X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FVamsasAppDatastore.java;h=fb6465cb93baacac99bd34d2306381e82d7049d4;hb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;hp=379982ade00bff0302da64259e741719b9d55ef7;hpb=6ab5d6082ba24bfa949ee3a44b100d7fed92c9ad;p=jalview.git diff --git a/src/jalview/io/VamsasAppDatastore.java b/src/jalview/io/VamsasAppDatastore.java index 379982a..fb6465c 100644 --- a/src/jalview/io/VamsasAppDatastore.java +++ b/src/jalview/io/VamsasAppDatastore.java @@ -1,25 +1,24 @@ /* - * 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 + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7) + * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle + * + * 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 . */ - package jalview.io; import jalview.bin.Cache; +import jalview.datamodel.AlignedCodonFrame; import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.AlignmentI; import jalview.datamodel.AlignmentView; @@ -31,17 +30,25 @@ 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.UrlLink; +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.Vector; +import java.util.jar.JarInputStream; +import java.util.jar.JarOutputStream; import uk.ac.vamsas.client.*; import uk.ac.vamsas.objects.core.*; +import uk.ac.vamsas.objects.utils.Properties; /* * @@ -50,7 +57,9 @@ import uk.ac.vamsas.objects.core.*; * "org.exolab.castor.serializer", "org.apache.xml.serialize.XMLSerilazizer"); } * */ - +/* + * TODO: check/verify consistency for vamsas sync with group associated alignment annotation + */ public class VamsasAppDatastore { /** @@ -59,33 +68,70 @@ public class VamsasAppDatastore public static final String JALVIEW_ANNOTATION_ROW = "JalviewAnnotation"; /** - * AlignmentAnnotation property to indicate that values should not be interpolated + * 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 + * 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"; - + 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) + 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]); + } } /** @@ -97,6 +143,37 @@ public class VamsasAppDatastore { 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 " @@ -178,29 +255,47 @@ public class VamsasAppDatastore * alignViewport to be stored * @param aFtitle * title for alignment + * @return true if alignment associated with viewport was stored/synchronized + * to document */ - public void storeVAMSAS(AlignViewport av, String aFtitle) + 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 (jal.getDataset() == null) + if (jds == null) { Cache.log.warn("Creating new dataset for an alignment."); jal.setDataset(null); + jds = jal.getDataset(); } - dataset = (DataSet) getjv2vObj(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. - jalview.datamodel.SequenceI[] jdatset = jal.getDataset() - .getSequencesArray(); + // 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]); @@ -214,10 +309,11 @@ public class VamsasAppDatastore } else { - if (dataset != vbound.getV_parent()) + if (vbound.getV_parent() != null + && dataset != vbound.getV_parent()) { throw new Error( - "IMPLEMENTATION ERROR: Cannot map an alignment of sequences from datasets into the vamsas document."); + "IMPLEMENTATION ERROR: Cannot map an alignment of sequences from different datasets into a single alignment in the vamsas document."); // This occurs because the dataset for the alignment we are // trying to } @@ -229,13 +325,15 @@ public class VamsasAppDatastore 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(jal.getDataset(), dataset); + bindjvvobj(jds, dataset); dataset.setProvenance(dummyProvenance()); - dataset.getProvenance().addEntry(provEntry); + // dataset.getProvenance().addEntry(provEntry); nw = true; } else @@ -244,100 +342,53 @@ public class VamsasAppDatastore } // 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; + Vector dssmods = new Vector(); 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()); - sequence.setDescription(jal.getDataset().getSequenceAt(i) - .getDescription()); - dataset.addSequence(sequence); - } - else + Datasetsequence dssync = new jalview.io.vamsas.Datasetsequence( + this, sq, dict, dataset); + sequence = (Sequence) dssync.getVobj(); + if (dssync.getModified()) { - // verify principal attributes. and update any new - // features/references. - System.out.println("update dataset sequence object."); + dssmods.addElement(sequence); } - 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.addSeqRef(sequence); // we have just created this annotation - // - so safe to use this - 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) + ; + } + if (dssmods.size() > 0) + { + if (!nw) { - DBRefEntry[] entries = sq.getDBRef(); - jalview.datamodel.DBRefEntry dbentry; - for (int db = 0; db < entries.length; db++) - { - Rangetype dbr = new jalview.io.vamsas.Dbref(this, - dbentry = entries[db], sq, sequence); - } - + 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 (!av.getAlignment().isAligned()) - return; // TODO: trees could be written - but for the moment we just skip - - // //////////////////////////////////////////// - // Save the Alignments + if (alignmentWillBeSkipped(av)) + { + // TODO: trees could be written - but for the moment we just + addToSkipList(av); + // add to the JalviewXML skipList and .. + return false; + } - Alignment alignment = (Alignment) getjv2vObj(av); // this is so we can get - // the alignviewport - // back if (alignment == null) { alignment = new Alignment(); - bindjvvobj(av, alignment); + bindjvvobj(av.getSequenceSetId(), alignment); if (alignment.getProvenance() == null) { alignment.setProvenance(new Provenance()); @@ -354,37 +405,76 @@ public class VamsasAppDatastore 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()); - if (getjv2vObj(jal.getSequenceAt(i).getDatasetSequence()) == null) - { - Cache.log - .warn("Serious. Unbound dataset sequence in alignment: " - + jal.getSequenceAt(i).getDatasetSequence()); - } - alseq.setRefid(getjv2vObj(jal.getSequenceAt(i) - .getDatasetSequence())); - alignment.addAlignmentSequence(alseq); - bindjvvobj(jal.getSequenceAt(i), alseq); + 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. - if (alignment.getModifiable() == null) // TODO: USE VAMSAS LIBRARY - // OBJECT LOCK METHODS + // TODO: Use isLocked methods + if (alignment.getModifiable() == null + || alignment.getModifiable().length() == 0) + // && !alignment.isDependedOn()) { - System.out.println("update alignment in document."); + 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."); } @@ -406,18 +496,18 @@ public class VamsasAppDatastore * 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) { + * 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); } } - * } + * 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); } } } */ } } @@ -437,6 +527,13 @@ public class VamsasAppDatastore { 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 @@ -479,8 +576,8 @@ public class VamsasAppDatastore 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. + // rangeAnnotationType initer/updater that + // takes a set of int ranges. vSeg.setStart(1); vSeg.setInclusive(true); vSeg.setEnd(jal.getWidth()); @@ -494,7 +591,7 @@ public class VamsasAppDatastore if (aa[i].graph != AlignmentAnnotation.NO_GRAPH) { an.setGroup(Integer.toString(aa[i].graphGroup)); // // JBPNote - // - + // - // originally we // were going to // store @@ -528,16 +625,17 @@ public class VamsasAppDatastore // of // utf8 // translation - ae.addValue(aa[i].annotations[a].value); + 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)); + 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); @@ -550,23 +648,30 @@ public class VamsasAppDatastore // 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(newProperty(THRESHOLD, "float", ""+aa[i].threshold.value)); - if (aa[i].threshold.label!=null) - an.addProperty(newProperty(THRESHOLD+"Name", "string", ""+aa[i].threshold.label)); + 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) + // LOCK METHODS) { // verify annotation - update (perhaps) Cache.log @@ -599,7 +704,8 @@ public class VamsasAppDatastore { TreePanel tp = (TreePanel) frames[t]; - if (tp.getAlignment() == jal) + if (tp.getViewPort().getSequenceSetId() + .equals(av.getSequenceSetId())) { DatastoreItem vtree = new jalview.io.vamsas.Tree(this, tp, jal, alignment); @@ -614,8 +720,266 @@ public class VamsasAppDatastore 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(AlignViewport av) + { + return (!av.getAlignment().isAligned()); + } + + private void addToSkipList(AlignViewport 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, Vector 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, @@ -669,8 +1033,7 @@ public class VamsasAppDatastore { // 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.setDict(uk.ac.vamsas.objects.utils.GlyphDictionary.PROTEIN_SS_3STATE); ss.setContent(String .valueOf(alan.annotations[a].secondaryStructure)); ae.addGlyph(ss); @@ -706,11 +1069,13 @@ public class VamsasAppDatastore // the Jalview // specific // bits. - if (alan.getThreshold()!=null && alan.getThreshold().displayed) + if (alan.getThreshold() != null && alan.getThreshold().displayed) { - an.addProperty(newProperty(THRESHOLD, "float", ""+alan.getThreshold().value)); - if (alan.getThreshold().label!=null) - an.addProperty(newProperty(THRESHOLD+"Name", "string", ""+alan.getThreshold().label)); + 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); @@ -719,7 +1084,7 @@ public class VamsasAppDatastore { // update reference sequence Annotation if (an.getModifiable() == null) // TODO: USE VAMSAS LIBRARY OBJECT LOCK - // METHODS) + // METHODS) { // verify existing alignment sequence annotation is up to date System.out.println("update dataset sequence annotation."); @@ -773,7 +1138,7 @@ public class VamsasAppDatastore * something extracted from another program, etc) */ an.setType(JALVIEW_ANNOTATION_ROW); // TODO: better fix - // this rough guess ;) + // this rough guess ;) alsref.addAlignmentSequenceAnnotation(an); bindjvvobj(alan, an); // These properties are directly supported by the @@ -787,7 +1152,7 @@ public class VamsasAppDatastore { // update reference sequence Annotation if (an.getModifiable() == null) // TODO: USE VAMSAS LIBRARY OBJECT LOCK - // METHODS) + // METHODS) { // verify existing alignment sequence annotation is up to date System.out.println("update alignment sequence annotation."); @@ -803,104 +1168,49 @@ public class VamsasAppDatastore /** * set vamsas annotation object type from jalview annotation + * * @param an * @param alan */ - private void setAnnotationType(RangeAnnotation an, AlignmentAnnotation 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(true); + } + else { - ((AlignmentSequenceAnnotation)an).setGraph(false); + ((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(true); + } + else { - ((uk.ac.vamsas.objects.core.AlignmentAnnotation)an).setGraph(false); + ((uk.ac.vamsas.objects.core.AlignmentAnnotation) an) + .setGraph(false); } } switch (alan.graph) { - case AlignmentAnnotation.BAR_GRAPH: - an.addProperty(newProperty(DISCRETE_ANNOTATION, "boolean","true")); - break; - case AlignmentAnnotation.LINE_GRAPH: - an.addProperty(newProperty(CONTINUOUS_ANNOTATION, "boolean","true")); - break; - default: - // don't add any kind of discrete or continous property info. - } - } - - 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"); + 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. } - 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; } /** @@ -939,40 +1249,317 @@ public class VamsasAppDatastore */ private boolean isJalviewOnly(AlignmentAnnotation annotation) { - return annotation.label.equals("Quality") + return annotation.autoCalculated || annotation.label.equals("Quality") || annotation.label.equals("Conservation") || annotation.label.equals("Consensus"); } + boolean dojvsync = true; + + // boolean dojvsync = false; // disables Jalview AppData IO /** - * 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 + * list of alignment views created when updating Jalview from document. */ - public AlignFrame getAlignFrameFor(AlignViewport av) + private Vector newAlignmentViews = new Vector(); + + /** + * update local jalview view settings from the stored appdata (if any) + */ + public void updateJalviewFromAppdata() { - if (Desktop.desktop != null) + // recover any existing Jalview data from appdata + // TODO: recover any PDB files stored as attachments in the vamsas session + // and initialise the Jalview2XML.alreadyLoadedPDB hashtable with mappings + // to temp files. { - javax.swing.JInternalFrame[] frames = Desktop.instance.getAllFrames(); + final IClientAppdata cappdata = cdoc.getClientAppdata(); + if (cappdata != null) + { + if (cappdata.hasClientAppdata()) + { + // TODO: how to check version of Jalview client app data and whether + // it has been modified + // client data is shared over all app clients + try + { + jalview.gui.Jalview2XML fromxml = new jalview.gui.Jalview2XML(); + fromxml.attemptversion1parse = false; + fromxml.setUniqueSetSuffix(""); + fromxml.setObjectMappingTables(vobj2jv, jv2vobj); // mapKeysToString + // and + // mapValuesToString + fromxml.setSkipList(skipList); + jalview.util.jarInputStreamProvider jprovider = new jalview.util.jarInputStreamProvider() + { + + public String getFilename() + { + + // TODO Get the vamsas session ID here + return "Jalview Vamsas Document Client Data"; + } + + public JarInputStream getJarInputStream() throws IOException + { + jalview.bin.Cache.log + .debug("Returning client input stream for Jalview from Vamsas Document."); + return new JarInputStream(cappdata.getClientInputStream()); + } + }; + if (dojvsync) + { + fromxml.LoadJalviewAlign(jprovider); + } + } catch (Exception e) + { + + } catch (OutOfMemoryError e) + { - for (int t = 0; t < frames.length; t++) + } catch (Error e) + { + + } + } + } + if (cappdata.hasUserAppdata()) { - if (frames[t] instanceof AlignFrame) + // TODO: how to check version of Jalview user app data and whether it + // has been modified + // user data overrides data shared over all app clients ? + try { - if (((AlignFrame) frames[t]).getViewport() == av) + jalview.gui.Jalview2XML fromxml = new jalview.gui.Jalview2XML(); + fromxml.attemptversion1parse = false; + fromxml.setUniqueSetSuffix(""); + fromxml.setSkipList(skipList); + fromxml.setObjectMappingTables(mapKeysToString(vobj2jv), + mapValuesToString(jv2vobj)); + jalview.util.jarInputStreamProvider jarstream = new jalview.util.jarInputStreamProvider() { - return (AlignFrame) frames[t]; + + public String getFilename() + { + + // TODO Get the vamsas session ID here + return "Jalview Vamsas Document User Data"; + } + + public JarInputStream getJarInputStream() throws IOException + { + jalview.bin.Cache.log + .debug("Returning user input stream for Jalview from Vamsas Document."); + return new JarInputStream(cappdata.getUserInputStream()); + } + }; + if (dojvsync) + { + fromxml.LoadJalviewAlign(jarstream); } + } catch (Exception e) + { + + } catch (OutOfMemoryError e) + { + + } catch (Error e) + { + } } + } - return null; + flushAlignViewports(); } - public void updateToJalview() + /** + * remove any spurious views generated by document synchronization + */ + private void flushAlignViewports() + { + // remove any additional viewports originally recovered from the vamsas + // document. + // search for all alignframes containing viewports generated from document + // sync, + // and if any contain more than one view, then remove the one generated by + // document update. + AlignViewport views[], av = null; + AlignFrame af = null; + Iterator newviews = newAlignmentViews.iterator(); + while (newviews.hasNext()) + { + av = (AlignViewport) newviews.next(); + af = Desktop.getAlignFrameFor(av); + // TODO implement this : af.getNumberOfViews + String seqsetidobj = av.getSequenceSetId(); + views = Desktop.getViewports(seqsetidobj); + Cache.log.debug("Found " + + (views == null ? " no " : "" + views.length) + + " views for '" + av.getSequenceSetId() + "'"); + if (views.length > 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; + AlignedCodonFrame[] 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 && mappings.length > 0) + { + jalview.structure.StructureSelectionManager + .getStructureSelectionManager(Desktop.instance).addMappings(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) + { + throw new Error( + "IMPLEMENTATION ERROR: old jalview object is not bound ! (" + + oldjvobject + ")"); + } + 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(); @@ -1008,25 +1595,12 @@ public class VamsasAppDatastore 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 + jalview.io.vamsas.Datasetsequence dssync = new Datasetsequence( + this, vdseq); + + jalview.datamodel.SequenceI dsseq = (SequenceI) dssync.getJvobj(); + if (dssync.isAddfromdoc()) { - 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) @@ -1037,6 +1611,7 @@ public class VamsasAppDatastore new jalview.io.vamsas.Dbref(this, dbref[db], vdseq, dsseq); } + dsseq.updatePDBIds(); } } @@ -1064,7 +1639,7 @@ public class VamsasAppDatastore { SequenceI dsSeq = (SequenceI) getvObj2jv((Vobject) dseta .getSeqRef(0)); // TODO: deal with group dataset - // annotations + // annotations if (dsSeq == null) { jalview.bin.Cache.log @@ -1077,13 +1652,8 @@ public class VamsasAppDatastore { if (dseta.getAnnotationElementCount() == 0) { - jalview.datamodel.SequenceFeature sf = (jalview.datamodel.SequenceFeature) getvObj2jv(dseta); - if (sf == null) - { - dsSeq - .addSequenceFeature(sf = getJalviewSeqFeature(dseta)); - bindjvvobj(sf, dseta); - } + new jalview.io.vamsas.Sequencefeature(this, dseta, dsSeq); + } else { @@ -1097,6 +1667,11 @@ public class VamsasAppDatastore } } } + else + { + Cache.log + .warn("Ignoring multiply referenced dataset sequence annotation for binding to datsaet sequence features."); + } } } if (dataset.getAlignmentCount() > 0) @@ -1107,17 +1682,23 @@ public class VamsasAppDatastore { uk.ac.vamsas.objects.core.Alignment alignment = dataset .getAlignment(al); - AlignViewport av = (AlignViewport) getvObj2jv(alignment); + // TODO check this handles multiple views properly + AlignViewport av = findViewport(alignment); + jalview.datamodel.AlignmentI jal = null; if (av != null) { - jal = av.getAlignment(); + // 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 newal = (jal == null) ? true : false; + boolean refreshal = false; Vector newasAnnots = new Vector(); char gapChar = ' '; // default for new alignments read in from the - // document + // document if (jal != null) { dsseqs = jal.getSequences(); // for merge/update @@ -1131,51 +1712,14 @@ public class VamsasAppDatastore 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 + jalview.datamodel.Sequence alseq = (jalview.datamodel.Sequence) getvObj2jv(valseq); + if (syncFromAlignmentSequence(valseq, valGapchar, gapChar, + dsseqs) && alseq != null) { - 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); + // updated to sequence from the document + jremain--; + refreshal = true; } if (valseq.getAlignmentSequenceAnnotationCount() > 0) { @@ -1184,38 +1728,39 @@ public class VamsasAppDatastore 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 + // 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. + // 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) + // VAMSAS LIBRARY + // OBJECT LOCK + // METHODS) { Cache.log .info("UNIMPLEMENTED: not recovering user modifiable sequence alignment annotation"); @@ -1281,8 +1826,8 @@ public class VamsasAppDatastore 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) + // LIBRARY OBJECT LOCK + // METHODS) { // TODO: user defined annotation is totally mutable... - so // load it up or throw away if locally edited. @@ -1295,8 +1840,11 @@ public class VamsasAppDatastore 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; } } } @@ -1308,17 +1856,20 @@ public class VamsasAppDatastore // /////////////////////////////// // construct alignment view alignFrame = new AlignFrame(jal, AlignFrame.DEFAULT_WIDTH, - AlignFrame.DEFAULT_HEIGHT); + AlignFrame.DEFAULT_HEIGHT, alignment.getVorbaId() + .toString()); av = alignFrame.getViewport(); - String title = alignment.getProvenance().getEntry( - alignment.getProvenance().getEntryCount() - 1) + 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")) + if (alignment.getProperty(p).getName().equals("title")) { title = alignment.getProperty(p).getContent(); } @@ -1328,21 +1879,25 @@ public class VamsasAppDatastore // alignment using its provenance. if (Cache.log.isDebugEnabled()) { - title = title + "(" - + alignment.getVorbaId() + ")"; - + title = title + "(" + alignment.getVorbaId() + ")"; + } - jalview.gui.Desktop.addInternalFrame(alignFrame, title - , + jalview.gui.Desktop.addInternalFrame(alignFrame, title, AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); - bindjvvobj(av, alignment); + bindjvvobj(av.getSequenceSetId(), alignment); } else { // find the alignFrame for jal. // TODO: fix this so we retrieve the alignFrame handing av - // *directly* - alignFrame = getAlignFrameFor(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 // ///////////////////////////////////// @@ -1355,17 +1910,28 @@ public class VamsasAppDatastore 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); + { + tp = alignFrame.ShowNewickTree(vstree.getNewickTree(), + vstree.getTitle(), vstree.getInputData(), 600, + 500, t * 20 + 50, t * 20 + 50); + } - if (tp!=null) + 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()); + Cache.log.warn("Cannot create tree for tree " + t + + " in document (" + + alignment.getTree(t).getVorbaId()); } } @@ -1388,6 +1954,19 @@ public class VamsasAppDatastore } } } + return newAlignmentViews.size(); + } + + public AlignViewport findViewport(Alignment alignment) + { + AlignViewport av = null; + AlignViewport[] avs = Desktop + .getViewports((String) getvObj2jv(alignment)); + if (avs != null) + { + av = avs[0]; + } + return av; } // bitfields - should be a template in j1.5 @@ -1431,7 +2010,7 @@ public class VamsasAppDatastore { 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. + // same annotation row as positions. if (annotation.getAnnotationElementCount() > 0) { @@ -1439,7 +2018,7 @@ public class VamsasAppDatastore 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) + // (|seg.start-seg.end|+1) if (pos >= 0 && pos < rangeMap.length) { int row = ae[aa].getAfter() ? 1 : 0; @@ -1464,9 +2043,9 @@ public class VamsasAppDatastore } } String dc = null; // ae[aa].getDisplayCharacter()==null ? "dc" : - // ae[aa].getDisplayCharacter(); + // ae[aa].getDisplayCharacter(); String ss = null; // ae[aa].getSecondaryStructure()==null ? "ss" : - // ae[aa].getSecondaryStructure(); + // ae[aa].getSecondaryStructure(); java.awt.Color colour = null; if (ae[aa].getGlyphCount() > 0) { @@ -1475,16 +2054,14 @@ public class VamsasAppDatastore { if (glyphs[g] .getDict() - .equals( - uk.ac.vamsas.objects.utils.GlyphDictionary.PROTEIN_SS_3STATE)) + .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)) + .equals(uk.ac.vamsas.objects.utils.GlyphDictionary.PROTEIN_HD_HYDRO)) { Cache.log.debug("ignoring hydrophobicity glyph marker."); AeContent[HASHPHOB] = true; @@ -1502,8 +2079,9 @@ public class VamsasAppDatastore } else { - Cache.log.debug("IMPLEMENTATION TODO: Ignoring unknown glyph type " - + glyphs[g].getDict()); + Cache.log + .debug("IMPLEMENTATION TODO: Ignoring unknown glyph type " + + glyphs[g].getDict()); } } } @@ -1515,21 +2093,21 @@ public class VamsasAppDatastore { Cache.log.warn("ignoring additional " + (ae[aa].getValueCount() - 1) - + "values in annotation element."); + + " 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); + (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); + (dc != null) ? dc : "", desc, + (ss != null) ? ss.charAt(0) : ' ', val, colour); } } else @@ -1548,7 +2126,7 @@ public class VamsasAppDatastore anot[0][i] = anot[1][i]; anot[0][i].description = anot[0][i].description + " (after)"; AeContent[HASDESCSTR] = true; // we have valid description string - // data + // data anot[1][i] = null; } } @@ -1600,46 +2178,48 @@ public class VamsasAppDatastore 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 + 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(); + 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)) { + interp = false; + } + else if (props[p].getName().equalsIgnoreCase(CONTINUOUS_ANNOTATION)) + { type = AlignmentAnnotation.LINE_GRAPH; - } else if - (props[p].getName().equalsIgnoreCase(THRESHOLD)) + } + else if (props[p].getName().equalsIgnoreCase(THRESHOLD)) { - Float val=null; - try { + Float val = null; + try + { val = new Float(props[p].getContent()); - }catch (Exception e) + } 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(); - } + 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")) + else if (props[p].getName().equalsIgnoreCase(THRESHOLD + "Name")) { - if (gl==null) + if (gl == null) gl = new GraphLine(0, "", java.awt.Color.black); gl.label = props[p].getContent(); } @@ -1676,17 +2256,21 @@ public class VamsasAppDatastore // 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((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) + if (type == 0) { - type = jalview.datamodel.AlignmentAnnotation.BAR_GRAPH; // default type of value annotation + type = jalview.datamodel.AlignmentAnnotation.BAR_GRAPH; // default + // type of + // value + // annotation if (has[HASHPHOB]) { // no hints - so we ensure HPHOB display is like this. @@ -1746,17 +2330,19 @@ public class VamsasAppDatastore if (!has[HASDC]) { if (!interp) - { - if (arow[i].description!=null && arow[i].description.length()<3) + { + 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. + } + else + { + // mark the position as a point used for the interpolation. arow[i].displayCharacter = arow[i].value + ""; - } + } } } } @@ -1765,22 +2351,28 @@ public class VamsasAppDatastore } else { - if (annotation.getAnnotationElementCount()==0) + 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. + // 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) // TODO: USE VAMSAS LIBRARY OBJECT - // LOCK METHODS) + if (annotation.getModifiable() == null + || annotation.getModifiable().length() == 0) // TODO: USE VAMSAS + // LIBRARY OBJECT + // LOCK METHODS) { jan.editable = true; } @@ -1789,7 +2381,13 @@ public class VamsasAppDatastore if (annotation.getGroup() != null && annotation.getGroup().length() > 0) { - jan.graphGroup = Integer.parseInt(annotation.getGroup()); + jan.graphGroup = Integer.parseInt(annotation.getGroup()); // TODO: + // group + // similarly + // named + // annotation + // together + // ? } } catch (Exception e) { @@ -1803,23 +2401,6 @@ public class VamsasAppDatastore 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 @@ -1938,10 +2519,8 @@ public class VamsasAppDatastore * @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 + * @param default unit for local + * @param default unit for mapped * @return MapList */ private jalview.util.MapList parsemapType(MapType maprange, int localu, @@ -2006,8 +2585,8 @@ public class VamsasAppDatastore * * 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(); + * 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()); @@ -2067,9 +2646,11 @@ public class VamsasAppDatastore return prov; } - void addProvenance(Provenance p, String action) + Entry addProvenance(Provenance p, String action) { - p.addEntry(dummyPEntry(action)); + Entry dentry = dummyPEntry(action); + p.addEntry(dentry); + return dentry; } public Entry getProvEntry() @@ -2107,7 +2688,15 @@ public class VamsasAppDatastore Cache.log.warn("Creating new dataset for an alignment."); jal.setDataset(null); } - dataset = (DataSet) getjv2vObj(jal.getDataset()); + 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. if (av.getAlignment().getCodonFrames() != null && av.getAlignment().getCodonFrames().length > 0) @@ -2116,7 +2705,8 @@ public class VamsasAppDatastore .getCodonFrames(); for (int cf = 0; cf < cframes.length; cf++) { - if (cframes[cf].getdnaSeqs().length > 0) + if (cframes[cf].getdnaSeqs() != null + && cframes[cf].getdnaSeqs().length > 0) { jalview.datamodel.SequenceI[] dmps = cframes[cf].getdnaSeqs(); jalview.datamodel.Mapping[] mps = cframes[cf].getProtMappings(); @@ -2132,7 +2722,7 @@ public class VamsasAppDatastore { Cache.log .warn("NO Vamsas Binding for local sequence! NOT CREATING MAPPING FOR " - + mfrom.getName() + + dmps[smp].getDisplayId(true) + " to " + mps[smp].getTo().getName()); } @@ -2146,4 +2736,43 @@ public class VamsasAppDatastore 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; + } }