--- /dev/null
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ */
+
+package jalview.io;
+
+import jalview.bin.Cache;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.AlignmentView;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.gui.AlignFrame;
+import jalview.gui.AlignViewport;
+import jalview.gui.Desktop;
+import jalview.gui.TreePanel;
+
+import java.util.HashMap;
+import java.util.Hashtable;
+import java.util.IdentityHashMap;
+import java.util.Vector;
+
+import uk.ac.vamsas.client.*;
+import uk.ac.vamsas.objects.core.*;
+
+/*
+ *
+ * static {
+ * org.exolab.castor.util.LocalConfiguration.getInstance().getProperties().setProperty(
+ * "org.exolab.castor.serializer", "org.apache.xml.serialize.XMLSerilazizer"); }
+ *
+ */
+
+public class VamsasAppDatastore
+{
+ Entry provEntry = null;
+
+ // AlignViewport av;
+
+ org.exolab.castor.types.Date date = new org.exolab.castor.types.Date(
+ new java.util.Date());
+
+ IClientDocument cdoc;
+
+ Hashtable vobj2jv;
+
+ IdentityHashMap jv2vobj;
+
+ public VamsasAppDatastore(IClientDocument 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(uk.ac.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, uk.ac.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() ?
+ uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_NA
+ : uk.ac.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()==null) // TODO: USE VAMSAS LIBRARY OBJECT LOCK METHODS
+ {
+ 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)
+ {
+ uk.ac.vamsas.objects.core.AlignmentSequence alsref = (uk.ac.vamsas.
+ objects.core.AlignmentSequence) getjv2vObj(aa[i].sequenceRef);
+ uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation an = (uk.ac.
+ 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 uk.ac.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(uk.ac.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()==null) // TODO: USE VAMSAS LIBRARY OBJECT LOCK METHODS)
+ {
+ // 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
+ uk.ac.vamsas.objects.core.AlignmentAnnotation an = (uk.ac.vamsas.
+ objects.core.AlignmentAnnotation) getjv2vObj(aa[i]);
+ if (an == null)
+ {
+ an = new uk.ac.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(uk.ac.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(""); // TODO: This is not the way the modifiable flag is supposed to be used.
+ }
+ 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()==null) // TODO: USE VAMSAS LIBRARY OBJECT LOCK METHODS)
+ {
+ // 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.instance.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()==null) // TODO: USE VAMSAS LIBRARY OBJECT LOCK METHODS)
+ {
+ // 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 uk.ac.vamsas.objects.core.Alignment)
+ {
+ // recover an AlignmentView for the input data
+ AlignViewport javport = (AlignViewport) getvObj2jv( (uk.ac.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.instance.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.getSequenceAsString().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(),
+ (int)dataset.getSequence(i).getStart(),
+ (int)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++)
+ {
+ uk.ac.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),
+ (int)valseq.getStart(),
+ (int)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()==null) // TODO: USE VAMSAS LIBRARY OBJECT LOCK METHODS)
+ {
+ 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)
+ {
+ uk.ac.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()==null) // TODO: USE VAMSAS LIBRARY OBJECT LOCK METHODS)
+ {
+ // 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(uk.ac.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 = (int) 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(uk.ac.vamsas.objects.utils.
+ GlyphDictionary.PROTEIN_SS_3STATE))
+ {
+ ss = glyphs[g].getContent();
+ AeContent[HASSECSTR] = true;
+ }
+ else if (glyphs[g].getDict().equals(uk.ac.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(uk.ac.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,
+ uk.ac.vamsas.objects.core.RangeAnnotation annotation)
+ {
+ jalview.datamodel.AlignmentAnnotation jan = null;
+ if (annotation == null)
+ {
+ return null;
+ }
+ // boolean hasSequenceRef=annotation.getClass().equals(uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation.class);
+ //boolean hasProvenance=hasSequenceRef || (annotation.getClass().equals(uk.ac.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(uk.ac.vamsas.objects.core.AlignmentAnnotation.class) && ((uk.ac.vamsas.objects.core.AlignmentAnnotation)annotation).getGraph())
+ || (hasSequenceRef=true && ((uk.ac.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()==null) // TODO: USE VAMSAS LIBRARY OBJECT LOCK METHODS)
+ {
+ jan.editable = true;
+ }
+
+ if (annotation.getPropertyCount() > 0)
+ {
+ // look for special jalview properties
+ uk.ac.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