package jalview.io;
-import org.vamsas.client.Vobject;
-import org.vamsas.client.VorbaId;
-import org.vamsas.objects.core.*;
-import org.vamsas.objects.utils.DocumentStuff;
-import org.vamsas.test.simpleclient.ClientDoc;
-
import jalview.bin.Cache;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
*/
public class VamsasDatastore {
- Entry provEntry = null;
-
- // AlignViewport av;
-
- org.exolab.castor.types.Date date = new org.exolab.castor.types.Date(
- new java.util.Date());
-
- ClientDoc cdoc;
-
- Hashtable vobj2jv;
-
- IdentityHashMap jv2vobj;
-
- public VamsasDatastore(ClientDoc cdoc, Hashtable vobj2jv,
- IdentityHashMap jv2vobj, Entry provEntry) {
- this.cdoc = cdoc;
- this.vobj2jv = vobj2jv;
- this.jv2vobj = jv2vobj;
- this.provEntry = provEntry;
- }
-
- /*
- * public void storeJalview(String file, AlignFrame af) { try { // 1. Load the
- * mapping information from the file Mapping map = new
- * Mapping(getClass().getClassLoader()); java.net.URL url =
- * getClass().getResource("/jalview_mapping.xml"); map.loadMapping(url); // 2.
- * Unmarshal the data // Unmarshaller unmar = new Unmarshaller();
- * //unmar.setIgnoreExtraElements(true); //unmar.setMapping(map); // uni =
- * (UniprotFile) unmar.unmarshal(new FileReader(file)); // 3. marshal the data
- * with the total price back and print the XML in the console Marshaller
- * marshaller = new Marshaller( new FileWriter(file) );
- *
- * marshaller.setMapping(map); marshaller.marshal(af); } catch (Exception e) {
- * e.printStackTrace(); } }
- *
- *
- */
- /**
- * @return the Vobject bound to Jalview datamodel object
- */
- protected Vobject getjv2vObj(Object jvobj) {
- if (jv2vobj.containsKey(jvobj))
- return cdoc.getObject((VorbaId) jv2vobj.get(jvobj));
- return null;
- }
-
- /**
- *
- * @param vobj
- * @return Jalview datamodel object bound to the vamsas document object
- */
- protected Object getvObj2jv(org.vamsas.client.Vobject vobj) {
- VorbaId id = vobj.getVorbaId();
- if (id == null)
- {
- id = cdoc.registerObject(vobj);
- Cache.log
- .debug("Registering new object and returning null for getvObj2jv");
- return null;
- }
- if (vobj2jv.containsKey(vobj.getVorbaId()))
- return vobj2jv.get(vobj.getVorbaId());
- return null;
- }
-
- protected void bindjvvobj(Object jvobj, org.vamsas.client.Vobject vobj) {
- VorbaId id = vobj.getVorbaId();
- if (id == null)
- {
- id = cdoc.registerObject(vobj);
- if (id==null || vobj.getVorbaId()==null)
- Cache.log.error("Failed to get id for "+(vobj.isRegisterable() ? "registerable" : "unregisterable") +" object "+vobj);
- }
-
- if (vobj2jv.containsKey(vobj.getVorbaId()) && !((VorbaId)vobj2jv.get(vobj.getVorbaId())).equals(jvobj)) {
- Cache.log.debug("Warning? Overwriting existing vamsas id binding for "+vobj.getVorbaId(), new Exception("Overwriting vamsas id binding."));
- }
- else if (jv2vobj.containsKey(jvobj) && !((VorbaId)jv2vobj.get(jvobj)).equals(vobj.getVorbaId()))
- {
- Cache.log.debug("Warning? Overwriting existing jalview object binding for "+jvobj, new Exception("Overwriting jalview object binding."));
- }
- /* Cache.log.error("Attempt to make conflicting object binding! "+vobj+" id " +vobj.getVorbaId()+" already bound to "+getvObj2jv(vobj)+" and "+jvobj+" already bound to "+getjv2vObj(jvobj),new Exception("Excessive call to bindjvvobj"));
- }*/
- // we just update the hash's regardless!
- vobj2jv.put(vobj.getVorbaId(), jvobj);
- // JBPNote - better implementing a hybrid invertible hash.
- jv2vobj.put(jvobj, vobj.getVorbaId());
- }
-
- /**
- * put the alignment viewed by AlignViewport into cdoc.
- *
- * @param av alignViewport to be stored
- * @param aFtitle title for alignment
- */
- public void storeVAMSAS(AlignViewport av, String aFtitle) {
- try
- {
- jalview.datamodel.AlignmentI jal = av.getAlignment();
- boolean nw = false;
- VAMSAS root = null; // will be resolved based on Dataset Parent.
- // /////////////////////////////////////////
- // SAVE THE DATASET
- if (jal.getDataset() == null)
- {
- Cache.log.warn("Creating new dataset for an alignment.");
- jal.setDataset(null);
- }
- DataSet dataset = (DataSet) getjv2vObj(jal.getDataset());
- if (dataset == null)
- {
- root = cdoc.getVamsasRoots()[0]; // default vamsas root for modifying.
- dataset = new DataSet();
- root.addDataSet(dataset);
- bindjvvobj(jal.getDataset(), dataset);
- dataset.setProvenance(dummyProvenance());
- dataset.getProvenance().addEntry(provEntry);
- nw = true;
- }
- else
- {
- root = (VAMSAS) dataset.getV_parent();
- }
- // update dataset
- Sequence sequence;
- DbRef dbref;
- // set new dataset and alignment sequences based on alignment Nucleotide
- // flag.
- // this *will* break when alignment contains both nucleotide and amino
- // acid sequences.
- String dict = jal.isNucleotide() ? org.vamsas.objects.utils.SymbolDictionary.STANDARD_NA
- : org.vamsas.objects.utils.SymbolDictionary.STANDARD_AA;
- for (int i = 0; i < jal.getHeight(); i++)
- {
- SequenceI sq = jal.getSequenceAt(i).getDatasetSequence(); // only insert
- // referenced
- // sequences
- // to dataset.
- sequence = (Sequence) getjv2vObj(sq);
- if (sequence == null)
- {
- sequence = new Sequence();
- bindjvvobj(sq, sequence);
- sq.setVamsasId(sequence.getVorbaId().getId());
- sequence.setSequence(sq.getSequenceAsString());
- sequence.setDictionary(dict);
- sequence.setName(jal.getDataset().getSequenceAt(i).getName());
- sequence.setStart(jal.getDataset().getSequenceAt(i).getStart());
- sequence.setEnd(jal.getDataset().getSequenceAt(i).getEnd());
- dataset.addSequence(sequence);
- }
- else
- {
- // verify principal attributes. and update any new
- // features/references.
- System.out.println("update dataset sequence object.");
- }
- if (sq.getSequenceFeatures() != null)
- {
- int sfSize = sq.getSequenceFeatures().length;
-
- for (int sf = 0; sf < sfSize; sf++)
- {
- jalview.datamodel.SequenceFeature feature = (jalview.datamodel.SequenceFeature) sq
- .getSequenceFeatures()[sf];
-
- DataSetAnnotations dsa = (DataSetAnnotations) getjv2vObj(feature);
- if (dsa == null)
- {
- dsa = (DataSetAnnotations) getDSAnnotationFromJalview(
- new DataSetAnnotations(), feature);
- if (dsa.getProvenance() == null)
- {
- dsa.setProvenance(new Provenance());
- }
- addProvenance(dsa.getProvenance(), "created"); // JBPNote - need
- // to update
- dsa.setSeqRef(sequence);
- bindjvvobj(feature, dsa);
- dataset.addDataSetAnnotations(dsa);
- }
- else
- {
- // todo: verify and update dataset annotations for sequence
- System.out.println("update dataset sequence annotations.");
- }
- }
- }
-
- if (sq.getDBRef() != null)
- {
- DBRefEntry[] entries = sq.getDBRef();
- jalview.datamodel.DBRefEntry dbentry;
- for (int db = 0; db < entries.length; db++)
- {
- dbentry = entries[db];
- dbref = (DbRef) getjv2vObj(dbentry);
- if (dbref == null)
- {
- dbref = new DbRef();
- bindjvvobj(dbentry, dbref);
- dbref.setAccessionId(dbentry.getAccessionId());
- dbref.setSource(dbentry.getSource());
- dbref.setVersion(dbentry.getVersion());
- /*
- * TODO: Maps are not yet supported by Jalview. Map vMap = new
- * Map(); vMap.set dbref.addMap(vMap);
- */
- sequence.addDbRef(dbref);
- }
- else
- {
- // TODO: verify and update dbrefs in vamsas document
- // there will be trouble when a dataset sequence is modified to
- // contain more residues than were originally referenced - we must
- // then make a number of dataset sequence entries
- System.out
- .println("update dataset sequence database references.");
- }
- }
-
- }
- }
- // dataset.setProvenance(getVamsasProvenance(jal.getDataset().getProvenance()));
- // ////////////////////////////////////////////
-
- // ////////////////////////////////////////////
- // Save the Alignments
-
- Alignment alignment = (Alignment) getjv2vObj(av); // this is so we can get the alignviewport back
- if (alignment == null)
- {
- alignment = new Alignment();
- bindjvvobj(av, alignment);
- if (alignment.getProvenance() == null)
- alignment.setProvenance(new Provenance());
- addProvenance(alignment.getProvenance(), "added"); // TODO: insert some
- // sensible source
- // here
- dataset.addAlignment(alignment);
- {
- Property title = new Property();
- title.setName("jalview:AlTitle");
- title.setType("string");
- title.setContent(aFtitle);
- alignment.addProperty(title);
- }
- alignment.setGapChar(String.valueOf(av.getGapCharacter()));
- AlignmentSequence alseq = null;
- for (int i = 0; i < jal.getHeight(); i++)
- {
- alseq = new AlignmentSequence();
- // TODO: VAMSAS: translate lowercase symbols to annotation ?
- alseq.setSequence(jal.getSequenceAt(i).getSequenceAsString());
- alseq.setName(jal.getSequenceAt(i).getName());
- alseq.setStart(jal.getSequenceAt(i).getStart());
- alseq.setEnd(jal.getSequenceAt(i).getEnd());
- alseq.setRefid(getjv2vObj(jal.getSequenceAt(i).getDatasetSequence()));
- alignment.addAlignmentSequence(alseq);
- bindjvvobj(jal.getSequenceAt(i), alseq);
- }
- }
- else
- {
- // todo: verify and update mutable alignment props.
- if (alignment.getModifiable())
- {
- System.out.println("update alignment in document.");
- }
- else
- {
- System.out
- .println("update edited alignment to new alignment in document.");
- }
- }
- // ////////////////////////////////////////////
- // SAVE Alignment Sequence Features
- for (int i = 0, iSize = alignment.getAlignmentSequenceCount(); i < iSize; i++)
- {
- AlignmentSequence valseq;
- SequenceI alseq = (SequenceI) getvObj2jv(valseq = alignment
- .getAlignmentSequence(i));
- if (alseq != null && alseq.getSequenceFeatures() != null)
- {
- jalview.datamodel.SequenceFeature[] features = alseq
- .getSequenceFeatures();
- for (int f = 0; f < features.length; f++)
- {
- if (features[f] != null)
- {
- AlignmentSequenceAnnotation valseqf = (AlignmentSequenceAnnotation) getjv2vObj(features[i]);
- if (valseqf == null)
- {
-
- valseqf = (AlignmentSequenceAnnotation) getDSAnnotationFromJalview(
- new AlignmentSequenceAnnotation(), features[i]);
- if (valseqf.getProvenance() == null)
- {
- valseqf.setProvenance(new Provenance());
- }
- addProvenance(valseqf.getProvenance(), "created"); // JBPNote -
- // need to
- // update
- bindjvvobj(features[i], valseqf);
- valseq.addAlignmentSequenceAnnotation(valseqf);
- }
- }
-
- }
- }
- }
-
- // ////////////////////////////////////////////
- // SAVE ANNOTATIONS
- if (jal.getAlignmentAnnotation() != null)
- {
- jalview.datamodel.AlignmentAnnotation[] aa = jal
- .getAlignmentAnnotation();
- java.util.HashMap AlSeqMaps = new HashMap(); // stores int maps from
- // alignment columns to
- // sequence positions.
- for (int i = 0; i < aa.length; i++)
- {
- if (aa[i] == null || isJalviewOnly(aa[i]))
- {
- continue;
- }
- if (aa[i].sequenceRef != null)
- {
- org.vamsas.objects.core.AlignmentSequence alsref = (org.vamsas.objects.core.AlignmentSequence) getjv2vObj(aa[i].sequenceRef);
- org.vamsas.objects.core.AlignmentSequenceAnnotation an = (org.vamsas.objects.core.AlignmentSequenceAnnotation) getjv2vObj(aa[i]);
- int[] gapMap = null;
- if (AlSeqMaps.containsKey(aa[i].sequenceRef))
- {
- gapMap = (int[]) AlSeqMaps.get(aa[i].sequenceRef);
- }
- else
- {
- gapMap = new int[aa[i].sequenceRef.getLength()];
- // map from alignment position to sequence position.
- int[] sgapMap = aa[i].sequenceRef.gapMap();
- for (int a = 0; a < sgapMap.length; a++)
- gapMap[sgapMap[a]] = a;
- }
- if (an == null)
- {
- an = new org.vamsas.objects.core.AlignmentSequenceAnnotation();
- Seg vSeg = new Seg();
- vSeg.setStart(1);
- vSeg.setInclusive(true);
- vSeg.setEnd(gapMap.length);
- an.addSeg(vSeg);
- an.setType("jalview:SecondaryStructurePrediction");// TODO: better fix this rough guess ;)
- alsref.addAlignmentSequenceAnnotation(an);
- bindjvvobj(aa[i],an);
- // LATER: much of this is verbatim from the alignmentAnnotation
- // method below. suggests refactoring to make rangeAnnotation the
- // base class
- an.setDescription(aa[i].description);
- if (aa[i].graph > 0)
- an.setGraph(true); // aa[i].graph);
- else
- an.setGraph(false);
- an.setLabel(aa[i].label);
- an.setProvenance(dummyProvenance()); // get provenance as user
- // created, or jnet, or
- // something else.
- an.setGroup(Integer.toString(aa[i].graphGroup)); // // JBPNote -
- // originally we
- // were going to
- // store
- // graphGroup in
- // the Jalview
- // specific
- // bits.
- AnnotationElement ae;
- for (int a = 0; a < aa[i].annotations.length; a++)
- {
- if (aa[i].annotations[a] == null)
- {
- continue;
- }
-
- ae = new AnnotationElement();
- ae.setDescription(aa[i].annotations[a].description);
- ae.addGlyph(new Glyph());
- ae.getGlyph(0)
- .setContent(aa[i].annotations[a].displayCharacter); // assume
- // jax-b
- // takes
- // care
- // of
- // utf8
- // translation
- if (aa[i].graph!=jalview.datamodel.AlignmentAnnotation.NO_GRAPH)
- ae.addValue(aa[i].annotations[a].value);
- ae.setPosition(gapMap[a]+1); // position w.r.t. AlignmentSequence
- // symbols
- if (aa[i].annotations[a].secondaryStructure != ' ')
- {
- // we only write an annotation where it really exists.
- Glyph ss = new Glyph();
- ss
- .setDict(org.vamsas.objects.utils.GlyphDictionary.PROTEIN_SS_3STATE);
- ss.setContent(String
- .valueOf(aa[i].annotations[a].secondaryStructure));
- ae.addGlyph(ss);
- }
- an.addAnnotationElement(ae);
- }
- }
- else
- {
- // update reference sequence Annotation
- if (an.getModifiable())
- {
- // verify existing alignment sequence annotation is up to date
- System.out.println("update alignment sequence annotation.");
- }
- else
- {
- // verify existing alignment sequence annotation is up to date
- System.out
- .println("make new alignment sequence annotation if modification has happened.");
- }
- }
- }
- else
- {
- // add Alignment Annotation
- org.vamsas.objects.core.AlignmentAnnotation an = (org.vamsas.objects.core.AlignmentAnnotation) getjv2vObj(aa[i]);
- if (an == null)
- {
- an = new org.vamsas.objects.core.AlignmentAnnotation();
- an.setType("jalview:AnnotationRow");
- an.setDescription(aa[i].description);
- alignment.addAlignmentAnnotation(an);
- Seg vSeg = new Seg();
- vSeg.setStart(1);
- vSeg.setInclusive(true);
- vSeg.setEnd(jal.getWidth());
- an.addSeg(vSeg);
- if (aa[i].graph > 0)
- an.setGraph(true); // aa[i].graph);
- an.setLabel(aa[i].label);
- an.setProvenance(dummyProvenance());
- if (aa[i].graph!=aa[i].NO_GRAPH) {
- an.setGroup(Integer.toString(aa[i].graphGroup)); // // JBPNote -
- // originally we
- // were going to
- // store
- // graphGroup in
- // the Jalview
- // specific
- // bits.
- an.setGraph(true);
- } else {
- an.setGraph(false);
- }
- AnnotationElement ae;
-
- for (int a = 0; a < aa[i].annotations.length; a++)
- {
- if ((aa[i] == null) || (aa[i].annotations[a] == null))
- {
- continue;
- }
-
- ae = new AnnotationElement();
- ae.setDescription(aa[i].annotations[a].description);
- ae.addGlyph(new Glyph());
- ae.getGlyph(0)
- .setContent(aa[i].annotations[a].displayCharacter); // assume
- // jax-b
- // takes
- // care
- // of
- // utf8
- // translation
- ae.addValue(aa[i].annotations[a].value);
- ae.setPosition(a+1);
- if (aa[i].annotations[a].secondaryStructure != ' ')
- {
- Glyph ss = new Glyph();
- ss
- .setDict(org.vamsas.objects.utils.GlyphDictionary.PROTEIN_SS_3STATE);
- ss.setContent(String
- .valueOf(aa[i].annotations[a].secondaryStructure));
- ae.addGlyph(ss);
- }
- an.addAnnotationElement(ae);
- }
- if (aa[i].editable) {
- //an.addProperty(newProperty("jalview:editable", null, "true"));
- an.setModifiable(true);
- }
- if (aa[i].graph!=jalview.datamodel.AlignmentAnnotation.NO_GRAPH) {
- an.setGraph(true);
- an.setGroup(Integer.toString(aa[i].graphGroup));
- an.addProperty(newProperty("jalview:graphType",null,
- ((aa[i].graph==jalview.datamodel.AlignmentAnnotation.BAR_GRAPH) ? "BAR_GRAPH" : "LINE_GRAPH")));
-
- /** and on and on..
- vProperty=new Property();
- vProperty.setName("jalview:graphThreshhold");
- vProperty.setContent(aa[i].threshold);
- */
-
- }
- }
- else
- {
- if (an.getModifiable())
- {
- // verify annotation - update (perhaps)
- Cache.log.info("update alignment sequence annotation. not yet implemented.");
- }
- else
- {
- // verify annotation - update (perhaps)
- Cache.log.info("updated alignment sequence annotation added.");
- }
- }
- }
- }
- }
- // /////////////////////////////////////////////////////
-
- // //////////////////////////////////////////////
- // /SAVE THE TREES
- // /////////////////////////////////
- // FIND ANY ASSOCIATED TREES
- if (Desktop.desktop != null)
- {
- javax.swing.JInternalFrame[] frames = Desktop.desktop.getAllFrames();
-
- for (int t = 0; t < frames.length; t++)
- {
- if (frames[t] instanceof TreePanel)
- {
- TreePanel tp = (TreePanel) frames[t];
-
- if (tp.getAlignment() == jal)
- {
- Tree tree = (Tree) getjv2vObj(tp);
- if (tree == null)
- {
- tree = new Tree();
- bindjvvobj(tp, tree);
- tree.setTitle(tp.getTitle());
- Newick newick = new Newick();
- // TODO: translate sequenceI to leaf mappings to vamsas
- // references - see tree specification in schema.
- newick.setContent(tp.getTree().toString());
- newick.setTitle(tp.getTitle());
- tree.addNewick(newick);
- tree.setProvenance(makeTreeProvenance(jal, tp));
- alignment.addTree(tree);
- }
- else
- {
- if (tree.getModifiable())
- {
- // verify any changes.
- System.out.println("Update tree in document.");
- }
- else
- {
- System.out
- .println("Add modified tree as new tree in document.");
- }
- }
- }
- }
- }
- }
- // Store Jalview specific stuff in the Jalview appData
- // not implemented in the SimpleDoc interface.
- }
-
- catch (Exception ex)
- {
- ex.printStackTrace();
- }
-
- }
-
- private Property newProperty(String name, String type, String content) {
- Property vProperty=new Property();
- vProperty.setName(name);
- if (type!=null)
- vProperty.setType(type);
- else
- vProperty.setType("String");
- vProperty.setContent(content);
- return vProperty;
- }
-
- /**
- * correctly create a RangeAnnotation from a jalview sequence feature
- *
- * @param dsa
- * (typically DataSetAnnotations or AlignmentSequenceAnnotation)
- * @param feature
- * (the feature to be mapped from)
- * @return
- */
- private RangeAnnotation getDSAnnotationFromJalview(RangeAnnotation dsa,
- SequenceFeature feature) {
- dsa.setType(feature.getType());
- Seg vSeg = new Seg();
- vSeg.setStart(feature.getBegin());
- vSeg.setEnd(feature.getEnd());
- vSeg.setInclusive(true);
- dsa.addSeg(vSeg);
- dsa.setDescription(feature.getDescription());
- dsa.setStatus(feature.getStatus());
- if (feature.links != null && feature.links.size() > 0)
- {
- for (int i = 0, iSize = feature.links.size(); i < iSize; i++)
- {
- String link = (String) feature.links.elementAt(i);
- int sep = link.indexOf('|');
- if (sep > -1)
- {
- Link vLink = new Link();
- if (sep > 0)
- vLink.setContent(link.substring(0, sep - 1));
- else
- vLink.setContent("");
- vLink.setHref(link.substring(sep + 1)); // TODO: validate href.
- dsa.addLink(vLink);
- }
- }
- }
- dsa.setGroup(feature.getFeatureGroup());
- return dsa;
- }
-
- /**
- * correctly creates provenance for trees calculated on an alignment by
- * jalview.
- *
- * @param jal
- * @param tp
- * @return
- */
- private Provenance makeTreeProvenance(AlignmentI jal, TreePanel tp) {
- Provenance prov = new Provenance();
- prov.addEntry(new Entry());
- prov.getEntry(0).setAction("imported "+tp.getTitle());
- prov.getEntry(0).setUser(provEntry.getUser());
- prov.getEntry(0).setApp(provEntry.getApp());
- prov.getEntry(0).setDate(provEntry.getDate());
- if (tp.getTree().hasOriginalSequenceData())
- {
- Input vInput = new Input();
- // LATER: check to see if tree input data is contained in this alignment -
- // or just correctly resolve the tree's seqData to the correct alignment in
- // the document.
- // vInput.setObjRef(getjv2vObj(jal));
- vInput.setObjRef(getjv2vObj(tp.getViewPort()));
- prov.getEntry(0).setAction("created "+tp.getTitle());
- prov.getEntry(0).addInput(vInput);
- vInput.setName("jalview:seqdist");
- prov.getEntry(0).addParam(new Param());
- prov.getEntry(0).getParam(0).setName("treeType");
- prov.getEntry(0).getParam(0).setType("utf8");
- prov.getEntry(0).getParam(0).setContent("NJ");
-
- int ranges[] = tp.getTree().seqData.getVisibleContigs();
- // VisibleContigs are with respect to alignment coordinates. Still need offsets
- int start= tp.getTree().seqData.getAlignmentOrigin();
- for (int r = 0; r < ranges.length; r += 2)
- {
- Seg visSeg = new Seg();
- visSeg.setStart(1+start+ranges[r]);
- visSeg.setEnd(start+ranges[r + 1]);
- visSeg.setInclusive(true);
- vInput.addSeg(visSeg);
- }
- }
- return prov;
- }
-
- /**
- *
- * @param tp
- * @return Object[] { AlignmentView, AlignmentI - reference alignment for
- * input }
- */
- private Object[] recoverInputData(Provenance tp) {
- for (int pe = 0; pe < tp.getEntryCount(); pe++)
- {
- if (tp.getEntry(pe).getInputCount() > 0)
- {
- if (tp.getEntry(pe).getInputCount() > 1)
- Cache.log.warn("Ignoring additional input spec in provenance entry "
- + tp.getEntry(pe).toString());
- // LATER: deal sensibly with multiple inputs.
- Input vInput = tp.getEntry(pe).getInput(0);
- if (vInput.getObjRef() instanceof org.vamsas.objects.core.Alignment)
- {
- // recover an AlignmentView for the input data
- AlignViewport javport = (AlignViewport) getvObj2jv((org.vamsas.client.Vobject) vInput
- .getObjRef());
- jalview.datamodel.AlignmentI jal = javport.getAlignment();
- jalview.datamodel.CigarArray view = javport.getAlignment().getCompactAlignment();
- int from = 1, to = jal.getWidth();
- int offset=0; // deleteRange modifies its frame of reference
- for (int r = 0, s = vInput.getSegCount(); r < s; r++)
- {
- Seg visSeg = vInput.getSeg(r);
- int se[] = getSegRange(visSeg,true); // jalview doesn't do bidirection alignments yet.
- if (to < se[1])
- Cache.log.warn("Ignoring invalid segment in InputData spec.");
- else
- {
- if (se[0] > from)
- {
- view.deleteRange(offset+from-1, offset+se[0] - 2);
- offset-=se[0]-from;
- }
- from = se[1] + 1;
- }
- }
- if (from < to)
- {
- view.deleteRange(offset+from-1, offset+to-1); // final deletion - TODO: check off by
- // one for to
- }
- return new Object[] { new AlignmentView(view), jal };
- }
- }
- }
- Cache.log.debug("Returning null for input data recovery from provenance.");
- return null;
- }
-
- /**
- * get start<end range of segment, adjusting for inclusivity flag and
- * polarity.
- *
- * @param visSeg
- * @param ensureDirection when true - always ensure start is less than end.
- * @return int[] { start, end, direction} where direction==1 for range running from end to start.
- */
- private int[] getSegRange(Seg visSeg, boolean ensureDirection) {
- boolean incl = visSeg.getInclusive();
- // adjust for inclusive flag.
- int pol = (visSeg.getStart() <= visSeg.getEnd()) ? 1 : -1; // polarity of
- // region.
- int start = visSeg.getStart() + (incl ? 0 : pol);
- int end = visSeg.getEnd() + (incl ? 0 : -pol);
- if (ensureDirection && pol==-1)
- {
- // jalview doesn't deal with inverted ranges, yet.
- int t = end;
- end = start;
- start = t;
- }
- return new int[] { start, end, pol<0 ? 1 : 0 };
- }
-
- /**
- *
- * @param annotation
- * @return true if annotation is not to be stored in document
- */
- private boolean isJalviewOnly(AlignmentAnnotation annotation) {
- return annotation.label.equals("Quality")
- || annotation.label.equals("Conservation")
- || annotation.label.equals("Consensus");
- }
- /**
- * This will return the first AlignFrame viewing AlignViewport av.
- * It will break if there are more than one AlignFrames viewing a particular av.
- * This also shouldn't be in the io package.
- * @param av
- * @return alignFrame for av
- */
- public AlignFrame getAlignFrameFor(AlignViewport av) {
- if (Desktop.desktop != null)
- {
- javax.swing.JInternalFrame[] frames = Desktop.desktop.getAllFrames();
-
- for (int t = 0; t < frames.length; t++)
- {
- if (frames[t] instanceof AlignFrame) {
- if (((AlignFrame) frames[t]).getViewport()==av)
- return (AlignFrame) frames[t];
- }
- }
- }
- return null;
- }
- public void updateToJalview() {
- VAMSAS _roots[] = cdoc.getVamsasRoots();
-
- for (int _root = 0; _root<_roots.length; _root++) {
- VAMSAS root = _roots[_root];
- boolean newds=false;
- for (int _ds=0,_nds=root.getDataSetCount(); _ds<_nds; _ds++) {
- // ///////////////////////////////////
- // ///LOAD DATASET
- DataSet dataset = root.getDataSet(_ds);
- int i, iSize = dataset.getSequenceCount();
- Vector dsseqs;
- jalview.datamodel.Alignment jdataset = (jalview.datamodel.Alignment) getvObj2jv(dataset);
- int jremain=0;
- if (jdataset==null) {
- Cache.log.debug("Initialising new jalview dataset fields");
- newds=true;
- dsseqs=new Vector();
- } else {
- Cache.log.debug("Update jalview dataset from vamsas.");
- jremain=jdataset.getHeight();
- dsseqs=jdataset.getSequences();
- }
-
- // TODO: test sequence merging - we preserve existing non vamsas
- // sequences but add in any new vamsas ones, and don't yet update any
- // sequence attributes
- for (i = 0; i < iSize ; i++)
- {
- Sequence vdseq = dataset.getSequence(i);
- jalview.datamodel.SequenceI dsseq = (SequenceI) getvObj2jv(vdseq);
- if (dsseq!=null) {
- if (!dsseq.getSequence().equals(vdseq.getSequence()))
- throw new Error("Broken! - mismatch of dataset sequence and jalview internal dataset sequence.");
- jremain--;
- } else {
- dsseq = new jalview.datamodel.Sequence(
- dataset.getSequence(i).getName(),
- dataset.getSequence(i).getSequence(),
- dataset.getSequence(i).getStart(),
- dataset.getSequence(i).getEnd() );
- dsseq.setDescription(dataset.getSequence(i).getDescription());
- bindjvvobj(dsseq, dataset.getSequence(i));
- dsseq.setVamsasId(dataset.getSequence(i).getVorbaId().getId());
- dsseqs.add(dsseq);
- }
- if (vdseq.getDbRefCount()>0) {
- DbRef [] dbref = vdseq.getDbRef();
- for(int db=0; db<dbref.length; db++)
- {
- jalview.datamodel.DBRefEntry dbr=(jalview.datamodel.DBRefEntry) getvObj2jv(dbref[db]);
- if (dbr==null) {
- // add new dbref
- dsseq.addDBRef(dbr= new jalview.datamodel.DBRefEntry
- (
- dbref[db].getSource().toString(),
- dbref[db].getVersion().toString(),
- dbref[db].getAccessionId().toString()));
- bindjvvobj(dbr, dbref[db]);
- }
- }
- }
- }
-
- if (newds) {
- SequenceI[] seqs = new SequenceI[dsseqs.size()];
- for (i=0,iSize=dsseqs.size(); i<iSize; i++) {
- seqs[i]=(SequenceI) dsseqs.elementAt(i);
- dsseqs.setElementAt(null, i);
- }
- jdataset = new jalview.datamodel.Alignment(seqs);
- Cache.log.debug("New vamsas dataset imported into jalview.");
- bindjvvobj(jdataset, dataset);
- }
- // ////////
- // add any new dataset sequence feature annotations
- if (dataset.getDataSetAnnotations() != null) {
- for (int dsa = 0; dsa < dataset.getDataSetAnnotationsCount(); dsa++) {
- DataSetAnnotations dseta=dataset.getDataSetAnnotations(dsa);
- SequenceI dsSeq=(SequenceI) getvObj2jv((Vobject) dseta.getSeqRef());
- if (dsSeq==null) {
- jalview.bin.Cache.log.warn("Couldn't resolve jalview sequenceI for dataset object reference "+((Vobject)dataset.getDataSetAnnotations(dsa).getSeqRef()).getVorbaId().getId());
- } else {
- if (dseta.getAnnotationElementCount()==0) {
- jalview.datamodel.SequenceFeature sf=(jalview.datamodel.SequenceFeature) getvObj2jv(dseta);
- if (sf==null) {
- dsSeq.addSequenceFeature(sf=getJalviewSeqFeature(dseta));
- bindjvvobj(sf, dseta);
- }
- } else {
- // TODO: deal with alignmentAnnotation style annotation
- // appearing on dataset sequences.
- // JBPNote: we could just add them to all alignments but
- // that may complicate cross references in the jalview
- // datamodel
- Cache.log.warn("Ignoring dataset annotation with annotationElements. Not yet supported in jalview.");
- }
- }
- }
- }
-
- if (dataset.getAlignmentCount()>0) {
- // LOAD ALIGNMENTS from DATASET
-
- for (int al=0,nal=dataset.getAlignmentCount(); al<nal; al++) {
- org.vamsas.objects.core.Alignment alignment = dataset.getAlignment(al);
- AlignViewport av = (AlignViewport) getvObj2jv(alignment);
- jalview.datamodel.AlignmentI jal=null;
- if (av!=null)
- jal = av.getAlignment();
- iSize = alignment.getAlignmentSequenceCount();
- boolean newal=(jal==null) ? true : false;
- Vector newasAnnots=new Vector();
- char gapChar=' '; // default for new alignments read in from the document
- if (jal!=null) {
- dsseqs=jal.getSequences(); // for merge/update
- gapChar=jal.getGapCharacter();
- } else {
- dsseqs=new Vector();
- }
- char valGapchar=alignment.getGapChar().charAt(0);
- for (i = 0; i < iSize; i++)
- {
- AlignmentSequence valseq = alignment.getAlignmentSequence(i);
- jalview.datamodel.SequenceI alseq = (SequenceI) getvObj2jv(valseq);
- if (alseq!=null) {
- //TODO: upperCase/LowerCase situation here ? do we allow it ?
- //if (!alseq.getSequence().equals(valseq.getSequence())) {
- // throw new Error("Broken! - mismatch of dataset sequence and jalview internal dataset sequence.");
- if (Cache.log.isDebugEnabled())
- Cache.log.debug("Updating apparently edited sequence "+alseq.getName());
- // this might go *horribly* wrong
- alseq.setSequence(new String(valseq.getSequence()).replace(valGapchar, gapChar));
- jremain--;
- } else {
- alseq = new jalview.datamodel.Sequence(
- valseq.getName(),
- valseq.getSequence().replace(valGapchar, gapChar),
- valseq.getStart(),
- valseq.getEnd() );
-
- Vobject datsetseq = (Vobject)valseq.getRefid();
- if (datsetseq!=null) {
- alseq.setDatasetSequence((SequenceI)getvObj2jv(datsetseq)); // exceptions if AlignemntSequence reference isn't a simple SequenceI
- } else {
- Cache.log.error("Invalid dataset sequence id (null) for alignment sequence "+valseq.getVorbaId());
- }
- bindjvvobj(alseq, valseq);
- alseq.setVamsasId(valseq.getVorbaId().getId());
- dsseqs.add(alseq);
- }
- if (valseq.getAlignmentSequenceAnnotationCount()>0) {
- AlignmentSequenceAnnotation[] vasannot=valseq.getAlignmentSequenceAnnotation();
- for (int a=0; a<vasannot.length; a++) {
- jalview.datamodel.AlignmentAnnotation asa = (jalview.datamodel.AlignmentAnnotation) getvObj2jv(vasannot[a]); // TODO: 1:many jalview alignment sequence annotations
- if (asa==null) {
- int se[] = getBounds(vasannot[a]);
- asa = getjAlignmentAnnotation(jal, vasannot[a]);
- asa.sequenceRef=alseq;
- asa.createSequenceMapping(alseq, alseq.getStart()+se[0], false); // TODO: verify that positions in alseqAnnotation correspond to ungapped residue positions.
- bindjvvobj(asa, vasannot[a]);
- newasAnnots.add(asa);
- } else {
- // update existing annotation - can do this in place
- if (vasannot[a].getModifiable()) {
- Cache.log.info("UNIMPLEMENTED: not recovering user modifiable sequence alignment annotation");
- // TODO: should at least replace with new one - otherwise things will break
- // basically do this:
- // int se[] = getBounds(vasannot[a]);
- // asa.update(getjAlignmentAnnotation(jal, vasannot[a])); // update from another annotation object in place.
- // asa.createSequenceMapping(alseq, se[0], false);
-
- }
- }
- }
- }
- }
- if (jal==null) {
- SequenceI[] seqs = new SequenceI[dsseqs.size()];
- for (i=0,iSize=dsseqs.size(); i<iSize; i++) {
- seqs[i]=(SequenceI) dsseqs.elementAt(i);
- dsseqs.setElementAt(null, i);
- }
- jal = new jalview.datamodel.Alignment(seqs);
- Cache.log.debug("New vamsas alignment imported into jalview "+alignment.getVorbaId().getId());
- jal.setDataset(jdataset);
- }
- if (newasAnnots!=null && newasAnnots.size()>0) {
- // Add the new sequence annotations in to the alignment.
- for (int an=0,anSize=newasAnnots.size(); an<anSize; an++) {
- jal.addAnnotation((AlignmentAnnotation) newasAnnots.elementAt(an));
- // TODO: check if anything has to be done - like calling adjustForAlignment or something.
- newasAnnots.setElementAt(null, an);
- }
- newasAnnots=null;
- }
- // //////////////////////////////////////////
- // //LOAD ANNOTATIONS FOR THE ALIGNMENT
- // ////////////////////////////////////
- if (alignment.getAlignmentAnnotationCount()>0)
- {
- org.vamsas.objects.core.AlignmentAnnotation[] an = alignment.getAlignmentAnnotation();
-
- for (int j = 0; j < an.length; j++)
- {
- jalview.datamodel.AlignmentAnnotation jan=(jalview.datamodel.AlignmentAnnotation) getvObj2jv(an[j]);
- if (jan!=null) {
- // update or stay the same.
- // TODO: should at least replace with a new one - otherwise things will break
- // basically do this:
- // jan.update(getjAlignmentAnnotation(jal, an[a])); // update from another annotation object in place.
-
- Cache.log.debug("update from vamsas alignment annotation to existing jalview alignment annotation.");
- if (an[j].getModifiable()) {
- // TODO: user defined annotation is totally mutable... - so load it up or throw away if locally edited.
- Cache.log.info("NOT IMPLEMENTED - Recovering user-modifiable annotation - yet...");
- }
- // TODO: compare annotation element rows
- // TODO: compare props.
- } else {
- jan = getjAlignmentAnnotation(jal, an[j]);
- jal.addAnnotation(jan);
- bindjvvobj(jan, an[j]);
- }
- }
- }
- AlignFrame alignFrame;
- if (av==null) {
- Cache.log.debug("New alignframe for alignment "+alignment.getVorbaId());
- // ///////////////////////////////
- // construct alignment view
- alignFrame = new AlignFrame(jal, AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
- av=alignFrame.getViewport();
- String title = alignment.getProvenance().getEntry(alignment.getProvenance().getEntryCount()-1).getAction();
- if (alignment.getPropertyCount()>0) {
- for (int p=0,pe=alignment.getPropertyCount(); p<pe; p++) {
- if (alignment.getProperty(p).getName().equals("jalview:AlTitle")) {
- title = alignment.getProperty(p).getContent();
- }
- }
- }
- // TODO: automatically create meaningful title for a vamsas alignment using its provenance.
- jalview.gui.Desktop.addInternalFrame(alignFrame, title + "("+alignment.getVorbaId()+")",
- AlignFrame.DEFAULT_WIDTH,
- AlignFrame.DEFAULT_HEIGHT);
- bindjvvobj(av, alignment);
- } else {
- // find the alignFrame for jal.
- // TODO: fix this so we retrieve the alignFrame handing av *directly*
- alignFrame=getAlignFrameFor(av);
- }
- // LOAD TREES
- // /////////////////////////////////////
- if (alignment.getTreeCount() > 0)
- {
-
- for (int t = 0; t < alignment.getTreeCount(); t++)
- {
- Tree tree = alignment.getTree(t);
- TreePanel tp=(TreePanel) getvObj2jv(tree);
- if (tp!=null) {
- Cache.log.info("Update from vamsas document to alignment associated tree not implemented yet.");
- } else {
- // make a new tree
- Object[] idata = this.recoverInputData(tree.getProvenance());
- try {
- AlignmentView inputData=null;
- if (idata!=null && idata[0]!=null)
- inputData = (AlignmentView) idata[0];
- tp = alignFrame.ShowNewickTree(
- new jalview.io.NewickFile(tree.getNewick(0).getContent()),
- tree.getNewick(0).getTitle()+" ("+tree.getVorbaId()+")",inputData,
- 600, 500,
- t * 20 + 50, t * 20 + 50);
- bindjvvobj(tp, tree);
- } catch (Exception e) {
- Cache.log.warn("Problems parsing treefile '"+tree.getNewick(0).getContent()+"'",e);
- }
- }
- }
- }
-
- }
- }
- }
- }
- }
- // bitfields - should be a template in j1.5
- private static int HASSECSTR=0;
- private static int HASVALS=1;
- private static int HASHPHOB=2;
- private static int HASDC=3;
- private static int HASDESCSTR=4;
- private static int HASTWOSTATE=5; // not used yet.
- /**
- * parses the AnnotationElements - if they exist - into jalview.datamodel.Annotation[] rows
- * Two annotation rows are made if there are distinct annotation for both at 'pos' and 'after pos' at any particular site.
- * @param annotation
- * @return { boolean[static int constants ], int[ae.length] - map to annotated object frame, jalview.datamodel.Annotation[], jalview.datamodel.Annotation[] (after)}
- */
- private Object[] parseRangeAnnotation(org.vamsas.objects.core.RangeAnnotation annotation) {
- // set these attributes by looking in the annotation to decide what kind of alignment annotation rows will be made
- // TODO: potentially we might make several annotation rows from one vamsas alignment annotation. the jv2Vobj binding mechanism
- // may not quite cope with this (without binding an array of annotations to a vamsas alignment annotation)
- // summary flags saying what we found over the set of annotation rows.
- boolean[] AeContent = new boolean[] { false, false, false, false, false};
- int[] rangeMap = getMapping(annotation);
- jalview.datamodel.Annotation[][] anot=new jalview.datamodel.Annotation[][] {
- new jalview.datamodel.Annotation[rangeMap.length],
- new jalview.datamodel.Annotation[rangeMap.length]
- };
- boolean mergeable=true; //false if 'after positions cant be placed on same annotation row as positions.
-
- if (annotation.getAnnotationElementCount()>0) {
- AnnotationElement ae[] = annotation.getAnnotationElement();
- for (int aa = 0; aa < ae.length; aa++)
- {
- int pos = ae[aa].getPosition()-1;// pos counts from 1 to (|seg.start-seg.end|+1)
- if (pos>=0 && pos<rangeMap.length) {
- int row=ae[aa].getAfter()?1:0;
- if (anot[row][pos]!=null) {
- // only time this should happen is if the After flag is set.
- Cache.log.debug("Ignoring duplicate annotation site at "+pos);
- continue;
- }
- if (anot[1-row][pos]!=null)
- mergeable=false;
- String desc = "";
- if (ae[aa].getDescription()!=null) {
- desc = ae[aa].getDescription();
- if (desc.length()>0) {
- // have imported valid description string
- AeContent[HASDESCSTR]=true;
- }
- }
- String dc = null;//ae[aa].getDisplayCharacter()==null ? "dc" : ae[aa].getDisplayCharacter();
- String ss = null;//ae[aa].getSecondaryStructure()==null ? "ss" : ae[aa].getSecondaryStructure();
- java.awt.Color colour = null;
- if (ae[aa].getGlyphCount()>0) {
- Glyph[] glyphs = ae[aa].getGlyph();
- for (int g=0; g<glyphs.length; g++) {
- if (glyphs[g].getDict().equals(org.vamsas.objects.utils.GlyphDictionary.PROTEIN_SS_3STATE)) {
- ss=glyphs[g].getContent();
- AeContent[HASSECSTR]=true;
- } else if (glyphs[g].getDict().equals(org.vamsas.objects.utils.GlyphDictionary.PROTEIN_HD_HYDRO)) {
- Cache.log.debug("ignoring hydrophobicity glyph marker.");
- AeContent[HASHPHOB]=true;
- char c=(dc=glyphs[g].getContent()).charAt(0);
- // dc may get overwritten - but we still set the colour.
- colour = new java.awt.Color(c=='+'?255:0,c=='.'?255:0,c=='-'?255:0);
-
- } else if (glyphs[g].getDict().equals(org.vamsas.objects.utils.GlyphDictionary.DEFAULT)) {
- dc = glyphs[g].getContent();
- AeContent[HASDC]=true;
- } else {
- Cache.log.debug("Ignoring unknown glyph type "+glyphs[g].getDict());
- }
- }
- }
- float val=0;
- if (ae[aa].getValueCount()>0) {
- AeContent[HASVALS]=true;
- if (ae[aa].getValueCount()>1) {
- Cache.log.warn("ignoring additional "+(ae[aa].getValueCount()-1)+"values in annotation element.");
- }
- val = ae[aa].getValue(0);
- }
- if (colour==null) {
- anot[row][pos]=new jalview.datamodel.Annotation((dc!=null) ? dc : "", desc, (ss!=null)?ss.charAt(0):' ', val);
- } else {
- anot[row][pos]=new jalview.datamodel.Annotation((dc!=null) ? dc : "", desc, (ss!=null)?ss.charAt(0):' ', val, colour);
- }
- } else {
- Cache.log.warn("Ignoring out of bound annotation element "+aa+" in "+annotation.getVorbaId().getId());
- }
- }
- // decide on how many annotation rows are needed.
- if (mergeable) {
- for (int i=0; i<anot[0].length;i++) {
- if (anot[1][i]!=null) {
- anot[0][i] = anot[1][i];
- anot[0][i].description = anot[0][i].description+" (after)";
- AeContent[HASDESCSTR]=true; // we have valid description string data
- anot[1][i] = null;
- }
- }
- anot[1] = null;
- } else {
- for (int i=0; i<anot[0].length;i++) {
- anot[1][i].description = anot[1][i].description+" (after)";
- }
- }
- return new Object[] { AeContent, rangeMap, anot[0], anot[1] };
- } else {
- // no annotations to parse. Just return an empty annotationElement[] array.
- return new Object[] { AeContent, rangeMap, anot[0], anot[1] };
- }
- // return null;
- }
- /**
- * @param jal the jalview alignment to which the annotation will be attached (ideally - freshly updated from corresponding vamsas alignment)
- * @param annotation
- * @return unbound jalview alignment annotation object.
- */
- private jalview.datamodel.AlignmentAnnotation getjAlignmentAnnotation(jalview.datamodel.AlignmentI jal, org.vamsas.objects.core.RangeAnnotation annotation) {
- jalview.datamodel.AlignmentAnnotation jan =null;
- if (annotation==null)
- return null;
- // boolean hasSequenceRef=annotation.getClass().equals(org.vamsas.objects.core.AlignmentSequenceAnnotation.class);
- //boolean hasProvenance=hasSequenceRef || (annotation.getClass().equals(org.vamsas.objects.core.AlignmentAnnotation.class));
- /*int se[] = getBounds(annotation);
- if (se==null)
- se=new int[] {0,jal.getWidth()-1};
- */
- Object[] parsedRangeAnnotation = parseRangeAnnotation(annotation);
- String a_label=annotation.getLabel();
- String a_descr=annotation.getDescription();
- if (a_label==null || a_label.length()==0) {
- a_label = annotation.getType();
- if (a_label.length()==0)
- a_label = "Unamed annotation";
- }
- if (a_descr==null || a_descr.length()==0) {
- a_descr = "Annotation of type '"+annotation.getType()+"'";
- }
- if (parsedRangeAnnotation==null) {
- Cache.log.debug("Inserting empty annotation row elements for a whole-alignment annotation.");
-
-
- } else {
- if (parsedRangeAnnotation[3]!=null) {
- Cache.log.warn("Ignoring 'After' annotation row in "+annotation.getVorbaId());
- }
- jalview.datamodel.Annotation[] arow = (jalview.datamodel.Annotation[]) parsedRangeAnnotation[2];
- boolean[] has=(boolean[])parsedRangeAnnotation[0];
- // VAMSAS: getGraph is only on derived annotation for alignments - in this way its 'odd' - there is already an existing TODO about removing this flag as being redundant
- /*if ((annotation.getClass().equals(org.vamsas.objects.core.AlignmentAnnotation.class) && ((org.vamsas.objects.core.AlignmentAnnotation)annotation).getGraph())
- || (hasSequenceRef=true && ((org.vamsas.objects.core.AlignmentSequenceAnnotation)annotation).getGraph())) {
- */
- if (has[HASVALS]) {
- // make bounds and automatic description strings for jalview user's benefit (these shouldn't be written back to vamsas document)
- boolean first=true;
- float min=0,max=1;
- int lastval=0;
- for (int i=0;i<arow.length; i++) {
- if (arow[i]!=null) {
- if (i-lastval>1) {
- // do some interpolation *between* points
- if (arow[lastval]!=null) {
- float interval = arow[i].value-arow[lastval].value;
- interval/=i-lastval;
- float base = arow[lastval].value;
- for (int ip=lastval+1,np=0; ip<i; np++,ip++) {
- arow[ip] = new jalview.datamodel.Annotation("","",' ', interval*np+base);
- // NB - Interpolated points don't get a tooltip and description.
- }
- }
- }
- lastval=i;
- // check range - shouldn't we have a min and max property in the annotation object ?
- if (first) { min=max=arow[i].value; first=false;}
- else { if (arow[i].value<min) { min=arow[i].value; }
- else if (arow[i].value>max) { max=arow[i].value; }
- }
- // make tooltip and display char value
- if (!has[HASDESCSTR]) arow[i].description = arow[i].value + "";
- if (!has[HASDC]) arow[i].displayCharacter=arow[i].value+"";
- }
- }
- int type=jalview.datamodel.AlignmentAnnotation.LINE_GRAPH;
- if (has[HASHPHOB]) {
- type = jalview.datamodel.AlignmentAnnotation.BAR_GRAPH;
- }
- jan = new jalview.datamodel.AlignmentAnnotation(a_label, a_descr, arow, min, max, type);
- } else {
- jan = new jalview.datamodel.AlignmentAnnotation(a_label, a_descr, arow);
- jan.setThreshold(null);
- }
- if (annotation.getLinkCount()>0) {
- Cache.log.warn("Ignoring "+annotation.getLinkCount()+"links added to AlignmentAnnotation.");
- }
- if (annotation.getModifiable()) {
- jan.editable=true;
- }
-
- if (annotation.getPropertyCount()>0) {
- // look for special jalview properties
- org.vamsas.objects.core.Property[] props=annotation.getProperty();
- for (int p=0;p<props.length; p++) {
- if (props[p].getName().equalsIgnoreCase("jalview:graphType")) {
- try {
- // probably a jalview annotation graph so recover the visualization hints.
- jan.graph = jalview.datamodel.AlignmentAnnotation.getGraphValueFromString(props[p].getContent());
- } catch (Exception e) {
- Cache.log.debug("Invalid graph type value in jalview:graphType property.");
- }
- try {
- if (annotation.getGroup()!=null && annotation.getGroup().length()>0)
- jan.graphGroup = Integer.parseInt(annotation.getGroup());
- } catch (Exception e) {
- Cache.log.info("UNIMPLEMENTED : Couldn't parse non-integer group value for setting graphGroup correctly.");
- }
- }
- }
- }
-
- return jan;
-
- }
-
- return null;
- }
-
- private SequenceFeature getJalviewSeqFeature(RangeAnnotation dseta) {
- int[] se = getBounds(dseta);
- SequenceFeature sf = new jalview.datamodel.SequenceFeature(dseta.getType(),
- dseta.getDescription(), dseta.getStatus(), se[0], se[1], dseta
- .getGroup());
- if (dseta.getLinkCount() > 0)
- {
- Link[] links = dseta.getLink();
- for (int i = 0; i < links.length; i++)
- {
- sf.addLink(links[i].getContent() + "|" + links[i].getHref());
- }
- }
- return sf;
- }
-
- /**
- * get real bounds of a RangeType's specification. start and end are an
- * inclusive range within which all segments and positions lie.
- * TODO: refactor to vamsas utils
- * @param dseta
- * @return int[] { start, end}
- */
- private int[] getBounds(RangeType dseta) {
- if (dseta != null)
- {
- int[] se = null;
- if (dseta.getSegCount()>0 && dseta.getPosCount()>0)
- throw new Error("Invalid vamsas RangeType - cannot resolve both lists of Pos and Seg from choice!");
- if (dseta.getSegCount() > 0)
- {
- se = getSegRange(dseta.getSeg(0),true);
- for (int s = 1, sSize = dseta.getSegCount(); s < sSize; s++)
- {
- int nse[] = getSegRange(dseta.getSeg(s), true);
- if (se[0] > nse[0])
- se[0] = nse[0];
- if (se[1] < nse[1])
- se[1] = nse[1];
- }
- }
- if (dseta.getPosCount() > 0)
- {
- // could do a polarity for pos range too. and pass back indication of discontinuities.
- int pos = dseta.getPos(0).getI();
- se = new int[] { pos, pos };
- for (int p = 0, pSize = dseta.getPosCount(); p < pSize; p++)
- {
- pos = dseta.getPos(p).getI();
- if (se[0] > pos)
- se[0] = pos;
- if (se[1] < pos)
- se[1] = pos;
- }
- }
- return se;
- }
- return null;
- }
- /**
- * map from a rangeType's internal frame to the referenced object's coordinate frame.
- * @param dseta
- * @return int [] { ref(pos)...} for all pos in rangeType's frame.
- */
- private int[] getMapping(RangeType dseta) {
- Vector posList=new Vector();
- if (dseta != null)
- {
- int[] se = null;
- if (dseta.getSegCount()>0 && dseta.getPosCount()>0)
- throw new Error("Invalid vamsas RangeType - cannot resolve both lists of Pos and Seg from choice!");
- if (dseta.getSegCount() > 0)
- {
- for (int s = 0, sSize = dseta.getSegCount(); s < sSize; s++)
- {
- se = getSegRange(dseta.getSeg(s), false);
- int se_end=se[1-se[2]]+(se[2]==0 ? 1 : -1);
- for (int p=se[se[2]]; p!=se_end; p+=se[2]==0 ? 1 : -1 ) {
- posList.add(new Integer(p));
- }
- }
- }
- else if (dseta.getPosCount() > 0)
- {
- int pos = dseta.getPos(0).getI();
-
- for (int p = 0, pSize = dseta.getPosCount(); p < pSize; p++)
- {
- pos = dseta.getPos(p).getI();
- posList.add(new Integer(pos));
- }
- }
- }
- if (posList!=null && posList.size()>0) {
- int[] range=new int[posList.size()];
- for (int i=0; i<range.length; i++)
- range[i] = ((Integer)posList.elementAt(i)).intValue();
- posList.clear();
- return range;
- }
- return null;
- }
- /* not needed now.
- * Provenance getVamsasProvenance(jalview.datamodel.Provenance jprov) {
- jalview.datamodel.ProvenanceEntry[] entries = null;
- // TODO: fix App and Action here.
- Provenance prov = new Provenance();
- org.exolab.castor.types.Date date = new org.exolab.castor.types.Date(
- new java.util.Date());
- Entry provEntry;
-
- if (jprov != null)
- {
- entries = jprov.getEntries();
- for (int i = 0; i < entries.length; i++)
- {
- provEntry = new Entry();
- try
- {
- date = new org.exolab.castor.types.Date(entries[i].getDate());
- } catch (Exception ex)
- {
- ex.printStackTrace();
-
- date = new org.exolab.castor.types.Date(entries[i].getDate());
- }
- provEntry.setDate(date);
- provEntry.setUser(entries[i].getUser());
- provEntry.setAction(entries[i].getAction());
- prov.addEntry(provEntry);
- }
- }
- else
- {
- provEntry = new Entry();
- provEntry.setDate(date);
- provEntry.setUser(System.getProperty("user.name")); // TODO: ext string
- provEntry.setApp("JVAPP"); // TODO: ext string
- provEntry.setAction(action);
- prov.addEntry(provEntry);
- }
-
- return prov;
- }
- */
- jalview.datamodel.Provenance getJalviewProvenance(Provenance prov) {
- // TODO: fix App and Action entries and check use of provenance in jalview.
- jalview.datamodel.Provenance jprov = new jalview.datamodel.Provenance();
- for (int i = 0; i < prov.getEntryCount(); i++)
- {
- jprov.addEntry(prov.getEntry(i).getUser(), prov.getEntry(i).getAction(),
- prov.getEntry(i).getDate().toDate(), prov.getEntry(i).getId());
- }
-
- return jprov;
- }
-
- /**
- *
- * @return default initial provenance list for a Jalview created vamsas
- * object.
- */
- Provenance dummyProvenance() {
- return dummyProvenance(null);
- }
-
- Entry dummyPEntry(String action) {
- Entry entry = new Entry();
- entry.setApp(this.provEntry.getApp());
- if (action != null)
- entry.setAction(action);
- else
- entry.setAction("created.");
- entry.setDate(new org.exolab.castor.types.Date(new java.util.Date()));
- entry.setUser(this.provEntry.getUser());
- return entry;
- }
-
- Provenance dummyProvenance(String action) {
- Provenance prov = new Provenance();
- prov.addEntry(dummyPEntry(action));
- return prov;
- }
-
- void addProvenance(Provenance p, String action) {
- p.addEntry(dummyPEntry(action));
- }
}
git://source.jalview.org / jalview.git / commitdiff