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 java.awt.Rectangle;
24 import java.io.BufferedReader;
25 import java.io.DataInputStream;
26 import java.io.DataOutputStream;
28 import java.io.FileInputStream;
29 import java.io.FileOutputStream;
30 import java.io.IOException;
31 import java.io.InputStreamReader;
32 import java.io.OutputStreamWriter;
33 import java.io.PrintWriter;
34 import java.lang.reflect.InvocationTargetException;
35 import java.net.MalformedURLException;
37 import java.util.ArrayList;
38 import java.util.Enumeration;
39 import java.util.HashMap;
40 import java.util.HashSet;
41 import java.util.Hashtable;
42 import java.util.IdentityHashMap;
43 import java.util.Iterator;
44 import java.util.LinkedHashMap;
45 import java.util.List;
47 import java.util.Map.Entry;
49 import java.util.StringTokenizer;
50 import java.util.Vector;
51 import java.util.jar.JarEntry;
52 import java.util.jar.JarInputStream;
53 import java.util.jar.JarOutputStream;
55 import javax.swing.JInternalFrame;
56 import javax.swing.JOptionPane;
57 import javax.swing.SwingUtilities;
59 import org.exolab.castor.xml.Unmarshaller;
61 import jalview.api.structures.JalviewStructureDisplayI;
62 import jalview.bin.Cache;
63 import jalview.datamodel.AlignedCodonFrame;
64 import jalview.datamodel.Alignment;
65 import jalview.datamodel.AlignmentAnnotation;
66 import jalview.datamodel.AlignmentI;
67 import jalview.datamodel.PDBEntry;
68 import jalview.datamodel.SequenceI;
69 import jalview.datamodel.StructureViewerModel;
70 import jalview.datamodel.StructureViewerModel.StructureData;
71 import jalview.schemabinding.version2.AlcodMap;
72 import jalview.schemabinding.version2.AlcodonFrame;
73 import jalview.schemabinding.version2.Annotation;
74 import jalview.schemabinding.version2.AnnotationColours;
75 import jalview.schemabinding.version2.AnnotationElement;
76 import jalview.schemabinding.version2.CalcIdParam;
77 import jalview.schemabinding.version2.DBRef;
78 import jalview.schemabinding.version2.Features;
79 import jalview.schemabinding.version2.Group;
80 import jalview.schemabinding.version2.HiddenColumns;
81 import jalview.schemabinding.version2.JGroup;
82 import jalview.schemabinding.version2.JSeq;
83 import jalview.schemabinding.version2.JalviewModel;
84 import jalview.schemabinding.version2.JalviewModelSequence;
85 import jalview.schemabinding.version2.MapListFrom;
86 import jalview.schemabinding.version2.MapListTo;
87 import jalview.schemabinding.version2.Mapping;
88 import jalview.schemabinding.version2.MappingChoice;
89 import jalview.schemabinding.version2.OtherData;
90 import jalview.schemabinding.version2.PdbentryItem;
91 import jalview.schemabinding.version2.Pdbids;
92 import jalview.schemabinding.version2.Property;
93 import jalview.schemabinding.version2.Sequence;
94 import jalview.schemabinding.version2.SequenceSet;
95 import jalview.schemabinding.version2.SequenceSetProperties;
96 import jalview.schemabinding.version2.Setting;
97 import jalview.schemabinding.version2.StructureState;
98 import jalview.schemabinding.version2.ThresholdLine;
99 import jalview.schemabinding.version2.Tree;
100 import jalview.schemabinding.version2.UserColours;
101 import jalview.schemabinding.version2.Viewport;
102 import jalview.schemes.AnnotationColourGradient;
103 import jalview.schemes.ColourSchemeI;
104 import jalview.schemes.ColourSchemeProperty;
105 import jalview.schemes.GraduatedColor;
106 import jalview.schemes.ResidueColourScheme;
107 import jalview.schemes.ResidueProperties;
108 import jalview.schemes.UserColourScheme;
109 import jalview.structure.StructureSelectionManager;
110 import jalview.structures.models.AAStructureBindingModel;
111 import jalview.util.MessageManager;
112 import jalview.util.Platform;
113 import jalview.util.jarInputStreamProvider;
114 import jalview.viewmodel.AlignmentViewport;
115 import jalview.viewmodel.seqfeatures.FeatureRendererSettings;
116 import jalview.viewmodel.seqfeatures.FeaturesDisplayed;
117 import jalview.ws.jws2.Jws2Discoverer;
118 import jalview.ws.jws2.dm.AAConSettings;
119 import jalview.ws.jws2.jabaws2.Jws2Instance;
120 import jalview.ws.params.ArgumentI;
121 import jalview.ws.params.AutoCalcSetting;
122 import jalview.ws.params.WsParamSetI;
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 position = ap.alignFrame.getBounds();
1063 view.setXpos(position.x);
1064 view.setYpos(position.y);
1065 view.setWidth(position.width);
1066 view.setHeight(position.height);
1068 view.setStartRes(av.startRes);
1069 view.setStartSeq(av.startSeq);
1071 if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme)
1073 view.setBgColour(setUserColourScheme(av.getGlobalColourScheme(),
1076 else if (av.getGlobalColourScheme() instanceof jalview.schemes.AnnotationColourGradient)
1078 AnnotationColours ac = constructAnnotationColours(
1079 (jalview.schemes.AnnotationColourGradient) av
1080 .getGlobalColourScheme(),
1083 view.setAnnotationColours(ac);
1084 view.setBgColour("AnnotationColourGradient");
1088 view.setBgColour(ColourSchemeProperty.getColourName(av
1089 .getGlobalColourScheme()));
1092 ColourSchemeI cs = av.getGlobalColourScheme();
1096 if (cs.conservationApplied())
1098 view.setConsThreshold(cs.getConservationInc());
1099 if (cs instanceof jalview.schemes.UserColourScheme)
1101 view.setBgColour(setUserColourScheme(cs, userColours, jms));
1105 if (cs instanceof ResidueColourScheme)
1107 view.setPidThreshold(cs.getThreshold());
1111 view.setConservationSelected(av.getConservationSelected());
1112 view.setPidSelected(av.getAbovePIDThreshold());
1113 view.setFontName(av.font.getName());
1114 view.setFontSize(av.font.getSize());
1115 view.setFontStyle(av.font.getStyle());
1116 view.setRenderGaps(av.isRenderGaps());
1117 view.setShowAnnotation(av.isShowAnnotation());
1118 view.setShowBoxes(av.getShowBoxes());
1119 view.setShowColourText(av.getColourText());
1120 view.setShowFullId(av.getShowJVSuffix());
1121 view.setRightAlignIds(av.isRightAlignIds());
1122 view.setShowSequenceFeatures(av.isShowSequenceFeatures());
1123 view.setShowText(av.getShowText());
1124 view.setShowUnconserved(av.getShowUnconserved());
1125 view.setWrapAlignment(av.getWrapAlignment());
1126 view.setTextCol1(av.getTextColour().getRGB());
1127 view.setTextCol2(av.getTextColour2().getRGB());
1128 view.setTextColThreshold(av.getThresholdTextColour());
1129 view.setShowConsensusHistogram(av.isShowConsensusHistogram());
1130 view.setShowSequenceLogo(av.isShowSequenceLogo());
1131 view.setNormaliseSequenceLogo(av.isNormaliseSequenceLogo());
1132 view.setShowGroupConsensus(av.isShowGroupConsensus());
1133 view.setShowGroupConservation(av.isShowGroupConservation());
1134 view.setShowNPfeatureTooltip(av.isShowNPFeats());
1135 view.setShowDbRefTooltip(av.isShowDBRefs());
1136 view.setFollowHighlight(av.followHighlight);
1137 view.setFollowSelection(av.followSelection);
1138 view.setIgnoreGapsinConsensus(av.isIgnoreGapsConsensus());
1139 if (av.getFeaturesDisplayed() != null)
1141 jalview.schemabinding.version2.FeatureSettings fs = new jalview.schemabinding.version2.FeatureSettings();
1143 String[] renderOrder = ap.getSeqPanel().seqCanvas
1144 .getFeatureRenderer().getRenderOrder()
1145 .toArray(new String[0]);
1147 Vector settingsAdded = new Vector();
1148 Object gstyle = null;
1149 GraduatedColor gcol = null;
1150 if (renderOrder != null)
1152 for (int ro = 0; ro < renderOrder.length; ro++)
1154 gstyle = ap.getSeqPanel().seqCanvas.getFeatureRenderer()
1155 .getFeatureStyle(renderOrder[ro]);
1156 Setting setting = new Setting();
1157 setting.setType(renderOrder[ro]);
1158 if (gstyle instanceof GraduatedColor)
1160 gcol = (GraduatedColor) gstyle;
1161 setting.setColour(gcol.getMaxColor().getRGB());
1162 setting.setMincolour(gcol.getMinColor().getRGB());
1163 setting.setMin(gcol.getMin());
1164 setting.setMax(gcol.getMax());
1165 setting.setColourByLabel(gcol.isColourByLabel());
1166 setting.setAutoScale(gcol.isAutoScale());
1167 setting.setThreshold(gcol.getThresh());
1168 setting.setThreshstate(gcol.getThreshType());
1172 setting.setColour(ap.getSeqPanel().seqCanvas
1173 .getFeatureRenderer()
1174 .getColour(renderOrder[ro]).getRGB());
1177 setting.setDisplay(av.getFeaturesDisplayed().isVisible(
1179 float rorder = ap.getSeqPanel().seqCanvas.getFeatureRenderer()
1180 .getOrder(renderOrder[ro]);
1183 setting.setOrder(rorder);
1185 fs.addSetting(setting);
1186 settingsAdded.addElement(renderOrder[ro]);
1190 // Make sure we save none displayed feature settings
1191 Iterator en = ap.getSeqPanel().seqCanvas.getFeatureRenderer()
1192 .getFeatureColours().keySet().iterator();
1193 while (en.hasNext())
1195 String key = en.next().toString();
1196 if (settingsAdded.contains(key))
1201 Setting setting = new Setting();
1202 setting.setType(key);
1203 setting.setColour(ap.getSeqPanel().seqCanvas.getFeatureRenderer()
1204 .getColour(key).getRGB());
1206 setting.setDisplay(false);
1207 float rorder = ap.getSeqPanel().seqCanvas.getFeatureRenderer()
1211 setting.setOrder(rorder);
1213 fs.addSetting(setting);
1214 settingsAdded.addElement(key);
1216 // is groups actually supposed to be a map here ?
1217 en = ap.getSeqPanel().seqCanvas.getFeatureRenderer()
1218 .getFeatureGroups().iterator();
1219 Vector groupsAdded = new Vector();
1220 while (en.hasNext())
1222 String grp = en.next().toString();
1223 if (groupsAdded.contains(grp))
1227 Group g = new Group();
1229 g.setDisplay(((Boolean) ap.getSeqPanel().seqCanvas
1230 .getFeatureRenderer().checkGroupVisibility(grp, false))
1233 groupsAdded.addElement(grp);
1235 jms.setFeatureSettings(fs);
1239 if (av.hasHiddenColumns())
1241 if (av.getColumnSelection() == null
1242 || av.getColumnSelection().getHiddenColumns() == null)
1244 warn("REPORT BUG: avoided null columnselection bug (DMAM reported). Please contact Jim about this.");
1248 for (int c = 0; c < av.getColumnSelection().getHiddenColumns()
1251 int[] region = av.getColumnSelection().getHiddenColumns()
1253 HiddenColumns hc = new HiddenColumns();
1254 hc.setStart(region[0]);
1255 hc.setEnd(region[1]);
1256 view.addHiddenColumns(hc);
1260 if (calcIdSet.size() > 0)
1262 for (String calcId : calcIdSet)
1264 if (calcId.trim().length() > 0)
1266 CalcIdParam cidp = createCalcIdParam(calcId, av);
1267 // Some calcIds have no parameters.
1270 view.addCalcIdParam(cidp);
1276 jms.addViewport(view);
1278 object.setJalviewModelSequence(jms);
1279 object.getVamsasModel().addSequenceSet(vamsasSet);
1281 if (jout != null && fileName != null)
1283 // We may not want to write the object to disk,
1284 // eg we can copy the alignViewport to a new view object
1285 // using save and then load
1288 JarEntry entry = new JarEntry(fileName);
1289 jout.putNextEntry(entry);
1290 PrintWriter pout = new PrintWriter(new OutputStreamWriter(jout,
1292 org.exolab.castor.xml.Marshaller marshaller = new org.exolab.castor.xml.Marshaller(
1294 marshaller.marshal(object);
1297 } catch (Exception ex)
1299 // TODO: raise error in GUI if marshalling failed.
1300 ex.printStackTrace();
1307 * Save the state of a structure viewer
1312 * the archive XML element under which to save the state
1315 * @param matchedFile
1319 protected String saveStructureState(AlignmentPanel ap, SequenceI jds,
1320 Pdbids pdb, PDBEntry entry, List<String> viewIds,
1321 String matchedFile, StructureViewerBase viewFrame)
1323 final AAStructureBindingModel bindingModel = viewFrame.getBinding();
1324 for (int peid = 0; peid < bindingModel.getPdbCount(); peid++)
1326 final PDBEntry pdbentry = bindingModel.getPdbEntry(peid);
1327 final String pdbId = pdbentry.getId();
1328 if (!pdbId.equals(entry.getId())
1329 && !(entry.getId().length() > 4 && entry.getId()
1330 .toLowerCase().startsWith(pdbId.toLowerCase())))
1334 if (matchedFile == null)
1336 matchedFile = pdbentry.getFile();
1338 else if (!matchedFile.equals(pdbentry.getFile()))
1341 .warn("Probably lost some PDB-Sequence mappings for this structure file (which apparently has same PDB Entry code): "
1342 + pdbentry.getFile());
1346 // can get at it if the ID
1347 // match is ambiguous (e.g.
1349 String statestring = viewFrame.getStateInfo();
1351 for (int smap = 0; smap < viewFrame.getBinding().getSequence()[peid].length; smap++)
1353 // if (jal.findIndex(jmol.jmb.sequence[peid][smap]) > -1)
1354 if (jds == viewFrame.getBinding().getSequence()[peid][smap])
1356 StructureState state = new StructureState();
1357 state.setVisible(true);
1358 state.setXpos(viewFrame.getX());
1359 state.setYpos(viewFrame.getY());
1360 state.setWidth(viewFrame.getWidth());
1361 state.setHeight(viewFrame.getHeight());
1362 final String viewId = viewFrame.getViewId();
1363 state.setViewId(viewId);
1364 state.setAlignwithAlignPanel(viewFrame.isUsedforaligment(ap));
1365 state.setColourwithAlignPanel(viewFrame.isUsedforcolourby(ap));
1366 state.setColourByJmol(viewFrame.isColouredByViewer());
1368 * Only store each structure viewer's state once in each XML document.
1370 if (!viewIds.contains(viewId))
1372 viewIds.add(viewId);
1373 state.setContent(statestring.replaceAll("\n", ""));
1377 state.setContent("# duplicate state");
1379 pdb.addStructureState(state);
1386 private AnnotationColours constructAnnotationColours(
1387 AnnotationColourGradient acg, List<UserColourScheme> userColours,
1388 JalviewModelSequence jms)
1390 AnnotationColours ac = new AnnotationColours();
1391 ac.setAboveThreshold(acg.getAboveThreshold());
1392 ac.setThreshold(acg.getAnnotationThreshold());
1393 ac.setAnnotation(acg.getAnnotation());
1394 if (acg.getBaseColour() instanceof jalview.schemes.UserColourScheme)
1396 ac.setColourScheme(setUserColourScheme(acg.getBaseColour(),
1401 ac.setColourScheme(ColourSchemeProperty.getColourName(acg
1405 ac.setMaxColour(acg.getMaxColour().getRGB());
1406 ac.setMinColour(acg.getMinColour().getRGB());
1407 ac.setPerSequence(acg.isSeqAssociated());
1408 ac.setPredefinedColours(acg.isPredefinedColours());
1412 private void storeAlignmentAnnotation(AlignmentAnnotation[] aa,
1413 IdentityHashMap groupRefs, AlignmentViewport av,
1414 Set<String> calcIdSet, boolean storeDS, SequenceSet vamsasSet)
1417 for (int i = 0; i < aa.length; i++)
1419 Annotation an = new Annotation();
1421 if (aa[i].annotationId != null)
1423 annotationIds.put(aa[i].annotationId, aa[i]);
1426 an.setId(aa[i].annotationId);
1428 an.setVisible(aa[i].visible);
1430 an.setDescription(aa[i].description);
1432 if (aa[i].sequenceRef != null)
1434 // TODO later annotation sequenceRef should be the XML ID of the
1435 // sequence rather than its display name
1436 an.setSequenceRef(aa[i].sequenceRef.getName());
1438 if (aa[i].groupRef != null)
1440 Object groupIdr = groupRefs.get(aa[i].groupRef);
1441 if (groupIdr == null)
1443 // make a locally unique String
1444 groupRefs.put(aa[i].groupRef,
1445 groupIdr = ("" + System.currentTimeMillis()
1446 + aa[i].groupRef.getName() + groupRefs.size()));
1448 an.setGroupRef(groupIdr.toString());
1451 // store all visualization attributes for annotation
1452 an.setGraphHeight(aa[i].graphHeight);
1453 an.setCentreColLabels(aa[i].centreColLabels);
1454 an.setScaleColLabels(aa[i].scaleColLabel);
1455 an.setShowAllColLabels(aa[i].showAllColLabels);
1456 an.setBelowAlignment(aa[i].belowAlignment);
1458 if (aa[i].graph > 0)
1461 an.setGraphType(aa[i].graph);
1462 an.setGraphGroup(aa[i].graphGroup);
1463 if (aa[i].getThreshold() != null)
1465 ThresholdLine line = new ThresholdLine();
1466 line.setLabel(aa[i].getThreshold().label);
1467 line.setValue(aa[i].getThreshold().value);
1468 line.setColour(aa[i].getThreshold().colour.getRGB());
1469 an.setThresholdLine(line);
1477 an.setLabel(aa[i].label);
1479 if (aa[i] == av.getAlignmentQualityAnnot()
1480 || aa[i] == av.getAlignmentConservationAnnotation()
1481 || aa[i] == av.getAlignmentConsensusAnnotation()
1482 || aa[i].autoCalculated)
1484 // new way of indicating autocalculated annotation -
1485 an.setAutoCalculated(aa[i].autoCalculated);
1487 if (aa[i].hasScore())
1489 an.setScore(aa[i].getScore());
1492 if (aa[i].getCalcId() != null)
1494 calcIdSet.add(aa[i].getCalcId());
1495 an.setCalcId(aa[i].getCalcId());
1497 if (aa[i].hasProperties())
1499 for (String pr : aa[i].getProperties())
1501 Property prop = new Property();
1503 prop.setValue(aa[i].getProperty(pr));
1504 an.addProperty(prop);
1508 AnnotationElement ae;
1509 if (aa[i].annotations != null)
1511 an.setScoreOnly(false);
1512 for (int a = 0; a < aa[i].annotations.length; a++)
1514 if ((aa[i] == null) || (aa[i].annotations[a] == null))
1519 ae = new AnnotationElement();
1520 if (aa[i].annotations[a].description != null)
1522 ae.setDescription(aa[i].annotations[a].description);
1524 if (aa[i].annotations[a].displayCharacter != null)
1526 ae.setDisplayCharacter(aa[i].annotations[a].displayCharacter);
1529 if (!Float.isNaN(aa[i].annotations[a].value))
1531 ae.setValue(aa[i].annotations[a].value);
1535 if (aa[i].annotations[a].secondaryStructure > ' ')
1537 ae.setSecondaryStructure(aa[i].annotations[a].secondaryStructure
1541 if (aa[i].annotations[a].colour != null
1542 && aa[i].annotations[a].colour != java.awt.Color.black)
1544 ae.setColour(aa[i].annotations[a].colour.getRGB());
1547 an.addAnnotationElement(ae);
1548 if (aa[i].autoCalculated)
1550 // only write one non-null entry into the annotation row -
1551 // sufficient to get the visualization attributes necessary to
1559 an.setScoreOnly(true);
1561 if (!storeDS || (storeDS && !aa[i].autoCalculated))
1563 // skip autocalculated annotation - these are only provided for
1565 vamsasSet.addAnnotation(an);
1571 private CalcIdParam createCalcIdParam(String calcId, AlignViewport av)
1573 AutoCalcSetting settings = av.getCalcIdSettingsFor(calcId);
1574 if (settings != null)
1576 CalcIdParam vCalcIdParam = new CalcIdParam();
1577 vCalcIdParam.setCalcId(calcId);
1578 vCalcIdParam.addServiceURL(settings.getServiceURI());
1579 // generic URI allowing a third party to resolve another instance of the
1580 // service used for this calculation
1581 for (String urls : settings.getServiceURLs())
1583 vCalcIdParam.addServiceURL(urls);
1585 vCalcIdParam.setVersion("1.0");
1586 if (settings.getPreset() != null)
1588 WsParamSetI setting = settings.getPreset();
1589 vCalcIdParam.setName(setting.getName());
1590 vCalcIdParam.setDescription(setting.getDescription());
1594 vCalcIdParam.setName("");
1595 vCalcIdParam.setDescription("Last used parameters");
1597 // need to be able to recover 1) settings 2) user-defined presets or
1598 // recreate settings from preset 3) predefined settings provided by
1599 // service - or settings that can be transferred (or discarded)
1600 vCalcIdParam.setParameters(settings.getWsParamFile().replace("\n",
1602 vCalcIdParam.setAutoUpdate(settings.isAutoUpdate());
1603 // todo - decide if updateImmediately is needed for any projects.
1605 return vCalcIdParam;
1610 private boolean recoverCalcIdParam(CalcIdParam calcIdParam,
1613 if (calcIdParam.getVersion().equals("1.0"))
1615 Jws2Instance service = Jws2Discoverer.getDiscoverer()
1616 .getPreferredServiceFor(calcIdParam.getServiceURL());
1617 if (service != null)
1619 WsParamSetI parmSet = null;
1622 parmSet = service.getParamStore().parseServiceParameterFile(
1623 calcIdParam.getName(), calcIdParam.getDescription(),
1624 calcIdParam.getServiceURL(),
1625 calcIdParam.getParameters().replace("|\\n|", "\n"));
1626 } catch (IOException x)
1628 warn("Couldn't parse parameter data for "
1629 + calcIdParam.getCalcId(), x);
1632 List<ArgumentI> argList = null;
1633 if (calcIdParam.getName().length() > 0)
1635 parmSet = service.getParamStore()
1636 .getPreset(calcIdParam.getName());
1637 if (parmSet != null)
1639 // TODO : check we have a good match with settings in AACon -
1640 // otherwise we'll need to create a new preset
1645 argList = parmSet.getArguments();
1648 AAConSettings settings = new AAConSettings(
1649 calcIdParam.isAutoUpdate(), service, parmSet, argList);
1650 av.setCalcIdSettingsFor(calcIdParam.getCalcId(), settings,
1651 calcIdParam.isNeedsUpdate());
1656 warn("Cannot resolve a service for the parameters used in this project. Try configuring a JABAWS server.");
1660 throw new Error(MessageManager.formatMessage(
1661 "error.unsupported_version_calcIdparam", new Object[]
1662 { calcIdParam.toString() }));
1666 * External mapping between jalview objects and objects yielding a valid and
1667 * unique object ID string. This is null for normal Jalview project IO, but
1668 * non-null when a jalview project is being read or written as part of a
1671 IdentityHashMap jv2vobj = null;
1674 * Construct a unique ID for jvobj using either existing bindings or if none
1675 * exist, the result of the hashcode call for the object.
1678 * jalview data object
1679 * @return unique ID for referring to jvobj
1681 private String makeHashCode(Object jvobj, String altCode)
1683 if (jv2vobj != null)
1685 Object id = jv2vobj.get(jvobj);
1688 return id.toString();
1690 // check string ID mappings
1691 if (jvids2vobj != null && jvobj instanceof String)
1693 id = jvids2vobj.get(jvobj);
1697 return id.toString();
1699 // give up and warn that something has gone wrong
1700 warn("Cannot find ID for object in external mapping : " + jvobj);
1706 * return local jalview object mapped to ID, if it exists
1710 * @return null or object bound to idcode
1712 private Object retrieveExistingObj(String idcode)
1714 if (idcode != null && vobj2jv != null)
1716 return vobj2jv.get(idcode);
1722 * binding from ID strings from external mapping table to jalview data model
1725 private Hashtable vobj2jv;
1727 private Sequence createVamsasSequence(String id, SequenceI jds)
1729 return createVamsasSequence(true, id, jds, null);
1732 private Sequence createVamsasSequence(boolean recurse, String id,
1733 SequenceI jds, SequenceI parentseq)
1735 Sequence vamsasSeq = new Sequence();
1736 vamsasSeq.setId(id);
1737 vamsasSeq.setName(jds.getName());
1738 vamsasSeq.setSequence(jds.getSequenceAsString());
1739 vamsasSeq.setDescription(jds.getDescription());
1740 jalview.datamodel.DBRefEntry[] dbrefs = null;
1741 if (jds.getDatasetSequence() != null)
1743 vamsasSeq.setDsseqid(seqHash(jds.getDatasetSequence()));
1744 if (jds.getDatasetSequence().getDBRef() != null)
1746 dbrefs = jds.getDatasetSequence().getDBRef();
1751 vamsasSeq.setDsseqid(id); // so we can tell which sequences really are
1752 // dataset sequences only
1753 dbrefs = jds.getDBRef();
1757 for (int d = 0; d < dbrefs.length; d++)
1759 DBRef dbref = new DBRef();
1760 dbref.setSource(dbrefs[d].getSource());
1761 dbref.setVersion(dbrefs[d].getVersion());
1762 dbref.setAccessionId(dbrefs[d].getAccessionId());
1763 if (dbrefs[d].hasMap())
1765 Mapping mp = createVamsasMapping(dbrefs[d].getMap(), parentseq,
1767 dbref.setMapping(mp);
1769 vamsasSeq.addDBRef(dbref);
1775 private Mapping createVamsasMapping(jalview.datamodel.Mapping jmp,
1776 SequenceI parentseq, SequenceI jds, boolean recurse)
1779 if (jmp.getMap() != null)
1783 jalview.util.MapList mlst = jmp.getMap();
1784 List<int[]> r = mlst.getFromRanges();
1785 for (int[] range : r)
1787 MapListFrom mfrom = new MapListFrom();
1788 mfrom.setStart(range[0]);
1789 mfrom.setEnd(range[1]);
1790 mp.addMapListFrom(mfrom);
1792 r = mlst.getToRanges();
1793 for (int[] range : r)
1795 MapListTo mto = new MapListTo();
1796 mto.setStart(range[0]);
1797 mto.setEnd(range[1]);
1798 mp.addMapListTo(mto);
1800 mp.setMapFromUnit(mlst.getFromRatio());
1801 mp.setMapToUnit(mlst.getToRatio());
1802 if (jmp.getTo() != null)
1804 MappingChoice mpc = new MappingChoice();
1806 && (parentseq != jmp.getTo() || parentseq
1807 .getDatasetSequence() != jmp.getTo()))
1809 mpc.setSequence(createVamsasSequence(false, seqHash(jmp.getTo()),
1815 SequenceI ps = null;
1816 if (parentseq != jmp.getTo()
1817 && parentseq.getDatasetSequence() != jmp.getTo())
1819 // chaining dbref rather than a handshaking one
1820 jmpid = seqHash(ps = jmp.getTo());
1824 jmpid = seqHash(ps = parentseq);
1826 mpc.setDseqFor(jmpid);
1827 if (!seqRefIds.containsKey(mpc.getDseqFor()))
1829 jalview.bin.Cache.log.debug("creatign new DseqFor ID");
1830 seqRefIds.put(mpc.getDseqFor(), ps);
1834 jalview.bin.Cache.log.debug("reusing DseqFor ID");
1837 mp.setMappingChoice(mpc);
1843 String setUserColourScheme(jalview.schemes.ColourSchemeI cs,
1844 List<UserColourScheme> userColours, JalviewModelSequence jms)
1847 jalview.schemes.UserColourScheme ucs = (jalview.schemes.UserColourScheme) cs;
1848 boolean newucs = false;
1849 if (!userColours.contains(ucs))
1851 userColours.add(ucs);
1854 id = "ucs" + userColours.indexOf(ucs);
1857 // actually create the scheme's entry in the XML model
1858 java.awt.Color[] colours = ucs.getColours();
1859 jalview.schemabinding.version2.UserColours uc = new jalview.schemabinding.version2.UserColours();
1860 jalview.schemabinding.version2.UserColourScheme jbucs = new jalview.schemabinding.version2.UserColourScheme();
1862 for (int i = 0; i < colours.length; i++)
1864 jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();
1865 col.setName(ResidueProperties.aa[i]);
1866 col.setRGB(jalview.util.Format.getHexString(colours[i]));
1867 jbucs.addColour(col);
1869 if (ucs.getLowerCaseColours() != null)
1871 colours = ucs.getLowerCaseColours();
1872 for (int i = 0; i < colours.length; i++)
1874 jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();
1875 col.setName(ResidueProperties.aa[i].toLowerCase());
1876 col.setRGB(jalview.util.Format.getHexString(colours[i]));
1877 jbucs.addColour(col);
1882 uc.setUserColourScheme(jbucs);
1883 jms.addUserColours(uc);
1889 jalview.schemes.UserColourScheme getUserColourScheme(
1890 JalviewModelSequence jms, String id)
1892 UserColours[] uc = jms.getUserColours();
1893 UserColours colours = null;
1895 for (int i = 0; i < uc.length; i++)
1897 if (uc[i].getId().equals(id))
1905 java.awt.Color[] newColours = new java.awt.Color[24];
1907 for (int i = 0; i < 24; i++)
1909 newColours[i] = new java.awt.Color(Integer.parseInt(colours
1910 .getUserColourScheme().getColour(i).getRGB(), 16));
1913 jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(
1916 if (colours.getUserColourScheme().getColourCount() > 24)
1918 newColours = new java.awt.Color[23];
1919 for (int i = 0; i < 23; i++)
1921 newColours[i] = new java.awt.Color(Integer.parseInt(colours
1922 .getUserColourScheme().getColour(i + 24).getRGB(), 16));
1924 ucs.setLowerCaseColours(newColours);
1931 * contains last error message (if any) encountered by XML loader.
1933 String errorMessage = null;
1936 * flag to control whether the Jalview2XML_V1 parser should be deferred to if
1937 * exceptions are raised during project XML parsing
1939 public boolean attemptversion1parse = true;
1942 * Load a jalview project archive from a jar file
1945 * - HTTP URL or filename
1947 public AlignFrame loadJalviewAlign(final String file)
1950 jalview.gui.AlignFrame af = null;
1954 // create list to store references for any new Jmol viewers created
1955 newStructureViewers = new Vector<JalviewStructureDisplayI>();
1956 // UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
1957 // Workaround is to make sure caller implements the JarInputStreamProvider
1959 // so we can re-open the jar input stream for each entry.
1961 jarInputStreamProvider jprovider = createjarInputStreamProvider(file);
1962 af = loadJalviewAlign(jprovider);
1964 } catch (MalformedURLException e)
1966 errorMessage = "Invalid URL format for '" + file + "'";
1972 SwingUtilities.invokeAndWait(new Runnable()
1976 setLoadingFinishedForNewStructureViewers();
1979 } catch (Exception x)
1987 private jarInputStreamProvider createjarInputStreamProvider(
1988 final String file) throws MalformedURLException
1991 errorMessage = null;
1992 uniqueSetSuffix = null;
1994 viewportsAdded.clear();
1995 frefedSequence = null;
1997 if (file.startsWith("http://"))
1999 url = new URL(file);
2001 final URL _url = url;
2002 return new jarInputStreamProvider()
2006 public JarInputStream getJarInputStream() throws IOException
2010 return new JarInputStream(_url.openStream());
2014 return new JarInputStream(new FileInputStream(file));
2019 public String getFilename()
2027 * Recover jalview session from a jalview project archive. Caller may
2028 * initialise uniqueSetSuffix, seqRefIds, viewportsAdded and frefedSequence
2029 * themselves. Any null fields will be initialised with default values,
2030 * non-null fields are left alone.
2035 public AlignFrame loadJalviewAlign(final jarInputStreamProvider jprovider)
2037 errorMessage = null;
2038 if (uniqueSetSuffix == null)
2040 uniqueSetSuffix = System.currentTimeMillis() % 100000 + "";
2042 if (seqRefIds == null)
2044 seqRefIds = new HashMap<String, SequenceI>();
2046 if (frefedSequence == null)
2048 frefedSequence = new Vector();
2051 AlignFrame af = null, _af = null;
2052 Map<String, AlignFrame> gatherToThisFrame = new HashMap<String, AlignFrame>();
2053 final String file = jprovider.getFilename();
2056 JarInputStream jin = null;
2057 JarEntry jarentry = null;
2062 jin = jprovider.getJarInputStream();
2063 for (int i = 0; i < entryCount; i++)
2065 jarentry = jin.getNextJarEntry();
2068 if (jarentry != null && jarentry.getName().endsWith(".xml"))
2070 InputStreamReader in = new InputStreamReader(jin, "UTF-8");
2071 JalviewModel object = new JalviewModel();
2073 Unmarshaller unmar = new Unmarshaller(object);
2074 unmar.setValidation(false);
2075 object = (JalviewModel) unmar.unmarshal(in);
2076 if (true) // !skipViewport(object))
2078 _af = loadFromObject(object, file, true, jprovider);
2079 if (object.getJalviewModelSequence().getViewportCount() > 0)
2082 if (af.viewport.isGatherViewsHere())
2084 gatherToThisFrame.put(af.viewport.getSequenceSetId(), af);
2090 else if (jarentry != null)
2092 // Some other file here.
2095 } while (jarentry != null);
2096 resolveFrefedSequences();
2097 } catch (java.io.FileNotFoundException ex)
2099 ex.printStackTrace();
2100 errorMessage = "Couldn't locate Jalview XML file : " + file;
2101 System.err.println("Exception whilst loading jalview XML file : "
2103 } catch (java.net.UnknownHostException 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 (Exception ex)
2111 System.err.println("Parsing as Jalview Version 2 file failed.");
2112 ex.printStackTrace(System.err);
2113 if (attemptversion1parse)
2115 // Is Version 1 Jar file?
2118 af = new Jalview2XML_V1(raiseGUI).LoadJalviewAlign(jprovider);
2119 } catch (Exception ex2)
2121 System.err.println("Exception whilst loading as jalviewXMLV1:");
2122 ex2.printStackTrace();
2126 if (Desktop.instance != null)
2128 Desktop.instance.stopLoading();
2132 System.out.println("Successfully loaded archive file");
2135 ex.printStackTrace();
2137 System.err.println("Exception whilst loading jalview XML file : "
2139 } catch (OutOfMemoryError e)
2141 // Don't use the OOM Window here
2142 errorMessage = "Out of memory loading jalview XML file";
2143 System.err.println("Out of memory whilst loading jalview XML file");
2144 e.printStackTrace();
2147 if (Desktop.instance != null)
2149 Desktop.instance.stopLoading();
2153 * Regather multiple views (with the same sequence set id) to the frame (if
2154 * any) that is flagged as the one to gather to, i.e. convert them to tabbed
2155 * views instead of separate frames. Note this doesn't restore a state where
2156 * some expanded views in turn have tabbed views - the last "first tab" read
2157 * in will play the role of gatherer for all.
2159 for (AlignFrame fr : gatherToThisFrame.values())
2161 Desktop.instance.gatherViews(fr);
2164 restoreSplitFrames();
2166 if (errorMessage != null)
2174 * Try to reconstruct and display SplitFrame windows, where each contains
2175 * complementary dna and protein alignments. Done by pairing up AlignFrame
2176 * objects (created earlier) which have complementary viewport ids associated.
2178 protected void restoreSplitFrames()
2180 List<SplitFrame> gatherTo = new ArrayList<SplitFrame>();
2181 List<AlignFrame> addedToSplitFrames = new ArrayList<AlignFrame>();
2182 Map<String, AlignFrame> dna = new HashMap<String, AlignFrame>();
2185 * Identify the DNA alignments
2187 for (Entry<Viewport, AlignFrame> candidate : splitFrameCandidates
2190 AlignFrame af = candidate.getValue();
2191 if (af.getViewport().getAlignment().isNucleotide())
2193 dna.put(candidate.getKey().getId(), af);
2198 * Try to match up the protein complements
2200 for (Entry<Viewport, AlignFrame> candidate : splitFrameCandidates
2203 AlignFrame af = candidate.getValue();
2204 if (!af.getViewport().getAlignment().isNucleotide())
2206 String complementId = candidate.getKey().getComplementId();
2207 // only non-null complements should be in the Map
2208 if (complementId != null && dna.containsKey(complementId))
2210 final AlignFrame dnaFrame = dna.get(complementId);
2211 SplitFrame sf = createSplitFrame(dnaFrame, af);
2212 addedToSplitFrames.add(dnaFrame);
2213 addedToSplitFrames.add(af);
2214 if (af.viewport.isGatherViewsHere())
2223 * Open any that we failed to pair up (which shouldn't happen!) as
2224 * standalone AlignFrame's.
2226 for (Entry<Viewport, AlignFrame> candidate : splitFrameCandidates
2229 AlignFrame af = candidate.getValue();
2230 if (!addedToSplitFrames.contains(af)) {
2231 Viewport view = candidate.getKey();
2232 Desktop.addInternalFrame(af, view.getTitle(), view.getWidth(),
2234 System.err.println("Failed to restore view " + view.getTitle()
2235 + " to split frame");
2240 * Gather back into tabbed views as flagged.
2242 for (SplitFrame sf : gatherTo)
2244 Desktop.instance.gatherViews(sf);
2247 splitFrameCandidates.clear();
2251 * Construct and display one SplitFrame holding DNA and protein alignments.
2254 * @param proteinFrame
2257 protected SplitFrame createSplitFrame(AlignFrame dnaFrame,
2258 AlignFrame proteinFrame)
2260 SplitFrame splitFrame = new SplitFrame(dnaFrame, proteinFrame);
2261 String title = MessageManager.getString("label.linked_view_title");
2262 int width = (int) dnaFrame.getBounds().getWidth();
2263 int height = (int) (dnaFrame.getBounds().getHeight()
2264 + proteinFrame.getBounds().getHeight() + 50);
2265 Desktop.addInternalFrame(splitFrame, title, width, height);
2270 * check errorMessage for a valid error message and raise an error box in the
2271 * GUI or write the current errorMessage to stderr and then clear the error
2274 protected void reportErrors()
2276 reportErrors(false);
2279 protected void reportErrors(final boolean saving)
2281 if (errorMessage != null)
2283 final String finalErrorMessage = errorMessage;
2286 javax.swing.SwingUtilities.invokeLater(new Runnable()
2291 JOptionPane.showInternalMessageDialog(Desktop.desktop,
2292 finalErrorMessage, "Error "
2293 + (saving ? "saving" : "loading")
2294 + " Jalview file", JOptionPane.WARNING_MESSAGE);
2300 System.err.println("Problem loading Jalview file: " + errorMessage);
2303 errorMessage = null;
2306 Map<String, String> alreadyLoadedPDB = new HashMap<String, String>();
2309 * when set, local views will be updated from view stored in JalviewXML
2310 * Currently (28th Sep 2008) things will go horribly wrong in vamsas document
2311 * sync if this is set to true.
2313 private final boolean updateLocalViews = false;
2315 String loadPDBFile(jarInputStreamProvider jprovider, String pdbId)
2317 if (alreadyLoadedPDB.containsKey(pdbId))
2319 return alreadyLoadedPDB.get(pdbId).toString();
2324 JarInputStream jin = jprovider.getJarInputStream();
2326 * if (jprovider.startsWith("http://")) { jin = new JarInputStream(new
2327 * URL(jprovider).openStream()); } else { jin = new JarInputStream(new
2328 * FileInputStream(jprovider)); }
2331 JarEntry entry = null;
2334 entry = jin.getNextJarEntry();
2335 } while (entry != null && !entry.getName().equals(pdbId));
2338 BufferedReader in = new BufferedReader(new InputStreamReader(jin));
2339 File outFile = File.createTempFile("jalview_pdb", ".txt");
2340 outFile.deleteOnExit();
2341 PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
2344 while ((data = in.readLine()) != null)
2351 } catch (Exception foo)
2356 String t = outFile.getAbsolutePath();
2357 alreadyLoadedPDB.put(pdbId, t);
2362 warn("Couldn't find PDB file entry in Jalview Jar for " + pdbId);
2364 } catch (Exception ex)
2366 ex.printStackTrace();
2372 private class JvAnnotRow
2374 public JvAnnotRow(int i, AlignmentAnnotation jaa)
2381 * persisted version of annotation row from which to take vis properties
2383 public jalview.datamodel.AlignmentAnnotation template;
2386 * original position of the annotation row in the alignment
2392 * Load alignment frame from jalview XML DOM object
2397 * filename source string
2398 * @param loadTreesAndStructures
2399 * when false only create Viewport
2401 * data source provider
2402 * @return alignment frame created from view stored in DOM
2404 AlignFrame loadFromObject(JalviewModel object, String file,
2405 boolean loadTreesAndStructures, jarInputStreamProvider jprovider)
2407 SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);
2408 Sequence[] vamsasSeq = vamsasSet.getSequence();
2410 JalviewModelSequence jms = object.getJalviewModelSequence();
2412 Viewport view = (jms.getViewportCount() > 0) ? jms.getViewport(0)
2415 // ////////////////////////////////
2418 List<SequenceI> hiddenSeqs = null;
2419 jalview.datamodel.Sequence jseq;
2421 List<SequenceI> tmpseqs = new ArrayList<SequenceI>();
2423 boolean multipleView = false;
2425 JSeq[] jseqs = object.getJalviewModelSequence().getJSeq();
2426 int vi = 0; // counter in vamsasSeq array
2427 for (int i = 0; i < jseqs.length; i++)
2429 String seqId = jseqs[i].getId();
2431 if (seqRefIds.get(seqId) != null)
2433 tmpseqs.add(seqRefIds.get(seqId));
2434 multipleView = true;
2438 jseq = new jalview.datamodel.Sequence(vamsasSeq[vi].getName(),
2439 vamsasSeq[vi].getSequence());
2440 jseq.setDescription(vamsasSeq[vi].getDescription());
2441 jseq.setStart(jseqs[i].getStart());
2442 jseq.setEnd(jseqs[i].getEnd());
2443 jseq.setVamsasId(uniqueSetSuffix + seqId);
2444 seqRefIds.put(vamsasSeq[vi].getId(), jseq);
2449 if (jseqs[i].getHidden())
2451 if (hiddenSeqs == null)
2453 hiddenSeqs = new ArrayList<SequenceI>();
2456 hiddenSeqs.add(seqRefIds.get(seqId));
2462 // Create the alignment object from the sequence set
2463 // ///////////////////////////////
2464 SequenceI[] orderedSeqs = tmpseqs
2465 .toArray(new SequenceI[tmpseqs.size()]);
2467 Alignment al = new Alignment(orderedSeqs);
2469 // / Add the alignment properties
2470 for (int i = 0; i < vamsasSet.getSequenceSetPropertiesCount(); i++)
2472 SequenceSetProperties ssp = vamsasSet.getSequenceSetProperties(i);
2473 al.setProperty(ssp.getKey(), ssp.getValue());
2477 // SequenceFeatures are added to the DatasetSequence,
2478 // so we must create or recover the dataset before loading features
2479 // ///////////////////////////////
2480 if (vamsasSet.getDatasetId() == null || vamsasSet.getDatasetId() == "")
2482 // older jalview projects do not have a dataset id.
2483 al.setDataset(null);
2487 // recover dataset - passing on flag indicating if this a 'viewless'
2488 // sequence set (a.k.a. a stored dataset for the project)
2489 recoverDatasetFor(vamsasSet, al, object.getJalviewModelSequence()
2490 .getViewportCount() == 0);
2492 // ///////////////////////////////
2494 Hashtable pdbloaded = new Hashtable(); // TODO nothing writes to this??
2497 // load sequence features, database references and any associated PDB
2498 // structures for the alignment
2499 for (int i = 0; i < vamsasSeq.length; i++)
2501 if (jseqs[i].getFeaturesCount() > 0)
2503 Features[] features = jseqs[i].getFeatures();
2504 for (int f = 0; f < features.length; f++)
2506 jalview.datamodel.SequenceFeature sf = new jalview.datamodel.SequenceFeature(
2507 features[f].getType(), features[f].getDescription(),
2508 features[f].getStatus(), features[f].getBegin(),
2509 features[f].getEnd(), features[f].getFeatureGroup());
2511 sf.setScore(features[f].getScore());
2512 for (int od = 0; od < features[f].getOtherDataCount(); od++)
2514 OtherData keyValue = features[f].getOtherData(od);
2515 if (keyValue.getKey().startsWith("LINK"))
2517 sf.addLink(keyValue.getValue());
2521 sf.setValue(keyValue.getKey(), keyValue.getValue());
2526 al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf);
2529 if (vamsasSeq[i].getDBRefCount() > 0)
2531 addDBRefs(al.getSequenceAt(i).getDatasetSequence(), vamsasSeq[i]);
2533 if (jseqs[i].getPdbidsCount() > 0)
2535 Pdbids[] ids = jseqs[i].getPdbids();
2536 for (int p = 0; p < ids.length; p++)
2538 jalview.datamodel.PDBEntry entry = new jalview.datamodel.PDBEntry();
2539 entry.setId(ids[p].getId());
2540 entry.setType(ids[p].getType());
2541 if (ids[p].getFile() != null)
2543 if (!pdbloaded.containsKey(ids[p].getFile()))
2545 entry.setFile(loadPDBFile(jprovider, ids[p].getId()));
2549 entry.setFile(pdbloaded.get(ids[p].getId()).toString());
2552 StructureSelectionManager.getStructureSelectionManager(
2553 Desktop.instance).registerPDBEntry(entry);
2554 al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
2558 } // end !multipleview
2560 // ///////////////////////////////
2561 // LOAD SEQUENCE MAPPINGS
2563 if (vamsasSet.getAlcodonFrameCount() > 0)
2565 // TODO Potentially this should only be done once for all views of an
2567 AlcodonFrame[] alc = vamsasSet.getAlcodonFrame();
2568 for (int i = 0; i < alc.length; i++)
2570 AlignedCodonFrame cf = new AlignedCodonFrame();
2571 if (alc[i].getAlcodMapCount() > 0)
2573 AlcodMap[] maps = alc[i].getAlcodMap();
2574 for (int m = 0; m < maps.length; m++)
2576 SequenceI dnaseq = seqRefIds.get(maps[m].getDnasq());
2578 jalview.datamodel.Mapping mapping = null;
2579 // attach to dna sequence reference.
2580 if (maps[m].getMapping() != null)
2582 mapping = addMapping(maps[m].getMapping());
2586 cf.addMap(dnaseq, mapping.getTo(), mapping.getMap());
2591 frefedSequence.add(new Object[]
2592 { maps[m].getDnasq(), cf, mapping });
2596 al.addCodonFrame(cf);
2600 // ////////////////////////////////
2602 List<JvAnnotRow> autoAlan = new ArrayList<JvAnnotRow>();
2604 * store any annotations which forward reference a group's ID
2606 Hashtable<String, ArrayList<jalview.datamodel.AlignmentAnnotation>> groupAnnotRefs = new Hashtable<String, ArrayList<jalview.datamodel.AlignmentAnnotation>>();
2608 if (vamsasSet.getAnnotationCount() > 0)
2610 Annotation[] an = vamsasSet.getAnnotation();
2612 for (int i = 0; i < an.length; i++)
2615 * test if annotation is automatically calculated for this view only
2617 boolean autoForView = false;
2618 if (an[i].getLabel().equals("Quality")
2619 || an[i].getLabel().equals("Conservation")
2620 || an[i].getLabel().equals("Consensus"))
2622 // Kludge for pre 2.5 projects which lacked the autocalculated flag
2624 if (!an[i].hasAutoCalculated())
2626 an[i].setAutoCalculated(true);
2630 || (an[i].hasAutoCalculated() && an[i].isAutoCalculated()))
2632 // remove ID - we don't recover annotation from other views for
2633 // view-specific annotation
2637 // set visiblity for other annotation in this view
2638 if (an[i].getId() != null
2639 && annotationIds.containsKey(an[i].getId()))
2641 AlignmentAnnotation jda = annotationIds.get(an[i].getId());
2642 // in principle Visible should always be true for annotation displayed
2643 // in multiple views
2644 if (an[i].hasVisible())
2646 jda.visible = an[i].getVisible();
2649 al.addAnnotation(jda);
2653 // Construct new annotation from model.
2654 AnnotationElement[] ae = an[i].getAnnotationElement();
2655 jalview.datamodel.Annotation[] anot = null;
2656 java.awt.Color firstColour = null;
2658 if (!an[i].getScoreOnly())
2660 anot = new jalview.datamodel.Annotation[al.getWidth()];
2661 for (int aa = 0; aa < ae.length && aa < anot.length; aa++)
2663 anpos = ae[aa].getPosition();
2665 if (anpos >= anot.length)
2670 anot[anpos] = new jalview.datamodel.Annotation(
2672 ae[aa].getDisplayCharacter(), ae[aa].getDescription(),
2673 (ae[aa].getSecondaryStructure() == null || ae[aa]
2674 .getSecondaryStructure().length() == 0) ? ' '
2675 : ae[aa].getSecondaryStructure().charAt(0),
2679 // JBPNote: Consider verifying dataflow for IO of secondary
2680 // structure annotation read from Stockholm files
2681 // this was added to try to ensure that
2682 // if (anot[ae[aa].getPosition()].secondaryStructure>' ')
2684 // anot[ae[aa].getPosition()].displayCharacter = "";
2686 anot[anpos].colour = new java.awt.Color(ae[aa].getColour());
2687 if (firstColour == null)
2689 firstColour = anot[anpos].colour;
2693 jalview.datamodel.AlignmentAnnotation jaa = null;
2695 if (an[i].getGraph())
2697 float llim = 0, hlim = 0;
2698 // if (autoForView || an[i].isAutoCalculated()) {
2701 jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
2702 an[i].getDescription(), anot, llim, hlim,
2703 an[i].getGraphType());
2705 jaa.graphGroup = an[i].getGraphGroup();
2706 jaa._linecolour = firstColour;
2707 if (an[i].getThresholdLine() != null)
2709 jaa.setThreshold(new jalview.datamodel.GraphLine(an[i]
2710 .getThresholdLine().getValue(), an[i]
2711 .getThresholdLine().getLabel(), new java.awt.Color(
2712 an[i].getThresholdLine().getColour())));
2715 if (autoForView || an[i].isAutoCalculated())
2717 // Hardwire the symbol display line to ensure that labels for
2718 // histograms are displayed
2724 jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
2725 an[i].getDescription(), anot);
2726 jaa._linecolour = firstColour;
2728 // register new annotation
2729 if (an[i].getId() != null)
2731 annotationIds.put(an[i].getId(), jaa);
2732 jaa.annotationId = an[i].getId();
2734 // recover sequence association
2735 if (an[i].getSequenceRef() != null)
2737 if (al.findName(an[i].getSequenceRef()) != null)
2739 jaa.createSequenceMapping(al.findName(an[i].getSequenceRef()),
2741 al.findName(an[i].getSequenceRef()).addAlignmentAnnotation(jaa);
2744 // and make a note of any group association
2745 if (an[i].getGroupRef() != null && an[i].getGroupRef().length() > 0)
2747 ArrayList<jalview.datamodel.AlignmentAnnotation> aal = groupAnnotRefs
2748 .get(an[i].getGroupRef());
2751 aal = new ArrayList<jalview.datamodel.AlignmentAnnotation>();
2752 groupAnnotRefs.put(an[i].getGroupRef(), aal);
2757 if (an[i].hasScore())
2759 jaa.setScore(an[i].getScore());
2761 if (an[i].hasVisible())
2763 jaa.visible = an[i].getVisible();
2766 if (an[i].hasCentreColLabels())
2768 jaa.centreColLabels = an[i].getCentreColLabels();
2771 if (an[i].hasScaleColLabels())
2773 jaa.scaleColLabel = an[i].getScaleColLabels();
2775 if (an[i].hasAutoCalculated() && an[i].isAutoCalculated())
2777 // newer files have an 'autoCalculated' flag and store calculation
2778 // state in viewport properties
2779 jaa.autoCalculated = true; // means annotation will be marked for
2780 // update at end of load.
2782 if (an[i].hasGraphHeight())
2784 jaa.graphHeight = an[i].getGraphHeight();
2786 if (an[i].hasBelowAlignment())
2788 jaa.belowAlignment = an[i].isBelowAlignment();
2790 jaa.setCalcId(an[i].getCalcId());
2791 if (an[i].getPropertyCount() > 0)
2793 for (jalview.schemabinding.version2.Property prop : an[i]
2796 jaa.setProperty(prop.getName(), prop.getValue());
2799 if (jaa.autoCalculated)
2801 autoAlan.add(new JvAnnotRow(i, jaa));
2804 // if (!autoForView)
2806 // add autocalculated group annotation and any user created annotation
2808 al.addAnnotation(jaa);
2812 // ///////////////////////
2814 // Create alignment markup and styles for this view
2815 if (jms.getJGroupCount() > 0)
2817 JGroup[] groups = jms.getJGroup();
2818 boolean addAnnotSchemeGroup = false;
2819 for (int i = 0; i < groups.length; i++)
2821 ColourSchemeI cs = null;
2823 if (groups[i].getColour() != null)
2825 if (groups[i].getColour().startsWith("ucs"))
2827 cs = getUserColourScheme(jms, groups[i].getColour());
2829 else if (groups[i].getColour().equals("AnnotationColourGradient")
2830 && groups[i].getAnnotationColours() != null)
2832 addAnnotSchemeGroup = true;
2837 cs = ColourSchemeProperty.getColour(al, groups[i].getColour());
2842 cs.setThreshold(groups[i].getPidThreshold(), true);
2846 Vector seqs = new Vector();
2848 for (int s = 0; s < groups[i].getSeqCount(); s++)
2850 String seqId = groups[i].getSeq(s) + "";
2851 jalview.datamodel.SequenceI ts = seqRefIds.get(seqId);
2855 seqs.addElement(ts);
2859 if (seqs.size() < 1)
2864 jalview.datamodel.SequenceGroup sg = new jalview.datamodel.SequenceGroup(
2865 seqs, groups[i].getName(), cs, groups[i].getDisplayBoxes(),
2866 groups[i].getDisplayText(), groups[i].getColourText(),
2867 groups[i].getStart(), groups[i].getEnd());
2869 sg.setOutlineColour(new java.awt.Color(groups[i].getOutlineColour()));
2871 sg.textColour = new java.awt.Color(groups[i].getTextCol1());
2872 sg.textColour2 = new java.awt.Color(groups[i].getTextCol2());
2873 sg.setShowNonconserved(groups[i].hasShowUnconserved() ? groups[i]
2874 .isShowUnconserved() : false);
2875 sg.thresholdTextColour = groups[i].getTextColThreshold();
2876 if (groups[i].hasShowConsensusHistogram())
2878 sg.setShowConsensusHistogram(groups[i].isShowConsensusHistogram());
2881 if (groups[i].hasShowSequenceLogo())
2883 sg.setshowSequenceLogo(groups[i].isShowSequenceLogo());
2885 if (groups[i].hasNormaliseSequenceLogo())
2887 sg.setNormaliseSequenceLogo(groups[i].isNormaliseSequenceLogo());
2889 if (groups[i].hasIgnoreGapsinConsensus())
2891 sg.setIgnoreGapsConsensus(groups[i].getIgnoreGapsinConsensus());
2893 if (groups[i].getConsThreshold() != 0)
2895 jalview.analysis.Conservation c = new jalview.analysis.Conservation(
2896 "All", ResidueProperties.propHash, 3,
2897 sg.getSequences(null), 0, sg.getWidth() - 1);
2899 c.verdict(false, 25);
2900 sg.cs.setConservation(c);
2903 if (groups[i].getId() != null && groupAnnotRefs.size() > 0)
2905 // re-instate unique group/annotation row reference
2906 ArrayList<jalview.datamodel.AlignmentAnnotation> jaal = groupAnnotRefs
2907 .get(groups[i].getId());
2910 for (jalview.datamodel.AlignmentAnnotation jaa : jaal)
2913 if (jaa.autoCalculated)
2915 // match up and try to set group autocalc alignment row for this
2917 if (jaa.label.startsWith("Consensus for "))
2919 sg.setConsensus(jaa);
2921 // match up and try to set group autocalc alignment row for this
2923 if (jaa.label.startsWith("Conservation for "))
2925 sg.setConservationRow(jaa);
2932 if (addAnnotSchemeGroup)
2934 // reconstruct the annotation colourscheme
2935 sg.cs = constructAnnotationColour(
2936 groups[i].getAnnotationColours(), null, al, jms, false);
2942 // only dataset in this model, so just return.
2945 // ///////////////////////////////
2948 // If we just load in the same jar file again, the sequenceSetId
2949 // will be the same, and we end up with multiple references
2950 // to the same sequenceSet. We must modify this id on load
2951 // so that each load of the file gives a unique id
2952 String uniqueSeqSetId = view.getSequenceSetId() + uniqueSetSuffix;
2953 String viewId = (view.getId() == null ? null : view.getId()
2955 AlignFrame af = null;
2956 AlignViewport av = null;
2957 // now check to see if we really need to create a new viewport.
2958 if (multipleView && viewportsAdded.size() == 0)
2960 // We recovered an alignment for which a viewport already exists.
2961 // TODO: fix up any settings necessary for overlaying stored state onto
2962 // state recovered from another document. (may not be necessary).
2963 // we may need a binding from a viewport in memory to one recovered from
2965 // and then recover its containing af to allow the settings to be applied.
2966 // TODO: fix for vamsas demo
2968 .println("About to recover a viewport for existing alignment: Sequence set ID is "
2970 Object seqsetobj = retrieveExistingObj(uniqueSeqSetId);
2971 if (seqsetobj != null)
2973 if (seqsetobj instanceof String)
2975 uniqueSeqSetId = (String) seqsetobj;
2977 .println("Recovered extant sequence set ID mapping for ID : New Sequence set ID is "
2983 .println("Warning : Collision between sequence set ID string and existing jalview object mapping.");
2989 * indicate that annotation colours are applied across all groups (pre
2990 * Jalview 2.8.1 behaviour)
2992 boolean doGroupAnnColour = isVersionStringLaterThan("2.8.1",
2993 object.getVersion());
2995 AlignmentPanel ap = null;
2996 boolean isnewview = true;
2999 // Check to see if this alignment already has a view id == viewId
3000 jalview.gui.AlignmentPanel views[] = Desktop
3001 .getAlignmentPanels(uniqueSeqSetId);
3002 if (views != null && views.length > 0)
3004 for (int v = 0; v < views.length; v++)
3006 if (views[v].av.getViewId().equalsIgnoreCase(viewId))
3008 // recover the existing alignpanel, alignframe, viewport
3009 af = views[v].alignFrame;
3012 // TODO: could even skip resetting view settings if we don't want to
3013 // change the local settings from other jalview processes
3022 af = loadViewport(file, jseqs, hiddenSeqs, al, jms, view,
3023 uniqueSeqSetId, viewId, autoAlan);
3028 // /////////////////////////////////////
3029 if (loadTreesAndStructures && jms.getTreeCount() > 0)
3033 for (int t = 0; t < jms.getTreeCount(); t++)
3036 Tree tree = jms.getTree(t);
3038 TreePanel tp = (TreePanel) retrieveExistingObj(tree.getId());
3041 tp = af.ShowNewickTree(
3042 new jalview.io.NewickFile(tree.getNewick()),
3043 tree.getTitle(), tree.getWidth(), tree.getHeight(),
3044 tree.getXpos(), tree.getYpos());
3045 if (tree.getId() != null)
3047 // perhaps bind the tree id to something ?
3052 // update local tree attributes ?
3053 // TODO: should check if tp has been manipulated by user - if so its
3054 // settings shouldn't be modified
3055 tp.setTitle(tree.getTitle());
3056 tp.setBounds(new Rectangle(tree.getXpos(), tree.getYpos(), tree
3057 .getWidth(), tree.getHeight()));
3058 tp.av = av; // af.viewport; // TODO: verify 'associate with all
3061 tp.treeCanvas.av = av; // af.viewport;
3062 tp.treeCanvas.ap = ap; // af.alignPanel;
3067 warn("There was a problem recovering stored Newick tree: \n"
3068 + tree.getNewick());
3072 tp.fitToWindow.setState(tree.getFitToWindow());
3073 tp.fitToWindow_actionPerformed(null);
3075 if (tree.getFontName() != null)
3077 tp.setTreeFont(new java.awt.Font(tree.getFontName(), tree
3078 .getFontStyle(), tree.getFontSize()));
3082 tp.setTreeFont(new java.awt.Font(view.getFontName(), view
3083 .getFontStyle(), tree.getFontSize()));
3086 tp.showPlaceholders(tree.getMarkUnlinked());
3087 tp.showBootstrap(tree.getShowBootstrap());
3088 tp.showDistances(tree.getShowDistances());
3090 tp.treeCanvas.threshold = tree.getThreshold();
3092 if (tree.getCurrentTree())
3094 af.viewport.setCurrentTree(tp.getTree());
3098 } catch (Exception ex)
3100 ex.printStackTrace();
3104 // //LOAD STRUCTURES
3105 if (loadTreesAndStructures)
3107 loadStructures(jprovider, jseqs, af, ap);
3109 // and finally return.
3114 * Load and link any saved structure viewers.
3121 protected void loadStructures(jarInputStreamProvider jprovider,
3122 JSeq[] jseqs, AlignFrame af, AlignmentPanel ap)
3125 * Run through all PDB ids on the alignment, and collect mappings between
3126 * distinct view ids and all sequences referring to that view.
3128 Map<String, StructureViewerModel> structureViewers = new LinkedHashMap<String, StructureViewerModel>();
3130 for (int i = 0; i < jseqs.length; i++)
3132 if (jseqs[i].getPdbidsCount() > 0)
3134 Pdbids[] ids = jseqs[i].getPdbids();
3135 for (int p = 0; p < ids.length; p++)
3137 final int structureStateCount = ids[p].getStructureStateCount();
3138 for (int s = 0; s < structureStateCount; s++)
3140 // check to see if we haven't already created this structure view
3141 final StructureState structureState = ids[p]
3142 .getStructureState(s);
3143 String sviewid = (structureState.getViewId() == null) ? null
3144 : structureState.getViewId() + uniqueSetSuffix;
3145 jalview.datamodel.PDBEntry jpdb = new jalview.datamodel.PDBEntry();
3146 // Originally : ids[p].getFile()
3147 // : TODO: verify external PDB file recovery still works in normal
3148 // jalview project load
3149 jpdb.setFile(loadPDBFile(jprovider, ids[p].getId()));
3150 jpdb.setId(ids[p].getId());
3152 int x = structureState.getXpos();
3153 int y = structureState.getYpos();
3154 int width = structureState.getWidth();
3155 int height = structureState.getHeight();
3157 // Probably don't need to do this anymore...
3158 // Desktop.desktop.getComponentAt(x, y);
3159 // TODO: NOW: check that this recovers the PDB file correctly.
3160 String pdbFile = loadPDBFile(jprovider, ids[p].getId());
3161 jalview.datamodel.SequenceI seq = seqRefIds.get(jseqs[i]
3163 if (sviewid == null)
3165 sviewid = "_jalview_pre2_4_" + x + "," + y + "," + width
3168 if (!structureViewers.containsKey(sviewid))
3170 structureViewers.put(sviewid, new StructureViewerModel(x, y,
3171 width, height, false, false, true));
3172 // Legacy pre-2.7 conversion JAL-823 :
3173 // do not assume any view has to be linked for colour by
3177 // assemble String[] { pdb files }, String[] { id for each
3178 // file }, orig_fileloc, SequenceI[][] {{ seqs_file 1 }, {
3179 // seqs_file 2}, boolean[] {
3180 // linkAlignPanel,superposeWithAlignpanel}} from hash
3181 StructureViewerModel jmoldat = structureViewers.get(sviewid);
3182 jmoldat.setAlignWithPanel(jmoldat.isAlignWithPanel()
3183 | (structureState.hasAlignwithAlignPanel() ? structureState
3184 .getAlignwithAlignPanel() : false));
3187 * Default colour by linked panel to false if not specified (e.g.
3188 * for pre-2.7 projects)
3190 boolean colourWithAlignPanel = jmoldat.isColourWithAlignPanel();
3191 colourWithAlignPanel |= (structureState
3192 .hasColourwithAlignPanel() ? structureState
3193 .getColourwithAlignPanel() : false);
3194 jmoldat.setColourWithAlignPanel(colourWithAlignPanel);
3197 * Default colour by viewer to true if not specified (e.g. for
3200 boolean colourByViewer = jmoldat.isColourByViewer();
3201 colourByViewer &= structureState.hasColourByJmol() ? structureState
3202 .getColourByJmol() : true;
3203 jmoldat.setColourByViewer(colourByViewer);
3205 if (jmoldat.getStateData().length() < structureState
3206 .getContent().length())
3209 jmoldat.setStateData(structureState.getContent());
3212 if (ids[p].getFile() != null)
3214 File mapkey = new File(ids[p].getFile());
3215 StructureData seqstrmaps = jmoldat.getFileData().get(mapkey);
3216 if (seqstrmaps == null)
3218 jmoldat.getFileData().put(
3220 seqstrmaps = jmoldat.new StructureData(pdbFile,
3223 if (!seqstrmaps.getSeqList().contains(seq))
3225 seqstrmaps.getSeqList().add(seq);
3231 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");
3238 // Instantiate the associated structure views
3239 for (Entry<String, StructureViewerModel> entry : structureViewers
3242 createOrLinkStructureViewer(entry, af, ap);
3252 protected void createOrLinkStructureViewer(
3253 Entry<String, StructureViewerModel> viewerData, AlignFrame af,
3256 final StructureViewerModel svattrib = viewerData.getValue();
3259 * Search for any viewer windows already open from other alignment views
3260 * that exactly match the stored structure state
3262 StructureViewerBase comp = findMatchingViewer(viewerData);
3266 linkStructureViewer(ap, comp, svattrib);
3271 * Pending an XML element for ViewerType, just check if stateData contains
3272 * "chimera" (part of the chimera session filename).
3274 if (svattrib.getStateData().indexOf("chimera") > -1)
3276 createChimeraViewer(viewerData, af);
3280 createJmolViewer(viewerData, af);
3285 * Create a new Chimera viewer.
3290 protected void createChimeraViewer(
3291 Entry<String, StructureViewerModel> viewerData, AlignFrame af)
3293 final StructureViewerModel data = viewerData.getValue();
3294 String chimeraSession = data.getStateData();
3296 if (new File(chimeraSession).exists())
3298 Set<Entry<File, StructureData>> fileData = data.getFileData()
3300 List<PDBEntry> pdbs = new ArrayList<PDBEntry>();
3301 List<SequenceI[]> allseqs = new ArrayList<SequenceI[]>();
3302 for (Entry<File, StructureData> pdb : fileData)
3304 String filePath = pdb.getValue().getFilePath();
3305 String pdbId = pdb.getValue().getPdbId();
3306 pdbs.add(new PDBEntry(filePath, pdbId));
3307 final List<SequenceI> seqList = pdb.getValue().getSeqList();
3308 SequenceI[] seqs = seqList.toArray(new SequenceI[seqList.size()]);
3312 boolean colourByChimera = data.isColourByViewer();
3313 boolean colourBySequence = data.isColourWithAlignPanel();
3315 // TODO can/should this be done via StructureViewer (like Jmol)?
3316 final PDBEntry[] pdbArray = pdbs.toArray(new PDBEntry[pdbs.size()]);
3317 final SequenceI[][] seqsArray = allseqs.toArray(new SequenceI[allseqs
3319 new ChimeraViewFrame(chimeraSession, af.alignPanel, pdbArray,
3320 seqsArray, colourByChimera, colourBySequence);
3324 Cache.log.error("Chimera session file " + chimeraSession
3330 * Create a new Jmol window. First parse the Jmol state to translate filenames
3331 * loaded into the view, and record the order in which files are shown in the
3332 * Jmol view, so we can add the sequence mappings in same order.
3337 protected void createJmolViewer(
3338 final Entry<String, StructureViewerModel> viewerData,
3341 final StructureViewerModel svattrib = viewerData.getValue();
3342 String state = svattrib.getStateData();
3343 List<String> pdbfilenames = new ArrayList<String>();
3344 List<SequenceI[]> seqmaps = new ArrayList<SequenceI[]>();
3345 List<String> pdbids = new ArrayList<String>();
3346 StringBuilder newFileLoc = new StringBuilder(64);
3347 int cp = 0, ncp, ecp;
3348 Map<File, StructureData> oldFiles = svattrib.getFileData();
3349 while ((ncp = state.indexOf("load ", cp)) > -1)
3353 // look for next filename in load statement
3354 newFileLoc.append(state.substring(cp,
3355 ncp = (state.indexOf("\"", ncp + 1) + 1)));
3356 String oldfilenam = state.substring(ncp,
3357 ecp = state.indexOf("\"", ncp));
3358 // recover the new mapping data for this old filename
3359 // have to normalize filename - since Jmol and jalview do
3361 // translation differently.
3362 StructureData filedat = oldFiles.get(new File(oldfilenam));
3363 newFileLoc.append(Platform.escapeString(filedat.getFilePath()));
3364 pdbfilenames.add(filedat.getFilePath());
3365 pdbids.add(filedat.getPdbId());
3366 seqmaps.add(filedat.getSeqList().toArray(new SequenceI[0]));
3367 newFileLoc.append("\"");
3368 cp = ecp + 1; // advance beyond last \" and set cursor so we can
3369 // look for next file statement.
3370 } while ((ncp = state.indexOf("/*file*/", cp)) > -1);
3374 // just append rest of state
3375 newFileLoc.append(state.substring(cp));
3379 System.err.print("Ignoring incomplete Jmol state for PDB ids: ");
3380 newFileLoc = new StringBuilder(state);
3381 newFileLoc.append("; load append ");
3382 for (File id : oldFiles.keySet())
3384 // add this and any other pdb files that should be present in
3386 StructureData filedat = oldFiles.get(id);
3387 newFileLoc.append(filedat.getFilePath());
3388 pdbfilenames.add(filedat.getFilePath());
3389 pdbids.add(filedat.getPdbId());
3390 seqmaps.add(filedat.getSeqList().toArray(new SequenceI[0]));
3391 newFileLoc.append(" \"");
3392 newFileLoc.append(filedat.getFilePath());
3393 newFileLoc.append("\"");
3396 newFileLoc.append(";");
3399 if (newFileLoc.length() > 0)
3401 int histbug = newFileLoc.indexOf("history = ");
3403 int diff = histbug == -1 ? -1 : newFileLoc.indexOf(";", histbug);
3404 String val = (diff == -1) ? null : newFileLoc
3405 .substring(histbug, diff);
3406 if (val != null && val.length() >= 4)
3408 if (val.contains("e"))
3410 if (val.trim().equals("true"))
3418 newFileLoc.replace(histbug, diff, val);
3422 final String[] pdbf = pdbfilenames.toArray(new String[pdbfilenames
3424 final String[] id = pdbids.toArray(new String[pdbids.size()]);
3425 final SequenceI[][] sq = seqmaps
3426 .toArray(new SequenceI[seqmaps.size()][]);
3427 final String fileloc = newFileLoc.toString();
3428 final String sviewid = viewerData.getKey();
3429 final AlignFrame alf = af;
3430 final Rectangle rect = new Rectangle(svattrib.getX(),
3431 svattrib.getY(), svattrib.getWidth(), svattrib.getHeight());
3434 javax.swing.SwingUtilities.invokeAndWait(new Runnable()
3439 JalviewStructureDisplayI sview = null;
3442 // JAL-1333 note - we probably can't migrate Jmol views to UCSF
3444 sview = new StructureViewer(alf.alignPanel
3445 .getStructureSelectionManager()).createView(
3446 StructureViewer.ViewerType.JMOL, pdbf, id, sq,
3447 alf.alignPanel, svattrib, fileloc, rect, sviewid);
3448 addNewStructureViewer(sview);
3449 } catch (OutOfMemoryError ex)
3451 new OOMWarning("restoring structure view for PDB id " + id,
3452 (OutOfMemoryError) ex.getCause());
3453 if (sview != null && sview.isVisible())
3455 sview.closeViewer();
3456 sview.setVisible(false);
3462 } catch (InvocationTargetException ex)
3464 warn("Unexpected error when opening Jmol view.", ex);
3466 } catch (InterruptedException e)
3468 // e.printStackTrace();
3474 * Returns any open frame that matches given structure viewer data. The match
3475 * is based on the unique viewId, or (for older project versions) the frame's
3481 protected StructureViewerBase findMatchingViewer(
3482 Entry<String, StructureViewerModel> viewerData)
3484 final String sviewid = viewerData.getKey();
3485 final StructureViewerModel svattrib = viewerData.getValue();
3486 StructureViewerBase comp = null;
3487 JInternalFrame[] frames = getAllFrames();
3488 for (JInternalFrame frame : frames)
3490 if (frame instanceof StructureViewerBase)
3493 * Post jalview 2.4 schema includes structure view id
3496 && ((StructureViewerBase) frame).getViewId()
3499 comp = (AppJmol) frame;
3503 * Otherwise test for matching position and size of viewer frame
3505 else if (frame.getX() == svattrib.getX()
3506 && frame.getY() == svattrib.getY()
3507 && frame.getHeight() == svattrib.getHeight()
3508 && frame.getWidth() == svattrib.getWidth())
3510 comp = (AppJmol) frame;
3519 * Link an AlignmentPanel to an existing structure viewer.
3524 * @param useinViewerSuperpos
3525 * @param usetoColourbyseq
3526 * @param viewerColouring
3528 protected void linkStructureViewer(AlignmentPanel ap,
3529 StructureViewerBase viewer, StructureViewerModel svattrib)
3531 // NOTE: if the jalview project is part of a shared session then
3532 // view synchronization should/could be done here.
3534 final boolean useinViewerSuperpos = svattrib.isAlignWithPanel();
3535 final boolean usetoColourbyseq = svattrib.isColourWithAlignPanel();
3536 final boolean viewerColouring = svattrib.isColourByViewer();
3537 Map<File, StructureData> oldFiles = svattrib.getFileData();
3540 * Add mapping for sequences in this view to an already open viewer
3542 final AAStructureBindingModel binding = viewer.getBinding();
3543 for (File id : oldFiles.keySet())
3545 // add this and any other pdb files that should be present in the
3547 StructureData filedat = oldFiles.get(id);
3548 String pdbFile = filedat.getFilePath();
3549 SequenceI[] seq = filedat.getSeqList().toArray(new SequenceI[0]);
3550 binding.getSsm().setMapping(seq, null, pdbFile,
3551 jalview.io.AppletFormatAdapter.FILE);
3552 binding.addSequenceForStructFile(pdbFile, seq);
3554 // and add the AlignmentPanel's reference to the view panel
3555 viewer.addAlignmentPanel(ap);
3556 if (useinViewerSuperpos)
3558 viewer.useAlignmentPanelForSuperposition(ap);
3562 viewer.excludeAlignmentPanelForSuperposition(ap);
3564 if (usetoColourbyseq)
3566 viewer.useAlignmentPanelForColourbyseq(ap, !viewerColouring);
3570 viewer.excludeAlignmentPanelForColourbyseq(ap);
3575 * Get all frames within the Desktop.
3579 protected JInternalFrame[] getAllFrames()
3581 JInternalFrame[] frames = null;
3582 // TODO is this necessary - is it safe - risk of hanging?
3587 frames = Desktop.desktop.getAllFrames();
3588 } catch (ArrayIndexOutOfBoundsException e)
3590 // occasional No such child exceptions are thrown here...
3594 } catch (InterruptedException f)
3598 } while (frames == null);
3605 * - minimum version we are comparing against
3607 * - version of data being processsed.
3608 * @return true if version is development/null or evaluates to the same or
3609 * later X.Y.Z (where X,Y,Z are like [0-9]+b?[0-9]*)
3611 private boolean isVersionStringLaterThan(String supported, String version)
3613 if (version == null || version.equalsIgnoreCase("DEVELOPMENT BUILD")
3614 || version.equalsIgnoreCase("Test")
3615 || version.equalsIgnoreCase("AUTOMATED BUILD"))
3617 System.err.println("Assuming project file with "
3618 + (version == null ? "null" : version)
3619 + " is compatible with Jalview version " + supported);
3624 StringTokenizer currentV = new StringTokenizer(supported, "."), fileV = new StringTokenizer(
3626 while (currentV.hasMoreTokens() && fileV.hasMoreTokens())
3628 // convert b to decimal to catch bugfix releases within a series
3629 String curT = currentV.nextToken().toLowerCase().replace('b', '.');
3630 String fileT = fileV.nextToken().toLowerCase().replace('b', '.');
3633 if (Float.valueOf(curT) > Float.valueOf(fileT))
3635 // current version is newer than the version that wrote the file
3638 } catch (NumberFormatException nfe)
3641 .println("** WARNING: Version comparison failed for tokens ("
3645 + ")\n** Current: '"
3646 + supported + "' and Version: '" + version + "'");
3649 if (currentV.hasMoreElements())
3651 // fileV has no minor version but identical series to current
3658 Vector<JalviewStructureDisplayI> newStructureViewers = null;
3660 protected void addNewStructureViewer(JalviewStructureDisplayI sview)
3662 if (newStructureViewers != null)
3664 sview.getBinding().setFinishedLoadingFromArchive(false);
3665 newStructureViewers.add(sview);
3669 protected void setLoadingFinishedForNewStructureViewers()
3671 if (newStructureViewers != null)
3673 for (JalviewStructureDisplayI sview : newStructureViewers)
3675 sview.getBinding().setFinishedLoadingFromArchive(true);
3677 newStructureViewers.clear();
3678 newStructureViewers = null;
3682 AlignFrame loadViewport(String file, JSeq[] JSEQ,
3683 List<SequenceI> hiddenSeqs, Alignment al,
3684 JalviewModelSequence jms, Viewport view, String uniqueSeqSetId,
3685 String viewId, List<JvAnnotRow> autoAlan)
3687 AlignFrame af = null;
3688 af = new AlignFrame(al, view.getWidth(), view.getHeight(),
3689 uniqueSeqSetId, viewId);
3691 af.setFileName(file, "Jalview");
3693 for (int i = 0; i < JSEQ.length; i++)
3695 af.viewport.setSequenceColour(af.viewport.getAlignment()
3696 .getSequenceAt(i), new java.awt.Color(JSEQ[i].getColour()));
3699 af.viewport.setGatherViewsHere(view.getGatheredViews());
3701 if (view.getSequenceSetId() != null)
3703 AlignmentViewport av = viewportsAdded.get(uniqueSeqSetId);
3705 af.viewport.setSequenceSetId(uniqueSeqSetId);
3708 // propagate shared settings to this new view
3709 af.viewport.setHistoryList(av.getHistoryList());
3710 af.viewport.setRedoList(av.getRedoList());
3714 viewportsAdded.put(uniqueSeqSetId, af.viewport);
3716 // TODO: check if this method can be called repeatedly without
3717 // side-effects if alignpanel already registered.
3718 PaintRefresher.Register(af.alignPanel, uniqueSeqSetId);
3720 // apply Hidden regions to view.
3721 if (hiddenSeqs != null)
3723 for (int s = 0; s < JSEQ.length; s++)
3725 jalview.datamodel.SequenceGroup hidden = new jalview.datamodel.SequenceGroup();
3727 for (int r = 0; r < JSEQ[s].getHiddenSequencesCount(); r++)
3730 al.getSequenceAt(JSEQ[s].getHiddenSequences(r)), false);
3732 af.viewport.hideRepSequences(al.getSequenceAt(s), hidden);
3735 // jalview.datamodel.SequenceI[] hseqs = new
3736 // jalview.datamodel.SequenceI[hiddenSeqs
3739 // for (int s = 0; s < hiddenSeqs.size(); s++)
3741 // hseqs[s] = (jalview.datamodel.SequenceI) hiddenSeqs.elementAt(s);
3744 SequenceI[] hseqs = hiddenSeqs.toArray(new SequenceI[hiddenSeqs
3746 af.viewport.hideSequence(hseqs);
3749 // recover view properties and display parameters
3750 if (view.getViewName() != null)
3752 af.viewport.viewName = view.getViewName();
3753 af.setInitialTabVisible();
3755 af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),
3758 af.viewport.setShowAnnotation(view.getShowAnnotation());
3759 af.viewport.setAbovePIDThreshold(view.getPidSelected());
3761 af.viewport.setColourText(view.getShowColourText());
3763 af.viewport.setConservationSelected(view.getConservationSelected());
3764 af.viewport.setShowJVSuffix(view.getShowFullId());
3765 af.viewport.setRightAlignIds(view.getRightAlignIds());
3766 af.viewport.setFont(
3767 new java.awt.Font(view.getFontName(), view.getFontStyle(), view
3768 .getFontSize()), true);
3769 // TODO: allow custom charWidth/Heights to be restored by updating them
3770 // after setting font - which means set above to false
3771 af.viewport.setRenderGaps(view.getRenderGaps());
3772 af.viewport.setWrapAlignment(view.getWrapAlignment());
3773 af.viewport.setShowAnnotation(view.getShowAnnotation());
3775 af.viewport.setShowBoxes(view.getShowBoxes());
3777 af.viewport.setShowText(view.getShowText());
3779 af.viewport.setTextColour(new java.awt.Color(view.getTextCol1()));
3780 af.viewport.setTextColour2(new java.awt.Color(view.getTextCol2()));
3781 af.viewport.setThresholdTextColour(view.getTextColThreshold());
3782 af.viewport.setShowUnconserved(view.hasShowUnconserved() ? view
3783 .isShowUnconserved() : false);
3784 af.viewport.setStartRes(view.getStartRes());
3785 af.viewport.setStartSeq(view.getStartSeq());
3786 af.alignPanel.updateLayout();
3787 ColourSchemeI cs = null;
3788 // apply colourschemes
3789 if (view.getBgColour() != null)
3791 if (view.getBgColour().startsWith("ucs"))
3793 cs = getUserColourScheme(jms, view.getBgColour());
3795 else if (view.getBgColour().startsWith("Annotation"))
3797 AnnotationColours viewAnnColour = view.getAnnotationColours();
3798 cs = constructAnnotationColour(viewAnnColour, af, al, jms, true);
3805 cs = ColourSchemeProperty.getColour(al, view.getBgColour());
3810 cs.setThreshold(view.getPidThreshold(), true);
3811 cs.setConsensus(af.viewport.getSequenceConsensusHash());
3815 af.viewport.setGlobalColourScheme(cs);
3816 af.viewport.setColourAppliesToAllGroups(false);
3818 if (view.getConservationSelected() && cs != null)
3820 cs.setConservationInc(view.getConsThreshold());
3823 af.changeColour(cs);
3825 af.viewport.setColourAppliesToAllGroups(true);
3827 af.viewport.setShowSequenceFeatures(view.getShowSequenceFeatures());
3829 if (view.hasCentreColumnLabels())
3831 af.viewport.setCentreColumnLabels(view.getCentreColumnLabels());
3833 if (view.hasIgnoreGapsinConsensus())
3835 af.viewport.setIgnoreGapsConsensus(view.getIgnoreGapsinConsensus(),
3838 if (view.hasFollowHighlight())
3840 af.viewport.followHighlight = view.getFollowHighlight();
3842 if (view.hasFollowSelection())
3844 af.viewport.followSelection = view.getFollowSelection();
3846 if (view.hasShowConsensusHistogram())
3848 af.viewport.setShowConsensusHistogram(view
3849 .getShowConsensusHistogram());
3853 af.viewport.setShowConsensusHistogram(true);
3855 if (view.hasShowSequenceLogo())
3857 af.viewport.setShowSequenceLogo(view.getShowSequenceLogo());
3861 af.viewport.setShowSequenceLogo(false);
3863 if (view.hasNormaliseSequenceLogo())
3865 af.viewport.setNormaliseSequenceLogo(view.getNormaliseSequenceLogo());
3867 if (view.hasShowDbRefTooltip())
3869 af.viewport.setShowDBRefs(view.getShowDbRefTooltip());
3871 if (view.hasShowNPfeatureTooltip())
3873 af.viewport.setShowNPFeats(view.hasShowNPfeatureTooltip());
3875 if (view.hasShowGroupConsensus())
3877 af.viewport.setShowGroupConsensus(view.getShowGroupConsensus());
3881 af.viewport.setShowGroupConsensus(false);
3883 if (view.hasShowGroupConservation())
3885 af.viewport.setShowGroupConservation(view.getShowGroupConservation());
3889 af.viewport.setShowGroupConservation(false);
3892 // recover featre settings
3893 if (jms.getFeatureSettings() != null)
3895 FeaturesDisplayed fdi;
3896 af.viewport.setFeaturesDisplayed(fdi = new FeaturesDisplayed());
3897 String[] renderOrder = new String[jms.getFeatureSettings()
3898 .getSettingCount()];
3899 Hashtable featureGroups = new Hashtable();
3900 Hashtable featureColours = new Hashtable();
3901 Hashtable featureOrder = new Hashtable();
3903 for (int fs = 0; fs < jms.getFeatureSettings().getSettingCount(); fs++)
3905 Setting setting = jms.getFeatureSettings().getSetting(fs);
3906 if (setting.hasMincolour())
3908 GraduatedColor gc = setting.hasMin() ? new GraduatedColor(
3909 new java.awt.Color(setting.getMincolour()),
3910 new java.awt.Color(setting.getColour()),
3911 setting.getMin(), setting.getMax()) : new GraduatedColor(
3912 new java.awt.Color(setting.getMincolour()),
3913 new java.awt.Color(setting.getColour()), 0, 1);
3914 if (setting.hasThreshold())
3916 gc.setThresh(setting.getThreshold());
3917 gc.setThreshType(setting.getThreshstate());
3919 gc.setAutoScaled(true); // default
3920 if (setting.hasAutoScale())
3922 gc.setAutoScaled(setting.getAutoScale());
3924 if (setting.hasColourByLabel())
3926 gc.setColourByLabel(setting.getColourByLabel());
3928 // and put in the feature colour table.
3929 featureColours.put(setting.getType(), gc);
3933 featureColours.put(setting.getType(),
3934 new java.awt.Color(setting.getColour()));
3936 renderOrder[fs] = setting.getType();
3937 if (setting.hasOrder())
3939 featureOrder.put(setting.getType(), setting.getOrder());
3943 featureOrder.put(setting.getType(), new Float(fs
3944 / jms.getFeatureSettings().getSettingCount()));
3946 if (setting.getDisplay())
3948 fdi.setVisible(setting.getType());
3951 Hashtable fgtable = new Hashtable();
3952 for (int gs = 0; gs < jms.getFeatureSettings().getGroupCount(); gs++)
3954 Group grp = jms.getFeatureSettings().getGroup(gs);
3955 fgtable.put(grp.getName(), new Boolean(grp.getDisplay()));
3957 // FeatureRendererSettings frs = new FeatureRendererSettings(renderOrder,
3958 // fgtable, featureColours, jms.getFeatureSettings().hasTransparency() ?
3959 // jms.getFeatureSettings().getTransparency() : 0.0, featureOrder);
3960 FeatureRendererSettings frs = new FeatureRendererSettings(
3961 renderOrder, fgtable, featureColours, 1.0f, featureOrder);
3962 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
3963 .transferSettings(frs);
3967 if (view.getHiddenColumnsCount() > 0)
3969 for (int c = 0; c < view.getHiddenColumnsCount(); c++)
3971 af.viewport.hideColumns(view.getHiddenColumns(c).getStart(), view
3972 .getHiddenColumns(c).getEnd() // +1
3976 if (view.getCalcIdParam() != null)
3978 for (CalcIdParam calcIdParam : view.getCalcIdParam())
3980 if (calcIdParam != null)
3982 if (recoverCalcIdParam(calcIdParam, af.viewport))
3987 warn("Couldn't recover parameters for "
3988 + calcIdParam.getCalcId());
3993 af.setMenusFromViewport(af.viewport);
3995 // TODO: we don't need to do this if the viewport is aready visible.
3997 * Add the AlignFrame to the desktop (it may be 'gathered' later), unless it
3998 * has a 'cdna/protein complement' view, in which case save it in order to
3999 * populate a SplitFrame once all views have been read in.
4001 String complementaryViewId = view.getComplementId();
4002 if (complementaryViewId == null)
4004 Desktop.addInternalFrame(af, view.getTitle(), view.getWidth(),
4006 // recompute any autoannotation
4007 af.alignPanel.updateAnnotation(false, true);
4008 reorderAutoannotation(af, al, autoAlan);
4009 af.alignPanel.alignmentChanged();
4013 splitFrameCandidates.put(view, af);
4018 private ColourSchemeI constructAnnotationColour(
4019 AnnotationColours viewAnnColour, AlignFrame af, Alignment al,
4020 JalviewModelSequence jms, boolean checkGroupAnnColour)
4022 boolean propagateAnnColour = false;
4023 ColourSchemeI cs = null;
4024 AlignmentI annAlignment = af != null ? af.viewport.getAlignment() : al;
4025 if (checkGroupAnnColour && al.getGroups() != null
4026 && al.getGroups().size() > 0)
4028 // pre 2.8.1 behaviour
4029 // check to see if we should transfer annotation colours
4030 propagateAnnColour = true;
4031 for (jalview.datamodel.SequenceGroup sg : al.getGroups())
4033 if (sg.cs instanceof AnnotationColourGradient)
4035 propagateAnnColour = false;
4039 // int find annotation
4040 if (annAlignment.getAlignmentAnnotation() != null)
4042 for (int i = 0; i < annAlignment.getAlignmentAnnotation().length; i++)
4044 if (annAlignment.getAlignmentAnnotation()[i].label
4045 .equals(viewAnnColour.getAnnotation()))
4047 if (annAlignment.getAlignmentAnnotation()[i].getThreshold() == null)
4049 annAlignment.getAlignmentAnnotation()[i]
4050 .setThreshold(new jalview.datamodel.GraphLine(
4051 viewAnnColour.getThreshold(), "Threshold",
4052 java.awt.Color.black)
4057 if (viewAnnColour.getColourScheme().equals("None"))
4059 cs = new AnnotationColourGradient(
4060 annAlignment.getAlignmentAnnotation()[i],
4061 new java.awt.Color(viewAnnColour.getMinColour()),
4062 new java.awt.Color(viewAnnColour.getMaxColour()),
4063 viewAnnColour.getAboveThreshold());
4065 else if (viewAnnColour.getColourScheme().startsWith("ucs"))
4067 cs = new AnnotationColourGradient(
4068 annAlignment.getAlignmentAnnotation()[i],
4069 getUserColourScheme(jms,
4070 viewAnnColour.getColourScheme()),
4071 viewAnnColour.getAboveThreshold());
4075 cs = new AnnotationColourGradient(
4076 annAlignment.getAlignmentAnnotation()[i],
4077 ColourSchemeProperty.getColour(al,
4078 viewAnnColour.getColourScheme()),
4079 viewAnnColour.getAboveThreshold());
4081 if (viewAnnColour.hasPerSequence())
4083 ((AnnotationColourGradient) cs).setSeqAssociated(viewAnnColour
4086 if (viewAnnColour.hasPredefinedColours())
4088 ((AnnotationColourGradient) cs)
4089 .setPredefinedColours(viewAnnColour
4090 .isPredefinedColours());
4092 if (propagateAnnColour && al.getGroups() != null)
4094 // Also use these settings for all the groups
4095 for (int g = 0; g < al.getGroups().size(); g++)
4097 jalview.datamodel.SequenceGroup sg = al.getGroups().get(g);
4105 * if (viewAnnColour.getColourScheme().equals("None" )) { sg.cs =
4106 * new AnnotationColourGradient(
4107 * annAlignment.getAlignmentAnnotation()[i], new
4108 * java.awt.Color(viewAnnColour. getMinColour()), new
4109 * java.awt.Color(viewAnnColour. getMaxColour()),
4110 * viewAnnColour.getAboveThreshold()); } else
4113 sg.cs = new AnnotationColourGradient(
4114 annAlignment.getAlignmentAnnotation()[i], sg.cs,
4115 viewAnnColour.getAboveThreshold());
4116 if (cs instanceof AnnotationColourGradient)
4118 if (viewAnnColour.hasPerSequence())
4120 ((AnnotationColourGradient) cs)
4121 .setSeqAssociated(viewAnnColour.isPerSequence());
4123 if (viewAnnColour.hasPredefinedColours())
4125 ((AnnotationColourGradient) cs)
4126 .setPredefinedColours(viewAnnColour
4127 .isPredefinedColours());
4143 private void reorderAutoannotation(AlignFrame af, Alignment al,
4144 List<JvAnnotRow> autoAlan)
4146 // copy over visualization settings for autocalculated annotation in the
4148 if (al.getAlignmentAnnotation() != null)
4151 * Kludge for magic autoannotation names (see JAL-811)
4153 String[] magicNames = new String[]
4154 { "Consensus", "Quality", "Conservation" };
4155 JvAnnotRow nullAnnot = new JvAnnotRow(-1, null);
4156 Hashtable<String, JvAnnotRow> visan = new Hashtable<String, JvAnnotRow>();
4157 for (String nm : magicNames)
4159 visan.put(nm, nullAnnot);
4161 for (JvAnnotRow auan : autoAlan)
4163 visan.put(auan.template.label
4164 + (auan.template.getCalcId() == null ? "" : "\t"
4165 + auan.template.getCalcId()), auan);
4167 int hSize = al.getAlignmentAnnotation().length;
4168 List<JvAnnotRow> reorder = new ArrayList<JvAnnotRow>();
4169 // work through any autoCalculated annotation already on the view
4170 // removing it if it should be placed in a different location on the
4171 // annotation panel.
4172 List<String> remains = new ArrayList<String>(visan.keySet());
4173 for (int h = 0; h < hSize; h++)
4175 jalview.datamodel.AlignmentAnnotation jalan = al
4176 .getAlignmentAnnotation()[h];
4177 if (jalan.autoCalculated)
4180 JvAnnotRow valan = visan.get(k = jalan.label);
4181 if (jalan.getCalcId() != null)
4183 valan = visan.get(k = jalan.label + "\t" + jalan.getCalcId());
4188 // delete the auto calculated row from the alignment
4189 al.deleteAnnotation(jalan, false);
4193 if (valan != nullAnnot)
4195 if (jalan != valan.template)
4197 // newly created autoannotation row instance
4198 // so keep a reference to the visible annotation row
4199 // and copy over all relevant attributes
4200 if (valan.template.graphHeight >= 0)
4203 jalan.graphHeight = valan.template.graphHeight;
4205 jalan.visible = valan.template.visible;
4207 reorder.add(new JvAnnotRow(valan.order, jalan));
4212 // Add any (possibly stale) autocalculated rows that were not appended to
4213 // the view during construction
4214 for (String other : remains)
4216 JvAnnotRow othera = visan.get(other);
4217 if (othera != nullAnnot && othera.template.getCalcId() != null
4218 && othera.template.getCalcId().length() > 0)
4220 reorder.add(othera);
4223 // now put the automatic annotation in its correct place
4224 int s = 0, srt[] = new int[reorder.size()];
4225 JvAnnotRow[] rws = new JvAnnotRow[reorder.size()];
4226 for (JvAnnotRow jvar : reorder)
4229 srt[s++] = jvar.order;
4232 jalview.util.QuickSort.sort(srt, rws);
4233 // and re-insert the annotation at its correct position
4234 for (JvAnnotRow jvar : rws)
4236 al.addAnnotation(jvar.template, jvar.order);
4238 af.alignPanel.adjustAnnotationHeight();
4242 Hashtable skipList = null;
4245 * TODO remove this method
4248 * @return AlignFrame bound to sequenceSetId from view, if one exists. private
4249 * AlignFrame getSkippedFrame(Viewport view) { if (skipList==null) {
4250 * throw new Error("Implementation Error. No skipList defined for this
4251 * Jalview2XML instance."); } return (AlignFrame)
4252 * skipList.get(view.getSequenceSetId()); }
4256 * Check if the Jalview view contained in object should be skipped or not.
4259 * @return true if view's sequenceSetId is a key in skipList
4261 private boolean skipViewport(JalviewModel object)
4263 if (skipList == null)
4268 if (skipList.containsKey(id = object.getJalviewModelSequence()
4269 .getViewport()[0].getSequenceSetId()))
4271 if (Cache.log != null && Cache.log.isDebugEnabled())
4273 Cache.log.debug("Skipping seuqence set id " + id);
4280 public void addToSkipList(AlignFrame af)
4282 if (skipList == null)
4284 skipList = new Hashtable();
4286 skipList.put(af.getViewport().getSequenceSetId(), af);
4289 public void clearSkipList()
4291 if (skipList != null)
4298 private void recoverDatasetFor(SequenceSet vamsasSet, Alignment al,
4299 boolean ignoreUnrefed)
4301 jalview.datamodel.Alignment ds = getDatasetFor(vamsasSet.getDatasetId());
4302 Vector dseqs = null;
4305 // create a list of new dataset sequences
4306 dseqs = new Vector();
4308 for (int i = 0, iSize = vamsasSet.getSequenceCount(); i < iSize; i++)
4310 Sequence vamsasSeq = vamsasSet.getSequence(i);
4311 ensureJalviewDatasetSequence(vamsasSeq, ds, dseqs, ignoreUnrefed);
4313 // create a new dataset
4316 SequenceI[] dsseqs = new SequenceI[dseqs.size()];
4317 dseqs.copyInto(dsseqs);
4318 ds = new jalview.datamodel.Alignment(dsseqs);
4319 debug("Created new dataset " + vamsasSet.getDatasetId()
4320 + " for alignment " + System.identityHashCode(al));
4321 addDatasetRef(vamsasSet.getDatasetId(), ds);
4323 // set the dataset for the newly imported alignment.
4324 if (al.getDataset() == null && !ignoreUnrefed)
4333 * sequence definition to create/merge dataset sequence for
4337 * vector to add new dataset sequence to
4339 private void ensureJalviewDatasetSequence(Sequence vamsasSeq,
4340 AlignmentI ds, Vector dseqs, boolean ignoreUnrefed)
4342 // JBP TODO: Check this is called for AlCodonFrames to support recovery of
4344 SequenceI sq = seqRefIds.get(vamsasSeq.getId());
4345 SequenceI dsq = null;
4346 if (sq != null && sq.getDatasetSequence() != null)
4348 dsq = sq.getDatasetSequence();
4350 if (sq == null && ignoreUnrefed)
4354 String sqid = vamsasSeq.getDsseqid();
4357 // need to create or add a new dataset sequence reference to this sequence
4360 dsq = seqRefIds.get(sqid);
4365 // make a new dataset sequence
4366 dsq = sq.createDatasetSequence();
4369 // make up a new dataset reference for this sequence
4370 sqid = seqHash(dsq);
4372 dsq.setVamsasId(uniqueSetSuffix + sqid);
4373 seqRefIds.put(sqid, dsq);
4378 dseqs.addElement(dsq);
4383 ds.addSequence(dsq);
4389 { // make this dataset sequence sq's dataset sequence
4390 sq.setDatasetSequence(dsq);
4391 // and update the current dataset alignment
4396 if (!dseqs.contains(dsq))
4403 if (ds.findIndex(dsq) < 0)
4405 ds.addSequence(dsq);
4412 // TODO: refactor this as a merge dataset sequence function
4413 // now check that sq (the dataset sequence) sequence really is the union of
4414 // all references to it
4415 // boolean pre = sq.getStart() < dsq.getStart();
4416 // boolean post = sq.getEnd() > dsq.getEnd();
4420 // StringBuffer sb = new StringBuffer();
4421 String newres = jalview.analysis.AlignSeq.extractGaps(
4422 jalview.util.Comparison.GapChars, sq.getSequenceAsString());
4423 if (!newres.equalsIgnoreCase(dsq.getSequenceAsString())
4424 && newres.length() > dsq.getLength())
4426 // Update with the longer sequence.
4430 * if (pre) { sb.insert(0, newres .substring(0, dsq.getStart() -
4431 * sq.getStart())); dsq.setStart(sq.getStart()); } if (post) {
4432 * sb.append(newres.substring(newres.length() - sq.getEnd() -
4433 * dsq.getEnd())); dsq.setEnd(sq.getEnd()); }
4435 dsq.setSequence(newres);
4437 // TODO: merges will never happen if we 'know' we have the real dataset
4438 // sequence - this should be detected when id==dssid
4440 .println("DEBUG Notice: Merged dataset sequence (if you see this often, post at http://issues.jalview.org/browse/JAL-1474)"); // ("
4441 // + (pre ? "prepended" : "") + " "
4442 // + (post ? "appended" : ""));
4447 java.util.Hashtable datasetIds = null;
4449 java.util.IdentityHashMap dataset2Ids = null;
4451 private Alignment getDatasetFor(String datasetId)
4453 if (datasetIds == null)
4455 datasetIds = new Hashtable();
4458 if (datasetIds.containsKey(datasetId))
4460 return (Alignment) datasetIds.get(datasetId);
4465 private void addDatasetRef(String datasetId, Alignment dataset)
4467 if (datasetIds == null)
4469 datasetIds = new Hashtable();
4471 datasetIds.put(datasetId, dataset);
4475 * make a new dataset ID for this jalview dataset alignment
4480 private String getDatasetIdRef(jalview.datamodel.Alignment dataset)
4482 if (dataset.getDataset() != null)
4484 warn("Serious issue! Dataset Object passed to getDatasetIdRef is not a Jalview DATASET alignment...");
4486 String datasetId = makeHashCode(dataset, null);
4487 if (datasetId == null)
4489 // make a new datasetId and record it
4490 if (dataset2Ids == null)
4492 dataset2Ids = new IdentityHashMap();
4496 datasetId = (String) dataset2Ids.get(dataset);
4498 if (datasetId == null)
4500 datasetId = "ds" + dataset2Ids.size() + 1;
4501 dataset2Ids.put(dataset, datasetId);
4507 private void addDBRefs(SequenceI datasetSequence, Sequence sequence)
4509 for (int d = 0; d < sequence.getDBRefCount(); d++)
4511 DBRef dr = sequence.getDBRef(d);
4512 jalview.datamodel.DBRefEntry entry = new jalview.datamodel.DBRefEntry(
4513 sequence.getDBRef(d).getSource(), sequence.getDBRef(d)
4514 .getVersion(), sequence.getDBRef(d).getAccessionId());
4515 if (dr.getMapping() != null)
4517 entry.setMap(addMapping(dr.getMapping()));
4519 datasetSequence.addDBRef(entry);
4523 private jalview.datamodel.Mapping addMapping(Mapping m)
4525 SequenceI dsto = null;
4526 // Mapping m = dr.getMapping();
4527 int fr[] = new int[m.getMapListFromCount() * 2];
4528 Enumeration f = m.enumerateMapListFrom();
4529 for (int _i = 0; f.hasMoreElements(); _i += 2)
4531 MapListFrom mf = (MapListFrom) f.nextElement();
4532 fr[_i] = mf.getStart();
4533 fr[_i + 1] = mf.getEnd();
4535 int fto[] = new int[m.getMapListToCount() * 2];
4536 f = m.enumerateMapListTo();
4537 for (int _i = 0; f.hasMoreElements(); _i += 2)
4539 MapListTo mf = (MapListTo) f.nextElement();
4540 fto[_i] = mf.getStart();
4541 fto[_i + 1] = mf.getEnd();
4543 jalview.datamodel.Mapping jmap = new jalview.datamodel.Mapping(dsto,
4544 fr, fto, (int) m.getMapFromUnit(), (int) m.getMapToUnit());
4545 if (m.getMappingChoice() != null)
4547 MappingChoice mc = m.getMappingChoice();
4548 if (mc.getDseqFor() != null)
4550 String dsfor = "" + mc.getDseqFor();
4551 if (seqRefIds.containsKey(dsfor))
4556 jmap.setTo(seqRefIds.get(dsfor));
4560 frefedSequence.add(new Object[]
4567 * local sequence definition
4569 Sequence ms = mc.getSequence();
4570 SequenceI djs = null;
4571 String sqid = ms.getDsseqid();
4572 if (sqid != null && sqid.length() > 0)
4575 * recover dataset sequence
4577 djs = seqRefIds.get(sqid);
4582 .println("Warning - making up dataset sequence id for DbRef sequence map reference");
4583 sqid = ((Object) ms).toString(); // make up a new hascode for
4584 // undefined dataset sequence hash
4585 // (unlikely to happen)
4591 * make a new dataset sequence and add it to refIds hash
4593 djs = new jalview.datamodel.Sequence(ms.getName(),
4595 djs.setStart(jmap.getMap().getToLowest());
4596 djs.setEnd(jmap.getMap().getToHighest());
4597 djs.setVamsasId(uniqueSetSuffix + sqid);
4599 seqRefIds.put(sqid, djs);
4602 jalview.bin.Cache.log.debug("about to recurse on addDBRefs.");
4611 public jalview.gui.AlignmentPanel copyAlignPanel(AlignmentPanel ap,
4612 boolean keepSeqRefs)
4615 jalview.schemabinding.version2.JalviewModel jm = saveState(ap, null,
4621 jm.getJalviewModelSequence().getViewport(0).setSequenceSetId(null);
4625 uniqueSetSuffix = "";
4626 jm.getJalviewModelSequence().getViewport(0).setId(null); // we don't
4631 if (this.frefedSequence == null)
4633 frefedSequence = new Vector();
4636 viewportsAdded.clear();
4638 AlignFrame af = loadFromObject(jm, null, false, null);
4639 af.alignPanels.clear();
4640 af.closeMenuItem_actionPerformed(true);
4643 * if(ap.av.getAlignment().getAlignmentAnnotation()!=null) { for(int i=0;
4644 * i<ap.av.getAlignment().getAlignmentAnnotation().length; i++) {
4645 * if(!ap.av.getAlignment().getAlignmentAnnotation()[i].autoCalculated) {
4646 * af.alignPanel.av.getAlignment().getAlignmentAnnotation()[i] =
4647 * ap.av.getAlignment().getAlignmentAnnotation()[i]; } } }
4650 return af.alignPanel;
4654 * flag indicating if hashtables should be cleared on finalization TODO this
4655 * flag may not be necessary
4657 private final boolean _cleartables = true;
4659 private Hashtable jvids2vobj;
4664 * @see java.lang.Object#finalize()
4667 protected void finalize() throws Throwable
4669 // really make sure we have no buried refs left.
4674 this.seqRefIds = null;
4675 this.seqsToIds = null;
4679 private void warn(String msg)
4684 private void warn(String msg, Exception e)
4686 if (Cache.log != null)
4690 Cache.log.warn(msg, e);
4694 Cache.log.warn(msg);
4699 System.err.println("Warning: " + msg);
4702 e.printStackTrace();
4707 private void debug(String string)
4709 debug(string, null);
4712 private void debug(String msg, Exception e)
4714 if (Cache.log != null)
4718 Cache.log.debug(msg, e);
4722 Cache.log.debug(msg);
4727 System.err.println("Warning: " + msg);
4730 e.printStackTrace();
4736 * set the object to ID mapping tables used to write/recover objects and XML
4737 * ID strings for the jalview project. If external tables are provided then
4738 * finalize and clearSeqRefs will not clear the tables when the Jalview2XML
4739 * object goes out of scope. - also populates the datasetIds hashtable with
4740 * alignment objects containing dataset sequences
4743 * Map from ID strings to jalview datamodel
4745 * Map from jalview datamodel to ID strings
4749 public void setObjectMappingTables(Hashtable vobj2jv,
4750 IdentityHashMap jv2vobj)
4752 this.jv2vobj = jv2vobj;
4753 this.vobj2jv = vobj2jv;
4754 Iterator ds = jv2vobj.keySet().iterator();
4756 while (ds.hasNext())
4758 Object jvobj = ds.next();
4759 id = jv2vobj.get(jvobj).toString();
4760 if (jvobj instanceof jalview.datamodel.Alignment)
4762 if (((jalview.datamodel.Alignment) jvobj).getDataset() == null)
4764 addDatasetRef(id, (jalview.datamodel.Alignment) jvobj);
4767 else if (jvobj instanceof jalview.datamodel.Sequence)
4769 // register sequence object so the XML parser can recover it.
4770 if (seqRefIds == null)
4772 seqRefIds = new HashMap<String, SequenceI>();
4774 if (seqsToIds == null)
4776 seqsToIds = new IdentityHashMap<SequenceI, String>();
4778 seqRefIds.put(jv2vobj.get(jvobj).toString(), (SequenceI) jvobj);
4779 seqsToIds.put((SequenceI) jvobj, id);
4781 else if (jvobj instanceof jalview.datamodel.AlignmentAnnotation)
4784 AlignmentAnnotation jvann = (AlignmentAnnotation) jvobj;
4785 annotationIds.put(anid = jv2vobj.get(jvobj).toString(), jvann);
4786 if (jvann.annotationId == null)
4788 jvann.annotationId = anid;
4790 if (!jvann.annotationId.equals(anid))
4792 // TODO verify that this is the correct behaviour
4793 this.warn("Overriding Annotation ID for " + anid
4794 + " from different id : " + jvann.annotationId);
4795 jvann.annotationId = anid;
4798 else if (jvobj instanceof String)
4800 if (jvids2vobj == null)
4802 jvids2vobj = new Hashtable();
4803 jvids2vobj.put(jvobj, jv2vobj.get(jvobj).toString());
4808 Cache.log.debug("Ignoring " + jvobj.getClass() + " (ID = " + id);
4814 * set the uniqueSetSuffix used to prefix/suffix object IDs for jalview
4815 * objects created from the project archive. If string is null (default for
4816 * construction) then suffix will be set automatically.
4820 public void setUniqueSetSuffix(String string)
4822 uniqueSetSuffix = string;
4827 * uses skipList2 as the skipList for skipping views on sequence sets
4828 * associated with keys in the skipList
4832 public void setSkipList(Hashtable skipList2)
4834 skipList = skipList2;