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 System.out.println("Writing jar entry " + fileName);
1621 JarEntry entry = new JarEntry(fileName);
1622 jout.putNextEntry(entry);
1623 PrintWriter pout = new PrintWriter(
1624 new OutputStreamWriter(jout, UTF_8));
1625 JAXBContext jaxbContext = JAXBContext
1626 .newInstance(JalviewModel.class);
1627 Marshaller jaxbMarshaller = jaxbContext.createMarshaller();
1629 // output pretty printed
1630 // jaxbMarshaller.setProperty(Marshaller.JAXB_FORMATTED_OUTPUT, true);
1631 jaxbMarshaller.marshal(
1632 new ObjectFactory().createJalviewModel(object), pout);
1634 // jaxbMarshaller.marshal(object, pout);
1635 // marshaller.marshal(object);
1638 } catch (Exception ex)
1640 // TODO: raise error in GUI if marshalling failed.
1641 System.err.println("Error writing Jalview project");
1642 ex.printStackTrace();
1649 * Save any Varna viewers linked to this sequence. Writes an rnaViewer element
1650 * for each viewer, with
1652 * <li>viewer geometry (position, size, split pane divider location)</li>
1653 * <li>index of the selected structure in the viewer (currently shows gapped
1655 * <li>the id of the annotation holding RNA secondary structure</li>
1656 * <li>(currently only one SS is shown per viewer, may be more in future)</li>
1658 * Varna viewer state is also written out (in native Varna XML) to separate
1659 * project jar entries. A separate entry is written for each RNA structure
1660 * displayed, with the naming convention
1662 * <li>rna_viewId_sequenceId_annotationId_[gapped|trimmed]</li>
1670 * @param storeDataset
1672 protected void saveRnaViewers(JarOutputStream jout, JSeq jseq,
1673 final SequenceI jds, List<String> viewIds, AlignmentPanel ap,
1674 boolean storeDataset)
1676 if (Desktop.desktop == null)
1680 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1681 for (int f = frames.length - 1; f > -1; f--)
1683 if (frames[f] instanceof AppVarna)
1685 AppVarna varna = (AppVarna) frames[f];
1687 * link the sequence to every viewer that is showing it and is linked to
1688 * its alignment panel
1690 if (varna.isListeningFor(jds) && ap == varna.getAlignmentPanel())
1692 String viewId = varna.getViewId();
1693 RnaViewer rna = new RnaViewer();
1694 rna.setViewId(viewId);
1695 rna.setTitle(varna.getTitle());
1696 rna.setXpos(varna.getX());
1697 rna.setYpos(varna.getY());
1698 rna.setWidth(varna.getWidth());
1699 rna.setHeight(varna.getHeight());
1700 rna.setDividerLocation(varna.getDividerLocation());
1701 rna.setSelectedRna(varna.getSelectedIndex());
1702 // jseq.addRnaViewer(rna);
1703 jseq.getRnaViewer().add(rna);
1706 * Store each Varna panel's state once in the project per sequence.
1707 * First time through only (storeDataset==false)
1709 // boolean storeSessions = false;
1710 // String sequenceViewId = viewId + seqsToIds.get(jds);
1711 // if (!storeDataset && !viewIds.contains(sequenceViewId))
1713 // viewIds.add(sequenceViewId);
1714 // storeSessions = true;
1716 for (RnaModel model : varna.getModels())
1718 if (model.seq == jds)
1721 * VARNA saves each view (sequence or alignment secondary
1722 * structure, gapped or trimmed) as a separate XML file
1724 String jarEntryName = rnaSessions.get(model);
1725 if (jarEntryName == null)
1728 String varnaStateFile = varna.getStateInfo(model.rna);
1729 jarEntryName = RNA_PREFIX + viewId + "_" + nextCounter();
1730 copyFileToJar(jout, varnaStateFile, jarEntryName);
1731 rnaSessions.put(model, jarEntryName);
1733 SecondaryStructure ss = new SecondaryStructure();
1734 String annotationId = varna.getAnnotation(jds).annotationId;
1735 ss.setAnnotationId(annotationId);
1736 ss.setViewerState(jarEntryName);
1737 ss.setGapped(model.gapped);
1738 ss.setTitle(model.title);
1739 // rna.addSecondaryStructure(ss);
1740 rna.getSecondaryStructure().add(ss);
1749 * Copy the contents of a file to a new entry added to the output jar
1753 * @param jarEntryName
1755 protected void copyFileToJar(JarOutputStream jout, String infilePath,
1756 String jarEntryName)
1758 DataInputStream dis = null;
1761 File file = new File(infilePath);
1762 if (file.exists() && jout != null)
1764 dis = new DataInputStream(new FileInputStream(file));
1765 byte[] data = new byte[(int) file.length()];
1766 dis.readFully(data);
1767 writeJarEntry(jout, jarEntryName, data);
1769 } catch (Exception ex)
1771 ex.printStackTrace();
1779 } catch (IOException e)
1788 * Write the data to a new entry of given name in the output jar file
1791 * @param jarEntryName
1793 * @throws IOException
1795 protected void writeJarEntry(JarOutputStream jout, String jarEntryName,
1796 byte[] data) throws IOException
1800 System.out.println("Writing jar entry " + jarEntryName);
1801 jout.putNextEntry(new JarEntry(jarEntryName));
1802 DataOutputStream dout = new DataOutputStream(jout);
1803 dout.write(data, 0, data.length);
1810 * Save the state of a structure viewer
1815 * the archive XML element under which to save the state
1818 * @param matchedFile
1822 protected String saveStructureState(AlignmentPanel ap, SequenceI jds,
1823 Pdbids pdb, PDBEntry entry, List<String> viewIds,
1824 String matchedFile, StructureViewerBase viewFrame)
1826 final AAStructureBindingModel bindingModel = viewFrame.getBinding();
1829 * Look for any bindings for this viewer to the PDB file of interest
1830 * (including part matches excluding chain id)
1832 for (int peid = 0; peid < bindingModel.getPdbCount(); peid++)
1834 final PDBEntry pdbentry = bindingModel.getPdbEntry(peid);
1835 final String pdbId = pdbentry.getId();
1836 if (!pdbId.equals(entry.getId())
1837 && !(entry.getId().length() > 4 && entry.getId().toLowerCase()
1838 .startsWith(pdbId.toLowerCase())))
1841 * not interested in a binding to a different PDB entry here
1845 if (matchedFile == null)
1847 matchedFile = pdbentry.getFile();
1849 else if (!matchedFile.equals(pdbentry.getFile()))
1852 "Probably lost some PDB-Sequence mappings for this structure file (which apparently has same PDB Entry code): "
1853 + pdbentry.getFile());
1857 // can get at it if the ID
1858 // match is ambiguous (e.g.
1861 for (int smap = 0; smap < viewFrame.getBinding()
1862 .getSequence()[peid].length; smap++)
1864 // if (jal.findIndex(jmol.jmb.sequence[peid][smap]) > -1)
1865 if (jds == viewFrame.getBinding().getSequence()[peid][smap])
1867 StructureState state = new StructureState();
1868 state.setVisible(true);
1869 state.setXpos(viewFrame.getX());
1870 state.setYpos(viewFrame.getY());
1871 state.setWidth(viewFrame.getWidth());
1872 state.setHeight(viewFrame.getHeight());
1873 final String viewId = viewFrame.getViewId();
1874 state.setViewId(viewId);
1875 state.setAlignwithAlignPanel(viewFrame.isUsedforaligment(ap));
1876 state.setColourwithAlignPanel(viewFrame.isUsedforcolourby(ap));
1877 state.setColourByJmol(viewFrame.isColouredByViewer());
1878 state.setType(viewFrame.getViewerType().toString());
1879 // pdb.addStructureState(state);
1880 pdb.getStructureState().add(state);
1888 * Populates the AnnotationColourScheme xml for save. This captures the
1889 * settings of the options in the 'Colour by Annotation' dialog.
1892 * @param userColours
1896 private AnnotationColourScheme constructAnnotationColours(
1897 AnnotationColourGradient acg, List<UserColourScheme> userColours,
1900 AnnotationColourScheme ac = new AnnotationColourScheme();
1901 ac.setAboveThreshold(acg.getAboveThreshold());
1902 ac.setThreshold(acg.getAnnotationThreshold());
1903 // 2.10.2 save annotationId (unique) not annotation label
1904 ac.setAnnotation(acg.getAnnotation().annotationId);
1905 if (acg.getBaseColour() instanceof UserColourScheme)
1908 setUserColourScheme(acg.getBaseColour(), userColours, jm));
1913 ColourSchemeProperty.getColourName(acg.getBaseColour()));
1916 ac.setMaxColour(acg.getMaxColour().getRGB());
1917 ac.setMinColour(acg.getMinColour().getRGB());
1918 ac.setPerSequence(acg.isSeqAssociated());
1919 ac.setPredefinedColours(acg.isPredefinedColours());
1923 private void storeAlignmentAnnotation(AlignmentAnnotation[] aa,
1924 IdentityHashMap<SequenceGroup, String> groupRefs,
1925 AlignmentViewport av, Set<String> calcIdSet, boolean storeDS,
1926 SequenceSet vamsasSet)
1929 for (int i = 0; i < aa.length; i++)
1931 Annotation an = new Annotation();
1933 AlignmentAnnotation annotation = aa[i];
1934 if (annotation.annotationId != null)
1936 annotationIds.put(annotation.annotationId, annotation);
1939 an.setId(annotation.annotationId);
1941 an.setVisible(annotation.visible);
1943 an.setDescription(annotation.description);
1945 if (annotation.sequenceRef != null)
1947 // 2.9 JAL-1781 xref on sequence id rather than name
1948 an.setSequenceRef(seqsToIds.get(annotation.sequenceRef));
1950 if (annotation.groupRef != null)
1952 String groupIdr = groupRefs.get(annotation.groupRef);
1953 if (groupIdr == null)
1955 // make a locally unique String
1956 groupRefs.put(annotation.groupRef,
1957 groupIdr = ("" + System.currentTimeMillis()
1958 + annotation.groupRef.getName()
1959 + groupRefs.size()));
1961 an.setGroupRef(groupIdr.toString());
1964 // store all visualization attributes for annotation
1965 an.setGraphHeight(annotation.graphHeight);
1966 an.setCentreColLabels(annotation.centreColLabels);
1967 an.setScaleColLabels(annotation.scaleColLabel);
1968 an.setShowAllColLabels(annotation.showAllColLabels);
1969 an.setBelowAlignment(annotation.belowAlignment);
1971 if (annotation.graph > 0)
1974 an.setGraphType(annotation.graph);
1975 an.setGraphGroup(annotation.graphGroup);
1976 if (annotation.getThreshold() != null)
1978 ThresholdLine line = new ThresholdLine();
1979 line.setLabel(annotation.getThreshold().label);
1980 line.setValue(annotation.getThreshold().value);
1981 line.setColour(annotation.getThreshold().colour.getRGB());
1982 an.setThresholdLine(line);
1990 an.setLabel(annotation.label);
1992 if (annotation == av.getAlignmentQualityAnnot()
1993 || annotation == av.getAlignmentConservationAnnotation()
1994 || annotation == av.getAlignmentConsensusAnnotation()
1995 || annotation.autoCalculated)
1997 // new way of indicating autocalculated annotation -
1998 an.setAutoCalculated(annotation.autoCalculated);
2000 if (annotation.hasScore())
2002 an.setScore(annotation.getScore());
2005 if (annotation.getCalcId() != null)
2007 calcIdSet.add(annotation.getCalcId());
2008 an.setCalcId(annotation.getCalcId());
2010 if (annotation.hasProperties())
2012 for (String pr : annotation.getProperties())
2014 jalview.xml.binding.jalview.Annotation.Property prop = new jalview.xml.binding.jalview.Annotation.Property();
2016 prop.setValue(annotation.getProperty(pr));
2017 // an.addProperty(prop);
2018 an.getProperty().add(prop);
2022 AnnotationElement ae;
2023 if (annotation.annotations != null)
2025 an.setScoreOnly(false);
2026 for (int a = 0; a < annotation.annotations.length; a++)
2028 if ((annotation == null) || (annotation.annotations[a] == null))
2033 ae = new AnnotationElement();
2034 if (annotation.annotations[a].description != null)
2036 ae.setDescription(annotation.annotations[a].description);
2038 if (annotation.annotations[a].displayCharacter != null)
2040 ae.setDisplayCharacter(
2041 annotation.annotations[a].displayCharacter);
2044 if (!Float.isNaN(annotation.annotations[a].value))
2046 ae.setValue(annotation.annotations[a].value);
2050 if (annotation.annotations[a].secondaryStructure > ' ')
2052 ae.setSecondaryStructure(
2053 annotation.annotations[a].secondaryStructure + "");
2056 if (annotation.annotations[a].colour != null
2057 && annotation.annotations[a].colour != java.awt.Color.black)
2059 ae.setColour(annotation.annotations[a].colour.getRGB());
2062 // an.addAnnotationElement(ae);
2063 an.getAnnotationElement().add(ae);
2064 if (annotation.autoCalculated)
2066 // only write one non-null entry into the annotation row -
2067 // sufficient to get the visualization attributes necessary to
2075 an.setScoreOnly(true);
2077 if (!storeDS || (storeDS && !annotation.autoCalculated))
2079 // skip autocalculated annotation - these are only provided for
2081 // vamsasSet.addAnnotation(an);
2082 vamsasSet.getAnnotation().add(an);
2088 private CalcIdParam createCalcIdParam(String calcId, AlignViewport av)
2090 AutoCalcSetting settings = av.getCalcIdSettingsFor(calcId);
2091 if (settings != null)
2093 CalcIdParam vCalcIdParam = new CalcIdParam();
2094 vCalcIdParam.setCalcId(calcId);
2095 // vCalcIdParam.addServiceURL(settings.getServiceURI());
2096 vCalcIdParam.getServiceURL().add(settings.getServiceURI());
2097 // generic URI allowing a third party to resolve another instance of the
2098 // service used for this calculation
2099 for (String url : settings.getServiceURLs())
2101 // vCalcIdParam.addServiceURL(urls);
2102 vCalcIdParam.getServiceURL().add(url);
2104 vCalcIdParam.setVersion("1.0");
2105 if (settings.getPreset() != null)
2107 WsParamSetI setting = settings.getPreset();
2108 vCalcIdParam.setName(setting.getName());
2109 vCalcIdParam.setDescription(setting.getDescription());
2113 vCalcIdParam.setName("");
2114 vCalcIdParam.setDescription("Last used parameters");
2116 // need to be able to recover 1) settings 2) user-defined presets or
2117 // recreate settings from preset 3) predefined settings provided by
2118 // service - or settings that can be transferred (or discarded)
2119 vCalcIdParam.setParameters(
2120 settings.getWsParamFile().replace("\n", "|\\n|"));
2121 vCalcIdParam.setAutoUpdate(settings.isAutoUpdate());
2122 // todo - decide if updateImmediately is needed for any projects.
2124 return vCalcIdParam;
2129 private boolean recoverCalcIdParam(CalcIdParam calcIdParam,
2132 if (calcIdParam.getVersion().equals("1.0"))
2134 final String[] calcIds = calcIdParam.getServiceURL().toArray(new String[0]);
2135 Jws2Instance service = Jws2Discoverer.getDiscoverer()
2136 .getPreferredServiceFor(calcIds);
2137 if (service != null)
2139 WsParamSetI parmSet = null;
2142 parmSet = service.getParamStore().parseServiceParameterFile(
2143 calcIdParam.getName(), calcIdParam.getDescription(),
2145 calcIdParam.getParameters().replace("|\\n|", "\n"));
2146 } catch (IOException x)
2148 warn("Couldn't parse parameter data for "
2149 + calcIdParam.getCalcId(), x);
2152 List<ArgumentI> argList = null;
2153 if (calcIdParam.getName().length() > 0)
2155 parmSet = service.getParamStore()
2156 .getPreset(calcIdParam.getName());
2157 if (parmSet != null)
2159 // TODO : check we have a good match with settings in AACon -
2160 // otherwise we'll need to create a new preset
2165 argList = parmSet.getArguments();
2168 AAConSettings settings = new AAConSettings(
2169 calcIdParam.isAutoUpdate(), service, parmSet, argList);
2170 av.setCalcIdSettingsFor(calcIdParam.getCalcId(), settings,
2171 calcIdParam.isNeedsUpdate());
2176 warn("Cannot resolve a service for the parameters used in this project. Try configuring a JABAWS server.");
2180 throw new Error(MessageManager.formatMessage(
2181 "error.unsupported_version_calcIdparam", new Object[]
2182 { calcIdParam.toString() }));
2186 * External mapping between jalview objects and objects yielding a valid and
2187 * unique object ID string. This is null for normal Jalview project IO, but
2188 * non-null when a jalview project is being read or written as part of a
2191 IdentityHashMap jv2vobj = null;
2194 * Construct a unique ID for jvobj using either existing bindings or if none
2195 * exist, the result of the hashcode call for the object.
2198 * jalview data object
2199 * @return unique ID for referring to jvobj
2201 private String makeHashCode(Object jvobj, String altCode)
2203 if (jv2vobj != null)
2205 Object id = jv2vobj.get(jvobj);
2208 return id.toString();
2210 // check string ID mappings
2211 if (jvids2vobj != null && jvobj instanceof String)
2213 id = jvids2vobj.get(jvobj);
2217 return id.toString();
2219 // give up and warn that something has gone wrong
2220 warn("Cannot find ID for object in external mapping : " + jvobj);
2226 * return local jalview object mapped to ID, if it exists
2230 * @return null or object bound to idcode
2232 private Object retrieveExistingObj(String idcode)
2234 if (idcode != null && vobj2jv != null)
2236 return vobj2jv.get(idcode);
2242 * binding from ID strings from external mapping table to jalview data model
2245 private Hashtable vobj2jv;
2247 private Sequence createVamsasSequence(String id, SequenceI jds)
2249 return createVamsasSequence(true, id, jds, null);
2252 private Sequence createVamsasSequence(boolean recurse, String id,
2253 SequenceI jds, SequenceI parentseq)
2255 Sequence vamsasSeq = new Sequence();
2256 vamsasSeq.setId(id);
2257 vamsasSeq.setName(jds.getName());
2258 vamsasSeq.setSequence(jds.getSequenceAsString());
2259 vamsasSeq.setDescription(jds.getDescription());
2260 jalview.datamodel.DBRefEntry[] dbrefs = null;
2261 if (jds.getDatasetSequence() != null)
2263 vamsasSeq.setDsseqid(seqHash(jds.getDatasetSequence()));
2267 // seqId==dsseqid so we can tell which sequences really are
2268 // dataset sequences only
2269 vamsasSeq.setDsseqid(id);
2270 dbrefs = jds.getDBRefs();
2271 if (parentseq == null)
2278 for (int d = 0; d < dbrefs.length; d++)
2280 DBRef dbref = new DBRef();
2281 dbref.setSource(dbrefs[d].getSource());
2282 dbref.setVersion(dbrefs[d].getVersion());
2283 dbref.setAccessionId(dbrefs[d].getAccessionId());
2284 if (dbrefs[d].hasMap())
2286 Mapping mp = createVamsasMapping(dbrefs[d].getMap(), parentseq,
2288 dbref.setMapping(mp);
2290 // vamsasSeq.addDBRef(dbref);
2291 vamsasSeq.getDBRef().add(dbref);
2297 private Mapping createVamsasMapping(jalview.datamodel.Mapping jmp,
2298 SequenceI parentseq, SequenceI jds, boolean recurse)
2301 if (jmp.getMap() != null)
2305 jalview.util.MapList mlst = jmp.getMap();
2306 List<int[]> r = mlst.getFromRanges();
2307 for (int[] range : r)
2309 MapListFrom mfrom = new MapListFrom();
2310 mfrom.setStart(range[0]);
2311 mfrom.setEnd(range[1]);
2312 // mp.addMapListFrom(mfrom);
2313 mp.getMapListFrom().add(mfrom);
2315 r = mlst.getToRanges();
2316 for (int[] range : r)
2318 MapListTo mto = new MapListTo();
2319 mto.setStart(range[0]);
2320 mto.setEnd(range[1]);
2321 // mp.addMapListTo(mto);
2322 mp.getMapListTo().add(mto);
2324 mp.setMapFromUnit(BigInteger.valueOf(mlst.getFromRatio()));
2325 mp.setMapToUnit(BigInteger.valueOf(mlst.getToRatio()));
2326 if (jmp.getTo() != null)
2328 // MappingChoice mpc = new MappingChoice();
2330 // check/create ID for the sequence referenced by getTo()
2333 SequenceI ps = null;
2334 if (parentseq != jmp.getTo()
2335 && parentseq.getDatasetSequence() != jmp.getTo())
2337 // chaining dbref rather than a handshaking one
2338 jmpid = seqHash(ps = jmp.getTo());
2342 jmpid = seqHash(ps = parentseq);
2344 // mpc.setDseqFor(jmpid);
2345 mp.setDseqFor(jmpid);
2346 if (!seqRefIds.containsKey(jmpid))
2348 jalview.bin.Cache.log.debug("creatign new DseqFor ID");
2349 seqRefIds.put(jmpid, ps);
2353 jalview.bin.Cache.log.debug("reusing DseqFor ID");
2356 // mp.setMappingChoice(mpc);
2362 String setUserColourScheme(jalview.schemes.ColourSchemeI cs,
2363 List<UserColourScheme> userColours, JalviewModel jm)
2366 jalview.schemes.UserColourScheme ucs = (jalview.schemes.UserColourScheme) cs;
2367 boolean newucs = false;
2368 if (!userColours.contains(ucs))
2370 userColours.add(ucs);
2373 id = "ucs" + userColours.indexOf(ucs);
2376 // actually create the scheme's entry in the XML model
2377 java.awt.Color[] colours = ucs.getColours();
2378 UserColours uc = new UserColours();
2379 // UserColourScheme jbucs = new UserColourScheme();
2380 JalviewUserColours jbucs = new JalviewUserColours();
2382 for (int i = 0; i < colours.length; i++)
2384 Colour col = new Colour();
2385 col.setName(ResidueProperties.aa[i]);
2386 col.setRGB(jalview.util.Format.getHexString(colours[i]));
2387 // jbucs.addColour(col);
2388 jbucs.getColour().add(col);
2390 if (ucs.getLowerCaseColours() != null)
2392 colours = ucs.getLowerCaseColours();
2393 for (int i = 0; i < colours.length; i++)
2395 Colour col = new Colour();
2396 col.setName(ResidueProperties.aa[i].toLowerCase());
2397 col.setRGB(jalview.util.Format.getHexString(colours[i]));
2398 // jbucs.addColour(col);
2399 jbucs.getColour().add(col);
2404 uc.setUserColourScheme(jbucs);
2405 // jm.addUserColours(uc);
2406 jm.getUserColours().add(uc);
2412 jalview.schemes.UserColourScheme getUserColourScheme(
2413 JalviewModel jm, String id)
2415 List<UserColours> uc = jm.getUserColours();
2416 UserColours colours = null;
2418 for (int i = 0; i < uc.length; i++)
2420 if (uc[i].getId().equals(id))
2427 for (UserColours c : uc)
2429 if (c.getId().equals(id))
2436 java.awt.Color[] newColours = new java.awt.Color[24];
2438 for (int i = 0; i < 24; i++)
2440 newColours[i] = new java.awt.Color(Integer.parseInt(
2441 // colours.getUserColourScheme().getColour(i).getRGB(), 16));
2442 colours.getUserColourScheme().getColour().get(i).getRGB(),
2446 jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(
2449 if (colours.getUserColourScheme().getColour().size()/*Count()*/ > 24)
2451 newColours = new java.awt.Color[23];
2452 for (int i = 0; i < 23; i++)
2454 newColours[i] = new java.awt.Color(Integer.parseInt(
2455 colours.getUserColourScheme().getColour().get(i + 24)
2459 ucs.setLowerCaseColours(newColours);
2466 * contains last error message (if any) encountered by XML loader.
2468 String errorMessage = null;
2471 * flag to control whether the Jalview2XML_V1 parser should be deferred to if
2472 * exceptions are raised during project XML parsing
2474 public boolean attemptversion1parse = false;
2477 * Load a jalview project archive from a jar file
2480 * - HTTP URL or filename
2482 public AlignFrame loadJalviewAlign(final Object file)
2485 jalview.gui.AlignFrame af = null;
2489 // create list to store references for any new Jmol viewers created
2490 newStructureViewers = new Vector<>();
2491 // UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
2492 // Workaround is to make sure caller implements the JarInputStreamProvider
2494 // so we can re-open the jar input stream for each entry.
2496 jarInputStreamProvider jprovider = createjarInputStreamProvider(file);
2497 af = loadJalviewAlign(jprovider);
2500 af.setMenusForViewport();
2502 } catch (MalformedURLException e)
2504 errorMessage = "Invalid URL format for '" + file + "'";
2510 SwingUtilities.invokeAndWait(new Runnable()
2515 setLoadingFinishedForNewStructureViewers();
2518 } catch (Exception x)
2520 System.err.println("Error loading alignment: " + x.getMessage());
2526 @SuppressWarnings("unused")
2527 private jarInputStreamProvider createjarInputStreamProvider(
2528 final Object ofile) throws MalformedURLException
2531 // BH 2018 allow for bytes already attached to File object
2532 final String file = ofile.toString();
2533 byte[] bytes = /** @j2sNative ofile._bytes ||*/null;
2534 if (bytes != null) {
2536 return new jarInputStreamProvider()
2540 public JarInputStream getJarInputStream() throws IOException
2542 return new JarInputStream(new ByteArrayInputStream(bytes));
2546 public String getFilename()
2554 errorMessage = null;
2555 uniqueSetSuffix = null;
2557 viewportsAdded.clear();
2558 frefedSequence = null;
2560 if (file.startsWith("http://"))
2562 url = new URL(file);
2564 final URL _url = url;
2565 return new jarInputStreamProvider()
2569 public JarInputStream getJarInputStream() throws IOException
2573 return new JarInputStream(_url.openStream());
2577 return new JarInputStream(new FileInputStream(file));
2582 public String getFilename()
2590 * Recover jalview session from a jalview project archive. Caller may
2591 * initialise uniqueSetSuffix, seqRefIds, viewportsAdded and frefedSequence
2592 * themselves. Any null fields will be initialised with default values,
2593 * non-null fields are left alone.
2598 public AlignFrame loadJalviewAlign(final jarInputStreamProvider jprovider)
2600 errorMessage = null;
2601 if (uniqueSetSuffix == null)
2603 uniqueSetSuffix = System.currentTimeMillis() % 100000 + "";
2605 if (seqRefIds == null)
2609 AlignFrame af = null, _af = null;
2610 IdentityHashMap<AlignmentI, AlignmentI> importedDatasets = new IdentityHashMap<>();
2611 Map<String, AlignFrame> gatherToThisFrame = new HashMap<>();
2612 final String file = jprovider.getFilename();
2615 JarInputStream jin = null;
2616 JarEntry jarentry = null;
2621 jin = jprovider.getJarInputStream();
2622 for (int i = 0; i < entryCount; i++)
2624 jarentry = jin.getNextJarEntry();
2627 if (jarentry != null && jarentry.getName().endsWith(".xml"))
2629 InputStreamReader in = new InputStreamReader(jin, UTF_8);
2630 // JalviewModel object = new JalviewModel();
2632 JAXBContext jc = JAXBContext
2633 .newInstance("jalview.xml.binding.jalview");
2634 XMLStreamReader streamReader = XMLInputFactory.newInstance()
2635 .createXMLStreamReader(jin);
2636 javax.xml.bind.Unmarshaller um = jc.createUnmarshaller();
2637 JAXBElement<JalviewModel> jbe = um
2638 .unmarshal(streamReader, JalviewModel.class);
2639 JalviewModel object = jbe.getValue();
2642 Unmarshaller unmar = new Unmarshaller(object);
2643 unmar.setValidation(false);
2644 object = (JalviewModel) unmar.unmarshal(in);
2646 if (true) // !skipViewport(object))
2648 _af = loadFromObject(object, file, true, jprovider);
2649 if (_af != null && object.getViewport().size() > 0)
2650 // getJalviewModelSequence().getViewportCount() > 0)
2654 // store a reference to the first view
2657 if (_af.getViewport().isGatherViewsHere())
2659 // if this is a gathered view, keep its reference since
2660 // after gathering views, only this frame will remain
2662 gatherToThisFrame.put(_af.getViewport().getSequenceSetId(),
2665 // Save dataset to register mappings once all resolved
2666 importedDatasets.put(
2667 af.getViewport().getAlignment().getDataset(),
2668 af.getViewport().getAlignment().getDataset());
2673 else if (jarentry != null)
2675 // Some other file here.
2678 } while (jarentry != null);
2679 resolveFrefedSequences();
2680 } catch (IOException ex)
2682 ex.printStackTrace();
2683 errorMessage = "Couldn't locate Jalview XML file : " + file;
2685 "Exception whilst loading jalview XML file : " + ex + "\n");
2686 } catch (Exception ex)
2688 System.err.println("Parsing as Jalview Version 2 file failed.");
2689 ex.printStackTrace(System.err);
2690 if (attemptversion1parse)
2692 // Is Version 1 Jar file?
2695 af = new Jalview2XML_V1(raiseGUI).LoadJalviewAlign(jprovider);
2696 } catch (Exception ex2)
2698 System.err.println("Exception whilst loading as jalviewXMLV1:");
2699 ex2.printStackTrace();
2703 if (Desktop.instance != null)
2705 Desktop.instance.stopLoading();
2709 System.out.println("Successfully loaded archive file");
2712 ex.printStackTrace();
2715 "Exception whilst loading jalview XML file : " + ex + "\n");
2716 } catch (OutOfMemoryError e)
2718 // Don't use the OOM Window here
2719 errorMessage = "Out of memory loading jalview XML file";
2720 System.err.println("Out of memory whilst loading jalview XML file");
2721 e.printStackTrace();
2725 * Regather multiple views (with the same sequence set id) to the frame (if
2726 * any) that is flagged as the one to gather to, i.e. convert them to tabbed
2727 * views instead of separate frames. Note this doesn't restore a state where
2728 * some expanded views in turn have tabbed views - the last "first tab" read
2729 * in will play the role of gatherer for all.
2731 for (AlignFrame fr : gatherToThisFrame.values())
2733 Desktop.instance.gatherViews(fr);
2736 restoreSplitFrames();
2737 for (AlignmentI ds : importedDatasets.keySet())
2739 if (ds.getCodonFrames() != null)
2741 StructureSelectionManager
2742 .getStructureSelectionManager(Desktop.instance)
2743 .registerMappings(ds.getCodonFrames());
2746 if (errorMessage != null)
2751 if (Desktop.instance != null)
2753 Desktop.instance.stopLoading();
2760 * Try to reconstruct and display SplitFrame windows, where each contains
2761 * complementary dna and protein alignments. Done by pairing up AlignFrame
2762 * objects (created earlier) which have complementary viewport ids associated.
2764 protected void restoreSplitFrames()
2766 List<SplitFrame> gatherTo = new ArrayList<>();
2767 List<AlignFrame> addedToSplitFrames = new ArrayList<>();
2768 Map<String, AlignFrame> dna = new HashMap<>();
2771 * Identify the DNA alignments
2773 for (Entry<Viewport, AlignFrame> candidate : splitFrameCandidates
2776 AlignFrame af = candidate.getValue();
2777 if (af.getViewport().getAlignment().isNucleotide())
2779 dna.put(candidate.getKey().getId(), af);
2784 * Try to match up the protein complements
2786 for (Entry<Viewport, AlignFrame> candidate : splitFrameCandidates
2789 AlignFrame af = candidate.getValue();
2790 if (!af.getViewport().getAlignment().isNucleotide())
2792 String complementId = candidate.getKey().getComplementId();
2793 // only non-null complements should be in the Map
2794 if (complementId != null && dna.containsKey(complementId))
2796 final AlignFrame dnaFrame = dna.get(complementId);
2797 SplitFrame sf = createSplitFrame(dnaFrame, af);
2798 addedToSplitFrames.add(dnaFrame);
2799 addedToSplitFrames.add(af);
2800 dnaFrame.setMenusForViewport();
2801 af.setMenusForViewport();
2802 if (af.getViewport().isGatherViewsHere())
2811 * Open any that we failed to pair up (which shouldn't happen!) as
2812 * standalone AlignFrame's.
2814 for (Entry<Viewport, AlignFrame> candidate : splitFrameCandidates
2817 AlignFrame af = candidate.getValue();
2818 if (!addedToSplitFrames.contains(af))
2820 Viewport view = candidate.getKey();
2821 Desktop.addInternalFrame(af, view.getTitle(),
2822 safeInt(view.getWidth()), safeInt(view.getHeight()));
2823 af.setMenusForViewport();
2824 System.err.println("Failed to restore view " + view.getTitle()
2825 + " to split frame");
2830 * Gather back into tabbed views as flagged.
2832 for (SplitFrame sf : gatherTo)
2834 Desktop.instance.gatherViews(sf);
2837 splitFrameCandidates.clear();
2841 * Construct and display one SplitFrame holding DNA and protein alignments.
2844 * @param proteinFrame
2847 protected SplitFrame createSplitFrame(AlignFrame dnaFrame,
2848 AlignFrame proteinFrame)
2850 SplitFrame splitFrame = new SplitFrame(dnaFrame, proteinFrame);
2851 String title = MessageManager.getString("label.linked_view_title");
2852 int width = (int) dnaFrame.getBounds().getWidth();
2853 int height = (int) (dnaFrame.getBounds().getHeight()
2854 + proteinFrame.getBounds().getHeight() + 50);
2857 * SplitFrame location is saved to both enclosed frames
2859 splitFrame.setLocation(dnaFrame.getX(), dnaFrame.getY());
2860 Desktop.addInternalFrame(splitFrame, title, width, height);
2863 * And compute cDNA consensus (couldn't do earlier with consensus as
2864 * mappings were not yet present)
2866 proteinFrame.getViewport().alignmentChanged(proteinFrame.alignPanel);
2872 * check errorMessage for a valid error message and raise an error box in the
2873 * GUI or write the current errorMessage to stderr and then clear the error
2876 protected void reportErrors()
2878 reportErrors(false);
2881 protected void reportErrors(final boolean saving)
2883 if (errorMessage != null)
2885 final String finalErrorMessage = errorMessage;
2888 javax.swing.SwingUtilities.invokeLater(new Runnable()
2893 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
2895 "Error " + (saving ? "saving" : "loading")
2897 JvOptionPane.WARNING_MESSAGE);
2903 System.err.println("Problem loading Jalview file: " + errorMessage);
2906 errorMessage = null;
2909 Map<String, String> alreadyLoadedPDB = new HashMap<>();
2912 * when set, local views will be updated from view stored in JalviewXML
2913 * Currently (28th Sep 2008) things will go horribly wrong in vamsas document
2914 * sync if this is set to true.
2916 private final boolean updateLocalViews = false;
2919 * Returns the path to a temporary file holding the PDB file for the given PDB
2920 * id. The first time of asking, searches for a file of that name in the
2921 * Jalview project jar, and copies it to a new temporary file. Any repeat
2922 * requests just return the path to the file previously created.
2928 String loadPDBFile(jarInputStreamProvider jprovider, String pdbId,
2931 if (alreadyLoadedPDB.containsKey(pdbId))
2933 return alreadyLoadedPDB.get(pdbId).toString();
2936 String tempFile = copyJarEntry(jprovider, pdbId, "jalview_pdb",
2938 if (tempFile != null)
2940 alreadyLoadedPDB.put(pdbId, tempFile);
2946 * Copies the jar entry of given name to a new temporary file and returns the
2947 * path to the file, or null if the entry is not found.
2950 * @param jarEntryName
2952 * a prefix for the temporary file name, must be at least three
2955 * null or original file - so new file can be given the same suffix
2959 protected String copyJarEntry(jarInputStreamProvider jprovider,
2960 String jarEntryName, String prefix, String origFile)
2962 BufferedReader in = null;
2963 PrintWriter out = null;
2964 String suffix = ".tmp";
2965 if (origFile == null)
2967 origFile = jarEntryName;
2969 int sfpos = origFile.lastIndexOf(".");
2970 if (sfpos > -1 && sfpos < (origFile.length() - 3))
2972 suffix = "." + origFile.substring(sfpos + 1);
2976 JarInputStream jin = jprovider.getJarInputStream();
2978 * if (jprovider.startsWith("http://")) { jin = new JarInputStream(new
2979 * URL(jprovider).openStream()); } else { jin = new JarInputStream(new
2980 * FileInputStream(jprovider)); }
2983 JarEntry entry = null;
2986 entry = jin.getNextJarEntry();
2987 } while (entry != null && !entry.getName().equals(jarEntryName));
2990 in = new BufferedReader(new InputStreamReader(jin, UTF_8));
2991 File outFile = File.createTempFile(prefix, suffix);
2992 outFile.deleteOnExit();
2993 out = new PrintWriter(new FileOutputStream(outFile));
2996 while ((data = in.readLine()) != null)
3001 String t = outFile.getAbsolutePath();
3006 warn("Couldn't find entry in Jalview Jar for " + jarEntryName);
3008 } catch (Exception ex)
3010 ex.printStackTrace();
3018 } catch (IOException e)
3032 private class JvAnnotRow
3034 public JvAnnotRow(int i, AlignmentAnnotation jaa)
3041 * persisted version of annotation row from which to take vis properties
3043 public jalview.datamodel.AlignmentAnnotation template;
3046 * original position of the annotation row in the alignment
3052 * Load alignment frame from jalview XML DOM object
3054 * @param jalviewModel
3057 * filename source string
3058 * @param loadTreesAndStructures
3059 * when false only create Viewport
3061 * data source provider
3062 * @return alignment frame created from view stored in DOM
3064 AlignFrame loadFromObject(JalviewModel jalviewModel, String file,
3065 boolean loadTreesAndStructures, jarInputStreamProvider jprovider)
3067 SequenceSet vamsasSet = jalviewModel.getVamsasModel().getSequenceSet().get(0);
3068 List<Sequence> vamsasSeqs = vamsasSet.getSequence();
3070 // JalviewModelSequence jms = object.getJalviewModelSequence();
3072 // Viewport view = (jms.getViewportCount() > 0) ? jms.getViewport(0)
3074 Viewport view = (jalviewModel.getViewport().size() > 0)
3075 ? jalviewModel.getViewport().get(0)
3078 // ////////////////////////////////
3081 List<SequenceI> hiddenSeqs = null;
3083 List<SequenceI> tmpseqs = new ArrayList<>();
3085 boolean multipleView = false;
3086 SequenceI referenceseqForView = null;
3087 // JSeq[] jseqs = object.getJalviewModelSequence().getJSeq();
3088 List<JSeq> jseqs = jalviewModel.getJSeq();
3089 int vi = 0; // counter in vamsasSeq array
3090 for (int i = 0; i < jseqs.size(); i++)
3092 JSeq jseq = jseqs.get(i);
3093 String seqId = jseq.getId();
3095 SequenceI tmpSeq = seqRefIds.get(seqId);
3098 if (!incompleteSeqs.containsKey(seqId))
3100 // may not need this check, but keep it for at least 2.9,1 release
3101 if (tmpSeq.getStart() != jseq.getStart()
3102 || tmpSeq.getEnd() != jseq.getEnd())
3105 "Warning JAL-2154 regression: updating start/end for sequence "
3106 + tmpSeq.toString() + " to " + jseq);
3111 incompleteSeqs.remove(seqId);
3113 if (vamsasSeqs.size() > vi
3114 && vamsasSeqs.get(vi).getId().equals(seqId))
3116 // most likely we are reading a dataset XML document so
3117 // update from vamsasSeq section of XML for this sequence
3118 tmpSeq.setName(vamsasSeqs.get(vi).getName());
3119 tmpSeq.setDescription(vamsasSeqs.get(vi).getDescription());
3120 tmpSeq.setSequence(vamsasSeqs.get(vi).getSequence());
3125 // reading multiple views, so vamsasSeq set is a subset of JSeq
3126 multipleView = true;
3128 tmpSeq.setStart(jseq.getStart());
3129 tmpSeq.setEnd(jseq.getEnd());
3130 tmpseqs.add(tmpSeq);
3134 Sequence vamsasSeq = vamsasSeqs.get(vi);
3135 tmpSeq = new jalview.datamodel.Sequence(vamsasSeq.getName(),
3136 vamsasSeq.getSequence());
3137 tmpSeq.setDescription(vamsasSeq.getDescription());
3138 tmpSeq.setStart(jseq.getStart());
3139 tmpSeq.setEnd(jseq.getEnd());
3140 tmpSeq.setVamsasId(uniqueSetSuffix + seqId);
3141 seqRefIds.put(vamsasSeq.getId(), tmpSeq);
3142 tmpseqs.add(tmpSeq);
3146 if (safeBoolean(jseq.isViewreference()))
3148 referenceseqForView = tmpseqs.get(tmpseqs.size() - 1);
3151 if (jseq.isHidden() != null && jseq.isHidden().booleanValue())
3153 if (hiddenSeqs == null)
3155 hiddenSeqs = new ArrayList<>();
3158 hiddenSeqs.add(tmpSeq);
3163 // Create the alignment object from the sequence set
3164 // ///////////////////////////////
3165 SequenceI[] orderedSeqs = tmpseqs
3166 .toArray(new SequenceI[tmpseqs.size()]);
3168 AlignmentI al = null;
3169 // so we must create or recover the dataset alignment before going further
3170 // ///////////////////////////////
3171 if (vamsasSet.getDatasetId() == null || vamsasSet.getDatasetId() == "")
3173 // older jalview projects do not have a dataset - so creat alignment and
3175 al = new Alignment(orderedSeqs);
3176 al.setDataset(null);
3180 boolean isdsal = jalviewModel.getViewport().isEmpty();
3183 // we are importing a dataset record, so
3184 // recover reference to an alignment already materialsed as dataset
3185 al = getDatasetFor(vamsasSet.getDatasetId());
3189 // materialse the alignment
3190 al = new Alignment(orderedSeqs);
3194 addDatasetRef(vamsasSet.getDatasetId(), al);
3197 // finally, verify all data in vamsasSet is actually present in al
3198 // passing on flag indicating if it is actually a stored dataset
3199 recoverDatasetFor(vamsasSet, al, isdsal);
3202 if (referenceseqForView != null)
3204 al.setSeqrep(referenceseqForView);
3206 // / Add the alignment properties
3207 for (int i = 0; i < vamsasSet.getSequenceSetProperties().size(); i++)
3209 SequenceSetProperties ssp = vamsasSet.getSequenceSetProperties()
3211 al.setProperty(ssp.getKey(), ssp.getValue());
3214 // ///////////////////////////////
3216 Hashtable pdbloaded = new Hashtable(); // TODO nothing writes to this??
3219 // load sequence features, database references and any associated PDB
3220 // structures for the alignment
3222 // prior to 2.10, this part would only be executed the first time a
3223 // sequence was encountered, but not afterwards.
3224 // now, for 2.10 projects, this is also done if the xml doc includes
3225 // dataset sequences not actually present in any particular view.
3227 for (int i = 0; i < vamsasSeqs.size(); i++)
3229 JSeq jseq = jseqs.get(i);
3230 if (jseq.getFeatures().size() > 0)
3232 List<Feature> features = jseq.getFeatures();
3233 for (int f = 0; f < features.size(); f++)
3235 Feature feat = features.get(f);
3236 SequenceFeature sf = new SequenceFeature(feat.getType(),
3237 feat.getDescription(), feat.getBegin(), feat.getEnd(),
3238 safeFloat(feat.getScore()), feat.getFeatureGroup());
3239 sf.setStatus(feat.getStatus());
3242 * load any feature attributes - include map-valued attributes
3244 Map<String, Map<String, String>> mapAttributes = new HashMap<>();
3245 for (int od = 0; od < feat.getOtherData().size(); od++)
3247 OtherData keyValue = feat.getOtherData().get(od);
3248 String attributeName = keyValue.getKey();
3249 String attributeValue = keyValue.getValue();
3250 if (attributeName.startsWith("LINK"))
3252 sf.addLink(attributeValue);
3256 String subAttribute = keyValue.getKey2();
3257 if (subAttribute == null)
3259 // simple string-valued attribute
3260 sf.setValue(attributeName, attributeValue);
3264 // attribute 'key' has sub-attribute 'key2'
3265 if (!mapAttributes.containsKey(attributeName))
3267 mapAttributes.put(attributeName, new HashMap<>());
3269 mapAttributes.get(attributeName).put(subAttribute,
3274 for (Entry<String, Map<String, String>> mapAttribute : mapAttributes
3277 sf.setValue(mapAttribute.getKey(), mapAttribute.getValue());
3280 // adds feature to datasequence's feature set (since Jalview 2.10)
3281 al.getSequenceAt(i).addSequenceFeature(sf);
3284 if (vamsasSeqs.get(i).getDBRef().size() > 0)
3286 // adds dbrefs to datasequence's set (since Jalview 2.10)
3288 al.getSequenceAt(i).getDatasetSequence() == null
3289 ? al.getSequenceAt(i)
3290 : al.getSequenceAt(i).getDatasetSequence(),
3293 if (jseq.getPdbids().size() > 0)
3295 List<Pdbids> ids = jseq.getPdbids();
3296 for (int p = 0; p < ids.size(); p++)
3298 Pdbids pdbid = ids.get(p);
3299 jalview.datamodel.PDBEntry entry = new jalview.datamodel.PDBEntry();
3300 entry.setId(pdbid.getId());
3301 if (pdbid.getType() != null)
3303 if (PDBEntry.Type.getType(pdbid.getType()) != null)
3305 entry.setType(PDBEntry.Type.getType(pdbid.getType()));
3309 entry.setType(PDBEntry.Type.FILE);
3312 // jprovider is null when executing 'New View'
3313 if (pdbid.getFile() != null && jprovider != null)
3315 if (!pdbloaded.containsKey(pdbid.getFile()))
3317 entry.setFile(loadPDBFile(jprovider, pdbid.getId(),
3322 entry.setFile(pdbloaded.get(pdbid.getId()).toString());
3326 if (pdbid.getPdbentryItem() != null)
3328 for (PdbentryItem item : pdbid.getPdbentryItem())
3330 for (Property pr : item.getProperty())
3332 entry.setProperty(pr.getName(), pr.getValue());
3337 for (Property prop : pdbid.getProperty())
3339 entry.setProperty(prop.getName(), prop.getValue());
3341 StructureSelectionManager
3342 .getStructureSelectionManager(Desktop.instance)
3343 .registerPDBEntry(entry);
3344 // adds PDBEntry to datasequence's set (since Jalview 2.10)
3345 if (al.getSequenceAt(i).getDatasetSequence() != null)
3347 al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
3351 al.getSequenceAt(i).addPDBId(entry);
3356 } // end !multipleview
3358 // ///////////////////////////////
3359 // LOAD SEQUENCE MAPPINGS
3361 if (vamsasSet.getAlcodonFrame().size() > 0)
3363 // TODO Potentially this should only be done once for all views of an
3365 List<AlcodonFrame> alc = vamsasSet.getAlcodonFrame();
3366 for (int i = 0; i < alc.size(); i++)
3368 AlignedCodonFrame cf = new AlignedCodonFrame();
3369 if (alc.get(i).getAlcodMap().size() > 0)
3371 List<AlcodMap> maps = alc.get(i).getAlcodMap();
3372 for (int m = 0; m < maps.size(); m++)
3374 AlcodMap map = maps.get(m);
3375 SequenceI dnaseq = seqRefIds.get(map.getDnasq());
3377 jalview.datamodel.Mapping mapping = null;
3378 // attach to dna sequence reference.
3379 if (map.getMapping() != null)
3381 mapping = addMapping(map.getMapping());
3382 if (dnaseq != null && mapping.getTo() != null)
3384 cf.addMap(dnaseq, mapping.getTo(), mapping.getMap());
3390 newAlcodMapRef(map.getDnasq(), cf, mapping));
3394 al.addCodonFrame(cf);
3399 // ////////////////////////////////
3401 List<JvAnnotRow> autoAlan = new ArrayList<>();
3404 * store any annotations which forward reference a group's ID
3406 Map<String, List<AlignmentAnnotation>> groupAnnotRefs = new Hashtable<>();
3408 if (vamsasSet.getAnnotation().size()/*Count()*/ > 0)
3410 List<Annotation> an = vamsasSet.getAnnotation();
3412 for (int i = 0; i < an.size(); i++)
3414 Annotation annotation = an.get(i);
3417 * test if annotation is automatically calculated for this view only
3419 boolean autoForView = false;
3420 if (annotation.getLabel().equals("Quality")
3421 || annotation.getLabel().equals("Conservation")
3422 || annotation.getLabel().equals("Consensus"))
3424 // Kludge for pre 2.5 projects which lacked the autocalculated flag
3426 // JAXB has no has() test; schema defaults value to false
3427 // if (!annotation.hasAutoCalculated())
3429 // annotation.setAutoCalculated(true);
3432 if (autoForView || annotation.isAutoCalculated())
3434 // remove ID - we don't recover annotation from other views for
3435 // view-specific annotation
3436 annotation.setId(null);
3439 // set visibility for other annotation in this view
3440 String annotationId = annotation.getId();
3441 if (annotationId != null && annotationIds.containsKey(annotationId))
3443 AlignmentAnnotation jda = annotationIds.get(annotationId);
3444 // in principle Visible should always be true for annotation displayed
3445 // in multiple views
3446 if (annotation.isVisible() != null)
3448 jda.visible = annotation.isVisible();
3451 al.addAnnotation(jda);
3455 // Construct new annotation from model.
3456 List<AnnotationElement> ae = annotation.getAnnotationElement();
3457 jalview.datamodel.Annotation[] anot = null;
3458 java.awt.Color firstColour = null;
3460 if (!annotation.isScoreOnly())
3462 anot = new jalview.datamodel.Annotation[al.getWidth()];
3463 for (int aa = 0; aa < ae.size() && aa < anot.length; aa++)
3465 AnnotationElement annElement = ae.get(aa);
3466 anpos = annElement.getPosition();
3468 if (anpos >= anot.length)
3473 float value = safeFloat(annElement.getValue());
3474 anot[anpos] = new jalview.datamodel.Annotation(
3475 annElement.getDisplayCharacter(),
3476 annElement.getDescription(),
3477 (annElement.getSecondaryStructure() == null
3478 || annElement.getSecondaryStructure()
3482 .getSecondaryStructure()
3485 anot[anpos].colour = new Color(safeInt(annElement.getColour()));
3486 if (firstColour == null)
3488 firstColour = anot[anpos].colour;
3492 jalview.datamodel.AlignmentAnnotation jaa = null;
3494 if (annotation.isGraph())
3496 float llim = 0, hlim = 0;
3497 // if (autoForView || an[i].isAutoCalculated()) {
3500 jaa = new jalview.datamodel.AlignmentAnnotation(
3501 annotation.getLabel(), annotation.getDescription(), anot,
3502 llim, hlim, safeInt(annotation.getGraphType()));
3504 jaa.graphGroup = safeInt(annotation.getGraphGroup());
3505 jaa._linecolour = firstColour;
3506 if (annotation.getThresholdLine() != null)
3508 jaa.setThreshold(new jalview.datamodel.GraphLine(
3509 safeFloat(annotation.getThresholdLine().getValue()),
3510 annotation.getThresholdLine().getLabel(),
3511 new java.awt.Color(safeInt(
3512 annotation.getThresholdLine().getColour()))));
3514 if (autoForView || annotation.isAutoCalculated())
3516 // Hardwire the symbol display line to ensure that labels for
3517 // histograms are displayed
3523 jaa = new jalview.datamodel.AlignmentAnnotation(
3524 annotation.getLabel(), annotation.getDescription(), anot);
3525 jaa._linecolour = firstColour;
3527 // register new annotation
3528 if (annotation.getId() != null)
3530 annotationIds.put(annotation.getId(), jaa);
3531 jaa.annotationId = annotation.getId();
3533 // recover sequence association
3534 String sequenceRef = annotation.getSequenceRef();
3535 if (sequenceRef != null)
3537 // from 2.9 sequenceRef is to sequence id (JAL-1781)
3538 SequenceI sequence = seqRefIds.get(sequenceRef);
3539 if (sequence == null)
3541 // in pre-2.9 projects sequence ref is to sequence name
3542 sequence = al.findName(sequenceRef);
3544 if (sequence != null)
3546 jaa.createSequenceMapping(sequence, 1, true);
3547 sequence.addAlignmentAnnotation(jaa);
3550 // and make a note of any group association
3551 if (annotation.getGroupRef() != null
3552 && annotation.getGroupRef().length() > 0)
3554 List<jalview.datamodel.AlignmentAnnotation> aal = groupAnnotRefs
3555 .get(annotation.getGroupRef());
3558 aal = new ArrayList<>();
3559 groupAnnotRefs.put(annotation.getGroupRef(), aal);
3564 if (annotation.getScore() != null)
3566 jaa.setScore(annotation.getScore().doubleValue());
3568 if (annotation.isVisible() != null)
3570 jaa.visible = annotation.isVisible().booleanValue();
3573 if (annotation.isCentreColLabels() != null)
3575 jaa.centreColLabels = annotation.isCentreColLabels()
3579 if (annotation.isScaleColLabels() != null)
3581 jaa.scaleColLabel = annotation.isScaleColLabels().booleanValue();
3583 if (annotation.isAutoCalculated())
3585 // newer files have an 'autoCalculated' flag and store calculation
3586 // state in viewport properties
3587 jaa.autoCalculated = true; // means annotation will be marked for
3588 // update at end of load.
3590 if (annotation.getGraphHeight() != null)
3592 jaa.graphHeight = annotation.getGraphHeight().intValue();
3594 jaa.belowAlignment = annotation.isBelowAlignment();
3595 jaa.setCalcId(annotation.getCalcId());
3596 if (annotation.getProperty().size() > 0)
3598 for (Annotation.Property prop : annotation
3601 jaa.setProperty(prop.getName(), prop.getValue());
3604 if (jaa.autoCalculated)
3606 autoAlan.add(new JvAnnotRow(i, jaa));
3609 // if (!autoForView)
3611 // add autocalculated group annotation and any user created annotation
3613 al.addAnnotation(jaa);
3617 // ///////////////////////
3619 // Create alignment markup and styles for this view
3620 if (jalviewModel.getJGroup().size() > 0)
3622 List<JGroup> groups = jalviewModel.getJGroup();
3623 boolean addAnnotSchemeGroup = false;
3624 for (int i = 0; i < groups.size(); i++)
3626 JGroup jGroup = groups.get(i);
3627 ColourSchemeI cs = null;
3628 if (jGroup.getColour() != null)
3630 if (jGroup.getColour().startsWith("ucs"))
3632 cs = getUserColourScheme(jalviewModel, jGroup.getColour());
3634 else if (jGroup.getColour().equals("AnnotationColourGradient")
3635 && jGroup.getAnnotationColours() != null)
3637 addAnnotSchemeGroup = true;
3641 cs = ColourSchemeProperty.getColourScheme(al,
3642 jGroup.getColour());
3645 int pidThreshold = safeInt(jGroup.getPidThreshold());
3647 Vector<SequenceI> seqs = new Vector<>();
3649 for (int s = 0; s < jGroup.getSeq().size(); s++)
3651 String seqId = jGroup.getSeq().get(s);
3652 SequenceI ts = seqRefIds.get(seqId);
3656 seqs.addElement(ts);
3660 if (seqs.size() < 1)
3665 SequenceGroup sg = new SequenceGroup(seqs, jGroup.getName(), cs,
3666 safeBoolean(jGroup.isDisplayBoxes()),
3667 safeBoolean(jGroup.isDisplayText()),
3668 safeBoolean(jGroup.isColourText()),
3669 safeInt(jGroup.getStart()), safeInt(jGroup.getEnd()));
3670 sg.getGroupColourScheme().setThreshold(pidThreshold, true);
3671 sg.getGroupColourScheme()
3672 .setConservationInc(safeInt(jGroup.getConsThreshold()));
3673 sg.setOutlineColour(new Color(safeInt(jGroup.getOutlineColour())));
3675 sg.textColour = new Color(safeInt(jGroup.getTextCol1()));
3676 sg.textColour2 = new Color(safeInt(jGroup.getTextCol2()));
3677 sg.setShowNonconserved(safeBoolean(jGroup.isShowUnconserved()));
3678 sg.thresholdTextColour = safeInt(jGroup.getTextColThreshold());
3679 // attributes with a default in the schema are never null
3680 sg.setShowConsensusHistogram(jGroup.isShowConsensusHistogram());
3681 sg.setshowSequenceLogo(jGroup.isShowSequenceLogo());
3682 sg.setNormaliseSequenceLogo(jGroup.isNormaliseSequenceLogo());
3683 sg.setIgnoreGapsConsensus(jGroup.isIgnoreGapsinConsensus());
3684 if (jGroup.getConsThreshold() != null
3685 && jGroup.getConsThreshold().intValue() != 0)
3687 Conservation c = new Conservation("All", sg.getSequences(null), 0,
3690 c.verdict(false, 25);
3691 sg.cs.setConservation(c);
3694 if (jGroup.getId() != null && groupAnnotRefs.size() > 0)
3696 // re-instate unique group/annotation row reference
3697 List<AlignmentAnnotation> jaal = groupAnnotRefs
3698 .get(jGroup.getId());
3701 for (AlignmentAnnotation jaa : jaal)
3704 if (jaa.autoCalculated)
3706 // match up and try to set group autocalc alignment row for this
3708 if (jaa.label.startsWith("Consensus for "))
3710 sg.setConsensus(jaa);
3712 // match up and try to set group autocalc alignment row for this
3714 if (jaa.label.startsWith("Conservation for "))
3716 sg.setConservationRow(jaa);
3723 if (addAnnotSchemeGroup)
3725 // reconstruct the annotation colourscheme
3726 sg.setColourScheme(constructAnnotationColour(
3727 jGroup.getAnnotationColours(), null, al, jalviewModel, false));
3733 // only dataset in this model, so just return.
3736 // ///////////////////////////////
3739 // If we just load in the same jar file again, the sequenceSetId
3740 // will be the same, and we end up with multiple references
3741 // to the same sequenceSet. We must modify this id on load
3742 // so that each load of the file gives a unique id
3743 String uniqueSeqSetId = view.getSequenceSetId() + uniqueSetSuffix;
3744 String viewId = (view.getId() == null ? null
3745 : view.getId() + uniqueSetSuffix);
3746 AlignFrame af = null;
3747 AlignViewport av = null;
3748 // now check to see if we really need to create a new viewport.
3749 if (multipleView && viewportsAdded.size() == 0)
3751 // We recovered an alignment for which a viewport already exists.
3752 // TODO: fix up any settings necessary for overlaying stored state onto
3753 // state recovered from another document. (may not be necessary).
3754 // we may need a binding from a viewport in memory to one recovered from
3756 // and then recover its containing af to allow the settings to be applied.
3757 // TODO: fix for vamsas demo
3759 "About to recover a viewport for existing alignment: Sequence set ID is "
3761 Object seqsetobj = retrieveExistingObj(uniqueSeqSetId);
3762 if (seqsetobj != null)
3764 if (seqsetobj instanceof String)
3766 uniqueSeqSetId = (String) seqsetobj;
3768 "Recovered extant sequence set ID mapping for ID : New Sequence set ID is "
3774 "Warning : Collision between sequence set ID string and existing jalview object mapping.");
3780 * indicate that annotation colours are applied across all groups (pre
3781 * Jalview 2.8.1 behaviour)
3783 boolean doGroupAnnColour = Jalview2XML.isVersionStringLaterThan("2.8.1",
3784 jalviewModel.getVersion());
3786 AlignmentPanel ap = null;
3787 boolean isnewview = true;
3790 // Check to see if this alignment already has a view id == viewId
3791 jalview.gui.AlignmentPanel views[] = Desktop
3792 .getAlignmentPanels(uniqueSeqSetId);
3793 if (views != null && views.length > 0)
3795 for (int v = 0; v < views.length; v++)
3797 if (views[v].av.getViewId().equalsIgnoreCase(viewId))
3799 // recover the existing alignpanel, alignframe, viewport
3800 af = views[v].alignFrame;
3803 // TODO: could even skip resetting view settings if we don't want to
3804 // change the local settings from other jalview processes
3813 af = loadViewport(file, jseqs, hiddenSeqs, al, jalviewModel, view,
3814 uniqueSeqSetId, viewId, autoAlan);
3815 av = af.getViewport();
3820 * Load any trees, PDB structures and viewers
3822 * Not done if flag is false (when this method is used for New View)
3824 if (loadTreesAndStructures)
3826 loadTrees(jalviewModel, view, af, av, ap);
3827 loadPDBStructures(jprovider, jseqs, af, ap);
3828 loadRnaViewers(jprovider, jseqs, ap);
3830 // and finally return.
3835 * Instantiate and link any saved RNA (Varna) viewers. The state of the Varna
3836 * panel is restored from separate jar entries, two (gapped and trimmed) per
3837 * sequence and secondary structure.
3839 * Currently each viewer shows just one sequence and structure (gapped and
3840 * trimmed), however this method is designed to support multiple sequences or
3841 * structures in viewers if wanted in future.
3847 private void loadRnaViewers(jarInputStreamProvider jprovider,
3848 List<JSeq> jseqs, AlignmentPanel ap)
3851 * scan the sequences for references to viewers; create each one the first
3852 * time it is referenced, add Rna models to existing viewers
3854 for (JSeq jseq : jseqs)
3856 for (int i = 0; i < jseq.getRnaViewer().size(); i++)
3858 RnaViewer viewer = jseq.getRnaViewer().get(i);
3859 AppVarna appVarna = findOrCreateVarnaViewer(viewer, uniqueSetSuffix,
3862 for (int j = 0; j < viewer.getSecondaryStructure().size(); j++)
3864 SecondaryStructure ss = viewer.getSecondaryStructure().get(j);
3865 SequenceI seq = seqRefIds.get(jseq.getId());
3866 AlignmentAnnotation ann = this.annotationIds
3867 .get(ss.getAnnotationId());
3870 * add the structure to the Varna display (with session state copied
3871 * from the jar to a temporary file)
3873 boolean gapped = safeBoolean(ss.isGapped());
3874 String rnaTitle = ss.getTitle();
3875 String sessionState = ss.getViewerState();
3876 String tempStateFile = copyJarEntry(jprovider, sessionState,
3878 RnaModel rna = new RnaModel(rnaTitle, ann, seq, null, gapped);
3879 appVarna.addModelSession(rna, rnaTitle, tempStateFile);
3881 appVarna.setInitialSelection(safeInt(viewer.getSelectedRna()));
3887 * Locate and return an already instantiated matching AppVarna, or create one
3891 * @param viewIdSuffix
3895 protected AppVarna findOrCreateVarnaViewer(RnaViewer viewer,
3896 String viewIdSuffix, AlignmentPanel ap)
3899 * on each load a suffix is appended to the saved viewId, to avoid conflicts
3900 * if load is repeated
3902 String postLoadId = viewer.getViewId() + viewIdSuffix;
3903 for (JInternalFrame frame : getAllFrames())
3905 if (frame instanceof AppVarna)
3907 AppVarna varna = (AppVarna) frame;
3908 if (postLoadId.equals(varna.getViewId()))
3910 // this viewer is already instantiated
3911 // could in future here add ap as another 'parent' of the
3912 // AppVarna window; currently just 1-to-many
3919 * viewer not found - make it
3921 RnaViewerModel model = new RnaViewerModel(postLoadId, viewer.getTitle(),
3922 safeInt(viewer.getXpos()), safeInt(viewer.getYpos()),
3923 safeInt(viewer.getWidth()), safeInt(viewer.getHeight()),
3924 safeInt(viewer.getDividerLocation()));
3925 AppVarna varna = new AppVarna(model, ap);
3931 * Load any saved trees
3939 protected void loadTrees(JalviewModel jm, Viewport view,
3940 AlignFrame af, AlignViewport av, AlignmentPanel ap)
3942 // TODO result of automated refactoring - are all these parameters needed?
3945 for (int t = 0; t < jm.getTree().size(); t++)
3948 Tree tree = jm.getTree().get(t);
3950 TreePanel tp = (TreePanel) retrieveExistingObj(tree.getId());
3953 tp = af.showNewickTree(new NewickFile(tree.getNewick()),
3954 tree.getTitle(), safeInt(tree.getWidth()),
3955 safeInt(tree.getHeight()), safeInt(tree.getXpos()),
3956 safeInt(tree.getYpos()));
3957 if (tree.getId() != null)
3959 // perhaps bind the tree id to something ?
3964 // update local tree attributes ?
3965 // TODO: should check if tp has been manipulated by user - if so its
3966 // settings shouldn't be modified
3967 tp.setTitle(tree.getTitle());
3968 tp.setBounds(new Rectangle(safeInt(tree.getXpos()),
3969 safeInt(tree.getYpos()), safeInt(tree.getWidth()),
3970 safeInt(tree.getHeight())));
3971 tp.setViewport(av); // af.viewport;
3972 // TODO: verify 'associate with all views' works still
3973 tp.getTreeCanvas().setViewport(av); // af.viewport;
3974 tp.getTreeCanvas().setAssociatedPanel(ap); // af.alignPanel;
3979 warn("There was a problem recovering stored Newick tree: \n"
3980 + tree.getNewick());
3984 tp.fitToWindow.setState(safeBoolean(tree.isFitToWindow()));
3985 tp.fitToWindow_actionPerformed(null);
3987 if (tree.getFontName() != null)
3990 new Font(tree.getFontName(), safeInt(tree.getFontStyle()),
3991 safeInt(tree.getFontSize())));
3996 new Font(view.getFontName(), safeInt(view.getFontStyle()),
3997 safeInt(view.getFontSize())));
4000 tp.showPlaceholders(safeBoolean(tree.isMarkUnlinked()));
4001 tp.showBootstrap(safeBoolean(tree.isShowBootstrap()));
4002 tp.showDistances(safeBoolean(tree.isShowDistances()));
4004 tp.getTreeCanvas().setThreshold(safeFloat(tree.getThreshold()));
4006 if (safeBoolean(tree.isCurrentTree()))
4008 af.getViewport().setCurrentTree(tp.getTree());
4012 } catch (Exception ex)
4014 ex.printStackTrace();
4019 * Load and link any saved structure viewers.
4026 protected void loadPDBStructures(jarInputStreamProvider jprovider,
4027 List<JSeq> jseqs, AlignFrame af, AlignmentPanel ap)
4030 * Run through all PDB ids on the alignment, and collect mappings between
4031 * distinct view ids and all sequences referring to that view.
4033 Map<String, StructureViewerModel> structureViewers = new LinkedHashMap<>();
4035 for (int i = 0; i < jseqs.size(); i++)
4037 JSeq jseq = jseqs.get(i);
4038 if (jseq.getPdbids().size() > 0)
4040 List<Pdbids> ids = jseq.getPdbids();
4041 for (int p = 0; p < ids.size(); p++)
4043 Pdbids pdbid = ids.get(p);
4044 final int structureStateCount = pdbid.getStructureState().size();
4045 for (int s = 0; s < structureStateCount; s++)
4047 // check to see if we haven't already created this structure view
4048 final StructureState structureState = pdbid
4049 .getStructureState().get(s);
4050 String sviewid = (structureState.getViewId() == null) ? null
4051 : structureState.getViewId() + uniqueSetSuffix;
4052 jalview.datamodel.PDBEntry jpdb = new jalview.datamodel.PDBEntry();
4053 // Originally : pdbid.getFile()
4054 // : TODO: verify external PDB file recovery still works in normal
4055 // jalview project load
4057 loadPDBFile(jprovider, pdbid.getId(), pdbid.getFile()));
4058 jpdb.setId(pdbid.getId());
4060 int x = safeInt(structureState.getXpos());
4061 int y = safeInt(structureState.getYpos());
4062 int width = safeInt(structureState.getWidth());
4063 int height = safeInt(structureState.getHeight());
4065 // Probably don't need to do this anymore...
4066 // Desktop.desktop.getComponentAt(x, y);
4067 // TODO: NOW: check that this recovers the PDB file correctly.
4068 String pdbFile = loadPDBFile(jprovider, pdbid.getId(),
4070 jalview.datamodel.SequenceI seq = seqRefIds
4071 .get(jseq.getId() + "");
4072 if (sviewid == null)
4074 sviewid = "_jalview_pre2_4_" + x + "," + y + "," + width + ","
4077 if (!structureViewers.containsKey(sviewid))
4079 structureViewers.put(sviewid,
4080 new StructureViewerModel(x, y, width, height, false,
4081 false, true, structureState.getViewId(),
4082 structureState.getType()));
4083 // Legacy pre-2.7 conversion JAL-823 :
4084 // do not assume any view has to be linked for colour by
4088 // assemble String[] { pdb files }, String[] { id for each
4089 // file }, orig_fileloc, SequenceI[][] {{ seqs_file 1 }, {
4090 // seqs_file 2}, boolean[] {
4091 // linkAlignPanel,superposeWithAlignpanel}} from hash
4092 StructureViewerModel jmoldat = structureViewers.get(sviewid);
4093 jmoldat.setAlignWithPanel(jmoldat.isAlignWithPanel()
4094 || structureState.isAlignwithAlignPanel());
4097 * Default colour by linked panel to false if not specified (e.g.
4098 * for pre-2.7 projects)
4100 boolean colourWithAlignPanel = jmoldat.isColourWithAlignPanel();
4101 colourWithAlignPanel |= structureState.isColourwithAlignPanel();
4102 jmoldat.setColourWithAlignPanel(colourWithAlignPanel);
4105 * Default colour by viewer to true if not specified (e.g. for
4108 boolean colourByViewer = jmoldat.isColourByViewer();
4109 colourByViewer &= structureState.isColourByJmol();
4110 jmoldat.setColourByViewer(colourByViewer);
4112 if (jmoldat.getStateData().length() < structureState
4113 .getValue()/*Content()*/.length())
4115 jmoldat.setStateData(structureState.getValue());// Content());
4117 if (pdbid.getFile() != null)
4119 File mapkey = new File(pdbid.getFile());
4120 StructureData seqstrmaps = jmoldat.getFileData().get(mapkey);
4121 if (seqstrmaps == null)
4123 jmoldat.getFileData().put(mapkey,
4124 seqstrmaps = jmoldat.new StructureData(pdbFile,
4127 if (!seqstrmaps.getSeqList().contains(seq))
4129 seqstrmaps.getSeqList().add(seq);
4135 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");
4142 // Instantiate the associated structure views
4143 for (Entry<String, StructureViewerModel> entry : structureViewers
4148 createOrLinkStructureViewer(entry, af, ap, jprovider);
4149 } catch (Exception e)
4152 "Error loading structure viewer: " + e.getMessage());
4153 // failed - try the next one
4165 protected void createOrLinkStructureViewer(
4166 Entry<String, StructureViewerModel> viewerData, AlignFrame af,
4167 AlignmentPanel ap, jarInputStreamProvider jprovider)
4169 final StructureViewerModel stateData = viewerData.getValue();
4172 * Search for any viewer windows already open from other alignment views
4173 * that exactly match the stored structure state
4175 StructureViewerBase comp = findMatchingViewer(viewerData);
4179 linkStructureViewer(ap, comp, stateData);
4184 * From 2.9: stateData.type contains JMOL or CHIMERA, data is in jar entry
4185 * "viewer_"+stateData.viewId
4187 if (ViewerType.CHIMERA.toString().equals(stateData.getType()))
4189 createChimeraViewer(viewerData, af, jprovider);
4194 * else Jmol (if pre-2.9, stateData contains JMOL state string)
4196 createJmolViewer(viewerData, af, jprovider);
4201 * Create a new Chimera viewer.
4207 protected void createChimeraViewer(
4208 Entry<String, StructureViewerModel> viewerData, AlignFrame af,
4209 jarInputStreamProvider jprovider)
4211 StructureViewerModel data = viewerData.getValue();
4212 String chimeraSessionFile = data.getStateData();
4215 * Copy Chimera session from jar entry "viewer_"+viewId to a temporary file
4217 * NB this is the 'saved' viewId as in the project file XML, _not_ the
4218 * 'uniquified' sviewid used to reconstruct the viewer here
4220 String viewerJarEntryName = getViewerJarEntryName(data.getViewId());
4221 chimeraSessionFile = copyJarEntry(jprovider, viewerJarEntryName,
4224 Set<Entry<File, StructureData>> fileData = data.getFileData()
4226 List<PDBEntry> pdbs = new ArrayList<>();
4227 List<SequenceI[]> allseqs = new ArrayList<>();
4228 for (Entry<File, StructureData> pdb : fileData)
4230 String filePath = pdb.getValue().getFilePath();
4231 String pdbId = pdb.getValue().getPdbId();
4232 // pdbs.add(new PDBEntry(filePath, pdbId));
4233 pdbs.add(new PDBEntry(pdbId, null, PDBEntry.Type.PDB, filePath));
4234 final List<SequenceI> seqList = pdb.getValue().getSeqList();
4235 SequenceI[] seqs = seqList.toArray(new SequenceI[seqList.size()]);
4239 boolean colourByChimera = data.isColourByViewer();
4240 boolean colourBySequence = data.isColourWithAlignPanel();
4242 // TODO use StructureViewer as a factory here, see JAL-1761
4243 final PDBEntry[] pdbArray = pdbs.toArray(new PDBEntry[pdbs.size()]);
4244 final SequenceI[][] seqsArray = allseqs
4245 .toArray(new SequenceI[allseqs.size()][]);
4246 String newViewId = viewerData.getKey();
4248 ChimeraViewFrame cvf = new ChimeraViewFrame(chimeraSessionFile,
4249 af.alignPanel, pdbArray, seqsArray, colourByChimera,
4250 colourBySequence, newViewId);
4251 cvf.setSize(data.getWidth(), data.getHeight());
4252 cvf.setLocation(data.getX(), data.getY());
4256 * Create a new Jmol window. First parse the Jmol state to translate filenames
4257 * loaded into the view, and record the order in which files are shown in the
4258 * Jmol view, so we can add the sequence mappings in same order.
4264 protected void createJmolViewer(
4265 final Entry<String, StructureViewerModel> viewerData,
4266 AlignFrame af, jarInputStreamProvider jprovider)
4268 final StructureViewerModel svattrib = viewerData.getValue();
4269 String state = svattrib.getStateData();
4272 * Pre-2.9: state element value is the Jmol state string
4274 * 2.9+: @type is "JMOL", state data is in a Jar file member named "viewer_"
4277 if (ViewerType.JMOL.toString().equals(svattrib.getType()))
4279 state = readJarEntry(jprovider,
4280 getViewerJarEntryName(svattrib.getViewId()));
4283 List<String> pdbfilenames = new ArrayList<>();
4284 List<SequenceI[]> seqmaps = new ArrayList<>();
4285 List<String> pdbids = new ArrayList<>();
4286 StringBuilder newFileLoc = new StringBuilder(64);
4287 int cp = 0, ncp, ecp;
4288 Map<File, StructureData> oldFiles = svattrib.getFileData();
4289 while ((ncp = state.indexOf("load ", cp)) > -1)
4293 // look for next filename in load statement
4294 newFileLoc.append(state.substring(cp,
4295 ncp = (state.indexOf("\"", ncp + 1) + 1)));
4296 String oldfilenam = state.substring(ncp,
4297 ecp = state.indexOf("\"", ncp));
4298 // recover the new mapping data for this old filename
4299 // have to normalize filename - since Jmol and jalview do
4301 // translation differently.
4302 StructureData filedat = oldFiles.get(new File(oldfilenam));
4303 if (filedat == null)
4305 String reformatedOldFilename = oldfilenam.replaceAll("/", "\\\\");
4306 filedat = oldFiles.get(new File(reformatedOldFilename));
4308 newFileLoc.append(Platform.escapeString(filedat.getFilePath()));
4309 pdbfilenames.add(filedat.getFilePath());
4310 pdbids.add(filedat.getPdbId());
4311 seqmaps.add(filedat.getSeqList().toArray(new SequenceI[0]));
4312 newFileLoc.append("\"");
4313 cp = ecp + 1; // advance beyond last \" and set cursor so we can
4314 // look for next file statement.
4315 } while ((ncp = state.indexOf("/*file*/", cp)) > -1);
4319 // just append rest of state
4320 newFileLoc.append(state.substring(cp));
4324 System.err.print("Ignoring incomplete Jmol state for PDB ids: ");
4325 newFileLoc = new StringBuilder(state);
4326 newFileLoc.append("; load append ");
4327 for (File id : oldFiles.keySet())
4329 // add this and any other pdb files that should be present in
4331 StructureData filedat = oldFiles.get(id);
4332 newFileLoc.append(filedat.getFilePath());
4333 pdbfilenames.add(filedat.getFilePath());
4334 pdbids.add(filedat.getPdbId());
4335 seqmaps.add(filedat.getSeqList().toArray(new SequenceI[0]));
4336 newFileLoc.append(" \"");
4337 newFileLoc.append(filedat.getFilePath());
4338 newFileLoc.append("\"");
4341 newFileLoc.append(";");
4344 if (newFileLoc.length() == 0)
4348 int histbug = newFileLoc.indexOf("history = ");
4352 * change "history = [true|false];" to "history = [1|0];"
4355 int diff = histbug == -1 ? -1 : newFileLoc.indexOf(";", histbug);
4356 String val = (diff == -1) ? null
4357 : newFileLoc.substring(histbug, diff);
4358 if (val != null && val.length() >= 4)
4360 if (val.contains("e")) // eh? what can it be?
4362 if (val.trim().equals("true"))
4370 newFileLoc.replace(histbug, diff, val);
4375 final String[] pdbf = pdbfilenames
4376 .toArray(new String[pdbfilenames.size()]);
4377 final String[] id = pdbids.toArray(new String[pdbids.size()]);
4378 final SequenceI[][] sq = seqmaps
4379 .toArray(new SequenceI[seqmaps.size()][]);
4380 final String fileloc = newFileLoc.toString();
4381 final String sviewid = viewerData.getKey();
4382 final AlignFrame alf = af;
4383 final Rectangle rect = new Rectangle(svattrib.getX(), svattrib.getY(),
4384 svattrib.getWidth(), svattrib.getHeight());
4387 javax.swing.SwingUtilities.invokeAndWait(new Runnable()
4392 JalviewStructureDisplayI sview = null;
4395 sview = new StructureViewer(
4396 alf.alignPanel.getStructureSelectionManager())
4397 .createView(StructureViewer.ViewerType.JMOL,
4398 pdbf, id, sq, alf.alignPanel, svattrib,
4399 fileloc, rect, sviewid);
4400 addNewStructureViewer(sview);
4401 } catch (OutOfMemoryError ex)
4403 new OOMWarning("restoring structure view for PDB id " + id,
4404 (OutOfMemoryError) ex.getCause());
4405 if (sview != null && sview.isVisible())
4407 sview.closeViewer(false);
4408 sview.setVisible(false);
4414 } catch (InvocationTargetException ex)
4416 warn("Unexpected error when opening Jmol view.", ex);
4418 } catch (InterruptedException e)
4420 // e.printStackTrace();
4426 * Generates a name for the entry in the project jar file to hold state
4427 * information for a structure viewer
4432 protected String getViewerJarEntryName(String viewId)
4434 return VIEWER_PREFIX + viewId;
4438 * Returns any open frame that matches given structure viewer data. The match
4439 * is based on the unique viewId, or (for older project versions) the frame's
4445 protected StructureViewerBase findMatchingViewer(
4446 Entry<String, StructureViewerModel> viewerData)
4448 final String sviewid = viewerData.getKey();
4449 final StructureViewerModel svattrib = viewerData.getValue();
4450 StructureViewerBase comp = null;
4451 JInternalFrame[] frames = getAllFrames();
4452 for (JInternalFrame frame : frames)
4454 if (frame instanceof StructureViewerBase)
4457 * Post jalview 2.4 schema includes structure view id
4459 if (sviewid != null && ((StructureViewerBase) frame).getViewId()
4462 comp = (StructureViewerBase) frame;
4463 break; // break added in 2.9
4466 * Otherwise test for matching position and size of viewer frame
4468 else if (frame.getX() == svattrib.getX()
4469 && frame.getY() == svattrib.getY()
4470 && frame.getHeight() == svattrib.getHeight()
4471 && frame.getWidth() == svattrib.getWidth())
4473 comp = (StructureViewerBase) frame;
4474 // no break in faint hope of an exact match on viewId
4482 * Link an AlignmentPanel to an existing structure viewer.
4487 * @param useinViewerSuperpos
4488 * @param usetoColourbyseq
4489 * @param viewerColouring
4491 protected void linkStructureViewer(AlignmentPanel ap,
4492 StructureViewerBase viewer, StructureViewerModel stateData)
4494 // NOTE: if the jalview project is part of a shared session then
4495 // view synchronization should/could be done here.
4497 final boolean useinViewerSuperpos = stateData.isAlignWithPanel();
4498 final boolean usetoColourbyseq = stateData.isColourWithAlignPanel();
4499 final boolean viewerColouring = stateData.isColourByViewer();
4500 Map<File, StructureData> oldFiles = stateData.getFileData();
4503 * Add mapping for sequences in this view to an already open viewer
4505 final AAStructureBindingModel binding = viewer.getBinding();
4506 for (File id : oldFiles.keySet())
4508 // add this and any other pdb files that should be present in the
4510 StructureData filedat = oldFiles.get(id);
4511 String pdbFile = filedat.getFilePath();
4512 SequenceI[] seq = filedat.getSeqList().toArray(new SequenceI[0]);
4513 binding.getSsm().setMapping(seq, null, pdbFile, DataSourceType.FILE,
4515 binding.addSequenceForStructFile(pdbFile, seq);
4517 // and add the AlignmentPanel's reference to the view panel
4518 viewer.addAlignmentPanel(ap);
4519 if (useinViewerSuperpos)
4521 viewer.useAlignmentPanelForSuperposition(ap);
4525 viewer.excludeAlignmentPanelForSuperposition(ap);
4527 if (usetoColourbyseq)
4529 viewer.useAlignmentPanelForColourbyseq(ap, !viewerColouring);
4533 viewer.excludeAlignmentPanelForColourbyseq(ap);
4538 * Get all frames within the Desktop.
4542 protected JInternalFrame[] getAllFrames()
4544 JInternalFrame[] frames = null;
4545 // TODO is this necessary - is it safe - risk of hanging?
4550 frames = Desktop.desktop.getAllFrames();
4551 } catch (ArrayIndexOutOfBoundsException e)
4553 // occasional No such child exceptions are thrown here...
4557 } catch (InterruptedException f)
4561 } while (frames == null);
4566 * Answers true if 'version' is equal to or later than 'supported', where each
4567 * is formatted as major/minor versions like "2.8.3" or "2.3.4b1" for bugfix
4568 * changes. Development and test values for 'version' are leniently treated
4572 * - minimum version we are comparing against
4574 * - version of data being processsed
4577 public static boolean isVersionStringLaterThan(String supported,
4580 if (supported == null || version == null
4581 || version.equalsIgnoreCase("DEVELOPMENT BUILD")
4582 || version.equalsIgnoreCase("Test")
4583 || version.equalsIgnoreCase("AUTOMATED BUILD"))
4585 System.err.println("Assuming project file with "
4586 + (version == null ? "null" : version)
4587 + " is compatible with Jalview version " + supported);
4592 return StringUtils.compareVersions(version, supported, "b") >= 0;
4596 Vector<JalviewStructureDisplayI> newStructureViewers = null;
4598 protected void addNewStructureViewer(JalviewStructureDisplayI sview)
4600 if (newStructureViewers != null)
4602 sview.getBinding().setFinishedLoadingFromArchive(false);
4603 newStructureViewers.add(sview);
4607 protected void setLoadingFinishedForNewStructureViewers()
4609 if (newStructureViewers != null)
4611 for (JalviewStructureDisplayI sview : newStructureViewers)
4613 sview.getBinding().setFinishedLoadingFromArchive(true);
4615 newStructureViewers.clear();
4616 newStructureViewers = null;
4620 AlignFrame loadViewport(String file, List<JSeq> JSEQ,
4621 List<SequenceI> hiddenSeqs, AlignmentI al,
4622 JalviewModel jm, Viewport view, String uniqueSeqSetId,
4623 String viewId, List<JvAnnotRow> autoAlan)
4625 AlignFrame af = null;
4626 af = new AlignFrame(al, safeInt(view.getWidth()),
4627 safeInt(view.getHeight()), uniqueSeqSetId, viewId);
4629 af.setFileName(file, FileFormat.Jalview);
4631 final AlignViewport viewport = af.getViewport();
4632 for (int i = 0; i < JSEQ.size(); i++)
4634 int colour = safeInt(JSEQ.get(i).getColour());
4635 viewport.setSequenceColour(viewport.getAlignment().getSequenceAt(i),
4641 viewport.setColourByReferenceSeq(true);
4642 viewport.setDisplayReferenceSeq(true);
4645 viewport.setGatherViewsHere(safeBoolean(view.isGatheredViews()));
4647 if (view.getSequenceSetId() != null)
4649 AlignmentViewport av = viewportsAdded.get(uniqueSeqSetId);
4651 viewport.setSequenceSetId(uniqueSeqSetId);
4654 // propagate shared settings to this new view
4655 viewport.setHistoryList(av.getHistoryList());
4656 viewport.setRedoList(av.getRedoList());
4660 viewportsAdded.put(uniqueSeqSetId, viewport);
4662 // TODO: check if this method can be called repeatedly without
4663 // side-effects if alignpanel already registered.
4664 PaintRefresher.Register(af.alignPanel, uniqueSeqSetId);
4666 // apply Hidden regions to view.
4667 if (hiddenSeqs != null)
4669 for (int s = 0; s < JSEQ.size(); s++)
4671 SequenceGroup hidden = new SequenceGroup();
4672 boolean isRepresentative = false;
4673 for (int r = 0; r < JSEQ.get(s).getHiddenSequences().size(); r++)
4675 isRepresentative = true;
4676 SequenceI sequenceToHide = al
4677 .getSequenceAt(JSEQ.get(s).getHiddenSequences().get(r));
4678 hidden.addSequence(sequenceToHide, false);
4679 // remove from hiddenSeqs list so we don't try to hide it twice
4680 hiddenSeqs.remove(sequenceToHide);
4682 if (isRepresentative)
4684 SequenceI representativeSequence = al.getSequenceAt(s);
4685 hidden.addSequence(representativeSequence, false);
4686 viewport.hideRepSequences(representativeSequence, hidden);
4690 SequenceI[] hseqs = hiddenSeqs
4691 .toArray(new SequenceI[hiddenSeqs.size()]);
4692 viewport.hideSequence(hseqs);
4695 // recover view properties and display parameters
4697 viewport.setShowAnnotation(safeBoolean(view.isShowAnnotation()));
4698 viewport.setAbovePIDThreshold(safeBoolean(view.isPidSelected()));
4699 final int pidThreshold = safeInt(view.getPidThreshold());
4700 viewport.setThreshold(pidThreshold);
4702 viewport.setColourText(safeBoolean(view.isShowColourText()));
4705 .setConservationSelected(
4706 safeBoolean(view.isConservationSelected()));
4707 viewport.setIncrement(safeInt(view.getConsThreshold()));
4708 viewport.setShowJVSuffix(safeBoolean(view.isShowFullId()));
4709 viewport.setRightAlignIds(safeBoolean(view.isRightAlignIds()));
4710 viewport.setFont(new Font(view.getFontName(),
4711 safeInt(view.getFontStyle()), safeInt(view.getFontSize())),
4713 ViewStyleI vs = viewport.getViewStyle();
4714 vs.setScaleProteinAsCdna(view.isScaleProteinAsCdna());
4715 viewport.setViewStyle(vs);
4716 // TODO: allow custom charWidth/Heights to be restored by updating them
4717 // after setting font - which means set above to false
4718 viewport.setRenderGaps(safeBoolean(view.isRenderGaps()));
4719 viewport.setWrapAlignment(safeBoolean(view.isWrapAlignment()));
4720 viewport.setShowAnnotation(safeBoolean(view.isShowAnnotation()));
4722 viewport.setShowBoxes(safeBoolean(view.isShowBoxes()));
4724 viewport.setShowText(safeBoolean(view.isShowText()));
4726 viewport.setTextColour(new Color(safeInt(view.getTextCol1())));
4727 viewport.setTextColour2(new Color(safeInt(view.getTextCol2())));
4728 viewport.setThresholdTextColour(safeInt(view.getTextColThreshold()));
4729 viewport.setShowUnconserved(view.isShowUnconserved());
4730 viewport.getRanges().setStartRes(safeInt(view.getStartRes()));
4732 if (view.getViewName() != null)
4734 viewport.setViewName(view.getViewName());
4735 af.setInitialTabVisible();
4737 af.setBounds(safeInt(view.getXpos()), safeInt(view.getYpos()),
4738 safeInt(view.getWidth()), safeInt(view.getHeight()));
4739 // startSeq set in af.alignPanel.updateLayout below
4740 af.alignPanel.updateLayout();
4741 ColourSchemeI cs = null;
4742 // apply colourschemes
4743 if (view.getBgColour() != null)
4745 if (view.getBgColour().startsWith("ucs"))
4747 cs = getUserColourScheme(jm, view.getBgColour());
4749 else if (view.getBgColour().startsWith("Annotation"))
4751 AnnotationColourScheme viewAnnColour = view.getAnnotationColours();
4752 cs = constructAnnotationColour(viewAnnColour, af, al, jm, true);
4759 cs = ColourSchemeProperty.getColourScheme(al, view.getBgColour());
4763 viewport.setGlobalColourScheme(cs);
4764 viewport.getResidueShading().setThreshold(pidThreshold,
4765 view.isIgnoreGapsinConsensus());
4766 viewport.getResidueShading()
4767 .setConsensus(viewport.getSequenceConsensusHash());
4768 viewport.setColourAppliesToAllGroups(false);
4770 if (safeBoolean(view.isConservationSelected()) && cs != null)
4772 viewport.getResidueShading()
4773 .setConservationInc(safeInt(view.getConsThreshold()));
4776 af.changeColour(cs);
4778 viewport.setColourAppliesToAllGroups(true);
4781 .setShowSequenceFeatures(
4782 safeBoolean(view.isShowSequenceFeatures()));
4784 viewport.setCentreColumnLabels(view.isCentreColumnLabels());
4785 viewport.setIgnoreGapsConsensus(view.isIgnoreGapsinConsensus(), null);
4786 viewport.setFollowHighlight(view.isFollowHighlight());
4787 viewport.followSelection = view.isFollowSelection();
4788 viewport.setShowConsensusHistogram(view.isShowConsensusHistogram());
4789 viewport.setShowSequenceLogo(view.isShowSequenceLogo());
4790 viewport.setNormaliseSequenceLogo(view.isNormaliseSequenceLogo());
4791 viewport.setShowDBRefs(safeBoolean(view.isShowDbRefTooltip()));
4792 viewport.setShowNPFeats(safeBoolean(view.isShowNPfeatureTooltip()));
4793 viewport.setShowGroupConsensus(view.isShowGroupConsensus());
4794 viewport.setShowGroupConservation(view.isShowGroupConservation());
4796 // recover feature settings
4797 if (jm.getFeatureSettings() != null)
4799 FeatureRenderer fr = af.alignPanel.getSeqPanel().seqCanvas
4800 .getFeatureRenderer();
4801 FeaturesDisplayed fdi;
4802 viewport.setFeaturesDisplayed(fdi = new FeaturesDisplayed());
4803 String[] renderOrder = new String[jm.getFeatureSettings()
4804 .getSetting().size()];
4805 Map<String, FeatureColourI> featureColours = new Hashtable<>();
4806 Map<String, Float> featureOrder = new Hashtable<>();
4808 for (int fs = 0; fs < jm.getFeatureSettings()
4809 .getSetting().size(); fs++)
4811 Setting setting = jm.getFeatureSettings().getSetting().get(fs);
4812 String featureType = setting.getType();
4815 * restore feature filters (if any)
4817 jalview.xml.binding.jalview.FeatureMatcherSet filters = setting
4819 if (filters != null)
4821 FeatureMatcherSetI filter = Jalview2XML
4822 .parseFilter(featureType, filters);
4823 if (!filter.isEmpty())
4825 fr.setFeatureFilter(featureType, filter);
4830 * restore feature colour scheme
4832 Color maxColour = new Color(setting.getColour());
4833 if (setting.getMincolour() != null)
4836 * minColour is always set unless a simple colour
4837 * (including for colour by label though it doesn't use it)
4839 Color minColour = new Color(setting.getMincolour().intValue());
4840 Color noValueColour = minColour;
4841 NoValueColour noColour = setting.getNoValueColour();
4842 if (noColour == NoValueColour.NONE)
4844 noValueColour = null;
4846 else if (noColour == NoValueColour.MAX)
4848 noValueColour = maxColour;
4850 float min = safeFloat(safeFloat(setting.getMin()));
4851 float max = setting.getMax() == null ? 1f
4852 : setting.getMax().floatValue();
4853 FeatureColourI gc = new FeatureColour(minColour, maxColour,
4854 noValueColour, min, max);
4855 if (setting.getAttributeName().size() > 0)
4857 gc.setAttributeName(setting.getAttributeName().toArray(
4858 new String[setting.getAttributeName().size()]));
4860 if (setting.getThreshold() != null)
4862 gc.setThreshold(setting.getThreshold().floatValue());
4863 int threshstate = safeInt(setting.getThreshstate());
4864 // -1 = None, 0 = Below, 1 = Above threshold
4865 if (threshstate == 0)
4867 gc.setBelowThreshold(true);
4869 else if (threshstate == 1)
4871 gc.setAboveThreshold(true);
4874 gc.setAutoScaled(true); // default
4875 if (setting.isAutoScale() != null)
4877 gc.setAutoScaled(setting.isAutoScale());
4879 if (setting.isColourByLabel() != null)
4881 gc.setColourByLabel(setting.isColourByLabel());
4883 // and put in the feature colour table.
4884 featureColours.put(featureType, gc);
4888 featureColours.put(featureType,
4889 new FeatureColour(maxColour));
4891 renderOrder[fs] = featureType;
4892 if (setting.getOrder() != null)
4894 featureOrder.put(featureType, setting.getOrder().floatValue());
4898 featureOrder.put(featureType, new Float(
4899 fs / jm.getFeatureSettings().getSetting().size()));
4901 if (safeBoolean(setting.isDisplay()))
4903 fdi.setVisible(featureType);
4906 Map<String, Boolean> fgtable = new Hashtable<>();
4907 for (int gs = 0; gs < jm.getFeatureSettings().getGroup().size(); gs++)
4909 Group grp = jm.getFeatureSettings().getGroup().get(gs);
4910 fgtable.put(grp.getName(), new Boolean(grp.isDisplay()));
4912 // FeatureRendererSettings frs = new FeatureRendererSettings(renderOrder,
4913 // fgtable, featureColours, jms.getFeatureSettings().hasTransparency() ?
4914 // jms.getFeatureSettings().getTransparency() : 0.0, featureOrder);
4915 FeatureRendererSettings frs = new FeatureRendererSettings(renderOrder,
4916 fgtable, featureColours, 1.0f, featureOrder);
4917 fr.transferSettings(frs);
4920 if (view.getHiddenColumns().size() > 0)
4922 for (int c = 0; c < view.getHiddenColumns().size(); c++)
4924 final HiddenColumns hc = view.getHiddenColumns().get(c);
4925 viewport.hideColumns(safeInt(hc.getStart()),
4926 safeInt(hc.getEnd()) /* +1 */);
4929 if (view.getCalcIdParam() != null)
4931 for (CalcIdParam calcIdParam : view.getCalcIdParam())
4933 if (calcIdParam != null)
4935 if (recoverCalcIdParam(calcIdParam, viewport))
4940 warn("Couldn't recover parameters for "
4941 + calcIdParam.getCalcId());
4946 af.setMenusFromViewport(viewport);
4947 af.setTitle(view.getTitle());
4948 // TODO: we don't need to do this if the viewport is aready visible.
4950 * Add the AlignFrame to the desktop (it may be 'gathered' later), unless it
4951 * has a 'cdna/protein complement' view, in which case save it in order to
4952 * populate a SplitFrame once all views have been read in.
4954 String complementaryViewId = view.getComplementId();
4955 if (complementaryViewId == null)
4957 Desktop.addInternalFrame(af, view.getTitle(),
4958 safeInt(view.getWidth()), safeInt(view.getHeight()));
4959 // recompute any autoannotation
4960 af.alignPanel.updateAnnotation(false, true);
4961 reorderAutoannotation(af, al, autoAlan);
4962 af.alignPanel.alignmentChanged();
4966 splitFrameCandidates.put(view, af);
4972 * Reads saved data to restore Colour by Annotation settings
4974 * @param viewAnnColour
4978 * @param checkGroupAnnColour
4981 private ColourSchemeI constructAnnotationColour(
4982 AnnotationColourScheme viewAnnColour, AlignFrame af,
4983 AlignmentI al, JalviewModel model, boolean checkGroupAnnColour)
4985 boolean propagateAnnColour = false;
4986 AlignmentI annAlignment = af != null ? af.getViewport().getAlignment()
4988 if (checkGroupAnnColour && al.getGroups() != null
4989 && al.getGroups().size() > 0)
4991 // pre 2.8.1 behaviour
4992 // check to see if we should transfer annotation colours
4993 propagateAnnColour = true;
4994 for (SequenceGroup sg : al.getGroups())
4996 if (sg.getColourScheme() instanceof AnnotationColourGradient)
4998 propagateAnnColour = false;
5004 * 2.10.2- : saved annotationId is AlignmentAnnotation.annotationId
5006 String annotationId = viewAnnColour.getAnnotation();
5007 AlignmentAnnotation matchedAnnotation = annotationIds.get(annotationId);
5010 * pre 2.10.2: saved annotationId is AlignmentAnnotation.label
5012 if (matchedAnnotation == null
5013 && annAlignment.getAlignmentAnnotation() != null)
5015 for (int i = 0; i < annAlignment.getAlignmentAnnotation().length; i++)
5018 .equals(annAlignment.getAlignmentAnnotation()[i].label))
5020 matchedAnnotation = annAlignment.getAlignmentAnnotation()[i];
5025 if (matchedAnnotation == null)
5027 System.err.println("Failed to match annotation colour scheme for "
5031 if (matchedAnnotation.getThreshold() == null)
5033 matchedAnnotation.setThreshold(
5034 new GraphLine(safeFloat(viewAnnColour.getThreshold()),
5035 "Threshold", Color.black));
5038 AnnotationColourGradient cs = null;
5039 if (viewAnnColour.getColourScheme().equals("None"))
5041 cs = new AnnotationColourGradient(matchedAnnotation,
5042 new Color(safeInt(viewAnnColour.getMinColour())),
5043 new Color(safeInt(viewAnnColour.getMaxColour())),
5044 safeInt(viewAnnColour.getAboveThreshold()));
5046 else if (viewAnnColour.getColourScheme().startsWith("ucs"))
5048 cs = new AnnotationColourGradient(matchedAnnotation,
5049 getUserColourScheme(model, viewAnnColour.getColourScheme()),
5050 safeInt(viewAnnColour.getAboveThreshold()));
5054 cs = new AnnotationColourGradient(matchedAnnotation,
5055 ColourSchemeProperty.getColourScheme(al,
5056 viewAnnColour.getColourScheme()),
5057 safeInt(viewAnnColour.getAboveThreshold()));
5060 boolean perSequenceOnly = safeBoolean(viewAnnColour.isPerSequence());
5061 boolean useOriginalColours = safeBoolean(
5062 viewAnnColour.isPredefinedColours());
5063 cs.setSeqAssociated(perSequenceOnly);
5064 cs.setPredefinedColours(useOriginalColours);
5066 if (propagateAnnColour && al.getGroups() != null)
5068 // Also use these settings for all the groups
5069 for (int g = 0; g < al.getGroups().size(); g++)
5071 SequenceGroup sg = al.getGroups().get(g);
5072 if (sg.getGroupColourScheme() == null)
5077 AnnotationColourGradient groupScheme = new AnnotationColourGradient(
5078 matchedAnnotation, sg.getColourScheme(),
5079 safeInt(viewAnnColour.getAboveThreshold()));
5080 sg.setColourScheme(groupScheme);
5081 groupScheme.setSeqAssociated(perSequenceOnly);
5082 groupScheme.setPredefinedColours(useOriginalColours);
5088 private void reorderAutoannotation(AlignFrame af, AlignmentI al,
5089 List<JvAnnotRow> autoAlan)
5091 // copy over visualization settings for autocalculated annotation in the
5093 if (al.getAlignmentAnnotation() != null)
5096 * Kludge for magic autoannotation names (see JAL-811)
5098 String[] magicNames = new String[] { "Consensus", "Quality",
5100 JvAnnotRow nullAnnot = new JvAnnotRow(-1, null);
5101 Hashtable<String, JvAnnotRow> visan = new Hashtable<>();
5102 for (String nm : magicNames)
5104 visan.put(nm, nullAnnot);
5106 for (JvAnnotRow auan : autoAlan)
5108 visan.put(auan.template.label
5109 + (auan.template.getCalcId() == null ? ""
5110 : "\t" + auan.template.getCalcId()),
5113 int hSize = al.getAlignmentAnnotation().length;
5114 List<JvAnnotRow> reorder = new ArrayList<>();
5115 // work through any autoCalculated annotation already on the view
5116 // removing it if it should be placed in a different location on the
5117 // annotation panel.
5118 List<String> remains = new ArrayList<>(visan.keySet());
5119 for (int h = 0; h < hSize; h++)
5121 jalview.datamodel.AlignmentAnnotation jalan = al
5122 .getAlignmentAnnotation()[h];
5123 if (jalan.autoCalculated)
5126 JvAnnotRow valan = visan.get(k = jalan.label);
5127 if (jalan.getCalcId() != null)
5129 valan = visan.get(k = jalan.label + "\t" + jalan.getCalcId());
5134 // delete the auto calculated row from the alignment
5135 al.deleteAnnotation(jalan, false);
5139 if (valan != nullAnnot)
5141 if (jalan != valan.template)
5143 // newly created autoannotation row instance
5144 // so keep a reference to the visible annotation row
5145 // and copy over all relevant attributes
5146 if (valan.template.graphHeight >= 0)
5149 jalan.graphHeight = valan.template.graphHeight;
5151 jalan.visible = valan.template.visible;
5153 reorder.add(new JvAnnotRow(valan.order, jalan));
5158 // Add any (possibly stale) autocalculated rows that were not appended to
5159 // the view during construction
5160 for (String other : remains)
5162 JvAnnotRow othera = visan.get(other);
5163 if (othera != nullAnnot && othera.template.getCalcId() != null
5164 && othera.template.getCalcId().length() > 0)
5166 reorder.add(othera);
5169 // now put the automatic annotation in its correct place
5170 int s = 0, srt[] = new int[reorder.size()];
5171 JvAnnotRow[] rws = new JvAnnotRow[reorder.size()];
5172 for (JvAnnotRow jvar : reorder)
5175 srt[s++] = jvar.order;
5178 jalview.util.QuickSort.sort(srt, rws);
5179 // and re-insert the annotation at its correct position
5180 for (JvAnnotRow jvar : rws)
5182 al.addAnnotation(jvar.template, jvar.order);
5184 af.alignPanel.adjustAnnotationHeight();
5188 Hashtable skipList = null;
5191 * TODO remove this method
5194 * @return AlignFrame bound to sequenceSetId from view, if one exists. private
5195 * AlignFrame getSkippedFrame(Viewport view) { if (skipList==null) {
5196 * throw new Error("Implementation Error. No skipList defined for this
5197 * Jalview2XML instance."); } return (AlignFrame)
5198 * skipList.get(view.getSequenceSetId()); }
5202 * Check if the Jalview view contained in object should be skipped or not.
5205 * @return true if view's sequenceSetId is a key in skipList
5207 private boolean skipViewport(JalviewModel object)
5209 if (skipList == null)
5213 String id = object.getViewport().get(0).getSequenceSetId();
5214 if (skipList.containsKey(id))
5216 if (Cache.log != null && Cache.log.isDebugEnabled())
5218 Cache.log.debug("Skipping seuqence set id " + id);
5225 public void addToSkipList(AlignFrame af)
5227 if (skipList == null)
5229 skipList = new Hashtable();
5231 skipList.put(af.getViewport().getSequenceSetId(), af);
5234 public void clearSkipList()
5236 if (skipList != null)
5243 private void recoverDatasetFor(SequenceSet vamsasSet, AlignmentI al,
5244 boolean ignoreUnrefed)
5246 jalview.datamodel.AlignmentI ds = getDatasetFor(
5247 vamsasSet.getDatasetId());
5248 Vector dseqs = null;
5251 // create a list of new dataset sequences
5252 dseqs = new Vector();
5254 for (int i = 0, iSize = vamsasSet.getSequence().size(); i < iSize; i++)
5256 Sequence vamsasSeq = vamsasSet.getSequence().get(i);
5257 ensureJalviewDatasetSequence(vamsasSeq, ds, dseqs, ignoreUnrefed, i);
5259 // create a new dataset
5262 SequenceI[] dsseqs = new SequenceI[dseqs.size()];
5263 dseqs.copyInto(dsseqs);
5264 ds = new jalview.datamodel.Alignment(dsseqs);
5265 debug("Created new dataset " + vamsasSet.getDatasetId()
5266 + " for alignment " + System.identityHashCode(al));
5267 addDatasetRef(vamsasSet.getDatasetId(), ds);
5269 // set the dataset for the newly imported alignment.
5270 if (al.getDataset() == null && !ignoreUnrefed)
5279 * sequence definition to create/merge dataset sequence for
5283 * vector to add new dataset sequence to
5284 * @param ignoreUnrefed
5285 * - when true, don't create new sequences from vamsasSeq if it's id
5286 * doesn't already have an asssociated Jalview sequence.
5288 * - used to reorder the sequence in the alignment according to the
5289 * vamsasSeq array ordering, to preserve ordering of dataset
5291 private void ensureJalviewDatasetSequence(Sequence vamsasSeq,
5292 AlignmentI ds, Vector dseqs, boolean ignoreUnrefed, int vseqpos)
5294 // JBP TODO: Check this is called for AlCodonFrames to support recovery of
5296 SequenceI sq = seqRefIds.get(vamsasSeq.getId());
5297 boolean reorder = false;
5298 SequenceI dsq = null;
5299 if (sq != null && sq.getDatasetSequence() != null)
5301 dsq = sq.getDatasetSequence();
5307 if (sq == null && ignoreUnrefed)
5311 String sqid = vamsasSeq.getDsseqid();
5314 // need to create or add a new dataset sequence reference to this sequence
5317 dsq = seqRefIds.get(sqid);
5322 // make a new dataset sequence
5323 dsq = sq.createDatasetSequence();
5326 // make up a new dataset reference for this sequence
5327 sqid = seqHash(dsq);
5329 dsq.setVamsasId(uniqueSetSuffix + sqid);
5330 seqRefIds.put(sqid, dsq);
5335 dseqs.addElement(dsq);
5340 ds.addSequence(dsq);
5346 { // make this dataset sequence sq's dataset sequence
5347 sq.setDatasetSequence(dsq);
5348 // and update the current dataset alignment
5353 if (!dseqs.contains(dsq))
5360 if (ds.findIndex(dsq) < 0)
5362 ds.addSequence(dsq);
5369 // TODO: refactor this as a merge dataset sequence function
5370 // now check that sq (the dataset sequence) sequence really is the union of
5371 // all references to it
5372 // boolean pre = sq.getStart() < dsq.getStart();
5373 // boolean post = sq.getEnd() > dsq.getEnd();
5377 // StringBuffer sb = new StringBuffer();
5378 String newres = jalview.analysis.AlignSeq.extractGaps(
5379 jalview.util.Comparison.GapChars, sq.getSequenceAsString());
5380 if (!newres.equalsIgnoreCase(dsq.getSequenceAsString())
5381 && newres.length() > dsq.getLength())
5383 // Update with the longer sequence.
5387 * if (pre) { sb.insert(0, newres .substring(0, dsq.getStart() -
5388 * sq.getStart())); dsq.setStart(sq.getStart()); } if (post) {
5389 * sb.append(newres.substring(newres.length() - sq.getEnd() -
5390 * dsq.getEnd())); dsq.setEnd(sq.getEnd()); }
5392 dsq.setSequence(newres);
5394 // TODO: merges will never happen if we 'know' we have the real dataset
5395 // sequence - this should be detected when id==dssid
5397 "DEBUG Notice: Merged dataset sequence (if you see this often, post at http://issues.jalview.org/browse/JAL-1474)"); // ("
5398 // + (pre ? "prepended" : "") + " "
5399 // + (post ? "appended" : ""));
5404 // sequence refs are identical. We may need to update the existing dataset
5405 // alignment with this one, though.
5406 if (ds != null && dseqs == null)
5408 int opos = ds.findIndex(dsq);
5409 SequenceI tseq = null;
5410 if (opos != -1 && vseqpos != opos)
5412 // remove from old position
5413 ds.deleteSequence(dsq);
5415 if (vseqpos < ds.getHeight())
5417 if (vseqpos != opos)
5419 // save sequence at destination position
5420 tseq = ds.getSequenceAt(vseqpos);
5421 ds.replaceSequenceAt(vseqpos, dsq);
5422 ds.addSequence(tseq);
5427 ds.addSequence(dsq);
5434 * TODO use AlignmentI here and in related methods - needs
5435 * AlignmentI.getDataset() changed to return AlignmentI instead of Alignment
5437 Hashtable<String, AlignmentI> datasetIds = null;
5439 IdentityHashMap<AlignmentI, String> dataset2Ids = null;
5441 private AlignmentI getDatasetFor(String datasetId)
5443 if (datasetIds == null)
5445 datasetIds = new Hashtable<>();
5448 if (datasetIds.containsKey(datasetId))
5450 return datasetIds.get(datasetId);
5455 private void addDatasetRef(String datasetId, AlignmentI dataset)
5457 if (datasetIds == null)
5459 datasetIds = new Hashtable<>();
5461 datasetIds.put(datasetId, dataset);
5465 * make a new dataset ID for this jalview dataset alignment
5470 private String getDatasetIdRef(AlignmentI dataset)
5472 if (dataset.getDataset() != null)
5474 warn("Serious issue! Dataset Object passed to getDatasetIdRef is not a Jalview DATASET alignment...");
5476 String datasetId = makeHashCode(dataset, null);
5477 if (datasetId == null)
5479 // make a new datasetId and record it
5480 if (dataset2Ids == null)
5482 dataset2Ids = new IdentityHashMap<>();
5486 datasetId = dataset2Ids.get(dataset);
5488 if (datasetId == null)
5490 datasetId = "ds" + dataset2Ids.size() + 1;
5491 dataset2Ids.put(dataset, datasetId);
5497 private void addDBRefs(SequenceI datasetSequence, Sequence sequence)
5499 for (int d = 0; d < sequence.getDBRef().size(); d++)
5501 DBRef dr = sequence.getDBRef().get(d);
5502 jalview.datamodel.DBRefEntry entry = new jalview.datamodel.DBRefEntry(
5503 dr.getSource(), dr.getVersion(), dr.getAccessionId());
5504 if (dr.getMapping() != null)
5506 entry.setMap(addMapping(dr.getMapping()));
5508 datasetSequence.addDBRef(entry);
5512 private jalview.datamodel.Mapping addMapping(Mapping m)
5514 SequenceI dsto = null;
5515 // Mapping m = dr.getMapping();
5516 int fr[] = new int[m.getMapListFrom().size() * 2];
5517 Iterator<MapListFrom> from = m.getMapListFrom().iterator();// enumerateMapListFrom();
5518 for (int _i = 0; from.hasNext(); _i += 2)
5520 MapListFrom mf = from.next();
5521 fr[_i] = mf.getStart();
5522 fr[_i + 1] = mf.getEnd();
5524 int fto[] = new int[m.getMapListTo().size() * 2];
5525 Iterator<MapListTo> to = m.getMapListTo().iterator();// enumerateMapListTo();
5526 for (int _i = 0; to.hasNext(); _i += 2)
5528 MapListTo mf = to.next();
5529 fto[_i] = mf.getStart();
5530 fto[_i + 1] = mf.getEnd();
5532 jalview.datamodel.Mapping jmap = new jalview.datamodel.Mapping(dsto, fr,
5533 fto, m.getMapFromUnit().intValue(),
5534 m.getMapToUnit().intValue());
5535 // if (m.getMappingChoice() != null)
5537 // MappingChoice mc = m.getMappingChoice();
5538 if (m.getDseqFor() != null)
5540 String dsfor = m.getDseqFor();
5541 if (seqRefIds.containsKey(dsfor))
5546 jmap.setTo(seqRefIds.get(dsfor));
5550 frefedSequence.add(newMappingRef(dsfor, jmap));
5556 * local sequence definition
5558 Sequence ms = m.getSequence();
5559 SequenceI djs = null;
5560 String sqid = ms.getDsseqid();
5561 if (sqid != null && sqid.length() > 0)
5564 * recover dataset sequence
5566 djs = seqRefIds.get(sqid);
5571 "Warning - making up dataset sequence id for DbRef sequence map reference");
5572 sqid = ((Object) ms).toString(); // make up a new hascode for
5573 // undefined dataset sequence hash
5574 // (unlikely to happen)
5580 * make a new dataset sequence and add it to refIds hash
5582 djs = new jalview.datamodel.Sequence(ms.getName(),
5584 djs.setStart(jmap.getMap().getToLowest());
5585 djs.setEnd(jmap.getMap().getToHighest());
5586 djs.setVamsasId(uniqueSetSuffix + sqid);
5588 incompleteSeqs.put(sqid, djs);
5589 seqRefIds.put(sqid, djs);
5592 jalview.bin.Cache.log.debug("about to recurse on addDBRefs.");
5601 * Provides a 'copy' of an alignment view (on action New View) by 'saving' the
5602 * view as XML (but not to file), and then reloading it
5607 public AlignmentPanel copyAlignPanel(AlignmentPanel ap)
5610 JalviewModel jm = saveState(ap, null, null, null);
5612 uniqueSetSuffix = "";
5613 // jm.getJalviewModelSequence().getViewport(0).setId(null);
5614 jm.getViewport().get(0).setId(null);
5615 // we don't overwrite the view we just copied
5617 if (this.frefedSequence == null)
5619 frefedSequence = new Vector<>();
5622 viewportsAdded.clear();
5624 AlignFrame af = loadFromObject(jm, null, false, null);
5625 af.getAlignPanels().clear();
5626 af.closeMenuItem_actionPerformed(true);
5629 * if(ap.av.getAlignment().getAlignmentAnnotation()!=null) { for(int i=0;
5630 * i<ap.av.getAlignment().getAlignmentAnnotation().length; i++) {
5631 * if(!ap.av.getAlignment().getAlignmentAnnotation()[i].autoCalculated) {
5632 * af.alignPanel.av.getAlignment().getAlignmentAnnotation()[i] =
5633 * ap.av.getAlignment().getAlignmentAnnotation()[i]; } } }
5636 return af.alignPanel;
5639 private Hashtable jvids2vobj;
5641 private void warn(String msg)
5646 private void warn(String msg, Exception e)
5648 if (Cache.log != null)
5652 Cache.log.warn(msg, e);
5656 Cache.log.warn(msg);
5661 System.err.println("Warning: " + msg);
5664 e.printStackTrace();
5669 private void debug(String string)
5671 debug(string, null);
5674 private void debug(String msg, Exception e)
5676 if (Cache.log != null)
5680 Cache.log.debug(msg, e);
5684 Cache.log.debug(msg);
5689 System.err.println("Warning: " + msg);
5692 e.printStackTrace();
5698 * set the object to ID mapping tables used to write/recover objects and XML
5699 * ID strings for the jalview project. If external tables are provided then
5700 * finalize and clearSeqRefs will not clear the tables when the Jalview2XML
5701 * object goes out of scope. - also populates the datasetIds hashtable with
5702 * alignment objects containing dataset sequences
5705 * Map from ID strings to jalview datamodel
5707 * Map from jalview datamodel to ID strings
5711 public void setObjectMappingTables(Hashtable vobj2jv,
5712 IdentityHashMap jv2vobj)
5714 this.jv2vobj = jv2vobj;
5715 this.vobj2jv = vobj2jv;
5716 Iterator ds = jv2vobj.keySet().iterator();
5718 while (ds.hasNext())
5720 Object jvobj = ds.next();
5721 id = jv2vobj.get(jvobj).toString();
5722 if (jvobj instanceof jalview.datamodel.Alignment)
5724 if (((jalview.datamodel.Alignment) jvobj).getDataset() == null)
5726 addDatasetRef(id, (jalview.datamodel.Alignment) jvobj);
5729 else if (jvobj instanceof jalview.datamodel.Sequence)
5731 // register sequence object so the XML parser can recover it.
5732 if (seqRefIds == null)
5734 seqRefIds = new HashMap<>();
5736 if (seqsToIds == null)
5738 seqsToIds = new IdentityHashMap<>();
5740 seqRefIds.put(jv2vobj.get(jvobj).toString(), (SequenceI) jvobj);
5741 seqsToIds.put((SequenceI) jvobj, id);
5743 else if (jvobj instanceof jalview.datamodel.AlignmentAnnotation)
5746 AlignmentAnnotation jvann = (AlignmentAnnotation) jvobj;
5747 annotationIds.put(anid = jv2vobj.get(jvobj).toString(), jvann);
5748 if (jvann.annotationId == null)
5750 jvann.annotationId = anid;
5752 if (!jvann.annotationId.equals(anid))
5754 // TODO verify that this is the correct behaviour
5755 this.warn("Overriding Annotation ID for " + anid
5756 + " from different id : " + jvann.annotationId);
5757 jvann.annotationId = anid;
5760 else if (jvobj instanceof String)
5762 if (jvids2vobj == null)
5764 jvids2vobj = new Hashtable();
5765 jvids2vobj.put(jvobj, jv2vobj.get(jvobj).toString());
5770 Cache.log.debug("Ignoring " + jvobj.getClass() + " (ID = " + id);
5776 * set the uniqueSetSuffix used to prefix/suffix object IDs for jalview
5777 * objects created from the project archive. If string is null (default for
5778 * construction) then suffix will be set automatically.
5782 public void setUniqueSetSuffix(String string)
5784 uniqueSetSuffix = string;
5789 * uses skipList2 as the skipList for skipping views on sequence sets
5790 * associated with keys in the skipList
5794 public void setSkipList(Hashtable skipList2)
5796 skipList = skipList2;
5800 * Reads the jar entry of given name and returns its contents, or null if the
5801 * entry is not found.
5804 * @param jarEntryName
5807 protected String readJarEntry(jarInputStreamProvider jprovider,
5808 String jarEntryName)
5810 String result = null;
5811 BufferedReader in = null;
5816 * Reopen the jar input stream and traverse its entries to find a matching
5819 JarInputStream jin = jprovider.getJarInputStream();
5820 JarEntry entry = null;
5823 entry = jin.getNextJarEntry();
5824 } while (entry != null && !entry.getName().equals(jarEntryName));
5828 StringBuilder out = new StringBuilder(256);
5829 in = new BufferedReader(new InputStreamReader(jin, UTF_8));
5832 while ((data = in.readLine()) != null)
5836 result = out.toString();
5840 warn("Couldn't find entry in Jalview Jar for " + jarEntryName);
5842 } catch (Exception ex)
5844 ex.printStackTrace();
5852 } catch (IOException e)
5863 * Returns an incrementing counter (0, 1, 2...)
5867 private synchronized int nextCounter()
5873 * Populates an XML model of the feature colour scheme for one feature type
5875 * @param featureType
5879 public static Colour marshalColour(
5880 String featureType, FeatureColourI fcol)
5882 Colour col = new Colour();
5883 if (fcol.isSimpleColour())
5885 col.setRGB(Format.getHexString(fcol.getColour()));
5889 col.setRGB(Format.getHexString(fcol.getMaxColour()));
5890 col.setMin(fcol.getMin());
5891 col.setMax(fcol.getMax());
5892 col.setMinRGB(jalview.util.Format.getHexString(fcol.getMinColour()));
5893 col.setAutoScale(fcol.isAutoScaled());
5894 col.setThreshold(fcol.getThreshold());
5895 col.setColourByLabel(fcol.isColourByLabel());
5896 col.setThreshType(fcol.isAboveThreshold() ? ThresholdType.ABOVE
5897 : (fcol.isBelowThreshold() ? ThresholdType.BELOW
5898 : ThresholdType.NONE));
5899 if (fcol.isColourByAttribute())
5901 final String[] attName = fcol.getAttributeName();
5902 col.getAttributeName().add(attName[0]);
5903 if (attName.length > 1)
5905 col.getAttributeName().add(attName[1]);
5908 Color noColour = fcol.getNoColour();
5909 if (noColour == null)
5911 col.setNoValueColour(NoValueColour.NONE);
5913 else if (noColour == fcol.getMaxColour())
5915 col.setNoValueColour(NoValueColour.MAX);
5919 col.setNoValueColour(NoValueColour.MIN);
5922 col.setName(featureType);
5927 * Populates an XML model of the feature filter(s) for one feature type
5929 * @param firstMatcher
5930 * the first (or only) match condition)
5932 * remaining match conditions (if any)
5934 * if true, conditions are and-ed, else or-ed
5936 public static jalview.xml.binding.jalview.FeatureMatcherSet marshalFilter(
5937 FeatureMatcherI firstMatcher, Iterator<FeatureMatcherI> filters,
5940 jalview.xml.binding.jalview.FeatureMatcherSet result = new jalview.xml.binding.jalview.FeatureMatcherSet();
5942 if (filters.hasNext())
5947 CompoundMatcher compound = new CompoundMatcher();
5948 compound.setAnd(and);
5949 jalview.xml.binding.jalview.FeatureMatcherSet matcher1 = marshalFilter(
5950 firstMatcher, Collections.emptyIterator(), and);
5951 // compound.addMatcherSet(matcher1);
5952 compound.getMatcherSet().add(matcher1);
5953 FeatureMatcherI nextMatcher = filters.next();
5954 jalview.xml.binding.jalview.FeatureMatcherSet matcher2 = marshalFilter(
5955 nextMatcher, filters, and);
5956 // compound.addMatcherSet(matcher2);
5957 compound.getMatcherSet().add(matcher2);
5958 result.setCompoundMatcher(compound);
5963 * single condition matcher
5965 // MatchCondition matcherModel = new MatchCondition();
5966 jalview.xml.binding.jalview.FeatureMatcher matcherModel = new jalview.xml.binding.jalview.FeatureMatcher();
5967 matcherModel.setCondition(
5968 firstMatcher.getMatcher().getCondition().getStableName());
5969 matcherModel.setValue(firstMatcher.getMatcher().getPattern());
5970 if (firstMatcher.isByAttribute())
5972 matcherModel.setBy(FilterBy.BY_ATTRIBUTE);
5973 // matcherModel.setAttributeName(firstMatcher.getAttribute());
5974 String[] attName = firstMatcher.getAttribute();
5975 matcherModel.getAttributeName().add(attName[0]); // attribute
5976 if (attName.length > 1)
5978 matcherModel.getAttributeName().add(attName[1]); // sub-attribute
5981 else if (firstMatcher.isByLabel())
5983 matcherModel.setBy(FilterBy.BY_LABEL);
5985 else if (firstMatcher.isByScore())
5987 matcherModel.setBy(FilterBy.BY_SCORE);
5989 result.setMatchCondition(matcherModel);
5996 * Loads one XML model of a feature filter to a Jalview object
5998 * @param featureType
5999 * @param matcherSetModel
6002 public static FeatureMatcherSetI parseFilter(
6004 jalview.xml.binding.jalview.FeatureMatcherSet matcherSetModel)
6006 FeatureMatcherSetI result = new FeatureMatcherSet();
6009 parseFilterConditions(result, matcherSetModel, true);
6010 } catch (IllegalStateException e)
6012 // mixing AND and OR conditions perhaps
6014 String.format("Error reading filter conditions for '%s': %s",
6015 featureType, e.getMessage()));
6016 // return as much as was parsed up to the error
6023 * Adds feature match conditions to matcherSet as unmarshalled from XML
6024 * (possibly recursively for compound conditions)
6027 * @param matcherSetModel
6029 * if true, multiple conditions are AND-ed, else they are OR-ed
6030 * @throws IllegalStateException
6031 * if AND and OR conditions are mixed
6033 protected static void parseFilterConditions(
6034 FeatureMatcherSetI matcherSet,
6035 jalview.xml.binding.jalview.FeatureMatcherSet matcherSetModel,
6038 jalview.xml.binding.jalview.FeatureMatcher mc = matcherSetModel
6039 .getMatchCondition();
6045 FilterBy filterBy = mc.getBy();
6046 Condition cond = Condition.fromString(mc.getCondition());
6047 String pattern = mc.getValue();
6048 FeatureMatcherI matchCondition = null;
6049 if (filterBy == FilterBy.BY_LABEL)
6051 matchCondition = FeatureMatcher.byLabel(cond, pattern);
6053 else if (filterBy == FilterBy.BY_SCORE)
6055 matchCondition = FeatureMatcher.byScore(cond, pattern);
6058 else if (filterBy == FilterBy.BY_ATTRIBUTE)
6060 final List<String> attributeName = mc.getAttributeName();
6061 String[] attNames = attributeName
6062 .toArray(new String[attributeName.size()]);
6063 matchCondition = FeatureMatcher.byAttribute(cond, pattern,
6068 * note this throws IllegalStateException if AND-ing to a
6069 * previously OR-ed compound condition, or vice versa
6073 matcherSet.and(matchCondition);
6077 matcherSet.or(matchCondition);
6083 * compound condition
6085 List<jalview.xml.binding.jalview.FeatureMatcherSet> matchers = matcherSetModel
6086 .getCompoundMatcher().getMatcherSet();
6087 boolean anded = matcherSetModel.getCompoundMatcher().isAnd();
6088 if (matchers.size() == 2)
6090 parseFilterConditions(matcherSet, matchers.get(0), anded);
6091 parseFilterConditions(matcherSet, matchers.get(1), anded);
6095 System.err.println("Malformed compound filter condition");
6101 * Loads one XML model of a feature colour to a Jalview object
6103 * @param colourModel
6106 public static FeatureColourI parseColour(Colour colourModel)
6108 FeatureColourI colour = null;
6110 if (colourModel.getMax() != null)
6112 Color mincol = null;
6113 Color maxcol = null;
6114 Color noValueColour = null;
6118 mincol = new Color(Integer.parseInt(colourModel.getMinRGB(), 16));
6119 maxcol = new Color(Integer.parseInt(colourModel.getRGB(), 16));
6120 } catch (Exception e)
6122 Cache.log.warn("Couldn't parse out graduated feature color.", e);
6125 NoValueColour noCol = colourModel.getNoValueColour();
6126 if (noCol == NoValueColour.MIN)
6128 noValueColour = mincol;
6130 else if (noCol == NoValueColour.MAX)
6132 noValueColour = maxcol;
6135 colour = new FeatureColour(mincol, maxcol, noValueColour,
6136 safeFloat(colourModel.getMin()),
6137 safeFloat(colourModel.getMax()));
6138 final List<String> attributeName = colourModel.getAttributeName();
6139 String[] attributes = attributeName
6140 .toArray(new String[attributeName.size()]);
6141 if (attributes != null && attributes.length > 0)
6143 colour.setAttributeName(attributes);
6145 if (colourModel.isAutoScale() != null)
6147 colour.setAutoScaled(colourModel.isAutoScale().booleanValue());
6149 if (colourModel.isColourByLabel() != null)
6151 colour.setColourByLabel(
6152 colourModel.isColourByLabel().booleanValue());
6154 if (colourModel.getThreshold() != null)
6156 colour.setThreshold(colourModel.getThreshold().floatValue());
6158 ThresholdType ttyp = colourModel.getThreshType();
6159 if (ttyp == ThresholdType.ABOVE)
6161 colour.setAboveThreshold(true);
6163 else if (ttyp == ThresholdType.BELOW)
6165 colour.setBelowThreshold(true);
6170 Color color = new Color(Integer.parseInt(colourModel.getRGB(), 16));
6171 colour = new FeatureColour(color);