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.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 "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();
464 "Sequence deletion from alignment is not implemented.");
472 addProvenance(alignment.getProvenance(), "Edited"); // TODO:
481 addProvenance(alignment.getProvenance(), "Attributes Edited"); // TODO:
491 System.out.println("update alignment in document.");
495 System.out.println("alignment in document left unchanged.");
500 // unbind alignment from view.
501 // create new binding and new alignment.
502 // mark trail on new alignment as being derived from old ?
504 "update edited alignment to new alignment in document.");
507 // ////////////////////////////////////////////
508 // SAVE Alignment Sequence Features
509 for (int i = 0, iSize = alignment
510 .getAlignmentSequenceCount(); i < iSize; i++)
512 AlignmentSequence valseq;
513 SequenceI alseq = (SequenceI) getvObj2jv(
514 valseq = alignment.getAlignmentSequence(i));
515 if (alseq != null && alseq.getSequenceFeatures() != null)
518 * We do not put local Alignment Sequence Features into the vamsas
522 * jalview.datamodel.SequenceFeature[] features = alseq
523 * .getSequenceFeatures(); for (int f = 0; f < features.length; f++) {
524 * if (features[f] != null) { AlignmentSequenceAnnotation valseqf = (
525 * AlignmentSequenceAnnotation) getjv2vObj(features[i]); if (valseqf
528 * valseqf = (AlignmentSequenceAnnotation) getDSAnnotationFromJalview(
529 * new AlignmentSequenceAnnotation(), features[i]);
530 * valseqf.setGraph(false);
531 * valseqf.addProperty(newProperty("jalview:feature"
532 * ,"boolean","true")); if (valseqf.getProvenance() == null) {
533 * valseqf.setProvenance(new Provenance()); }
534 * addProvenance(valseqf.getProvenance(), "created"); // JBPNote - //
535 * need to // update bindjvvobj(features[i], valseqf);
536 * valseq.addAlignmentSequenceAnnotation(valseqf); } } }
541 // ////////////////////////////////////////////
543 if (jal.getAlignmentAnnotation() != null)
545 jalview.datamodel.AlignmentAnnotation[] aa = jal
546 .getAlignmentAnnotation();
547 java.util.HashMap AlSeqMaps = new HashMap(); // stores int maps from
548 // alignment columns to
549 // sequence positions.
550 for (int i = 0; i < aa.length; i++)
552 if (aa[i] == null || isJalviewOnly(aa[i]))
556 if (aa[i].groupRef != null)
558 // TODO: store any group associated annotation references
560 "Group associated sequence annotation is not stored in VAMSAS document.");
563 if (aa[i].sequenceRef != null)
565 // Deal with sequence associated annotation
566 Vobject sref = getjv2vObj(aa[i].sequenceRef);
567 if (sref instanceof uk.ac.vamsas.objects.core.AlignmentSequence)
569 saveAlignmentSequenceAnnotation(AlSeqMaps,
570 (AlignmentSequence) sref, aa[i]);
574 // first find the alignment sequence to associate this with.
575 for (SequenceI jvalsq : av.getAlignment().getSequences())
577 // saveDatasetSequenceAnnotation(AlSeqMaps,(uk.ac.vamsas.objects.core.Sequence)
579 if (jvalsq.getDatasetSequence() == aa[i].sequenceRef)
581 Vobject alsref = getjv2vObj(jvalsq);
582 saveAlignmentSequenceAnnotation(AlSeqMaps,
583 (AlignmentSequence) alsref, aa[i]);
592 // add Alignment Annotation
593 uk.ac.vamsas.objects.core.AlignmentAnnotation an = (uk.ac.vamsas.objects.core.AlignmentAnnotation) getjv2vObj(
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());
644 .setContent(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();
660 uk.ac.vamsas.objects.utils.GlyphDictionary.PROTEIN_SS_3STATE);
661 ss.setContent(String.valueOf(
662 aa[i].annotations[a].secondaryStructure));
665 an.addAnnotationElement(ae);
669 // an.addProperty(newProperty("jalview:editable", null,
671 // an.setModifiable(""); // TODO: This is not the way the
672 // modifiable flag is supposed to be used.
674 setAnnotationType(an, aa[i]);
676 if (aa[i].graph != jalview.datamodel.AlignmentAnnotation.NO_GRAPH)
679 an.setGroup(Integer.toString(aa[i].graphGroup));
680 if (aa[i].threshold != null && aa[i].threshold.displayed)
682 an.addProperty(Properties.newProperty(THRESHOLD,
683 Properties.FLOATTYPE,
684 "" + aa[i].threshold.value));
685 if (aa[i].threshold.label != null)
687 an.addProperty(Properties.newProperty(
688 THRESHOLD + "Name", Properties.STRINGTYPE,
689 "" + aa[i].threshold.label));
698 if (an.getModifiable() == null) // TODO: USE VAMSAS LIBRARY OBJECT
701 // verify annotation - update (perhaps)
703 "update alignment sequence annotation. not yet implemented.");
707 // verify annotation - update (perhaps)
709 "updated alignment sequence annotation added.");
715 // /////////////////////////////////////////////////////
717 // //////////////////////////////////////////////
719 // /////////////////////////////////
720 // FIND ANY ASSOCIATED TREES
721 if (Desktop.desktop != null)
723 javax.swing.JInternalFrame[] frames = Desktop.instance
726 for (int t = 0; t < frames.length; t++)
728 if (frames[t] instanceof TreePanel)
730 TreePanel tp = (TreePanel) frames[t];
732 if (tp.getViewPort().getSequenceSetId()
733 .equals(av.getSequenceSetId()))
735 DatastoreItem vtree = new jalview.io.vamsas.Tree(this, tp,
741 // Store Jalview specific stuff in the Jalview appData
742 // not implemented in the SimpleDoc interface.
747 ex.printStackTrace();
754 * very quick test to see if the viewport would be stored in the vamsas
755 * document. Reasons for not storing include the unaligned flag being false
756 * (for all sequences, including the hidden ones!)
759 * @return true if alignment associated with this view will be stored in
762 public boolean alignmentWillBeSkipped(AlignmentViewport av)
764 return (!av.getAlignment().isAligned());
767 private void addToSkipList(AlignmentViewport av)
769 if (skipList == null)
771 skipList = new Hashtable();
773 skipList.put(av.getSequenceSetId(), av);
777 * remove docseqs from the given alignment marking provenance appropriately
778 * and removing any references to the sequences.
783 private void removeValignmentSequences(Alignment alignment,
786 // delete these from document. This really needs to be a generic document
787 // API function derived by CASTOR.
788 Enumeration en = docseqs.elements();
789 while (en.hasMoreElements())
791 alignment.removeAlignmentSequence(
792 (AlignmentSequence) en.nextElement());
794 Entry pe = addProvenance(alignment.getProvenance(),
795 "Removed " + docseqs.size() + " sequences");
796 en = alignment.enumerateAlignmentAnnotation();
797 Vector toremove = new Vector();
798 while (en.hasMoreElements())
800 uk.ac.vamsas.objects.core.AlignmentAnnotation alan = (uk.ac.vamsas.objects.core.AlignmentAnnotation) en
802 if (alan.getSeqrefsCount() > 0)
805 Vector storem = new Vector();
806 Enumeration sr = alan.enumerateSeqrefs();
807 while (sr.hasMoreElements())
809 Object alsr = sr.nextElement();
810 if (docseqs.contains(alsr))
812 storem.addElement(alsr);
815 // remove references to the deleted sequences
816 sr = storem.elements();
817 while (sr.hasMoreElements())
819 alan.removeSeqrefs(sr.nextElement());
822 if (alan.getSeqrefsCount() == 0)
824 // should then delete alan from dataset
825 toremove.addElement(alan);
829 // remove any annotation that used to be associated to a specific bunch of
831 en = toremove.elements();
832 while (en.hasMoreElements())
834 alignment.removeAlignmentAnnotation(
835 (uk.ac.vamsas.objects.core.AlignmentAnnotation) en
838 // TODO: search through alignment annotations to remove any references to
839 // this alignment sequence
843 * sync a jalview alignment seuqence into a vamsas alignment assumes all lock
844 * transformation/bindings have been sorted out before hand. creates/syncs the
845 * vamsas alignment sequence for jvalsq and adds it to the alignment if
846 * necessary. unbounddocseq is a duplicate of the vamsas alignment sequences
847 * and these are removed after being processed w.r.t a bound jvalsq
850 private boolean syncToAlignmentSequence(SequenceI jvalsq,
851 Alignment alignment, Vector unbounddocseq)
853 boolean modal = false;
854 // todo: islocked method here
855 boolean up2doc = false;
856 AlignmentSequence alseq = (AlignmentSequence) getjv2vObj(jvalsq);
859 alseq = new AlignmentSequence();
864 if (unbounddocseq != null)
866 unbounddocseq.removeElement(alseq);
869 // boolean locked = (alignment.getModifiable()==null ||
870 // alignment.getModifiable().length()>0);
871 // TODO: VAMSAS: translate lowercase symbols to annotation ?
872 if (up2doc || !alseq.getSequence().equals(jvalsq.getSequenceAsString()))
874 alseq.setSequence(jvalsq.getSequenceAsString());
875 alseq.setStart(jvalsq.getStart());
876 alseq.setEnd(jvalsq.getEnd());
879 if (up2doc || !alseq.getName().equals(jvalsq.getName()))
882 alseq.setName(jvalsq.getName());
884 if (jvalsq.getDescription() != null && (alseq.getDescription() == null
885 || !jvalsq.getDescription().equals(alseq.getDescription())))
888 alseq.setDescription(jvalsq.getDescription());
890 if (getjv2vObj(jvalsq.getDatasetSequence()) == null)
893 "Serious Implementation error - Unbound dataset sequence in alignment: "
894 + jvalsq.getDatasetSequence());
896 alseq.setRefid(getjv2vObj(jvalsq.getDatasetSequence()));
900 alignment.addAlignmentSequence(alseq);
901 bindjvvobj(jvalsq, alseq);
903 return up2doc || modal;
907 * locally sync a jalview alignment seuqence from a vamsas alignment assumes
908 * all lock transformation/bindings have been sorted out before hand.
909 * creates/syncs the jvalsq from the alignment sequence
911 private boolean syncFromAlignmentSequence(AlignmentSequence valseq,
912 char valGapchar, char gapChar, List<SequenceI> dsseqs)
915 boolean modal = false;
916 // todo: islocked method here
917 boolean upFromdoc = false;
918 jalview.datamodel.SequenceI alseq = (SequenceI) getvObj2jv(valseq);
926 // boolean locked = (alignment.getModifiable()==null ||
927 // alignment.getModifiable().length()>0);
928 // TODO: VAMSAS: translate lowercase symbols to annotation ?
930 || !valseq.getSequence().equals(alseq.getSequenceAsString()))
932 // this might go *horribly* wrong
933 alseq.setSequence(new String(valseq.getSequence())
934 .replace(valGapchar, gapChar));
935 alseq.setStart((int) valseq.getStart());
936 alseq.setEnd((int) valseq.getEnd());
939 if (!valseq.getName().equals(alseq.getName()))
942 alseq.setName(valseq.getName());
944 if (alseq.getDescription() == null || (valseq.getDescription() != null
945 && !alseq.getDescription().equals(valseq.getDescription())))
947 alseq.setDescription(valseq.getDescription());
950 if (modal && Console.isDebugEnabled())
953 "Updating apparently edited sequence " + alseq.getName());
958 alseq = new jalview.datamodel.Sequence(valseq.getName(),
959 valseq.getSequence().replace(valGapchar, gapChar),
960 (int) valseq.getStart(), (int) valseq.getEnd());
962 Vobject datsetseq = (Vobject) valseq.getRefid();
963 if (datsetseq != null)
965 alseq.setDatasetSequence((SequenceI) getvObj2jv(datsetseq)); // exceptions
966 if (valseq.getDescription() != null)
968 alseq.setDescription(valseq.getDescription());
972 // inherit description line from dataset.
973 if (alseq.getDatasetSequence().getDescription() != null)
975 alseq.setDescription(
976 alseq.getDatasetSequence().getDescription());
990 "Invalid dataset sequence id (null) for alignment sequence "
991 + valseq.getVorbaId());
993 bindjvvobj(alseq, valseq);
994 alseq.setVamsasId(valseq.getVorbaId().getId());
997 Vobject datsetseq = (Vobject) valseq.getRefid();
998 if (datsetseq != null)
1000 if (datsetseq != alseq.getDatasetSequence())
1004 alseq.setDatasetSequence((SequenceI) getvObj2jv(datsetseq)); // exceptions
1006 return upFromdoc || modal;
1009 private void initRangeAnnotationType(RangeAnnotation an,
1010 AlignmentAnnotation alan, int[] gapMap)
1012 Seg vSeg = new Seg();
1014 vSeg.setInclusive(true);
1015 vSeg.setEnd(gapMap.length);
1018 // LATER: much of this is verbatim from the alignmentAnnotation
1019 // method below. suggests refactoring to make rangeAnnotation the
1021 an.setDescription(alan.description);
1022 an.setLabel(alan.label);
1023 an.setGroup(Integer.toString(alan.graphGroup));
1032 AnnotationElement ae;
1033 for (int a = 0; a < alan.annotations.length; a++)
1035 if (alan.annotations[a] == null)
1040 ae = new AnnotationElement();
1041 ae.setDescription(alan.annotations[a].description);
1042 ae.addGlyph(new Glyph());
1043 ae.getGlyph(0).setContent(alan.annotations[a].displayCharacter); // assume
1050 if (alan.graph != jalview.datamodel.AlignmentAnnotation.NO_GRAPH)
1052 ae.addValue(alan.annotations[a].value);
1054 ae.setPosition(gapMap[a] + 1); // position w.r.t. AlignmentSequence
1056 if (alan.annotations[a].secondaryStructure != ' ')
1058 // we only write an annotation where it really exists.
1059 Glyph ss = new Glyph();
1061 uk.ac.vamsas.objects.utils.GlyphDictionary.PROTEIN_SS_3STATE);
1063 String.valueOf(alan.annotations[a].secondaryStructure));
1066 an.addAnnotationElement(ae);
1071 private void saveDatasetSequenceAnnotation(HashMap AlSeqMaps,
1072 uk.ac.vamsas.objects.core.Sequence sref, AlignmentAnnotation alan)
1076 // objects.core.AlignmentSequence alsref = (uk.ac.vamsas.
1077 // objects.core.AlignmentSequence) sref;
1078 uk.ac.vamsas.objects.core.DataSetAnnotations an = (uk.ac.vamsas.objects.core.DataSetAnnotations) getjv2vObj(
1080 int[] gapMap = getGapMap(AlSeqMaps, alan);
1083 an = new uk.ac.vamsas.objects.core.DataSetAnnotations();
1084 initRangeAnnotationType(an, alan, gapMap);
1086 an.setProvenance(dummyProvenance()); // get provenance as user
1087 // created, or jnet, or
1089 setAnnotationType(an, alan);
1090 an.setGroup(Integer.toString(alan.graphGroup)); // // JBPNote -
1098 if (alan.getThreshold() != null && alan.getThreshold().displayed)
1100 an.addProperty(Properties.newProperty(THRESHOLD,
1101 Properties.FLOATTYPE, "" + alan.getThreshold().value));
1102 if (alan.getThreshold().label != null)
1104 an.addProperty(Properties.newProperty(THRESHOLD + "Name",
1105 Properties.STRINGTYPE, "" + alan.getThreshold().label));
1108 ((DataSet) sref.getV_parent()).addDataSetAnnotations(an);
1109 bindjvvobj(alan, an);
1113 // update reference sequence Annotation
1114 if (an.getModifiable() == null) // TODO: USE VAMSAS LIBRARY OBJECT LOCK
1117 // verify existing alignment sequence annotation is up to date
1118 System.out.println("update dataset sequence annotation.");
1122 // verify existing alignment sequence annotation is up to date
1124 "make new alignment dataset sequence annotation if modification has happened.");
1130 private int[] getGapMap(HashMap AlSeqMaps, AlignmentAnnotation alan)
1133 if (AlSeqMaps.containsKey(alan.sequenceRef))
1135 gapMap = (int[]) AlSeqMaps.get(alan.sequenceRef);
1139 gapMap = new int[alan.sequenceRef.getLength()];
1140 // map from alignment position to sequence position.
1141 int[] sgapMap = alan.sequenceRef.gapMap();
1142 for (int a = 0; a < sgapMap.length; a++)
1144 gapMap[sgapMap[a]] = a;
1150 private void saveAlignmentSequenceAnnotation(HashMap AlSeqMaps,
1151 AlignmentSequence alsref, AlignmentAnnotation alan)
1155 // objects.core.AlignmentSequence alsref = (uk.ac.vamsas.
1156 // objects.core.AlignmentSequence) sref;
1157 uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation an = (uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation) getjv2vObj(
1159 int[] gapMap = getGapMap(AlSeqMaps, alan);
1162 an = new uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation();
1163 initRangeAnnotationType(an, alan, gapMap);
1165 * I mean here that we don't actually have a semantic 'type' for the
1166 * annotation (this might be - score, intrinsic property, measurement,
1167 * something extracted from another program, etc)
1169 an.setType(JALVIEW_ANNOTATION_ROW); // TODO: better fix
1170 // this rough guess ;)
1171 alsref.addAlignmentSequenceAnnotation(an);
1172 bindjvvobj(alan, an);
1173 // These properties are directly supported by the
1174 // AlignmentSequenceAnnotation type.
1175 setAnnotationType(an, alan);
1176 an.setProvenance(dummyProvenance()); // get provenance as user
1177 // created, or jnet, or
1182 // update reference sequence Annotation
1183 if (an.getModifiable() == null) // TODO: USE VAMSAS LIBRARY OBJECT LOCK
1186 // verify existing alignment sequence annotation is up to date
1187 System.out.println("update alignment sequence annotation.");
1191 // verify existing alignment sequence annotation is up to date
1193 "make new alignment sequence annotation if modification has happened.");
1199 * set vamsas annotation object type from jalview annotation
1204 private void setAnnotationType(RangeAnnotation an,
1205 AlignmentAnnotation alan)
1207 if (an instanceof AlignmentSequenceAnnotation)
1209 if (alan.graph != AlignmentAnnotation.NO_GRAPH)
1211 ((AlignmentSequenceAnnotation) an).setGraph(true);
1215 ((AlignmentSequenceAnnotation) an).setGraph(false);
1218 if (an instanceof uk.ac.vamsas.objects.core.AlignmentAnnotation)
1220 if (alan.graph != AlignmentAnnotation.NO_GRAPH)
1222 ((uk.ac.vamsas.objects.core.AlignmentAnnotation) an).setGraph(true);
1226 ((uk.ac.vamsas.objects.core.AlignmentAnnotation) an)
1232 case AlignmentAnnotation.BAR_GRAPH:
1233 an.addProperty(Properties.newProperty(DISCRETE_ANNOTATION,
1234 Properties.BOOLEANTYPE, "true"));
1236 case AlignmentAnnotation.LINE_GRAPH:
1237 an.addProperty(Properties.newProperty(CONTINUOUS_ANNOTATION,
1238 Properties.BOOLEANTYPE, "true"));
1241 // don't add any kind of discrete or continous property info.
1246 * get start<end range of segment, adjusting for inclusivity flag and
1250 * @param ensureDirection
1251 * when true - always ensure start is less than end.
1252 * @return int[] { start, end, direction} where direction==1 for range running
1253 * from end to start.
1255 private int[] getSegRange(Seg visSeg, boolean ensureDirection)
1257 boolean incl = visSeg.getInclusive();
1258 // adjust for inclusive flag.
1259 int pol = (visSeg.getStart() <= visSeg.getEnd()) ? 1 : -1; // polarity of
1261 int start = visSeg.getStart() + (incl ? 0 : pol);
1262 int end = visSeg.getEnd() + (incl ? 0 : -pol);
1263 if (ensureDirection && pol == -1)
1265 // jalview doesn't deal with inverted ranges, yet.
1270 return new int[] { start, end, pol < 0 ? 1 : 0 };
1276 * @return true if annotation is not to be stored in document
1278 private boolean isJalviewOnly(AlignmentAnnotation annotation)
1280 return annotation.autoCalculated || annotation.label.equals("Quality")
1281 || annotation.label.equals("Conservation")
1282 || annotation.label.equals("Consensus");
1285 boolean dojvsync = true;
1287 // boolean dojvsync = false; // disables Jalview AppData IO
1289 * list of alignment views created when updating Jalview from document.
1291 private final Vector newAlignmentViews = new Vector();
1294 * update local jalview view settings from the stored appdata (if any)
1296 public void updateJalviewFromAppdata()
1298 // recover any existing Jalview data from appdata
1299 // TODO: recover any PDB files stored as attachments in the vamsas session
1300 // and initialise the Jalview2XML.alreadyLoadedPDB hashtable with mappings
1303 final IClientAppdata cappdata = cdoc.getClientAppdata();
1304 if (cappdata != null)
1306 if (cappdata.hasClientAppdata())
1308 // TODO: how to check version of Jalview client app data and whether
1309 // it has been modified
1310 // client data is shared over all app clients
1313 // jalview.gui.Jalview2XML fromxml = new jalview.gui.Jalview2XML();
1314 Jalview2XML fromxml = new Jalview2XML();
1315 fromxml.attemptversion1parse = false;
1316 fromxml.setUniqueSetSuffix("");
1317 fromxml.setObjectMappingTables(vobj2jv, jv2vobj); // mapKeysToString
1319 // mapValuesToString
1320 fromxml.setSkipList(skipList);
1321 jalview.util.jarInputStreamProvider jprovider = new jalview.util.jarInputStreamProvider()
1325 public String getFilename()
1328 // TODO Get the vamsas session ID here
1329 return "Jalview Vamsas Document Client Data";
1333 public JarInputStream getJarInputStream() throws IOException
1336 "Returning client input stream for Jalview from Vamsas Document.");
1337 return new JarInputStream(cappdata.getClientInputStream());
1342 fromxml.loadJalviewAlign(jprovider);
1344 } catch (Exception e)
1347 } catch (OutOfMemoryError e)
1356 if (cappdata.hasUserAppdata())
1358 // TODO: how to check version of Jalview user app data and whether it
1359 // has been modified
1360 // user data overrides data shared over all app clients ?
1363 Jalview2XML fromxml = new Jalview2XML();
1364 fromxml.attemptversion1parse = false;
1365 fromxml.setUniqueSetSuffix("");
1366 fromxml.setSkipList(skipList);
1367 fromxml.setObjectMappingTables(mapKeysToString(vobj2jv),
1368 mapValuesToString(jv2vobj));
1369 jalview.util.jarInputStreamProvider jarstream = new jalview.util.jarInputStreamProvider()
1373 public String getFilename()
1376 // TODO Get the vamsas session ID here
1377 return "Jalview Vamsas Document User Data";
1381 public JarInputStream getJarInputStream() throws IOException
1384 "Returning user input stream for Jalview from Vamsas Document.");
1385 return new JarInputStream(cappdata.getUserInputStream());
1390 fromxml.loadJalviewAlign(jarstream);
1392 } catch (Exception e)
1395 } catch (OutOfMemoryError e)
1405 flushAlignViewports();
1409 * remove any spurious views generated by document synchronization
1411 private void flushAlignViewports()
1413 // remove any additional viewports originally recovered from the vamsas
1415 // search for all alignframes containing viewports generated from document
1417 // and if any contain more than one view, then remove the one generated by
1419 AlignmentViewport views[], av = null;
1420 AlignFrame af = null;
1421 Iterator newviews = newAlignmentViews.iterator();
1422 while (newviews.hasNext())
1424 av = (AlignmentViewport) newviews.next();
1425 af = Desktop.getAlignFrameFor(av);
1426 // TODO implement this : af.getNumberOfViews
1427 String seqsetidobj = av.getSequenceSetId();
1428 views = Desktop.getViewports(seqsetidobj);
1429 Console.debug("Found " + (views == null ? " no " : "" + views.length)
1430 + " views for '" + av.getSequenceSetId() + "'");
1431 if (views.length > 1)
1433 // we need to close the original document view.
1435 // work out how to do this by seeing if the views are gathered.
1436 // pretty clunky but the only way to do this without adding more flags
1437 // to the align frames.
1438 boolean gathered = false;
1439 String newviewid = null;
1440 List<AlignedCodonFrame> mappings = av.getAlignment()
1442 for (int i = 0; i < views.length; i++)
1446 AlignFrame viewframe = Desktop.getAlignFrameFor(views[i]);
1447 if (viewframe == af)
1451 newviewid = views[i].getSequenceSetId();
1455 // lose the reference to the vamsas document created view
1459 // close the view generated by the vamsas document synchronization
1466 af.closeMenuItem_actionPerformed(false);
1468 replaceJvObjMapping(seqsetidobj, newviewid);
1469 seqsetidobj = newviewid;
1470 // not sure if we need to do this:
1472 if (false) // mappings != null)
1474 // ensure sequence mappings from vamsas document view still
1476 if (mappings != null)
1478 jalview.structure.StructureSelectionManager
1479 .getStructureSelectionManager(Desktop.instance)
1480 .registerMappings(mappings);
1484 // ensure vamsas object binds to the stored views retrieved from
1486 // jalview.structure.StructureSelectionManager
1487 // .getStructureSelectionManager()
1488 // .addStructureViewerListener(viewframe.alignPanel);
1493 newAlignmentViews.clear();
1497 * replaces oldjvobject with newjvobject in the Jalview Object <> VorbaID
1500 * @param oldjvobject
1501 * @param newjvobject
1504 private void replaceJvObjMapping(Object oldjvobject, Object newjvobject)
1506 Object vobject = jv2vobj.remove(oldjvobject);
1507 if (vobject == null)
1509 // NOTE: this happens if user deletes object in one session then updates
1510 // from another client
1511 throw new Error(MessageManager.formatMessage(
1512 "error.implementation_error_old_jalview_object_not_bound",
1514 { oldjvobject.toString() }));
1516 if (newjvobject != null)
1518 jv2vobj.put(newjvobject, vobject);
1519 vobj2jv.put(vobject, newjvobject);
1524 * Update the jalview client and user appdata from the local jalview settings
1526 public void updateJalviewClientAppdata()
1528 final IClientAppdata cappdata = cdoc.getClientAppdata();
1529 if (cappdata != null)
1533 Jalview2XML jxml = new Jalview2XML();
1534 jxml.setObjectMappingTables(mapKeysToString(vobj2jv),
1535 mapValuesToString(jv2vobj));
1536 jxml.setSkipList(skipList);
1540 new JarOutputStream(cappdata.getClientOutputStream()));
1543 } catch (Exception e)
1545 // TODO raise GUI warning if user requests it.
1547 "Couldn't update jalview client application data. Giving up - local settings probably lost.",
1554 "Couldn't access client application data for vamsas session. This is probably a vamsas client bug.");
1559 * translate the Vobject keys to strings for use in Jalview2XML
1564 private IdentityHashMap mapValuesToString(IdentityHashMap jv2vobj2)
1566 IdentityHashMap mapped = new IdentityHashMap();
1567 Iterator keys = jv2vobj2.keySet().iterator();
1568 while (keys.hasNext())
1570 Object key = keys.next();
1571 mapped.put(key, jv2vobj2.get(key).toString());
1577 * translate the Vobject values to strings for use in Jalview2XML
1580 * @return hashtable with string values
1582 private Hashtable mapKeysToString(Hashtable vobj2jv2)
1584 Hashtable mapped = new Hashtable();
1585 Iterator keys = vobj2jv2.keySet().iterator();
1586 while (keys.hasNext())
1588 Object key = keys.next();
1589 mapped.put(key.toString(), vobj2jv2.get(key));
1595 * synchronize Jalview from the vamsas document
1597 * @return number of new views from document
1599 public int updateToJalview()
1601 VAMSAS _roots[] = cdoc.getVamsasRoots();
1603 for (int _root = 0; _root < _roots.length; _root++)
1605 VAMSAS root = _roots[_root];
1606 boolean newds = false;
1607 for (int _ds = 0, _nds = root.getDataSetCount(); _ds < _nds; _ds++)
1609 // ///////////////////////////////////
1611 DataSet dataset = root.getDataSet(_ds);
1612 int i, iSize = dataset.getSequenceCount();
1613 List<SequenceI> dsseqs;
1614 jalview.datamodel.Alignment jdataset = (jalview.datamodel.Alignment) getvObj2jv(
1617 if (jdataset == null)
1619 Console.debug("Initialising new jalview dataset fields");
1621 dsseqs = new Vector();
1625 Console.debug("Update jalview dataset from vamsas.");
1626 jremain = jdataset.getHeight();
1627 dsseqs = jdataset.getSequences();
1630 // TODO: test sequence merging - we preserve existing non vamsas
1631 // sequences but add in any new vamsas ones, and don't yet update any
1632 // sequence attributes
1633 for (i = 0; i < iSize; i++)
1635 Sequence vdseq = dataset.getSequence(i);
1636 jalview.io.vamsas.Datasetsequence dssync = new Datasetsequence(
1639 jalview.datamodel.SequenceI dsseq = (SequenceI) dssync.getJvobj();
1640 if (dssync.isAddfromdoc())
1644 if (vdseq.getDbRefCount() > 0)
1646 DbRef[] dbref = vdseq.getDbRef();
1647 for (int db = 0; db < dbref.length; db++)
1649 new jalview.io.vamsas.Dbref(this, dbref[db], vdseq, dsseq);
1652 dsseq.updatePDBIds();
1658 SequenceI[] seqs = new SequenceI[dsseqs.size()];
1659 for (i = 0, iSize = dsseqs.size(); i < iSize; i++)
1661 seqs[i] = dsseqs.get(i);
1662 dsseqs.set(i, null);
1664 jdataset = new jalview.datamodel.Alignment(seqs);
1665 Console.debug("New vamsas dataset imported into jalview.");
1666 bindjvvobj(jdataset, dataset);
1669 // add any new dataset sequence feature annotations
1670 if (dataset.getDataSetAnnotations() != null)
1672 for (int dsa = 0; dsa < dataset
1673 .getDataSetAnnotationsCount(); dsa++)
1675 DataSetAnnotations dseta = dataset.getDataSetAnnotations(dsa);
1676 // TODO: deal with group annotation on datset sequences.
1677 if (dseta.getSeqRefCount() == 1)
1679 SequenceI dsSeq = (SequenceI) getvObj2jv(
1680 (Vobject) dseta.getSeqRef(0)); // TODO: deal with group
1686 "Couldn't resolve jalview sequenceI for dataset object reference "
1687 + ((Vobject) dataset
1688 .getDataSetAnnotations(dsa)
1689 .getSeqRef(0)).getVorbaId()
1694 if (dseta.getAnnotationElementCount() == 0)
1696 new jalview.io.vamsas.Sequencefeature(this, dseta, dsSeq);
1701 // TODO: deal with alignmentAnnotation style annotation
1702 // appearing on dataset sequences.
1703 // JBPNote: we could just add them to all alignments but
1704 // that may complicate cross references in the jalview
1707 "Ignoring dataset annotation with annotationElements. Not yet supported in jalview.");
1714 "Ignoring multiply referenced dataset sequence annotation for binding to datsaet sequence features.");
1718 if (dataset.getAlignmentCount() > 0)
1720 // LOAD ALIGNMENTS from DATASET
1722 for (int al = 0, nal = dataset
1723 .getAlignmentCount(); al < nal; al++)
1725 uk.ac.vamsas.objects.core.Alignment alignment = dataset
1727 // TODO check this handles multiple views properly
1728 AlignmentViewport av = findViewport(alignment);
1730 jalview.datamodel.AlignmentI jal = null;
1733 // TODO check that correct alignment object is retrieved when
1734 // hidden seqs exist.
1735 jal = (av.hasHiddenRows()) ? av.getAlignment()
1736 .getHiddenSequences().getFullAlignment()
1737 : av.getAlignment();
1739 iSize = alignment.getAlignmentSequenceCount();
1740 boolean refreshal = false;
1741 Vector newasAnnots = new Vector();
1742 char gapChar = ' '; // default for new alignments read in from the
1746 dsseqs = jal.getSequences(); // for merge/update
1747 gapChar = jal.getGapCharacter();
1751 dsseqs = new Vector();
1753 char valGapchar = alignment.getGapChar().charAt(0);
1754 for (i = 0; i < iSize; i++)
1756 AlignmentSequence valseq = alignment.getAlignmentSequence(i);
1757 jalview.datamodel.Sequence alseq = (jalview.datamodel.Sequence) getvObj2jv(
1759 if (syncFromAlignmentSequence(valseq, valGapchar, gapChar,
1760 dsseqs) && alseq != null)
1763 // updated to sequence from the document
1767 if (valseq.getAlignmentSequenceAnnotationCount() > 0)
1769 AlignmentSequenceAnnotation[] vasannot = valseq
1770 .getAlignmentSequenceAnnotation();
1771 for (int a = 0; a < vasannot.length; a++)
1773 jalview.datamodel.AlignmentAnnotation asa = (jalview.datamodel.AlignmentAnnotation) getvObj2jv(
1774 vasannot[a]); // TODO:
1782 int se[] = getBounds(vasannot[a]);
1783 asa = getjAlignmentAnnotation(jal, vasannot[a]);
1784 asa.setSequenceRef(alseq);
1785 asa.createSequenceMapping(alseq, se[0], false); // TODO:
1796 alseq.addAlignmentAnnotation(asa);
1797 bindjvvobj(asa, vasannot[a]);
1799 newasAnnots.add(asa);
1803 // update existing annotation - can do this in place
1804 if (vasannot[a].getModifiable() == null) // TODO: USE
1810 "UNIMPLEMENTED: not recovering user modifiable sequence alignment annotation");
1811 // TODO: should at least replace with new one - otherwise
1812 // things will break
1813 // basically do this:
1814 // int se[] = getBounds(vasannot[a]);
1815 // asa.update(getjAlignmentAnnotation(jal, vasannot[a]));
1816 // // update from another annotation object in place.
1817 // asa.createSequenceMapping(alseq, se[0], false);
1826 SequenceI[] seqs = new SequenceI[dsseqs.size()];
1827 for (i = 0, iSize = dsseqs.size(); i < iSize; i++)
1829 seqs[i] = dsseqs.get(i);
1830 dsseqs.set(i, null);
1832 jal = new jalview.datamodel.Alignment(seqs);
1833 Console.debug("New vamsas alignment imported into jalview "
1834 + alignment.getVorbaId().getId());
1835 jal.setDataset(jdataset);
1837 if (newasAnnots != null && newasAnnots.size() > 0)
1839 // Add the new sequence annotations in to the alignment.
1840 for (int an = 0, anSize = newasAnnots
1841 .size(); an < anSize; an++)
1844 (AlignmentAnnotation) newasAnnots.elementAt(an));
1845 // TODO: check if anything has to be done - like calling
1846 // adjustForAlignment or something.
1847 newasAnnots.setElementAt(null, an);
1851 // //////////////////////////////////////////
1852 // //LOAD ANNOTATIONS FOR THE ALIGNMENT
1853 // ////////////////////////////////////
1854 if (alignment.getAlignmentAnnotationCount() > 0)
1856 uk.ac.vamsas.objects.core.AlignmentAnnotation[] an = alignment
1857 .getAlignmentAnnotation();
1859 for (int j = 0; j < an.length; j++)
1861 jalview.datamodel.AlignmentAnnotation jan = (jalview.datamodel.AlignmentAnnotation) getvObj2jv(
1865 // update or stay the same.
1866 // TODO: should at least replace with a new one - otherwise
1867 // things will break
1868 // basically do this:
1869 // jan.update(getjAlignmentAnnotation(jal, an[a])); // update
1870 // from another annotation object in place.
1873 "update from vamsas alignment annotation to existing jalview alignment annotation.");
1874 if (an[j].getModifiable() == null) // TODO: USE VAMSAS
1875 // LIBRARY OBJECT LOCK
1878 // TODO: user defined annotation is totally mutable... - so
1879 // load it up or throw away if locally edited.
1881 "NOT IMPLEMENTED - Recovering user-modifiable annotation - yet...");
1883 // TODO: compare annotation element rows
1884 // TODO: compare props.
1888 jan = getjAlignmentAnnotation(jal, an[j]);
1889 // TODO: ensure we add the alignment annotation before the
1890 // automatic annotation rows
1891 jal.addAnnotation(jan);
1892 bindjvvobj(jan, an[j]);
1897 AlignFrame alignFrame;
1900 Console.debug("New alignframe for alignment "
1901 + alignment.getVorbaId());
1902 // ///////////////////////////////
1903 // construct alignment view
1904 alignFrame = new AlignFrame(jal, AlignFrame.DEFAULT_WIDTH,
1905 AlignFrame.DEFAULT_HEIGHT,
1906 alignment.getVorbaId().toString());
1907 av = alignFrame.getViewport();
1908 newAlignmentViews.addElement(av);
1909 String title = alignment.getProvenance()
1911 alignment.getProvenance().getEntryCount() - 1)
1913 if (alignment.getPropertyCount() > 0)
1915 for (int p = 0, pe = alignment
1916 .getPropertyCount(); p < pe; p++)
1918 if (alignment.getProperty(p).getName().equals("title"))
1920 title = alignment.getProperty(p).getContent();
1924 // TODO: automatically create meaningful title for a vamsas
1925 // alignment using its provenance.
1926 if (Console.isDebugEnabled())
1928 title = title + "(" + alignment.getVorbaId() + ")";
1931 jalview.gui.Desktop.addInternalFrame(alignFrame, title,
1932 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
1933 bindjvvobj(av.getSequenceSetId(), alignment);
1937 // find the alignFrame for jal.
1938 // TODO: fix this so we retrieve the alignFrame handing av
1939 // *directly* (JBPNote - don't understand this now)
1940 // TODO: make sure all associated views are refreshed
1941 alignFrame = Desktop.getAlignFrameFor(av);
1944 av.alignmentChanged(alignFrame.alignPanel);
1945 alignFrame.alignPanel.adjustAnnotationHeight();
1949 // /////////////////////////////////////
1950 if (alignment.getTreeCount() > 0)
1953 for (int t = 0; t < alignment.getTreeCount(); t++)
1955 jalview.io.vamsas.Tree vstree = new jalview.io.vamsas.Tree(
1956 this, alignFrame, alignment.getTree(t));
1957 TreePanel tp = null;
1958 if (vstree.isValidTree())
1960 tp = alignFrame.showNewickTree(vstree.getNewickTree(),
1961 vstree.getTitle(), vstree.getInputData(), 600,
1962 500, t * 20 + 50, t * 20 + 50);
1967 bindjvvobj(tp, alignment.getTree(t));
1970 vstree.UpdateSequenceTreeMap(tp);
1971 } catch (RuntimeException e)
1973 Console.warn("update of labels failed.", e);
1978 Console.warn("Cannot create tree for tree " + t
1980 + alignment.getTree(t).getVorbaId());
1988 // we do sequenceMappings last because they span all datasets in a vamsas
1990 for (int _ds = 0, _nds = root.getDataSetCount(); _ds < _nds; _ds++)
1992 DataSet dataset = root.getDataSet(_ds);
1993 if (dataset.getSequenceMappingCount() > 0)
1995 for (int sm = 0, smCount = dataset
1996 .getSequenceMappingCount(); sm < smCount; sm++)
1998 Rangetype seqmap = new jalview.io.vamsas.Sequencemapping(this,
1999 dataset.getSequenceMapping(sm));
2004 return newAlignmentViews.size();
2007 public AlignmentViewport findViewport(Alignment alignment)
2009 AlignmentViewport av = null;
2010 AlignmentViewport[] avs = Desktop
2011 .getViewports((String) getvObj2jv(alignment));
2019 // bitfields - should be a template in j1.5
2020 private static int HASSECSTR = 0;
2022 private static int HASVALS = 1;
2024 private static int HASHPHOB = 2;
2026 private static int HASDC = 3;
2028 private static int HASDESCSTR = 4;
2030 private static int HASTWOSTATE = 5; // not used yet.
2033 * parses the AnnotationElements - if they exist - into
2034 * jalview.datamodel.Annotation[] rows Two annotation rows are made if there
2035 * are distinct annotation for both at 'pos' and 'after pos' at any particular
2039 * @return { boolean[static int constants ], int[ae.length] - map to annotated
2040 * object frame, jalview.datamodel.Annotation[],
2041 * jalview.datamodel.Annotation[] (after)}
2043 private Object[] parseRangeAnnotation(
2044 uk.ac.vamsas.objects.core.RangeAnnotation annotation)
2046 // set these attributes by looking in the annotation to decide what kind of
2047 // alignment annotation rows will be made
2048 // TODO: potentially we might make several annotation rows from one vamsas
2049 // alignment annotation. the jv2Vobj binding mechanism
2050 // may not quite cope with this (without binding an array of annotations to
2051 // a vamsas alignment annotation)
2052 // summary flags saying what we found over the set of annotation rows.
2053 boolean[] AeContent = new boolean[] { false, false, false, false,
2055 int[] rangeMap = getMapping(annotation);
2056 jalview.datamodel.Annotation[][] anot = new jalview.datamodel.Annotation[][] {
2057 new jalview.datamodel.Annotation[rangeMap.length],
2058 new jalview.datamodel.Annotation[rangeMap.length] };
2059 boolean mergeable = true; // false if 'after positions cant be placed on
2060 // same annotation row as positions.
2062 if (annotation.getAnnotationElementCount() > 0)
2064 AnnotationElement ae[] = annotation.getAnnotationElement();
2065 for (int aa = 0; aa < ae.length; aa++)
2067 int pos = (int) ae[aa].getPosition() - 1; // pos counts from 1 to
2068 // (|seg.start-seg.end|+1)
2069 if (pos >= 0 && pos < rangeMap.length)
2071 int row = ae[aa].getAfter() ? 1 : 0;
2072 if (anot[row][pos] != null)
2074 // only time this should happen is if the After flag is set.
2075 Console.debug("Ignoring duplicate annotation site at " + pos);
2078 if (anot[1 - row][pos] != null)
2083 if (ae[aa].getDescription() != null)
2085 desc = ae[aa].getDescription();
2086 if (desc.length() > 0)
2088 // have imported valid description string
2089 AeContent[HASDESCSTR] = true;
2092 String dc = null; // ae[aa].getDisplayCharacter()==null ? "dc" :
2093 // ae[aa].getDisplayCharacter();
2094 String ss = null; // ae[aa].getSecondaryStructure()==null ? "ss" :
2095 // ae[aa].getSecondaryStructure();
2096 java.awt.Color colour = null;
2097 if (ae[aa].getGlyphCount() > 0)
2099 Glyph[] glyphs = ae[aa].getGlyph();
2100 for (int g = 0; g < glyphs.length; g++)
2102 if (glyphs[g].getDict().equals(
2103 uk.ac.vamsas.objects.utils.GlyphDictionary.PROTEIN_SS_3STATE))
2105 ss = glyphs[g].getContent();
2106 AeContent[HASSECSTR] = true;
2108 else if (glyphs[g].getDict().equals(
2109 uk.ac.vamsas.objects.utils.GlyphDictionary.PROTEIN_HD_HYDRO))
2111 Console.debug("ignoring hydrophobicity glyph marker.");
2112 AeContent[HASHPHOB] = true;
2113 char c = (dc = glyphs[g].getContent()).charAt(0);
2114 // dc may get overwritten - but we still set the colour.
2115 colour = new java.awt.Color(c == '+' ? 255 : 0,
2116 c == '.' ? 255 : 0, c == '-' ? 255 : 0);
2119 else if (glyphs[g].getDict().equals(
2120 uk.ac.vamsas.objects.utils.GlyphDictionary.DEFAULT))
2122 dc = glyphs[g].getContent();
2123 AeContent[HASDC] = true;
2128 "IMPLEMENTATION TODO: Ignoring unknown glyph type "
2129 + glyphs[g].getDict());
2134 if (ae[aa].getValueCount() > 0)
2136 AeContent[HASVALS] = true;
2137 if (ae[aa].getValueCount() > 1)
2140 "ignoring additional " + (ae[aa].getValueCount() - 1)
2141 + " values in annotation element.");
2143 val = ae[aa].getValue(0);
2147 anot[row][pos] = new jalview.datamodel.Annotation(
2148 (dc != null) ? dc : "", desc,
2149 (ss != null) ? ss.charAt(0) : ' ', val);
2153 anot[row][pos] = new jalview.datamodel.Annotation(
2154 (dc != null) ? dc : "", desc,
2155 (ss != null) ? ss.charAt(0) : ' ', val, colour);
2160 Console.warn("Ignoring out of bound annotation element " + aa
2161 + " in " + annotation.getVorbaId().getId());
2164 // decide on how many annotation rows are needed.
2167 for (int i = 0; i < anot[0].length; i++)
2169 if (anot[1][i] != null)
2171 anot[0][i] = anot[1][i];
2172 anot[0][i].description = anot[0][i].description + " (after)";
2173 AeContent[HASDESCSTR] = true; // we have valid description string
2182 for (int i = 0; i < anot[0].length; i++)
2184 anot[1][i].description = anot[1][i].description + " (after)";
2187 return new Object[] { AeContent, rangeMap, anot[0], anot[1] };
2191 // no annotations to parse. Just return an empty annotationElement[]
2193 return new Object[] { AeContent, rangeMap, anot[0], anot[1] };
2200 * the jalview alignment to which the annotation will be attached
2201 * (ideally - freshly updated from corresponding vamsas alignment)
2203 * @return unbound jalview alignment annotation object.
2205 private jalview.datamodel.AlignmentAnnotation getjAlignmentAnnotation(
2206 jalview.datamodel.AlignmentI jal,
2207 uk.ac.vamsas.objects.core.RangeAnnotation annotation)
2209 if (annotation == null)
2214 // hasSequenceRef=annotation.getClass().equals(uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation.class);
2215 // boolean hasProvenance=hasSequenceRef ||
2216 // (annotation.getClass().equals(uk.ac.vamsas.objects.core.AlignmentAnnotation.class));
2218 * int se[] = getBounds(annotation); if (se==null) se=new int[]
2219 * {0,jal.getWidth()-1};
2221 Object[] parsedRangeAnnotation = parseRangeAnnotation(annotation);
2222 String a_label = annotation.getLabel();
2223 String a_descr = annotation.getDescription();
2224 GraphLine gl = null;
2226 boolean interp = true; // cleared if annotation is DISCRETE
2227 // set type and other attributes from properties
2228 if (annotation.getPropertyCount() > 0)
2230 // look for special jalview properties
2231 uk.ac.vamsas.objects.core.Property[] props = annotation.getProperty();
2232 for (int p = 0; p < props.length; p++)
2234 if (props[p].getName().equalsIgnoreCase(DISCRETE_ANNOTATION))
2236 type = AlignmentAnnotation.BAR_GRAPH;
2239 else if (props[p].getName().equalsIgnoreCase(CONTINUOUS_ANNOTATION))
2241 type = AlignmentAnnotation.LINE_GRAPH;
2243 else if (props[p].getName().equalsIgnoreCase(THRESHOLD))
2248 val = Float.valueOf(props[p].getContent());
2249 } catch (Exception e)
2251 Console.warn("Failed to parse threshold property");
2257 gl = new GraphLine(val.floatValue(), "",
2258 java.awt.Color.black);
2262 gl.value = val.floatValue();
2266 else if (props[p].getName().equalsIgnoreCase(THRESHOLD + "Name"))
2270 gl = new GraphLine(0, "", java.awt.Color.black);
2272 gl.label = props[p].getContent();
2276 jalview.datamodel.AlignmentAnnotation jan = null;
2277 if (a_label == null || a_label.length() == 0)
2279 a_label = annotation.getType();
2280 if (a_label.length() == 0)
2282 a_label = "Unamed annotation";
2285 if (a_descr == null || a_descr.length() == 0)
2287 a_descr = "Annotation of type '" + annotation.getType() + "'";
2289 if (parsedRangeAnnotation == null)
2292 "Inserting empty annotation row elements for a whole-alignment annotation.");
2296 if (parsedRangeAnnotation[3] != null)
2298 Console.warn("Ignoring 'After' annotation row in "
2299 + annotation.getVorbaId());
2301 jalview.datamodel.Annotation[] arow = (jalview.datamodel.Annotation[]) parsedRangeAnnotation[2];
2302 boolean[] has = (boolean[]) parsedRangeAnnotation[0];
2303 // VAMSAS: getGraph is only on derived annotation for alignments - in this
2304 // way its 'odd' - there is already an existing TODO about removing this
2305 // flag as being redundant
2307 * if((annotation.getClass().equals(uk.ac.vamsas.objects.core.
2308 * AlignmentAnnotation.class) &&
2309 * ((uk.ac.vamsas.objects.core.AlignmentAnnotation)annotation).getGraph())
2310 * || (hasSequenceRef=true &&
2311 * ((uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation
2312 * )annotation).getGraph())) {
2318 type = jalview.datamodel.AlignmentAnnotation.BAR_GRAPH; // default
2324 // no hints - so we ensure HPHOB display is like this.
2325 type = jalview.datamodel.AlignmentAnnotation.BAR_GRAPH;
2328 // make bounds and automatic description strings for jalview user's
2329 // benefit (these shouldn't be written back to vamsas document)
2330 boolean first = true;
2331 float min = 0, max = 1;
2333 for (int i = 0; i < arow.length; i++)
2335 if (arow[i] != null)
2337 if (i - lastval > 1 && interp)
2339 // do some interpolation *between* points
2340 if (arow[lastval] != null)
2342 float interval = arow[i].value - arow[lastval].value;
2343 interval /= i - lastval;
2344 float base = arow[lastval].value;
2345 for (int ip = lastval + 1, np = 0; ip < i; np++, ip++)
2347 arow[ip] = new jalview.datamodel.Annotation("", "", ' ',
2348 interval * np + base);
2349 // NB - Interpolated points don't get a tooltip and
2355 // check range - shouldn't we have a min and max property in the
2356 // annotation object ?
2359 min = max = arow[i].value;
2364 if (arow[i].value < min)
2366 min = arow[i].value;
2368 else if (arow[i].value > max)
2370 max = arow[i].value;
2373 // make tooltip and display char value
2374 if (!has[HASDESCSTR])
2376 arow[i].description = arow[i].value + "";
2382 if (arow[i].description != null
2383 && arow[i].description.length() < 3)
2385 // copy over the description as the display char.
2386 arow[i].displayCharacter = new String(
2387 arow[i].description);
2392 // mark the position as a point used for the interpolation.
2393 arow[i].displayCharacter = arow[i].value + "";
2398 jan = new jalview.datamodel.AlignmentAnnotation(a_label, a_descr,
2399 arow, min, max, type);
2403 if (annotation.getAnnotationElementCount() == 0)
2405 // empty annotation array
2406 // TODO: alignment 'features' compare rangeType spec to alignment
2407 // width - if it is not complete, then mark regions on the annotation
2410 jan = new jalview.datamodel.AlignmentAnnotation(a_label, a_descr,
2412 jan.setThreshold(null);
2413 jan.annotationId = annotation.getVorbaId().toString(); // keep all the
2416 if (annotation.getLinkCount() > 0)
2418 Console.warn("Ignoring " + annotation.getLinkCount()
2419 + "links added to AlignmentAnnotation.");
2421 if (annotation.getModifiable() == null
2422 || annotation.getModifiable().length() == 0) // TODO: USE VAMSAS
2426 jan.editable = true;
2430 if (annotation.getGroup() != null
2431 && annotation.getGroup().length() > 0)
2433 jan.graphGroup = Integer.parseInt(annotation.getGroup()); // TODO:
2441 } catch (Exception e)
2444 "UNIMPLEMENTED : Couldn't parse non-integer group value for setting graphGroup correctly.");
2454 * get real bounds of a RangeType's specification. start and end are an
2455 * inclusive range within which all segments and positions lie. TODO: refactor
2459 * @return int[] { start, end}
2461 private int[] getBounds(RangeType dseta)
2466 if (dseta.getSegCount() > 0 && dseta.getPosCount() > 0)
2468 throw new Error(MessageManager.getString(
2469 "error.invalid_vamsas_rangetype_cannot_resolve_lists"));
2471 if (dseta.getSegCount() > 0)
2473 se = getSegRange(dseta.getSeg(0), true);
2474 for (int s = 1, sSize = dseta.getSegCount(); s < sSize; s++)
2476 int nse[] = getSegRange(dseta.getSeg(s), true);
2487 if (dseta.getPosCount() > 0)
2489 // could do a polarity for pos range too. and pass back indication of
2491 int pos = dseta.getPos(0).getI();
2492 se = new int[] { pos, pos };
2493 for (int p = 0, pSize = dseta.getPosCount(); p < pSize; p++)
2495 pos = dseta.getPos(p).getI();
2512 * map from a rangeType's internal frame to the referenced object's coordinate
2516 * @return int [] { ref(pos)...} for all pos in rangeType's frame.
2518 private int[] getMapping(RangeType dseta)
2520 Vector posList = new Vector();
2524 if (dseta.getSegCount() > 0 && dseta.getPosCount() > 0)
2526 throw new Error(MessageManager.getString(
2527 "error.invalid_vamsas_rangetype_cannot_resolve_lists"));
2529 if (dseta.getSegCount() > 0)
2531 for (int s = 0, sSize = dseta.getSegCount(); s < sSize; s++)
2533 se = getSegRange(dseta.getSeg(s), false);
2534 int se_end = se[1 - se[2]] + (se[2] == 0 ? 1 : -1);
2535 for (int p = se[se[2]]; p != se_end; p += se[2] == 0 ? 1 : -1)
2537 posList.add(Integer.valueOf(p));
2541 else if (dseta.getPosCount() > 0)
2543 int pos = dseta.getPos(0).getI();
2545 for (int p = 0, pSize = dseta.getPosCount(); p < pSize; p++)
2547 pos = dseta.getPos(p).getI();
2548 posList.add(Integer.valueOf(pos));
2552 if (posList != null && posList.size() > 0)
2554 int[] range = new int[posList.size()];
2555 for (int i = 0; i < range.length; i++)
2557 range[i] = ((Integer) posList.elementAt(i)).intValue();
2568 * where the from range is the local mapped range, and the to range
2569 * is the 'mapped' range in the MapRangeType
2576 private jalview.util.MapList parsemapType(MapType maprange, int localu,
2579 jalview.util.MapList ml = null;
2580 int[] localRange = getMapping(maprange.getLocal());
2581 int[] mappedRange = getMapping(maprange.getMapped());
2582 long lu = maprange.getLocal().hasUnit() ? maprange.getLocal().getUnit()
2584 long mu = maprange.getMapped().hasUnit()
2585 ? maprange.getMapped().getUnit()
2587 ml = new jalview.util.MapList(localRange, mappedRange, (int) lu,
2593 * initialise a range type object from a set of start/end inclusive intervals
2598 private void initRangeType(RangeType mrt, List<int[]> ranges)
2600 for (int[] range : ranges)
2602 Seg vSeg = new Seg();
2603 vSeg.setStart(range[0]);
2604 vSeg.setEnd(range[1]);
2610 * initialise a MapType object from a MapList object.
2616 private void initMapType(MapType maprange, jalview.util.MapList ml,
2619 maprange.setLocal(new Local());
2620 maprange.setMapped(new Mapped());
2621 initRangeType(maprange.getLocal(), ml.getFromRanges());
2622 initRangeType(maprange.getMapped(), ml.getToRanges());
2625 maprange.getLocal().setUnit(ml.getFromRatio());
2626 maprange.getLocal().setUnit(ml.getToRatio());
2631 * not needed now. Provenance getVamsasProvenance(jalview.datamodel.Provenance
2632 * jprov) { jalview.datamodel.ProvenanceEntry[] entries = null; // TODO: fix
2633 * App and Action here. Provenance prov = new Provenance();
2634 * org.exolab.castor.types.Date date = new org.exolab.castor.types.Date( new
2635 * java.util.Date()); Entry provEntry;
2637 * if (jprov != null) { entries = jprov.getEntries(); for (int i = 0; i <
2638 * entries.length; i++) { provEntry = new Entry(); try { date = new
2639 * org.exolab.castor.types.Date(entries[i].getDate()); } catch (Exception ex)
2640 * { ex.printStackTrace();
2642 * date = new org.exolab.castor.types.Date(entries[i].getDate()); }
2643 * provEntry.setDate(date); provEntry.setUser(entries[i].getUser());
2644 * provEntry.setAction(entries[i].getAction()); prov.addEntry(provEntry); } }
2645 * else { provEntry = new Entry(); provEntry.setDate(date);
2646 * provEntry.setUser(System.getProperty("user.name")); // TODO: ext string
2647 * provEntry.setApp("JVAPP"); // TODO: ext string provEntry.setAction(action);
2648 * prov.addEntry(provEntry); }
2652 jalview.datamodel.Provenance getJalviewProvenance(Provenance prov)
2654 // TODO: fix App and Action entries and check use of provenance in jalview.
2655 jalview.datamodel.Provenance jprov = new jalview.datamodel.Provenance();
2656 for (int i = 0; i < prov.getEntryCount(); i++)
2658 jprov.addEntry(prov.getEntry(i).getUser(),
2659 prov.getEntry(i).getAction(), prov.getEntry(i).getDate(),
2660 prov.getEntry(i).getId());
2668 * @return default initial provenance list for a Jalview created vamsas
2671 Provenance dummyProvenance()
2673 return dummyProvenance(null);
2676 Entry dummyPEntry(String action)
2678 Entry entry = new Entry();
2679 entry.setApp(this.provEntry.getApp());
2682 entry.setAction(action);
2686 entry.setAction("created.");
2688 entry.setDate(new java.util.Date());
2689 entry.setUser(this.provEntry.getUser());
2693 Provenance dummyProvenance(String action)
2695 Provenance prov = new Provenance();
2696 prov.addEntry(dummyPEntry(action));
2700 Entry addProvenance(Provenance p, String action)
2702 Entry dentry = dummyPEntry(action);
2707 public Entry getProvEntry()
2712 public IClientDocument getClientDocument()
2717 public IdentityHashMap getJvObjectBinding()
2722 public Hashtable getVamsasObjectBinding()
2727 public void storeSequenceMappings(AlignmentViewport viewport,
2728 String title) throws Exception
2730 AlignmentViewport av = viewport;
2733 jalview.datamodel.AlignmentI jal = av.getAlignment();
2734 // /////////////////////////////////////////
2736 DataSet dataset = null;
2737 if (jal.getDataset() == null)
2739 Console.warn("Creating new dataset for an alignment.");
2740 jal.setDataset(null);
2742 dataset = (DataSet) ((Alignment) getjv2vObj(
2743 viewport.getSequenceSetId())).getV_parent(); // jal.getDataset());
2744 if (dataset == null)
2746 dataset = (DataSet) getjv2vObj(jal.getDataset());
2748 "Can't find the correct dataset for the alignment in this view. Creating new one.");
2751 // Store any sequence mappings.
2752 List<AlignedCodonFrame> cframes = av.getAlignment().getCodonFrames();
2753 if (cframes != null)
2755 for (AlignedCodonFrame acf : cframes)
2757 if (acf.getdnaSeqs() != null && acf.getdnaSeqs().length > 0)
2759 jalview.datamodel.SequenceI[] dmps = acf.getdnaSeqs();
2760 jalview.datamodel.Mapping[] mps = acf.getProtMappings();
2761 for (int smp = 0; smp < mps.length; smp++)
2763 uk.ac.vamsas.objects.core.SequenceType mfrom = (SequenceType) getjv2vObj(
2767 new jalview.io.vamsas.Sequencemapping(this, mps[smp], mfrom,
2773 "NO Vamsas Binding for local sequence! NOT CREATING MAPPING FOR "
2774 + dmps[smp].getDisplayId(true) + " to "
2775 + mps[smp].getTo().getName());
2781 } catch (Exception e)
2783 throw new Exception(MessageManager.formatMessage(
2784 "exception.couldnt_store_sequence_mappings", new String[]
2789 public void clearSkipList()
2791 if (skipList != null)
2798 * @return the skipList
2800 public Hashtable getSkipList()
2807 * the skipList to set
2809 public void setSkipList(Hashtable skipList)
2811 this.skipList = skipList;
2815 * registry for datastoreItems
2817 DatastoreRegistry dsReg = new DatastoreRegistry();
2819 public DatastoreRegistry getDatastoreRegisty()
2823 dsReg = new DatastoreRegistry();