/* * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * * Jalview 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 3 * of the License, or (at your option) any later version. * * Jalview 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 Jalview. If not, see . * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.io; import jalview.bin.Cache; import jalview.datamodel.AlignedCodonFrame; import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.GraphLine; import jalview.datamodel.SequenceI; import jalview.gui.AlignFrame; import jalview.gui.AlignViewport; import jalview.gui.Desktop; import jalview.gui.TreePanel; import jalview.io.vamsas.Datasetsequence; import jalview.io.vamsas.DatastoreItem; import jalview.io.vamsas.DatastoreRegistry; import jalview.io.vamsas.Rangetype; import jalview.util.MessageManager; import jalview.viewmodel.AlignmentViewport; import java.io.IOException; import java.util.Enumeration; import java.util.HashMap; import java.util.Hashtable; import java.util.IdentityHashMap; import java.util.Iterator; import java.util.List; import java.util.Vector; import java.util.jar.JarInputStream; import java.util.jar.JarOutputStream; import uk.ac.vamsas.client.IClientAppdata; import uk.ac.vamsas.client.IClientDocument; import uk.ac.vamsas.client.Vobject; import uk.ac.vamsas.client.VorbaId; import uk.ac.vamsas.objects.core.Alignment; import uk.ac.vamsas.objects.core.AlignmentSequence; import uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation; import uk.ac.vamsas.objects.core.AnnotationElement; import uk.ac.vamsas.objects.core.DataSet; import uk.ac.vamsas.objects.core.DataSetAnnotations; import uk.ac.vamsas.objects.core.DbRef; import uk.ac.vamsas.objects.core.Entry; import uk.ac.vamsas.objects.core.Glyph; import uk.ac.vamsas.objects.core.Local; import uk.ac.vamsas.objects.core.MapType; import uk.ac.vamsas.objects.core.Mapped; import uk.ac.vamsas.objects.core.Property; import uk.ac.vamsas.objects.core.Provenance; import uk.ac.vamsas.objects.core.RangeAnnotation; import uk.ac.vamsas.objects.core.RangeType; import uk.ac.vamsas.objects.core.Seg; import uk.ac.vamsas.objects.core.Sequence; import uk.ac.vamsas.objects.core.SequenceType; import uk.ac.vamsas.objects.core.VAMSAS; import uk.ac.vamsas.objects.utils.Properties; /* * * static { * org.exolab.castor.util.LocalConfiguration.getInstance().getProperties().setProperty( * "org.exolab.castor.serializer", "org.apache.xml.serialize.XMLSerilazizer"); } * */ /* * TODO: check/verify consistency for vamsas sync with group associated alignment annotation */ public class VamsasAppDatastore { /** * Type used for general jalview generated annotation added to vamsas document */ public static final String JALVIEW_ANNOTATION_ROW = "JalviewAnnotation"; /** * AlignmentAnnotation property to indicate that values should not be * interpolated */ public static final String DISCRETE_ANNOTATION = "discrete"; /** * continuous property - optional to specify that annotation should be * represented as a continous graph line */ private static final String CONTINUOUS_ANNOTATION = "continuous"; private static final String THRESHOLD = "threshold"; /** * template for provenance entries written to vamsas session document */ Entry provEntry = null; /** * Instance of the session document being synchronized with */ IClientDocument cdoc; /** * map Vorba (vamsas object xml ref) IDs to live jalview object references */ Hashtable vobj2jv; /** * map live jalview object references to Vorba IDs */ IdentityHashMap jv2vobj; /** * map jalview sequence set ID (which is vorba ID for alignment) to last * recorded hash value for the alignment viewport (the undo/redo hash value) */ Hashtable alignRDHash; public VamsasAppDatastore(IClientDocument cdoc, Hashtable vobj2jv, IdentityHashMap jv2vobj, Entry provEntry, Hashtable alignRDHash) { this.cdoc = cdoc; this.vobj2jv = vobj2jv; this.jv2vobj = jv2vobj; this.provEntry = provEntry; this.alignRDHash = alignRDHash; buildSkipList(); } /** * the skipList used to skip over views from Jalview Appdata's that we've * already syncrhonized */ Hashtable skipList; private void buildSkipList() { skipList = new Hashtable(); AlignFrame[] al = Desktop.getAlignFrames(); for (int f = 0; al != null && f < al.length; f++) { skipList.put(al[f].getViewport().getSequenceSetId(), al[f]); } } /** * @return the Vobject bound to Jalview datamodel object */ protected Vobject getjv2vObj(Object jvobj) { if (jv2vobj.containsKey(jvobj)) { return cdoc.getObject((VorbaId) jv2vobj.get(jvobj)); } // check if we're working with a string - then workaround // the use of IdentityHashTable because different strings // have different object IDs. if (jvobj instanceof String) { Object seqsetidobj = null; seqsetidobj = getVamsasObjectBinding().get(jvobj); if (seqsetidobj != null) { if (seqsetidobj instanceof String) { // what is expected. object returned by av.getSequenceSetId() - // reverse lookup to get the 'registered' instance of this string Vobject obj = getjv2vObj(seqsetidobj); if (obj != null && !(obj instanceof Alignment)) { Cache.log.warn( "IMPLEMENTATION ERROR?: Unexpected mapping for unmapped jalview string object content:" + seqsetidobj + " to object " + obj); } return obj; } else { Cache.log.warn("Unexpected mapping for Jalview String Object ID " + seqsetidobj + " to another jalview dataset object " + seqsetidobj); } } } if (Cache.log.isDebugEnabled()) { Cache.log.debug( "Returning null VorbaID binding for jalview object " + 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 || cdoc.getObject(id) != vobj) { 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(MessageManager.getString( "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! Cache.log.debug("Binding " + vobj.getVorbaId() + " to " + jvobj); 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 * @return true if alignment associated with viewport was stored/synchronized * to document */ public boolean storeVAMSAS(AlignViewport av, String aFtitle) { try { jalview.datamodel.AlignmentI jal = av.getAlignment(); jalview.datamodel.AlignmentI jds = jal.getDataset(); boolean nw = false; VAMSAS root = null; // will be resolved based on Dataset Parent. // ///////////////////////////////////////// // SAVE THE DATASET DataSet dataset = null; if (jds == null) { Cache.log.warn("Creating new dataset for an alignment."); jal.setDataset(null); jds = jal.getDataset(); } // try and get alignment and association for sequence set id Alignment alignment = (Alignment) getjv2vObj(av.getSequenceSetId()); if (alignment != null) { dataset = (DataSet) alignment.getV_parent(); } else { // is the dataset already registered dataset = (DataSet) getjv2vObj(jds); } if (dataset == null) { // it might be that one of the dataset sequences does actually have a // binding, so search for it indirectly. If it does, then the local // jalview dataset // must be merged with the existing vamsas dataset. jalview.datamodel.SequenceI[] jdatset = jds.getSequencesArray(); for (int i = 0; i < jdatset.length; i++) { Vobject vbound = getjv2vObj(jdatset[i]); if (vbound != null) { if (vbound instanceof uk.ac.vamsas.objects.core.Sequence) { if (dataset == null) { dataset = (DataSet) vbound.getV_parent(); } else { if (vbound.getV_parent() != null && dataset != vbound.getV_parent()) { throw new Error(MessageManager.getString( "error.implementation_error_cannot_map_alignment_sequences")); // This occurs because the dataset for the alignment we are // trying to } } } } } } if (dataset == null) { Cache.log.warn("Creating new vamsas dataset for alignment view " + av.getSequenceSetId()); // we create a new dataset on the default vamsas root. root = cdoc.getVamsasRoots()[0]; // default vamsas root for modifying. dataset = new DataSet(); root.addDataSet(dataset); bindjvvobj(jds, dataset); dataset.setProvenance(dummyProvenance()); // dataset.getProvenance().addEntry(provEntry); nw = true; } else { root = (VAMSAS) dataset.getV_parent(); } // update dataset Sequence sequence; // 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; Vector dssmods = new Vector(); for (int i = 0; i < jal.getHeight(); i++) { SequenceI sq = jal.getSequenceAt(i).getDatasetSequence(); // only insert // referenced // sequences // to dataset. Datasetsequence dssync = new jalview.io.vamsas.Datasetsequence(this, sq, dict, dataset); sequence = (Sequence) dssync.getVobj(); if (dssync.getModified()) { dssmods.addElement(sequence); } ; } if (dssmods.size() > 0) { if (!nw) { Entry pentry = this.addProvenance(dataset.getProvenance(), "updated sequences"); // pentry.addInput(vInput); could write in which sequences were // modified. dssmods.removeAllElements(); } } // dataset.setProvenance(getVamsasProvenance(jal.getDataset().getProvenance())); // //////////////////////////////////////////// if (alignmentWillBeSkipped(av)) { // TODO: trees could be written - but for the moment we just addToSkipList(av); // add to the JalviewXML skipList and .. return false; } if (alignment == null) { alignment = new Alignment(); bindjvvobj(av.getSequenceSetId(), 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("title"); title.setType("string"); title.setContent(aFtitle); alignment.addProperty(title); } alignment.setGapChar(String.valueOf(av.getGapCharacter())); for (int i = 0; i < jal.getHeight(); i++) { syncToAlignmentSequence(jal.getSequenceAt(i), alignment, null); } alignRDHash.put(av.getSequenceSetId(), av.getUndoRedoHash()); } else { // always prepare to clone the alignment boolean alismod = av.isUndoRedoHashModified( (long[]) alignRDHash.get(av.getSequenceSetId())); // todo: verify and update mutable alignment props. // TODO: Use isLocked methods if (alignment.getModifiable() == null || alignment.getModifiable().length() == 0) // && !alignment.isDependedOn()) { boolean modified = false; // check existing sequences in local and in document. Vector docseqs = new Vector( alignment.getAlignmentSequenceAsReference()); for (int i = 0; i < jal.getHeight(); i++) { modified |= syncToAlignmentSequence(jal.getSequenceAt(i), alignment, docseqs); } if (docseqs.size() > 0) { // removeValignmentSequences(alignment, docseqs); docseqs.removeAllElements(); System.out.println( "Sequence deletion from alignment is not implemented."); } if (modified) { if (alismod) { // info in the undo addProvenance(alignment.getProvenance(), "Edited"); // TODO: // insert // something // sensible // here again } else { // info in the undo addProvenance(alignment.getProvenance(), "Attributes Edited"); // TODO: // insert // something // sensible // here // again } } if (alismod) { System.out.println("update alignment in document."); } else { System.out.println("alignment in document left unchanged."); } } else { // unbind alignment from view. // create new binding and new alignment. // mark trail on new alignment as being derived from old ? 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) { /* * We do not put local Alignment Sequence Features into the vamsas * document yet. * * * 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]); * valseqf.setGraph(false); * valseqf.addProperty(newProperty("jalview:feature" * ,"boolean","true")); 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].groupRef != null) { // TODO: store any group associated annotation references Cache.log.warn( "Group associated sequence annotation is not stored in VAMSAS document."); continue; } if (aa[i].sequenceRef != null) { // Deal with sequence associated annotation Vobject sref = getjv2vObj(aa[i].sequenceRef); if (sref instanceof uk.ac.vamsas.objects.core.AlignmentSequence) { saveAlignmentSequenceAnnotation(AlSeqMaps, (AlignmentSequence) sref, aa[i]); } else { // first find the alignment sequence to associate this with. for (SequenceI jvalsq : av.getAlignment().getSequences()) { // saveDatasetSequenceAnnotation(AlSeqMaps,(uk.ac.vamsas.objects.core.Sequence) // sref, aa[i]); if (jvalsq.getDatasetSequence() == aa[i].sequenceRef) { Vobject alsref = getjv2vObj(jvalsq); saveAlignmentSequenceAnnotation(AlSeqMaps, (AlignmentSequence) alsref, aa[i]); break; } ; } } } 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_ANNOTATION_ROW); an.setDescription(aa[i].description); alignment.addAlignmentAnnotation(an); Seg vSeg = new Seg(); // TODO: refactor to have a default // rangeAnnotationType initer/updater that // takes a set of int ranges. 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 != AlignmentAnnotation.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 if (an.isGraph()) { 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. } setAnnotationType(an, aa[i]); if (aa[i].graph != jalview.datamodel.AlignmentAnnotation.NO_GRAPH) { an.setGraph(true); an.setGroup(Integer.toString(aa[i].graphGroup)); if (aa[i].threshold != null && aa[i].threshold.displayed) { an.addProperty(Properties.newProperty(THRESHOLD, Properties.FLOATTYPE, "" + aa[i].threshold.value)); if (aa[i].threshold.label != null) { an.addProperty(Properties.newProperty( THRESHOLD + "Name", Properties.STRINGTYPE, "" + aa[i].threshold.label)); } } } } 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.getViewPort().getSequenceSetId() .equals(av.getSequenceSetId())) { DatastoreItem vtree = new jalview.io.vamsas.Tree(this, tp, jal, alignment); } } } } // Store Jalview specific stuff in the Jalview appData // not implemented in the SimpleDoc interface. } catch (Exception ex) { ex.printStackTrace(); return false; } return true; } /** * very quick test to see if the viewport would be stored in the vamsas * document. Reasons for not storing include the unaligned flag being false * (for all sequences, including the hidden ones!) * * @param av * @return true if alignment associated with this view will be stored in * document. */ public boolean alignmentWillBeSkipped(AlignmentViewport av) { return (!av.getAlignment().isAligned()); } private void addToSkipList(AlignmentViewport av) { if (skipList == null) { skipList = new Hashtable(); } skipList.put(av.getSequenceSetId(), av); } /** * remove docseqs from the given alignment marking provenance appropriately * and removing any references to the sequences. * * @param alignment * @param docseqs */ private void removeValignmentSequences(Alignment alignment, Vector docseqs) { // delete these from document. This really needs to be a generic document // API function derived by CASTOR. Enumeration en = docseqs.elements(); while (en.hasMoreElements()) { alignment.removeAlignmentSequence( (AlignmentSequence) en.nextElement()); } Entry pe = addProvenance(alignment.getProvenance(), "Removed " + docseqs.size() + " sequences"); en = alignment.enumerateAlignmentAnnotation(); Vector toremove = new Vector(); while (en.hasMoreElements()) { uk.ac.vamsas.objects.core.AlignmentAnnotation alan = (uk.ac.vamsas.objects.core.AlignmentAnnotation) en .nextElement(); if (alan.getSeqrefsCount() > 0) { int p = 0; Vector storem = new Vector(); Enumeration sr = alan.enumerateSeqrefs(); while (sr.hasMoreElements()) { Object alsr = sr.nextElement(); if (docseqs.contains(alsr)) { storem.addElement(alsr); } } // remove references to the deleted sequences sr = storem.elements(); while (sr.hasMoreElements()) { alan.removeSeqrefs(sr.nextElement()); } if (alan.getSeqrefsCount() == 0) { // should then delete alan from dataset toremove.addElement(alan); } } } // remove any annotation that used to be associated to a specific bunch of // sequences en = toremove.elements(); while (en.hasMoreElements()) { alignment.removeAlignmentAnnotation( (uk.ac.vamsas.objects.core.AlignmentAnnotation) en .nextElement()); } // TODO: search through alignment annotations to remove any references to // this alignment sequence } /** * sync a jalview alignment seuqence into a vamsas alignment assumes all lock * transformation/bindings have been sorted out before hand. creates/syncs the * vamsas alignment sequence for jvalsq and adds it to the alignment if * necessary. unbounddocseq is a duplicate of the vamsas alignment sequences * and these are removed after being processed w.r.t a bound jvalsq * */ private boolean syncToAlignmentSequence(SequenceI jvalsq, Alignment alignment, Vector unbounddocseq) { boolean modal = false; // todo: islocked method here boolean up2doc = false; AlignmentSequence alseq = (AlignmentSequence) getjv2vObj(jvalsq); if (alseq == null) { alseq = new AlignmentSequence(); up2doc = true; } else { if (unbounddocseq != null) { unbounddocseq.removeElement(alseq); } } // boolean locked = (alignment.getModifiable()==null || // alignment.getModifiable().length()>0); // TODO: VAMSAS: translate lowercase symbols to annotation ? if (up2doc || !alseq.getSequence().equals(jvalsq.getSequenceAsString())) { alseq.setSequence(jvalsq.getSequenceAsString()); alseq.setStart(jvalsq.getStart()); alseq.setEnd(jvalsq.getEnd()); modal = true; } if (up2doc || !alseq.getName().equals(jvalsq.getName())) { modal = true; alseq.setName(jvalsq.getName()); } if (jvalsq.getDescription() != null && (alseq.getDescription() == null || !jvalsq.getDescription().equals(alseq.getDescription()))) { modal = true; alseq.setDescription(jvalsq.getDescription()); } if (getjv2vObj(jvalsq.getDatasetSequence()) == null) { Cache.log.warn( "Serious Implementation error - Unbound dataset sequence in alignment: " + jvalsq.getDatasetSequence()); } alseq.setRefid(getjv2vObj(jvalsq.getDatasetSequence())); if (up2doc) { alignment.addAlignmentSequence(alseq); bindjvvobj(jvalsq, alseq); } return up2doc || modal; } /** * locally sync a jalview alignment seuqence from a vamsas alignment assumes * all lock transformation/bindings have been sorted out before hand. * creates/syncs the jvalsq from the alignment sequence */ private boolean syncFromAlignmentSequence(AlignmentSequence valseq, char valGapchar, char gapChar, List dsseqs) { boolean modal = false; // todo: islocked method here boolean upFromdoc = false; jalview.datamodel.SequenceI alseq = (SequenceI) getvObj2jv(valseq); if (alseq == null) { upFromdoc = true; } if (alseq != null) { // boolean locked = (alignment.getModifiable()==null || // alignment.getModifiable().length()>0); // TODO: VAMSAS: translate lowercase symbols to annotation ? if (upFromdoc || !valseq.getSequence().equals(alseq.getSequenceAsString())) { // this might go *horribly* wrong alseq.setSequence(new String(valseq.getSequence()) .replace(valGapchar, gapChar)); alseq.setStart((int) valseq.getStart()); alseq.setEnd((int) valseq.getEnd()); modal = true; } if (!valseq.getName().equals(alseq.getName())) { modal = true; alseq.setName(valseq.getName()); } if (alseq.getDescription() == null || (valseq.getDescription() != null && !alseq.getDescription().equals(valseq.getDescription()))) { alseq.setDescription(valseq.getDescription()); modal = true; } if (modal && Cache.log.isDebugEnabled()) { Cache.log.debug( "Updating apparently edited sequence " + alseq.getName()); } } 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 (valseq.getDescription() != null) { alseq.setDescription(valseq.getDescription()); } else { // inherit description line from dataset. if (alseq.getDatasetSequence().getDescription() != null) { alseq.setDescription( alseq.getDatasetSequence().getDescription()); } } // 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); } Vobject datsetseq = (Vobject) valseq.getRefid(); if (datsetseq != null) { if (datsetseq != alseq.getDatasetSequence()) { modal = true; } alseq.setDatasetSequence((SequenceI) getvObj2jv(datsetseq)); // exceptions } return upFromdoc || modal; } private void initRangeAnnotationType(RangeAnnotation an, AlignmentAnnotation alan, int[] gapMap) { Seg vSeg = new Seg(); vSeg.setStart(1); vSeg.setInclusive(true); vSeg.setEnd(gapMap.length); an.addSeg(vSeg); // LATER: much of this is verbatim from the alignmentAnnotation // method below. suggests refactoring to make rangeAnnotation the // base class an.setDescription(alan.description); an.setLabel(alan.label); an.setGroup(Integer.toString(alan.graphGroup)); // // JBPNote - // originally we // were going to // store // graphGroup in // the Jalview // specific // bits. AnnotationElement ae; for (int a = 0; a < alan.annotations.length; a++) { if (alan.annotations[a] == null) { continue; } ae = new AnnotationElement(); ae.setDescription(alan.annotations[a].description); ae.addGlyph(new Glyph()); ae.getGlyph(0).setContent(alan.annotations[a].displayCharacter); // assume // jax-b // takes // care // of // utf8 // translation if (alan.graph != jalview.datamodel.AlignmentAnnotation.NO_GRAPH) { ae.addValue(alan.annotations[a].value); } ae.setPosition(gapMap[a] + 1); // position w.r.t. AlignmentSequence // symbols if (alan.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(alan.annotations[a].secondaryStructure)); ae.addGlyph(ss); } an.addAnnotationElement(ae); } } private void saveDatasetSequenceAnnotation(HashMap AlSeqMaps, uk.ac.vamsas.objects.core.Sequence sref, AlignmentAnnotation alan) { // { // uk.ac.vamsas. // objects.core.AlignmentSequence alsref = (uk.ac.vamsas. // objects.core.AlignmentSequence) sref; uk.ac.vamsas.objects.core.DataSetAnnotations an = (uk.ac.vamsas.objects.core.DataSetAnnotations) getjv2vObj( alan); int[] gapMap = getGapMap(AlSeqMaps, alan); if (an == null) { an = new uk.ac.vamsas.objects.core.DataSetAnnotations(); initRangeAnnotationType(an, alan, gapMap); an.setProvenance(dummyProvenance()); // get provenance as user // created, or jnet, or // something else. setAnnotationType(an, alan); an.setGroup(Integer.toString(alan.graphGroup)); // // JBPNote - // originally we // were going to // store // graphGroup in // the Jalview // specific // bits. if (alan.getThreshold() != null && alan.getThreshold().displayed) { an.addProperty(Properties.newProperty(THRESHOLD, Properties.FLOATTYPE, "" + alan.getThreshold().value)); if (alan.getThreshold().label != null) { an.addProperty(Properties.newProperty(THRESHOLD + "Name", Properties.STRINGTYPE, "" + alan.getThreshold().label)); } } ((DataSet) sref.getV_parent()).addDataSetAnnotations(an); bindjvvobj(alan, an); } 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 dataset sequence annotation."); } else { // verify existing alignment sequence annotation is up to date System.out.println( "make new alignment dataset sequence annotation if modification has happened."); } } } private int[] getGapMap(HashMap AlSeqMaps, AlignmentAnnotation alan) { int[] gapMap; if (AlSeqMaps.containsKey(alan.sequenceRef)) { gapMap = (int[]) AlSeqMaps.get(alan.sequenceRef); } else { gapMap = new int[alan.sequenceRef.getLength()]; // map from alignment position to sequence position. int[] sgapMap = alan.sequenceRef.gapMap(); for (int a = 0; a < sgapMap.length; a++) { gapMap[sgapMap[a]] = a; } } return gapMap; } private void saveAlignmentSequenceAnnotation(HashMap AlSeqMaps, AlignmentSequence alsref, AlignmentAnnotation alan) { // { // uk.ac.vamsas. // objects.core.AlignmentSequence alsref = (uk.ac.vamsas. // objects.core.AlignmentSequence) sref; uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation an = (uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation) getjv2vObj( alan); int[] gapMap = getGapMap(AlSeqMaps, alan); if (an == null) { an = new uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation(); initRangeAnnotationType(an, alan, gapMap); /** * I mean here that we don't actually have a semantic 'type' for the * annotation (this might be - score, intrinsic property, measurement, * something extracted from another program, etc) */ an.setType(JALVIEW_ANNOTATION_ROW); // TODO: better fix // this rough guess ;) alsref.addAlignmentSequenceAnnotation(an); bindjvvobj(alan, an); // These properties are directly supported by the // AlignmentSequenceAnnotation type. setAnnotationType(an, alan); an.setProvenance(dummyProvenance()); // get provenance as user // created, or jnet, or // something else. } 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."); } } } /** * set vamsas annotation object type from jalview annotation * * @param an * @param alan */ private void setAnnotationType(RangeAnnotation an, AlignmentAnnotation alan) { if (an instanceof AlignmentSequenceAnnotation) { if (alan.graph != AlignmentAnnotation.NO_GRAPH) { ((AlignmentSequenceAnnotation) an).setGraph(true); } else { ((AlignmentSequenceAnnotation) an).setGraph(false); } } if (an instanceof uk.ac.vamsas.objects.core.AlignmentAnnotation) { if (alan.graph != AlignmentAnnotation.NO_GRAPH) { ((uk.ac.vamsas.objects.core.AlignmentAnnotation) an).setGraph(true); } else { ((uk.ac.vamsas.objects.core.AlignmentAnnotation) an) .setGraph(false); } } switch (alan.graph) { case AlignmentAnnotation.BAR_GRAPH: an.addProperty(Properties.newProperty(DISCRETE_ANNOTATION, Properties.BOOLEANTYPE, "true")); break; case AlignmentAnnotation.LINE_GRAPH: an.addProperty(Properties.newProperty(CONTINUOUS_ANNOTATION, Properties.BOOLEANTYPE, "true")); break; default: // don't add any kind of discrete or continous property info. } } /** * get start 1) { // we need to close the original document view. // work out how to do this by seeing if the views are gathered. // pretty clunky but the only way to do this without adding more flags // to the align frames. boolean gathered = false; String newviewid = null; List mappings = av.getAlignment() .getCodonFrames(); for (int i = 0; i < views.length; i++) { if (views[i] != av) { AlignFrame viewframe = Desktop.getAlignFrameFor(views[i]); if (viewframe == af) { gathered = true; } newviewid = views[i].getSequenceSetId(); } else { // lose the reference to the vamsas document created view views[i] = null; } } // close the view generated by the vamsas document synchronization if (gathered) { af.closeView(av); } else { af.closeMenuItem_actionPerformed(false); } replaceJvObjMapping(seqsetidobj, newviewid); seqsetidobj = newviewid; // not sure if we need to do this: if (false) // mappings != null) { // ensure sequence mappings from vamsas document view still // active if (mappings != null) { jalview.structure.StructureSelectionManager .getStructureSelectionManager(Desktop.instance) .registerMappings(mappings); } } } // ensure vamsas object binds to the stored views retrieved from // Jalview appdata // jalview.structure.StructureSelectionManager // .getStructureSelectionManager() // .addStructureViewerListener(viewframe.alignPanel); } newviews = null; newAlignmentViews.clear(); } /** * replaces oldjvobject with newjvobject in the Jalview Object <> VorbaID * binding tables * * @param oldjvobject * @param newjvobject * (may be null) */ private void replaceJvObjMapping(Object oldjvobject, Object newjvobject) { Object vobject = jv2vobj.remove(oldjvobject); if (vobject == null) { // NOTE: this happens if user deletes object in one session then updates // from another client throw new Error(MessageManager.formatMessage( "error.implementation_error_old_jalview_object_not_bound", new String[] { oldjvobject.toString() })); } if (newjvobject != null) { jv2vobj.put(newjvobject, vobject); vobj2jv.put(vobject, newjvobject); } } /** * Update the jalview client and user appdata from the local jalview settings */ public void updateJalviewClientAppdata() { final IClientAppdata cappdata = cdoc.getClientAppdata(); if (cappdata != null) { try { jalview.gui.Jalview2XML jxml = new jalview.gui.Jalview2XML(); jxml.setObjectMappingTables(mapKeysToString(vobj2jv), mapValuesToString(jv2vobj)); jxml.setSkipList(skipList); if (dojvsync) { jxml.saveState( new JarOutputStream(cappdata.getClientOutputStream())); } } catch (Exception e) { // TODO raise GUI warning if user requests it. jalview.bin.Cache.log.error( "Couldn't update jalview client application data. Giving up - local settings probably lost.", e); } } else { jalview.bin.Cache.log.error( "Couldn't access client application data for vamsas session. This is probably a vamsas client bug."); } } /** * translate the Vobject keys to strings for use in Jalview2XML * * @param jv2vobj2 * @return */ private IdentityHashMap mapValuesToString(IdentityHashMap jv2vobj2) { IdentityHashMap mapped = new IdentityHashMap(); Iterator keys = jv2vobj2.keySet().iterator(); while (keys.hasNext()) { Object key = keys.next(); mapped.put(key, jv2vobj2.get(key).toString()); } return mapped; } /** * translate the Vobject values to strings for use in Jalview2XML * * @param vobj2jv2 * @return hashtable with string values */ private Hashtable mapKeysToString(Hashtable vobj2jv2) { Hashtable mapped = new Hashtable(); Iterator keys = vobj2jv2.keySet().iterator(); while (keys.hasNext()) { Object key = keys.next(); mapped.put(key.toString(), vobj2jv2.get(key)); } return mapped; } /** * synchronize Jalview from the vamsas document * * @return number of new views from document */ public int 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(); List 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.io.vamsas.Datasetsequence dssync = new Datasetsequence( this, vdseq); jalview.datamodel.SequenceI dsseq = (SequenceI) dssync.getJvobj(); if (dssync.isAddfromdoc()) { dsseqs.add(dsseq); } if (vdseq.getDbRefCount() > 0) { DbRef[] dbref = vdseq.getDbRef(); for (int db = 0; db < dbref.length; db++) { new jalview.io.vamsas.Dbref(this, dbref[db], vdseq, dsseq); } dsseq.updatePDBIds(); } } if (newds) { SequenceI[] seqs = new SequenceI[dsseqs.size()]; for (i = 0, iSize = dsseqs.size(); i < iSize; i++) { seqs[i] = dsseqs.get(i); dsseqs.set(i, null); } 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); // TODO: deal with group annotation on datset sequences. if (dseta.getSeqRefCount() == 1) { SequenceI dsSeq = (SequenceI) getvObj2jv( (Vobject) dseta.getSeqRef(0)); // TODO: deal with group // dataset // annotations if (dsSeq == null) { jalview.bin.Cache.log.warn( "Couldn't resolve jalview sequenceI for dataset object reference " + ((Vobject) dataset .getDataSetAnnotations(dsa) .getSeqRef(0)).getVorbaId() .getId()); } else { if (dseta.getAnnotationElementCount() == 0) { new jalview.io.vamsas.Sequencefeature(this, dseta, dsSeq); } 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."); } } } else { Cache.log.warn( "Ignoring multiply referenced dataset sequence annotation for binding to datsaet sequence features."); } } } 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); // TODO check this handles multiple views properly AlignmentViewport av = findViewport(alignment); jalview.datamodel.AlignmentI jal = null; if (av != null) { // TODO check that correct alignment object is retrieved when // hidden seqs exist. jal = (av.hasHiddenRows()) ? av.getAlignment() .getHiddenSequences().getFullAlignment() : av.getAlignment(); } iSize = alignment.getAlignmentSequenceCount(); boolean refreshal = 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.Sequence alseq = (jalview.datamodel.Sequence) getvObj2jv( valseq); if (syncFromAlignmentSequence(valseq, valGapchar, gapChar, dsseqs) && alseq != null) { // updated to sequence from the document jremain--; refreshal = true; } 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.setSequenceRef(alseq); asa.createSequenceMapping(alseq, se[0], false); // TODO: // verify // that // positions // in // alseqAnnotation // correspond // to // ungapped // residue // positions. alseq.addAlignmentAnnotation(asa); bindjvvobj(asa, vasannot[a]); refreshal = true; 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] = dsseqs.get(i); dsseqs.set(i, null); } 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]); // TODO: ensure we add the alignment annotation before the // automatic annotation rows jal.addAnnotation(jan); bindjvvobj(jan, an[j]); refreshal = true; } } } 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, alignment.getVorbaId().toString()); av = alignFrame.getViewport(); newAlignmentViews.addElement(av); 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("title")) { title = alignment.getProperty(p).getContent(); } } } // TODO: automatically create meaningful title for a vamsas // alignment using its provenance. if (Cache.log.isDebugEnabled()) { title = title + "(" + alignment.getVorbaId() + ")"; } jalview.gui.Desktop.addInternalFrame(alignFrame, title, AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); bindjvvobj(av.getSequenceSetId(), alignment); } else { // find the alignFrame for jal. // TODO: fix this so we retrieve the alignFrame handing av // *directly* (JBPNote - don't understand this now) // TODO: make sure all associated views are refreshed alignFrame = Desktop.getAlignFrameFor(av); if (refreshal) { av.alignmentChanged(alignFrame.alignPanel); alignFrame.alignPanel.adjustAnnotationHeight(); } } // LOAD TREES // ///////////////////////////////////// if (alignment.getTreeCount() > 0) { for (int t = 0; t < alignment.getTreeCount(); t++) { jalview.io.vamsas.Tree vstree = new jalview.io.vamsas.Tree( this, alignFrame, alignment.getTree(t)); TreePanel tp = null; if (vstree.isValidTree()) { tp = alignFrame.showNewickTree(vstree.getNewickTree(), vstree.getTitle(), vstree.getInputData(), 600, 500, t * 20 + 50, t * 20 + 50); } if (tp != null) { bindjvvobj(tp, alignment.getTree(t)); try { vstree.UpdateSequenceTreeMap(tp); } catch (RuntimeException e) { Cache.log.warn("update of labels failed.", e); } } else { Cache.log.warn("Cannot create tree for tree " + t + " in document (" + alignment.getTree(t).getVorbaId()); } } } } } } // we do sequenceMappings last because they span all datasets in a vamsas // root for (int _ds = 0, _nds = root.getDataSetCount(); _ds < _nds; _ds++) { DataSet dataset = root.getDataSet(_ds); if (dataset.getSequenceMappingCount() > 0) { for (int sm = 0, smCount = dataset .getSequenceMappingCount(); sm < smCount; sm++) { Rangetype seqmap = new jalview.io.vamsas.Sequencemapping(this, dataset.getSequenceMapping(sm)); } } } } return newAlignmentViews.size(); } public AlignmentViewport findViewport(Alignment alignment) { AlignmentViewport av = null; AlignmentViewport[] avs = Desktop .getViewports((String) getvObj2jv(alignment)); if (avs != null) { av = avs[0]; } return av; } // 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( "IMPLEMENTATION TODO: 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) { 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(); GraphLine gl = null; int type = 0; boolean interp = true; // cleared if annotation is DISCRETE // set type and other attributes from properties 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(DISCRETE_ANNOTATION)) { type = AlignmentAnnotation.BAR_GRAPH; interp = false; } else if (props[p].getName().equalsIgnoreCase(CONTINUOUS_ANNOTATION)) { type = AlignmentAnnotation.LINE_GRAPH; } else if (props[p].getName().equalsIgnoreCase(THRESHOLD)) { Float val = null; try { val = new Float(props[p].getContent()); } catch (Exception e) { Cache.log.warn("Failed to parse threshold property"); } if (val != null) { if (gl == null) { gl = new GraphLine(val.floatValue(), "", java.awt.Color.black); } else { gl.value = val.floatValue(); } } } else if (props[p].getName().equalsIgnoreCase(THRESHOLD + "Name")) { if (gl == null) { gl = new GraphLine(0, "", java.awt.Color.black); } gl.label = props[p].getContent(); } } } jalview.datamodel.AlignmentAnnotation jan = null; 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]) { if (type == 0) { type = jalview.datamodel.AlignmentAnnotation.BAR_GRAPH; // default // type of // value // annotation if (has[HASHPHOB]) { // no hints - so we ensure HPHOB display is like this. type = jalview.datamodel.AlignmentAnnotation.BAR_GRAPH; } } // 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 && interp) { // 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]) { if (!interp) { if (arow[i].description != null && arow[i].description.length() < 3) { // copy over the description as the display char. arow[i].displayCharacter = new String( arow[i].description); } } else { // mark the position as a point used for the interpolation. arow[i].displayCharacter = arow[i].value + ""; } } } } jan = new jalview.datamodel.AlignmentAnnotation(a_label, a_descr, arow, min, max, type); } else { if (annotation.getAnnotationElementCount() == 0) { // empty annotation array // TODO: alignment 'features' compare rangeType spec to alignment // width - if it is not complete, then mark regions on the annotation // row. } jan = new jalview.datamodel.AlignmentAnnotation(a_label, a_descr, arow); jan.setThreshold(null); jan.annotationId = annotation.getVorbaId().toString(); // keep all the // ids together. } if (annotation.getLinkCount() > 0) { Cache.log.warn("Ignoring " + annotation.getLinkCount() + "links added to AlignmentAnnotation."); } if (annotation.getModifiable() == null || annotation.getModifiable().length() == 0) // TODO: USE VAMSAS // LIBRARY OBJECT // LOCK METHODS) { jan.editable = true; } try { if (annotation.getGroup() != null && annotation.getGroup().length() > 0) { jan.graphGroup = Integer.parseInt(annotation.getGroup()); // TODO: // group // similarly // named // annotation // together // ? } } catch (Exception e) { Cache.log.info( "UNIMPLEMENTED : Couldn't parse non-integer group value for setting graphGroup correctly."); } return jan; } return null; } /** * 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(MessageManager.getString( "error.invalid_vamsas_rangetype_cannot_resolve_lists")); } 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(MessageManager.getString( "error.invalid_vamsas_rangetype_cannot_resolve_lists")); } 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; } /** * * @param maprange * where the from range is the local mapped range, and the to range * is the 'mapped' range in the MapRangeType * @param default * unit for local * @param default * unit for mapped * @return MapList */ private jalview.util.MapList parsemapType(MapType maprange, int localu, int mappedu) { jalview.util.MapList ml = null; int[] localRange = getMapping(maprange.getLocal()); int[] mappedRange = getMapping(maprange.getMapped()); long lu = maprange.getLocal().hasUnit() ? maprange.getLocal().getUnit() : localu; long mu = maprange.getMapped().hasUnit() ? maprange.getMapped().getUnit() : mappedu; ml = new jalview.util.MapList(localRange, mappedRange, (int) lu, (int) mu); return ml; } /** * initialise a range type object from a set of start/end inclusive intervals * * @param mrt * @param ranges */ private void initRangeType(RangeType mrt, List ranges) { for (int[] range : ranges) { Seg vSeg = new Seg(); vSeg.setStart(range[0]); vSeg.setEnd(range[1]); mrt.addSeg(vSeg); } } /** * initialise a MapType object from a MapList object. * * @param maprange * @param ml * @param setUnits */ private void initMapType(MapType maprange, jalview.util.MapList ml, boolean setUnits) { maprange.setLocal(new Local()); maprange.setMapped(new Mapped()); initRangeType(maprange.getLocal(), ml.getFromRanges()); initRangeType(maprange.getMapped(), ml.getToRanges()); if (setUnits) { maprange.getLocal().setUnit(ml.getFromRatio()); maprange.getLocal().setUnit(ml.getToRatio()); } } /* * 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(), 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 java.util.Date()); entry.setUser(this.provEntry.getUser()); return entry; } Provenance dummyProvenance(String action) { Provenance prov = new Provenance(); prov.addEntry(dummyPEntry(action)); return prov; } Entry addProvenance(Provenance p, String action) { Entry dentry = dummyPEntry(action); p.addEntry(dentry); return dentry; } public Entry getProvEntry() { return provEntry; } public IClientDocument getClientDocument() { return cdoc; } public IdentityHashMap getJvObjectBinding() { return jv2vobj; } public Hashtable getVamsasObjectBinding() { return vobj2jv; } public void storeSequenceMappings(AlignmentViewport viewport, String title) throws Exception { AlignmentViewport av = viewport; try { jalview.datamodel.AlignmentI jal = av.getAlignment(); // ///////////////////////////////////////// // SAVE THE DATASET DataSet dataset = null; if (jal.getDataset() == null) { Cache.log.warn("Creating new dataset for an alignment."); jal.setDataset(null); } dataset = (DataSet) ((Alignment) getjv2vObj( viewport.getSequenceSetId())).getV_parent(); // jal.getDataset()); if (dataset == null) { dataset = (DataSet) getjv2vObj(jal.getDataset()); Cache.log.error( "Can't find the correct dataset for the alignment in this view. Creating new one."); } // Store any sequence mappings. List cframes = av.getAlignment().getCodonFrames(); if (cframes != null) { for (AlignedCodonFrame acf : cframes) { if (acf.getdnaSeqs() != null && acf.getdnaSeqs().length > 0) { jalview.datamodel.SequenceI[] dmps = acf.getdnaSeqs(); jalview.datamodel.Mapping[] mps = acf.getProtMappings(); for (int smp = 0; smp < mps.length; smp++) { uk.ac.vamsas.objects.core.SequenceType mfrom = (SequenceType) getjv2vObj( dmps[smp]); if (mfrom != null) { new jalview.io.vamsas.Sequencemapping(this, mps[smp], mfrom, dataset); } else { Cache.log.warn( "NO Vamsas Binding for local sequence! NOT CREATING MAPPING FOR " + dmps[smp].getDisplayId(true) + " to " + mps[smp].getTo().getName()); } } } } } } catch (Exception e) { throw new Exception(MessageManager.formatMessage( "exception.couldnt_store_sequence_mappings", new String[] { title }), e); } } public void clearSkipList() { if (skipList != null) { skipList.clear(); } } /** * @return the skipList */ public Hashtable getSkipList() { return skipList; } /** * @param skipList * the skipList to set */ public void setSkipList(Hashtable skipList) { this.skipList = skipList; } /** * registry for datastoreItems */ DatastoreRegistry dsReg = new DatastoreRegistry(); public DatastoreRegistry getDatastoreRegisty() { if (dsReg == null) { dsReg = new DatastoreRegistry(); } return dsReg; } }