don't recover annotation from other views for
3423 // view-specific annotation
3424 annotation.setId(null);
3427 // set visibility for other annotation in this view
3428 String annotationId = annotation.getId();
3429 if (annotationId != null && annotationIds.containsKey(annotationId))
3431 AlignmentAnnotation jda = annotationIds.get(annotationId);
3432 // in principle Visible should always be true for annotation displayed
3433 // in multiple views
3434 if (annotation.isVisible() != null)
3436 jda.visible = annotation.isVisible();
3439 al.addAnnotation(jda);
3443 // Construct new annotation from model.
3444 List<AnnotationElement> ae = annotation.getAnnotationElement();
3445 jalview.datamodel.Annotation[] anot = null;
3446 java.awt.Color firstColour = null;
3448 if (!annotation.isScoreOnly())
3450 anot = new jalview.datamodel.Annotation[al.getWidth()];
3451 for (int aa = 0; aa < ae.size() && aa < anot.length; aa++)
3453 AnnotationElement annElement = ae.get(aa);
3454 anpos = annElement.getPosition();
3456 if (anpos >= anot.length)
3461 float value = safeFloat(annElement.getValue());
3462 anot[anpos] = new jalview.datamodel.Annotation(
3463 annElement.getDisplayCharacter(),
3464 annElement.getDescription(),
3465 (annElement.getSecondaryStructure() == null
3466 || annElement.getSecondaryStructure()
3470 .getSecondaryStructure()
3473 anot[anpos].colour = new Color(safeInt(annElement.getColour()));
3474 if (firstColour == null)
3476 firstColour = anot[anpos].colour;
3480 jalview.datamodel.AlignmentAnnotation jaa = null;
3482 if (annotation.isGraph())
3484 float llim = 0, hlim = 0;
3485 // if (autoForView || an[i].isAutoCalculated()) {
3488 jaa = new jalview.datamodel.AlignmentAnnotation(
3489 annotation.getLabel(), annotation.getDescription(), anot,
3490 llim, hlim, safeInt(annotation.getGraphType()));
3492 jaa.graphGroup = safeInt(annotation.getGraphGroup());
3493 jaa._linecolour = firstColour;
3494 if (annotation.getThresholdLine() != null)
3496 jaa.setThreshold(new jalview.datamodel.GraphLine(
3497 safeFloat(annotation.getThresholdLine().getValue()),
3498 annotation.getThresholdLine().getLabel(),
3499 new java.awt.Color(safeInt(
3500 annotation.getThresholdLine().getColour()))));
3502 if (autoForView || annotation.isAutoCalculated())
3504 // Hardwire the symbol display line to ensure that labels for
3505 // histograms are displayed
3511 jaa = new jalview.datamodel.AlignmentAnnotation(
3512 annotation.getLabel(), annotation.getDescription(), anot);
3513 jaa._linecolour = firstColour;
3515 // register new annotation
3516 if (annotation.getId() != null)
3518 annotationIds.put(annotation.getId(), jaa);
3519 jaa.annotationId = annotation.getId();
3521 // recover sequence association
3522 String sequenceRef = annotation.getSequenceRef();
3523 if (sequenceRef != null)
3525 // from 2.9 sequenceRef is to sequence id (JAL-1781)
3526 SequenceI sequence = seqRefIds.get(sequenceRef);
3527 if (sequence == null)
3529 // in pre-2.9 projects sequence ref is to sequence name
3530 sequence = al.findName(sequenceRef);
3532 if (sequence != null)
3534 jaa.createSequenceMapping(sequence, 1, true);
3535 sequence.addAlignmentAnnotation(jaa);
3538 // and make a note of any group association
3539 if (annotation.getGroupRef() != null
3540 && annotation.getGroupRef().length() > 0)
3542 List<jalview.datamodel.AlignmentAnnotation> aal = groupAnnotRefs
3543 .get(annotation.getGroupRef());
3546 aal = new ArrayList<>();
3547 groupAnnotRefs.put(annotation.getGroupRef(), aal);
3552 if (annotation.getScore() != null)
3554 jaa.setScore(annotation.getScore().doubleValue());
3556 if (annotation.isVisible() != null)
3558 jaa.visible = annotation.isVisible().booleanValue();
3561 if (annotation.isCentreColLabels() != null)
3563 jaa.centreColLabels = annotation.isCentreColLabels()
3567 if (annotation.isScaleColLabels() != null)
3569 jaa.scaleColLabel = annotation.isScaleColLabels().booleanValue();
3571 if (annotation.isAutoCalculated())
3573 // newer files have an 'autoCalculated' flag and store calculation
3574 // state in viewport properties
3575 jaa.autoCalculated = true; // means annotation will be marked for
3576 // update at end of load.
3578 if (annotation.getGraphHeight() != null)
3580 jaa.graphHeight = annotation.getGraphHeight().intValue();
3582 jaa.belowAlignment = annotation.isBelowAlignment();
3583 jaa.setCalcId(annotation.getCalcId());
3584 if (annotation.getProperty().size() > 0)
3586 for (Annotation.Property prop : annotation
3589 jaa.setProperty(prop.getName(), prop.getValue());
3592 if (jaa.autoCalculated)
3594 autoAlan.add(new JvAnnotRow(i, jaa));
3597 // if (!autoForView)
3599 // add autocalculated group annotation and any user created annotation
3601 al.addAnnotation(jaa);
3605 // ///////////////////////
3607 // Create alignment markup and styles for this view
3608 if (jalviewModel.getJGroup().size() > 0)
3610 List<JGroup> groups = jalviewModel.getJGroup();
3611 boolean addAnnotSchemeGroup = false;
3612 for (int i = 0; i < groups.size(); i++)
3614 JGroup jGroup = groups.get(i);
3615 ColourSchemeI cs = null;
3616 if (jGroup.getColour() != null)
3618 if (jGroup.getColour().startsWith("ucs"))
3620 cs = getUserColourScheme(jalviewModel, jGroup.getColour());
3622 else if (jGroup.getColour().equals("AnnotationColourGradient")
3623 && jGroup.getAnnotationColours() != null)
3625 addAnnotSchemeGroup = true;
3629 cs = ColourSchemeProperty.getColourScheme(al,
3630 jGroup.getColour());
3633 int pidThreshold = safeInt(jGroup.getPidThreshold());
3635 Vector<SequenceI> seqs = new Vector<>();
3637 for (int s = 0; s < jGroup.getSeq().size(); s++)
3639 String seqId = jGroup.getSeq().get(s);
3640 SequenceI ts = seqRefIds.get(seqId);
3644 seqs.addElement(ts);
3648 if (seqs.size() < 1)
3653 SequenceGroup sg = new SequenceGroup(seqs, jGroup.getName(), cs,
3654 safeBoolean(jGroup.isDisplayBoxes()),
3655 safeBoolean(jGroup.isDisplayText()),
3656 safeBoolean(jGroup.isColourText()),
3657 safeInt(jGroup.getStart()), safeInt(jGroup.getEnd()));
3658 sg.getGroupColourScheme().setThreshold(pidThreshold, true);
3659 sg.getGroupColourScheme()
3660 .setConservationInc(safeInt(jGroup.getConsThreshold()));
3661 sg.setOutlineColour(new Color(safeInt(jGroup.getOutlineColour())));
3663 sg.textColour = new Color(safeInt(jGroup.getTextCol1()));
3664 sg.textColour2 = new Color(safeInt(jGroup.getTextCol2()));
3665 sg.setShowNonconserved(safeBoolean(jGroup.isShowUnconserved()));
3666 sg.thresholdTextColour = safeInt(jGroup.getTextColThreshold());
3667 // attributes with a default in the schema are never null
3668 sg.setShowConsensusHistogram(jGroup.isShowConsensusHistogram());
3669 sg.setshowSequenceLogo(jGroup.isShowSequenceLogo());
3670 sg.setNormaliseSequenceLogo(jGroup.isNormaliseSequenceLogo());
3671 sg.setIgnoreGapsConsensus(jGroup.isIgnoreGapsinConsensus());
3672 if (jGroup.getConsThreshold() != null
3673 && jGroup.getConsThreshold().intValue() != 0)
3675 Conservation c = new Conservation("All", sg.getSequences(null), 0,
3678 c.verdict(false, 25);
3679 sg.cs.setConservation(c);
3682 if (jGroup.getId() != null && groupAnnotRefs.size() > 0)
3684 // re-instate unique group/annotation row reference
3685 List<AlignmentAnnotation> jaal = groupAnnotRefs
3686 .get(jGroup.getId());
3689 for (AlignmentAnnotation jaa : jaal)
3692 if (jaa.autoCalculated)
3694 // match up and try to set group autocalc alignment row for this
3696 if (jaa.label.startsWith("Consensus for "))
3698 sg.setConsensus(jaa);
3700 // match up and try to set group autocalc alignment row for this
3702 if (jaa.label.startsWith("Conservation for "))
3704 sg.setConservationRow(jaa);
3711 if (addAnnotSchemeGroup)
3713 // reconstruct the annotation colourscheme
3714 sg.setColourScheme(constructAnnotationColour(
3715 jGroup.getAnnotationColours(), null, al, jalviewModel, false));
3721 // only dataset in this model, so just return.
3724 // ///////////////////////////////
3727 // If we just load in the same jar file again, the sequenceSetId
3728 // will be the same, and we end up with multiple references
3729 // to the same sequenceSet. We must modify this id on load
3730 // so that each load of the file gives a unique id
3731 String uniqueSeqSetId = view.getSequenceSetId() + uniqueSetSuffix;
3732 String viewId = (view.getId() == null ? null
3733 : view.getId() + uniqueSetSuffix);
3734 AlignFrame af = null;
3735 AlignViewport av = null;
3736 // now check to see if we really need to create a new viewport.
3737 if (multipleView && viewportsAdded.size() == 0)
3739 // We recovered an alignment for which a viewport already exists.
3740 // TODO: fix up any settings necessary for overlaying stored state onto
3741 // state recovered from another document. (may not be necessary).
3742 // we may need a binding from a viewport in memory to one recovered from
3744 // and then recover its containing af to allow the settings to be applied.
3745 // TODO: fix for vamsas demo
3747 "About to recover a viewport for existing alignment: Sequence set ID is "
3749 Object seqsetobj = retrieveExistingObj(uniqueSeqSetId);
3750 if (seqsetobj != null)
3752 if (seqsetobj instanceof String)
3754 uniqueSeqSetId = (String) seqsetobj;
3756 "Recovered extant sequence set ID mapping for ID : New Sequence set ID is "
3762 "Warning : Collision between sequence set ID string and existing jalview object mapping.");
3768 * indicate that annotation colours are applied across all groups (pre
3769 * Jalview 2.8.1 behaviour)
3771 boolean doGroupAnnColour = Jalview2XML.isVersionStringLaterThan("2.8.1",
3772 jalviewModel.getVersion());
3774 AlignmentPanel ap = null;
3775 boolean isnewview = true;
3778 // Check to see if this alignment already has a view id == viewId
3779 jalview.gui.AlignmentPanel views[] = Desktop
3780 .getAlignmentPanels(uniqueSeqSetId);
3781 if (views != null && views.length > 0)
3783 for (int v = 0; v < views.length; v++)
3785 if (views[v].av.getViewId().equalsIgnoreCase(viewId))
3787 // recover the existing alignpanel, alignframe, viewport
3788 af = views[v].alignFrame;
3791 // TODO: could even skip resetting view settings if we don't want to
3792 // change the local settings from other jalview processes
3801 af = loadViewport(file, jseqs, hiddenSeqs, al, jalviewModel, view,
3802 uniqueSeqSetId, viewId, autoAlan);
3803 av = af.getViewport();
3808 * Load any trees, PDB structures and viewers
3810 * Not done if flag is false (when this method is used for New View)
3812 if (loadTreesAndStructures)
3814 loadTrees(jalviewModel, view, af, av, ap);
3815 loadPDBStructures(jprovider, jseqs, af, ap);
3816 loadRnaViewers(jprovider, jseqs, ap);
3818 // and finally return.
3823 * Instantiate and link any saved RNA (Varna) viewers. The state of the Varna
3824 * panel is restored from separate jar entries, two (gapped and trimmed) per
3825 * sequence and secondary structure.
3827 * Currently each viewer shows just one sequence and structure (gapped and
3828 * trimmed), however this method is designed to support multiple sequences or
3829 * structures in viewers if wanted in future.
3835 private void loadRnaViewers(jarInputStreamProvider jprovider,
3836 List<JSeq> jseqs, AlignmentPanel ap)
3839 * scan the sequences for references to viewers; create each one the first
3840 * time it is referenced, add Rna models to existing viewers
3842 for (JSeq jseq : jseqs)
3844 for (int i = 0; i < jseq.getRnaViewer().size(); i++)
3846 RnaViewer viewer = jseq.getRnaViewer().get(i);
3847 AppVarna appVarna = findOrCreateVarnaViewer(viewer, uniqueSetSuffix,
3850 for (int j = 0; j < viewer.getSecondaryStructure().size(); j++)
3852 SecondaryStructure ss = viewer.getSecondaryStructure().get(j);
3853 SequenceI seq = seqRefIds.get(jseq.getId());
3854 AlignmentAnnotation ann = this.annotationIds
3855 .get(ss.getAnnotationId());
3858 * add the structure to the Varna display (with session state copied
3859 * from the jar to a temporary file)
3861 boolean gapped = safeBoolean(ss.isGapped());
3862 String rnaTitle = ss.getTitle();
3863 String sessionState = ss.getViewerState();
3864 String tempStateFile = copyJarEntry(jprovider, sessionState,
3866 RnaModel rna = new RnaModel(rnaTitle, ann, seq, null, gapped);
3867 appVarna.addModelSession(rna, rnaTitle, tempStateFile);
3869 appVarna.setInitialSelection(safeInt(viewer.getSelectedRna()));
3875 * Locate and return an already instantiated matching AppVarna, or create one
3879 * @param viewIdSuffix
3883 protected AppVarna findOrCreateVarnaViewer(RnaViewer viewer,
3884 String viewIdSuffix, AlignmentPanel ap)
3887 * on each load a suffix is appended to the saved viewId, to avoid conflicts
3888 * if load is repeated
3890 String postLoadId = viewer.getViewId() + viewIdSuffix;
3891 for (JInternalFrame frame : getAllFrames())
3893 if (frame instanceof AppVarna)
3895 AppVarna varna = (AppVarna) frame;
3896 if (postLoadId.equals(varna.getViewId()))
3898 // this viewer is already instantiated
3899 // could in future here add ap as another 'parent' of the
3900 // AppVarna window; currently just 1-to-many
3907 * viewer not found - make it
3909 RnaViewerModel model = new RnaViewerModel(postLoadId, viewer.getTitle(),
3910 safeInt(viewer.getXpos()), safeInt(viewer.getYpos()),
3911 safeInt(viewer.getWidth()), safeInt(viewer.getHeight()),
3912 safeInt(viewer.getDividerLocation()));
3913 AppVarna varna = new AppVarna(model, ap);
3919 * Load any saved trees
3927 protected void loadTrees(JalviewModel jm, Viewport view,
3928 AlignFrame af, AlignViewport av, AlignmentPanel ap)
3930 // TODO result of automated refactoring - are all these parameters needed?
3933 for (int t = 0; t < jm.getTree().size(); t++)
3936 Tree tree = jm.getTree().get(t);
3938 TreePanel tp = (TreePanel) retrieveExistingObj(tree.getId());
3941 tp = af.showNewickTree(new NewickFile(tree.getNewick()),
3942 tree.getTitle(), safeInt(tree.getWidth()),
3943 safeInt(tree.getHeight()), safeInt(tree.getXpos()),
3944 safeInt(tree.getYpos()));
3945 if (tree.getId() != null)
3947 // perhaps bind the tree id to something ?
3952 // update local tree attributes ?
3953 // TODO: should check if tp has been manipulated by user - if so its
3954 // settings shouldn't be modified
3955 tp.setTitle(tree.getTitle());
3956 tp.setBounds(new Rectangle(safeInt(tree.getXpos()),
3957 safeInt(tree.getYpos()), safeInt(tree.getWidth()),
3958 safeInt(tree.getHeight())));
3959 tp.setViewport(av); // af.viewport;
3960 // TODO: verify 'associate with all views' works still
3961 tp.getTreeCanvas().setViewport(av); // af.viewport;
3962 tp.getTreeCanvas().setAssociatedPanel(ap); // af.alignPanel;
3967 warn("There was a problem recovering stored Newick tree: \n"
3968 + tree.getNewick());
3972 tp.fitToWindow.setState(safeBoolean(tree.isFitToWindow()));
3973 tp.fitToWindow_actionPerformed(null);
3975 if (tree.getFontName() != null)
3978 new Font(tree.getFontName(), safeInt(tree.getFontStyle()),
3979 safeInt(tree.getFontSize())));
3984 new Font(view.getFontName(), safeInt(view.getFontStyle()),
3985 safeInt(view.getFontSize())));
3988 tp.showPlaceholders(safeBoolean(tree.isMarkUnlinked()));
3989 tp.showBootstrap(safeBoolean(tree.isShowBootstrap()));
3990 tp.showDistances(safeBoolean(tree.isShowDistances()));
3992 tp.getTreeCanvas().setThreshold(safeFloat(tree.getThreshold()));
3994 if (safeBoolean(tree.isCurrentTree()))
3996 af.getViewport().setCurrentTree(tp.getTree());
4000 } catch (Exception ex)
4002 ex.printStackTrace();
4007 * Load and link any saved structure viewers.
4014 protected void loadPDBStructures(jarInputStreamProvider jprovider,
4015 List<JSeq> jseqs, AlignFrame af, AlignmentPanel ap)
4018 * Run through all PDB ids on the alignment, and collect mappings between
4019 * distinct view ids and all sequences referring to that view.
4021 Map<String, StructureViewerModel> structureViewers = new LinkedHashMap<>();
4023 for (int i = 0; i < jseqs.size(); i++)
4025 JSeq jseq = jseqs.get(i);
4026 if (jseq.getPdbids().size() > 0)
4028 List<Pdbids> ids = jseq.getPdbids();
4029 for (int p = 0; p < ids.size(); p++)
4031 Pdbids pdbid = ids.get(p);
4032 final int structureStateCount = pdbid.getStructureState().size();
4033 for (int s = 0; s < structureStateCount; s++)
4035 // check to see if we haven't already created this structure view
4036 final StructureState structureState = pdbid
4037 .getStructureState().get(s);
4038 String sviewid = (structureState.getViewId() == null) ? null
4039 : structureState.getViewId() + uniqueSetSuffix;
4040 jalview.datamodel.PDBEntry jpdb = new jalview.datamodel.PDBEntry();
4041 // Originally : pdbid.getFile()
4042 // : TODO: verify external PDB file recovery still works in normal
4043 // jalview project load
4045 loadPDBFile(jprovider, pdbid.getId(), pdbid.getFile()));
4046 jpdb.setId(pdbid.getId());
4048 int x = safeInt(structureState.getXpos());
4049 int y = safeInt(structureState.getYpos());
4050 int width = safeInt(structureState.getWidth());
4051 int height = safeInt(structureState.getHeight());
4053 // Probably don't need to do this anymore...
4054 // Desktop.desktop.getComponentAt(x, y);
4055 // TODO: NOW: check that this recovers the PDB file correctly.
4056 String pdbFile = loadPDBFile(jprovider, pdbid.getId(),
4058 jalview.datamodel.SequenceI seq = seqRefIds
4059 .get(jseq.getId() + "");
4060 if (sviewid == null)
4062 sviewid = "_jalview_pre2_4_" + x + "," + y + "," + width + ","
4065 if (!structureViewers.containsKey(sviewid))
4067 structureViewers.put(sviewid,
4068 new StructureViewerModel(x, y, width, height, false,
4069 false, true, structureState.getViewId(),
4070 structureState.getType()));
4071 // Legacy pre-2.7 conversion JAL-823 :
4072 // do not assume any view has to be linked for colour by
4076 // assemble String[] { pdb files }, String[] { id for each
4077 // file }, orig_fileloc, SequenceI[][] {{ seqs_file 1 }, {
4078 // seqs_file 2}, boolean[] {
4079 // linkAlignPanel,superposeWithAlignpanel}} from hash
4080 StructureViewerModel jmoldat = structureViewers.get(sviewid);
4081 jmoldat.setAlignWithPanel(jmoldat.isAlignWithPanel()
4082 || structureState.isAlignwithAlignPanel());
4085 * Default colour by linked panel to false if not specified (e.g.
4086 * for pre-2.7 projects)
4088 boolean colourWithAlignPanel = jmoldat.isColourWithAlignPanel();
4089 colourWithAlignPanel |= structureState.isColourwithAlignPanel();
4090 jmoldat.setColourWithAlignPanel(colourWithAlignPanel);
4093 * Default colour by viewer to true if not specified (e.g. for
4096 boolean colourByViewer = jmoldat.isColourByViewer();
4097 colourByViewer &= structureState.isColourByJmol();
4098 jmoldat.setColourByViewer(colourByViewer);
4100 if (jmoldat.getStateData().length() < structureState
4101 .getValue()/*Content()*/.length())
4103 jmoldat.setStateData(structureState.getValue());// Content());
4105 if (pdbid.getFile() != null)
4107 File mapkey = new File(pdbid.getFile());
4108 StructureData seqstrmaps = jmoldat.getFileData().get(mapkey);
4109 if (seqstrmaps == null)
4111 jmoldat.getFileData().put(mapkey,
4112 seqstrmaps = jmoldat.new StructureData(pdbFile,
4115 if (!seqstrmaps.getSeqList().contains(seq))
4117 seqstrmaps.getSeqList().add(seq);
4123 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");
4130 // Instantiate the associated structure views
4131 for (Entry<String, StructureViewerModel> entry : structureViewers
4136 createOrLinkStructureViewer(entry, af, ap, jprovider);
4137 } catch (Exception e)
4140 "Error loading structure viewer: " + e.getMessage());
4141 // failed - try the next one
4153 protected void createOrLinkStructureViewer(
4154 Entry<String, StructureViewerModel> viewerData, AlignFrame af,
4155 AlignmentPanel ap, jarInputStreamProvider jprovider)
4157 final StructureViewerModel stateData = viewerData.getValue();
4160 * Search for any viewer windows already open from other alignment views
4161 * that exactly match the stored structure state
4163 StructureViewerBase comp = findMatchingViewer(viewerData);
4167 linkStructureViewer(ap, comp, stateData);
4172 * From 2.9: stateData.type contains JMOL or CHIMERA, data is in jar entry
4173 * "viewer_"+stateData.viewId
4175 if (ViewerType.CHIMERA.toString().equals(stateData.getType()))
4177 createChimeraViewer(viewerData, af, jprovider);
4182 * else Jmol (if pre-2.9, stateData contains JMOL state string)
4184 createJmolViewer(viewerData, af, jprovider);
4189 * Create a new Chimera viewer.
4195 protected void createChimeraViewer(
4196 Entry<String, StructureViewerModel> viewerData, AlignFrame af,
4197 jarInputStreamProvider jprovider)
4199 StructureViewerModel data = viewerData.getValue();
4200 String chimeraSessionFile = data.getStateData();
4203 * Copy Chimera session from jar entry "viewer_"+viewId to a temporary file
4205 * NB this is the 'saved' viewId as in the project file XML, _not_ the
4206 * 'uniquified' sviewid used to reconstruct the viewer here
4208 String viewerJarEntryName = getViewerJarEntryName(data.getViewId());
4209 chimeraSessionFile = copyJarEntry(jprovider, viewerJarEntryName,
4212 Set<Entry<File, StructureData>> fileData = data.getFileData()
4214 List<PDBEntry> pdbs = new ArrayList<>();
4215 List<SequenceI[]> allseqs = new ArrayList<>();
4216 for (Entry<File, StructureData> pdb : fileData)
4218 String filePath = pdb.getValue().getFilePath();
4219 String pdbId = pdb.getValue().getPdbId();
4220 // pdbs.add(new PDBEntry(filePath, pdbId));
4221 pdbs.add(new PDBEntry(pdbId, null, PDBEntry.Type.PDB, filePath));
4222 final List<SequenceI> seqList = pdb.getValue().getSeqList();
4223 SequenceI[] seqs = seqList.toArray(new SequenceI[seqList.size()]);
4227 boolean colourByChimera = data.isColourByViewer();
4228 boolean colourBySequence = data.isColourWithAlignPanel();
4230 // TODO use StructureViewer as a factory here, see JAL-1761
4231 final PDBEntry[] pdbArray = pdbs.toArray(new PDBEntry[pdbs.size()]);
4232 final SequenceI[][] seqsArray = allseqs
4233 .toArray(new SequenceI[allseqs.size()][]);
4234 String newViewId = viewerData.getKey();
4236 ChimeraViewFrame cvf = new ChimeraViewFrame(chimeraSessionFile,
4237 af.alignPanel, pdbArray, seqsArray, colourByChimera,
4238 colourBySequence, newViewId);
4239 cvf.setSize(data.getWidth(), data.getHeight());
4240 cvf.setLocation(data.getX(), data.getY());
4244 * Create a new Jmol window. First parse the Jmol state to translate filenames
4245 * loaded into the view, and record the order in which files are shown in the
4246 * Jmol view, so we can add the sequence mappings in same order.
4252 protected void createJmolViewer(
4253 final Entry<String, StructureViewerModel> viewerData,
4254 AlignFrame af, jarInputStreamProvider jprovider)
4256 final StructureViewerModel svattrib = viewerData.getValue();
4257 String state = svattrib.getStateData();
4260 * Pre-2.9: state element value is the Jmol state string
4262 * 2.9+: @type is "JMOL", state data is in a Jar file member named "viewer_"
4265 if (ViewerType.JMOL.toString().equals(svattrib.getType()))
4267 state = readJarEntry(jprovider,
4268 getViewerJarEntryName(svattrib.getViewId()));
4271 List<String> pdbfilenames = new ArrayList<>();
4272 List<SequenceI[]> seqmaps = new ArrayList<>();
4273 List<String> pdbids = new ArrayList<>();
4274 StringBuilder newFileLoc = new StringBuilder(64);
4275 int cp = 0, ncp, ecp;
4276 Map<File, StructureData> oldFiles = svattrib.getFileData();
4277 while ((ncp = state.indexOf("load ", cp)) > -1)
4281 // look for next filename in load statement
4282 newFileLoc.append(state.substring(cp,
4283 ncp = (state.indexOf("\"", ncp + 1) + 1)));
4284 String oldfilenam = state.substring(ncp,
4285 ecp = state.indexOf("\"", ncp));
4286 // recover the new mapping data for this old filename
4287 // have to normalize filename - since Jmol and jalview do
4289 // translation differently.
4290 StructureData filedat = oldFiles.get(new File(oldfilenam));
4291 if (filedat == null)
4293 String reformatedOldFilename = oldfilenam.replaceAll("/", "\\\\");
4294 filedat = oldFiles.get(new File(reformatedOldFilename));
4296 newFileLoc.append(Platform.escapeString(filedat.getFilePath()));
4297 pdbfilenames.add(filedat.getFilePath());
4298 pdbids.add(filedat.getPdbId());
4299 seqmaps.add(filedat.getSeqList().toArray(new SequenceI[0]));
4300 newFileLoc.append("\"");
4301 cp = ecp + 1; // advance beyond last \" and set cursor so we can
4302 // look for next file statement.
4303 } while ((ncp = state.indexOf("/*file*/", cp)) > -1);
4307 // just append rest of state
4308 newFileLoc.append(state.substring(cp));
4312 System.err.print("Ignoring incomplete Jmol state for PDB ids: ");
4313 newFileLoc = new StringBuilder(state);
4314 newFileLoc.append("; load append ");
4315 for (File id : oldFiles.keySet())
4317 // add this and any other pdb files that should be present in
4319 StructureData filedat = oldFiles.get(id);
4320 newFileLoc.append(filedat.getFilePath());
4321 pdbfilenames.add(filedat.getFilePath());
4322 pdbids.add(filedat.getPdbId());
4323 seqmaps.add(filedat.getSeqList().toArray(new SequenceI[0]));
4324 newFileLoc.append(" \"");
4325 newFileLoc.append(filedat.getFilePath());
4326 newFileLoc.append("\"");
4329 newFileLoc.append(";");
4332 if (newFileLoc.length() == 0)
4336 int histbug = newFileLoc.indexOf("history = ");
4340 * change "history = [true|false];" to "history = [1|0];"
4343 int diff = histbug == -1 ? -1 : newFileLoc.indexOf(";", histbug);
4344 String val = (diff == -1) ? null
4345 : newFileLoc.substring(histbug, diff);
4346 if (val != null && val.length() >= 4)
4348 if (val.contains("e")) // eh? what can it be?
4350 if (val.trim().equals("true"))
4358 newFileLoc.replace(histbug, diff, val);
4363 final String[] pdbf = pdbfilenames
4364 .toArray(new String[pdbfilenames.size()]);
4365 final String[] id = pdbids.toArray(new String[pdbids.size()]);
4366 final SequenceI[][] sq = seqmaps
4367 .toArray(new SequenceI[seqmaps.size()][]);
4368 final String fileloc = newFileLoc.toString();
4369 final String sviewid = viewerData.getKey();
4370 final AlignFrame alf = af;
4371 final Rectangle rect = new Rectangle(svattrib.getX(), svattrib.getY(),
4372 svattrib.getWidth(), svattrib.getHeight());
4375 javax.swing.SwingUtilities.invokeAndWait(new Runnable()
4380 JalviewStructureDisplayI sview = null;
4383 sview = new StructureViewer(
4384 alf.alignPanel.getStructureSelectionManager())
4385 .createView(StructureViewer.ViewerType.JMOL,
4386 pdbf, id, sq, alf.alignPanel, svattrib,
4387 fileloc, rect, sviewid);
4388 addNewStructureViewer(sview);
4389 } catch (OutOfMemoryError ex)
4391 new OOMWarning("restoring structure view for PDB id " + id,
4392 (OutOfMemoryError) ex.getCause());
4393 if (sview != null && sview.isVisible())
4395 sview.closeViewer(false);
4396 sview.setVisible(false);
4402 } catch (InvocationTargetException ex)
4404 warn("Unexpected error when opening Jmol view.", ex);
4406 } catch (InterruptedException e)
4408 // e.printStackTrace();
4414 * Generates a name for the entry in the project jar file to hold state
4415 * information for a structure viewer
4420 protected String getViewerJarEntryName(String viewId)
4422 return VIEWER_PREFIX + viewId;
4426 * Returns any open frame that matches given structure viewer data. The match
4427 * is based on the unique viewId, or (for older project versions) the frame's
4433 protected StructureViewerBase findMatchingViewer(
4434 Entry<String, StructureViewerModel> viewerData)
4436 final String sviewid = viewerData.getKey();
4437 final StructureViewerModel svattrib = viewerData.getValue();
4438 StructureViewerBase comp = null;
4439 JInternalFrame[] frames = getAllFrames();
4440 for (JInternalFrame frame : frames)
4442 if (frame instanceof StructureViewerBase)
4445 * Post jalview 2.4 schema includes structure view id
4447 if (sviewid != null && ((StructureViewerBase) frame).getViewId()
4450 comp = (StructureViewerBase) frame;
4451 break; // break added in 2.9
4454 * Otherwise test for matching position and size of viewer frame
4456 else if (frame.getX() == svattrib.getX()
4457 && frame.getY() == svattrib.getY()
4458 && frame.getHeight() == svattrib.getHeight()
4459 && frame.getWidth() == svattrib.getWidth())
4461 comp = (StructureViewerBase) frame;
4462 // no break in faint hope of an exact match on viewId
4470 * Link an AlignmentPanel to an existing structure viewer.
4475 * @param useinViewerSuperpos
4476 * @param usetoColourbyseq
4477 * @param viewerColouring
4479 protected void linkStructureViewer(AlignmentPanel ap,
4480 StructureViewerBase viewer, StructureViewerModel stateData)
4482 // NOTE: if the jalview project is part of a shared session then
4483 // view synchronization should/could be done here.
4485 final boolean useinViewerSuperpos = stateData.isAlignWithPanel();
4486 final boolean usetoColourbyseq = stateData.isColourWithAlignPanel();
4487 final boolean viewerColouring = stateData.isColourByViewer();
4488 Map<File, StructureData> oldFiles = stateData.getFileData();
4491 * Add mapping for sequences in this view to an already open viewer
4493 final AAStructureBindingModel binding = viewer.getBinding();
4494 for (File id : oldFiles.keySet())
4496 // add this and any other pdb files that should be present in the
4498 StructureData filedat = oldFiles.get(id);
4499 String pdbFile = filedat.getFilePath();
4500 SequenceI[] seq = filedat.getSeqList().toArray(new SequenceI[0]);
4501 binding.getSsm().setMapping(seq, null, pdbFile, DataSourceType.FILE,
4503 binding.addSequenceForStructFile(pdbFile, seq);
4505 // and add the AlignmentPanel's reference to the view panel
4506 viewer.addAlignmentPanel(ap);
4507 if (useinViewerSuperpos)
4509 viewer.useAlignmentPanelForSuperposition(ap);
4513 viewer.excludeAlignmentPanelForSuperposition(ap);
4515 if (usetoColourbyseq)
4517 viewer.useAlignmentPanelForColourbyseq(ap, !viewerColouring);
4521 viewer.excludeAlignmentPanelForColourbyseq(ap);
4526 * Get all frames within the Desktop.
4530 protected JInternalFrame[] getAllFrames()
4532 JInternalFrame[] frames = null;
4533 // TODO is this necessary - is it safe - risk of hanging?
4538 frames = Desktop.desktop.getAllFrames();
4539 } catch (ArrayIndexOutOfBoundsException e)
4541 // occasional No such child exceptions are thrown here...
4545 } catch (InterruptedException f)
4549 } while (frames == null);
4554 * Answers true if 'version' is equal to or later than 'supported', where each
4555 * is formatted as major/minor versions like "2.8.3" or "2.3.4b1" for bugfix
4556 * changes. Development and test values for 'version' are leniently treated
4560 * - minimum version we are comparing against
4562 * - version of data being processsed
4565 public static boolean isVersionStringLaterThan(String supported,
4568 if (supported == null || version == null
4569 || version.equalsIgnoreCase("DEVELOPMENT BUILD")
4570 || version.equalsIgnoreCase("Test")
4571 || version.equalsIgnoreCase("AUTOMATED BUILD"))
4573 System.err.println("Assuming project file with "
4574 + (version == null ? "null" : version)
4575 + " is compatible with Jalview version " + supported);
4580 return StringUtils.compareVersions(version, supported, "b") >= 0;
4584 Vector<JalviewStructureDisplayI> newStructureViewers = null;
4586 protected void addNewStructureViewer(JalviewStructureDisplayI sview)
4588 if (newStructureViewers != null)
4590 sview.getBinding().setFinishedLoadingFromArchive(false);
4591 newStructureViewers.add(sview);
4595 protected void setLoadingFinishedForNewStructureViewers()
4597 if (newStructureViewers != null)
4599 for (JalviewStructureDisplayI sview : newStructureViewers)
4601 sview.getBinding().setFinishedLoadingFromArchive(true);
4603 newStructureViewers.clear();
4604 newStructureViewers = null;
4608 AlignFrame loadViewport(String file, List<JSeq> JSEQ,
4609 List<SequenceI> hiddenSeqs, AlignmentI al,
4610 JalviewModel jm, Viewport view, String uniqueSeqSetId,
4611 String viewId, List<JvAnnotRow> autoAlan)
4613 AlignFrame af = null;
4614 af = new AlignFrame(al, safeInt(view.getWidth()),
4615 safeInt(view.getHeight()), uniqueSeqSetId, viewId);
4617 af.setFileName(file, FileFormat.Jalview);
4619 final AlignViewport viewport = af.getViewport();
4620 for (int i = 0; i < JSEQ.size(); i++)
4622 int colour = safeInt(JSEQ.get(i).getColour());
4623 viewport.setSequenceColour(viewport.getAlignment().getSequenceAt(i),
4629 viewport.setColourByReferenceSeq(true);
4630 viewport.setDisplayReferenceSeq(true);
4633 viewport.setGatherViewsHere(safeBoolean(view.isGatheredViews()));
4635 if (view.getSequenceSetId() != null)
4637 AlignmentViewport av = viewportsAdded.get(uniqueSeqSetId);
4639 viewport.setSequenceSetId(uniqueSeqSetId);
4642 // propagate shared settings to this new view
4643 viewport.setHistoryList(av.getHistoryList());
4644 viewport.setRedoList(av.getRedoList());
4648 viewportsAdded.put(uniqueSeqSetId, viewport);
4650 // TODO: check if this method can be called repeatedly without
4651 // side-effects if alignpanel already registered.
4652 PaintRefresher.Register(af.alignPanel, uniqueSeqSetId);
4654 // apply Hidden regions to view.
4655 if (hiddenSeqs != null)
4657 for (int s = 0; s < JSEQ.size(); s++)
4659 SequenceGroup hidden = new SequenceGroup();
4660 boolean isRepresentative = false;
4661 for (int r = 0; r < JSEQ.get(s).getHiddenSequences().size(); r++)
4663 isRepresentative = true;
4664 SequenceI sequenceToHide = al
4665 .getSequenceAt(JSEQ.get(s).getHiddenSequences().get(r));
4666 hidden.addSequence(sequenceToHide, false);
4667 // remove from hiddenSeqs list so we don't try to hide it twice
4668 hiddenSeqs.remove(sequenceToHide);
4670 if (isRepresentative)
4672 SequenceI representativeSequence = al.getSequenceAt(s);
4673 hidden.addSequence(representativeSequence, false);
4674 viewport.hideRepSequences(representativeSequence, hidden);
4678 SequenceI[] hseqs = hiddenSeqs
4679 .toArray(new SequenceI[hiddenSeqs.size()]);
4680 viewport.hideSequence(hseqs);
4683 // recover view properties and display parameters
4685 viewport.setShowAnnotation(safeBoolean(view.isShowAnnotation()));
4686 viewport.setAbovePIDThreshold(safeBoolean(view.isPidSelected()));
4687 final int pidThreshold = safeInt(view.getPidThreshold());
4688 viewport.setThreshold(pidThreshold);
4690 viewport.setColourText(safeBoolean(view.isShowColourText()));
4693 .setConservationSelected(
4694 safeBoolean(view.isConservationSelected()));
4695 viewport.setIncrement(safeInt(view.getConsThreshold()));
4696 viewport.setShowJVSuffix(safeBoolean(view.isShowFullId()));
4697 viewport.setRightAlignIds(safeBoolean(view.isRightAlignIds()));
4698 viewport.setFont(new Font(view.getFontName(),
4699 safeInt(view.getFontStyle()), safeInt(view.getFontSize())),
4701 ViewStyleI vs = viewport.getViewStyle();
4702 vs.setScaleProteinAsCdna(view.isScaleProteinAsCdna());
4703 viewport.setViewStyle(vs);
4704 // TODO: allow custom charWidth/Heights to be restored by updating them
4705 // after setting font - which means set above to false
4706 viewport.setRenderGaps(safeBoolean(view.isRenderGaps()));
4707 viewport.setWrapAlignment(safeBoolean(view.isWrapAlignment()));
4708 viewport.setShowAnnotation(safeBoolean(view.isShowAnnotation()));
4710 viewport.setShowBoxes(safeBoolean(view.isShowBoxes()));
4712 viewport.setShowText(safeBoolean(view.isShowText()));
4714 viewport.setTextColour(new Color(safeInt(view.getTextCol1())));
4715 viewport.setTextColour2(new Color(safeInt(view.getTextCol2())));
4716 viewport.setThresholdTextColour(safeInt(view.getTextColThreshold()));
4717 viewport.setShowUnconserved(view.isShowUnconserved());
4718 viewport.getRanges().setStartRes(safeInt(view.getStartRes()));
4720 if (view.getViewName() != null)
4722 viewport.setViewName(view.getViewName());
4723 af.setInitialTabVisible();
4725 af.setBounds(safeInt(view.getXpos()), safeInt(view.getYpos()),
4726 safeInt(view.getWidth()), safeInt(view.getHeight()));
4727 // startSeq set in af.alignPanel.updateLayout below
4728 af.alignPanel.updateLayout();
4729 ColourSchemeI cs = null;
4730 // apply colourschemes
4731 if (view.getBgColour() != null)
4733 if (view.getBgColour().startsWith("ucs"))
4735 cs = getUserColourScheme(jm, view.getBgColour());
4737 else if (view.getBgColour().startsWith("Annotation"))
4739 AnnotationColourScheme viewAnnColour = view.getAnnotationColours();
4740 cs = constructAnnotationColour(viewAnnColour, af, al, jm, true);
4747 cs = ColourSchemeProperty.getColourScheme(al, view.getBgColour());
4751 viewport.setGlobalColourScheme(cs);
4752 viewport.getResidueShading().setThreshold(pidThreshold,
4753 view.isIgnoreGapsinConsensus());
4754 viewport.getResidueShading()
4755 .setConsensus(viewport.getSequenceConsensusHash());
4756 viewport.setColourAppliesToAllGroups(false);
4758 if (safeBoolean(view.isConservationSelected()) && cs != null)
4760 viewport.getResidueShading()
4761 .setConservationInc(safeInt(view.getConsThreshold()));
4764 af.changeColour(cs);
4766 viewport.setColourAppliesToAllGroups(true);
4769 .setShowSequenceFeatures(
4770 safeBoolean(view.isShowSequenceFeatures()));
4772 viewport.setCentreColumnLabels(view.isCentreColumnLabels());
4773 viewport.setIgnoreGapsConsensus(view.isIgnoreGapsinConsensus(), null);
4774 viewport.setFollowHighlight(view.isFollowHighlight());
4775 viewport.followSelection = view.isFollowSelection();
4776 viewport.setShowConsensusHistogram(view.isShowConsensusHistogram());
4777 viewport.setShowSequenceLogo(view.isShowSequenceLogo());
4778 viewport.setNormaliseSequenceLogo(view.isNormaliseSequenceLogo());
4779 viewport.setShowDBRefs(safeBoolean(view.isShowDbRefTooltip()));
4780 viewport.setShowNPFeats(safeBoolean(view.isShowNPfeatureTooltip()));
4781 viewport.setShowGroupConsensus(view.isShowGroupConsensus());
4782 viewport.setShowGroupConservation(view.isShowGroupConservation());
4784 // recover feature settings
4785 if (jm.getFeatureSettings() != null)
4787 FeatureRenderer fr = af.alignPanel.getSeqPanel().seqCanvas
4788 .getFeatureRenderer();
4789 FeaturesDisplayed fdi;
4790 viewport.setFeaturesDisplayed(fdi = new FeaturesDisplayed());
4791 String[] renderOrder = new String[jm.getFeatureSettings()
4792 .getSetting().size()];
4793 Map<String, FeatureColourI> featureColours = new Hashtable<>();
4794 Map<String, Float> featureOrder = new Hashtable<>();
4796 for (int fs = 0; fs < jm.getFeatureSettings()
4797 .getSetting().size(); fs++)
4799 Setting setting = jm.getFeatureSettings().getSetting().get(fs);
4800 String featureType = setting.getType();
4803 * restore feature filters (if any)
4805 jalview.xml.binding.jalview.FeatureMatcherSet filters = setting
4807 if (filters != null)
4809 FeatureMatcherSetI filter = Jalview2XML
4810 .parseFilter(featureType, filters);
4811 if (!filter.isEmpty())
4813 fr.setFeatureFilter(featureType, filter);
4818 * restore feature colour scheme
4820 Color maxColour = new Color(setting.getColour());
4821 if (setting.getMincolour() != null)
4824 * minColour is always set unless a simple colour
4825 * (including for colour by label though it doesn't use it)
4827 Color minColour = new Color(setting.getMincolour().intValue());
4828 Color noValueColour = minColour;
4829 NoValueColour noColour = setting.getNoValueColour();
4830 if (noColour == NoValueColour.NONE)
4832 noValueColour = null;
4834 else if (noColour == NoValueColour.MAX)
4836 noValueColour = maxColour;
4838 float min = safeFloat(safeFloat(setting.getMin()));
4839 float max = setting.getMax() == null ? 1f
4840 : setting.getMax().floatValue();
4841 FeatureColourI gc = new FeatureColour(minColour, maxColour,
4842 noValueColour, min, max);
4843 if (setting.getAttributeName().size() > 0)
4845 gc.setAttributeName(setting.getAttributeName().toArray(
4846 new String[setting.getAttributeName().size()]));
4848 if (setting.getThreshold() != null)
4850 gc.setThreshold(setting.getThreshold().floatValue());
4851 int threshstate = safeInt(setting.getThreshstate());
4852 // -1 = None, 0 = Below, 1 = Above threshold
4853 if (threshstate == 0)
4855 gc.setBelowThreshold(true);
4857 else if (threshstate == 1)
4859 gc.setAboveThreshold(true);
4862 gc.setAutoScaled(true); // default
4863 if (setting.isAutoScale() != null)
4865 gc.setAutoScaled(setting.isAutoScale());
4867 if (setting.isColourByLabel() != null)
4869 gc.setColourByLabel(setting.isColourByLabel());
4871 // and put in the feature colour table.
4872 featureColours.put(featureType, gc);
4876 featureColours.put(featureType,
4877 new FeatureColour(maxColour));
4879 renderOrder[fs] = featureType;
4880 if (setting.getOrder() != null)
4882 featureOrder.put(featureType, setting.getOrder().floatValue());
4886 featureOrder.put(featureType, new Float(
4887 fs / jm.getFeatureSettings().getSetting().size()));
4889 if (safeBoolean(setting.isDisplay()))
4891 fdi.setVisible(featureType);
4894 Map<String, Boolean> fgtable = new Hashtable<>();
4895 for (int gs = 0; gs < jm.getFeatureSettings().getGroup().size(); gs++)
4897 Group grp = jm.getFeatureSettings().getGroup().get(gs);
4898 fgtable.put(grp.getName(), new Boolean(grp.isDisplay()));
4900 // FeatureRendererSettings frs = new FeatureRendererSettings(renderOrder,
4901 // fgtable, featureColours, jms.getFeatureSettings().hasTransparency() ?
4902 // jms.getFeatureSettings().getTransparency() : 0.0, featureOrder);
4903 FeatureRendererSettings frs = new FeatureRendererSettings(renderOrder,
4904 fgtable, featureColours, 1.0f, featureOrder);
4905 fr.transferSettings(frs);
4908 if (view.getHiddenColumns().size() > 0)
4910 for (int c = 0; c < view.getHiddenColumns().size(); c++)
4912 final HiddenColumns hc = view.getHiddenColumns().get(c);
4913 viewport.hideColumns(safeInt(hc.getStart()),
4914 safeInt(hc.getEnd()) /* +1 */);
4917 if (view.getCalcIdParam() != null)
4919 for (CalcIdParam calcIdParam : view.getCalcIdParam())
4921 if (calcIdParam != null)
4923 if (recoverCalcIdParam(calcIdParam, viewport))
4928 warn("Couldn't recover parameters for "
4929 + calcIdParam.getCalcId());
4934 af.setMenusFromViewport(viewport);
4935 af.setTitle(view.getTitle());
4936 // TODO: we don't need to do this if the viewport is aready visible.
4938 * Add the AlignFrame to the desktop (it may be 'gathered' later), unless it
4939 * has a 'cdna/protein complement' view, in which case save it in order to
4940 * populate a SplitFrame once all views have been read in.
4942 String complementaryViewId = view.getComplementId();
4943 if (complementaryViewId == null)
4945 Desktop.addInternalFrame(af, view.getTitle(),
4946 safeInt(view.getWidth()), safeInt(view.getHeight()));
4947 // recompute any autoannotation
4948 af.alignPanel.updateAnnotation(false, true);
4949 reorderAutoannotation(af, al, autoAlan);
4950 af.alignPanel.alignmentChanged();
4954 splitFrameCandidates.put(view, af);
4960 * Reads saved data to restore Colour by Annotation settings
4962 * @param viewAnnColour
4966 * @param checkGroupAnnColour
4969 private ColourSchemeI constructAnnotationColour(
4970 AnnotationColourScheme viewAnnColour, AlignFrame af,
4971 AlignmentI al, JalviewModel model, boolean checkGroupAnnColour)
4973 boolean propagateAnnColour = false;
4974 AlignmentI annAlignment = af != null ? af.getViewport().getAlignment()
4976 if (checkGroupAnnColour && al.getGroups() != null
4977 && al.getGroups().size() > 0)
4979 // pre 2.8.1 behaviour
4980 // check to see if we should transfer annotation colours
4981 propagateAnnColour = true;
4982 for (SequenceGroup sg : al.getGroups())
4984 if (sg.getColourScheme() instanceof AnnotationColourGradient)
4986 propagateAnnColour = false;
4992 * 2.10.2- : saved annotationId is AlignmentAnnotation.annotationId
4994 String annotationId = viewAnnColour.getAnnotation();
4995 AlignmentAnnotation matchedAnnotation = annotationIds.get(annotationId);
4998 * pre 2.10.2: saved annotationId is AlignmentAnnotation.label
5000 if (matchedAnnotation == null
5001 && annAlignment.getAlignmentAnnotation() != null)
5003 for (int i = 0; i < annAlignment.getAlignmentAnnotation().length; i++)
5006 .equals(annAlignment.getAlignmentAnnotation()[i].label))
5008 matchedAnnotation = annAlignment.getAlignmentAnnotation()[i];
5013 if (matchedAnnotation == null)
5015 System.err.println("Failed to match annotation colour scheme for "
5019 if (matchedAnnotation.getThreshold() == null)
5021 matchedAnnotation.setThreshold(
5022 new GraphLine(safeFloat(viewAnnColour.getThreshold()),
5023 "Threshold", Color.black));
5026 AnnotationColourGradient cs = null;
5027 if (viewAnnColour.getColourScheme().equals("None"))
5029 cs = new AnnotationColourGradient(matchedAnnotation,
5030 new Color(safeInt(viewAnnColour.getMinColour())),
5031 new Color(safeInt(viewAnnColour.getMaxColour())),
5032 safeInt(viewAnnColour.getAboveThreshold()));
5034 else if (viewAnnColour.getColourScheme().startsWith("ucs"))
5036 cs = new AnnotationColourGradient(matchedAnnotation,
5037 getUserColourScheme(model, viewAnnColour.getColourScheme()),
5038 safeInt(viewAnnColour.getAboveThreshold()));
5042 cs = new AnnotationColourGradient(matchedAnnotation,
5043 ColourSchemeProperty.getColourScheme(al,
5044 viewAnnColour.getColourScheme()),
5045 safeInt(viewAnnColour.getAboveThreshold()));
5048 boolean perSequenceOnly = safeBoolean(viewAnnColour.isPerSequence());
5049 boolean useOriginalColours = safeBoolean(
5050 viewAnnColour.isPredefinedColours());
5051 cs.setSeqAssociated(perSequenceOnly);
5052 cs.setPredefinedColours(useOriginalColours);
5054 if (propagateAnnColour && al.getGroups() != null)
5056 // Also use these settings for all the groups
5057 for (int g = 0; g < al.getGroups().size(); g++)
5059 SequenceGroup sg = al.getGroups().get(g);
5060 if (sg.getGroupColourScheme() == null)
5065 AnnotationColourGradient groupScheme = new AnnotationColourGradient(
5066 matchedAnnotation, sg.getColourScheme(),
5067 safeInt(viewAnnColour.getAboveThreshold()));
5068 sg.setColourScheme(groupScheme);
5069 groupScheme.setSeqAssociated(perSequenceOnly);
5070 groupScheme.setPredefinedColours(useOriginalColours);
5076 private void reorderAutoannotation(AlignFrame af, AlignmentI al,
5077 List<JvAnnotRow> autoAlan)
5079 // copy over visualization settings for autocalculated annotation in the
5081 if (al.getAlignmentAnnotation() != null)
5084 * Kludge for magic autoannotation names (see JAL-811)
5086 String[] magicNames = new String[] { "Consensus", "Quality",
5088 JvAnnotRow nullAnnot = new JvAnnotRow(-1, null);
5089 Hashtable<String, JvAnnotRow> visan = new Hashtable<>();
5090 for (String nm : magicNames)
5092 visan.put(nm, nullAnnot);
5094 for (JvAnnotRow auan : autoAlan)
5096 visan.put(auan.template.label
5097 + (auan.template.getCalcId() == null ? ""
5098 : "\t" + auan.template.getCalcId()),
5101 int hSize = al.getAlignmentAnnotation().length;
5102 List<JvAnnotRow> reorder = new ArrayList<>();
5103 // work through any autoCalculated annotation already on the view
5104 // removing it if it should be placed in a different location on the
5105 // annotation panel.
5106 List<String> remains = new ArrayList<>(visan.keySet());
5107 for (int h = 0; h < hSize; h++)
5109 jalview.datamodel.AlignmentAnnotation jalan = al
5110 .getAlignmentAnnotation()[h];
5111 if (jalan.autoCalculated)
5114 JvAnnotRow valan = visan.get(k = jalan.label);
5115 if (jalan.getCalcId() != null)
5117 valan = visan.get(k = jalan.label + "\t" + jalan.getCalcId());
5122 // delete the auto calculated row from the alignment
5123 al.deleteAnnotation(jalan, false);
5127 if (valan != nullAnnot)
5129 if (jalan != valan.template)
5131 // newly created autoannotation row instance
5132 // so keep a reference to the visible annotation row
5133 // and copy over all relevant attributes
5134 if (valan.template.graphHeight >= 0)
5137 jalan.graphHeight = valan.template.graphHeight;
5139 jalan.visible = valan.template.visible;
5141 reorder.add(new JvAnnotRow(valan.order, jalan));
5146 // Add any (possibly stale) autocalculated rows that were not appended to
5147 // the view during construction
5148 for (String other : remains)
5150 JvAnnotRow othera = visan.get(other);
5151 if (othera != nullAnnot && othera.template.getCalcId() != null
5152 && othera.template.getCalcId().length() > 0)
5154 reorder.add(othera);
5157 // now put the automatic annotation in its correct place
5158 int s = 0, srt[] = new int[reorder.size()];
5159 JvAnnotRow[] rws = new JvAnnotRow[reorder.size()];
5160 for (JvAnnotRow jvar : reorder)
5163 srt[s++] = jvar.order;
5166 jalview.util.QuickSort.sort(srt, rws);
5167 // and re-insert the annotation at its correct position
5168 for (JvAnnotRow jvar : rws)
5170 al.addAnnotation(jvar.template, jvar.order);
5172 af.alignPanel.adjustAnnotationHeight();
5176 Hashtable skipList = null;
5179 * TODO remove this method
5182 * @return AlignFrame bound to sequenceSetId from view, if one exists. private
5183 * AlignFrame getSkippedFrame(Viewport view) { if (skipList==null) {
5184 * throw new Error("Implementation Error. No skipList defined for this
5185 * Jalview2XML instance."); } return (AlignFrame)
5186 * skipList.get(view.getSequenceSetId()); }
5190 * Check if the Jalview view contained in object should be skipped or not.
5193 * @return true if view's sequenceSetId is a key in skipList
5195 private boolean skipViewport(JalviewModel object)
5197 if (skipList == null)
5201 String id = object.getViewport().get(0).getSequenceSetId();
5202 if (skipList.containsKey(id))
5204 if (Cache.log != null && Cache.log.isDebugEnabled())
5206 Cache.log.debug("Skipping seuqence set id " + id);
5213 public void addToSkipList(AlignFrame af)
5215 if (skipList == null)
5217 skipList = new Hashtable();
5219 skipList.put(af.getViewport().getSequenceSetId(), af);
5222 public void clearSkipList()
5224 if (skipList != null)
5231 private void recoverDatasetFor(SequenceSet vamsasSet, AlignmentI al,
5232 boolean ignoreUnrefed)
5234 jalview.datamodel.AlignmentI ds = getDatasetFor(
5235 vamsasSet.getDatasetId());
5236 Vector dseqs = null;
5239 // create a list of new dataset sequences
5240 dseqs = new Vector();
5242 for (int i = 0, iSize = vamsasSet.getSequence().size(); i < iSize; i++)
5244 Sequence vamsasSeq = vamsasSet.getSequence().get(i);
5245 ensureJalviewDatasetSequence(vamsasSeq, ds, dseqs, ignoreUnrefed, i);
5247 // create a new dataset
5250 SequenceI[] dsseqs = new SequenceI[dseqs.size()];
5251 dseqs.copyInto(dsseqs);
5252 ds = new jalview.datamodel.Alignment(dsseqs);
5253 debug("Created new dataset " + vamsasSet.getDatasetId()
5254 + " for alignment " + System.identityHashCode(al));
5255 addDatasetRef(vamsasSet.getDatasetId(), ds);
5257 // set the dataset for the newly imported alignment.
5258 if (al.getDataset() == null && !ignoreUnrefed)
5267 * sequence definition to create/merge dataset sequence for
5271 * vector to add new dataset sequence to
5272 * @param ignoreUnrefed
5273 * - when true, don't create new sequences from vamsasSeq if it's id
5274 * doesn't already have an asssociated Jalview sequence.
5276 * - used to reorder the sequence in the alignment according to the
5277 * vamsasSeq array ordering, to preserve ordering of dataset
5279 private void ensureJalviewDatasetSequence(Sequence vamsasSeq,
5280 AlignmentI ds, Vector dseqs, boolean ignoreUnrefed, int vseqpos)
5282 // JBP TODO: Check this is called for AlCodonFrames to support recovery of
5284 SequenceI sq = seqRefIds.get(vamsasSeq.getId());
5285 boolean reorder = false;
5286 SequenceI dsq = null;
5287 if (sq != null && sq.getDatasetSequence() != null)
5289 dsq = sq.getDatasetSequence();
5295 if (sq == null && ignoreUnrefed)
5299 String sqid = vamsasSeq.getDsseqid();
5302 // need to create or add a new dataset sequence reference to this sequence
5305 dsq = seqRefIds.get(sqid);
5310 // make a new dataset sequence
5311 dsq = sq.createDatasetSequence();
5314 // make up a new dataset reference for this sequence
5315 sqid = seqHash(dsq);
5317 dsq.setVamsasId(uniqueSetSuffix + sqid);
5318 seqRefIds.put(sqid, dsq);
5323 dseqs.addElement(dsq);
5328 ds.addSequence(dsq);
5334 { // make this dataset sequence sq's dataset sequence
5335 sq.setDatasetSequence(dsq);
5336 // and update the current dataset alignment
5341 if (!dseqs.contains(dsq))
5348 if (ds.findIndex(dsq) < 0)
5350 ds.addSequence(dsq);
5357 // TODO: refactor this as a merge dataset sequence function
5358 // now check that sq (the dataset sequence) sequence really is the union of
5359 // all references to it
5360 // boolean pre = sq.getStart() < dsq.getStart();
5361 // boolean post = sq.getEnd() > dsq.getEnd();
5365 // StringBuffer sb = new StringBuffer();
5366 String newres = jalview.analysis.AlignSeq.extractGaps(
5367 jalview.util.Comparison.GapChars, sq.getSequenceAsString());
5368 if (!newres.equalsIgnoreCase(dsq.getSequenceAsString())
5369 && newres.length() > dsq.getLength())
5371 // Update with the longer sequence.
5375 * if (pre) { sb.insert(0, newres .substring(0, dsq.getStart() -
5376 * sq.getStart())); dsq.setStart(sq.getStart()); } if (post) {
5377 * sb.append(newres.substring(newres.length() - sq.getEnd() -
5378 * dsq.getEnd())); dsq.setEnd(sq.getEnd()); }
5380 dsq.setSequence(newres);
5382 // TODO: merges will never happen if we 'know' we have the real dataset
5383 // sequence - this should be detected when id==dssid
5385 "DEBUG Notice: Merged dataset sequence (if you see this often, post at http://issues.jalview.org/browse/JAL-1474)"); // ("
5386 // + (pre ? "prepended" : "") + " "
5387 // + (post ? "appended" : ""));
5392 // sequence refs are identical. We may need to update the existing dataset
5393 // alignment with this one, though.
5394 if (ds != null && dseqs == null)
5396 int opos = ds.findIndex(dsq);
5397 SequenceI tseq = null;
5398 if (opos != -1 && vseqpos != opos)
5400 // remove from old position
5401 ds.deleteSequence(dsq);
5403 if (vseqpos < ds.getHeight())
5405 if (vseqpos != opos)
5407 // save sequence at destination position
5408 tseq = ds.getSequenceAt(vseqpos);
5409 ds.replaceSequenceAt(vseqpos, dsq);
5410 ds.addSequence(tseq);
5415 ds.addSequence(dsq);
5422 * TODO use AlignmentI here and in related methods - needs
5423 * AlignmentI.getDataset() changed to return AlignmentI instead of Alignment
5425 Hashtable<String, AlignmentI> datasetIds = null;
5427 IdentityHashMap<AlignmentI, String> dataset2Ids = null;
5429 private AlignmentI getDatasetFor(String datasetId)
5431 if (datasetIds == null)
5433 datasetIds = new Hashtable<>();
5436 if (datasetIds.containsKey(datasetId))
5438 return datasetIds.get(datasetId);
5443 private void addDatasetRef(String datasetId, AlignmentI dataset)
5445 if (datasetIds == null)
5447 datasetIds = new Hashtable<>();
5449 datasetIds.put(datasetId, dataset);
5453 * make a new dataset ID for this jalview dataset alignment
5458 private String getDatasetIdRef(AlignmentI dataset)
5460 if (dataset.getDataset() != null)
5462 warn("Serious issue! Dataset Object passed to getDatasetIdRef is not a Jalview DATASET alignment...");
5464 String datasetId = makeHashCode(dataset, null);
5465 if (datasetId == null)
5467 // make a new datasetId and record it
5468 if (dataset2Ids == null)
5470 dataset2Ids = new IdentityHashMap<>();
5474 datasetId = dataset2Ids.get(dataset);
5476 if (datasetId == null)
5478 datasetId = "ds" + dataset2Ids.size() + 1;
5479 dataset2Ids.put(dataset, datasetId);
5485 private void addDBRefs(SequenceI datasetSequence, Sequence sequence)
5487 for (int d = 0; d < sequence.getDBRef().size(); d++)
5489 DBRef dr = sequence.getDBRef().get(d);
5490 jalview.datamodel.DBRefEntry entry = new jalview.datamodel.DBRefEntry(
5491 dr.getSource(), dr.getVersion(), dr.getAccessionId());
5492 if (dr.getMapping() != null)
5494 entry.setMap(addMapping(dr.getMapping()));
5496 datasetSequence.addDBRef(entry);
5500 private jalview.datamodel.Mapping addMapping(Mapping m)
5502 SequenceI dsto = null;
5503 // Mapping m = dr.getMapping();
5504 int fr[] = new int[m.getMapListFrom().size() * 2];
5505 Iterator<MapListFrom> from = m.getMapListFrom().iterator();// enumerateMapListFrom();
5506 for (int _i = 0; from.hasNext(); _i += 2)
5508 MapListFrom mf = from.next();
5509 fr[_i] = mf.getStart();
5510 fr[_i + 1] = mf.getEnd();
5512 int fto[] = new int[m.getMapListTo().size() * 2];
5513 Iterator<MapListTo> to = m.getMapListTo().iterator();// enumerateMapListTo();
5514 for (int _i = 0; to.hasNext(); _i += 2)
5516 MapListTo mf = to.next();
5517 fto[_i] = mf.getStart();
5518 fto[_i + 1] = mf.getEnd();
5520 jalview.datamodel.Mapping jmap = new jalview.datamodel.Mapping(dsto, fr,
5521 fto, m.getMapFromUnit().intValue(),
5522 m.getMapToUnit().intValue());
5523 // if (m.getMappingChoice() != null)
5525 // MappingChoice mc = m.getMappingChoice();
5526 if (m.getDseqFor() != null)
5528 String dsfor = m.getDseqFor();
5529 if (seqRefIds.containsKey(dsfor))
5534 jmap.setTo(seqRefIds.get(dsfor));
5538 frefedSequence.add(newMappingRef(dsfor, jmap));
5544 * local sequence definition
5546 Sequence ms = m.getSequence();
5547 SequenceI djs = null;
5548 String sqid = ms.getDsseqid();
5549 if (sqid != null && sqid.length() > 0)
5552 * recover dataset sequence
5554 djs = seqRefIds.get(sqid);
5559 "Warning - making up dataset sequence id for DbRef sequence map reference");
5560 sqid = ((Object) ms).toString(); // make up a new hascode for
5561 // undefined dataset sequence hash
5562 // (unlikely to happen)
5568 * make a new dataset sequence and add it to refIds hash
5570 djs = new jalview.datamodel.Sequence(ms.getName(),
5572 djs.setStart(jmap.getMap().getToLowest());
5573 djs.setEnd(jmap.getMap().getToHighest());
5574 djs.setVamsasId(uniqueSetSuffix + sqid);
5576 incompleteSeqs.put(sqid, djs);
5577 seqRefIds.put(sqid, djs);
5580 jalview.bin.Cache.log.debug("about to recurse on addDBRefs.");
5589 * Provides a 'copy' of an alignment view (on action New View) by 'saving' the
5590 * view as XML (but not to file), and then reloading it
5595 public AlignmentPanel copyAlignPanel(AlignmentPanel ap)
5598 JalviewModel jm = saveState(ap, null, null, null);
5600 uniqueSetSuffix = "";
5601 // jm.getJalviewModelSequence().getViewport(0).setId(null);
5602 jm.getViewport().get(0).setId(null);
5603 // we don't overwrite the view we just copied
5605 if (this.frefedSequence == null)
5607 frefedSequence = new Vector<>();
5610 viewportsAdded.clear();
5612 AlignFrame af = loadFromObject(jm, null, false, null);
5613 af.getAlignPanels().clear();
5614 af.closeMenuItem_actionPerformed(true);
5617 * if(ap.av.getAlignment().getAlignmentAnnotation()!=null) { for(int i=0;
5618 * i<ap.av.getAlignment().getAlignmentAnnotation().length; i++) {
5619 * if(!ap.av.getAlignment().getAlignmentAnnotation()[i].autoCalculated) {
5620 * af.alignPanel.av.getAlignment().getAlignmentAnnotation()[i] =
5621 * ap.av.getAlignment().getAlignmentAnnotation()[i]; } } }
5624 return af.alignPanel;
5627 private Hashtable jvids2vobj;
5629 private void warn(String msg)
5634 private void warn(String msg, Exception e)
5636 if (Cache.log != null)
5640 Cache.log.warn(msg, e);
5644 Cache.log.warn(msg);
5649 System.err.println("Warning: " + msg);
5652 e.printStackTrace();
5657 private void debug(String string)
5659 debug(string, null);
5662 private void debug(String msg, Exception e)
5664 if (Cache.log != null)
5668 Cache.log.debug(msg, e);
5672 Cache.log.debug(msg);
5677 System.err.println("Warning: " + msg);
5680 e.printStackTrace();
5686 * set the object to ID mapping tables used to write/recover objects and XML
5687 * ID strings for the jalview project. If external tables are provided then
5688 * finalize and clearSeqRefs will not clear the tables when the Jalview2XML
5689 * object goes out of scope. - also populates the datasetIds hashtable with
5690 * alignment objects containing dataset sequences
5693 * Map from ID strings to jalview datamodel
5695 * Map from jalview datamodel to ID strings
5699 public void setObjectMappingTables(Hashtable vobj2jv,
5700 IdentityHashMap jv2vobj)
5702 this.jv2vobj = jv2vobj;
5703 this.vobj2jv = vobj2jv;
5704 Iterator ds = jv2vobj.keySet().iterator();
5706 while (ds.hasNext())
5708 Object jvobj = ds.next();
5709 id = jv2vobj.get(jvobj).toString();
5710 if (jvobj instanceof jalview.datamodel.Alignment)
5712 if (((jalview.datamodel.Alignment) jvobj).getDataset() == null)
5714 addDatasetRef(id, (jalview.datamodel.Alignment) jvobj);
5717 else if (jvobj instanceof jalview.datamodel.Sequence)
5719 // register sequence object so the XML parser can recover it.
5720 if (seqRefIds == null)
5722 seqRefIds = new HashMap<>();
5724 if (seqsToIds == null)
5726 seqsToIds = new IdentityHashMap<>();
5728 seqRefIds.put(jv2vobj.get(jvobj).toString(), (SequenceI) jvobj);
5729 seqsToIds.put((SequenceI) jvobj, id);
5731 else if (jvobj instanceof jalview.datamodel.AlignmentAnnotation)
5734 AlignmentAnnotation jvann = (AlignmentAnnotation) jvobj;
5735 annotationIds.put(anid = jv2vobj.get(jvobj).toString(), jvann);
5736 if (jvann.annotationId == null)
5738 jvann.annotationId = anid;
5740 if (!jvann.annotationId.equals(anid))
5742 // TODO verify that this is the correct behaviour
5743 this.warn("Overriding Annotation ID for " + anid
5744 + " from different id : " + jvann.annotationId);
5745 jvann.annotationId = anid;
5748 else if (jvobj instanceof String)
5750 if (jvids2vobj == null)
5752 jvids2vobj = new Hashtable();
5753 jvids2vobj.put(jvobj, jv2vobj.get(jvobj).toString());
5758 Cache.log.debug("Ignoring " + jvobj.getClass() + " (ID = " + id);
5764 * set the uniqueSetSuffix used to prefix/suffix object IDs for jalview
5765 * objects created from the project archive. If string is null (default for
5766 * construction) then suffix will be set automatically.
5770 public void setUniqueSetSuffix(String string)
5772 uniqueSetSuffix = string;
5777 * uses skipList2 as the skipList for skipping views on sequence sets
5778 * associated with keys in the skipList
5782 public void setSkipList(Hashtable skipList2)
5784 skipList = skipList2;
5788 * Reads the jar entry of given name and returns its contents, or null if the
5789 * entry is not found.
5792 * @param jarEntryName
5795 protected String readJarEntry(jarInputStreamProvider jprovider,
5796 String jarEntryName)
5798 String result = null;
5799 BufferedReader in = null;
5804 * Reopen the jar input stream and traverse its entries to find a matching
5807 JarInputStream jin = jprovider.getJarInputStream();
5808 JarEntry entry = null;
5811 entry = jin.getNextJarEntry();
5812 System.out.println("Jalview2XML#readJarEntry: jarentry=" + (entry == null ? null : entry.getName()));
5813 } while (entry != null && !entry.getName().equals(jarEntryName));
5817 StringBuilder out = new StringBuilder(256);
5818 in = new BufferedReader(new InputStreamReader(jin, UTF_8));
5821 while ((data = in.readLine()) != null)
5825 result = out.toString();
5829 warn("Couldn't find entry in Jalview Jar for " + jarEntryName);
5831 } catch (Exception ex)
5833 ex.printStackTrace();
5841 } catch (IOException e)
5852 * Returns an incrementing counter (0, 1, 2...)
5856 private synchronized int nextCounter()
5862 * Populates an XML model of the feature colour scheme for one feature type
5864 * @param featureType
5868 public static Colour marshalColour(
5869 String featureType, FeatureColourI fcol)
5871 Colour col = new Colour();
5872 if (fcol.isSimpleColour())
5874 col.setRGB(Format.getHexString(fcol.getColour()));
5878 col.setRGB(Format.getHexString(fcol.getMaxColour()));
5879 col.setMin(fcol.getMin());
5880 col.setMax(fcol.getMax());
5881 col.setMinRGB(jalview.util.Format.getHexString(fcol.getMinColour()));
5882 col.setAutoScale(fcol.isAutoScaled());
5883 col.setThreshold(fcol.getThreshold());
5884 col.setColourByLabel(fcol.isColourByLabel());
5885 col.setThreshType(fcol.isAboveThreshold() ? ThresholdType.ABOVE
5886 : (fcol.isBelowThreshold() ? ThresholdType.BELOW
5887 : ThresholdType.NONE));
5888 if (fcol.isColourByAttribute())
5890 final String[] attName = fcol.getAttributeName();
5891 col.getAttributeName().add(attName[0]);
5892 if (attName.length > 1)
5894 col.getAttributeName().add(attName[1]);
5897 Color noColour = fcol.getNoColour();
5898 if (noColour == null)
5900 col.setNoValueColour(NoValueColour.NONE);
5902 else if (noColour == fcol.getMaxColour())
5904 col.setNoValueColour(NoValueColour.MAX);
5908 col.setNoValueColour(NoValueColour.MIN);
5911 col.setName(featureType);
5916 * Populates an XML model of the feature filter(s) for one feature type
5918 * @param firstMatcher
5919 * the first (or only) match condition)
5921 * remaining match conditions (if any)
5923 * if true, conditions are and-ed, else or-ed
5925 public static jalview.xml.binding.jalview.FeatureMatcherSet marshalFilter(
5926 FeatureMatcherI firstMatcher, Iterator<FeatureMatcherI> filters,
5929 jalview.xml.binding.jalview.FeatureMatcherSet result = new jalview.xml.binding.jalview.FeatureMatcherSet();
5931 if (filters.hasNext())
5936 CompoundMatcher compound = new CompoundMatcher();
5937 compound.setAnd(and);
5938 jalview.xml.binding.jalview.FeatureMatcherSet matcher1 = marshalFilter(
5939 firstMatcher, Collections.emptyIterator(), and);
5940 // compound.addMatcherSet(matcher1);
5941 compound.getMatcherSet().add(matcher1);
5942 FeatureMatcherI nextMatcher = filters.next();
5943 jalview.xml.binding.jalview.FeatureMatcherSet matcher2 = marshalFilter(
5944 nextMatcher, filters, and);
5945 // compound.addMatcherSet(matcher2);
5946 compound.getMatcherSet().add(matcher2);
5947 result.setCompoundMatcher(compound);
5952 * single condition matcher
5954 // MatchCondition matcherModel = new MatchCondition();
5955 jalview.xml.binding.jalview.FeatureMatcher matcherModel = new jalview.xml.binding.jalview.FeatureMatcher();
5956 matcherModel.setCondition(
5957 firstMatcher.getMatcher().getCondition().getStableName());
5958 matcherModel.setValue(firstMatcher.getMatcher().getPattern());
5959 if (firstMatcher.isByAttribute())
5961 matcherModel.setBy(FilterBy.BY_ATTRIBUTE);
5962 // matcherModel.setAttributeName(firstMatcher.getAttribute());
5963 String[] attName = firstMatcher.getAttribute();
5964 matcherModel.getAttributeName().add(attName[0]); // attribute
5965 if (attName.length > 1)
5967 matcherModel.getAttributeName().add(attName[1]); // sub-attribute
5970 else if (firstMatcher.isByLabel())
5972 matcherModel.setBy(FilterBy.BY_LABEL);
5974 else if (firstMatcher.isByScore())
5976 matcherModel.setBy(FilterBy.BY_SCORE);
5978 result.setMatchCondition(matcherModel);
5985 * Loads one XML model of a feature filter to a Jalview object
5987 * @param featureType
5988 * @param matcherSetModel
5991 public static FeatureMatcherSetI parseFilter(
5993 jalview.xml.binding.jalview.FeatureMatcherSet matcherSetModel)
5995 FeatureMatcherSetI result = new FeatureMatcherSet();
5998 parseFilterConditions(result, matcherSetModel, true);
5999 } catch (IllegalStateException e)
6001 // mixing AND and OR conditions perhaps
6003 String.format("Error reading filter conditions for '%s': %s",
6004 featureType, e.getMessage()));
6005 // return as much as was parsed up to the error
6012 * Adds feature match conditions to matcherSet as unmarshalled from XML
6013 * (possibly recursively for compound conditions)
6016 * @param matcherSetModel
6018 * if true, multiple conditions are AND-ed, else they are OR-ed
6019 * @throws IllegalStateException
6020 * if AND and OR conditions are mixed
6022 protected static void parseFilterConditions(
6023 FeatureMatcherSetI matcherSet,
6024 jalview.xml.binding.jalview.FeatureMatcherSet matcherSetModel,
6027 jalview.xml.binding.jalview.FeatureMatcher mc = matcherSetModel
6028 .getMatchCondition();
6034 FilterBy filterBy = mc.getBy();
6035 Condition cond = Condition.fromString(mc.getCondition());
6036 String pattern = mc.getValue();
6037 FeatureMatcherI matchCondition = null;
6038 if (filterBy == FilterBy.BY_LABEL)
6040 matchCondition = FeatureMatcher.byLabel(cond, pattern);
6042 else if (filterBy == FilterBy.BY_SCORE)
6044 matchCondition = FeatureMatcher.byScore(cond, pattern);
6047 else if (filterBy == FilterBy.BY_ATTRIBUTE)
6049 final List<String> attributeName = mc.getAttributeName();
6050 String[] attNames = attributeName
6051 .toArray(new String[attributeName.size()]);
6052 matchCondition = FeatureMatcher.byAttribute(cond, pattern,
6057 * note this throws IllegalStateException if AND-ing to a
6058 * previously OR-ed compound condition, or vice versa
6062 matcherSet.and(matchCondition);
6066 matcherSet.or(matchCondition);
6072 * compound condition
6074 List<jalview.xml.binding.jalview.FeatureMatcherSet> matchers = matcherSetModel
6075 .getCompoundMatcher().getMatcherSet();
6076 boolean anded = matcherSetModel.getCompoundMatcher().isAnd();
6077 if (matchers.size() == 2)
6079 parseFilterConditions(matcherSet, matchers.get(0), anded);
6080 parseFilterConditions(matcherSet, matchers.get(1), anded);
6084 System.err.println("Malformed compound filter condition");
6090 * Loads one XML model of a feature colour to a Jalview object
6092 * @param colourModel
6095 public static FeatureColourI parseColour(Colour colourModel)
6097 FeatureColourI colour = null;
6099 if (colourModel.getMax() != null)
6101 Color mincol = null;
6102 Color maxcol = null;
6103 Color noValueColour = null;
6107 mincol = new Color(Integer.parseInt(colourModel.getMinRGB(), 16));
6108 maxcol = new Color(Integer.parseInt(colourModel.getRGB(), 16));
6109 } catch (Exception e)
6111 Cache.log.warn("Couldn't parse out graduated feature color.", e);
6114 NoValueColour noCol = colourModel.getNoValueColour();
6115 if (noCol == NoValueColour.MIN)
6117 noValueColour = mincol;
6119 else if (noCol == NoValueColour.MAX)
6121 noValueColour = maxcol;
6124 colour = new FeatureColour(mincol, maxcol, noValueColour,
6125 safeFloat(colourModel.getMin()),
6126 safeFloat(colourModel.getMax()));
6127 final List<String> attributeName = colourModel.getAttributeName();
6128 String[] attributes = attributeName
6129 .toArray(new String[attributeName.size()]);
6130 if (attributes != null && attributes.length > 0)
6132 colour.setAttributeName(attributes);
6134 if (colourModel.isAutoScale() != null)
6136 colour.setAutoScaled(colourModel.isAutoScale().booleanValue());
6138 if (colourModel.isColourByLabel() != null)
6140 colour.setColourByLabel(
6141 colourModel.isColourByLabel().booleanValue());
6143 if (colourModel.getThreshold() != null)
6145 colour.setThreshold(colourModel.getThreshold().floatValue());
6147 ThresholdType ttyp = colourModel.getThreshType();
6148 if (ttyp == ThresholdType.ABOVE)
6150 colour.setAboveThreshold(true);
6152 else if (ttyp == ThresholdType.BELOW)
6154 colour.setBelowThreshold(true);
6159 Color color = new Color(Integer.parseInt(colourModel.getRGB(), 16));
6160 colour = new FeatureColour(color);