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.
23 import jalview.api.structures.JalviewStructureDisplayI;
24 import jalview.bin.Cache;
25 import jalview.datamodel.AlignedCodonFrame;
26 import jalview.datamodel.Alignment;
27 import jalview.datamodel.AlignmentAnnotation;
28 import jalview.datamodel.AlignmentI;
29 import jalview.datamodel.PDBEntry;
30 import jalview.datamodel.SequenceI;
31 import jalview.datamodel.StructureViewerModel;
32 import jalview.datamodel.StructureViewerModel.StructureData;
33 import jalview.schemabinding.version2.AlcodMap;
34 import jalview.schemabinding.version2.AlcodonFrame;
35 import jalview.schemabinding.version2.Annotation;
36 import jalview.schemabinding.version2.AnnotationColours;
37 import jalview.schemabinding.version2.AnnotationElement;
38 import jalview.schemabinding.version2.CalcIdParam;
39 import jalview.schemabinding.version2.DBRef;
40 import jalview.schemabinding.version2.Features;
41 import jalview.schemabinding.version2.Group;
42 import jalview.schemabinding.version2.HiddenColumns;
43 import jalview.schemabinding.version2.JGroup;
44 import jalview.schemabinding.version2.JSeq;
45 import jalview.schemabinding.version2.JalviewModel;
46 import jalview.schemabinding.version2.JalviewModelSequence;
47 import jalview.schemabinding.version2.MapListFrom;
48 import jalview.schemabinding.version2.MapListTo;
49 import jalview.schemabinding.version2.Mapping;
50 import jalview.schemabinding.version2.MappingChoice;
51 import jalview.schemabinding.version2.OtherData;
52 import jalview.schemabinding.version2.PdbentryItem;
53 import jalview.schemabinding.version2.Pdbids;
54 import jalview.schemabinding.version2.Property;
55 import jalview.schemabinding.version2.Sequence;
56 import jalview.schemabinding.version2.SequenceSet;
57 import jalview.schemabinding.version2.SequenceSetProperties;
58 import jalview.schemabinding.version2.Setting;
59 import jalview.schemabinding.version2.StructureState;
60 import jalview.schemabinding.version2.ThresholdLine;
61 import jalview.schemabinding.version2.Tree;
62 import jalview.schemabinding.version2.UserColours;
63 import jalview.schemabinding.version2.Viewport;
64 import jalview.schemes.AnnotationColourGradient;
65 import jalview.schemes.ColourSchemeI;
66 import jalview.schemes.ColourSchemeProperty;
67 import jalview.schemes.GraduatedColor;
68 import jalview.schemes.ResidueColourScheme;
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.MessageManager;
74 import jalview.util.Platform;
75 import jalview.util.jarInputStreamProvider;
76 import jalview.viewmodel.AlignmentViewport;
77 import jalview.viewmodel.seqfeatures.FeatureRendererSettings;
78 import jalview.viewmodel.seqfeatures.FeaturesDisplayed;
79 import jalview.ws.jws2.Jws2Discoverer;
80 import jalview.ws.jws2.dm.AAConSettings;
81 import jalview.ws.jws2.jabaws2.Jws2Instance;
82 import jalview.ws.params.ArgumentI;
83 import jalview.ws.params.AutoCalcSetting;
84 import jalview.ws.params.WsParamSetI;
86 import java.awt.Rectangle;
87 import java.io.BufferedReader;
88 import java.io.DataInputStream;
89 import java.io.DataOutputStream;
91 import java.io.FileInputStream;
92 import java.io.FileOutputStream;
93 import java.io.IOException;
94 import java.io.InputStreamReader;
95 import java.io.OutputStreamWriter;
96 import java.io.PrintWriter;
97 import java.lang.reflect.InvocationTargetException;
98 import java.net.MalformedURLException;
100 import java.util.ArrayList;
101 import java.util.Enumeration;
102 import java.util.HashMap;
103 import java.util.HashSet;
104 import java.util.Hashtable;
105 import java.util.IdentityHashMap;
106 import java.util.Iterator;
107 import java.util.LinkedHashMap;
108 import java.util.List;
109 import java.util.Map;
110 import java.util.Map.Entry;
111 import java.util.Set;
112 import java.util.StringTokenizer;
113 import java.util.Vector;
114 import java.util.jar.JarEntry;
115 import java.util.jar.JarInputStream;
116 import java.util.jar.JarOutputStream;
118 import javax.swing.JInternalFrame;
119 import javax.swing.JOptionPane;
120 import javax.swing.SwingUtilities;
122 import org.exolab.castor.xml.Unmarshaller;
125 * Write out the current jalview desktop state as a Jalview XML stream.
127 * Note: the vamsas objects referred to here are primitive versions of the
128 * VAMSAS project schema elements - they are not the same and most likely never
132 * @version $Revision: 1.134 $
134 public class Jalview2XML
137 * SequenceI reference -> XML ID string in jalview XML. Populated as XML reps
138 * of sequence objects are created.
140 IdentityHashMap<SequenceI, String> seqsToIds = null;
143 * jalview XML Sequence ID to jalview sequence object reference (both dataset
144 * and alignment sequences. Populated as XML reps of sequence objects are
147 Map<String, SequenceI> seqRefIds = null;
149 Vector frefedSequence = null;
151 boolean raiseGUI = true; // whether errors are raised in dialog boxes or not
154 * Map of reconstructed AlignFrame objects that appear to have come from
155 * SplitFrame objects (have a dna/protein complement view).
157 private Map<Viewport, AlignFrame> splitFrameCandidates = new HashMap<Viewport, AlignFrame>();
160 * create/return unique hash string for sq
163 * @return new or existing unique string for sq
165 String seqHash(SequenceI sq)
167 if (seqsToIds == null)
171 if (seqsToIds.containsKey(sq))
173 return seqsToIds.get(sq);
177 // create sequential key
178 String key = "sq" + (seqsToIds.size() + 1);
179 key = makeHashCode(sq, key); // check we don't have an external reference
181 seqsToIds.put(sq, key);
190 if (seqRefIds != null)
194 if (seqsToIds != null)
204 warn("clearSeqRefs called when _cleartables was not set. Doing nothing.");
205 // seqRefIds = new Hashtable();
206 // seqsToIds = new IdentityHashMap();
212 if (seqsToIds == null)
214 seqsToIds = new IdentityHashMap<SequenceI, String>();
216 if (seqRefIds == null)
218 seqRefIds = new HashMap<String, SequenceI>();
226 public Jalview2XML(boolean raiseGUI)
228 this.raiseGUI = raiseGUI;
231 public void resolveFrefedSequences()
233 if (frefedSequence.size() > 0)
235 int r = 0, rSize = frefedSequence.size();
238 Object[] ref = (Object[]) frefedSequence.elementAt(r);
241 String sref = (String) ref[0];
242 if (seqRefIds.containsKey(sref))
244 if (ref[1] instanceof jalview.datamodel.Mapping)
246 SequenceI seq = seqRefIds.get(sref);
247 while (seq.getDatasetSequence() != null)
249 seq = seq.getDatasetSequence();
251 ((jalview.datamodel.Mapping) ref[1]).setTo(seq);
255 if (ref[1] instanceof jalview.datamodel.AlignedCodonFrame)
257 SequenceI seq = seqRefIds.get(sref);
258 while (seq.getDatasetSequence() != null)
260 seq = seq.getDatasetSequence();
263 && ref[2] instanceof jalview.datamodel.Mapping)
265 jalview.datamodel.Mapping mp = (jalview.datamodel.Mapping) ref[2];
266 ((jalview.datamodel.AlignedCodonFrame) ref[1]).addMap(
267 seq, mp.getTo(), mp.getMap());
272 .println("IMPLEMENTATION ERROR: Unimplemented forward sequence references for AlcodonFrames involving "
273 + ref[2].getClass() + " type objects.");
279 .println("IMPLEMENTATION ERROR: Unimplemented forward sequence references for "
280 + ref[1].getClass() + " type objects.");
283 frefedSequence.remove(r);
289 .println("IMPLEMENTATION WARNING: Unresolved forward reference for hash string "
291 + " with objecttype "
292 + ref[1].getClass());
299 frefedSequence.remove(r);
307 * This maintains a map of viewports, the key being the seqSetId. Important to
308 * set historyItem and redoList for multiple views
310 Map<String, AlignViewport> viewportsAdded = new HashMap<String, AlignViewport>();
312 Map<String, AlignmentAnnotation> annotationIds = new HashMap<String, AlignmentAnnotation>();
314 String uniqueSetSuffix = "";
317 * List of pdbfiles added to Jar
319 List<String> pdbfiles = null;
321 // SAVES SEVERAL ALIGNMENT WINDOWS TO SAME JARFILE
322 public void saveState(File statefile)
324 FileOutputStream fos = null;
327 fos = new FileOutputStream(statefile);
328 JarOutputStream jout = new JarOutputStream(fos);
331 } catch (Exception e)
333 // TODO: inform user of the problem - they need to know if their data was
335 if (errorMessage == null)
337 errorMessage = "Couldn't write Jalview Archive to output file '"
338 + statefile + "' - See console error log for details";
342 errorMessage += "(output file was '" + statefile + "')";
352 } catch (IOException e)
362 * Writes a jalview project archive to the given Jar output stream.
366 public void saveState(JarOutputStream jout)
368 AlignFrame[] frames = Desktop.getAlignFrames(); // Desktop.desktop.getAllFrames();
375 Hashtable<String, AlignFrame> dsses = new Hashtable<String, AlignFrame>();
380 // NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS
381 // //////////////////////////////////////////////////
383 Vector shortNames = new Vector();
386 for (int i = frames.length - 1; i > -1; i--)
388 AlignFrame af = frames[i];
392 .containsKey(af.getViewport().getSequenceSetId()))
397 String shortName = af.getTitle();
399 if (shortName.indexOf(File.separatorChar) > -1)
401 shortName = shortName.substring(shortName
402 .lastIndexOf(File.separatorChar) + 1);
407 while (shortNames.contains(shortName))
409 if (shortName.endsWith("_" + (count - 1)))
411 shortName = shortName.substring(0, shortName.lastIndexOf("_"));
414 shortName = shortName.concat("_" + count);
418 shortNames.addElement(shortName);
420 if (!shortName.endsWith(".xml"))
422 shortName = shortName + ".xml";
425 int ap, apSize = af.alignPanels.size();
427 for (ap = 0; ap < apSize; ap++)
429 AlignmentPanel apanel = af.alignPanels.get(ap);
430 String fileName = apSize == 1 ? shortName : ap + shortName;
431 if (!fileName.endsWith(".xml"))
433 fileName = fileName + ".xml";
436 saveState(apanel, fileName, jout);
438 String dssid = getDatasetIdRef(af.getViewport().getAlignment()
440 if (!dsses.containsKey(dssid))
442 dsses.put(dssid, af);
447 writeDatasetFor(dsses, "" + jout.hashCode() + " " + uniqueSetSuffix,
453 } catch (Exception foo)
458 } catch (Exception ex)
460 // TODO: inform user of the problem - they need to know if their data was
462 if (errorMessage == null)
464 errorMessage = "Couldn't write Jalview Archive - see error output for details";
466 ex.printStackTrace();
470 // USE THIS METHOD TO SAVE A SINGLE ALIGNMENT WINDOW
471 public boolean saveAlignment(AlignFrame af, String jarFile,
477 int apSize = af.alignPanels.size();
478 FileOutputStream fos = new FileOutputStream(jarFile);
479 JarOutputStream jout = new JarOutputStream(fos);
480 Hashtable<String, AlignFrame> dsses = new Hashtable<String, AlignFrame>();
481 for (AlignmentPanel apanel : af.alignPanels)
483 String jfileName = apSize == 1 ? fileName : fileName + ap;
485 if (!jfileName.endsWith(".xml"))
487 jfileName = jfileName + ".xml";
489 saveState(apanel, jfileName, jout);
490 String dssid = getDatasetIdRef(af.getViewport().getAlignment()
492 if (!dsses.containsKey(dssid))
494 dsses.put(dssid, af);
497 writeDatasetFor(dsses, fileName, jout);
501 } catch (Exception foo)
507 } catch (Exception ex)
509 errorMessage = "Couldn't Write alignment view to Jalview Archive - see error output for details";
510 ex.printStackTrace();
515 private void writeDatasetFor(Hashtable<String, AlignFrame> dsses,
516 String fileName, JarOutputStream jout)
519 for (String dssids : dsses.keySet())
521 AlignFrame _af = dsses.get(dssids);
522 String jfileName = fileName + " Dataset for " + _af.getTitle();
523 if (!jfileName.endsWith(".xml"))
525 jfileName = jfileName + ".xml";
527 saveState(_af.alignPanel, jfileName, true, jout);
532 * create a JalviewModel from an alignment view and marshall it to a
536 * panel to create jalview model for
538 * name of alignment panel written to output stream
544 public JalviewModel saveState(AlignmentPanel ap, String fileName,
545 JarOutputStream jout)
547 return saveState(ap, fileName, false, jout);
551 * create a JalviewModel from an alignment view and marshall it to a
555 * panel to create jalview model for
557 * name of alignment panel written to output stream
559 * when true, only write the dataset for the alignment, not the data
560 * associated with the view.
566 public JalviewModel saveState(AlignmentPanel ap, String fileName,
567 boolean storeDS, JarOutputStream jout)
570 List<String> viewIds = new ArrayList<String>();
571 List<UserColourScheme> userColours = new ArrayList<UserColourScheme>();
573 AlignViewport av = ap.av;
575 JalviewModel object = new JalviewModel();
576 object.setVamsasModel(new jalview.schemabinding.version2.VamsasModel());
578 object.setCreationDate(new java.util.Date(System.currentTimeMillis()));
579 object.setVersion(jalview.bin.Cache.getDefault("VERSION",
580 "Development Build"));
582 jalview.datamodel.AlignmentI jal = av.getAlignment();
584 if (av.hasHiddenRows())
586 jal = jal.getHiddenSequences().getFullAlignment();
589 SequenceSet vamsasSet = new SequenceSet();
591 JalviewModelSequence jms = new JalviewModelSequence();
593 vamsasSet.setGapChar(jal.getGapCharacter() + "");
595 if (jal.getDataset() != null)
597 // dataset id is the dataset's hashcode
598 vamsasSet.setDatasetId(getDatasetIdRef(jal.getDataset()));
601 // switch jal and the dataset
602 jal = jal.getDataset();
605 if (jal.getProperties() != null)
607 Enumeration en = jal.getProperties().keys();
608 while (en.hasMoreElements())
610 String key = en.nextElement().toString();
611 SequenceSetProperties ssp = new SequenceSetProperties();
613 ssp.setValue(jal.getProperties().get(key).toString());
614 vamsasSet.addSequenceSetProperties(ssp);
619 Set<String> calcIdSet = new HashSet<String>();
623 jalview.datamodel.SequenceI jds, jdatasq;
624 for (int i = 0; i < jal.getHeight(); i++)
626 jds = jal.getSequenceAt(i);
627 jdatasq = jds.getDatasetSequence() == null ? jds : jds
628 .getDatasetSequence();
631 if (seqRefIds.get(id) != null)
633 // This happens for two reasons: 1. multiple views are being serialised.
634 // 2. the hashCode has collided with another sequence's code. This DOES
635 // HAPPEN! (PF00072.15.stk does this)
636 // JBPNote: Uncomment to debug writing out of files that do not read
637 // back in due to ArrayOutOfBoundExceptions.
638 // System.err.println("vamsasSeq backref: "+id+"");
639 // System.err.println(jds.getName()+"
640 // "+jds.getStart()+"-"+jds.getEnd()+" "+jds.getSequenceAsString());
641 // System.err.println("Hashcode: "+seqHash(jds));
642 // SequenceI rsq = (SequenceI) seqRefIds.get(id + "");
643 // System.err.println(rsq.getName()+"
644 // "+rsq.getStart()+"-"+rsq.getEnd()+" "+rsq.getSequenceAsString());
645 // System.err.println("Hashcode: "+seqHash(rsq));
649 vamsasSeq = createVamsasSequence(id, jds);
650 vamsasSet.addSequence(vamsasSeq);
651 seqRefIds.put(id, jds);
655 jseq.setStart(jds.getStart());
656 jseq.setEnd(jds.getEnd());
657 jseq.setColour(av.getSequenceColour(jds).getRGB());
659 jseq.setId(id); // jseq id should be a string not a number
662 // Store any sequences this sequence represents
663 if (av.hasHiddenRows())
665 jseq.setHidden(av.getAlignment().getHiddenSequences()
668 if (av.isHiddenRepSequence(jal.getSequenceAt(i)))
670 jalview.datamodel.SequenceI[] reps = av
671 .getRepresentedSequences(jal.getSequenceAt(i))
672 .getSequencesInOrder(jal);
674 for (int h = 0; h < reps.length; h++)
676 if (reps[h] != jal.getSequenceAt(i))
678 jseq.addHiddenSequences(jal.findIndex(reps[h]));
685 if (jds.getSequenceFeatures() != null)
687 jalview.datamodel.SequenceFeature[] sf = jds
688 .getSequenceFeatures();
690 while (index < sf.length)
692 Features features = new Features();
694 features.setBegin(sf[index].getBegin());
695 features.setEnd(sf[index].getEnd());
696 features.setDescription(sf[index].getDescription());
697 features.setType(sf[index].getType());
698 features.setFeatureGroup(sf[index].getFeatureGroup());
699 features.setScore(sf[index].getScore());
700 if (sf[index].links != null)
702 for (int l = 0; l < sf[index].links.size(); l++)
704 OtherData keyValue = new OtherData();
705 keyValue.setKey("LINK_" + l);
706 keyValue.setValue(sf[index].links.elementAt(l).toString());
707 features.addOtherData(keyValue);
710 if (sf[index].otherDetails != null)
713 Enumeration keys = sf[index].otherDetails.keys();
714 while (keys.hasMoreElements())
716 key = keys.nextElement().toString();
717 OtherData keyValue = new OtherData();
718 keyValue.setKey(key);
719 keyValue.setValue(sf[index].otherDetails.get(key).toString());
720 features.addOtherData(keyValue);
724 jseq.addFeatures(features);
729 if (jdatasq.getPDBId() != null)
731 Enumeration en = jdatasq.getPDBId().elements();
732 while (en.hasMoreElements())
734 Pdbids pdb = new Pdbids();
735 jalview.datamodel.PDBEntry entry = (jalview.datamodel.PDBEntry) en
738 pdb.setId(entry.getId());
739 pdb.setType(entry.getType());
742 * Store any structure views associated with this sequence. This
743 * section copes with duplicate entries in the project, so a dataset
744 * only view *should* be coped with sensibly.
746 // This must have been loaded, is it still visible?
747 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
748 String matchedFile = null;
749 for (int f = frames.length - 1; f > -1; f--)
751 if (frames[f] instanceof StructureViewerBase)
753 StructureViewerBase viewFrame = (StructureViewerBase) frames[f];
754 matchedFile = saveStructureState(ap, jds, pdb, entry,
755 viewIds, matchedFile, viewFrame);
759 if (matchedFile != null || entry.getFile() != null)
761 if (entry.getFile() != null)
764 matchedFile = entry.getFile();
766 pdb.setFile(matchedFile); // entry.getFile());
767 if (pdbfiles == null)
769 pdbfiles = new ArrayList<String>();
772 if (!pdbfiles.contains(entry.getId()))
774 pdbfiles.add(entry.getId());
775 DataInputStream dis = null;
778 File file = new File(matchedFile);
779 if (file.exists() && jout != null)
781 byte[] data = new byte[(int) file.length()];
782 jout.putNextEntry(new JarEntry(entry.getId()));
783 dis = new DataInputStream(new FileInputStream(file));
786 DataOutputStream dout = new DataOutputStream(jout);
787 dout.write(data, 0, data.length);
791 } catch (Exception ex)
793 ex.printStackTrace();
801 } catch (IOException e)
811 if (entry.getProperty() != null)
813 PdbentryItem item = new PdbentryItem();
814 Hashtable properties = entry.getProperty();
815 Enumeration en2 = properties.keys();
816 while (en2.hasMoreElements())
818 Property prop = new Property();
819 String key = en2.nextElement().toString();
821 prop.setValue(properties.get(key).toString());
822 item.addProperty(prop);
824 pdb.addPdbentryItem(item);
834 if (!storeDS && av.hasHiddenRows())
836 jal = av.getAlignment();
839 if (jal.getCodonFrames() != null)
841 Set<AlignedCodonFrame> jac = jal.getCodonFrames();
842 for (AlignedCodonFrame acf : jac)
844 AlcodonFrame alc = new AlcodonFrame();
845 vamsasSet.addAlcodonFrame(alc);
846 if (acf.getProtMappings() != null
847 && acf.getProtMappings().length > 0)
849 SequenceI[] dnas = acf.getdnaSeqs();
850 jalview.datamodel.Mapping[] pmaps = acf.getProtMappings();
851 for (int m = 0; m < pmaps.length; m++)
853 AlcodMap alcmap = new AlcodMap();
854 alcmap.setDnasq(seqHash(dnas[m]));
855 alcmap.setMapping(createVamsasMapping(pmaps[m], dnas[m], null,
857 alc.addAlcodMap(alcmap);
862 // AlcodonFrame alc = new AlcodonFrame();
863 // vamsasSet.addAlcodonFrame(alc);
864 // for (int p = 0; p < acf.aaWidth; p++)
866 // Alcodon cmap = new Alcodon();
867 // if (acf.codons[p] != null)
869 // // Null codons indicate a gapped column in the translated peptide
871 // cmap.setPos1(acf.codons[p][0]);
872 // cmap.setPos2(acf.codons[p][1]);
873 // cmap.setPos3(acf.codons[p][2]);
875 // alc.addAlcodon(cmap);
877 // if (acf.getProtMappings() != null
878 // && acf.getProtMappings().length > 0)
880 // SequenceI[] dnas = acf.getdnaSeqs();
881 // jalview.datamodel.Mapping[] pmaps = acf.getProtMappings();
882 // for (int m = 0; m < pmaps.length; m++)
884 // AlcodMap alcmap = new AlcodMap();
885 // alcmap.setDnasq(seqHash(dnas[m]));
886 // alcmap.setMapping(createVamsasMapping(pmaps[m], dnas[m], null,
888 // alc.addAlcodMap(alcmap);
895 // /////////////////////////////////
896 if (!storeDS && av.currentTree != null)
898 // FIND ANY ASSOCIATED TREES
899 // NOT IMPLEMENTED FOR HEADLESS STATE AT PRESENT
900 if (Desktop.desktop != null)
902 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
904 for (int t = 0; t < frames.length; t++)
906 if (frames[t] instanceof TreePanel)
908 TreePanel tp = (TreePanel) frames[t];
910 if (tp.treeCanvas.av.getAlignment() == jal)
912 Tree tree = new Tree();
913 tree.setTitle(tp.getTitle());
914 tree.setCurrentTree((av.currentTree == tp.getTree()));
915 tree.setNewick(tp.getTree().toString());
916 tree.setThreshold(tp.treeCanvas.threshold);
918 tree.setFitToWindow(tp.fitToWindow.getState());
919 tree.setFontName(tp.getTreeFont().getName());
920 tree.setFontSize(tp.getTreeFont().getSize());
921 tree.setFontStyle(tp.getTreeFont().getStyle());
922 tree.setMarkUnlinked(tp.placeholdersMenu.getState());
924 tree.setShowBootstrap(tp.bootstrapMenu.getState());
925 tree.setShowDistances(tp.distanceMenu.getState());
927 tree.setHeight(tp.getHeight());
928 tree.setWidth(tp.getWidth());
929 tree.setXpos(tp.getX());
930 tree.setYpos(tp.getY());
931 tree.setId(makeHashCode(tp, null));
940 * store forward refs from an annotationRow to any groups
942 IdentityHashMap groupRefs = new IdentityHashMap();
945 for (SequenceI sq : jal.getSequences())
947 // Store annotation on dataset sequences only
948 jalview.datamodel.AlignmentAnnotation[] aa = sq.getAnnotation();
949 if (aa != null && aa.length > 0)
951 storeAlignmentAnnotation(aa, groupRefs, av, calcIdSet, storeDS,
958 if (jal.getAlignmentAnnotation() != null)
960 // Store the annotation shown on the alignment.
961 jalview.datamodel.AlignmentAnnotation[] aa = jal
962 .getAlignmentAnnotation();
963 storeAlignmentAnnotation(aa, groupRefs, av, calcIdSet, storeDS,
968 if (jal.getGroups() != null)
970 JGroup[] groups = new JGroup[jal.getGroups().size()];
972 for (jalview.datamodel.SequenceGroup sg : jal.getGroups())
974 groups[++i] = new JGroup();
976 groups[i].setStart(sg.getStartRes());
977 groups[i].setEnd(sg.getEndRes());
978 groups[i].setName(sg.getName());
979 if (groupRefs.containsKey(sg))
981 // group has references so set it's ID field
982 groups[i].setId(groupRefs.get(sg).toString());
986 if (sg.cs.conservationApplied())
988 groups[i].setConsThreshold(sg.cs.getConservationInc());
990 if (sg.cs instanceof jalview.schemes.UserColourScheme)
992 groups[i].setColour(setUserColourScheme(sg.cs, userColours,
998 .setColour(ColourSchemeProperty.getColourName(sg.cs));
1001 else if (sg.cs instanceof jalview.schemes.AnnotationColourGradient)
1003 groups[i].setColour("AnnotationColourGradient");
1004 groups[i].setAnnotationColours(constructAnnotationColours(
1005 (jalview.schemes.AnnotationColourGradient) sg.cs,
1008 else if (sg.cs instanceof jalview.schemes.UserColourScheme)
1011 .setColour(setUserColourScheme(sg.cs, userColours, jms));
1015 groups[i].setColour(ColourSchemeProperty.getColourName(sg.cs));
1018 groups[i].setPidThreshold(sg.cs.getThreshold());
1021 groups[i].setOutlineColour(sg.getOutlineColour().getRGB());
1022 groups[i].setDisplayBoxes(sg.getDisplayBoxes());
1023 groups[i].setDisplayText(sg.getDisplayText());
1024 groups[i].setColourText(sg.getColourText());
1025 groups[i].setTextCol1(sg.textColour.getRGB());
1026 groups[i].setTextCol2(sg.textColour2.getRGB());
1027 groups[i].setTextColThreshold(sg.thresholdTextColour);
1028 groups[i].setShowUnconserved(sg.getShowNonconserved());
1029 groups[i].setIgnoreGapsinConsensus(sg.getIgnoreGapsConsensus());
1030 groups[i].setShowConsensusHistogram(sg.isShowConsensusHistogram());
1031 groups[i].setShowSequenceLogo(sg.isShowSequenceLogo());
1032 groups[i].setNormaliseSequenceLogo(sg.isNormaliseSequenceLogo());
1033 for (int s = 0; s < sg.getSize(); s++)
1035 jalview.datamodel.Sequence seq = (jalview.datamodel.Sequence) sg
1037 groups[i].addSeq(seqHash(seq));
1041 jms.setJGroup(groups);
1045 // /////////SAVE VIEWPORT
1046 Viewport view = new Viewport();
1047 view.setTitle(ap.alignFrame.getTitle());
1048 view.setSequenceSetId(makeHashCode(av.getSequenceSetId(),
1049 av.getSequenceSetId()));
1050 view.setId(av.getViewId());
1051 if (av.getCodingComplement() != null)
1053 view.setComplementId(av.getCodingComplement().getViewId());
1055 view.setViewName(av.viewName);
1056 view.setGatheredViews(av.isGatherViewsHere());
1058 Rectangle position = ap.av.getExplodedGeometry();
1059 if (position != null)
1061 view.setXpos(position.x);
1062 view.setYpos(position.y);
1063 view.setWidth(position.width);
1064 view.setHeight(position.height);
1068 view.setXpos(ap.alignFrame.getBounds().x);
1069 view.setYpos(ap.alignFrame.getBounds().y);
1070 view.setWidth(ap.alignFrame.getBounds().width);
1071 view.setHeight(ap.alignFrame.getBounds().height);
1074 view.setStartRes(av.startRes);
1075 view.setStartSeq(av.startSeq);
1077 if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme)
1079 view.setBgColour(setUserColourScheme(av.getGlobalColourScheme(),
1082 else if (av.getGlobalColourScheme() instanceof jalview.schemes.AnnotationColourGradient)
1084 AnnotationColours ac = constructAnnotationColours(
1085 (jalview.schemes.AnnotationColourGradient) av
1086 .getGlobalColourScheme(),
1089 view.setAnnotationColours(ac);
1090 view.setBgColour("AnnotationColourGradient");
1094 view.setBgColour(ColourSchemeProperty.getColourName(av
1095 .getGlobalColourScheme()));
1098 ColourSchemeI cs = av.getGlobalColourScheme();
1102 if (cs.conservationApplied())
1104 view.setConsThreshold(cs.getConservationInc());
1105 if (cs instanceof jalview.schemes.UserColourScheme)
1107 view.setBgColour(setUserColourScheme(cs, userColours, jms));
1111 if (cs instanceof ResidueColourScheme)
1113 view.setPidThreshold(cs.getThreshold());
1117 view.setConservationSelected(av.getConservationSelected());
1118 view.setPidSelected(av.getAbovePIDThreshold());
1119 view.setFontName(av.font.getName());
1120 view.setFontSize(av.font.getSize());
1121 view.setFontStyle(av.font.getStyle());
1122 view.setRenderGaps(av.isRenderGaps());
1123 view.setShowAnnotation(av.isShowAnnotation());
1124 view.setShowBoxes(av.getShowBoxes());
1125 view.setShowColourText(av.getColourText());
1126 view.setShowFullId(av.getShowJVSuffix());
1127 view.setRightAlignIds(av.isRightAlignIds());
1128 view.setShowSequenceFeatures(av.isShowSequenceFeatures());
1129 view.setShowText(av.getShowText());
1130 view.setShowUnconserved(av.getShowUnconserved());
1131 view.setWrapAlignment(av.getWrapAlignment());
1132 view.setTextCol1(av.getTextColour().getRGB());
1133 view.setTextCol2(av.getTextColour2().getRGB());
1134 view.setTextColThreshold(av.getThresholdTextColour());
1135 view.setShowConsensusHistogram(av.isShowConsensusHistogram());
1136 view.setShowSequenceLogo(av.isShowSequenceLogo());
1137 view.setNormaliseSequenceLogo(av.isNormaliseSequenceLogo());
1138 view.setShowGroupConsensus(av.isShowGroupConsensus());
1139 view.setShowGroupConservation(av.isShowGroupConservation());
1140 view.setShowNPfeatureTooltip(av.isShowNPFeats());
1141 view.setShowDbRefTooltip(av.isShowDBRefs());
1142 view.setFollowHighlight(av.followHighlight);
1143 view.setFollowSelection(av.followSelection);
1144 view.setIgnoreGapsinConsensus(av.isIgnoreGapsConsensus());
1145 if (av.getFeaturesDisplayed() != null)
1147 jalview.schemabinding.version2.FeatureSettings fs = new jalview.schemabinding.version2.FeatureSettings();
1149 String[] renderOrder = ap.getSeqPanel().seqCanvas
1150 .getFeatureRenderer().getRenderOrder()
1151 .toArray(new String[0]);
1153 Vector settingsAdded = new Vector();
1154 Object gstyle = null;
1155 GraduatedColor gcol = null;
1156 if (renderOrder != null)
1158 for (int ro = 0; ro < renderOrder.length; ro++)
1160 gstyle = ap.getSeqPanel().seqCanvas.getFeatureRenderer()
1161 .getFeatureStyle(renderOrder[ro]);
1162 Setting setting = new Setting();
1163 setting.setType(renderOrder[ro]);
1164 if (gstyle instanceof GraduatedColor)
1166 gcol = (GraduatedColor) gstyle;
1167 setting.setColour(gcol.getMaxColor().getRGB());
1168 setting.setMincolour(gcol.getMinColor().getRGB());
1169 setting.setMin(gcol.getMin());
1170 setting.setMax(gcol.getMax());
1171 setting.setColourByLabel(gcol.isColourByLabel());
1172 setting.setAutoScale(gcol.isAutoScale());
1173 setting.setThreshold(gcol.getThresh());
1174 setting.setThreshstate(gcol.getThreshType());
1178 setting.setColour(ap.getSeqPanel().seqCanvas
1179 .getFeatureRenderer()
1180 .getColour(renderOrder[ro]).getRGB());
1183 setting.setDisplay(av.getFeaturesDisplayed().isVisible(
1185 float rorder = ap.getSeqPanel().seqCanvas.getFeatureRenderer()
1186 .getOrder(renderOrder[ro]);
1189 setting.setOrder(rorder);
1191 fs.addSetting(setting);
1192 settingsAdded.addElement(renderOrder[ro]);
1196 // Make sure we save none displayed feature settings
1197 Iterator en = ap.getSeqPanel().seqCanvas.getFeatureRenderer()
1198 .getFeatureColours().keySet().iterator();
1199 while (en.hasNext())
1201 String key = en.next().toString();
1202 if (settingsAdded.contains(key))
1207 Setting setting = new Setting();
1208 setting.setType(key);
1209 setting.setColour(ap.getSeqPanel().seqCanvas.getFeatureRenderer()
1210 .getColour(key).getRGB());
1212 setting.setDisplay(false);
1213 float rorder = ap.getSeqPanel().seqCanvas.getFeatureRenderer()
1217 setting.setOrder(rorder);
1219 fs.addSetting(setting);
1220 settingsAdded.addElement(key);
1222 // is groups actually supposed to be a map here ?
1223 en = ap.getSeqPanel().seqCanvas.getFeatureRenderer()
1224 .getFeatureGroups().iterator();
1225 Vector groupsAdded = new Vector();
1226 while (en.hasNext())
1228 String grp = en.next().toString();
1229 if (groupsAdded.contains(grp))
1233 Group g = new Group();
1235 g.setDisplay(((Boolean) ap.getSeqPanel().seqCanvas
1236 .getFeatureRenderer().checkGroupVisibility(grp, false))
1239 groupsAdded.addElement(grp);
1241 jms.setFeatureSettings(fs);
1245 if (av.hasHiddenColumns())
1247 if (av.getColumnSelection() == null
1248 || av.getColumnSelection().getHiddenColumns() == null)
1250 warn("REPORT BUG: avoided null columnselection bug (DMAM reported). Please contact Jim about this.");
1254 for (int c = 0; c < av.getColumnSelection().getHiddenColumns()
1257 int[] region = av.getColumnSelection().getHiddenColumns()
1259 HiddenColumns hc = new HiddenColumns();
1260 hc.setStart(region[0]);
1261 hc.setEnd(region[1]);
1262 view.addHiddenColumns(hc);
1266 if (calcIdSet.size() > 0)
1268 for (String calcId : calcIdSet)
1270 if (calcId.trim().length() > 0)
1272 CalcIdParam cidp = createCalcIdParam(calcId, av);
1273 // Some calcIds have no parameters.
1276 view.addCalcIdParam(cidp);
1282 jms.addViewport(view);
1284 object.setJalviewModelSequence(jms);
1285 object.getVamsasModel().addSequenceSet(vamsasSet);
1287 if (jout != null && fileName != null)
1289 // We may not want to write the object to disk,
1290 // eg we can copy the alignViewport to a new view object
1291 // using save and then load
1294 JarEntry entry = new JarEntry(fileName);
1295 jout.putNextEntry(entry);
1296 PrintWriter pout = new PrintWriter(new OutputStreamWriter(jout,
1298 org.exolab.castor.xml.Marshaller marshaller = new org.exolab.castor.xml.Marshaller(
1300 marshaller.marshal(object);
1303 } catch (Exception ex)
1305 // TODO: raise error in GUI if marshalling failed.
1306 ex.printStackTrace();
1313 * Save the state of a structure viewer
1318 * the archive XML element under which to save the state
1321 * @param matchedFile
1325 protected String saveStructureState(AlignmentPanel ap, SequenceI jds,
1326 Pdbids pdb, PDBEntry entry, List<String> viewIds,
1327 String matchedFile, StructureViewerBase viewFrame)
1329 final AAStructureBindingModel bindingModel = viewFrame.getBinding();
1330 for (int peid = 0; peid < bindingModel.getPdbCount(); peid++)
1332 final PDBEntry pdbentry = bindingModel.getPdbEntry(peid);
1333 final String pdbId = pdbentry.getId();
1334 if (!pdbId.equals(entry.getId())
1335 && !(entry.getId().length() > 4 && entry.getId()
1336 .toLowerCase().startsWith(pdbId.toLowerCase())))
1340 if (matchedFile == null)
1342 matchedFile = pdbentry.getFile();
1344 else if (!matchedFile.equals(pdbentry.getFile()))
1347 .warn("Probably lost some PDB-Sequence mappings for this structure file (which apparently has same PDB Entry code): "
1348 + pdbentry.getFile());
1352 // can get at it if the ID
1353 // match is ambiguous (e.g.
1355 String statestring = viewFrame.getStateInfo();
1357 for (int smap = 0; smap < viewFrame.getBinding().getSequence()[peid].length; smap++)
1359 // if (jal.findIndex(jmol.jmb.sequence[peid][smap]) > -1)
1360 if (jds == viewFrame.getBinding().getSequence()[peid][smap])
1362 StructureState state = new StructureState();
1363 state.setVisible(true);
1364 state.setXpos(viewFrame.getX());
1365 state.setYpos(viewFrame.getY());
1366 state.setWidth(viewFrame.getWidth());
1367 state.setHeight(viewFrame.getHeight());
1368 final String viewId = viewFrame.getViewId();
1369 state.setViewId(viewId);
1370 state.setAlignwithAlignPanel(viewFrame.isUsedforaligment(ap));
1371 state.setColourwithAlignPanel(viewFrame.isUsedforcolourby(ap));
1372 state.setColourByJmol(viewFrame.isColouredByViewer());
1374 * Only store each structure viewer's state once in each XML document.
1376 if (!viewIds.contains(viewId))
1378 viewIds.add(viewId);
1379 state.setContent(statestring.replaceAll("\n", ""));
1383 state.setContent("# duplicate state");
1385 pdb.addStructureState(state);
1392 private AnnotationColours constructAnnotationColours(
1393 AnnotationColourGradient acg, List<UserColourScheme> userColours,
1394 JalviewModelSequence jms)
1396 AnnotationColours ac = new AnnotationColours();
1397 ac.setAboveThreshold(acg.getAboveThreshold());
1398 ac.setThreshold(acg.getAnnotationThreshold());
1399 ac.setAnnotation(acg.getAnnotation());
1400 if (acg.getBaseColour() instanceof jalview.schemes.UserColourScheme)
1402 ac.setColourScheme(setUserColourScheme(acg.getBaseColour(),
1407 ac.setColourScheme(ColourSchemeProperty.getColourName(acg
1411 ac.setMaxColour(acg.getMaxColour().getRGB());
1412 ac.setMinColour(acg.getMinColour().getRGB());
1413 ac.setPerSequence(acg.isSeqAssociated());
1414 ac.setPredefinedColours(acg.isPredefinedColours());
1418 private void storeAlignmentAnnotation(AlignmentAnnotation[] aa,
1419 IdentityHashMap groupRefs, AlignmentViewport av,
1420 Set<String> calcIdSet, boolean storeDS, SequenceSet vamsasSet)
1423 for (int i = 0; i < aa.length; i++)
1425 Annotation an = new Annotation();
1427 if (aa[i].annotationId != null)
1429 annotationIds.put(aa[i].annotationId, aa[i]);
1432 an.setId(aa[i].annotationId);
1434 an.setVisible(aa[i].visible);
1436 an.setDescription(aa[i].description);
1438 if (aa[i].sequenceRef != null)
1440 // TODO later annotation sequenceRef should be the XML ID of the
1441 // sequence rather than its display name
1442 an.setSequenceRef(aa[i].sequenceRef.getName());
1444 if (aa[i].groupRef != null)
1446 Object groupIdr = groupRefs.get(aa[i].groupRef);
1447 if (groupIdr == null)
1449 // make a locally unique String
1450 groupRefs.put(aa[i].groupRef,
1451 groupIdr = ("" + System.currentTimeMillis()
1452 + aa[i].groupRef.getName() + groupRefs.size()));
1454 an.setGroupRef(groupIdr.toString());
1457 // store all visualization attributes for annotation
1458 an.setGraphHeight(aa[i].graphHeight);
1459 an.setCentreColLabels(aa[i].centreColLabels);
1460 an.setScaleColLabels(aa[i].scaleColLabel);
1461 an.setShowAllColLabels(aa[i].showAllColLabels);
1462 an.setBelowAlignment(aa[i].belowAlignment);
1464 if (aa[i].graph > 0)
1467 an.setGraphType(aa[i].graph);
1468 an.setGraphGroup(aa[i].graphGroup);
1469 if (aa[i].getThreshold() != null)
1471 ThresholdLine line = new ThresholdLine();
1472 line.setLabel(aa[i].getThreshold().label);
1473 line.setValue(aa[i].getThreshold().value);
1474 line.setColour(aa[i].getThreshold().colour.getRGB());
1475 an.setThresholdLine(line);
1483 an.setLabel(aa[i].label);
1485 if (aa[i] == av.getAlignmentQualityAnnot()
1486 || aa[i] == av.getAlignmentConservationAnnotation()
1487 || aa[i] == av.getAlignmentConsensusAnnotation()
1488 || aa[i].autoCalculated)
1490 // new way of indicating autocalculated annotation -
1491 an.setAutoCalculated(aa[i].autoCalculated);
1493 if (aa[i].hasScore())
1495 an.setScore(aa[i].getScore());
1498 if (aa[i].getCalcId() != null)
1500 calcIdSet.add(aa[i].getCalcId());
1501 an.setCalcId(aa[i].getCalcId());
1503 if (aa[i].hasProperties())
1505 for (String pr : aa[i].getProperties())
1507 Property prop = new Property();
1509 prop.setValue(aa[i].getProperty(pr));
1510 an.addProperty(prop);
1514 AnnotationElement ae;
1515 if (aa[i].annotations != null)
1517 an.setScoreOnly(false);
1518 for (int a = 0; a < aa[i].annotations.length; a++)
1520 if ((aa[i] == null) || (aa[i].annotations[a] == null))
1525 ae = new AnnotationElement();
1526 if (aa[i].annotations[a].description != null)
1528 ae.setDescription(aa[i].annotations[a].description);
1530 if (aa[i].annotations[a].displayCharacter != null)
1532 ae.setDisplayCharacter(aa[i].annotations[a].displayCharacter);
1535 if (!Float.isNaN(aa[i].annotations[a].value))
1537 ae.setValue(aa[i].annotations[a].value);
1541 if (aa[i].annotations[a].secondaryStructure > ' ')
1543 ae.setSecondaryStructure(aa[i].annotations[a].secondaryStructure
1547 if (aa[i].annotations[a].colour != null
1548 && aa[i].annotations[a].colour != java.awt.Color.black)
1550 ae.setColour(aa[i].annotations[a].colour.getRGB());
1553 an.addAnnotationElement(ae);
1554 if (aa[i].autoCalculated)
1556 // only write one non-null entry into the annotation row -
1557 // sufficient to get the visualization attributes necessary to
1565 an.setScoreOnly(true);
1567 if (!storeDS || (storeDS && !aa[i].autoCalculated))
1569 // skip autocalculated annotation - these are only provided for
1571 vamsasSet.addAnnotation(an);
1577 private CalcIdParam createCalcIdParam(String calcId, AlignViewport av)
1579 AutoCalcSetting settings = av.getCalcIdSettingsFor(calcId);
1580 if (settings != null)
1582 CalcIdParam vCalcIdParam = new CalcIdParam();
1583 vCalcIdParam.setCalcId(calcId);
1584 vCalcIdParam.addServiceURL(settings.getServiceURI());
1585 // generic URI allowing a third party to resolve another instance of the
1586 // service used for this calculation
1587 for (String urls : settings.getServiceURLs())
1589 vCalcIdParam.addServiceURL(urls);
1591 vCalcIdParam.setVersion("1.0");
1592 if (settings.getPreset() != null)
1594 WsParamSetI setting = settings.getPreset();
1595 vCalcIdParam.setName(setting.getName());
1596 vCalcIdParam.setDescription(setting.getDescription());
1600 vCalcIdParam.setName("");
1601 vCalcIdParam.setDescription("Last used parameters");
1603 // need to be able to recover 1) settings 2) user-defined presets or
1604 // recreate settings from preset 3) predefined settings provided by
1605 // service - or settings that can be transferred (or discarded)
1606 vCalcIdParam.setParameters(settings.getWsParamFile().replace("\n",
1608 vCalcIdParam.setAutoUpdate(settings.isAutoUpdate());
1609 // todo - decide if updateImmediately is needed for any projects.
1611 return vCalcIdParam;
1616 private boolean recoverCalcIdParam(CalcIdParam calcIdParam,
1619 if (calcIdParam.getVersion().equals("1.0"))
1621 Jws2Instance service = Jws2Discoverer.getDiscoverer()
1622 .getPreferredServiceFor(calcIdParam.getServiceURL());
1623 if (service != null)
1625 WsParamSetI parmSet = null;
1628 parmSet = service.getParamStore().parseServiceParameterFile(
1629 calcIdParam.getName(), calcIdParam.getDescription(),
1630 calcIdParam.getServiceURL(),
1631 calcIdParam.getParameters().replace("|\\n|", "\n"));
1632 } catch (IOException x)
1634 warn("Couldn't parse parameter data for "
1635 + calcIdParam.getCalcId(), x);
1638 List<ArgumentI> argList = null;
1639 if (calcIdParam.getName().length() > 0)
1641 parmSet = service.getParamStore()
1642 .getPreset(calcIdParam.getName());
1643 if (parmSet != null)
1645 // TODO : check we have a good match with settings in AACon -
1646 // otherwise we'll need to create a new preset
1651 argList = parmSet.getArguments();
1654 AAConSettings settings = new AAConSettings(
1655 calcIdParam.isAutoUpdate(), service, parmSet, argList);
1656 av.setCalcIdSettingsFor(calcIdParam.getCalcId(), settings,
1657 calcIdParam.isNeedsUpdate());
1662 warn("Cannot resolve a service for the parameters used in this project. Try configuring a JABAWS server.");
1666 throw new Error(MessageManager.formatMessage(
1667 "error.unsupported_version_calcIdparam", new Object[]
1668 { calcIdParam.toString() }));
1672 * External mapping between jalview objects and objects yielding a valid and
1673 * unique object ID string. This is null for normal Jalview project IO, but
1674 * non-null when a jalview project is being read or written as part of a
1677 IdentityHashMap jv2vobj = null;
1680 * Construct a unique ID for jvobj using either existing bindings or if none
1681 * exist, the result of the hashcode call for the object.
1684 * jalview data object
1685 * @return unique ID for referring to jvobj
1687 private String makeHashCode(Object jvobj, String altCode)
1689 if (jv2vobj != null)
1691 Object id = jv2vobj.get(jvobj);
1694 return id.toString();
1696 // check string ID mappings
1697 if (jvids2vobj != null && jvobj instanceof String)
1699 id = jvids2vobj.get(jvobj);
1703 return id.toString();
1705 // give up and warn that something has gone wrong
1706 warn("Cannot find ID for object in external mapping : " + jvobj);
1712 * return local jalview object mapped to ID, if it exists
1716 * @return null or object bound to idcode
1718 private Object retrieveExistingObj(String idcode)
1720 if (idcode != null && vobj2jv != null)
1722 return vobj2jv.get(idcode);
1728 * binding from ID strings from external mapping table to jalview data model
1731 private Hashtable vobj2jv;
1733 private Sequence createVamsasSequence(String id, SequenceI jds)
1735 return createVamsasSequence(true, id, jds, null);
1738 private Sequence createVamsasSequence(boolean recurse, String id,
1739 SequenceI jds, SequenceI parentseq)
1741 Sequence vamsasSeq = new Sequence();
1742 vamsasSeq.setId(id);
1743 vamsasSeq.setName(jds.getName());
1744 vamsasSeq.setSequence(jds.getSequenceAsString());
1745 vamsasSeq.setDescription(jds.getDescription());
1746 jalview.datamodel.DBRefEntry[] dbrefs = null;
1747 if (jds.getDatasetSequence() != null)
1749 vamsasSeq.setDsseqid(seqHash(jds.getDatasetSequence()));
1750 if (jds.getDatasetSequence().getDBRef() != null)
1752 dbrefs = jds.getDatasetSequence().getDBRef();
1757 vamsasSeq.setDsseqid(id); // so we can tell which sequences really are
1758 // dataset sequences only
1759 dbrefs = jds.getDBRef();
1763 for (int d = 0; d < dbrefs.length; d++)
1765 DBRef dbref = new DBRef();
1766 dbref.setSource(dbrefs[d].getSource());
1767 dbref.setVersion(dbrefs[d].getVersion());
1768 dbref.setAccessionId(dbrefs[d].getAccessionId());
1769 if (dbrefs[d].hasMap())
1771 Mapping mp = createVamsasMapping(dbrefs[d].getMap(), parentseq,
1773 dbref.setMapping(mp);
1775 vamsasSeq.addDBRef(dbref);
1781 private Mapping createVamsasMapping(jalview.datamodel.Mapping jmp,
1782 SequenceI parentseq, SequenceI jds, boolean recurse)
1785 if (jmp.getMap() != null)
1789 jalview.util.MapList mlst = jmp.getMap();
1790 List<int[]> r = mlst.getFromRanges();
1791 for (int[] range : r)
1793 MapListFrom mfrom = new MapListFrom();
1794 mfrom.setStart(range[0]);
1795 mfrom.setEnd(range[1]);
1796 mp.addMapListFrom(mfrom);
1798 r = mlst.getToRanges();
1799 for (int[] range : r)
1801 MapListTo mto = new MapListTo();
1802 mto.setStart(range[0]);
1803 mto.setEnd(range[1]);
1804 mp.addMapListTo(mto);
1806 mp.setMapFromUnit(mlst.getFromRatio());
1807 mp.setMapToUnit(mlst.getToRatio());
1808 if (jmp.getTo() != null)
1810 MappingChoice mpc = new MappingChoice();
1812 && (parentseq != jmp.getTo() || parentseq
1813 .getDatasetSequence() != jmp.getTo()))
1815 mpc.setSequence(createVamsasSequence(false, seqHash(jmp.getTo()),
1821 SequenceI ps = null;
1822 if (parentseq != jmp.getTo()
1823 && parentseq.getDatasetSequence() != jmp.getTo())
1825 // chaining dbref rather than a handshaking one
1826 jmpid = seqHash(ps = jmp.getTo());
1830 jmpid = seqHash(ps = parentseq);
1832 mpc.setDseqFor(jmpid);
1833 if (!seqRefIds.containsKey(mpc.getDseqFor()))
1835 jalview.bin.Cache.log.debug("creatign new DseqFor ID");
1836 seqRefIds.put(mpc.getDseqFor(), ps);
1840 jalview.bin.Cache.log.debug("reusing DseqFor ID");
1843 mp.setMappingChoice(mpc);
1849 String setUserColourScheme(jalview.schemes.ColourSchemeI cs,
1850 List<UserColourScheme> userColours, JalviewModelSequence jms)
1853 jalview.schemes.UserColourScheme ucs = (jalview.schemes.UserColourScheme) cs;
1854 boolean newucs = false;
1855 if (!userColours.contains(ucs))
1857 userColours.add(ucs);
1860 id = "ucs" + userColours.indexOf(ucs);
1863 // actually create the scheme's entry in the XML model
1864 java.awt.Color[] colours = ucs.getColours();
1865 jalview.schemabinding.version2.UserColours uc = new jalview.schemabinding.version2.UserColours();
1866 jalview.schemabinding.version2.UserColourScheme jbucs = new jalview.schemabinding.version2.UserColourScheme();
1868 for (int i = 0; i < colours.length; i++)
1870 jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();
1871 col.setName(ResidueProperties.aa[i]);
1872 col.setRGB(jalview.util.Format.getHexString(colours[i]));
1873 jbucs.addColour(col);
1875 if (ucs.getLowerCaseColours() != null)
1877 colours = ucs.getLowerCaseColours();
1878 for (int i = 0; i < colours.length; i++)
1880 jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();
1881 col.setName(ResidueProperties.aa[i].toLowerCase());
1882 col.setRGB(jalview.util.Format.getHexString(colours[i]));
1883 jbucs.addColour(col);
1888 uc.setUserColourScheme(jbucs);
1889 jms.addUserColours(uc);
1895 jalview.schemes.UserColourScheme getUserColourScheme(
1896 JalviewModelSequence jms, String id)
1898 UserColours[] uc = jms.getUserColours();
1899 UserColours colours = null;
1901 for (int i = 0; i < uc.length; i++)
1903 if (uc[i].getId().equals(id))
1911 java.awt.Color[] newColours = new java.awt.Color[24];
1913 for (int i = 0; i < 24; i++)
1915 newColours[i] = new java.awt.Color(Integer.parseInt(colours
1916 .getUserColourScheme().getColour(i).getRGB(), 16));
1919 jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(
1922 if (colours.getUserColourScheme().getColourCount() > 24)
1924 newColours = new java.awt.Color[23];
1925 for (int i = 0; i < 23; i++)
1927 newColours[i] = new java.awt.Color(Integer.parseInt(colours
1928 .getUserColourScheme().getColour(i + 24).getRGB(), 16));
1930 ucs.setLowerCaseColours(newColours);
1937 * contains last error message (if any) encountered by XML loader.
1939 String errorMessage = null;
1942 * flag to control whether the Jalview2XML_V1 parser should be deferred to if
1943 * exceptions are raised during project XML parsing
1945 public boolean attemptversion1parse = true;
1948 * Load a jalview project archive from a jar file
1951 * - HTTP URL or filename
1953 public AlignFrame loadJalviewAlign(final String file)
1956 jalview.gui.AlignFrame af = null;
1960 // create list to store references for any new Jmol viewers created
1961 newStructureViewers = new Vector<JalviewStructureDisplayI>();
1962 // UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
1963 // Workaround is to make sure caller implements the JarInputStreamProvider
1965 // so we can re-open the jar input stream for each entry.
1967 jarInputStreamProvider jprovider = createjarInputStreamProvider(file);
1968 af = loadJalviewAlign(jprovider);
1970 } catch (MalformedURLException e)
1972 errorMessage = "Invalid URL format for '" + file + "'";
1978 SwingUtilities.invokeAndWait(new Runnable()
1982 setLoadingFinishedForNewStructureViewers();
1985 } catch (Exception x)
1993 private jarInputStreamProvider createjarInputStreamProvider(
1994 final String file) throws MalformedURLException
1997 errorMessage = null;
1998 uniqueSetSuffix = null;
2000 viewportsAdded.clear();
2001 frefedSequence = null;
2003 if (file.startsWith("http://"))
2005 url = new URL(file);
2007 final URL _url = url;
2008 return new jarInputStreamProvider()
2012 public JarInputStream getJarInputStream() throws IOException
2016 return new JarInputStream(_url.openStream());
2020 return new JarInputStream(new FileInputStream(file));
2025 public String getFilename()
2033 * Recover jalview session from a jalview project archive. Caller may
2034 * initialise uniqueSetSuffix, seqRefIds, viewportsAdded and frefedSequence
2035 * themselves. Any null fields will be initialised with default values,
2036 * non-null fields are left alone.
2041 public AlignFrame loadJalviewAlign(final jarInputStreamProvider jprovider)
2043 errorMessage = null;
2044 if (uniqueSetSuffix == null)
2046 uniqueSetSuffix = System.currentTimeMillis() % 100000 + "";
2048 if (seqRefIds == null)
2050 seqRefIds = new HashMap<String, SequenceI>();
2052 if (frefedSequence == null)
2054 frefedSequence = new Vector();
2057 AlignFrame af = null, _af = null;
2058 Map<String, AlignFrame> gatherToThisFrame = new HashMap<String, AlignFrame>();
2059 final String file = jprovider.getFilename();
2062 JarInputStream jin = null;
2063 JarEntry jarentry = null;
2068 jin = jprovider.getJarInputStream();
2069 for (int i = 0; i < entryCount; i++)
2071 jarentry = jin.getNextJarEntry();
2074 if (jarentry != null && jarentry.getName().endsWith(".xml"))
2076 InputStreamReader in = new InputStreamReader(jin, "UTF-8");
2077 JalviewModel object = new JalviewModel();
2079 Unmarshaller unmar = new Unmarshaller(object);
2080 unmar.setValidation(false);
2081 object = (JalviewModel) unmar.unmarshal(in);
2082 if (true) // !skipViewport(object))
2084 _af = loadFromObject(object, file, true, jprovider);
2085 if (object.getJalviewModelSequence().getViewportCount() > 0)
2088 if (af.viewport.isGatherViewsHere())
2090 gatherToThisFrame.put(af.viewport.getSequenceSetId(), af);
2096 else if (jarentry != null)
2098 // Some other file here.
2101 } while (jarentry != null);
2102 resolveFrefedSequences();
2103 } catch (java.io.FileNotFoundException ex)
2105 ex.printStackTrace();
2106 errorMessage = "Couldn't locate Jalview XML file : " + file;
2107 System.err.println("Exception whilst loading jalview XML file : "
2109 } catch (java.net.UnknownHostException ex)
2111 ex.printStackTrace();
2112 errorMessage = "Couldn't locate Jalview XML file : " + file;
2113 System.err.println("Exception whilst loading jalview XML file : "
2115 } catch (Exception ex)
2117 System.err.println("Parsing as Jalview Version 2 file failed.");
2118 ex.printStackTrace(System.err);
2119 if (attemptversion1parse)
2121 // Is Version 1 Jar file?
2124 af = new Jalview2XML_V1(raiseGUI).LoadJalviewAlign(jprovider);
2125 } catch (Exception ex2)
2127 System.err.println("Exception whilst loading as jalviewXMLV1:");
2128 ex2.printStackTrace();
2132 if (Desktop.instance != null)
2134 Desktop.instance.stopLoading();
2138 System.out.println("Successfully loaded archive file");
2141 ex.printStackTrace();
2143 System.err.println("Exception whilst loading jalview XML file : "
2145 } catch (OutOfMemoryError e)
2147 // Don't use the OOM Window here
2148 errorMessage = "Out of memory loading jalview XML file";
2149 System.err.println("Out of memory whilst loading jalview XML file");
2150 e.printStackTrace();
2153 if (Desktop.instance != null)
2155 Desktop.instance.stopLoading();
2159 * Regather multiple views (with the same sequence set id) to the frame (if
2160 * any) that is flagged as the one to gather to, i.e. convert them to tabbed
2161 * views instead of separate frames. Note this doesn't restore a state where
2162 * some expanded views in turn have tabbed views - the last "first tab" read
2163 * in will play the role of gatherer for all.
2165 for (AlignFrame fr : gatherToThisFrame.values())
2167 Desktop.instance.gatherViews(fr);
2170 restoreSplitFrames();
2172 if (errorMessage != null)
2180 * Try to reconstruct and display SplitFrame windows, where each contains
2181 * complementary dna and protein alignments. Done by pairing up AlignFrame
2182 * objects (created earlier) which have complementary viewport ids associated.
2184 protected void restoreSplitFrames()
2186 List<SplitFrame> gatherTo = new ArrayList<SplitFrame>();
2187 List<AlignFrame> addedToSplitFrames = new ArrayList<AlignFrame>();
2188 Map<String, AlignFrame> dna = new HashMap<String, AlignFrame>();
2191 * Identify the DNA alignments
2193 for (Entry<Viewport, AlignFrame> candidate : splitFrameCandidates
2196 AlignFrame af = candidate.getValue();
2197 if (af.getViewport().getAlignment().isNucleotide())
2199 dna.put(candidate.getKey().getId(), af);
2204 * Try to match up the protein complements
2206 for (Entry<Viewport, AlignFrame> candidate : splitFrameCandidates
2209 AlignFrame af = candidate.getValue();
2210 if (!af.getViewport().getAlignment().isNucleotide())
2212 String complementId = candidate.getKey().getComplementId();
2213 // only non-null complements should be in the Map
2214 if (complementId != null && dna.containsKey(complementId))
2216 final AlignFrame dnaFrame = dna.get(complementId);
2217 SplitFrame sf = createSplitFrame(dnaFrame, af);
2218 addedToSplitFrames.add(dnaFrame);
2219 addedToSplitFrames.add(af);
2220 if (af.viewport.isGatherViewsHere())
2229 * Open any that we failed to pair up (which shouldn't happen!) as
2230 * standalone AlignFrame's.
2232 for (Entry<Viewport, AlignFrame> candidate : splitFrameCandidates
2235 AlignFrame af = candidate.getValue();
2236 if (!addedToSplitFrames.contains(af)) {
2237 Viewport view = candidate.getKey();
2238 Desktop.addInternalFrame(af, view.getTitle(), view.getWidth(),
2240 System.err.println("Failed to restore view " + view.getTitle()
2241 + " to split frame");
2246 * Gather back into tabbed views as flagged.
2248 for (SplitFrame sf : gatherTo)
2250 Desktop.instance.gatherViews(sf);
2253 splitFrameCandidates.clear();
2257 * Construct and display one SplitFrame holding DNA and protein alignments.
2260 * @param proteinFrame
2263 protected SplitFrame createSplitFrame(AlignFrame dnaFrame,
2264 AlignFrame proteinFrame)
2266 SplitFrame splitFrame = new SplitFrame(dnaFrame, proteinFrame);
2267 String title = MessageManager.getString("label.linked_view_title");
2268 Desktop.addInternalFrame(splitFrame, title, -1, -1);
2273 * check errorMessage for a valid error message and raise an error box in the
2274 * GUI or write the current errorMessage to stderr and then clear the error
2277 protected void reportErrors()
2279 reportErrors(false);
2282 protected void reportErrors(final boolean saving)
2284 if (errorMessage != null)
2286 final String finalErrorMessage = errorMessage;
2289 javax.swing.SwingUtilities.invokeLater(new Runnable()
2294 JOptionPane.showInternalMessageDialog(Desktop.desktop,
2295 finalErrorMessage, "Error "
2296 + (saving ? "saving" : "loading")
2297 + " Jalview file", JOptionPane.WARNING_MESSAGE);
2303 System.err.println("Problem loading Jalview file: " + errorMessage);
2306 errorMessage = null;
2309 Map<String, String> alreadyLoadedPDB = new HashMap<String, String>();
2312 * when set, local views will be updated from view stored in JalviewXML
2313 * Currently (28th Sep 2008) things will go horribly wrong in vamsas document
2314 * sync if this is set to true.
2316 private final boolean updateLocalViews = false;
2318 String loadPDBFile(jarInputStreamProvider jprovider, String pdbId)
2320 if (alreadyLoadedPDB.containsKey(pdbId))
2322 return alreadyLoadedPDB.get(pdbId).toString();
2327 JarInputStream jin = jprovider.getJarInputStream();
2329 * if (jprovider.startsWith("http://")) { jin = new JarInputStream(new
2330 * URL(jprovider).openStream()); } else { jin = new JarInputStream(new
2331 * FileInputStream(jprovider)); }
2334 JarEntry entry = null;
2337 entry = jin.getNextJarEntry();
2338 } while (entry != null && !entry.getName().equals(pdbId));
2341 BufferedReader in = new BufferedReader(new InputStreamReader(jin));
2342 File outFile = File.createTempFile("jalview_pdb", ".txt");
2343 outFile.deleteOnExit();
2344 PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
2347 while ((data = in.readLine()) != null)
2354 } catch (Exception foo)
2359 String t = outFile.getAbsolutePath();
2360 alreadyLoadedPDB.put(pdbId, t);
2365 warn("Couldn't find PDB file entry in Jalview Jar for " + pdbId);
2367 } catch (Exception ex)
2369 ex.printStackTrace();
2375 private class JvAnnotRow
2377 public JvAnnotRow(int i, AlignmentAnnotation jaa)
2384 * persisted version of annotation row from which to take vis properties
2386 public jalview.datamodel.AlignmentAnnotation template;
2389 * original position of the annotation row in the alignment
2395 * Load alignment frame from jalview XML DOM object
2400 * filename source string
2401 * @param loadTreesAndStructures
2402 * when false only create Viewport
2404 * data source provider
2405 * @return alignment frame created from view stored in DOM
2407 AlignFrame loadFromObject(JalviewModel object, String file,
2408 boolean loadTreesAndStructures, jarInputStreamProvider jprovider)
2410 SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);
2411 Sequence[] vamsasSeq = vamsasSet.getSequence();
2413 JalviewModelSequence jms = object.getJalviewModelSequence();
2415 Viewport view = (jms.getViewportCount() > 0) ? jms.getViewport(0)
2418 // ////////////////////////////////
2421 List<SequenceI> hiddenSeqs = null;
2422 jalview.datamodel.Sequence jseq;
2424 List<SequenceI> tmpseqs = new ArrayList<SequenceI>();
2426 boolean multipleView = false;
2428 JSeq[] jseqs = object.getJalviewModelSequence().getJSeq();
2429 int vi = 0; // counter in vamsasSeq array
2430 for (int i = 0; i < jseqs.length; i++)
2432 String seqId = jseqs[i].getId();
2434 if (seqRefIds.get(seqId) != null)
2436 tmpseqs.add(seqRefIds.get(seqId));
2437 multipleView = true;
2441 jseq = new jalview.datamodel.Sequence(vamsasSeq[vi].getName(),
2442 vamsasSeq[vi].getSequence());
2443 jseq.setDescription(vamsasSeq[vi].getDescription());
2444 jseq.setStart(jseqs[i].getStart());
2445 jseq.setEnd(jseqs[i].getEnd());
2446 jseq.setVamsasId(uniqueSetSuffix + seqId);
2447 seqRefIds.put(vamsasSeq[vi].getId(), jseq);
2452 if (jseqs[i].getHidden())
2454 if (hiddenSeqs == null)
2456 hiddenSeqs = new ArrayList<SequenceI>();
2459 hiddenSeqs.add(seqRefIds.get(seqId));
2465 // Create the alignment object from the sequence set
2466 // ///////////////////////////////
2467 SequenceI[] orderedSeqs = tmpseqs
2468 .toArray(new SequenceI[tmpseqs.size()]);
2470 Alignment al = new Alignment(orderedSeqs);
2472 // / Add the alignment properties
2473 for (int i = 0; i < vamsasSet.getSequenceSetPropertiesCount(); i++)
2475 SequenceSetProperties ssp = vamsasSet.getSequenceSetProperties(i);
2476 al.setProperty(ssp.getKey(), ssp.getValue());
2480 // SequenceFeatures are added to the DatasetSequence,
2481 // so we must create or recover the dataset before loading features
2482 // ///////////////////////////////
2483 if (vamsasSet.getDatasetId() == null || vamsasSet.getDatasetId() == "")
2485 // older jalview projects do not have a dataset id.
2486 al.setDataset(null);
2490 // recover dataset - passing on flag indicating if this a 'viewless'
2491 // sequence set (a.k.a. a stored dataset for the project)
2492 recoverDatasetFor(vamsasSet, al, object.getJalviewModelSequence()
2493 .getViewportCount() == 0);
2495 // ///////////////////////////////
2497 Hashtable pdbloaded = new Hashtable(); // TODO nothing writes to this??
2500 // load sequence features, database references and any associated PDB
2501 // structures for the alignment
2502 for (int i = 0; i < vamsasSeq.length; i++)
2504 if (jseqs[i].getFeaturesCount() > 0)
2506 Features[] features = jseqs[i].getFeatures();
2507 for (int f = 0; f < features.length; f++)
2509 jalview.datamodel.SequenceFeature sf = new jalview.datamodel.SequenceFeature(
2510 features[f].getType(), features[f].getDescription(),
2511 features[f].getStatus(), features[f].getBegin(),
2512 features[f].getEnd(), features[f].getFeatureGroup());
2514 sf.setScore(features[f].getScore());
2515 for (int od = 0; od < features[f].getOtherDataCount(); od++)
2517 OtherData keyValue = features[f].getOtherData(od);
2518 if (keyValue.getKey().startsWith("LINK"))
2520 sf.addLink(keyValue.getValue());
2524 sf.setValue(keyValue.getKey(), keyValue.getValue());
2529 al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf);
2532 if (vamsasSeq[i].getDBRefCount() > 0)
2534 addDBRefs(al.getSequenceAt(i).getDatasetSequence(), vamsasSeq[i]);
2536 if (jseqs[i].getPdbidsCount() > 0)
2538 Pdbids[] ids = jseqs[i].getPdbids();
2539 for (int p = 0; p < ids.length; p++)
2541 jalview.datamodel.PDBEntry entry = new jalview.datamodel.PDBEntry();
2542 entry.setId(ids[p].getId());
2543 entry.setType(ids[p].getType());
2544 if (ids[p].getFile() != null)
2546 if (!pdbloaded.containsKey(ids[p].getFile()))
2548 entry.setFile(loadPDBFile(jprovider, ids[p].getId()));
2552 entry.setFile(pdbloaded.get(ids[p].getId()).toString());
2555 StructureSelectionManager.getStructureSelectionManager(
2556 Desktop.instance).registerPDBEntry(entry);
2557 al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
2561 } // end !multipleview
2563 // ///////////////////////////////
2564 // LOAD SEQUENCE MAPPINGS
2566 if (vamsasSet.getAlcodonFrameCount() > 0)
2568 // TODO Potentially this should only be done once for all views of an
2570 AlcodonFrame[] alc = vamsasSet.getAlcodonFrame();
2571 for (int i = 0; i < alc.length; i++)
2573 AlignedCodonFrame cf = new AlignedCodonFrame();
2574 if (alc[i].getAlcodMapCount() > 0)
2576 AlcodMap[] maps = alc[i].getAlcodMap();
2577 for (int m = 0; m < maps.length; m++)
2579 SequenceI dnaseq = seqRefIds.get(maps[m].getDnasq());
2581 jalview.datamodel.Mapping mapping = null;
2582 // attach to dna sequence reference.
2583 if (maps[m].getMapping() != null)
2585 mapping = addMapping(maps[m].getMapping());
2589 cf.addMap(dnaseq, mapping.getTo(), mapping.getMap());
2594 frefedSequence.add(new Object[]
2595 { maps[m].getDnasq(), cf, mapping });
2599 al.addCodonFrame(cf);
2603 // ////////////////////////////////
2605 List<JvAnnotRow> autoAlan = new ArrayList<JvAnnotRow>();
2607 * store any annotations which forward reference a group's ID
2609 Hashtable<String, ArrayList<jalview.datamodel.AlignmentAnnotation>> groupAnnotRefs = new Hashtable<String, ArrayList<jalview.datamodel.AlignmentAnnotation>>();
2611 if (vamsasSet.getAnnotationCount() > 0)
2613 Annotation[] an = vamsasSet.getAnnotation();
2615 for (int i = 0; i < an.length; i++)
2618 * test if annotation is automatically calculated for this view only
2620 boolean autoForView = false;
2621 if (an[i].getLabel().equals("Quality")
2622 || an[i].getLabel().equals("Conservation")
2623 || an[i].getLabel().equals("Consensus"))
2625 // Kludge for pre 2.5 projects which lacked the autocalculated flag
2627 if (!an[i].hasAutoCalculated())
2629 an[i].setAutoCalculated(true);
2633 || (an[i].hasAutoCalculated() && an[i].isAutoCalculated()))
2635 // remove ID - we don't recover annotation from other views for
2636 // view-specific annotation
2640 // set visiblity for other annotation in this view
2641 if (an[i].getId() != null
2642 && annotationIds.containsKey(an[i].getId()))
2644 AlignmentAnnotation jda = annotationIds.get(an[i].getId());
2645 // in principle Visible should always be true for annotation displayed
2646 // in multiple views
2647 if (an[i].hasVisible())
2649 jda.visible = an[i].getVisible();
2652 al.addAnnotation(jda);
2656 // Construct new annotation from model.
2657 AnnotationElement[] ae = an[i].getAnnotationElement();
2658 jalview.datamodel.Annotation[] anot = null;
2659 java.awt.Color firstColour = null;
2661 if (!an[i].getScoreOnly())
2663 anot = new jalview.datamodel.Annotation[al.getWidth()];
2664 for (int aa = 0; aa < ae.length && aa < anot.length; aa++)
2666 anpos = ae[aa].getPosition();
2668 if (anpos >= anot.length)
2673 anot[anpos] = new jalview.datamodel.Annotation(
2675 ae[aa].getDisplayCharacter(), ae[aa].getDescription(),
2676 (ae[aa].getSecondaryStructure() == null || ae[aa]
2677 .getSecondaryStructure().length() == 0) ? ' '
2678 : ae[aa].getSecondaryStructure().charAt(0),
2682 // JBPNote: Consider verifying dataflow for IO of secondary
2683 // structure annotation read from Stockholm files
2684 // this was added to try to ensure that
2685 // if (anot[ae[aa].getPosition()].secondaryStructure>' ')
2687 // anot[ae[aa].getPosition()].displayCharacter = "";
2689 anot[anpos].colour = new java.awt.Color(ae[aa].getColour());
2690 if (firstColour == null)
2692 firstColour = anot[anpos].colour;
2696 jalview.datamodel.AlignmentAnnotation jaa = null;
2698 if (an[i].getGraph())
2700 float llim = 0, hlim = 0;
2701 // if (autoForView || an[i].isAutoCalculated()) {
2704 jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
2705 an[i].getDescription(), anot, llim, hlim,
2706 an[i].getGraphType());
2708 jaa.graphGroup = an[i].getGraphGroup();
2709 jaa._linecolour = firstColour;
2710 if (an[i].getThresholdLine() != null)
2712 jaa.setThreshold(new jalview.datamodel.GraphLine(an[i]
2713 .getThresholdLine().getValue(), an[i]
2714 .getThresholdLine().getLabel(), new java.awt.Color(
2715 an[i].getThresholdLine().getColour())));
2718 if (autoForView || an[i].isAutoCalculated())
2720 // Hardwire the symbol display line to ensure that labels for
2721 // histograms are displayed
2727 jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
2728 an[i].getDescription(), anot);
2729 jaa._linecolour = firstColour;
2731 // register new annotation
2732 if (an[i].getId() != null)
2734 annotationIds.put(an[i].getId(), jaa);
2735 jaa.annotationId = an[i].getId();
2737 // recover sequence association
2738 if (an[i].getSequenceRef() != null)
2740 if (al.findName(an[i].getSequenceRef()) != null)
2742 jaa.createSequenceMapping(al.findName(an[i].getSequenceRef()),
2744 al.findName(an[i].getSequenceRef()).addAlignmentAnnotation(jaa);
2747 // and make a note of any group association
2748 if (an[i].getGroupRef() != null && an[i].getGroupRef().length() > 0)
2750 ArrayList<jalview.datamodel.AlignmentAnnotation> aal = groupAnnotRefs
2751 .get(an[i].getGroupRef());
2754 aal = new ArrayList<jalview.datamodel.AlignmentAnnotation>();
2755 groupAnnotRefs.put(an[i].getGroupRef(), aal);
2760 if (an[i].hasScore())
2762 jaa.setScore(an[i].getScore());
2764 if (an[i].hasVisible())
2766 jaa.visible = an[i].getVisible();
2769 if (an[i].hasCentreColLabels())
2771 jaa.centreColLabels = an[i].getCentreColLabels();
2774 if (an[i].hasScaleColLabels())
2776 jaa.scaleColLabel = an[i].getScaleColLabels();
2778 if (an[i].hasAutoCalculated() && an[i].isAutoCalculated())
2780 // newer files have an 'autoCalculated' flag and store calculation
2781 // state in viewport properties
2782 jaa.autoCalculated = true; // means annotation will be marked for
2783 // update at end of load.
2785 if (an[i].hasGraphHeight())
2787 jaa.graphHeight = an[i].getGraphHeight();
2789 if (an[i].hasBelowAlignment())
2791 jaa.belowAlignment = an[i].isBelowAlignment();
2793 jaa.setCalcId(an[i].getCalcId());
2794 if (an[i].getPropertyCount() > 0)
2796 for (jalview.schemabinding.version2.Property prop : an[i]
2799 jaa.setProperty(prop.getName(), prop.getValue());
2802 if (jaa.autoCalculated)
2804 autoAlan.add(new JvAnnotRow(i, jaa));
2807 // if (!autoForView)
2809 // add autocalculated group annotation and any user created annotation
2811 al.addAnnotation(jaa);
2815 // ///////////////////////
2817 // Create alignment markup and styles for this view
2818 if (jms.getJGroupCount() > 0)
2820 JGroup[] groups = jms.getJGroup();
2821 boolean addAnnotSchemeGroup = false;
2822 for (int i = 0; i < groups.length; i++)
2824 ColourSchemeI cs = null;
2826 if (groups[i].getColour() != null)
2828 if (groups[i].getColour().startsWith("ucs"))
2830 cs = getUserColourScheme(jms, groups[i].getColour());
2832 else if (groups[i].getColour().equals("AnnotationColourGradient")
2833 && groups[i].getAnnotationColours() != null)
2835 addAnnotSchemeGroup = true;
2840 cs = ColourSchemeProperty.getColour(al, groups[i].getColour());
2845 cs.setThreshold(groups[i].getPidThreshold(), true);
2849 Vector seqs = new Vector();
2851 for (int s = 0; s < groups[i].getSeqCount(); s++)
2853 String seqId = groups[i].getSeq(s) + "";
2854 jalview.datamodel.SequenceI ts = seqRefIds.get(seqId);
2858 seqs.addElement(ts);
2862 if (seqs.size() < 1)
2867 jalview.datamodel.SequenceGroup sg = new jalview.datamodel.SequenceGroup(
2868 seqs, groups[i].getName(), cs, groups[i].getDisplayBoxes(),
2869 groups[i].getDisplayText(), groups[i].getColourText(),
2870 groups[i].getStart(), groups[i].getEnd());
2872 sg.setOutlineColour(new java.awt.Color(groups[i].getOutlineColour()));
2874 sg.textColour = new java.awt.Color(groups[i].getTextCol1());
2875 sg.textColour2 = new java.awt.Color(groups[i].getTextCol2());
2876 sg.setShowNonconserved(groups[i].hasShowUnconserved() ? groups[i]
2877 .isShowUnconserved() : false);
2878 sg.thresholdTextColour = groups[i].getTextColThreshold();
2879 if (groups[i].hasShowConsensusHistogram())
2881 sg.setShowConsensusHistogram(groups[i].isShowConsensusHistogram());
2884 if (groups[i].hasShowSequenceLogo())
2886 sg.setshowSequenceLogo(groups[i].isShowSequenceLogo());
2888 if (groups[i].hasNormaliseSequenceLogo())
2890 sg.setNormaliseSequenceLogo(groups[i].isNormaliseSequenceLogo());
2892 if (groups[i].hasIgnoreGapsinConsensus())
2894 sg.setIgnoreGapsConsensus(groups[i].getIgnoreGapsinConsensus());
2896 if (groups[i].getConsThreshold() != 0)
2898 jalview.analysis.Conservation c = new jalview.analysis.Conservation(
2899 "All", ResidueProperties.propHash, 3,
2900 sg.getSequences(null), 0, sg.getWidth() - 1);
2902 c.verdict(false, 25);
2903 sg.cs.setConservation(c);
2906 if (groups[i].getId() != null && groupAnnotRefs.size() > 0)
2908 // re-instate unique group/annotation row reference
2909 ArrayList<jalview.datamodel.AlignmentAnnotation> jaal = groupAnnotRefs
2910 .get(groups[i].getId());
2913 for (jalview.datamodel.AlignmentAnnotation jaa : jaal)
2916 if (jaa.autoCalculated)
2918 // match up and try to set group autocalc alignment row for this
2920 if (jaa.label.startsWith("Consensus for "))
2922 sg.setConsensus(jaa);
2924 // match up and try to set group autocalc alignment row for this
2926 if (jaa.label.startsWith("Conservation for "))
2928 sg.setConservationRow(jaa);
2935 if (addAnnotSchemeGroup)
2937 // reconstruct the annotation colourscheme
2938 sg.cs = constructAnnotationColour(
2939 groups[i].getAnnotationColours(), null, al, jms, false);
2945 // only dataset in this model, so just return.
2948 // ///////////////////////////////
2951 // If we just load in the same jar file again, the sequenceSetId
2952 // will be the same, and we end up with multiple references
2953 // to the same sequenceSet. We must modify this id on load
2954 // so that each load of the file gives a unique id
2955 String uniqueSeqSetId = view.getSequenceSetId() + uniqueSetSuffix;
2956 String viewId = (view.getId() == null ? null : view.getId()
2958 AlignFrame af = null;
2959 AlignViewport av = null;
2960 // now check to see if we really need to create a new viewport.
2961 if (multipleView && viewportsAdded.size() == 0)
2963 // We recovered an alignment for which a viewport already exists.
2964 // TODO: fix up any settings necessary for overlaying stored state onto
2965 // state recovered from another document. (may not be necessary).
2966 // we may need a binding from a viewport in memory to one recovered from
2968 // and then recover its containing af to allow the settings to be applied.
2969 // TODO: fix for vamsas demo
2971 .println("About to recover a viewport for existing alignment: Sequence set ID is "
2973 Object seqsetobj = retrieveExistingObj(uniqueSeqSetId);
2974 if (seqsetobj != null)
2976 if (seqsetobj instanceof String)
2978 uniqueSeqSetId = (String) seqsetobj;
2980 .println("Recovered extant sequence set ID mapping for ID : New Sequence set ID is "
2986 .println("Warning : Collision between sequence set ID string and existing jalview object mapping.");
2992 * indicate that annotation colours are applied across all groups (pre
2993 * Jalview 2.8.1 behaviour)
2995 boolean doGroupAnnColour = isVersionStringLaterThan("2.8.1",
2996 object.getVersion());
2998 AlignmentPanel ap = null;
2999 boolean isnewview = true;
3002 // Check to see if this alignment already has a view id == viewId
3003 jalview.gui.AlignmentPanel views[] = Desktop
3004 .getAlignmentPanels(uniqueSeqSetId);
3005 if (views != null && views.length > 0)
3007 for (int v = 0; v < views.length; v++)
3009 if (views[v].av.getViewId().equalsIgnoreCase(viewId))
3011 // recover the existing alignpanel, alignframe, viewport
3012 af = views[v].alignFrame;
3015 // TODO: could even skip resetting view settings if we don't want to
3016 // change the local settings from other jalview processes
3025 af = loadViewport(file, jseqs, hiddenSeqs, al, jms, view,
3026 uniqueSeqSetId, viewId, autoAlan);
3031 // /////////////////////////////////////
3032 if (loadTreesAndStructures && jms.getTreeCount() > 0)
3036 for (int t = 0; t < jms.getTreeCount(); t++)
3039 Tree tree = jms.getTree(t);
3041 TreePanel tp = (TreePanel) retrieveExistingObj(tree.getId());
3044 tp = af.ShowNewickTree(
3045 new jalview.io.NewickFile(tree.getNewick()),
3046 tree.getTitle(), tree.getWidth(), tree.getHeight(),
3047 tree.getXpos(), tree.getYpos());
3048 if (tree.getId() != null)
3050 // perhaps bind the tree id to something ?
3055 // update local tree attributes ?
3056 // TODO: should check if tp has been manipulated by user - if so its
3057 // settings shouldn't be modified
3058 tp.setTitle(tree.getTitle());
3059 tp.setBounds(new Rectangle(tree.getXpos(), tree.getYpos(), tree
3060 .getWidth(), tree.getHeight()));
3061 tp.av = av; // af.viewport; // TODO: verify 'associate with all
3064 tp.treeCanvas.av = av; // af.viewport;
3065 tp.treeCanvas.ap = ap; // af.alignPanel;
3070 warn("There was a problem recovering stored Newick tree: \n"
3071 + tree.getNewick());
3075 tp.fitToWindow.setState(tree.getFitToWindow());
3076 tp.fitToWindow_actionPerformed(null);
3078 if (tree.getFontName() != null)
3080 tp.setTreeFont(new java.awt.Font(tree.getFontName(), tree
3081 .getFontStyle(), tree.getFontSize()));
3085 tp.setTreeFont(new java.awt.Font(view.getFontName(), view
3086 .getFontStyle(), tree.getFontSize()));
3089 tp.showPlaceholders(tree.getMarkUnlinked());
3090 tp.showBootstrap(tree.getShowBootstrap());
3091 tp.showDistances(tree.getShowDistances());
3093 tp.treeCanvas.threshold = tree.getThreshold();
3095 if (tree.getCurrentTree())
3097 af.viewport.setCurrentTree(tp.getTree());
3101 } catch (Exception ex)
3103 ex.printStackTrace();
3107 // //LOAD STRUCTURES
3108 if (loadTreesAndStructures)
3110 loadStructures(jprovider, jseqs, af, ap);
3112 // and finally return.
3117 * Load and link any saved structure viewers.
3124 protected void loadStructures(jarInputStreamProvider jprovider,
3125 JSeq[] jseqs, AlignFrame af, AlignmentPanel ap)
3128 * Run through all PDB ids on the alignment, and collect mappings between
3129 * distinct view ids and all sequences referring to that view.
3131 Map<String, StructureViewerModel> structureViewers = new LinkedHashMap<String, StructureViewerModel>();
3133 for (int i = 0; i < jseqs.length; i++)
3135 if (jseqs[i].getPdbidsCount() > 0)
3137 Pdbids[] ids = jseqs[i].getPdbids();
3138 for (int p = 0; p < ids.length; p++)
3140 final int structureStateCount = ids[p].getStructureStateCount();
3141 for (int s = 0; s < structureStateCount; s++)
3143 // check to see if we haven't already created this structure view
3144 final StructureState structureState = ids[p]
3145 .getStructureState(s);
3146 String sviewid = (structureState.getViewId() == null) ? null
3147 : structureState.getViewId() + uniqueSetSuffix;
3148 jalview.datamodel.PDBEntry jpdb = new jalview.datamodel.PDBEntry();
3149 // Originally : ids[p].getFile()
3150 // : TODO: verify external PDB file recovery still works in normal
3151 // jalview project load
3152 jpdb.setFile(loadPDBFile(jprovider, ids[p].getId()));
3153 jpdb.setId(ids[p].getId());
3155 int x = structureState.getXpos();
3156 int y = structureState.getYpos();
3157 int width = structureState.getWidth();
3158 int height = structureState.getHeight();
3160 // Probably don't need to do this anymore...
3161 // Desktop.desktop.getComponentAt(x, y);
3162 // TODO: NOW: check that this recovers the PDB file correctly.
3163 String pdbFile = loadPDBFile(jprovider, ids[p].getId());
3164 jalview.datamodel.SequenceI seq = seqRefIds.get(jseqs[i]
3166 if (sviewid == null)
3168 sviewid = "_jalview_pre2_4_" + x + "," + y + "," + width
3171 if (!structureViewers.containsKey(sviewid))
3173 structureViewers.put(sviewid, new StructureViewerModel(x, y,
3174 width, height, false, false, true));
3175 // Legacy pre-2.7 conversion JAL-823 :
3176 // do not assume any view has to be linked for colour by
3180 // assemble String[] { pdb files }, String[] { id for each
3181 // file }, orig_fileloc, SequenceI[][] {{ seqs_file 1 }, {
3182 // seqs_file 2}, boolean[] {
3183 // linkAlignPanel,superposeWithAlignpanel}} from hash
3184 StructureViewerModel jmoldat = structureViewers.get(sviewid);
3185 jmoldat.setAlignWithPanel(jmoldat.isAlignWithPanel()
3186 | (structureState.hasAlignwithAlignPanel() ? structureState
3187 .getAlignwithAlignPanel() : false));
3190 * Default colour by linked panel to false if not specified (e.g.
3191 * for pre-2.7 projects)
3193 boolean colourWithAlignPanel = jmoldat.isColourWithAlignPanel();
3194 colourWithAlignPanel |= (structureState
3195 .hasColourwithAlignPanel() ? structureState
3196 .getColourwithAlignPanel() : false);
3197 jmoldat.setColourWithAlignPanel(colourWithAlignPanel);
3200 * Default colour by viewer to true if not specified (e.g. for
3203 boolean colourByViewer = jmoldat.isColourByViewer();
3204 colourByViewer &= structureState.hasColourByJmol() ? structureState
3205 .getColourByJmol() : true;
3206 jmoldat.setColourByViewer(colourByViewer);
3208 if (jmoldat.getStateData().length() < structureState
3209 .getContent().length())
3212 jmoldat.setStateData(structureState.getContent());
3215 if (ids[p].getFile() != null)
3217 File mapkey = new File(ids[p].getFile());
3218 StructureData seqstrmaps = jmoldat.getFileData().get(mapkey);
3219 if (seqstrmaps == null)
3221 jmoldat.getFileData().put(
3223 seqstrmaps = jmoldat.new StructureData(pdbFile,
3226 if (!seqstrmaps.getSeqList().contains(seq))
3228 seqstrmaps.getSeqList().add(seq);
3234 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");
3241 // Instantiate the associated structure views
3242 for (Entry<String, StructureViewerModel> entry : structureViewers
3245 createOrLinkStructureViewer(entry, af, ap);
3255 protected void createOrLinkStructureViewer(
3256 Entry<String, StructureViewerModel> viewerData, AlignFrame af,
3259 final StructureViewerModel svattrib = viewerData.getValue();
3262 * Search for any viewer windows already open from other alignment views
3263 * that exactly match the stored structure state
3265 StructureViewerBase comp = findMatchingViewer(viewerData);
3269 linkStructureViewer(ap, comp, svattrib);
3274 * Pending an XML element for ViewerType, just check if stateData contains
3275 * "chimera" (part of the chimera session filename).
3277 if (svattrib.getStateData().indexOf("chimera") > -1)
3279 createChimeraViewer(viewerData, af);
3283 createJmolViewer(viewerData, af);
3288 * Create a new Chimera viewer.
3293 protected void createChimeraViewer(
3294 Entry<String, StructureViewerModel> viewerData, AlignFrame af)
3296 final StructureViewerModel data = viewerData.getValue();
3297 String chimeraSession = data.getStateData();
3299 if (new File(chimeraSession).exists())
3301 Set<Entry<File, StructureData>> fileData = data.getFileData()
3303 List<PDBEntry> pdbs = new ArrayList<PDBEntry>();
3304 List<SequenceI[]> allseqs = new ArrayList<SequenceI[]>();
3305 for (Entry<File, StructureData> pdb : fileData)
3307 String filePath = pdb.getValue().getFilePath();
3308 String pdbId = pdb.getValue().getPdbId();
3309 pdbs.add(new PDBEntry(filePath, pdbId));
3310 final List<SequenceI> seqList = pdb.getValue().getSeqList();
3311 SequenceI[] seqs = seqList.toArray(new SequenceI[seqList.size()]);
3315 boolean colourByChimera = data.isColourByViewer();
3316 boolean colourBySequence = data.isColourWithAlignPanel();
3318 // TODO can/should this be done via StructureViewer (like Jmol)?
3319 final PDBEntry[] pdbArray = pdbs.toArray(new PDBEntry[pdbs.size()]);
3320 final SequenceI[][] seqsArray = allseqs.toArray(new SequenceI[allseqs
3322 new ChimeraViewFrame(chimeraSession, af.alignPanel, pdbArray,
3323 seqsArray, colourByChimera, colourBySequence);
3327 Cache.log.error("Chimera session file " + chimeraSession
3333 * Create a new Jmol window. First parse the Jmol state to translate filenames
3334 * loaded into the view, and record the order in which files are shown in the
3335 * Jmol view, so we can add the sequence mappings in same order.
3340 protected void createJmolViewer(
3341 final Entry<String, StructureViewerModel> viewerData,
3344 final StructureViewerModel svattrib = viewerData.getValue();
3345 String state = svattrib.getStateData();
3346 List<String> pdbfilenames = new ArrayList<String>();
3347 List<SequenceI[]> seqmaps = new ArrayList<SequenceI[]>();
3348 List<String> pdbids = new ArrayList<String>();
3349 StringBuilder newFileLoc = new StringBuilder(64);
3350 int cp = 0, ncp, ecp;
3351 Map<File, StructureData> oldFiles = svattrib.getFileData();
3352 while ((ncp = state.indexOf("load ", cp)) > -1)
3356 // look for next filename in load statement
3357 newFileLoc.append(state.substring(cp,
3358 ncp = (state.indexOf("\"", ncp + 1) + 1)));
3359 String oldfilenam = state.substring(ncp,
3360 ecp = state.indexOf("\"", ncp));
3361 // recover the new mapping data for this old filename
3362 // have to normalize filename - since Jmol and jalview do
3364 // translation differently.
3365 StructureData filedat = oldFiles.get(new File(oldfilenam));
3366 newFileLoc.append(Platform.escapeString(filedat.getFilePath()));
3367 pdbfilenames.add(filedat.getFilePath());
3368 pdbids.add(filedat.getPdbId());
3369 seqmaps.add(filedat.getSeqList().toArray(new SequenceI[0]));
3370 newFileLoc.append("\"");
3371 cp = ecp + 1; // advance beyond last \" and set cursor so we can
3372 // look for next file statement.
3373 } while ((ncp = state.indexOf("/*file*/", cp)) > -1);
3377 // just append rest of state
3378 newFileLoc.append(state.substring(cp));
3382 System.err.print("Ignoring incomplete Jmol state for PDB ids: ");
3383 newFileLoc = new StringBuilder(state);
3384 newFileLoc.append("; load append ");
3385 for (File id : oldFiles.keySet())
3387 // add this and any other pdb files that should be present in
3389 StructureData filedat = oldFiles.get(id);
3390 newFileLoc.append(filedat.getFilePath());
3391 pdbfilenames.add(filedat.getFilePath());
3392 pdbids.add(filedat.getPdbId());
3393 seqmaps.add(filedat.getSeqList().toArray(new SequenceI[0]));
3394 newFileLoc.append(" \"");
3395 newFileLoc.append(filedat.getFilePath());
3396 newFileLoc.append("\"");
3399 newFileLoc.append(";");
3402 if (newFileLoc.length() > 0)
3404 int histbug = newFileLoc.indexOf("history = ");
3406 int diff = histbug == -1 ? -1 : newFileLoc.indexOf(";", histbug);
3407 String val = (diff == -1) ? null : newFileLoc
3408 .substring(histbug, diff);
3409 if (val != null && val.length() >= 4)
3411 if (val.contains("e"))
3413 if (val.trim().equals("true"))
3421 newFileLoc.replace(histbug, diff, val);
3425 final String[] pdbf = pdbfilenames.toArray(new String[pdbfilenames
3427 final String[] id = pdbids.toArray(new String[pdbids.size()]);
3428 final SequenceI[][] sq = seqmaps
3429 .toArray(new SequenceI[seqmaps.size()][]);
3430 final String fileloc = newFileLoc.toString();
3431 final String sviewid = viewerData.getKey();
3432 final AlignFrame alf = af;
3433 final Rectangle rect = new Rectangle(svattrib.getX(),
3434 svattrib.getY(), svattrib.getWidth(), svattrib.getHeight());
3437 javax.swing.SwingUtilities.invokeAndWait(new Runnable()
3442 JalviewStructureDisplayI sview = null;
3445 // JAL-1333 note - we probably can't migrate Jmol views to UCSF
3447 sview = new StructureViewer(alf.alignPanel
3448 .getStructureSelectionManager()).createView(
3449 StructureViewer.ViewerType.JMOL, pdbf, id, sq,
3450 alf.alignPanel, svattrib, fileloc, rect, sviewid);
3451 addNewStructureViewer(sview);
3452 } catch (OutOfMemoryError ex)
3454 new OOMWarning("restoring structure view for PDB id " + id,
3455 (OutOfMemoryError) ex.getCause());
3456 if (sview != null && sview.isVisible())
3458 sview.closeViewer();
3459 sview.setVisible(false);
3465 } catch (InvocationTargetException ex)
3467 warn("Unexpected error when opening Jmol view.", ex);
3469 } catch (InterruptedException e)
3471 // e.printStackTrace();
3477 * Returns any open frame that matches given structure viewer data. The match
3478 * is based on the unique viewId, or (for older project versions) the frame's
3484 protected StructureViewerBase findMatchingViewer(
3485 Entry<String, StructureViewerModel> viewerData)
3487 final String sviewid = viewerData.getKey();
3488 final StructureViewerModel svattrib = viewerData.getValue();
3489 StructureViewerBase comp = null;
3490 JInternalFrame[] frames = getAllFrames();
3491 for (JInternalFrame frame : frames)
3493 if (frame instanceof StructureViewerBase)
3496 * Post jalview 2.4 schema includes structure view id
3499 && ((StructureViewerBase) frame).getViewId()
3502 comp = (AppJmol) frame;
3506 * Otherwise test for matching position and size of viewer frame
3508 else if (frame.getX() == svattrib.getX()
3509 && frame.getY() == svattrib.getY()
3510 && frame.getHeight() == svattrib.getHeight()
3511 && frame.getWidth() == svattrib.getWidth())
3513 comp = (AppJmol) frame;
3522 * Link an AlignmentPanel to an existing structure viewer.
3527 * @param useinViewerSuperpos
3528 * @param usetoColourbyseq
3529 * @param viewerColouring
3531 protected void linkStructureViewer(AlignmentPanel ap,
3532 StructureViewerBase viewer, StructureViewerModel svattrib)
3534 // NOTE: if the jalview project is part of a shared session then
3535 // view synchronization should/could be done here.
3537 final boolean useinViewerSuperpos = svattrib.isAlignWithPanel();
3538 final boolean usetoColourbyseq = svattrib.isColourWithAlignPanel();
3539 final boolean viewerColouring = svattrib.isColourByViewer();
3540 Map<File, StructureData> oldFiles = svattrib.getFileData();
3543 * Add mapping for sequences in this view to an already open viewer
3545 final AAStructureBindingModel binding = viewer.getBinding();
3546 for (File id : oldFiles.keySet())
3548 // add this and any other pdb files that should be present in the
3550 StructureData filedat = oldFiles.get(id);
3551 String pdbFile = filedat.getFilePath();
3552 SequenceI[] seq = filedat.getSeqList().toArray(new SequenceI[0]);
3553 binding.getSsm().setMapping(seq, null, pdbFile,
3554 jalview.io.AppletFormatAdapter.FILE);
3555 binding.addSequenceForStructFile(pdbFile, seq);
3557 // and add the AlignmentPanel's reference to the view panel
3558 viewer.addAlignmentPanel(ap);
3559 if (useinViewerSuperpos)
3561 viewer.useAlignmentPanelForSuperposition(ap);
3565 viewer.excludeAlignmentPanelForSuperposition(ap);
3567 if (usetoColourbyseq)
3569 viewer.useAlignmentPanelForColourbyseq(ap, !viewerColouring);
3573 viewer.excludeAlignmentPanelForColourbyseq(ap);
3578 * Get all frames within the Desktop.
3582 protected JInternalFrame[] getAllFrames()
3584 JInternalFrame[] frames = null;
3585 // TODO is this necessary - is it safe - risk of hanging?
3590 frames = Desktop.desktop.getAllFrames();
3591 } catch (ArrayIndexOutOfBoundsException e)
3593 // occasional No such child exceptions are thrown here...
3597 } catch (InterruptedException f)
3601 } while (frames == null);
3608 * - minimum version we are comparing against
3610 * - version of data being processsed.
3611 * @return true if version is development/null or evaluates to the same or
3612 * later X.Y.Z (where X,Y,Z are like [0-9]+b?[0-9]*)
3614 private boolean isVersionStringLaterThan(String supported, String version)
3616 if (version == null || version.equalsIgnoreCase("DEVELOPMENT BUILD")
3617 || version.equalsIgnoreCase("Test")
3618 || version.equalsIgnoreCase("AUTOMATED BUILD"))
3620 System.err.println("Assuming project file with "
3621 + (version == null ? "null" : version)
3622 + " is compatible with Jalview version " + supported);
3627 StringTokenizer currentV = new StringTokenizer(supported, "."), fileV = new StringTokenizer(
3629 while (currentV.hasMoreTokens() && fileV.hasMoreTokens())
3631 // convert b to decimal to catch bugfix releases within a series
3632 String curT = currentV.nextToken().toLowerCase().replace('b', '.');
3633 String fileT = fileV.nextToken().toLowerCase().replace('b', '.');
3636 if (Float.valueOf(curT) > Float.valueOf(fileT))
3638 // current version is newer than the version that wrote the file
3641 } catch (NumberFormatException nfe)
3644 .println("** WARNING: Version comparison failed for tokens ("
3648 + ")\n** Current: '"
3649 + supported + "' and Version: '" + version + "'");
3652 if (currentV.hasMoreElements())
3654 // fileV has no minor version but identical series to current
3661 Vector<JalviewStructureDisplayI> newStructureViewers = null;
3663 protected void addNewStructureViewer(JalviewStructureDisplayI sview)
3665 if (newStructureViewers != null)
3667 sview.getBinding().setFinishedLoadingFromArchive(false);
3668 newStructureViewers.add(sview);
3672 protected void setLoadingFinishedForNewStructureViewers()
3674 if (newStructureViewers != null)
3676 for (JalviewStructureDisplayI sview : newStructureViewers)
3678 sview.getBinding().setFinishedLoadingFromArchive(true);
3680 newStructureViewers.clear();
3681 newStructureViewers = null;
3685 AlignFrame loadViewport(String file, JSeq[] JSEQ,
3686 List<SequenceI> hiddenSeqs, Alignment al,
3687 JalviewModelSequence jms, Viewport view, String uniqueSeqSetId,
3688 String viewId, List<JvAnnotRow> autoAlan)
3690 AlignFrame af = null;
3691 af = new AlignFrame(al, view.getWidth(), view.getHeight(),
3692 uniqueSeqSetId, viewId);
3694 af.setFileName(file, "Jalview");
3696 for (int i = 0; i < JSEQ.length; i++)
3698 af.viewport.setSequenceColour(af.viewport.getAlignment()
3699 .getSequenceAt(i), new java.awt.Color(JSEQ[i].getColour()));
3702 af.viewport.setGatherViewsHere(view.getGatheredViews());
3704 if (view.getSequenceSetId() != null)
3706 AlignmentViewport av = viewportsAdded.get(uniqueSeqSetId);
3708 af.viewport.setSequenceSetId(uniqueSeqSetId);
3711 // propagate shared settings to this new view
3712 af.viewport.setHistoryList(av.getHistoryList());
3713 af.viewport.setRedoList(av.getRedoList());
3717 viewportsAdded.put(uniqueSeqSetId, af.viewport);
3719 // TODO: check if this method can be called repeatedly without
3720 // side-effects if alignpanel already registered.
3721 PaintRefresher.Register(af.alignPanel, uniqueSeqSetId);
3723 // apply Hidden regions to view.
3724 if (hiddenSeqs != null)
3726 for (int s = 0; s < JSEQ.length; s++)
3728 jalview.datamodel.SequenceGroup hidden = new jalview.datamodel.SequenceGroup();
3730 for (int r = 0; r < JSEQ[s].getHiddenSequencesCount(); r++)
3733 al.getSequenceAt(JSEQ[s].getHiddenSequences(r)), false);
3735 af.viewport.hideRepSequences(al.getSequenceAt(s), hidden);
3738 // jalview.datamodel.SequenceI[] hseqs = new
3739 // jalview.datamodel.SequenceI[hiddenSeqs
3742 // for (int s = 0; s < hiddenSeqs.size(); s++)
3744 // hseqs[s] = (jalview.datamodel.SequenceI) hiddenSeqs.elementAt(s);
3747 SequenceI[] hseqs = hiddenSeqs.toArray(new SequenceI[hiddenSeqs
3749 af.viewport.hideSequence(hseqs);
3752 // recover view properties and display parameters
3753 if (view.getViewName() != null)
3755 af.viewport.viewName = view.getViewName();
3756 af.setInitialTabVisible();
3758 af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),
3761 af.viewport.setShowAnnotation(view.getShowAnnotation());
3762 af.viewport.setAbovePIDThreshold(view.getPidSelected());
3764 af.viewport.setColourText(view.getShowColourText());
3766 af.viewport.setConservationSelected(view.getConservationSelected());
3767 af.viewport.setShowJVSuffix(view.getShowFullId());
3768 af.viewport.setRightAlignIds(view.getRightAlignIds());
3769 af.viewport.setFont(
3770 new java.awt.Font(view.getFontName(), view.getFontStyle(), view
3771 .getFontSize()), true);
3772 // TODO: allow custom charWidth/Heights to be restored by updating them
3773 // after setting font - which means set above to false
3774 af.viewport.setRenderGaps(view.getRenderGaps());
3775 af.viewport.setWrapAlignment(view.getWrapAlignment());
3776 af.viewport.setShowAnnotation(view.getShowAnnotation());
3778 af.viewport.setShowBoxes(view.getShowBoxes());
3780 af.viewport.setShowText(view.getShowText());
3782 af.viewport.setTextColour(new java.awt.Color(view.getTextCol1()));
3783 af.viewport.setTextColour2(new java.awt.Color(view.getTextCol2()));
3784 af.viewport.setThresholdTextColour(view.getTextColThreshold());
3785 af.viewport.setShowUnconserved(view.hasShowUnconserved() ? view
3786 .isShowUnconserved() : false);
3787 af.viewport.setStartRes(view.getStartRes());
3788 af.viewport.setStartSeq(view.getStartSeq());
3789 af.alignPanel.updateLayout();
3790 ColourSchemeI cs = null;
3791 // apply colourschemes
3792 if (view.getBgColour() != null)
3794 if (view.getBgColour().startsWith("ucs"))
3796 cs = getUserColourScheme(jms, view.getBgColour());
3798 else if (view.getBgColour().startsWith("Annotation"))
3800 AnnotationColours viewAnnColour = view.getAnnotationColours();
3801 cs = constructAnnotationColour(viewAnnColour, af, al, jms, true);
3808 cs = ColourSchemeProperty.getColour(al, view.getBgColour());
3813 cs.setThreshold(view.getPidThreshold(), true);
3814 cs.setConsensus(af.viewport.getSequenceConsensusHash());
3818 af.viewport.setGlobalColourScheme(cs);
3819 af.viewport.setColourAppliesToAllGroups(false);
3821 if (view.getConservationSelected() && cs != null)
3823 cs.setConservationInc(view.getConsThreshold());
3826 af.changeColour(cs);
3828 af.viewport.setColourAppliesToAllGroups(true);
3830 af.viewport.setShowSequenceFeatures(view.getShowSequenceFeatures());
3832 if (view.hasCentreColumnLabels())
3834 af.viewport.setCentreColumnLabels(view.getCentreColumnLabels());
3836 if (view.hasIgnoreGapsinConsensus())
3838 af.viewport.setIgnoreGapsConsensus(view.getIgnoreGapsinConsensus(),
3841 if (view.hasFollowHighlight())
3843 af.viewport.followHighlight = view.getFollowHighlight();
3845 if (view.hasFollowSelection())
3847 af.viewport.followSelection = view.getFollowSelection();
3849 if (view.hasShowConsensusHistogram())
3851 af.viewport.setShowConsensusHistogram(view
3852 .getShowConsensusHistogram());
3856 af.viewport.setShowConsensusHistogram(true);
3858 if (view.hasShowSequenceLogo())
3860 af.viewport.setShowSequenceLogo(view.getShowSequenceLogo());
3864 af.viewport.setShowSequenceLogo(false);
3866 if (view.hasNormaliseSequenceLogo())
3868 af.viewport.setNormaliseSequenceLogo(view.getNormaliseSequenceLogo());
3870 if (view.hasShowDbRefTooltip())
3872 af.viewport.setShowDBRefs(view.getShowDbRefTooltip());
3874 if (view.hasShowNPfeatureTooltip())
3876 af.viewport.setShowNPFeats(view.hasShowNPfeatureTooltip());
3878 if (view.hasShowGroupConsensus())
3880 af.viewport.setShowGroupConsensus(view.getShowGroupConsensus());
3884 af.viewport.setShowGroupConsensus(false);
3886 if (view.hasShowGroupConservation())
3888 af.viewport.setShowGroupConservation(view.getShowGroupConservation());
3892 af.viewport.setShowGroupConservation(false);
3895 // recover featre settings
3896 if (jms.getFeatureSettings() != null)
3898 FeaturesDisplayed fdi;
3899 af.viewport.setFeaturesDisplayed(fdi = new FeaturesDisplayed());
3900 String[] renderOrder = new String[jms.getFeatureSettings()
3901 .getSettingCount()];
3902 Hashtable featureGroups = new Hashtable();
3903 Hashtable featureColours = new Hashtable();
3904 Hashtable featureOrder = new Hashtable();
3906 for (int fs = 0; fs < jms.getFeatureSettings().getSettingCount(); fs++)
3908 Setting setting = jms.getFeatureSettings().getSetting(fs);
3909 if (setting.hasMincolour())
3911 GraduatedColor gc = setting.hasMin() ? new GraduatedColor(
3912 new java.awt.Color(setting.getMincolour()),
3913 new java.awt.Color(setting.getColour()),
3914 setting.getMin(), setting.getMax()) : new GraduatedColor(
3915 new java.awt.Color(setting.getMincolour()),
3916 new java.awt.Color(setting.getColour()), 0, 1);
3917 if (setting.hasThreshold())
3919 gc.setThresh(setting.getThreshold());
3920 gc.setThreshType(setting.getThreshstate());
3922 gc.setAutoScaled(true); // default
3923 if (setting.hasAutoScale())
3925 gc.setAutoScaled(setting.getAutoScale());
3927 if (setting.hasColourByLabel())
3929 gc.setColourByLabel(setting.getColourByLabel());
3931 // and put in the feature colour table.
3932 featureColours.put(setting.getType(), gc);
3936 featureColours.put(setting.getType(),
3937 new java.awt.Color(setting.getColour()));
3939 renderOrder[fs] = setting.getType();
3940 if (setting.hasOrder())
3942 featureOrder.put(setting.getType(), setting.getOrder());
3946 featureOrder.put(setting.getType(), new Float(fs
3947 / jms.getFeatureSettings().getSettingCount()));
3949 if (setting.getDisplay())
3951 fdi.setVisible(setting.getType());
3954 Hashtable fgtable = new Hashtable();
3955 for (int gs = 0; gs < jms.getFeatureSettings().getGroupCount(); gs++)
3957 Group grp = jms.getFeatureSettings().getGroup(gs);
3958 fgtable.put(grp.getName(), new Boolean(grp.getDisplay()));
3960 // FeatureRendererSettings frs = new FeatureRendererSettings(renderOrder,
3961 // fgtable, featureColours, jms.getFeatureSettings().hasTransparency() ?
3962 // jms.getFeatureSettings().getTransparency() : 0.0, featureOrder);
3963 FeatureRendererSettings frs = new FeatureRendererSettings(
3964 renderOrder, fgtable, featureColours, 1.0f, featureOrder);
3965 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
3966 .transferSettings(frs);
3970 if (view.getHiddenColumnsCount() > 0)
3972 for (int c = 0; c < view.getHiddenColumnsCount(); c++)
3974 af.viewport.hideColumns(view.getHiddenColumns(c).getStart(), view
3975 .getHiddenColumns(c).getEnd() // +1
3979 if (view.getCalcIdParam() != null)
3981 for (CalcIdParam calcIdParam : view.getCalcIdParam())
3983 if (calcIdParam != null)
3985 if (recoverCalcIdParam(calcIdParam, af.viewport))
3990 warn("Couldn't recover parameters for "
3991 + calcIdParam.getCalcId());
3996 af.setMenusFromViewport(af.viewport);
3998 // TODO: we don't need to do this if the viewport is aready visible.
4000 * Add the AlignFrame to the desktop (it may be 'gathered' later), unless it
4001 * has a 'cdna/protein complement' view, in which case save it in order to
4002 * populate a SplitFrame once all views have been read in.
4004 String complementaryViewId = view.getComplementId();
4005 if (complementaryViewId == null)
4007 Desktop.addInternalFrame(af, view.getTitle(), view.getWidth(),
4009 // recompute any autoannotation
4010 af.alignPanel.updateAnnotation(false, true);
4011 reorderAutoannotation(af, al, autoAlan);
4012 af.alignPanel.alignmentChanged();
4016 splitFrameCandidates.put(view, af);
4021 private ColourSchemeI constructAnnotationColour(
4022 AnnotationColours viewAnnColour, AlignFrame af, Alignment al,
4023 JalviewModelSequence jms, boolean checkGroupAnnColour)
4025 boolean propagateAnnColour = false;
4026 ColourSchemeI cs = null;
4027 AlignmentI annAlignment = af != null ? af.viewport.getAlignment() : al;
4028 if (checkGroupAnnColour && al.getGroups() != null
4029 && al.getGroups().size() > 0)
4031 // pre 2.8.1 behaviour
4032 // check to see if we should transfer annotation colours
4033 propagateAnnColour = true;
4034 for (jalview.datamodel.SequenceGroup sg : al.getGroups())
4036 if (sg.cs instanceof AnnotationColourGradient)
4038 propagateAnnColour = false;
4042 // int find annotation
4043 if (annAlignment.getAlignmentAnnotation() != null)
4045 for (int i = 0; i < annAlignment.getAlignmentAnnotation().length; i++)
4047 if (annAlignment.getAlignmentAnnotation()[i].label
4048 .equals(viewAnnColour.getAnnotation()))
4050 if (annAlignment.getAlignmentAnnotation()[i].getThreshold() == null)
4052 annAlignment.getAlignmentAnnotation()[i]
4053 .setThreshold(new jalview.datamodel.GraphLine(
4054 viewAnnColour.getThreshold(), "Threshold",
4055 java.awt.Color.black)
4060 if (viewAnnColour.getColourScheme().equals("None"))
4062 cs = new AnnotationColourGradient(
4063 annAlignment.getAlignmentAnnotation()[i],
4064 new java.awt.Color(viewAnnColour.getMinColour()),
4065 new java.awt.Color(viewAnnColour.getMaxColour()),
4066 viewAnnColour.getAboveThreshold());
4068 else if (viewAnnColour.getColourScheme().startsWith("ucs"))
4070 cs = new AnnotationColourGradient(
4071 annAlignment.getAlignmentAnnotation()[i],
4072 getUserColourScheme(jms,
4073 viewAnnColour.getColourScheme()),
4074 viewAnnColour.getAboveThreshold());
4078 cs = new AnnotationColourGradient(
4079 annAlignment.getAlignmentAnnotation()[i],
4080 ColourSchemeProperty.getColour(al,
4081 viewAnnColour.getColourScheme()),
4082 viewAnnColour.getAboveThreshold());
4084 if (viewAnnColour.hasPerSequence())
4086 ((AnnotationColourGradient) cs).setSeqAssociated(viewAnnColour
4089 if (viewAnnColour.hasPredefinedColours())
4091 ((AnnotationColourGradient) cs)
4092 .setPredefinedColours(viewAnnColour
4093 .isPredefinedColours());
4095 if (propagateAnnColour && al.getGroups() != null)
4097 // Also use these settings for all the groups
4098 for (int g = 0; g < al.getGroups().size(); g++)
4100 jalview.datamodel.SequenceGroup sg = al.getGroups().get(g);
4108 * if (viewAnnColour.getColourScheme().equals("None" )) { sg.cs =
4109 * new AnnotationColourGradient(
4110 * annAlignment.getAlignmentAnnotation()[i], new
4111 * java.awt.Color(viewAnnColour. getMinColour()), new
4112 * java.awt.Color(viewAnnColour. getMaxColour()),
4113 * viewAnnColour.getAboveThreshold()); } else
4116 sg.cs = new AnnotationColourGradient(
4117 annAlignment.getAlignmentAnnotation()[i], sg.cs,
4118 viewAnnColour.getAboveThreshold());
4119 if (cs instanceof AnnotationColourGradient)
4121 if (viewAnnColour.hasPerSequence())
4123 ((AnnotationColourGradient) cs)
4124 .setSeqAssociated(viewAnnColour.isPerSequence());
4126 if (viewAnnColour.hasPredefinedColours())
4128 ((AnnotationColourGradient) cs)
4129 .setPredefinedColours(viewAnnColour
4130 .isPredefinedColours());
4146 private void reorderAutoannotation(AlignFrame af, Alignment al,
4147 List<JvAnnotRow> autoAlan)
4149 // copy over visualization settings for autocalculated annotation in the
4151 if (al.getAlignmentAnnotation() != null)
4154 * Kludge for magic autoannotation names (see JAL-811)
4156 String[] magicNames = new String[]
4157 { "Consensus", "Quality", "Conservation" };
4158 JvAnnotRow nullAnnot = new JvAnnotRow(-1, null);
4159 Hashtable<String, JvAnnotRow> visan = new Hashtable<String, JvAnnotRow>();
4160 for (String nm : magicNames)
4162 visan.put(nm, nullAnnot);
4164 for (JvAnnotRow auan : autoAlan)
4166 visan.put(auan.template.label
4167 + (auan.template.getCalcId() == null ? "" : "\t"
4168 + auan.template.getCalcId()), auan);
4170 int hSize = al.getAlignmentAnnotation().length;
4171 List<JvAnnotRow> reorder = new ArrayList<JvAnnotRow>();
4172 // work through any autoCalculated annotation already on the view
4173 // removing it if it should be placed in a different location on the
4174 // annotation panel.
4175 List<String> remains = new ArrayList<String>(visan.keySet());
4176 for (int h = 0; h < hSize; h++)
4178 jalview.datamodel.AlignmentAnnotation jalan = al
4179 .getAlignmentAnnotation()[h];
4180 if (jalan.autoCalculated)
4183 JvAnnotRow valan = visan.get(k = jalan.label);
4184 if (jalan.getCalcId() != null)
4186 valan = visan.get(k = jalan.label + "\t" + jalan.getCalcId());
4191 // delete the auto calculated row from the alignment
4192 al.deleteAnnotation(jalan, false);
4196 if (valan != nullAnnot)
4198 if (jalan != valan.template)
4200 // newly created autoannotation row instance
4201 // so keep a reference to the visible annotation row
4202 // and copy over all relevant attributes
4203 if (valan.template.graphHeight >= 0)
4206 jalan.graphHeight = valan.template.graphHeight;
4208 jalan.visible = valan.template.visible;
4210 reorder.add(new JvAnnotRow(valan.order, jalan));
4215 // Add any (possibly stale) autocalculated rows that were not appended to
4216 // the view during construction
4217 for (String other : remains)
4219 JvAnnotRow othera = visan.get(other);
4220 if (othera != nullAnnot && othera.template.getCalcId() != null
4221 && othera.template.getCalcId().length() > 0)
4223 reorder.add(othera);
4226 // now put the automatic annotation in its correct place
4227 int s = 0, srt[] = new int[reorder.size()];
4228 JvAnnotRow[] rws = new JvAnnotRow[reorder.size()];
4229 for (JvAnnotRow jvar : reorder)
4232 srt[s++] = jvar.order;
4235 jalview.util.QuickSort.sort(srt, rws);
4236 // and re-insert the annotation at its correct position
4237 for (JvAnnotRow jvar : rws)
4239 al.addAnnotation(jvar.template, jvar.order);
4241 af.alignPanel.adjustAnnotationHeight();
4245 Hashtable skipList = null;
4248 * TODO remove this method
4251 * @return AlignFrame bound to sequenceSetId from view, if one exists. private
4252 * AlignFrame getSkippedFrame(Viewport view) { if (skipList==null) {
4253 * throw new Error("Implementation Error. No skipList defined for this
4254 * Jalview2XML instance."); } return (AlignFrame)
4255 * skipList.get(view.getSequenceSetId()); }
4259 * Check if the Jalview view contained in object should be skipped or not.
4262 * @return true if view's sequenceSetId is a key in skipList
4264 private boolean skipViewport(JalviewModel object)
4266 if (skipList == null)
4271 if (skipList.containsKey(id = object.getJalviewModelSequence()
4272 .getViewport()[0].getSequenceSetId()))
4274 if (Cache.log != null && Cache.log.isDebugEnabled())
4276 Cache.log.debug("Skipping seuqence set id " + id);
4283 public void addToSkipList(AlignFrame af)
4285 if (skipList == null)
4287 skipList = new Hashtable();
4289 skipList.put(af.getViewport().getSequenceSetId(), af);
4292 public void clearSkipList()
4294 if (skipList != null)
4301 private void recoverDatasetFor(SequenceSet vamsasSet, Alignment al,
4302 boolean ignoreUnrefed)
4304 jalview.datamodel.Alignment ds = getDatasetFor(vamsasSet.getDatasetId());
4305 Vector dseqs = null;
4308 // create a list of new dataset sequences
4309 dseqs = new Vector();
4311 for (int i = 0, iSize = vamsasSet.getSequenceCount(); i < iSize; i++)
4313 Sequence vamsasSeq = vamsasSet.getSequence(i);
4314 ensureJalviewDatasetSequence(vamsasSeq, ds, dseqs, ignoreUnrefed);
4316 // create a new dataset
4319 SequenceI[] dsseqs = new SequenceI[dseqs.size()];
4320 dseqs.copyInto(dsseqs);
4321 ds = new jalview.datamodel.Alignment(dsseqs);
4322 debug("Created new dataset " + vamsasSet.getDatasetId()
4323 + " for alignment " + System.identityHashCode(al));
4324 addDatasetRef(vamsasSet.getDatasetId(), ds);
4326 // set the dataset for the newly imported alignment.
4327 if (al.getDataset() == null && !ignoreUnrefed)
4336 * sequence definition to create/merge dataset sequence for
4340 * vector to add new dataset sequence to
4342 private void ensureJalviewDatasetSequence(Sequence vamsasSeq,
4343 AlignmentI ds, Vector dseqs, boolean ignoreUnrefed)
4345 // JBP TODO: Check this is called for AlCodonFrames to support recovery of
4347 SequenceI sq = seqRefIds.get(vamsasSeq.getId());
4348 SequenceI dsq = null;
4349 if (sq != null && sq.getDatasetSequence() != null)
4351 dsq = sq.getDatasetSequence();
4353 if (sq == null && ignoreUnrefed)
4357 String sqid = vamsasSeq.getDsseqid();
4360 // need to create or add a new dataset sequence reference to this sequence
4363 dsq = seqRefIds.get(sqid);
4368 // make a new dataset sequence
4369 dsq = sq.createDatasetSequence();
4372 // make up a new dataset reference for this sequence
4373 sqid = seqHash(dsq);
4375 dsq.setVamsasId(uniqueSetSuffix + sqid);
4376 seqRefIds.put(sqid, dsq);
4381 dseqs.addElement(dsq);
4386 ds.addSequence(dsq);
4392 { // make this dataset sequence sq's dataset sequence
4393 sq.setDatasetSequence(dsq);
4394 // and update the current dataset alignment
4399 if (!dseqs.contains(dsq))
4406 if (ds.findIndex(dsq) < 0)
4408 ds.addSequence(dsq);
4415 // TODO: refactor this as a merge dataset sequence function
4416 // now check that sq (the dataset sequence) sequence really is the union of
4417 // all references to it
4418 // boolean pre = sq.getStart() < dsq.getStart();
4419 // boolean post = sq.getEnd() > dsq.getEnd();
4423 // StringBuffer sb = new StringBuffer();
4424 String newres = jalview.analysis.AlignSeq.extractGaps(
4425 jalview.util.Comparison.GapChars, sq.getSequenceAsString());
4426 if (!newres.equalsIgnoreCase(dsq.getSequenceAsString())
4427 && newres.length() > dsq.getLength())
4429 // Update with the longer sequence.
4433 * if (pre) { sb.insert(0, newres .substring(0, dsq.getStart() -
4434 * sq.getStart())); dsq.setStart(sq.getStart()); } if (post) {
4435 * sb.append(newres.substring(newres.length() - sq.getEnd() -
4436 * dsq.getEnd())); dsq.setEnd(sq.getEnd()); }
4438 dsq.setSequence(newres);
4440 // TODO: merges will never happen if we 'know' we have the real dataset
4441 // sequence - this should be detected when id==dssid
4443 .println("DEBUG Notice: Merged dataset sequence (if you see this often, post at http://issues.jalview.org/browse/JAL-1474)"); // ("
4444 // + (pre ? "prepended" : "") + " "
4445 // + (post ? "appended" : ""));
4450 java.util.Hashtable datasetIds = null;
4452 java.util.IdentityHashMap dataset2Ids = null;
4454 private Alignment getDatasetFor(String datasetId)
4456 if (datasetIds == null)
4458 datasetIds = new Hashtable();
4461 if (datasetIds.containsKey(datasetId))
4463 return (Alignment) datasetIds.get(datasetId);
4468 private void addDatasetRef(String datasetId, Alignment dataset)
4470 if (datasetIds == null)
4472 datasetIds = new Hashtable();
4474 datasetIds.put(datasetId, dataset);
4478 * make a new dataset ID for this jalview dataset alignment
4483 private String getDatasetIdRef(jalview.datamodel.Alignment dataset)
4485 if (dataset.getDataset() != null)
4487 warn("Serious issue! Dataset Object passed to getDatasetIdRef is not a Jalview DATASET alignment...");
4489 String datasetId = makeHashCode(dataset, null);
4490 if (datasetId == null)
4492 // make a new datasetId and record it
4493 if (dataset2Ids == null)
4495 dataset2Ids = new IdentityHashMap();
4499 datasetId = (String) dataset2Ids.get(dataset);
4501 if (datasetId == null)
4503 datasetId = "ds" + dataset2Ids.size() + 1;
4504 dataset2Ids.put(dataset, datasetId);
4510 private void addDBRefs(SequenceI datasetSequence, Sequence sequence)
4512 for (int d = 0; d < sequence.getDBRefCount(); d++)
4514 DBRef dr = sequence.getDBRef(d);
4515 jalview.datamodel.DBRefEntry entry = new jalview.datamodel.DBRefEntry(
4516 sequence.getDBRef(d).getSource(), sequence.getDBRef(d)
4517 .getVersion(), sequence.getDBRef(d).getAccessionId());
4518 if (dr.getMapping() != null)
4520 entry.setMap(addMapping(dr.getMapping()));
4522 datasetSequence.addDBRef(entry);
4526 private jalview.datamodel.Mapping addMapping(Mapping m)
4528 SequenceI dsto = null;
4529 // Mapping m = dr.getMapping();
4530 int fr[] = new int[m.getMapListFromCount() * 2];
4531 Enumeration f = m.enumerateMapListFrom();
4532 for (int _i = 0; f.hasMoreElements(); _i += 2)
4534 MapListFrom mf = (MapListFrom) f.nextElement();
4535 fr[_i] = mf.getStart();
4536 fr[_i + 1] = mf.getEnd();
4538 int fto[] = new int[m.getMapListToCount() * 2];
4539 f = m.enumerateMapListTo();
4540 for (int _i = 0; f.hasMoreElements(); _i += 2)
4542 MapListTo mf = (MapListTo) f.nextElement();
4543 fto[_i] = mf.getStart();
4544 fto[_i + 1] = mf.getEnd();
4546 jalview.datamodel.Mapping jmap = new jalview.datamodel.Mapping(dsto,
4547 fr, fto, (int) m.getMapFromUnit(), (int) m.getMapToUnit());
4548 if (m.getMappingChoice() != null)
4550 MappingChoice mc = m.getMappingChoice();
4551 if (mc.getDseqFor() != null)
4553 String dsfor = "" + mc.getDseqFor();
4554 if (seqRefIds.containsKey(dsfor))
4559 jmap.setTo(seqRefIds.get(dsfor));
4563 frefedSequence.add(new Object[]
4570 * local sequence definition
4572 Sequence ms = mc.getSequence();
4573 SequenceI djs = null;
4574 String sqid = ms.getDsseqid();
4575 if (sqid != null && sqid.length() > 0)
4578 * recover dataset sequence
4580 djs = seqRefIds.get(sqid);
4585 .println("Warning - making up dataset sequence id for DbRef sequence map reference");
4586 sqid = ((Object) ms).toString(); // make up a new hascode for
4587 // undefined dataset sequence hash
4588 // (unlikely to happen)
4594 * make a new dataset sequence and add it to refIds hash
4596 djs = new jalview.datamodel.Sequence(ms.getName(),
4598 djs.setStart(jmap.getMap().getToLowest());
4599 djs.setEnd(jmap.getMap().getToHighest());
4600 djs.setVamsasId(uniqueSetSuffix + sqid);
4602 seqRefIds.put(sqid, djs);
4605 jalview.bin.Cache.log.debug("about to recurse on addDBRefs.");
4614 public jalview.gui.AlignmentPanel copyAlignPanel(AlignmentPanel ap,
4615 boolean keepSeqRefs)
4618 jalview.schemabinding.version2.JalviewModel jm = saveState(ap, null,
4624 jm.getJalviewModelSequence().getViewport(0).setSequenceSetId(null);
4628 uniqueSetSuffix = "";
4629 jm.getJalviewModelSequence().getViewport(0).setId(null); // we don't
4634 if (this.frefedSequence == null)
4636 frefedSequence = new Vector();
4639 viewportsAdded.clear();
4641 AlignFrame af = loadFromObject(jm, null, false, null);
4642 af.alignPanels.clear();
4643 af.closeMenuItem_actionPerformed(true);
4646 * if(ap.av.getAlignment().getAlignmentAnnotation()!=null) { for(int i=0;
4647 * i<ap.av.getAlignment().getAlignmentAnnotation().length; i++) {
4648 * if(!ap.av.getAlignment().getAlignmentAnnotation()[i].autoCalculated) {
4649 * af.alignPanel.av.getAlignment().getAlignmentAnnotation()[i] =
4650 * ap.av.getAlignment().getAlignmentAnnotation()[i]; } } }
4653 return af.alignPanel;
4657 * flag indicating if hashtables should be cleared on finalization TODO this
4658 * flag may not be necessary
4660 private final boolean _cleartables = true;
4662 private Hashtable jvids2vobj;
4667 * @see java.lang.Object#finalize()
4670 protected void finalize() throws Throwable
4672 // really make sure we have no buried refs left.
4677 this.seqRefIds = null;
4678 this.seqsToIds = null;
4682 private void warn(String msg)
4687 private void warn(String msg, Exception e)
4689 if (Cache.log != null)
4693 Cache.log.warn(msg, e);
4697 Cache.log.warn(msg);
4702 System.err.println("Warning: " + msg);
4705 e.printStackTrace();
4710 private void debug(String string)
4712 debug(string, null);
4715 private void debug(String msg, Exception e)
4717 if (Cache.log != null)
4721 Cache.log.debug(msg, e);
4725 Cache.log.debug(msg);
4730 System.err.println("Warning: " + msg);
4733 e.printStackTrace();
4739 * set the object to ID mapping tables used to write/recover objects and XML
4740 * ID strings for the jalview project. If external tables are provided then
4741 * finalize and clearSeqRefs will not clear the tables when the Jalview2XML
4742 * object goes out of scope. - also populates the datasetIds hashtable with
4743 * alignment objects containing dataset sequences
4746 * Map from ID strings to jalview datamodel
4748 * Map from jalview datamodel to ID strings
4752 public void setObjectMappingTables(Hashtable vobj2jv,
4753 IdentityHashMap jv2vobj)
4755 this.jv2vobj = jv2vobj;
4756 this.vobj2jv = vobj2jv;
4757 Iterator ds = jv2vobj.keySet().iterator();
4759 while (ds.hasNext())
4761 Object jvobj = ds.next();
4762 id = jv2vobj.get(jvobj).toString();
4763 if (jvobj instanceof jalview.datamodel.Alignment)
4765 if (((jalview.datamodel.Alignment) jvobj).getDataset() == null)
4767 addDatasetRef(id, (jalview.datamodel.Alignment) jvobj);
4770 else if (jvobj instanceof jalview.datamodel.Sequence)
4772 // register sequence object so the XML parser can recover it.
4773 if (seqRefIds == null)
4775 seqRefIds = new HashMap<String, SequenceI>();
4777 if (seqsToIds == null)
4779 seqsToIds = new IdentityHashMap<SequenceI, String>();
4781 seqRefIds.put(jv2vobj.get(jvobj).toString(), (SequenceI) jvobj);
4782 seqsToIds.put((SequenceI) jvobj, id);
4784 else if (jvobj instanceof jalview.datamodel.AlignmentAnnotation)
4787 AlignmentAnnotation jvann = (AlignmentAnnotation) jvobj;
4788 annotationIds.put(anid = jv2vobj.get(jvobj).toString(), jvann);
4789 if (jvann.annotationId == null)
4791 jvann.annotationId = anid;
4793 if (!jvann.annotationId.equals(anid))
4795 // TODO verify that this is the correct behaviour
4796 this.warn("Overriding Annotation ID for " + anid
4797 + " from different id : " + jvann.annotationId);
4798 jvann.annotationId = anid;
4801 else if (jvobj instanceof String)
4803 if (jvids2vobj == null)
4805 jvids2vobj = new Hashtable();
4806 jvids2vobj.put(jvobj, jv2vobj.get(jvobj).toString());
4811 Cache.log.debug("Ignoring " + jvobj.getClass() + " (ID = " + id);
4817 * set the uniqueSetSuffix used to prefix/suffix object IDs for jalview
4818 * objects created from the project archive. If string is null (default for
4819 * construction) then suffix will be set automatically.
4823 public void setUniqueSetSuffix(String string)
4825 uniqueSetSuffix = string;
4830 * uses skipList2 as the skipList for skipping views on sequence sets
4831 * associated with keys in the skipList
4835 public void setSkipList(Hashtable skipList2)
4837 skipList = skipList2;