2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 import jalview.bin.Cache;
24 import jalview.datamodel.AlignedCodonFrame;
25 import jalview.datamodel.AlignmentAnnotation;
26 import jalview.datamodel.GraphLine;
27 import jalview.datamodel.SequenceI;
28 import jalview.gui.AlignFrame;
29 import jalview.gui.AlignViewport;
30 import jalview.gui.Desktop;
31 import jalview.gui.TreePanel;
32 import jalview.io.vamsas.Datasetsequence;
33 import jalview.io.vamsas.DatastoreItem;
34 import jalview.io.vamsas.DatastoreRegistry;
35 import jalview.io.vamsas.Rangetype;
36 import jalview.util.MessageManager;
37 import jalview.viewmodel.AlignmentViewport;
39 import java.io.IOException;
40 import java.util.Enumeration;
41 import java.util.HashMap;
42 import java.util.Hashtable;
43 import java.util.IdentityHashMap;
44 import java.util.Iterator;
45 import java.util.List;
47 import java.util.Vector;
48 import java.util.jar.JarInputStream;
49 import java.util.jar.JarOutputStream;
51 import uk.ac.vamsas.client.IClientAppdata;
52 import uk.ac.vamsas.client.IClientDocument;
53 import uk.ac.vamsas.client.Vobject;
54 import uk.ac.vamsas.client.VorbaId;
55 import uk.ac.vamsas.objects.core.Alignment;
56 import uk.ac.vamsas.objects.core.AlignmentSequence;
57 import uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation;
58 import uk.ac.vamsas.objects.core.AnnotationElement;
59 import uk.ac.vamsas.objects.core.DataSet;
60 import uk.ac.vamsas.objects.core.DataSetAnnotations;
61 import uk.ac.vamsas.objects.core.DbRef;
62 import uk.ac.vamsas.objects.core.Entry;
63 import uk.ac.vamsas.objects.core.Glyph;
64 import uk.ac.vamsas.objects.core.Local;
65 import uk.ac.vamsas.objects.core.MapType;
66 import uk.ac.vamsas.objects.core.Mapped;
67 import uk.ac.vamsas.objects.core.Property;
68 import uk.ac.vamsas.objects.core.Provenance;
69 import uk.ac.vamsas.objects.core.RangeAnnotation;
70 import uk.ac.vamsas.objects.core.RangeType;
71 import uk.ac.vamsas.objects.core.Seg;
72 import uk.ac.vamsas.objects.core.Sequence;
73 import uk.ac.vamsas.objects.core.SequenceType;
74 import uk.ac.vamsas.objects.core.VAMSAS;
75 import uk.ac.vamsas.objects.utils.Properties;
80 * org.exolab.castor.util.LocalConfiguration.getInstance().getProperties().setProperty(
81 * "org.exolab.castor.serializer", "org.apache.xml.serialize.XMLSerilazizer"); }
85 * TODO: check/verify consistency for vamsas sync with group associated alignment annotation
87 public class VamsasAppDatastore
90 * Type used for general jalview generated annotation added to vamsas document
92 public static final String JALVIEW_ANNOTATION_ROW = "JalviewAnnotation";
95 * AlignmentAnnotation property to indicate that values should not be
98 public static final String DISCRETE_ANNOTATION = "discrete";
101 * continuous property - optional to specify that annotation should be
102 * represented as a continous graph line
104 private static final String CONTINUOUS_ANNOTATION = "continuous";
106 private static final String THRESHOLD = "threshold";
109 * template for provenance entries written to vamsas session document
111 Entry provEntry = null;
114 * Instance of the session document being synchronized with
116 IClientDocument cdoc;
119 * map Vorba (vamsas object xml ref) IDs to live jalview object references
124 * map live jalview object references to Vorba IDs
126 IdentityHashMap jv2vobj;
129 * map jalview sequence set ID (which is vorba ID for alignment) to last
130 * recorded hash value for the alignment viewport (the undo/redo hash value)
132 Hashtable alignRDHash;
134 public VamsasAppDatastore(IClientDocument cdoc, Hashtable vobj2jv,
135 IdentityHashMap jv2vobj, Entry provEntry, Hashtable alignRDHash)
138 this.vobj2jv = vobj2jv;
139 this.jv2vobj = jv2vobj;
140 this.provEntry = provEntry;
141 this.alignRDHash = alignRDHash;
146 * the skipList used to skip over views from Jalview Appdata's that we've
147 * already syncrhonized
151 private void buildSkipList()
153 skipList = new Hashtable();
154 AlignFrame[] al = Desktop.getAlignFrames();
155 for (int f = 0; al != null && f < al.length; f++)
157 skipList.put(al[f].getViewport().getSequenceSetId(), al[f]);
162 * @return the Vobject bound to Jalview datamodel object
164 protected Vobject getjv2vObj(Object jvobj)
166 if (jv2vobj.containsKey(jvobj))
168 return cdoc.getObject((VorbaId) jv2vobj.get(jvobj));
170 // check if we're working with a string - then workaround
171 // the use of IdentityHashTable because different strings
172 // have different object IDs.
173 if (jvobj instanceof String)
175 Object seqsetidobj = null;
176 seqsetidobj = getVamsasObjectBinding().get(jvobj);
177 if (seqsetidobj != null)
179 if (seqsetidobj instanceof String)
181 // what is expected. object returned by av.getSequenceSetId() -
182 // reverse lookup to get the 'registered' instance of this string
183 Vobject obj = getjv2vObj(seqsetidobj);
184 if (obj != null && !(obj instanceof Alignment))
187 .warn("IMPLEMENTATION ERROR?: Unexpected mapping for unmapped jalview string object content:"
188 + seqsetidobj + " to object " + obj);
194 Cache.log.warn("Unexpected mapping for Jalview String Object ID "
195 + seqsetidobj + " to another jalview dataset object "
201 if (Cache.log.isDebugEnabled())
203 Cache.log.debug("Returning null VorbaID binding for jalview object "
212 * @return Jalview datamodel object bound to the vamsas document object
214 protected Object getvObj2jv(uk.ac.vamsas.client.Vobject vobj)
216 VorbaId id = vobj.getVorbaId();
219 id = cdoc.registerObject(vobj);
221 .debug("Registering new object and returning null for getvObj2jv");
224 if (vobj2jv.containsKey(vobj.getVorbaId()))
226 return vobj2jv.get(vobj.getVorbaId());
231 protected void bindjvvobj(Object jvobj, uk.ac.vamsas.client.Vobject vobj)
233 VorbaId id = vobj.getVorbaId();
236 id = cdoc.registerObject(vobj);
237 if (id == null || vobj.getVorbaId() == null
238 || cdoc.getObject(id) != vobj)
240 Cache.log.error("Failed to get id for "
241 + (vobj.isRegisterable() ? "registerable"
242 : "unregisterable") + " object " + vobj);
246 if (vobj2jv.containsKey(vobj.getVorbaId())
247 && !((VorbaId) vobj2jv.get(vobj.getVorbaId())).equals(jvobj))
250 .debug("Warning? Overwriting existing vamsas id binding for "
254 .getString("exception.overwriting_vamsas_id_binding")));
256 else if (jv2vobj.containsKey(jvobj)
257 && !((VorbaId) jv2vobj.get(jvobj)).equals(vobj.getVorbaId()))
260 "Warning? Overwriting existing jalview object binding for "
261 + jvobj, new Exception(
262 "Overwriting jalview object binding."));
265 * Cache.log.error("Attempt to make conflicting object binding! "+vobj+" id "
266 * +vobj.getVorbaId()+" already bound to "+getvObj2jv(vobj)+" and "+jvobj+"
267 * already bound to "+getjv2vObj(jvobj),new Exception("Excessive call to
270 // we just update the hash's regardless!
271 Cache.log.debug("Binding " + vobj.getVorbaId() + " to " + jvobj);
272 vobj2jv.put(vobj.getVorbaId(), jvobj);
273 // JBPNote - better implementing a hybrid invertible hash.
274 jv2vobj.put(jvobj, vobj.getVorbaId());
278 * put the alignment viewed by AlignViewport into cdoc.
281 * alignViewport to be stored
283 * title for alignment
284 * @return true if alignment associated with viewport was stored/synchronized
287 public boolean storeVAMSAS(AlignViewport av, String aFtitle)
291 jalview.datamodel.AlignmentI jal = av.getAlignment();
292 jalview.datamodel.AlignmentI jds = jal.getDataset();
294 VAMSAS root = null; // will be resolved based on Dataset Parent.
295 // /////////////////////////////////////////
297 DataSet dataset = null;
300 Cache.log.warn("Creating new dataset for an alignment.");
301 jal.setDataset(null);
302 jds = jal.getDataset();
305 // try and get alignment and association for sequence set id
307 Alignment alignment = (Alignment) getjv2vObj(av.getSequenceSetId());
308 if (alignment != null)
310 dataset = (DataSet) alignment.getV_parent();
314 // is the dataset already registered
315 dataset = (DataSet) getjv2vObj(jds);
320 // it might be that one of the dataset sequences does actually have a
321 // binding, so search for it indirectly. If it does, then the local
323 // must be merged with the existing vamsas dataset.
324 jalview.datamodel.SequenceI[] jdatset = jds.getSequencesArray();
325 for (int i = 0; i < jdatset.length; i++)
327 Vobject vbound = getjv2vObj(jdatset[i]);
330 if (vbound instanceof uk.ac.vamsas.objects.core.Sequence)
334 dataset = (DataSet) vbound.getV_parent();
338 if (vbound.getV_parent() != null
339 && dataset != vbound.getV_parent())
343 .getString("error.implementation_error_cannot_map_alignment_sequences"));
344 // This occurs because the dataset for the alignment we are
355 Cache.log.warn("Creating new vamsas dataset for alignment view "
356 + av.getSequenceSetId());
357 // we create a new dataset on the default vamsas root.
358 root = cdoc.getVamsasRoots()[0]; // default vamsas root for modifying.
359 dataset = new DataSet();
360 root.addDataSet(dataset);
361 bindjvvobj(jds, dataset);
362 dataset.setProvenance(dummyProvenance());
363 // dataset.getProvenance().addEntry(provEntry);
368 root = (VAMSAS) dataset.getV_parent();
372 // set new dataset and alignment sequences based on alignment Nucleotide
374 // this *will* break when alignment contains both nucleotide and amino
376 String dict = jal.isNucleotide() ? uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_NA
377 : uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_AA;
378 Vector dssmods = new Vector();
379 for (int i = 0; i < jal.getHeight(); i++)
381 SequenceI sq = jal.getSequenceAt(i).getDatasetSequence(); // only insert
385 Datasetsequence dssync = new jalview.io.vamsas.Datasetsequence(
386 this, sq, dict, dataset);
387 sequence = (Sequence) dssync.getVobj();
388 if (dssync.getModified())
390 dssmods.addElement(sequence);
394 if (dssmods.size() > 0)
398 Entry pentry = this.addProvenance(dataset.getProvenance(),
399 "updated sequences");
400 // pentry.addInput(vInput); could write in which sequences were
402 dssmods.removeAllElements();
405 // dataset.setProvenance(getVamsasProvenance(jal.getDataset().getProvenance()));
406 // ////////////////////////////////////////////
407 if (alignmentWillBeSkipped(av))
409 // TODO: trees could be written - but for the moment we just
411 // add to the JalviewXML skipList and ..
415 if (alignment == null)
417 alignment = new Alignment();
418 bindjvvobj(av.getSequenceSetId(), alignment);
419 if (alignment.getProvenance() == null)
421 alignment.setProvenance(new Provenance());
423 addProvenance(alignment.getProvenance(), "added"); // TODO: insert some
426 dataset.addAlignment(alignment);
428 Property title = new Property();
429 title.setName("title");
430 title.setType("string");
431 title.setContent(aFtitle);
432 alignment.addProperty(title);
434 alignment.setGapChar(String.valueOf(av.getGapCharacter()));
435 for (int i = 0; i < jal.getHeight(); i++)
437 syncToAlignmentSequence(jal.getSequenceAt(i), alignment, null);
439 alignRDHash.put(av.getSequenceSetId(), av.getUndoRedoHash());
443 // always prepare to clone the alignment
444 boolean alismod = av.isUndoRedoHashModified((long[]) alignRDHash
445 .get(av.getSequenceSetId()));
446 // todo: verify and update mutable alignment props.
447 // TODO: Use isLocked methods
448 if (alignment.getModifiable() == null
449 || alignment.getModifiable().length() == 0)
450 // && !alignment.isDependedOn())
452 boolean modified = false;
453 // check existing sequences in local and in document.
454 Vector docseqs = new Vector(
455 alignment.getAlignmentSequenceAsReference());
456 for (int i = 0; i < jal.getHeight(); i++)
458 modified |= syncToAlignmentSequence(jal.getSequenceAt(i),
461 if (docseqs.size() > 0)
463 // removeValignmentSequences(alignment, docseqs);
464 docseqs.removeAllElements();
466 .println("Sequence deletion from alignment is not implemented.");
474 addProvenance(alignment.getProvenance(), "Edited"); // TODO:
483 addProvenance(alignment.getProvenance(), "Attributes Edited"); // TODO:
493 System.out.println("update alignment in document.");
497 System.out.println("alignment in document left unchanged.");
502 // unbind alignment from view.
503 // create new binding and new alignment.
504 // mark trail on new alignment as being derived from old ?
506 .println("update edited alignment to new alignment in document.");
509 // ////////////////////////////////////////////
510 // SAVE Alignment Sequence Features
511 for (int i = 0, iSize = alignment.getAlignmentSequenceCount(); i < iSize; i++)
513 AlignmentSequence valseq;
514 SequenceI alseq = (SequenceI) getvObj2jv(valseq = alignment
515 .getAlignmentSequence(i));
516 if (alseq != null && alseq.getSequenceFeatures() != null)
519 * We do not put local Alignment Sequence Features into the vamsas
523 * jalview.datamodel.SequenceFeature[] features = alseq
524 * .getSequenceFeatures(); for (int f = 0; f < features.length; f++) {
525 * if (features[f] != null) { AlignmentSequenceAnnotation valseqf = (
526 * AlignmentSequenceAnnotation) getjv2vObj(features[i]); if (valseqf
529 * valseqf = (AlignmentSequenceAnnotation) getDSAnnotationFromJalview(
530 * new AlignmentSequenceAnnotation(), features[i]);
531 * valseqf.setGraph(false);
532 * valseqf.addProperty(newProperty("jalview:feature"
533 * ,"boolean","true")); if (valseqf.getProvenance() == null) {
534 * valseqf.setProvenance(new Provenance()); }
535 * addProvenance(valseqf.getProvenance(), "created"); // JBPNote - //
536 * need to // update bindjvvobj(features[i], valseqf);
537 * valseq.addAlignmentSequenceAnnotation(valseqf); } } }
542 // ////////////////////////////////////////////
544 if (jal.getAlignmentAnnotation() != null)
546 jalview.datamodel.AlignmentAnnotation[] aa = jal
547 .getAlignmentAnnotation();
548 java.util.HashMap AlSeqMaps = new HashMap(); // stores int maps from
549 // alignment columns to
550 // sequence positions.
551 for (int i = 0; i < aa.length; i++)
553 if (aa[i] == null || isJalviewOnly(aa[i]))
557 if (aa[i].groupRef != null)
559 // TODO: store any group associated annotation references
561 .warn("Group associated sequence annotation is not stored in VAMSAS document.");
564 if (aa[i].sequenceRef != null)
566 // Deal with sequence associated annotation
567 Vobject sref = getjv2vObj(aa[i].sequenceRef);
568 if (sref instanceof uk.ac.vamsas.objects.core.AlignmentSequence)
570 saveAlignmentSequenceAnnotation(AlSeqMaps,
571 (AlignmentSequence) sref, aa[i]);
575 // first find the alignment sequence to associate this with.
576 for (SequenceI jvalsq : av.getAlignment().getSequences())
578 // saveDatasetSequenceAnnotation(AlSeqMaps,(uk.ac.vamsas.objects.core.Sequence)
580 if (jvalsq.getDatasetSequence() == aa[i].sequenceRef)
582 Vobject alsref = getjv2vObj(jvalsq);
583 saveAlignmentSequenceAnnotation(AlSeqMaps,
584 (AlignmentSequence) alsref, aa[i]);
593 // add Alignment Annotation
594 uk.ac.vamsas.objects.core.AlignmentAnnotation an = (uk.ac.vamsas.objects.core.AlignmentAnnotation) getjv2vObj(aa[i]);
597 an = new uk.ac.vamsas.objects.core.AlignmentAnnotation();
598 an.setType(JALVIEW_ANNOTATION_ROW);
599 an.setDescription(aa[i].description);
600 alignment.addAlignmentAnnotation(an);
601 Seg vSeg = new Seg(); // TODO: refactor to have a default
602 // rangeAnnotationType initer/updater that
603 // takes a set of int ranges.
605 vSeg.setInclusive(true);
606 vSeg.setEnd(jal.getWidth());
610 an.setGraph(true); // aa[i].graph);
612 an.setLabel(aa[i].label);
613 an.setProvenance(dummyProvenance());
614 if (aa[i].graph != AlignmentAnnotation.NO_GRAPH)
616 an.setGroup(Integer.toString(aa[i].graphGroup)); // // JBPNote
631 AnnotationElement ae;
633 for (int a = 0; a < aa[i].annotations.length; a++)
635 if ((aa[i] == null) || (aa[i].annotations[a] == null))
640 ae = new AnnotationElement();
641 ae.setDescription(aa[i].annotations[a].description);
642 ae.addGlyph(new Glyph());
643 ae.getGlyph(0).setContent(
644 aa[i].annotations[a].displayCharacter); // assume
653 ae.addValue(aa[i].annotations[a].value);
655 ae.setPosition(a + 1);
656 if (aa[i].annotations[a].secondaryStructure != ' ')
658 Glyph ss = new Glyph();
659 ss.setDict(uk.ac.vamsas.objects.utils.GlyphDictionary.PROTEIN_SS_3STATE);
661 .valueOf(aa[i].annotations[a].secondaryStructure));
664 an.addAnnotationElement(ae);
668 // an.addProperty(newProperty("jalview:editable", null,
670 // an.setModifiable(""); // TODO: This is not the way the
671 // modifiable flag is supposed to be used.
673 setAnnotationType(an, aa[i]);
675 if (aa[i].graph != jalview.datamodel.AlignmentAnnotation.NO_GRAPH)
678 an.setGroup(Integer.toString(aa[i].graphGroup));
679 if (aa[i].threshold != null && aa[i].threshold.displayed)
681 an.addProperty(Properties.newProperty(THRESHOLD,
682 Properties.FLOATTYPE, "" + aa[i].threshold.value));
683 if (aa[i].threshold.label != null)
685 an.addProperty(Properties.newProperty(THRESHOLD
686 + "Name", Properties.STRINGTYPE, ""
687 + aa[i].threshold.label));
696 if (an.getModifiable() == null) // TODO: USE VAMSAS LIBRARY OBJECT
699 // verify annotation - update (perhaps)
701 .info("update alignment sequence annotation. not yet implemented.");
705 // verify annotation - update (perhaps)
707 .info("updated alignment sequence annotation added.");
713 // /////////////////////////////////////////////////////
715 // //////////////////////////////////////////////
717 // /////////////////////////////////
718 // FIND ANY ASSOCIATED TREES
719 if (Desktop.desktop != null)
721 javax.swing.JInternalFrame[] frames = Desktop.instance
724 for (int t = 0; t < frames.length; t++)
726 if (frames[t] instanceof TreePanel)
728 TreePanel tp = (TreePanel) frames[t];
730 if (tp.getViewPort().getSequenceSetId()
731 .equals(av.getSequenceSetId()))
733 DatastoreItem vtree = new jalview.io.vamsas.Tree(this, tp,
739 // Store Jalview specific stuff in the Jalview appData
740 // not implemented in the SimpleDoc interface.
745 ex.printStackTrace();
752 * very quick test to see if the viewport would be stored in the vamsas
753 * document. Reasons for not storing include the unaligned flag being false
754 * (for all sequences, including the hidden ones!)
757 * @return true if alignment associated with this view will be stored in
760 public boolean alignmentWillBeSkipped(AlignmentViewport av)
762 return (!av.getAlignment().isAligned());
765 private void addToSkipList(AlignmentViewport av)
767 if (skipList == null)
769 skipList = new Hashtable();
771 skipList.put(av.getSequenceSetId(), av);
775 * remove docseqs from the given alignment marking provenance appropriately
776 * and removing any references to the sequences.
781 private void removeValignmentSequences(Alignment alignment, Vector docseqs)
783 // delete these from document. This really needs to be a generic document
784 // API function derived by CASTOR.
785 Enumeration en = docseqs.elements();
786 while (en.hasMoreElements())
788 alignment.removeAlignmentSequence((AlignmentSequence) en
791 Entry pe = addProvenance(alignment.getProvenance(), "Removed "
792 + docseqs.size() + " sequences");
793 en = alignment.enumerateAlignmentAnnotation();
794 Vector toremove = new Vector();
795 while (en.hasMoreElements())
797 uk.ac.vamsas.objects.core.AlignmentAnnotation alan = (uk.ac.vamsas.objects.core.AlignmentAnnotation) en
799 if (alan.getSeqrefsCount() > 0)
802 Vector storem = new Vector();
803 Enumeration sr = alan.enumerateSeqrefs();
804 while (sr.hasMoreElements())
806 Object alsr = sr.nextElement();
807 if (docseqs.contains(alsr))
809 storem.addElement(alsr);
812 // remove references to the deleted sequences
813 sr = storem.elements();
814 while (sr.hasMoreElements())
816 alan.removeSeqrefs(sr.nextElement());
819 if (alan.getSeqrefsCount() == 0)
821 // should then delete alan from dataset
822 toremove.addElement(alan);
826 // remove any annotation that used to be associated to a specific bunch of
828 en = toremove.elements();
829 while (en.hasMoreElements())
832 .removeAlignmentAnnotation((uk.ac.vamsas.objects.core.AlignmentAnnotation) en
835 // TODO: search through alignment annotations to remove any references to
836 // this alignment sequence
840 * sync a jalview alignment seuqence into a vamsas alignment assumes all lock
841 * transformation/bindings have been sorted out before hand. creates/syncs the
842 * vamsas alignment sequence for jvalsq and adds it to the alignment if
843 * necessary. unbounddocseq is a duplicate of the vamsas alignment sequences
844 * and these are removed after being processed w.r.t a bound jvalsq
847 private boolean syncToAlignmentSequence(SequenceI jvalsq,
848 Alignment alignment, Vector unbounddocseq)
850 boolean modal = false;
851 // todo: islocked method here
852 boolean up2doc = false;
853 AlignmentSequence alseq = (AlignmentSequence) getjv2vObj(jvalsq);
856 alseq = new AlignmentSequence();
861 if (unbounddocseq != null)
863 unbounddocseq.removeElement(alseq);
866 // boolean locked = (alignment.getModifiable()==null ||
867 // alignment.getModifiable().length()>0);
868 // TODO: VAMSAS: translate lowercase symbols to annotation ?
869 if (up2doc || !alseq.getSequence().equals(jvalsq.getSequenceAsString()))
871 alseq.setSequence(jvalsq.getSequenceAsString());
872 alseq.setStart(jvalsq.getStart());
873 alseq.setEnd(jvalsq.getEnd());
876 if (up2doc || !alseq.getName().equals(jvalsq.getName()))
879 alseq.setName(jvalsq.getName());
881 if (jvalsq.getDescription() != null
882 && (alseq.getDescription() == null || !jvalsq.getDescription()
883 .equals(alseq.getDescription())))
886 alseq.setDescription(jvalsq.getDescription());
888 if (getjv2vObj(jvalsq.getDatasetSequence()) == null)
891 .warn("Serious Implementation error - Unbound dataset sequence in alignment: "
892 + jvalsq.getDatasetSequence());
894 alseq.setRefid(getjv2vObj(jvalsq.getDatasetSequence()));
898 alignment.addAlignmentSequence(alseq);
899 bindjvvobj(jvalsq, alseq);
901 return up2doc || modal;
905 * locally sync a jalview alignment seuqence from a vamsas alignment assumes
906 * all lock transformation/bindings have been sorted out before hand.
907 * creates/syncs the jvalsq from the alignment sequence
909 private boolean syncFromAlignmentSequence(AlignmentSequence valseq,
910 char valGapchar, char gapChar, List<SequenceI> dsseqs)
913 boolean modal = false;
914 // todo: islocked method here
915 boolean upFromdoc = false;
916 jalview.datamodel.SequenceI alseq = (SequenceI) getvObj2jv(valseq);
924 // boolean locked = (alignment.getModifiable()==null ||
925 // alignment.getModifiable().length()>0);
926 // TODO: VAMSAS: translate lowercase symbols to annotation ?
928 || !valseq.getSequence().equals(alseq.getSequenceAsString()))
930 // this might go *horribly* wrong
931 alseq.setSequence(new String(valseq.getSequence()).replace(
932 valGapchar, gapChar));
933 alseq.setStart((int) valseq.getStart());
934 alseq.setEnd((int) valseq.getEnd());
937 if (!valseq.getName().equals(alseq.getName()))
940 alseq.setName(valseq.getName());
942 if (alseq.getDescription() == null
943 || (valseq.getDescription() != null && !alseq
944 .getDescription().equals(valseq.getDescription())))
946 alseq.setDescription(valseq.getDescription());
949 if (modal && Cache.log.isDebugEnabled())
951 Cache.log.debug("Updating apparently edited sequence "
957 alseq = new jalview.datamodel.Sequence(valseq.getName(), valseq
958 .getSequence().replace(valGapchar, gapChar),
959 (int) valseq.getStart(), (int) valseq.getEnd());
961 Vobject datsetseq = (Vobject) valseq.getRefid();
962 if (datsetseq != null)
964 alseq.setDatasetSequence((SequenceI) getvObj2jv(datsetseq)); // exceptions
965 if (valseq.getDescription() != null)
967 alseq.setDescription(valseq.getDescription());
971 // inherit description line from dataset.
972 if (alseq.getDatasetSequence().getDescription() != null)
974 alseq.setDescription(alseq.getDatasetSequence()
989 .error("Invalid dataset sequence id (null) for alignment sequence "
990 + valseq.getVorbaId());
992 bindjvvobj(alseq, valseq);
993 alseq.setVamsasId(valseq.getVorbaId().getId());
996 Vobject datsetseq = (Vobject) valseq.getRefid();
997 if (datsetseq != null)
999 if (datsetseq != alseq.getDatasetSequence())
1003 alseq.setDatasetSequence((SequenceI) getvObj2jv(datsetseq)); // exceptions
1005 return upFromdoc || modal;
1008 private void initRangeAnnotationType(RangeAnnotation an,
1009 AlignmentAnnotation alan, int[] gapMap)
1011 Seg vSeg = new Seg();
1013 vSeg.setInclusive(true);
1014 vSeg.setEnd(gapMap.length);
1017 // LATER: much of this is verbatim from the alignmentAnnotation
1018 // method below. suggests refactoring to make rangeAnnotation the
1020 an.setDescription(alan.description);
1021 an.setLabel(alan.label);
1022 an.setGroup(Integer.toString(alan.graphGroup));
1031 AnnotationElement ae;
1032 for (int a = 0; a < alan.annotations.length; a++)
1034 if (alan.annotations[a] == null)
1039 ae = new AnnotationElement();
1040 ae.setDescription(alan.annotations[a].description);
1041 ae.addGlyph(new Glyph());
1042 ae.getGlyph(0).setContent(alan.annotations[a].displayCharacter); // assume
1049 if (alan.graph != jalview.datamodel.AlignmentAnnotation.NO_GRAPH)
1051 ae.addValue(alan.annotations[a].value);
1053 ae.setPosition(gapMap[a] + 1); // position w.r.t. AlignmentSequence
1055 if (alan.annotations[a].secondaryStructure != ' ')
1057 // we only write an annotation where it really exists.
1058 Glyph ss = new Glyph();
1059 ss.setDict(uk.ac.vamsas.objects.utils.GlyphDictionary.PROTEIN_SS_3STATE);
1060 ss.setContent(String
1061 .valueOf(alan.annotations[a].secondaryStructure));
1064 an.addAnnotationElement(ae);
1069 private void saveDatasetSequenceAnnotation(HashMap AlSeqMaps,
1070 uk.ac.vamsas.objects.core.Sequence sref, AlignmentAnnotation alan)
1074 // objects.core.AlignmentSequence alsref = (uk.ac.vamsas.
1075 // objects.core.AlignmentSequence) sref;
1076 uk.ac.vamsas.objects.core.DataSetAnnotations an = (uk.ac.vamsas.objects.core.DataSetAnnotations) getjv2vObj(alan);
1077 int[] gapMap = getGapMap(AlSeqMaps, alan);
1080 an = new uk.ac.vamsas.objects.core.DataSetAnnotations();
1081 initRangeAnnotationType(an, alan, gapMap);
1083 an.setProvenance(dummyProvenance()); // get provenance as user
1084 // created, or jnet, or
1086 setAnnotationType(an, alan);
1087 an.setGroup(Integer.toString(alan.graphGroup)); // // JBPNote -
1095 if (alan.getThreshold() != null && alan.getThreshold().displayed)
1097 an.addProperty(Properties.newProperty(THRESHOLD,
1098 Properties.FLOATTYPE, "" + alan.getThreshold().value));
1099 if (alan.getThreshold().label != null)
1101 an.addProperty(Properties.newProperty(THRESHOLD + "Name",
1102 Properties.STRINGTYPE, "" + alan.getThreshold().label));
1105 ((DataSet) sref.getV_parent()).addDataSetAnnotations(an);
1106 bindjvvobj(alan, an);
1110 // update reference sequence Annotation
1111 if (an.getModifiable() == null) // TODO: USE VAMSAS LIBRARY OBJECT LOCK
1114 // verify existing alignment sequence annotation is up to date
1115 System.out.println("update dataset sequence annotation.");
1119 // verify existing alignment sequence annotation is up to date
1121 .println("make new alignment dataset sequence annotation if modification has happened.");
1127 private int[] getGapMap(HashMap AlSeqMaps, AlignmentAnnotation alan)
1130 if (AlSeqMaps.containsKey(alan.sequenceRef))
1132 gapMap = (int[]) AlSeqMaps.get(alan.sequenceRef);
1136 gapMap = new int[alan.sequenceRef.getLength()];
1137 // map from alignment position to sequence position.
1138 int[] sgapMap = alan.sequenceRef.gapMap();
1139 for (int a = 0; a < sgapMap.length; a++)
1141 gapMap[sgapMap[a]] = a;
1147 private void saveAlignmentSequenceAnnotation(HashMap AlSeqMaps,
1148 AlignmentSequence alsref, AlignmentAnnotation alan)
1152 // objects.core.AlignmentSequence alsref = (uk.ac.vamsas.
1153 // objects.core.AlignmentSequence) sref;
1154 uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation an = (uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation) getjv2vObj(alan);
1155 int[] gapMap = getGapMap(AlSeqMaps, alan);
1158 an = new uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation();
1159 initRangeAnnotationType(an, alan, gapMap);
1161 * I mean here that we don't actually have a semantic 'type' for the
1162 * annotation (this might be - score, intrinsic property, measurement,
1163 * something extracted from another program, etc)
1165 an.setType(JALVIEW_ANNOTATION_ROW); // TODO: better fix
1166 // this rough guess ;)
1167 alsref.addAlignmentSequenceAnnotation(an);
1168 bindjvvobj(alan, an);
1169 // These properties are directly supported by the
1170 // AlignmentSequenceAnnotation type.
1171 setAnnotationType(an, alan);
1172 an.setProvenance(dummyProvenance()); // get provenance as user
1173 // created, or jnet, or
1178 // update reference sequence Annotation
1179 if (an.getModifiable() == null) // TODO: USE VAMSAS LIBRARY OBJECT LOCK
1182 // verify existing alignment sequence annotation is up to date
1183 System.out.println("update alignment sequence annotation.");
1187 // verify existing alignment sequence annotation is up to date
1189 .println("make new alignment sequence annotation if modification has happened.");
1195 * set vamsas annotation object type from jalview annotation
1200 private void setAnnotationType(RangeAnnotation an,
1201 AlignmentAnnotation alan)
1203 if (an instanceof AlignmentSequenceAnnotation)
1205 if (alan.graph != AlignmentAnnotation.NO_GRAPH)
1207 ((AlignmentSequenceAnnotation) an).setGraph(true);
1211 ((AlignmentSequenceAnnotation) an).setGraph(false);
1214 if (an instanceof uk.ac.vamsas.objects.core.AlignmentAnnotation)
1216 if (alan.graph != AlignmentAnnotation.NO_GRAPH)
1218 ((uk.ac.vamsas.objects.core.AlignmentAnnotation) an).setGraph(true);
1222 ((uk.ac.vamsas.objects.core.AlignmentAnnotation) an)
1228 case AlignmentAnnotation.BAR_GRAPH:
1229 an.addProperty(Properties.newProperty(DISCRETE_ANNOTATION,
1230 Properties.BOOLEANTYPE, "true"));
1232 case AlignmentAnnotation.LINE_GRAPH:
1233 an.addProperty(Properties.newProperty(CONTINUOUS_ANNOTATION,
1234 Properties.BOOLEANTYPE, "true"));
1237 // don't add any kind of discrete or continous property info.
1242 * get start<end range of segment, adjusting for inclusivity flag and
1246 * @param ensureDirection
1247 * when true - always ensure start is less than end.
1248 * @return int[] { start, end, direction} where direction==1 for range running
1249 * from end to start.
1251 private int[] getSegRange(Seg visSeg, boolean ensureDirection)
1253 boolean incl = visSeg.getInclusive();
1254 // adjust for inclusive flag.
1255 int pol = (visSeg.getStart() <= visSeg.getEnd()) ? 1 : -1; // polarity of
1257 int start = visSeg.getStart() + (incl ? 0 : pol);
1258 int end = visSeg.getEnd() + (incl ? 0 : -pol);
1259 if (ensureDirection && pol == -1)
1261 // jalview doesn't deal with inverted ranges, yet.
1266 return new int[] { start, end, pol < 0 ? 1 : 0 };
1272 * @return true if annotation is not to be stored in document
1274 private boolean isJalviewOnly(AlignmentAnnotation annotation)
1276 return annotation.autoCalculated || annotation.label.equals("Quality")
1277 || annotation.label.equals("Conservation")
1278 || annotation.label.equals("Consensus");
1281 boolean dojvsync = true;
1283 // boolean dojvsync = false; // disables Jalview AppData IO
1285 * list of alignment views created when updating Jalview from document.
1287 private final Vector newAlignmentViews = new Vector();
1290 * update local jalview view settings from the stored appdata (if any)
1292 public void updateJalviewFromAppdata()
1294 // recover any existing Jalview data from appdata
1295 // TODO: recover any PDB files stored as attachments in the vamsas session
1296 // and initialise the Jalview2XML.alreadyLoadedPDB hashtable with mappings
1299 final IClientAppdata cappdata = cdoc.getClientAppdata();
1300 if (cappdata != null)
1302 if (cappdata.hasClientAppdata())
1304 // TODO: how to check version of Jalview client app data and whether
1305 // it has been modified
1306 // client data is shared over all app clients
1309 jalview.gui.Jalview2XML fromxml = new jalview.gui.Jalview2XML();
1310 fromxml.attemptversion1parse = false;
1311 fromxml.setUniqueSetSuffix("");
1312 fromxml.setObjectMappingTables(vobj2jv, jv2vobj); // mapKeysToString
1314 // mapValuesToString
1315 fromxml.setSkipList(skipList);
1316 jalview.util.jarInputStreamProvider jprovider = new jalview.util.jarInputStreamProvider()
1320 public String getFilename()
1323 // TODO Get the vamsas session ID here
1324 return "Jalview Vamsas Document Client Data";
1328 public JarInputStream getJarInputStream() throws IOException
1330 jalview.bin.Cache.log
1331 .debug("Returning client input stream for Jalview from Vamsas Document.");
1332 return new JarInputStream(cappdata.getClientInputStream());
1337 fromxml.loadJalviewAlign(jprovider);
1339 } catch (Exception e)
1342 } catch (OutOfMemoryError e)
1351 if (cappdata.hasUserAppdata())
1353 // TODO: how to check version of Jalview user app data and whether it
1354 // has been modified
1355 // user data overrides data shared over all app clients ?
1358 jalview.gui.Jalview2XML fromxml = new jalview.gui.Jalview2XML();
1359 fromxml.attemptversion1parse = false;
1360 fromxml.setUniqueSetSuffix("");
1361 fromxml.setSkipList(skipList);
1362 fromxml.setObjectMappingTables(mapKeysToString(vobj2jv),
1363 mapValuesToString(jv2vobj));
1364 jalview.util.jarInputStreamProvider jarstream = new jalview.util.jarInputStreamProvider()
1368 public String getFilename()
1371 // TODO Get the vamsas session ID here
1372 return "Jalview Vamsas Document User Data";
1376 public JarInputStream getJarInputStream() throws IOException
1378 jalview.bin.Cache.log
1379 .debug("Returning user input stream for Jalview from Vamsas Document.");
1380 return new JarInputStream(cappdata.getUserInputStream());
1385 fromxml.loadJalviewAlign(jarstream);
1387 } catch (Exception e)
1390 } catch (OutOfMemoryError e)
1400 flushAlignViewports();
1404 * remove any spurious views generated by document synchronization
1406 private void flushAlignViewports()
1408 // remove any additional viewports originally recovered from the vamsas
1410 // search for all alignframes containing viewports generated from document
1412 // and if any contain more than one view, then remove the one generated by
1414 AlignmentViewport views[], av = null;
1415 AlignFrame af = null;
1416 Iterator newviews = newAlignmentViews.iterator();
1417 while (newviews.hasNext())
1419 av = (AlignmentViewport) newviews.next();
1420 af = Desktop.getAlignFrameFor(av);
1421 // TODO implement this : af.getNumberOfViews
1422 String seqsetidobj = av.getSequenceSetId();
1423 views = Desktop.getViewports(seqsetidobj);
1424 Cache.log.debug("Found "
1425 + (views == null ? " no " : "" + views.length)
1426 + " views for '" + av.getSequenceSetId() + "'");
1427 if (views.length > 1)
1429 // we need to close the original document view.
1431 // work out how to do this by seeing if the views are gathered.
1432 // pretty clunky but the only way to do this without adding more flags
1433 // to the align frames.
1434 boolean gathered = false;
1435 String newviewid = null;
1436 Set<AlignedCodonFrame> mappings = av.getAlignment()
1438 for (int i = 0; i < views.length; i++)
1442 AlignFrame viewframe = Desktop.getAlignFrameFor(views[i]);
1443 if (viewframe == af)
1447 newviewid = views[i].getSequenceSetId();
1451 // lose the reference to the vamsas document created view
1455 // close the view generated by the vamsas document synchronization
1462 af.closeMenuItem_actionPerformed(false);
1464 replaceJvObjMapping(seqsetidobj, newviewid);
1465 seqsetidobj = newviewid;
1466 // not sure if we need to do this:
1468 if (false) // mappings != null)
1470 // ensure sequence mappings from vamsas document view still
1472 if (mappings != null)
1474 jalview.structure.StructureSelectionManager
1475 .getStructureSelectionManager(Desktop.instance)
1476 .registerMappings(mappings);
1480 // ensure vamsas object binds to the stored views retrieved from
1482 // jalview.structure.StructureSelectionManager
1483 // .getStructureSelectionManager()
1484 // .addStructureViewerListener(viewframe.alignPanel);
1489 newAlignmentViews.clear();
1493 * replaces oldjvobject with newjvobject in the Jalview Object <> VorbaID
1496 * @param oldjvobject
1497 * @param newjvobject
1500 private void replaceJvObjMapping(Object oldjvobject, Object newjvobject)
1502 Object vobject = jv2vobj.remove(oldjvobject);
1503 if (vobject == null)
1505 // NOTE: this happens if user deletes object in one session then updates
1506 // from another client
1507 throw new Error(MessageManager.formatMessage(
1508 "error.implementation_error_old_jalview_object_not_bound",
1509 new String[] { oldjvobject.toString() }));
1511 if (newjvobject != null)
1513 jv2vobj.put(newjvobject, vobject);
1514 vobj2jv.put(vobject, newjvobject);
1519 * Update the jalview client and user appdata from the local jalview settings
1521 public void updateJalviewClientAppdata()
1523 final IClientAppdata cappdata = cdoc.getClientAppdata();
1524 if (cappdata != null)
1528 jalview.gui.Jalview2XML jxml = new jalview.gui.Jalview2XML();
1529 jxml.setObjectMappingTables(mapKeysToString(vobj2jv),
1530 mapValuesToString(jv2vobj));
1531 jxml.setSkipList(skipList);
1534 jxml.saveState(new JarOutputStream(cappdata
1535 .getClientOutputStream()));
1538 } catch (Exception e)
1540 // TODO raise GUI warning if user requests it.
1541 jalview.bin.Cache.log
1542 .error("Couldn't update jalview client application data. Giving up - local settings probably lost.",
1548 jalview.bin.Cache.log
1549 .error("Couldn't access client application data for vamsas session. This is probably a vamsas client bug.");
1554 * translate the Vobject keys to strings for use in Jalview2XML
1559 private IdentityHashMap mapValuesToString(IdentityHashMap jv2vobj2)
1561 IdentityHashMap mapped = new IdentityHashMap();
1562 Iterator keys = jv2vobj2.keySet().iterator();
1563 while (keys.hasNext())
1565 Object key = keys.next();
1566 mapped.put(key, jv2vobj2.get(key).toString());
1572 * translate the Vobject values to strings for use in Jalview2XML
1575 * @return hashtable with string values
1577 private Hashtable mapKeysToString(Hashtable vobj2jv2)
1579 Hashtable mapped = new Hashtable();
1580 Iterator keys = vobj2jv2.keySet().iterator();
1581 while (keys.hasNext())
1583 Object key = keys.next();
1584 mapped.put(key.toString(), vobj2jv2.get(key));
1590 * synchronize Jalview from the vamsas document
1592 * @return number of new views from document
1594 public int updateToJalview()
1596 VAMSAS _roots[] = cdoc.getVamsasRoots();
1598 for (int _root = 0; _root < _roots.length; _root++)
1600 VAMSAS root = _roots[_root];
1601 boolean newds = false;
1602 for (int _ds = 0, _nds = root.getDataSetCount(); _ds < _nds; _ds++)
1604 // ///////////////////////////////////
1606 DataSet dataset = root.getDataSet(_ds);
1607 int i, iSize = dataset.getSequenceCount();
1608 List<SequenceI> dsseqs;
1609 jalview.datamodel.Alignment jdataset = (jalview.datamodel.Alignment) getvObj2jv(dataset);
1611 if (jdataset == null)
1613 Cache.log.debug("Initialising new jalview dataset fields");
1615 dsseqs = new Vector();
1619 Cache.log.debug("Update jalview dataset from vamsas.");
1620 jremain = jdataset.getHeight();
1621 dsseqs = jdataset.getSequences();
1624 // TODO: test sequence merging - we preserve existing non vamsas
1625 // sequences but add in any new vamsas ones, and don't yet update any
1626 // sequence attributes
1627 for (i = 0; i < iSize; i++)
1629 Sequence vdseq = dataset.getSequence(i);
1630 jalview.io.vamsas.Datasetsequence dssync = new Datasetsequence(
1633 jalview.datamodel.SequenceI dsseq = (SequenceI) dssync.getJvobj();
1634 if (dssync.isAddfromdoc())
1638 if (vdseq.getDbRefCount() > 0)
1640 DbRef[] dbref = vdseq.getDbRef();
1641 for (int db = 0; db < dbref.length; db++)
1643 new jalview.io.vamsas.Dbref(this, dbref[db], vdseq, dsseq);
1646 dsseq.updatePDBIds();
1652 SequenceI[] seqs = new SequenceI[dsseqs.size()];
1653 for (i = 0, iSize = dsseqs.size(); i < iSize; i++)
1655 seqs[i] = dsseqs.get(i);
1656 dsseqs.set(i, null);
1658 jdataset = new jalview.datamodel.Alignment(seqs);
1659 Cache.log.debug("New vamsas dataset imported into jalview.");
1660 bindjvvobj(jdataset, dataset);
1663 // add any new dataset sequence feature annotations
1664 if (dataset.getDataSetAnnotations() != null)
1666 for (int dsa = 0; dsa < dataset.getDataSetAnnotationsCount(); dsa++)
1668 DataSetAnnotations dseta = dataset.getDataSetAnnotations(dsa);
1669 // TODO: deal with group annotation on datset sequences.
1670 if (dseta.getSeqRefCount() == 1)
1672 SequenceI dsSeq = (SequenceI) getvObj2jv((Vobject) dseta
1673 .getSeqRef(0)); // TODO: deal with group dataset
1677 jalview.bin.Cache.log
1678 .warn("Couldn't resolve jalview sequenceI for dataset object reference "
1679 + ((Vobject) dataset.getDataSetAnnotations(
1680 dsa).getSeqRef(0)).getVorbaId()
1685 if (dseta.getAnnotationElementCount() == 0)
1687 new jalview.io.vamsas.Sequencefeature(this, dseta, dsSeq);
1692 // TODO: deal with alignmentAnnotation style annotation
1693 // appearing on dataset sequences.
1694 // JBPNote: we could just add them to all alignments but
1695 // that may complicate cross references in the jalview
1698 .warn("Ignoring dataset annotation with annotationElements. Not yet supported in jalview.");
1705 .warn("Ignoring multiply referenced dataset sequence annotation for binding to datsaet sequence features.");
1709 if (dataset.getAlignmentCount() > 0)
1711 // LOAD ALIGNMENTS from DATASET
1713 for (int al = 0, nal = dataset.getAlignmentCount(); al < nal; al++)
1715 uk.ac.vamsas.objects.core.Alignment alignment = dataset
1717 // TODO check this handles multiple views properly
1718 AlignmentViewport av = findViewport(alignment);
1720 jalview.datamodel.AlignmentI jal = null;
1723 // TODO check that correct alignment object is retrieved when
1724 // hidden seqs exist.
1725 jal = (av.hasHiddenRows()) ? av.getAlignment()
1726 .getHiddenSequences().getFullAlignment() : av
1729 iSize = alignment.getAlignmentSequenceCount();
1730 boolean refreshal = false;
1731 Vector newasAnnots = new Vector();
1732 char gapChar = ' '; // default for new alignments read in from the
1736 dsseqs = jal.getSequences(); // for merge/update
1737 gapChar = jal.getGapCharacter();
1741 dsseqs = new Vector();
1743 char valGapchar = alignment.getGapChar().charAt(0);
1744 for (i = 0; i < iSize; i++)
1746 AlignmentSequence valseq = alignment.getAlignmentSequence(i);
1747 jalview.datamodel.Sequence alseq = (jalview.datamodel.Sequence) getvObj2jv(valseq);
1748 if (syncFromAlignmentSequence(valseq, valGapchar, gapChar,
1749 dsseqs) && alseq != null)
1752 // updated to sequence from the document
1756 if (valseq.getAlignmentSequenceAnnotationCount() > 0)
1758 AlignmentSequenceAnnotation[] vasannot = valseq
1759 .getAlignmentSequenceAnnotation();
1760 for (int a = 0; a < vasannot.length; a++)
1762 jalview.datamodel.AlignmentAnnotation asa = (jalview.datamodel.AlignmentAnnotation) getvObj2jv(vasannot[a]); // TODO:
1770 int se[] = getBounds(vasannot[a]);
1771 asa = getjAlignmentAnnotation(jal, vasannot[a]);
1772 asa.setSequenceRef(alseq);
1773 asa.createSequenceMapping(alseq, se[0], false); // TODO:
1784 alseq.addAlignmentAnnotation(asa);
1785 bindjvvobj(asa, vasannot[a]);
1787 newasAnnots.add(asa);
1791 // update existing annotation - can do this in place
1792 if (vasannot[a].getModifiable() == null) // TODO: USE
1798 .info("UNIMPLEMENTED: not recovering user modifiable sequence alignment annotation");
1799 // TODO: should at least replace with new one - otherwise
1800 // things will break
1801 // basically do this:
1802 // int se[] = getBounds(vasannot[a]);
1803 // asa.update(getjAlignmentAnnotation(jal, vasannot[a]));
1804 // // update from another annotation object in place.
1805 // asa.createSequenceMapping(alseq, se[0], false);
1814 SequenceI[] seqs = new SequenceI[dsseqs.size()];
1815 for (i = 0, iSize = dsseqs.size(); i < iSize; i++)
1817 seqs[i] = dsseqs.get(i);
1818 dsseqs.set(i, null);
1820 jal = new jalview.datamodel.Alignment(seqs);
1821 Cache.log.debug("New vamsas alignment imported into jalview "
1822 + alignment.getVorbaId().getId());
1823 jal.setDataset(jdataset);
1825 if (newasAnnots != null && newasAnnots.size() > 0)
1827 // Add the new sequence annotations in to the alignment.
1828 for (int an = 0, anSize = newasAnnots.size(); an < anSize; an++)
1830 jal.addAnnotation((AlignmentAnnotation) newasAnnots
1832 // TODO: check if anything has to be done - like calling
1833 // adjustForAlignment or something.
1834 newasAnnots.setElementAt(null, an);
1838 // //////////////////////////////////////////
1839 // //LOAD ANNOTATIONS FOR THE ALIGNMENT
1840 // ////////////////////////////////////
1841 if (alignment.getAlignmentAnnotationCount() > 0)
1843 uk.ac.vamsas.objects.core.AlignmentAnnotation[] an = alignment
1844 .getAlignmentAnnotation();
1846 for (int j = 0; j < an.length; j++)
1848 jalview.datamodel.AlignmentAnnotation jan = (jalview.datamodel.AlignmentAnnotation) getvObj2jv(an[j]);
1851 // update or stay the same.
1852 // TODO: should at least replace with a new one - otherwise
1853 // things will break
1854 // basically do this:
1855 // jan.update(getjAlignmentAnnotation(jal, an[a])); // update
1856 // from another annotation object in place.
1859 .debug("update from vamsas alignment annotation to existing jalview alignment annotation.");
1860 if (an[j].getModifiable() == null) // TODO: USE VAMSAS
1861 // LIBRARY OBJECT LOCK
1864 // TODO: user defined annotation is totally mutable... - so
1865 // load it up or throw away if locally edited.
1867 .info("NOT IMPLEMENTED - Recovering user-modifiable annotation - yet...");
1869 // TODO: compare annotation element rows
1870 // TODO: compare props.
1874 jan = getjAlignmentAnnotation(jal, an[j]);
1875 // TODO: ensure we add the alignment annotation before the
1876 // automatic annotation rows
1877 jal.addAnnotation(jan);
1878 bindjvvobj(jan, an[j]);
1883 AlignFrame alignFrame;
1886 Cache.log.debug("New alignframe for alignment "
1887 + alignment.getVorbaId());
1888 // ///////////////////////////////
1889 // construct alignment view
1890 alignFrame = new AlignFrame(jal, AlignFrame.DEFAULT_WIDTH,
1891 AlignFrame.DEFAULT_HEIGHT, alignment.getVorbaId()
1893 av = alignFrame.getViewport();
1894 newAlignmentViews.addElement(av);
1895 String title = alignment
1898 alignment.getProvenance().getEntryCount() - 1)
1900 if (alignment.getPropertyCount() > 0)
1902 for (int p = 0, pe = alignment.getPropertyCount(); p < pe; p++)
1904 if (alignment.getProperty(p).getName().equals("title"))
1906 title = alignment.getProperty(p).getContent();
1910 // TODO: automatically create meaningful title for a vamsas
1911 // alignment using its provenance.
1912 if (Cache.log.isDebugEnabled())
1914 title = title + "(" + alignment.getVorbaId() + ")";
1917 jalview.gui.Desktop.addInternalFrame(alignFrame, title,
1918 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
1919 bindjvvobj(av.getSequenceSetId(), alignment);
1923 // find the alignFrame for jal.
1924 // TODO: fix this so we retrieve the alignFrame handing av
1925 // *directly* (JBPNote - don't understand this now)
1926 // TODO: make sure all associated views are refreshed
1927 alignFrame = Desktop.getAlignFrameFor(av);
1930 av.alignmentChanged(alignFrame.alignPanel);
1931 alignFrame.alignPanel.adjustAnnotationHeight();
1935 // /////////////////////////////////////
1936 if (alignment.getTreeCount() > 0)
1939 for (int t = 0; t < alignment.getTreeCount(); t++)
1941 jalview.io.vamsas.Tree vstree = new jalview.io.vamsas.Tree(
1942 this, alignFrame, alignment.getTree(t));
1943 TreePanel tp = null;
1944 if (vstree.isValidTree())
1946 tp = alignFrame.ShowNewickTree(vstree.getNewickTree(),
1947 vstree.getTitle(), vstree.getInputData(), 600,
1948 500, t * 20 + 50, t * 20 + 50);
1953 bindjvvobj(tp, alignment.getTree(t));
1956 vstree.UpdateSequenceTreeMap(tp);
1957 } catch (RuntimeException e)
1959 Cache.log.warn("update of labels failed.", e);
1964 Cache.log.warn("Cannot create tree for tree " + t
1966 + alignment.getTree(t).getVorbaId());
1974 // we do sequenceMappings last because they span all datasets in a vamsas
1976 for (int _ds = 0, _nds = root.getDataSetCount(); _ds < _nds; _ds++)
1978 DataSet dataset = root.getDataSet(_ds);
1979 if (dataset.getSequenceMappingCount() > 0)
1981 for (int sm = 0, smCount = dataset.getSequenceMappingCount(); sm < smCount; sm++)
1983 Rangetype seqmap = new jalview.io.vamsas.Sequencemapping(this,
1984 dataset.getSequenceMapping(sm));
1989 return newAlignmentViews.size();
1992 public AlignmentViewport findViewport(Alignment alignment)
1994 AlignmentViewport av = null;
1995 AlignmentViewport[] avs = Desktop
1996 .getViewports((String) getvObj2jv(alignment));
2004 // bitfields - should be a template in j1.5
2005 private static int HASSECSTR = 0;
2007 private static int HASVALS = 1;
2009 private static int HASHPHOB = 2;
2011 private static int HASDC = 3;
2013 private static int HASDESCSTR = 4;
2015 private static int HASTWOSTATE = 5; // not used yet.
2018 * parses the AnnotationElements - if they exist - into
2019 * jalview.datamodel.Annotation[] rows Two annotation rows are made if there
2020 * are distinct annotation for both at 'pos' and 'after pos' at any particular
2024 * @return { boolean[static int constants ], int[ae.length] - map to annotated
2025 * object frame, jalview.datamodel.Annotation[],
2026 * jalview.datamodel.Annotation[] (after)}
2028 private Object[] parseRangeAnnotation(
2029 uk.ac.vamsas.objects.core.RangeAnnotation annotation)
2031 // set these attributes by looking in the annotation to decide what kind of
2032 // alignment annotation rows will be made
2033 // TODO: potentially we might make several annotation rows from one vamsas
2034 // alignment annotation. the jv2Vobj binding mechanism
2035 // may not quite cope with this (without binding an array of annotations to
2036 // a vamsas alignment annotation)
2037 // summary flags saying what we found over the set of annotation rows.
2038 boolean[] AeContent = new boolean[] { false, false, false, false, false };
2039 int[] rangeMap = getMapping(annotation);
2040 jalview.datamodel.Annotation[][] anot = new jalview.datamodel.Annotation[][]
2041 { new jalview.datamodel.Annotation[rangeMap.length],
2042 new jalview.datamodel.Annotation[rangeMap.length] };
2043 boolean mergeable = true; // false if 'after positions cant be placed on
2044 // same annotation row as positions.
2046 if (annotation.getAnnotationElementCount() > 0)
2048 AnnotationElement ae[] = annotation.getAnnotationElement();
2049 for (int aa = 0; aa < ae.length; aa++)
2051 int pos = (int) ae[aa].getPosition() - 1; // pos counts from 1 to
2052 // (|seg.start-seg.end|+1)
2053 if (pos >= 0 && pos < rangeMap.length)
2055 int row = ae[aa].getAfter() ? 1 : 0;
2056 if (anot[row][pos] != null)
2058 // only time this should happen is if the After flag is set.
2059 Cache.log.debug("Ignoring duplicate annotation site at " + pos);
2062 if (anot[1 - row][pos] != null)
2067 if (ae[aa].getDescription() != null)
2069 desc = ae[aa].getDescription();
2070 if (desc.length() > 0)
2072 // have imported valid description string
2073 AeContent[HASDESCSTR] = true;
2076 String dc = null; // ae[aa].getDisplayCharacter()==null ? "dc" :
2077 // ae[aa].getDisplayCharacter();
2078 String ss = null; // ae[aa].getSecondaryStructure()==null ? "ss" :
2079 // ae[aa].getSecondaryStructure();
2080 java.awt.Color colour = null;
2081 if (ae[aa].getGlyphCount() > 0)
2083 Glyph[] glyphs = ae[aa].getGlyph();
2084 for (int g = 0; g < glyphs.length; g++)
2088 .equals(uk.ac.vamsas.objects.utils.GlyphDictionary.PROTEIN_SS_3STATE))
2090 ss = glyphs[g].getContent();
2091 AeContent[HASSECSTR] = true;
2095 .equals(uk.ac.vamsas.objects.utils.GlyphDictionary.PROTEIN_HD_HYDRO))
2097 Cache.log.debug("ignoring hydrophobicity glyph marker.");
2098 AeContent[HASHPHOB] = true;
2099 char c = (dc = glyphs[g].getContent()).charAt(0);
2100 // dc may get overwritten - but we still set the colour.
2101 colour = new java.awt.Color(c == '+' ? 255 : 0,
2102 c == '.' ? 255 : 0, c == '-' ? 255 : 0);
2105 else if (glyphs[g].getDict().equals(
2106 uk.ac.vamsas.objects.utils.GlyphDictionary.DEFAULT))
2108 dc = glyphs[g].getContent();
2109 AeContent[HASDC] = true;
2114 .debug("IMPLEMENTATION TODO: Ignoring unknown glyph type "
2115 + glyphs[g].getDict());
2120 if (ae[aa].getValueCount() > 0)
2122 AeContent[HASVALS] = true;
2123 if (ae[aa].getValueCount() > 1)
2125 Cache.log.warn("ignoring additional "
2126 + (ae[aa].getValueCount() - 1)
2127 + " values in annotation element.");
2129 val = ae[aa].getValue(0);
2133 anot[row][pos] = new jalview.datamodel.Annotation(
2134 (dc != null) ? dc : "", desc,
2135 (ss != null) ? ss.charAt(0) : ' ', val);
2139 anot[row][pos] = new jalview.datamodel.Annotation(
2140 (dc != null) ? dc : "", desc,
2141 (ss != null) ? ss.charAt(0) : ' ', val, colour);
2146 Cache.log.warn("Ignoring out of bound annotation element " + aa
2147 + " in " + annotation.getVorbaId().getId());
2150 // decide on how many annotation rows are needed.
2153 for (int i = 0; i < anot[0].length; i++)
2155 if (anot[1][i] != null)
2157 anot[0][i] = anot[1][i];
2158 anot[0][i].description = anot[0][i].description + " (after)";
2159 AeContent[HASDESCSTR] = true; // we have valid description string
2168 for (int i = 0; i < anot[0].length; i++)
2170 anot[1][i].description = anot[1][i].description + " (after)";
2173 return new Object[] { AeContent, rangeMap, anot[0], anot[1] };
2177 // no annotations to parse. Just return an empty annotationElement[]
2179 return new Object[] { AeContent, rangeMap, anot[0], anot[1] };
2186 * the jalview alignment to which the annotation will be attached
2187 * (ideally - freshly updated from corresponding vamsas alignment)
2189 * @return unbound jalview alignment annotation object.
2191 private jalview.datamodel.AlignmentAnnotation getjAlignmentAnnotation(
2192 jalview.datamodel.AlignmentI jal,
2193 uk.ac.vamsas.objects.core.RangeAnnotation annotation)
2195 if (annotation == null)
2200 // hasSequenceRef=annotation.getClass().equals(uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation.class);
2201 // boolean hasProvenance=hasSequenceRef ||
2202 // (annotation.getClass().equals(uk.ac.vamsas.objects.core.AlignmentAnnotation.class));
2204 * int se[] = getBounds(annotation); if (se==null) se=new int[]
2205 * {0,jal.getWidth()-1};
2207 Object[] parsedRangeAnnotation = parseRangeAnnotation(annotation);
2208 String a_label = annotation.getLabel();
2209 String a_descr = annotation.getDescription();
2210 GraphLine gl = null;
2212 boolean interp = true; // cleared if annotation is DISCRETE
2213 // set type and other attributes from properties
2214 if (annotation.getPropertyCount() > 0)
2216 // look for special jalview properties
2217 uk.ac.vamsas.objects.core.Property[] props = annotation.getProperty();
2218 for (int p = 0; p < props.length; p++)
2220 if (props[p].getName().equalsIgnoreCase(DISCRETE_ANNOTATION))
2222 type = AlignmentAnnotation.BAR_GRAPH;
2225 else if (props[p].getName().equalsIgnoreCase(CONTINUOUS_ANNOTATION))
2227 type = AlignmentAnnotation.LINE_GRAPH;
2229 else if (props[p].getName().equalsIgnoreCase(THRESHOLD))
2234 val = new Float(props[p].getContent());
2235 } catch (Exception e)
2237 Cache.log.warn("Failed to parse threshold property");
2243 gl = new GraphLine(val.floatValue(), "", java.awt.Color.black);
2247 gl.value = val.floatValue();
2251 else if (props[p].getName().equalsIgnoreCase(THRESHOLD + "Name"))
2255 gl = new GraphLine(0, "", java.awt.Color.black);
2257 gl.label = props[p].getContent();
2261 jalview.datamodel.AlignmentAnnotation jan = null;
2262 if (a_label == null || a_label.length() == 0)
2264 a_label = annotation.getType();
2265 if (a_label.length() == 0)
2267 a_label = "Unamed annotation";
2270 if (a_descr == null || a_descr.length() == 0)
2272 a_descr = "Annotation of type '" + annotation.getType() + "'";
2274 if (parsedRangeAnnotation == null)
2277 .debug("Inserting empty annotation row elements for a whole-alignment annotation.");
2281 if (parsedRangeAnnotation[3] != null)
2283 Cache.log.warn("Ignoring 'After' annotation row in "
2284 + annotation.getVorbaId());
2286 jalview.datamodel.Annotation[] arow = (jalview.datamodel.Annotation[]) parsedRangeAnnotation[2];
2287 boolean[] has = (boolean[]) parsedRangeAnnotation[0];
2288 // VAMSAS: getGraph is only on derived annotation for alignments - in this
2289 // way its 'odd' - there is already an existing TODO about removing this
2290 // flag as being redundant
2292 * if((annotation.getClass().equals(uk.ac.vamsas.objects.core.
2293 * AlignmentAnnotation.class) &&
2294 * ((uk.ac.vamsas.objects.core.AlignmentAnnotation)annotation).getGraph())
2295 * || (hasSequenceRef=true &&
2296 * ((uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation
2297 * )annotation).getGraph())) {
2303 type = jalview.datamodel.AlignmentAnnotation.BAR_GRAPH; // default
2309 // no hints - so we ensure HPHOB display is like this.
2310 type = jalview.datamodel.AlignmentAnnotation.BAR_GRAPH;
2313 // make bounds and automatic description strings for jalview user's
2314 // benefit (these shouldn't be written back to vamsas document)
2315 boolean first = true;
2316 float min = 0, max = 1;
2318 for (int i = 0; i < arow.length; i++)
2320 if (arow[i] != null)
2322 if (i - lastval > 1 && interp)
2324 // do some interpolation *between* points
2325 if (arow[lastval] != null)
2327 float interval = arow[i].value - arow[lastval].value;
2328 interval /= i - lastval;
2329 float base = arow[lastval].value;
2330 for (int ip = lastval + 1, np = 0; ip < i; np++, ip++)
2332 arow[ip] = new jalview.datamodel.Annotation("", "", ' ',
2333 interval * np + base);
2334 // NB - Interpolated points don't get a tooltip and
2340 // check range - shouldn't we have a min and max property in the
2341 // annotation object ?
2344 min = max = arow[i].value;
2349 if (arow[i].value < min)
2351 min = arow[i].value;
2353 else if (arow[i].value > max)
2355 max = arow[i].value;
2358 // make tooltip and display char value
2359 if (!has[HASDESCSTR])
2361 arow[i].description = arow[i].value + "";
2367 if (arow[i].description != null
2368 && arow[i].description.length() < 3)
2370 // copy over the description as the display char.
2371 arow[i].displayCharacter = new String(arow[i].description);
2376 // mark the position as a point used for the interpolation.
2377 arow[i].displayCharacter = arow[i].value + "";
2382 jan = new jalview.datamodel.AlignmentAnnotation(a_label, a_descr,
2383 arow, min, max, type);
2387 if (annotation.getAnnotationElementCount() == 0)
2389 // empty annotation array
2390 // TODO: alignment 'features' compare rangeType spec to alignment
2391 // width - if it is not complete, then mark regions on the annotation
2394 jan = new jalview.datamodel.AlignmentAnnotation(a_label, a_descr,
2396 jan.setThreshold(null);
2397 jan.annotationId = annotation.getVorbaId().toString(); // keep all the
2400 if (annotation.getLinkCount() > 0)
2402 Cache.log.warn("Ignoring " + annotation.getLinkCount()
2403 + "links added to AlignmentAnnotation.");
2405 if (annotation.getModifiable() == null
2406 || annotation.getModifiable().length() == 0) // TODO: USE VAMSAS
2410 jan.editable = true;
2414 if (annotation.getGroup() != null
2415 && annotation.getGroup().length() > 0)
2417 jan.graphGroup = Integer.parseInt(annotation.getGroup()); // TODO:
2425 } catch (Exception e)
2428 .info("UNIMPLEMENTED : Couldn't parse non-integer group value for setting graphGroup correctly.");
2438 * get real bounds of a RangeType's specification. start and end are an
2439 * inclusive range within which all segments and positions lie. TODO: refactor
2443 * @return int[] { start, end}
2445 private int[] getBounds(RangeType dseta)
2450 if (dseta.getSegCount() > 0 && dseta.getPosCount() > 0)
2454 .getString("error.invalid_vamsas_rangetype_cannot_resolve_lists"));
2456 if (dseta.getSegCount() > 0)
2458 se = getSegRange(dseta.getSeg(0), true);
2459 for (int s = 1, sSize = dseta.getSegCount(); s < sSize; s++)
2461 int nse[] = getSegRange(dseta.getSeg(s), true);
2472 if (dseta.getPosCount() > 0)
2474 // could do a polarity for pos range too. and pass back indication of
2476 int pos = dseta.getPos(0).getI();
2477 se = new int[] { pos, pos };
2478 for (int p = 0, pSize = dseta.getPosCount(); p < pSize; p++)
2480 pos = dseta.getPos(p).getI();
2497 * map from a rangeType's internal frame to the referenced object's coordinate
2501 * @return int [] { ref(pos)...} for all pos in rangeType's frame.
2503 private int[] getMapping(RangeType dseta)
2505 Vector posList = new Vector();
2509 if (dseta.getSegCount() > 0 && dseta.getPosCount() > 0)
2513 .getString("error.invalid_vamsas_rangetype_cannot_resolve_lists"));
2515 if (dseta.getSegCount() > 0)
2517 for (int s = 0, sSize = dseta.getSegCount(); s < sSize; s++)
2519 se = getSegRange(dseta.getSeg(s), false);
2520 int se_end = se[1 - se[2]] + (se[2] == 0 ? 1 : -1);
2521 for (int p = se[se[2]]; p != se_end; p += se[2] == 0 ? 1 : -1)
2523 posList.add(new Integer(p));
2527 else if (dseta.getPosCount() > 0)
2529 int pos = dseta.getPos(0).getI();
2531 for (int p = 0, pSize = dseta.getPosCount(); p < pSize; p++)
2533 pos = dseta.getPos(p).getI();
2534 posList.add(new Integer(pos));
2538 if (posList != null && posList.size() > 0)
2540 int[] range = new int[posList.size()];
2541 for (int i = 0; i < range.length; i++)
2543 range[i] = ((Integer) posList.elementAt(i)).intValue();
2554 * where the from range is the local mapped range, and the to range
2555 * is the 'mapped' range in the MapRangeType
2556 * @param default unit for local
2557 * @param default unit for mapped
2560 private jalview.util.MapList parsemapType(MapType maprange, int localu,
2563 jalview.util.MapList ml = null;
2564 int[] localRange = getMapping(maprange.getLocal());
2565 int[] mappedRange = getMapping(maprange.getMapped());
2566 long lu = maprange.getLocal().hasUnit() ? maprange.getLocal().getUnit()
2568 long mu = maprange.getMapped().hasUnit() ? maprange.getMapped()
2569 .getUnit() : mappedu;
2570 ml = new jalview.util.MapList(localRange, mappedRange, (int) lu,
2576 * initialise a range type object from a set of start/end inclusive intervals
2581 private void initRangeType(RangeType mrt, List<int[]> ranges)
2583 for (int[] range : ranges)
2585 Seg vSeg = new Seg();
2586 vSeg.setStart(range[0]);
2587 vSeg.setEnd(range[1]);
2593 * initialise a MapType object from a MapList object.
2599 private void initMapType(MapType maprange, jalview.util.MapList ml,
2602 maprange.setLocal(new Local());
2603 maprange.setMapped(new Mapped());
2604 initRangeType(maprange.getLocal(), ml.getFromRanges());
2605 initRangeType(maprange.getMapped(), ml.getToRanges());
2608 maprange.getLocal().setUnit(ml.getFromRatio());
2609 maprange.getLocal().setUnit(ml.getToRatio());
2614 * not needed now. Provenance getVamsasProvenance(jalview.datamodel.Provenance
2615 * jprov) { jalview.datamodel.ProvenanceEntry[] entries = null; // TODO: fix
2616 * App and Action here. Provenance prov = new Provenance();
2617 * org.exolab.castor.types.Date date = new org.exolab.castor.types.Date( new
2618 * java.util.Date()); Entry provEntry;
2620 * if (jprov != null) { entries = jprov.getEntries(); for (int i = 0; i <
2621 * entries.length; i++) { provEntry = new Entry(); try { date = new
2622 * org.exolab.castor.types.Date(entries[i].getDate()); } catch (Exception ex)
2623 * { ex.printStackTrace();
2625 * date = new org.exolab.castor.types.Date(entries[i].getDate()); }
2626 * provEntry.setDate(date); provEntry.setUser(entries[i].getUser());
2627 * provEntry.setAction(entries[i].getAction()); prov.addEntry(provEntry); } }
2628 * else { provEntry = new Entry(); provEntry.setDate(date);
2629 * provEntry.setUser(System.getProperty("user.name")); // TODO: ext string
2630 * provEntry.setApp("JVAPP"); // TODO: ext string provEntry.setAction(action);
2631 * prov.addEntry(provEntry); }
2635 jalview.datamodel.Provenance getJalviewProvenance(Provenance prov)
2637 // TODO: fix App and Action entries and check use of provenance in jalview.
2638 jalview.datamodel.Provenance jprov = new jalview.datamodel.Provenance();
2639 for (int i = 0; i < prov.getEntryCount(); i++)
2641 jprov.addEntry(prov.getEntry(i).getUser(), prov.getEntry(i)
2642 .getAction(), prov.getEntry(i).getDate(), prov.getEntry(i)
2651 * @return default initial provenance list for a Jalview created vamsas
2654 Provenance dummyProvenance()
2656 return dummyProvenance(null);
2659 Entry dummyPEntry(String action)
2661 Entry entry = new Entry();
2662 entry.setApp(this.provEntry.getApp());
2665 entry.setAction(action);
2669 entry.setAction("created.");
2671 entry.setDate(new java.util.Date());
2672 entry.setUser(this.provEntry.getUser());
2676 Provenance dummyProvenance(String action)
2678 Provenance prov = new Provenance();
2679 prov.addEntry(dummyPEntry(action));
2683 Entry addProvenance(Provenance p, String action)
2685 Entry dentry = dummyPEntry(action);
2690 public Entry getProvEntry()
2695 public IClientDocument getClientDocument()
2700 public IdentityHashMap getJvObjectBinding()
2705 public Hashtable getVamsasObjectBinding()
2710 public void storeSequenceMappings(AlignmentViewport viewport, String title)
2713 AlignmentViewport av = viewport;
2716 jalview.datamodel.AlignmentI jal = av.getAlignment();
2717 // /////////////////////////////////////////
2719 DataSet dataset = null;
2720 if (jal.getDataset() == null)
2722 Cache.log.warn("Creating new dataset for an alignment.");
2723 jal.setDataset(null);
2725 dataset = (DataSet) ((Alignment) getjv2vObj(viewport
2726 .getSequenceSetId())).getV_parent(); // jal.getDataset());
2727 if (dataset == null)
2729 dataset = (DataSet) getjv2vObj(jal.getDataset());
2731 .error("Can't find the correct dataset for the alignment in this view. Creating new one.");
2734 // Store any sequence mappings.
2735 Set<AlignedCodonFrame> cframes = av.getAlignment().getCodonFrames();
2736 if (cframes != null)
2738 for (AlignedCodonFrame acf : cframes)
2740 if (acf.getdnaSeqs() != null && acf.getdnaSeqs().length > 0)
2742 jalview.datamodel.SequenceI[] dmps = acf.getdnaSeqs();
2743 jalview.datamodel.Mapping[] mps = acf.getProtMappings();
2744 for (int smp = 0; smp < mps.length; smp++)
2746 uk.ac.vamsas.objects.core.SequenceType mfrom = (SequenceType) getjv2vObj(dmps[smp]);
2749 new jalview.io.vamsas.Sequencemapping(this, mps[smp],
2755 .warn("NO Vamsas Binding for local sequence! NOT CREATING MAPPING FOR "
2756 + dmps[smp].getDisplayId(true)
2758 + mps[smp].getTo().getName());
2764 } catch (Exception e)
2766 throw new Exception(MessageManager.formatMessage(
2767 "exception.couldnt_store_sequence_mappings",
2768 new String[] { title }), e);
2772 public void clearSkipList()
2774 if (skipList != null)
2781 * @return the skipList
2783 public Hashtable getSkipList()
2790 * the skipList to set
2792 public void setSkipList(Hashtable skipList)
2794 this.skipList = skipList;
2798 * registry for datastoreItems
2800 DatastoreRegistry dsReg = new DatastoreRegistry();
2802 public DatastoreRegistry getDatastoreRegisty()
2806 dsReg = new DatastoreRegistry();