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.Console;
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.project.Jalview2XML;
37 import jalview.util.MessageManager;
38 import jalview.viewmodel.AlignmentViewport;
40 import java.io.IOException;
41 import java.util.Enumeration;
42 import java.util.HashMap;
43 import java.util.Hashtable;
44 import java.util.IdentityHashMap;
45 import java.util.Iterator;
46 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.getDesktopAlignFrames();
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 "IMPLEMENTATION ERROR?: Unexpected mapping for unmapped jalview string object content:"
188 + seqsetidobj + " to object " + obj);
194 Console.warn("Unexpected mapping for Jalview String Object ID "
195 + seqsetidobj + " to another jalview dataset object "
201 if (Console.isDebugEnabled())
204 "Returning null VorbaID binding for jalview object " + jvobj);
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 "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 Console.error("Failed to get id for "
241 + (vobj.isRegisterable() ? "registerable"
243 + " object " + vobj);
247 if (vobj2jv.containsKey(vobj.getVorbaId())
248 && !((VorbaId) vobj2jv.get(vobj.getVorbaId())).equals(jvobj))
251 "Warning? Overwriting existing vamsas id binding for "
253 new Exception(MessageManager.getString(
254 "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 "
262 new Exception("Overwriting jalview object binding."));
265 * Cache.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 Console.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 Console.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())
342 "IMPLEMENTATION ERROR: Cannot map an alignment of sequences from different datasets into a single alignment in the vamsas document.");
352 Console.warn("Creating new vamsas dataset for alignment view "
353 + av.getSequenceSetId());
354 // we create a new dataset on the default vamsas root.
355 root = cdoc.getVamsasRoots()[0]; // default vamsas root for modifying.
356 dataset = new DataSet();
357 root.addDataSet(dataset);
358 bindjvvobj(jds, dataset);
359 dataset.setProvenance(dummyProvenance());
360 // dataset.getProvenance().addEntry(provEntry);
365 root = (VAMSAS) dataset.getV_parent();
369 // set new dataset and alignment sequences based on alignment Nucleotide
371 // this *will* break when alignment contains both nucleotide and amino
373 String dict = jal.isNucleotide()
374 ? uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_NA
375 : uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_AA;
376 Vector dssmods = new Vector();
377 for (int i = 0; i < jal.getHeight(); i++)
379 SequenceI sq = jal.getSequenceAt(i).getDatasetSequence(); // only insert
383 Datasetsequence dssync = new jalview.io.vamsas.Datasetsequence(this,
385 sequence = (Sequence) dssync.getVobj();
386 if (dssync.getModified())
388 dssmods.addElement(sequence);
392 if (dssmods.size() > 0)
396 Entry pentry = this.addProvenance(dataset.getProvenance(),
397 "updated sequences");
398 // pentry.addInput(vInput); could write in which sequences were
400 dssmods.removeAllElements();
403 // dataset.setProvenance(getVamsasProvenance(jal.getDataset().getProvenance()));
404 // ////////////////////////////////////////////
405 if (alignmentWillBeSkipped(av))
407 // TODO: trees could be written - but for the moment we just
409 // add to the JalviewXML skipList and ..
413 if (alignment == null)
415 alignment = new Alignment();
416 bindjvvobj(av.getSequenceSetId(), alignment);
417 if (alignment.getProvenance() == null)
419 alignment.setProvenance(new Provenance());
421 addProvenance(alignment.getProvenance(), "added"); // TODO: insert some
424 dataset.addAlignment(alignment);
426 Property title = new Property();
427 title.setName("title");
428 title.setType("string");
429 title.setContent(aFtitle);
430 alignment.addProperty(title);
432 alignment.setGapChar(String.valueOf(av.getGapCharacter()));
433 for (int i = 0; i < jal.getHeight(); i++)
435 syncToAlignmentSequence(jal.getSequenceAt(i), alignment, null);
437 alignRDHash.put(av.getSequenceSetId(), av.getUndoRedoHash());
441 // always prepare to clone the alignment
442 boolean alismod = av.isUndoRedoHashModified(
443 (long[]) alignRDHash.get(av.getSequenceSetId()));
444 // todo: verify and update mutable alignment props.
445 // TODO: Use isLocked methods
446 if (alignment.getModifiable() == null
447 || alignment.getModifiable().length() == 0)
448 // && !alignment.isDependedOn())
450 boolean modified = false;
451 // check existing sequences in local and in document.
452 Vector docseqs = new Vector(
453 alignment.getAlignmentSequenceAsReference());
454 for (int i = 0; i < jal.getHeight(); i++)
456 modified |= syncToAlignmentSequence(jal.getSequenceAt(i),
459 if (docseqs.size() > 0)
461 // removeValignmentSequences(alignment, docseqs);
462 docseqs.removeAllElements();
463 jalview.bin.Console.outPrintln(
464 "Sequence deletion from alignment is not implemented.");
472 addProvenance(alignment.getProvenance(), "Edited"); // TODO:
481 addProvenance(alignment.getProvenance(), "Attributes Edited"); // TODO:
491 jalview.bin.Console.outPrintln("update alignment in document.");
496 .outPrintln("alignment in document left unchanged.");
501 // unbind alignment from view.
502 // create new binding and new alignment.
503 // mark trail on new alignment as being derived from old ?
504 jalview.bin.Console.outPrintln(
505 "update edited alignment to new alignment in document.");
508 // ////////////////////////////////////////////
509 // SAVE Alignment Sequence Features
510 for (int i = 0, iSize = alignment
511 .getAlignmentSequenceCount(); i < iSize; i++)
513 AlignmentSequence valseq;
514 SequenceI alseq = (SequenceI) getvObj2jv(
515 valseq = alignment.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 "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(
598 an = new uk.ac.vamsas.objects.core.AlignmentAnnotation();
599 an.setType(JALVIEW_ANNOTATION_ROW);
600 an.setDescription(aa[i].description);
601 alignment.addAlignmentAnnotation(an);
602 Seg vSeg = new Seg(); // TODO: refactor to have a default
603 // rangeAnnotationType initer/updater that
604 // takes a set of int ranges.
606 vSeg.setInclusive(true);
607 vSeg.setEnd(jal.getWidth());
611 an.setGraph(true); // aa[i].graph);
613 an.setLabel(aa[i].label);
614 an.setProvenance(dummyProvenance());
615 if (aa[i].graph != AlignmentAnnotation.NO_GRAPH)
617 an.setGroup(Integer.toString(aa[i].graphGroup)); // // JBPNote
632 AnnotationElement ae;
634 for (int a = 0; a < aa[i].annotations.length; a++)
636 if ((aa[i] == null) || (aa[i].annotations[a] == null))
641 ae = new AnnotationElement();
642 ae.setDescription(aa[i].annotations[a].description);
643 ae.addGlyph(new Glyph());
645 .setContent(aa[i].annotations[a].displayCharacter); // assume
654 ae.addValue(aa[i].annotations[a].value);
656 ae.setPosition(a + 1);
657 if (aa[i].annotations[a].secondaryStructure != ' ')
659 Glyph ss = new Glyph();
661 uk.ac.vamsas.objects.utils.GlyphDictionary.PROTEIN_SS_3STATE);
662 ss.setContent(String.valueOf(
663 aa[i].annotations[a].secondaryStructure));
666 an.addAnnotationElement(ae);
670 // an.addProperty(newProperty("jalview:editable", null,
672 // an.setModifiable(""); // TODO: This is not the way the
673 // modifiable flag is supposed to be used.
675 setAnnotationType(an, aa[i]);
677 if (aa[i].graph != jalview.datamodel.AlignmentAnnotation.NO_GRAPH)
680 an.setGroup(Integer.toString(aa[i].graphGroup));
681 if (aa[i].threshold != null && aa[i].threshold.displayed)
683 an.addProperty(Properties.newProperty(THRESHOLD,
684 Properties.FLOATTYPE,
685 "" + aa[i].threshold.value));
686 if (aa[i].threshold.label != null)
688 an.addProperty(Properties.newProperty(
689 THRESHOLD + "Name", Properties.STRINGTYPE,
690 "" + aa[i].threshold.label));
699 if (an.getModifiable() == null) // TODO: USE VAMSAS LIBRARY OBJECT
702 // verify annotation - update (perhaps)
704 "update alignment sequence annotation. not yet implemented.");
708 // verify annotation - update (perhaps)
710 "updated alignment sequence annotation added.");
716 // /////////////////////////////////////////////////////
718 // //////////////////////////////////////////////
720 // /////////////////////////////////
721 // FIND ANY ASSOCIATED TREES
722 if (Desktop.desktop != null)
724 javax.swing.JInternalFrame[] frames = Desktop.instance
727 for (int t = 0; t < frames.length; t++)
729 if (frames[t] instanceof TreePanel)
731 TreePanel tp = (TreePanel) frames[t];
733 if (tp.getViewPort().getSequenceSetId()
734 .equals(av.getSequenceSetId()))
736 DatastoreItem vtree = new jalview.io.vamsas.Tree(this, tp,
742 // Store Jalview specific stuff in the Jalview appData
743 // not implemented in the SimpleDoc interface.
748 ex.printStackTrace();
755 * very quick test to see if the viewport would be stored in the vamsas
756 * document. Reasons for not storing include the unaligned flag being false
757 * (for all sequences, including the hidden ones!)
760 * @return true if alignment associated with this view will be stored in
763 public boolean alignmentWillBeSkipped(AlignmentViewport av)
765 return (!av.getAlignment().isAligned());
768 private void addToSkipList(AlignmentViewport av)
770 if (skipList == null)
772 skipList = new Hashtable();
774 skipList.put(av.getSequenceSetId(), av);
778 * remove docseqs from the given alignment marking provenance appropriately
779 * and removing any references to the sequences.
784 private void removeValignmentSequences(Alignment alignment,
787 // delete these from document. This really needs to be a generic document
788 // API function derived by CASTOR.
789 Enumeration en = docseqs.elements();
790 while (en.hasMoreElements())
792 alignment.removeAlignmentSequence(
793 (AlignmentSequence) en.nextElement());
795 Entry pe = addProvenance(alignment.getProvenance(),
796 "Removed " + docseqs.size() + " sequences");
797 en = alignment.enumerateAlignmentAnnotation();
798 Vector toremove = new Vector();
799 while (en.hasMoreElements())
801 uk.ac.vamsas.objects.core.AlignmentAnnotation alan = (uk.ac.vamsas.objects.core.AlignmentAnnotation) en
803 if (alan.getSeqrefsCount() > 0)
806 Vector storem = new Vector();
807 Enumeration sr = alan.enumerateSeqrefs();
808 while (sr.hasMoreElements())
810 Object alsr = sr.nextElement();
811 if (docseqs.contains(alsr))
813 storem.addElement(alsr);
816 // remove references to the deleted sequences
817 sr = storem.elements();
818 while (sr.hasMoreElements())
820 alan.removeSeqrefs(sr.nextElement());
823 if (alan.getSeqrefsCount() == 0)
825 // should then delete alan from dataset
826 toremove.addElement(alan);
830 // remove any annotation that used to be associated to a specific bunch of
832 en = toremove.elements();
833 while (en.hasMoreElements())
835 alignment.removeAlignmentAnnotation(
836 (uk.ac.vamsas.objects.core.AlignmentAnnotation) en
839 // TODO: search through alignment annotations to remove any references to
840 // this alignment sequence
844 * sync a jalview alignment seuqence into a vamsas alignment assumes all lock
845 * transformation/bindings have been sorted out before hand. creates/syncs the
846 * vamsas alignment sequence for jvalsq and adds it to the alignment if
847 * necessary. unbounddocseq is a duplicate of the vamsas alignment sequences
848 * and these are removed after being processed w.r.t a bound jvalsq
851 private boolean syncToAlignmentSequence(SequenceI jvalsq,
852 Alignment alignment, Vector unbounddocseq)
854 boolean modal = false;
855 // todo: islocked method here
856 boolean up2doc = false;
857 AlignmentSequence alseq = (AlignmentSequence) getjv2vObj(jvalsq);
860 alseq = new AlignmentSequence();
865 if (unbounddocseq != null)
867 unbounddocseq.removeElement(alseq);
870 // boolean locked = (alignment.getModifiable()==null ||
871 // alignment.getModifiable().length()>0);
872 // TODO: VAMSAS: translate lowercase symbols to annotation ?
873 if (up2doc || !alseq.getSequence().equals(jvalsq.getSequenceAsString()))
875 alseq.setSequence(jvalsq.getSequenceAsString());
876 alseq.setStart(jvalsq.getStart());
877 alseq.setEnd(jvalsq.getEnd());
880 if (up2doc || !alseq.getName().equals(jvalsq.getName()))
883 alseq.setName(jvalsq.getName());
885 if (jvalsq.getDescription() != null && (alseq.getDescription() == null
886 || !jvalsq.getDescription().equals(alseq.getDescription())))
889 alseq.setDescription(jvalsq.getDescription());
891 if (getjv2vObj(jvalsq.getDatasetSequence()) == null)
894 "Serious Implementation error - Unbound dataset sequence in alignment: "
895 + jvalsq.getDatasetSequence());
897 alseq.setRefid(getjv2vObj(jvalsq.getDatasetSequence()));
901 alignment.addAlignmentSequence(alseq);
902 bindjvvobj(jvalsq, alseq);
904 return up2doc || modal;
908 * locally sync a jalview alignment seuqence from a vamsas alignment assumes
909 * all lock transformation/bindings have been sorted out before hand.
910 * creates/syncs the jvalsq from the alignment sequence
912 private boolean syncFromAlignmentSequence(AlignmentSequence valseq,
913 char valGapchar, char gapChar, List<SequenceI> dsseqs)
916 boolean modal = false;
917 // todo: islocked method here
918 boolean upFromdoc = false;
919 jalview.datamodel.SequenceI alseq = (SequenceI) getvObj2jv(valseq);
927 // boolean locked = (alignment.getModifiable()==null ||
928 // alignment.getModifiable().length()>0);
929 // TODO: VAMSAS: translate lowercase symbols to annotation ?
931 || !valseq.getSequence().equals(alseq.getSequenceAsString()))
933 // this might go *horribly* wrong
934 alseq.setSequence(new String(valseq.getSequence())
935 .replace(valGapchar, gapChar));
936 alseq.setStart((int) valseq.getStart());
937 alseq.setEnd((int) valseq.getEnd());
940 if (!valseq.getName().equals(alseq.getName()))
943 alseq.setName(valseq.getName());
945 if (alseq.getDescription() == null || (valseq.getDescription() != null
946 && !alseq.getDescription().equals(valseq.getDescription())))
948 alseq.setDescription(valseq.getDescription());
951 if (modal && Console.isDebugEnabled())
954 "Updating apparently edited sequence " + alseq.getName());
959 alseq = new jalview.datamodel.Sequence(valseq.getName(),
960 valseq.getSequence().replace(valGapchar, gapChar),
961 (int) valseq.getStart(), (int) valseq.getEnd());
963 Vobject datsetseq = (Vobject) valseq.getRefid();
964 if (datsetseq != null)
966 alseq.setDatasetSequence((SequenceI) getvObj2jv(datsetseq)); // exceptions
967 if (valseq.getDescription() != null)
969 alseq.setDescription(valseq.getDescription());
973 // inherit description line from dataset.
974 if (alseq.getDatasetSequence().getDescription() != null)
976 alseq.setDescription(
977 alseq.getDatasetSequence().getDescription());
991 "Invalid dataset sequence id (null) for alignment sequence "
992 + valseq.getVorbaId());
994 bindjvvobj(alseq, valseq);
995 alseq.setVamsasId(valseq.getVorbaId().getId());
998 Vobject datsetseq = (Vobject) valseq.getRefid();
999 if (datsetseq != null)
1001 if (datsetseq != alseq.getDatasetSequence())
1005 alseq.setDatasetSequence((SequenceI) getvObj2jv(datsetseq)); // exceptions
1007 return upFromdoc || modal;
1010 private void initRangeAnnotationType(RangeAnnotation an,
1011 AlignmentAnnotation alan, int[] gapMap)
1013 Seg vSeg = new Seg();
1015 vSeg.setInclusive(true);
1016 vSeg.setEnd(gapMap.length);
1019 // LATER: much of this is verbatim from the alignmentAnnotation
1020 // method below. suggests refactoring to make rangeAnnotation the
1022 an.setDescription(alan.description);
1023 an.setLabel(alan.label);
1024 an.setGroup(Integer.toString(alan.graphGroup));
1033 AnnotationElement ae;
1034 for (int a = 0; a < alan.annotations.length; a++)
1036 if (alan.annotations[a] == null)
1041 ae = new AnnotationElement();
1042 ae.setDescription(alan.annotations[a].description);
1043 ae.addGlyph(new Glyph());
1044 ae.getGlyph(0).setContent(alan.annotations[a].displayCharacter); // assume
1051 if (alan.graph != jalview.datamodel.AlignmentAnnotation.NO_GRAPH)
1053 ae.addValue(alan.annotations[a].value);
1055 ae.setPosition(gapMap[a] + 1); // position w.r.t. AlignmentSequence
1057 if (alan.annotations[a].secondaryStructure != ' ')
1059 // we only write an annotation where it really exists.
1060 Glyph ss = new Glyph();
1062 uk.ac.vamsas.objects.utils.GlyphDictionary.PROTEIN_SS_3STATE);
1064 String.valueOf(alan.annotations[a].secondaryStructure));
1067 an.addAnnotationElement(ae);
1072 private void saveDatasetSequenceAnnotation(HashMap AlSeqMaps,
1073 uk.ac.vamsas.objects.core.Sequence sref, AlignmentAnnotation alan)
1077 // objects.core.AlignmentSequence alsref = (uk.ac.vamsas.
1078 // objects.core.AlignmentSequence) sref;
1079 uk.ac.vamsas.objects.core.DataSetAnnotations an = (uk.ac.vamsas.objects.core.DataSetAnnotations) getjv2vObj(
1081 int[] gapMap = getGapMap(AlSeqMaps, alan);
1084 an = new uk.ac.vamsas.objects.core.DataSetAnnotations();
1085 initRangeAnnotationType(an, alan, gapMap);
1087 an.setProvenance(dummyProvenance()); // get provenance as user
1088 // created, or jnet, or
1090 setAnnotationType(an, alan);
1091 an.setGroup(Integer.toString(alan.graphGroup)); // // JBPNote -
1099 if (alan.getThreshold() != null && alan.getThreshold().displayed)
1101 an.addProperty(Properties.newProperty(THRESHOLD,
1102 Properties.FLOATTYPE, "" + alan.getThreshold().value));
1103 if (alan.getThreshold().label != null)
1105 an.addProperty(Properties.newProperty(THRESHOLD + "Name",
1106 Properties.STRINGTYPE, "" + alan.getThreshold().label));
1109 ((DataSet) sref.getV_parent()).addDataSetAnnotations(an);
1110 bindjvvobj(alan, an);
1114 // update reference sequence Annotation
1115 if (an.getModifiable() == null) // TODO: USE VAMSAS LIBRARY OBJECT LOCK
1118 // verify existing alignment sequence annotation is up to date
1120 .outPrintln("update dataset sequence annotation.");
1124 // verify existing alignment sequence annotation is up to date
1125 jalview.bin.Console.outPrintln(
1126 "make new alignment dataset sequence annotation if modification has happened.");
1132 private int[] getGapMap(HashMap AlSeqMaps, AlignmentAnnotation alan)
1135 if (AlSeqMaps.containsKey(alan.sequenceRef))
1137 gapMap = (int[]) AlSeqMaps.get(alan.sequenceRef);
1141 gapMap = new int[alan.sequenceRef.getLength()];
1142 // map from alignment position to sequence position.
1143 int[] sgapMap = alan.sequenceRef.gapMap();
1144 for (int a = 0; a < sgapMap.length; a++)
1146 gapMap[sgapMap[a]] = a;
1152 private void saveAlignmentSequenceAnnotation(HashMap AlSeqMaps,
1153 AlignmentSequence alsref, AlignmentAnnotation alan)
1157 // objects.core.AlignmentSequence alsref = (uk.ac.vamsas.
1158 // objects.core.AlignmentSequence) sref;
1159 uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation an = (uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation) getjv2vObj(
1161 int[] gapMap = getGapMap(AlSeqMaps, alan);
1164 an = new uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation();
1165 initRangeAnnotationType(an, alan, gapMap);
1167 * I mean here that we don't actually have a semantic 'type' for the
1168 * annotation (this might be - score, intrinsic property, measurement,
1169 * something extracted from another program, etc)
1171 an.setType(JALVIEW_ANNOTATION_ROW); // TODO: better fix
1172 // this rough guess ;)
1173 alsref.addAlignmentSequenceAnnotation(an);
1174 bindjvvobj(alan, an);
1175 // These properties are directly supported by the
1176 // AlignmentSequenceAnnotation type.
1177 setAnnotationType(an, alan);
1178 an.setProvenance(dummyProvenance()); // get provenance as user
1179 // created, or jnet, or
1184 // update reference sequence Annotation
1185 if (an.getModifiable() == null) // TODO: USE VAMSAS LIBRARY OBJECT LOCK
1188 // verify existing alignment sequence annotation is up to date
1190 .outPrintln("update alignment sequence annotation.");
1194 // verify existing alignment sequence annotation is up to date
1195 jalview.bin.Console.outPrintln(
1196 "make new alignment sequence annotation if modification has happened.");
1202 * set vamsas annotation object type from jalview annotation
1207 private void setAnnotationType(RangeAnnotation an,
1208 AlignmentAnnotation alan)
1210 if (an instanceof AlignmentSequenceAnnotation)
1212 if (alan.graph != AlignmentAnnotation.NO_GRAPH)
1214 ((AlignmentSequenceAnnotation) an).setGraph(true);
1218 ((AlignmentSequenceAnnotation) an).setGraph(false);
1221 if (an instanceof uk.ac.vamsas.objects.core.AlignmentAnnotation)
1223 if (alan.graph != AlignmentAnnotation.NO_GRAPH)
1225 ((uk.ac.vamsas.objects.core.AlignmentAnnotation) an).setGraph(true);
1229 ((uk.ac.vamsas.objects.core.AlignmentAnnotation) an)
1235 case AlignmentAnnotation.BAR_GRAPH:
1236 an.addProperty(Properties.newProperty(DISCRETE_ANNOTATION,
1237 Properties.BOOLEANTYPE, "true"));
1239 case AlignmentAnnotation.LINE_GRAPH:
1240 an.addProperty(Properties.newProperty(CONTINUOUS_ANNOTATION,
1241 Properties.BOOLEANTYPE, "true"));
1244 // don't add any kind of discrete or continous property info.
1249 * get start<end range of segment, adjusting for inclusivity flag and
1253 * @param ensureDirection
1254 * when true - always ensure start is less than end.
1255 * @return int[] { start, end, direction} where direction==1 for range running
1256 * from end to start.
1258 private int[] getSegRange(Seg visSeg, boolean ensureDirection)
1260 boolean incl = visSeg.getInclusive();
1261 // adjust for inclusive flag.
1262 int pol = (visSeg.getStart() <= visSeg.getEnd()) ? 1 : -1; // polarity of
1264 int start = visSeg.getStart() + (incl ? 0 : pol);
1265 int end = visSeg.getEnd() + (incl ? 0 : -pol);
1266 if (ensureDirection && pol == -1)
1268 // jalview doesn't deal with inverted ranges, yet.
1273 return new int[] { start, end, pol < 0 ? 1 : 0 };
1279 * @return true if annotation is not to be stored in document
1281 private boolean isJalviewOnly(AlignmentAnnotation annotation)
1283 return annotation.autoCalculated || annotation.label.equals("Quality")
1284 || annotation.label.equals("Conservation")
1285 || annotation.label.equals("Consensus");
1288 boolean dojvsync = true;
1290 // boolean dojvsync = false; // disables Jalview AppData IO
1292 * list of alignment views created when updating Jalview from document.
1294 private final Vector newAlignmentViews = new Vector();
1297 * update local jalview view settings from the stored appdata (if any)
1299 public void updateJalviewFromAppdata()
1301 // recover any existing Jalview data from appdata
1302 // TODO: recover any PDB files stored as attachments in the vamsas session
1303 // and initialise the Jalview2XML.alreadyLoadedPDB hashtable with mappings
1306 final IClientAppdata cappdata = cdoc.getClientAppdata();
1307 if (cappdata != null)
1309 if (cappdata.hasClientAppdata())
1311 // TODO: how to check version of Jalview client app data and whether
1312 // it has been modified
1313 // client data is shared over all app clients
1316 // jalview.gui.Jalview2XML fromxml = new jalview.gui.Jalview2XML();
1317 Jalview2XML fromxml = new Jalview2XML();
1318 fromxml.attemptversion1parse = false;
1319 fromxml.setUniqueSetSuffix("");
1320 fromxml.setObjectMappingTables(vobj2jv, jv2vobj); // mapKeysToString
1322 // mapValuesToString
1323 fromxml.setSkipList(skipList);
1324 jalview.util.jarInputStreamProvider jprovider = new jalview.util.jarInputStreamProvider()
1328 public String getFilename()
1331 // TODO Get the vamsas session ID here
1332 return "Jalview Vamsas Document Client Data";
1336 public JarInputStream getJarInputStream() throws IOException
1339 "Returning client input stream for Jalview from Vamsas Document.");
1340 return new JarInputStream(cappdata.getClientInputStream());
1345 fromxml.loadJalviewAlign(jprovider);
1347 } catch (Exception e)
1350 } catch (OutOfMemoryError e)
1359 if (cappdata.hasUserAppdata())
1361 // TODO: how to check version of Jalview user app data and whether it
1362 // has been modified
1363 // user data overrides data shared over all app clients ?
1366 Jalview2XML fromxml = new Jalview2XML();
1367 fromxml.attemptversion1parse = false;
1368 fromxml.setUniqueSetSuffix("");
1369 fromxml.setSkipList(skipList);
1370 fromxml.setObjectMappingTables(mapKeysToString(vobj2jv),
1371 mapValuesToString(jv2vobj));
1372 jalview.util.jarInputStreamProvider jarstream = new jalview.util.jarInputStreamProvider()
1376 public String getFilename()
1379 // TODO Get the vamsas session ID here
1380 return "Jalview Vamsas Document User Data";
1384 public JarInputStream getJarInputStream() throws IOException
1387 "Returning user input stream for Jalview from Vamsas Document.");
1388 return new JarInputStream(cappdata.getUserInputStream());
1393 fromxml.loadJalviewAlign(jarstream);
1395 } catch (Exception e)
1398 } catch (OutOfMemoryError e)
1408 flushAlignViewports();
1412 * remove any spurious views generated by document synchronization
1414 private void flushAlignViewports()
1416 // remove any additional viewports originally recovered from the vamsas
1418 // search for all alignframes containing viewports generated from document
1420 // and if any contain more than one view, then remove the one generated by
1422 AlignmentViewport views[], av = null;
1423 AlignFrame af = null;
1424 Iterator newviews = newAlignmentViews.iterator();
1425 while (newviews.hasNext())
1427 av = (AlignmentViewport) newviews.next();
1428 af = Desktop.getAlignFrameFor(av);
1429 // TODO implement this : af.getNumberOfViews
1430 String seqsetidobj = av.getSequenceSetId();
1431 views = Desktop.getViewports(seqsetidobj);
1432 Console.debug("Found " + (views == null ? " no " : "" + views.length)
1433 + " views for '" + av.getSequenceSetId() + "'");
1434 if (views.length > 1)
1436 // we need to close the original document view.
1438 // work out how to do this by seeing if the views are gathered.
1439 // pretty clunky but the only way to do this without adding more flags
1440 // to the align frames.
1441 boolean gathered = false;
1442 String newviewid = null;
1443 List<AlignedCodonFrame> mappings = av.getAlignment()
1445 for (int i = 0; i < views.length; i++)
1449 AlignFrame viewframe = Desktop.getAlignFrameFor(views[i]);
1450 if (viewframe == af)
1454 newviewid = views[i].getSequenceSetId();
1458 // lose the reference to the vamsas document created view
1462 // close the view generated by the vamsas document synchronization
1469 af.closeMenuItem_actionPerformed(false);
1471 replaceJvObjMapping(seqsetidobj, newviewid);
1472 seqsetidobj = newviewid;
1473 // not sure if we need to do this:
1475 if (false) // mappings != null)
1477 // ensure sequence mappings from vamsas document view still
1479 if (mappings != null)
1481 jalview.structure.StructureSelectionManager
1482 .getStructureSelectionManager(Desktop.instance)
1483 .registerMappings(mappings);
1487 // ensure vamsas object binds to the stored views retrieved from
1489 // jalview.structure.StructureSelectionManager
1490 // .getStructureSelectionManager()
1491 // .addStructureViewerListener(viewframe.alignPanel);
1496 newAlignmentViews.clear();
1500 * replaces oldjvobject with newjvobject in the Jalview Object <> VorbaID
1503 * @param oldjvobject
1504 * @param newjvobject
1507 private void replaceJvObjMapping(Object oldjvobject, Object newjvobject)
1509 Object vobject = jv2vobj.remove(oldjvobject);
1510 if (vobject == null)
1512 // NOTE: this happens if user deletes object in one session then updates
1513 // from another client
1514 throw new Error(MessageManager.formatMessage(
1515 "error.implementation_error_old_jalview_object_not_bound",
1517 { oldjvobject.toString() }));
1519 if (newjvobject != null)
1521 jv2vobj.put(newjvobject, vobject);
1522 vobj2jv.put(vobject, newjvobject);
1527 * Update the jalview client and user appdata from the local jalview settings
1529 public void updateJalviewClientAppdata()
1531 final IClientAppdata cappdata = cdoc.getClientAppdata();
1532 if (cappdata != null)
1536 Jalview2XML jxml = new Jalview2XML();
1537 jxml.setObjectMappingTables(mapKeysToString(vobj2jv),
1538 mapValuesToString(jv2vobj));
1539 jxml.setSkipList(skipList);
1543 new JarOutputStream(cappdata.getClientOutputStream()));
1546 } catch (Exception e)
1548 // TODO raise GUI warning if user requests it.
1550 "Couldn't update jalview client application data. Giving up - local settings probably lost.",
1557 "Couldn't access client application data for vamsas session. This is probably a vamsas client bug.");
1562 * translate the Vobject keys to strings for use in Jalview2XML
1567 private IdentityHashMap mapValuesToString(IdentityHashMap jv2vobj2)
1569 IdentityHashMap mapped = new IdentityHashMap();
1570 Iterator keys = jv2vobj2.keySet().iterator();
1571 while (keys.hasNext())
1573 Object key = keys.next();
1574 mapped.put(key, jv2vobj2.get(key).toString());
1580 * translate the Vobject values to strings for use in Jalview2XML
1583 * @return hashtable with string values
1585 private Hashtable mapKeysToString(Hashtable vobj2jv2)
1587 Hashtable mapped = new Hashtable();
1588 Iterator keys = vobj2jv2.keySet().iterator();
1589 while (keys.hasNext())
1591 Object key = keys.next();
1592 mapped.put(key.toString(), vobj2jv2.get(key));
1598 * synchronize Jalview from the vamsas document
1600 * @return number of new views from document
1602 public int updateToJalview()
1604 VAMSAS _roots[] = cdoc.getVamsasRoots();
1606 for (int _root = 0; _root < _roots.length; _root++)
1608 VAMSAS root = _roots[_root];
1609 boolean newds = false;
1610 for (int _ds = 0, _nds = root.getDataSetCount(); _ds < _nds; _ds++)
1612 // ///////////////////////////////////
1614 DataSet dataset = root.getDataSet(_ds);
1615 int i, iSize = dataset.getSequenceCount();
1616 List<SequenceI> dsseqs;
1617 jalview.datamodel.Alignment jdataset = (jalview.datamodel.Alignment) getvObj2jv(
1620 if (jdataset == null)
1622 Console.debug("Initialising new jalview dataset fields");
1624 dsseqs = new Vector();
1628 Console.debug("Update jalview dataset from vamsas.");
1629 jremain = jdataset.getHeight();
1630 dsseqs = jdataset.getSequences();
1633 // TODO: test sequence merging - we preserve existing non vamsas
1634 // sequences but add in any new vamsas ones, and don't yet update any
1635 // sequence attributes
1636 for (i = 0; i < iSize; i++)
1638 Sequence vdseq = dataset.getSequence(i);
1639 jalview.io.vamsas.Datasetsequence dssync = new Datasetsequence(
1642 jalview.datamodel.SequenceI dsseq = (SequenceI) dssync.getJvobj();
1643 if (dssync.isAddfromdoc())
1647 if (vdseq.getDbRefCount() > 0)
1649 DbRef[] dbref = vdseq.getDbRef();
1650 for (int db = 0; db < dbref.length; db++)
1652 new jalview.io.vamsas.Dbref(this, dbref[db], vdseq, dsseq);
1655 dsseq.updatePDBIds();
1661 SequenceI[] seqs = new SequenceI[dsseqs.size()];
1662 for (i = 0, iSize = dsseqs.size(); i < iSize; i++)
1664 seqs[i] = dsseqs.get(i);
1665 dsseqs.set(i, null);
1667 jdataset = new jalview.datamodel.Alignment(seqs);
1668 Console.debug("New vamsas dataset imported into jalview.");
1669 bindjvvobj(jdataset, dataset);
1672 // add any new dataset sequence feature annotations
1673 if (dataset.getDataSetAnnotations() != null)
1675 for (int dsa = 0; dsa < dataset
1676 .getDataSetAnnotationsCount(); dsa++)
1678 DataSetAnnotations dseta = dataset.getDataSetAnnotations(dsa);
1679 // TODO: deal with group annotation on datset sequences.
1680 if (dseta.getSeqRefCount() == 1)
1682 SequenceI dsSeq = (SequenceI) getvObj2jv(
1683 (Vobject) dseta.getSeqRef(0)); // TODO: deal with group
1689 "Couldn't resolve jalview sequenceI for dataset object reference "
1690 + ((Vobject) dataset
1691 .getDataSetAnnotations(dsa)
1692 .getSeqRef(0)).getVorbaId()
1697 if (dseta.getAnnotationElementCount() == 0)
1699 new jalview.io.vamsas.Sequencefeature(this, dseta, dsSeq);
1704 // TODO: deal with alignmentAnnotation style annotation
1705 // appearing on dataset sequences.
1706 // JBPNote: we could just add them to all alignments but
1707 // that may complicate cross references in the jalview
1710 "Ignoring dataset annotation with annotationElements. Not yet supported in jalview.");
1717 "Ignoring multiply referenced dataset sequence annotation for binding to datsaet sequence features.");
1721 if (dataset.getAlignmentCount() > 0)
1723 // LOAD ALIGNMENTS from DATASET
1725 for (int al = 0, nal = dataset
1726 .getAlignmentCount(); al < nal; al++)
1728 uk.ac.vamsas.objects.core.Alignment alignment = dataset
1730 // TODO check this handles multiple views properly
1731 AlignmentViewport av = findViewport(alignment);
1733 jalview.datamodel.AlignmentI jal = null;
1736 // TODO check that correct alignment object is retrieved when
1737 // hidden seqs exist.
1738 jal = (av.hasHiddenRows()) ? av.getAlignment()
1739 .getHiddenSequences().getFullAlignment()
1740 : av.getAlignment();
1742 iSize = alignment.getAlignmentSequenceCount();
1743 boolean refreshal = false;
1744 Vector newasAnnots = new Vector();
1745 char gapChar = ' '; // default for new alignments read in from the
1749 dsseqs = jal.getSequences(); // for merge/update
1750 gapChar = jal.getGapCharacter();
1754 dsseqs = new Vector();
1756 char valGapchar = alignment.getGapChar().charAt(0);
1757 for (i = 0; i < iSize; i++)
1759 AlignmentSequence valseq = alignment.getAlignmentSequence(i);
1760 jalview.datamodel.Sequence alseq = (jalview.datamodel.Sequence) getvObj2jv(
1762 if (syncFromAlignmentSequence(valseq, valGapchar, gapChar,
1763 dsseqs) && alseq != null)
1766 // updated to sequence from the document
1770 if (valseq.getAlignmentSequenceAnnotationCount() > 0)
1772 AlignmentSequenceAnnotation[] vasannot = valseq
1773 .getAlignmentSequenceAnnotation();
1774 for (int a = 0; a < vasannot.length; a++)
1776 jalview.datamodel.AlignmentAnnotation asa = (jalview.datamodel.AlignmentAnnotation) getvObj2jv(
1777 vasannot[a]); // TODO:
1785 int se[] = getBounds(vasannot[a]);
1786 asa = getjAlignmentAnnotation(jal, vasannot[a]);
1787 asa.setSequenceRef(alseq);
1788 asa.createSequenceMapping(alseq, se[0], false); // TODO:
1799 alseq.addAlignmentAnnotation(asa);
1800 bindjvvobj(asa, vasannot[a]);
1802 newasAnnots.add(asa);
1806 // update existing annotation - can do this in place
1807 if (vasannot[a].getModifiable() == null) // TODO: USE
1813 "UNIMPLEMENTED: not recovering user modifiable sequence alignment annotation");
1814 // TODO: should at least replace with new one - otherwise
1815 // things will break
1816 // basically do this:
1817 // int se[] = getBounds(vasannot[a]);
1818 // asa.update(getjAlignmentAnnotation(jal, vasannot[a]));
1819 // // update from another annotation object in place.
1820 // asa.createSequenceMapping(alseq, se[0], false);
1829 SequenceI[] seqs = new SequenceI[dsseqs.size()];
1830 for (i = 0, iSize = dsseqs.size(); i < iSize; i++)
1832 seqs[i] = dsseqs.get(i);
1833 dsseqs.set(i, null);
1835 jal = new jalview.datamodel.Alignment(seqs);
1836 Console.debug("New vamsas alignment imported into jalview "
1837 + alignment.getVorbaId().getId());
1838 jal.setDataset(jdataset);
1840 if (newasAnnots != null && newasAnnots.size() > 0)
1842 // Add the new sequence annotations in to the alignment.
1843 for (int an = 0, anSize = newasAnnots
1844 .size(); an < anSize; an++)
1847 (AlignmentAnnotation) newasAnnots.elementAt(an));
1848 // TODO: check if anything has to be done - like calling
1849 // adjustForAlignment or something.
1850 newasAnnots.setElementAt(null, an);
1854 // //////////////////////////////////////////
1855 // //LOAD ANNOTATIONS FOR THE ALIGNMENT
1856 // ////////////////////////////////////
1857 if (alignment.getAlignmentAnnotationCount() > 0)
1859 uk.ac.vamsas.objects.core.AlignmentAnnotation[] an = alignment
1860 .getAlignmentAnnotation();
1862 for (int j = 0; j < an.length; j++)
1864 jalview.datamodel.AlignmentAnnotation jan = (jalview.datamodel.AlignmentAnnotation) getvObj2jv(
1868 // update or stay the same.
1869 // TODO: should at least replace with a new one - otherwise
1870 // things will break
1871 // basically do this:
1872 // jan.update(getjAlignmentAnnotation(jal, an[a])); // update
1873 // from another annotation object in place.
1876 "update from vamsas alignment annotation to existing jalview alignment annotation.");
1877 if (an[j].getModifiable() == null) // TODO: USE VAMSAS
1878 // LIBRARY OBJECT LOCK
1881 // TODO: user defined annotation is totally mutable... - so
1882 // load it up or throw away if locally edited.
1884 "NOT IMPLEMENTED - Recovering user-modifiable annotation - yet...");
1886 // TODO: compare annotation element rows
1887 // TODO: compare props.
1891 jan = getjAlignmentAnnotation(jal, an[j]);
1892 // TODO: ensure we add the alignment annotation before the
1893 // automatic annotation rows
1894 jal.addAnnotation(jan);
1895 bindjvvobj(jan, an[j]);
1900 AlignFrame alignFrame;
1903 Console.debug("New alignframe for alignment "
1904 + alignment.getVorbaId());
1905 // ///////////////////////////////
1906 // construct alignment view
1907 alignFrame = new AlignFrame(jal, AlignFrame.DEFAULT_WIDTH,
1908 AlignFrame.DEFAULT_HEIGHT,
1909 alignment.getVorbaId().toString());
1910 av = alignFrame.getViewport();
1911 newAlignmentViews.addElement(av);
1912 String title = alignment.getProvenance()
1914 alignment.getProvenance().getEntryCount() - 1)
1916 if (alignment.getPropertyCount() > 0)
1918 for (int p = 0, pe = alignment
1919 .getPropertyCount(); p < pe; p++)
1921 if (alignment.getProperty(p).getName().equals("title"))
1923 title = alignment.getProperty(p).getContent();
1927 // TODO: automatically create meaningful title for a vamsas
1928 // alignment using its provenance.
1929 if (Console.isDebugEnabled())
1931 title = title + "(" + alignment.getVorbaId() + ")";
1934 jalview.gui.Desktop.addInternalFrame(alignFrame, title,
1935 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
1936 bindjvvobj(av.getSequenceSetId(), alignment);
1940 // find the alignFrame for jal.
1941 // TODO: fix this so we retrieve the alignFrame handing av
1942 // *directly* (JBPNote - don't understand this now)
1943 // TODO: make sure all associated views are refreshed
1944 alignFrame = Desktop.getAlignFrameFor(av);
1947 av.alignmentChanged(alignFrame.alignPanel);
1948 alignFrame.alignPanel.adjustAnnotationHeight();
1952 // /////////////////////////////////////
1953 if (alignment.getTreeCount() > 0)
1956 for (int t = 0; t < alignment.getTreeCount(); t++)
1958 jalview.io.vamsas.Tree vstree = new jalview.io.vamsas.Tree(
1959 this, alignFrame, alignment.getTree(t));
1960 TreePanel tp = null;
1961 if (vstree.isValidTree())
1963 tp = alignFrame.showNewickTree(vstree.getNewickTree(),
1964 vstree.getTitle(), vstree.getInputData(), 600,
1965 500, t * 20 + 50, t * 20 + 50);
1970 bindjvvobj(tp, alignment.getTree(t));
1973 vstree.UpdateSequenceTreeMap(tp);
1974 } catch (RuntimeException e)
1976 Console.warn("update of labels failed.", e);
1981 Console.warn("Cannot create tree for tree " + t
1983 + alignment.getTree(t).getVorbaId());
1991 // we do sequenceMappings last because they span all datasets in a vamsas
1993 for (int _ds = 0, _nds = root.getDataSetCount(); _ds < _nds; _ds++)
1995 DataSet dataset = root.getDataSet(_ds);
1996 if (dataset.getSequenceMappingCount() > 0)
1998 for (int sm = 0, smCount = dataset
1999 .getSequenceMappingCount(); sm < smCount; sm++)
2001 Rangetype seqmap = new jalview.io.vamsas.Sequencemapping(this,
2002 dataset.getSequenceMapping(sm));
2007 return newAlignmentViews.size();
2010 public AlignmentViewport findViewport(Alignment alignment)
2012 AlignmentViewport av = null;
2013 AlignmentViewport[] avs = Desktop
2014 .getViewports((String) getvObj2jv(alignment));
2022 // bitfields - should be a template in j1.5
2023 private static int HASSECSTR = 0;
2025 private static int HASVALS = 1;
2027 private static int HASHPHOB = 2;
2029 private static int HASDC = 3;
2031 private static int HASDESCSTR = 4;
2033 private static int HASTWOSTATE = 5; // not used yet.
2036 * parses the AnnotationElements - if they exist - into
2037 * jalview.datamodel.Annotation[] rows Two annotation rows are made if there
2038 * are distinct annotation for both at 'pos' and 'after pos' at any particular
2042 * @return { boolean[static int constants ], int[ae.length] - map to annotated
2043 * object frame, jalview.datamodel.Annotation[],
2044 * jalview.datamodel.Annotation[] (after)}
2046 private Object[] parseRangeAnnotation(
2047 uk.ac.vamsas.objects.core.RangeAnnotation annotation)
2049 // set these attributes by looking in the annotation to decide what kind of
2050 // alignment annotation rows will be made
2051 // TODO: potentially we might make several annotation rows from one vamsas
2052 // alignment annotation. the jv2Vobj binding mechanism
2053 // may not quite cope with this (without binding an array of annotations to
2054 // a vamsas alignment annotation)
2055 // summary flags saying what we found over the set of annotation rows.
2056 boolean[] AeContent = new boolean[] { false, false, false, false,
2058 int[] rangeMap = getMapping(annotation);
2059 jalview.datamodel.Annotation[][] anot = new jalview.datamodel.Annotation[][] {
2060 new jalview.datamodel.Annotation[rangeMap.length],
2061 new jalview.datamodel.Annotation[rangeMap.length] };
2062 boolean mergeable = true; // false if 'after positions cant be placed on
2063 // same annotation row as positions.
2065 if (annotation.getAnnotationElementCount() > 0)
2067 AnnotationElement ae[] = annotation.getAnnotationElement();
2068 for (int aa = 0; aa < ae.length; aa++)
2070 int pos = (int) ae[aa].getPosition() - 1; // pos counts from 1 to
2071 // (|seg.start-seg.end|+1)
2072 if (pos >= 0 && pos < rangeMap.length)
2074 int row = ae[aa].getAfter() ? 1 : 0;
2075 if (anot[row][pos] != null)
2077 // only time this should happen is if the After flag is set.
2078 Console.debug("Ignoring duplicate annotation site at " + pos);
2081 if (anot[1 - row][pos] != null)
2086 if (ae[aa].getDescription() != null)
2088 desc = ae[aa].getDescription();
2089 if (desc.length() > 0)
2091 // have imported valid description string
2092 AeContent[HASDESCSTR] = true;
2095 String dc = null; // ae[aa].getDisplayCharacter()==null ? "dc" :
2096 // ae[aa].getDisplayCharacter();
2097 String ss = null; // ae[aa].getSecondaryStructure()==null ? "ss" :
2098 // ae[aa].getSecondaryStructure();
2099 java.awt.Color colour = null;
2100 if (ae[aa].getGlyphCount() > 0)
2102 Glyph[] glyphs = ae[aa].getGlyph();
2103 for (int g = 0; g < glyphs.length; g++)
2105 if (glyphs[g].getDict().equals(
2106 uk.ac.vamsas.objects.utils.GlyphDictionary.PROTEIN_SS_3STATE))
2108 ss = glyphs[g].getContent();
2109 AeContent[HASSECSTR] = true;
2111 else if (glyphs[g].getDict().equals(
2112 uk.ac.vamsas.objects.utils.GlyphDictionary.PROTEIN_HD_HYDRO))
2114 Console.debug("ignoring hydrophobicity glyph marker.");
2115 AeContent[HASHPHOB] = true;
2116 char c = (dc = glyphs[g].getContent()).charAt(0);
2117 // dc may get overwritten - but we still set the colour.
2118 colour = new java.awt.Color(c == '+' ? 255 : 0,
2119 c == '.' ? 255 : 0, c == '-' ? 255 : 0);
2122 else if (glyphs[g].getDict().equals(
2123 uk.ac.vamsas.objects.utils.GlyphDictionary.DEFAULT))
2125 dc = glyphs[g].getContent();
2126 AeContent[HASDC] = true;
2131 "IMPLEMENTATION TODO: Ignoring unknown glyph type "
2132 + glyphs[g].getDict());
2137 if (ae[aa].getValueCount() > 0)
2139 AeContent[HASVALS] = true;
2140 if (ae[aa].getValueCount() > 1)
2143 "ignoring additional " + (ae[aa].getValueCount() - 1)
2144 + " values in annotation element.");
2146 val = ae[aa].getValue(0);
2150 anot[row][pos] = new jalview.datamodel.Annotation(
2151 (dc != null) ? dc : "", desc,
2152 (ss != null) ? ss.charAt(0) : ' ', val);
2156 anot[row][pos] = new jalview.datamodel.Annotation(
2157 (dc != null) ? dc : "", desc,
2158 (ss != null) ? ss.charAt(0) : ' ', val, colour);
2163 Console.warn("Ignoring out of bound annotation element " + aa
2164 + " in " + annotation.getVorbaId().getId());
2167 // decide on how many annotation rows are needed.
2170 for (int i = 0; i < anot[0].length; i++)
2172 if (anot[1][i] != null)
2174 anot[0][i] = anot[1][i];
2175 anot[0][i].description = anot[0][i].description + " (after)";
2176 AeContent[HASDESCSTR] = true; // we have valid description string
2185 for (int i = 0; i < anot[0].length; i++)
2187 anot[1][i].description = anot[1][i].description + " (after)";
2190 return new Object[] { AeContent, rangeMap, anot[0], anot[1] };
2194 // no annotations to parse. Just return an empty annotationElement[]
2196 return new Object[] { AeContent, rangeMap, anot[0], anot[1] };
2203 * the jalview alignment to which the annotation will be attached
2204 * (ideally - freshly updated from corresponding vamsas alignment)
2206 * @return unbound jalview alignment annotation object.
2208 private jalview.datamodel.AlignmentAnnotation getjAlignmentAnnotation(
2209 jalview.datamodel.AlignmentI jal,
2210 uk.ac.vamsas.objects.core.RangeAnnotation annotation)
2212 if (annotation == null)
2217 // hasSequenceRef=annotation.getClass().equals(uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation.class);
2218 // boolean hasProvenance=hasSequenceRef ||
2219 // (annotation.getClass().equals(uk.ac.vamsas.objects.core.AlignmentAnnotation.class));
2221 * int se[] = getBounds(annotation); if (se==null) se=new int[]
2222 * {0,jal.getWidth()-1};
2224 Object[] parsedRangeAnnotation = parseRangeAnnotation(annotation);
2225 String a_label = annotation.getLabel();
2226 String a_descr = annotation.getDescription();
2227 GraphLine gl = null;
2229 boolean interp = true; // cleared if annotation is DISCRETE
2230 // set type and other attributes from properties
2231 if (annotation.getPropertyCount() > 0)
2233 // look for special jalview properties
2234 uk.ac.vamsas.objects.core.Property[] props = annotation.getProperty();
2235 for (int p = 0; p < props.length; p++)
2237 if (props[p].getName().equalsIgnoreCase(DISCRETE_ANNOTATION))
2239 type = AlignmentAnnotation.BAR_GRAPH;
2242 else if (props[p].getName().equalsIgnoreCase(CONTINUOUS_ANNOTATION))
2244 type = AlignmentAnnotation.LINE_GRAPH;
2246 else if (props[p].getName().equalsIgnoreCase(THRESHOLD))
2251 val = Float.valueOf(props[p].getContent());
2252 } catch (Exception e)
2254 Console.warn("Failed to parse threshold property");
2260 gl = new GraphLine(val.floatValue(), "",
2261 java.awt.Color.black);
2265 gl.value = val.floatValue();
2269 else if (props[p].getName().equalsIgnoreCase(THRESHOLD + "Name"))
2273 gl = new GraphLine(0, "", java.awt.Color.black);
2275 gl.label = props[p].getContent();
2279 jalview.datamodel.AlignmentAnnotation jan = null;
2280 if (a_label == null || a_label.length() == 0)
2282 a_label = annotation.getType();
2283 if (a_label.length() == 0)
2285 a_label = "Unamed annotation";
2288 if (a_descr == null || a_descr.length() == 0)
2290 a_descr = "Annotation of type '" + annotation.getType() + "'";
2292 if (parsedRangeAnnotation == null)
2295 "Inserting empty annotation row elements for a whole-alignment annotation.");
2299 if (parsedRangeAnnotation[3] != null)
2301 Console.warn("Ignoring 'After' annotation row in "
2302 + annotation.getVorbaId());
2304 jalview.datamodel.Annotation[] arow = (jalview.datamodel.Annotation[]) parsedRangeAnnotation[2];
2305 boolean[] has = (boolean[]) parsedRangeAnnotation[0];
2306 // VAMSAS: getGraph is only on derived annotation for alignments - in this
2307 // way its 'odd' - there is already an existing TODO about removing this
2308 // flag as being redundant
2310 * if((annotation.getClass().equals(uk.ac.vamsas.objects.core.
2311 * AlignmentAnnotation.class) &&
2312 * ((uk.ac.vamsas.objects.core.AlignmentAnnotation)annotation).getGraph())
2313 * || (hasSequenceRef=true &&
2314 * ((uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation
2315 * )annotation).getGraph())) {
2321 type = jalview.datamodel.AlignmentAnnotation.BAR_GRAPH; // default
2327 // no hints - so we ensure HPHOB display is like this.
2328 type = jalview.datamodel.AlignmentAnnotation.BAR_GRAPH;
2331 // make bounds and automatic description strings for jalview user's
2332 // benefit (these shouldn't be written back to vamsas document)
2333 boolean first = true;
2334 float min = 0, max = 1;
2336 for (int i = 0; i < arow.length; i++)
2338 if (arow[i] != null)
2340 if (i - lastval > 1 && interp)
2342 // do some interpolation *between* points
2343 if (arow[lastval] != null)
2345 float interval = arow[i].value - arow[lastval].value;
2346 interval /= i - lastval;
2347 float base = arow[lastval].value;
2348 for (int ip = lastval + 1, np = 0; ip < i; np++, ip++)
2350 arow[ip] = new jalview.datamodel.Annotation("", "", ' ',
2351 interval * np + base);
2352 // NB - Interpolated points don't get a tooltip and
2358 // check range - shouldn't we have a min and max property in the
2359 // annotation object ?
2362 min = max = arow[i].value;
2367 if (arow[i].value < min)
2369 min = arow[i].value;
2371 else if (arow[i].value > max)
2373 max = arow[i].value;
2376 // make tooltip and display char value
2377 if (!has[HASDESCSTR])
2379 arow[i].description = arow[i].value + "";
2385 if (arow[i].description != null
2386 && arow[i].description.length() < 3)
2388 // copy over the description as the display char.
2389 arow[i].displayCharacter = new String(
2390 arow[i].description);
2395 // mark the position as a point used for the interpolation.
2396 arow[i].displayCharacter = arow[i].value + "";
2401 jan = new jalview.datamodel.AlignmentAnnotation(a_label, a_descr,
2402 arow, min, max, type);
2406 if (annotation.getAnnotationElementCount() == 0)
2408 // empty annotation array
2409 // TODO: alignment 'features' compare rangeType spec to alignment
2410 // width - if it is not complete, then mark regions on the annotation
2413 jan = new jalview.datamodel.AlignmentAnnotation(a_label, a_descr,
2415 jan.setThreshold(null);
2416 jan.annotationId = annotation.getVorbaId().toString(); // keep all the
2419 if (annotation.getLinkCount() > 0)
2421 Console.warn("Ignoring " + annotation.getLinkCount()
2422 + "links added to AlignmentAnnotation.");
2424 if (annotation.getModifiable() == null
2425 || annotation.getModifiable().length() == 0) // TODO: USE VAMSAS
2429 jan.editable = true;
2433 if (annotation.getGroup() != null
2434 && annotation.getGroup().length() > 0)
2436 jan.graphGroup = Integer.parseInt(annotation.getGroup()); // TODO:
2444 } catch (Exception e)
2447 "UNIMPLEMENTED : Couldn't parse non-integer group value for setting graphGroup correctly.");
2457 * get real bounds of a RangeType's specification. start and end are an
2458 * inclusive range within which all segments and positions lie. TODO: refactor
2462 * @return int[] { start, end}
2464 private int[] getBounds(RangeType dseta)
2469 if (dseta.getSegCount() > 0 && dseta.getPosCount() > 0)
2471 throw new Error(MessageManager.getString(
2472 "error.invalid_vamsas_rangetype_cannot_resolve_lists"));
2474 if (dseta.getSegCount() > 0)
2476 se = getSegRange(dseta.getSeg(0), true);
2477 for (int s = 1, sSize = dseta.getSegCount(); s < sSize; s++)
2479 int nse[] = getSegRange(dseta.getSeg(s), true);
2490 if (dseta.getPosCount() > 0)
2492 // could do a polarity for pos range too. and pass back indication of
2494 int pos = dseta.getPos(0).getI();
2495 se = new int[] { pos, pos };
2496 for (int p = 0, pSize = dseta.getPosCount(); p < pSize; p++)
2498 pos = dseta.getPos(p).getI();
2515 * map from a rangeType's internal frame to the referenced object's coordinate
2519 * @return int [] { ref(pos)...} for all pos in rangeType's frame.
2521 private int[] getMapping(RangeType dseta)
2523 Vector posList = new Vector();
2527 if (dseta.getSegCount() > 0 && dseta.getPosCount() > 0)
2529 throw new Error(MessageManager.getString(
2530 "error.invalid_vamsas_rangetype_cannot_resolve_lists"));
2532 if (dseta.getSegCount() > 0)
2534 for (int s = 0, sSize = dseta.getSegCount(); s < sSize; s++)
2536 se = getSegRange(dseta.getSeg(s), false);
2537 int se_end = se[1 - se[2]] + (se[2] == 0 ? 1 : -1);
2538 for (int p = se[se[2]]; p != se_end; p += se[2] == 0 ? 1 : -1)
2540 posList.add(Integer.valueOf(p));
2544 else if (dseta.getPosCount() > 0)
2546 int pos = dseta.getPos(0).getI();
2548 for (int p = 0, pSize = dseta.getPosCount(); p < pSize; p++)
2550 pos = dseta.getPos(p).getI();
2551 posList.add(Integer.valueOf(pos));
2555 if (posList != null && posList.size() > 0)
2557 int[] range = new int[posList.size()];
2558 for (int i = 0; i < range.length; i++)
2560 range[i] = ((Integer) posList.elementAt(i)).intValue();
2571 * where the from range is the local mapped range, and the to range
2572 * is the 'mapped' range in the MapRangeType
2579 private jalview.util.MapList parsemapType(MapType maprange, int localu,
2582 jalview.util.MapList ml = null;
2583 int[] localRange = getMapping(maprange.getLocal());
2584 int[] mappedRange = getMapping(maprange.getMapped());
2585 long lu = maprange.getLocal().hasUnit() ? maprange.getLocal().getUnit()
2587 long mu = maprange.getMapped().hasUnit()
2588 ? maprange.getMapped().getUnit()
2590 ml = new jalview.util.MapList(localRange, mappedRange, (int) lu,
2596 * initialise a range type object from a set of start/end inclusive intervals
2601 private void initRangeType(RangeType mrt, List<int[]> ranges)
2603 for (int[] range : ranges)
2605 Seg vSeg = new Seg();
2606 vSeg.setStart(range[0]);
2607 vSeg.setEnd(range[1]);
2613 * initialise a MapType object from a MapList object.
2619 private void initMapType(MapType maprange, jalview.util.MapList ml,
2622 maprange.setLocal(new Local());
2623 maprange.setMapped(new Mapped());
2624 initRangeType(maprange.getLocal(), ml.getFromRanges());
2625 initRangeType(maprange.getMapped(), ml.getToRanges());
2628 maprange.getLocal().setUnit(ml.getFromRatio());
2629 maprange.getLocal().setUnit(ml.getToRatio());
2634 * not needed now. Provenance getVamsasProvenance(jalview.datamodel.Provenance
2635 * jprov) { jalview.datamodel.ProvenanceEntry[] entries = null; // TODO: fix
2636 * App and Action here. Provenance prov = new Provenance();
2637 * org.exolab.castor.types.Date date = new org.exolab.castor.types.Date( new
2638 * java.util.Date()); Entry provEntry;
2640 * if (jprov != null) { entries = jprov.getEntries(); for (int i = 0; i <
2641 * entries.length; i++) { provEntry = new Entry(); try { date = new
2642 * org.exolab.castor.types.Date(entries[i].getDate()); } catch (Exception ex)
2643 * { ex.printStackTrace();
2645 * date = new org.exolab.castor.types.Date(entries[i].getDate()); }
2646 * provEntry.setDate(date); provEntry.setUser(entries[i].getUser());
2647 * provEntry.setAction(entries[i].getAction()); prov.addEntry(provEntry); } }
2648 * else { provEntry = new Entry(); provEntry.setDate(date);
2649 * provEntry.setUser(System.getProperty("user.name")); // TODO: ext string
2650 * provEntry.setApp("JVAPP"); // TODO: ext string provEntry.setAction(action);
2651 * prov.addEntry(provEntry); }
2655 jalview.datamodel.Provenance getJalviewProvenance(Provenance prov)
2657 // TODO: fix App and Action entries and check use of provenance in jalview.
2658 jalview.datamodel.Provenance jprov = new jalview.datamodel.Provenance();
2659 for (int i = 0; i < prov.getEntryCount(); i++)
2661 jprov.addEntry(prov.getEntry(i).getUser(),
2662 prov.getEntry(i).getAction(), prov.getEntry(i).getDate(),
2663 prov.getEntry(i).getId());
2671 * @return default initial provenance list for a Jalview created vamsas
2674 Provenance dummyProvenance()
2676 return dummyProvenance(null);
2679 Entry dummyPEntry(String action)
2681 Entry entry = new Entry();
2682 entry.setApp(this.provEntry.getApp());
2685 entry.setAction(action);
2689 entry.setAction("created.");
2691 entry.setDate(new java.util.Date());
2692 entry.setUser(this.provEntry.getUser());
2696 Provenance dummyProvenance(String action)
2698 Provenance prov = new Provenance();
2699 prov.addEntry(dummyPEntry(action));
2703 Entry addProvenance(Provenance p, String action)
2705 Entry dentry = dummyPEntry(action);
2710 public Entry getProvEntry()
2715 public IClientDocument getClientDocument()
2720 public IdentityHashMap getJvObjectBinding()
2725 public Hashtable getVamsasObjectBinding()
2730 public void storeSequenceMappings(AlignmentViewport viewport,
2731 String title) throws Exception
2733 AlignmentViewport av = viewport;
2736 jalview.datamodel.AlignmentI jal = av.getAlignment();
2737 // /////////////////////////////////////////
2739 DataSet dataset = null;
2740 if (jal.getDataset() == null)
2742 Console.warn("Creating new dataset for an alignment.");
2743 jal.setDataset(null);
2745 dataset = (DataSet) ((Alignment) getjv2vObj(
2746 viewport.getSequenceSetId())).getV_parent(); // jal.getDataset());
2747 if (dataset == null)
2749 dataset = (DataSet) getjv2vObj(jal.getDataset());
2751 "Can't find the correct dataset for the alignment in this view. Creating new one.");
2754 // Store any sequence mappings.
2755 List<AlignedCodonFrame> cframes = av.getAlignment().getCodonFrames();
2756 if (cframes != null)
2758 for (AlignedCodonFrame acf : cframes)
2760 if (acf.getdnaSeqs() != null && acf.getdnaSeqs().length > 0)
2762 jalview.datamodel.SequenceI[] dmps = acf.getdnaSeqs();
2763 jalview.datamodel.Mapping[] mps = acf.getProtMappings();
2764 for (int smp = 0; smp < mps.length; smp++)
2766 uk.ac.vamsas.objects.core.SequenceType mfrom = (SequenceType) getjv2vObj(
2770 new jalview.io.vamsas.Sequencemapping(this, mps[smp], mfrom,
2776 "NO Vamsas Binding for local sequence! NOT CREATING MAPPING FOR "
2777 + dmps[smp].getDisplayId(true) + " to "
2778 + mps[smp].getTo().getName());
2784 } catch (Exception e)
2786 throw new Exception(MessageManager.formatMessage(
2787 "exception.couldnt_store_sequence_mappings", new String[]
2792 public void clearSkipList()
2794 if (skipList != null)
2801 * @return the skipList
2803 public Hashtable getSkipList()
2810 * the skipList to set
2812 public void setSkipList(Hashtable skipList)
2814 this.skipList = skipList;
2818 * registry for datastoreItems
2820 DatastoreRegistry dsReg = new DatastoreRegistry();
2822 public DatastoreRegistry getDatastoreRegisty()
2826 dsReg = new DatastoreRegistry();