X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FVamsasAppDatastore.java;h=6e0dab0263a285d0d4d13d068d0c5ac5e1748e9c;hb=a1984b1c8c273ed33c7ce9283039f4027dcae2de;hp=8f26680543c8e6c94208e5fa4c2f3297ebb8bf80;hpb=a1704bd1ca00e4c24f91a1d0cd4f502c84d0a9f2;p=jalview.git diff --git a/src/jalview/io/VamsasAppDatastore.java b/src/jalview/io/VamsasAppDatastore.java index 8f26680..6e0dab0 100644 --- a/src/jalview/io/VamsasAppDatastore.java +++ b/src/jalview/io/VamsasAppDatastore.java @@ -1,56 +1,89 @@ /* - * 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 + * 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. - * - * 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. - * + * + * 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 this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + * 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.AlignmentI; -import jalview.datamodel.AlignmentView; -import jalview.datamodel.DBRefEntry; import jalview.datamodel.GraphLine; -import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceI; import jalview.gui.AlignFrame; import jalview.gui.AlignViewport; import jalview.gui.Desktop; import jalview.gui.TreePanel; +import jalview.io.vamsas.Datasetsequence; import jalview.io.vamsas.DatastoreItem; +import jalview.io.vamsas.DatastoreRegistry; import jalview.io.vamsas.Rangetype; +import jalview.project.Jalview2XML; +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 uk.ac.vamsas.client.*; -import uk.ac.vamsas.objects.core.*; +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 { /** @@ -59,26 +92,43 @@ 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, @@ -88,7 +138,24 @@ public class VamsasAppDatastore this.vobj2jv = vobj2jv; this.jv2vobj = jv2vobj; this.provEntry = provEntry; - this.alignRDHash = alignRDHash; + 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]); + } } /** @@ -100,10 +167,41 @@ public class VamsasAppDatastore { return cdoc.getObject((VorbaId) jv2vobj.get(jvobj)); } - if (Cache.log.isDebugEnabled()) + // 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.warn( + "IMPLEMENTATION ERROR?: Unexpected mapping for unmapped jalview string object content:" + + seqsetidobj + " to object " + obj); + } + return obj; + } + else + { + Cache.warn("Unexpected mapping for Jalview String Object ID " + + seqsetidobj + " to another jalview dataset object " + + seqsetidobj); + } + } + } + + if (Cache.isDebugEnabled()) { - Cache.log.debug("Returning null VorbaID binding for jalview object " - + jvobj); + Cache.debug( + "Returning null VorbaID binding for jalview object " + jvobj); } return null; } @@ -119,8 +217,8 @@ public class VamsasAppDatastore if (id == null) { id = cdoc.registerObject(vobj); - Cache.log - .debug("Registering new object and returning null for getvObj2jv"); + Cache.debug( + "Registering new object and returning null for getvObj2jv"); return null; } if (vobj2jv.containsKey(vobj.getVorbaId())) @@ -139,36 +237,38 @@ public class VamsasAppDatastore if (id == null || vobj.getVorbaId() == null || cdoc.getObject(id) != vobj) { - Cache.log.error("Failed to get id for " + Cache.error("Failed to get id for " + (vobj.isRegisterable() ? "registerable" - : "unregisterable") + " object " + vobj); + : "unregisterable") + + " object " + vobj); } } if (vobj2jv.containsKey(vobj.getVorbaId()) && !((VorbaId) vobj2jv.get(vobj.getVorbaId())).equals(jvobj)) { - Cache.log.debug( + Cache.debug( "Warning? Overwriting existing vamsas id binding for " - + vobj.getVorbaId(), new Exception( - "Overwriting vamsas id binding.")); + + 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( + Cache.debug( "Warning? Overwriting existing jalview object binding for " - + jvobj, new Exception( - "Overwriting jalview object binding.")); + + jvobj, + new Exception("Overwriting jalview object binding.")); } /* - * Cache.log.error("Attempt to make conflicting object binding! "+vobj+" id " + * Cache.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); + Cache.debug("Binding " + vobj.getVorbaId() + " to " + jvobj); vobj2jv.put(vobj.getVorbaId(), jvobj); // JBPNote - better implementing a hybrid invertible hash. jv2vobj.put(jvobj, vobj.getVorbaId()); @@ -181,29 +281,47 @@ 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."); + Cache.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(); } - dataset = (DataSet) getjv2vObj(jal.getDataset()); + 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]); @@ -217,12 +335,11 @@ 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."); - // This occurs because the dataset for the alignment we are - // trying to + "IMPLEMENTATION ERROR: Cannot map an alignment of sequences from different datasets into a single alignment in the vamsas document."); } } } @@ -232,11 +349,13 @@ public class VamsasAppDatastore if (dataset == null) { + Cache.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); nw = true; @@ -247,12 +366,12 @@ 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 + 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++) @@ -261,122 +380,36 @@ public class VamsasAppDatastore // referenced // sequences // to dataset. - sequence = (Sequence) getjv2vObj(sq); - if (sequence == null) + Datasetsequence dssync = new jalview.io.vamsas.Datasetsequence(this, + sq, dict, dataset); + sequence = (Sequence) dssync.getVobj(); + if (dssync.getModified()) { - sequence = new Sequence(); - bindjvvobj(sq, sequence); - sq.setVamsasId(sequence.getVorbaId().getId()); - sequence.setSequence(sq.getSequenceAsString()); - sequence.setDictionary(dict); - sequence.setName(sq.getName()); - sequence.setStart(sq.getStart()); - sequence.setEnd(sq.getEnd()); - sequence.setDescription(sq.getDescription()); - dataset.addSequence(sequence); - dssmods.addElement(dssmods); - } - else - { - boolean dsmod = false; - // verify and update principal attributes. - if (sq.getDescription()!=null && (sequence.getDescription()==null || !sequence.getDescription().equals(sq.getDescription()))) - { - sequence.setDescription(sq.getDescription()); - dsmod = true; - } - if (sequence.getSequence()==null || !sequence.getSequence().equals(sq.getSequenceAsString())) - { - if (sequence.getStart()!=sq.getStart() || sequence.getEnd()!=sq.getEnd()) - { - // update modified sequence. - sequence.setSequence(sq.getSequenceAsString()); - sequence.setStart(sq.getStart()); - sequence.setEnd(sq.getEnd()); - dsmod = true; - } - } - if (!dict.equals(sequence.getDictionary())) - { - sequence.setDictionary(dict); - dsmod = true; - } - if (!sequence.getName().equals(sq.getName())) - { - sequence.setName(sq.getName()); - dsmod = true; - } - if (dsmod) - { - dssmods.addElement(sequence); - } - } - // add or update any new features/references on dataset sequence - if (sq.getSequenceFeatures() != null) - { - int sfSize = sq.getSequenceFeatures().length; - - for (int sf = 0; sf < sfSize; sf++) - { - // TODO: update/modifiable synchronizer - 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) - { - 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); - } - + dssmods.addElement(sequence); } + ; } - if (dssmods.size()>0) + if (dssmods.size() > 0) { if (!nw) { - Entry pentry = this.addProvenance(dataset.getProvenance(), "updated sequences"); - // pentry.addInput(vInput); could write in which sequences were modified. + 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.getSequenceSetId()); // this is so we can get - // the alignviewport - // back if (alignment == null) { alignment = new Alignment(); @@ -399,49 +432,86 @@ public class VamsasAppDatastore alignment.setGapChar(String.valueOf(av.getGapCharacter())); for (int i = 0; i < jal.getHeight(); i++) { - syncToAlignmentSequence(jal.getSequenceAt(i), alignment); + syncToAlignmentSequence(jal.getSequenceAt(i), alignment, null); } - alignRDHash.put(av.getSequenceSetId(),av.getUndoRedoHash()); + alignRDHash.put(av.getSequenceSetId(), av.getUndoRedoHash()); } else { - boolean alismod = av.isUndoRedoHashModified((long[]) alignRDHash.get(av.getSequenceSetId())); + // 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) + 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); + 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 { + 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 + addProvenance(alignment.getProvenance(), "Attributes Edited"); // TODO: + // insert + // something + // sensible + // here + // again } } - System.out.println("update alignment in document."); + if (alismod) + { + System.out.println("update alignment in document."); + } + else + { + System.out.println("alignment in document left unchanged."); + } } else { - System.out - .println("update edited alignment to new alignment in document."); + // 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++) + for (int i = 0, iSize = alignment + .getAlignmentSequenceCount(); i < iSize; i++) { AlignmentSequence valseq; - SequenceI alseq = (SequenceI) getvObj2jv(valseq = alignment - .getAlignmentSequence(i)); + SequenceI alseq = (SequenceI) getvObj2jv( + valseq = alignment.getAlignmentSequence(i)); if (alseq != null && alseq.getSequenceFeatures() != null) { /* @@ -452,18 +522,18 @@ 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); } } } */ } } @@ -483,6 +553,13 @@ public class VamsasAppDatastore { continue; } + if (aa[i].groupRef != null) + { + // TODO: store any group associated annotation references + Cache.warn( + "Group associated sequence annotation is not stored in VAMSAS document."); + continue; + } if (aa[i].sequenceRef != null) { // Deal with sequence associated annotation @@ -495,12 +572,8 @@ public class VamsasAppDatastore else { // first find the alignment sequence to associate this with. - SequenceI jvalsq = null; - Enumeration jval = av.getAlignment().getSequences() - .elements(); - while (jval.hasMoreElements()) + for (SequenceI jvalsq : av.getAlignment().getSequences()) { - jvalsq = (SequenceI) jval.nextElement(); // saveDatasetSequenceAnnotation(AlSeqMaps,(uk.ac.vamsas.objects.core.Sequence) // sref, aa[i]); if (jvalsq.getDatasetSequence() == aa[i].sequenceRef) @@ -517,7 +590,8 @@ public class VamsasAppDatastore else { // add Alignment Annotation - uk.ac.vamsas.objects.core.AlignmentAnnotation an = (uk.ac.vamsas.objects.core.AlignmentAnnotation) getjv2vObj(aa[i]); + 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(); @@ -525,8 +599,8 @@ 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()); @@ -540,7 +614,7 @@ public class VamsasAppDatastore if (aa[i].graph != AlignmentAnnotation.NO_GRAPH) { an.setGroup(Integer.toString(aa[i].graphGroup)); // // JBPNote - // - + // - // originally we // were going to // store @@ -566,24 +640,26 @@ public class VamsasAppDatastore ae = new AnnotationElement(); ae.setDescription(aa[i].annotations[a].description); ae.addGlyph(new Glyph()); - ae.getGlyph(0).setContent( - aa[i].annotations[a].displayCharacter); // assume + ae.getGlyph(0) + .setContent(aa[i].annotations[a].displayCharacter); // assume // jax-b // takes // care // 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); @@ -596,33 +672,41 @@ 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 - .info("update alignment sequence annotation. not yet implemented."); + Cache.info( + "update alignment sequence annotation. not yet implemented."); } else { // verify annotation - update (perhaps) - Cache.log - .info("updated alignment sequence annotation added."); + Cache.info( + "updated alignment sequence annotation added."); } } } @@ -645,7 +729,8 @@ 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); @@ -660,27 +745,129 @@ 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(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. + * 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) + Alignment alignment, Vector unbounddocseq) { boolean modal = false; // todo: islocked method here - boolean up2doc=false; + boolean up2doc = false; AlignmentSequence alseq = (AlignmentSequence) getjv2vObj(jvalsq); - if (alseq==null) + if (alseq == null) { alseq = new AlignmentSequence(); up2doc = true; } - // boolean locked = (alignment.getModifiable()==null || alignment.getModifiable().length()>0); + 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())) { @@ -694,53 +881,57 @@ public class VamsasAppDatastore modal = true; alseq.setName(jvalsq.getName()); } - if (jvalsq.getDescription()!=null && (alseq.getDescription()==null || !jvalsq.getDescription().equals(alseq.getDescription()))) + 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()); + Cache.warn( + "Serious Implementation error - Unbound dataset sequence in alignment: " + + jvalsq.getDatasetSequence()); } - alseq.setRefid(getjv2vObj(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 + * 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) - + private boolean syncFromAlignmentSequence(AlignmentSequence valseq, + char valGapchar, char gapChar, List dsseqs) + { boolean modal = false; // todo: islocked method here - boolean upFromdoc=false; + boolean upFromdoc = false; jalview.datamodel.SequenceI alseq = (SequenceI) getvObj2jv(valseq); - if (alseq==null) + if (alseq == null) { upFromdoc = true; } if (alseq != null) { - // boolean locked = (alignment.getModifiable()==null || alignment.getModifiable().length()>0); + // boolean locked = (alignment.getModifiable()==null || + // alignment.getModifiable().length()>0); // TODO: VAMSAS: translate lowercase symbols to annotation ? - if (upFromdoc || !valseq.getSequence().equals(alseq.getSequenceAsString())) + if (upFromdoc + || !valseq.getSequence().equals(alseq.getSequenceAsString())) { // this might go *horribly* wrong - alseq.setSequence(new String(valseq.getSequence()).replace( - valGapchar, gapChar)); + alseq.setSequence(new String(valseq.getSequence()) + .replace(valGapchar, gapChar)); alseq.setStart((int) valseq.getStart()); alseq.setEnd((int) valseq.getEnd()); modal = true; @@ -750,17 +941,16 @@ public class VamsasAppDatastore modal = true; alseq.setName(valseq.getName()); } - if (alseq.getDescription()==null - || (valseq.getDescription()==null - || alseq.getDescription().equals(valseq.getDescription()))) + if (alseq.getDescription() == null || (valseq.getDescription() != null + && !alseq.getDescription().equals(valseq.getDescription()))) { alseq.setDescription(valseq.getDescription()); modal = true; } - if (modal && Cache.log.isDebugEnabled()) + if (modal && Cache.isDebugEnabled()) { - Cache.log.debug("Updating apparently edited sequence " - + alseq.getName()); + Cache.debug( + "Updating apparently edited sequence " + alseq.getName()); } } else @@ -772,20 +962,32 @@ public class VamsasAppDatastore Vobject datsetseq = (Vobject) valseq.getRefid(); if (datsetseq != null) { - alseq - .setDatasetSequence((SequenceI) getvObj2jv(datsetseq)); // exceptions - // if - // AlignemntSequence - // reference - // isn't - // a - // simple - // SequenceI + 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 " + Cache.error( + "Invalid dataset sequence id (null) for alignment sequence " + valseq.getVorbaId()); } bindjvvobj(alseq, valseq); @@ -799,8 +1001,7 @@ public class VamsasAppDatastore { modal = true; } - alseq - .setDatasetSequence((SequenceI) getvObj2jv(datsetseq)); // exceptions + alseq.setDatasetSequence((SequenceI) getvObj2jv(datsetseq)); // exceptions } return upFromdoc || modal; } @@ -856,10 +1057,10 @@ 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.setContent(String - .valueOf(alan.annotations[a].secondaryStructure)); + 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); @@ -874,7 +1075,8 @@ public class VamsasAppDatastore // 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); + uk.ac.vamsas.objects.core.DataSetAnnotations an = (uk.ac.vamsas.objects.core.DataSetAnnotations) getjv2vObj( + alan); int[] gapMap = getGapMap(AlSeqMaps, alan); if (an == null) { @@ -893,11 +1095,15 @@ 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); @@ -906,7 +1112,7 @@ 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."); @@ -914,8 +1120,8 @@ public class VamsasAppDatastore else { // verify existing alignment sequence annotation is up to date - System.out - .println("make new alignment dataset sequence annotation if modification has happened."); + System.out.println( + "make new alignment dataset sequence annotation if modification has happened."); } } @@ -948,7 +1154,8 @@ public class VamsasAppDatastore // 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); + uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation an = (uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation) getjv2vObj( + alan); int[] gapMap = getGapMap(AlSeqMaps, alan); if (an == null) { @@ -960,7 +1167,7 @@ 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 @@ -974,7 +1181,7 @@ 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."); @@ -982,114 +1189,59 @@ public class VamsasAppDatastore else { // verify existing alignment sequence annotation is up to date - System.out - .println("make new alignment sequence annotation if modification has happened."); + 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) + 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. + 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. } } - private Property newProperty(String name, String type, String content) - { - Property vProperty = new Property(); - vProperty.setName(name); - if (type != null) - { - vProperty.setType(type); - } - else - { - vProperty.setType("String"); - } - vProperty.setContent(content); - return vProperty; - } - - /** - * correctly create a RangeAnnotation from a jalview sequence feature - * - * @param dsa - * (typically DataSetAnnotations or AlignmentSequenceAnnotation) - * @param feature - * (the feature to be mapped from) - * @return - */ - private RangeAnnotation getDSAnnotationFromJalview(RangeAnnotation dsa, - SequenceFeature feature) - { - dsa.setType(feature.getType()); - Seg vSeg = new Seg(); - vSeg.setStart(feature.getBegin()); - vSeg.setEnd(feature.getEnd()); - vSeg.setInclusive(true); - dsa.addSeg(vSeg); - dsa.setDescription(feature.getDescription()); - dsa.setStatus(feature.getStatus()); - if (feature.links != null && feature.links.size() > 0) - { - for (int i = 0, iSize = feature.links.size(); i < iSize; i++) - { - String link = (String) feature.links.elementAt(i); - int sep = link.indexOf('|'); - if (sep > -1) - { - Link vLink = new Link(); - if (sep > 0) - { - vLink.setContent(link.substring(0, sep - 1)); - } - else - { - vLink.setContent(""); - } - vLink.setHref(link.substring(sep + 1)); // TODO: validate href. - dsa.addLink(vLink); - } - } - } - dsa.setGroup(feature.getFeatureGroup()); - return dsa; - } - /** * 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 + { + Jalview2XML jxml = new 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. + Cache.error( + "Couldn't update jalview client application data. Giving up - local settings probably lost.", + e); + } + } + else + { + Cache.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(); @@ -1173,18 +1610,19 @@ public class VamsasAppDatastore // ///LOAD DATASET DataSet dataset = root.getDataSet(_ds); int i, iSize = dataset.getSequenceCount(); - Vector dsseqs; - jalview.datamodel.Alignment jdataset = (jalview.datamodel.Alignment) getvObj2jv(dataset); + 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"); + Cache.debug("Initialising new jalview dataset fields"); newds = true; dsseqs = new Vector(); } else { - Cache.log.debug("Update jalview dataset from vamsas."); + Cache.debug("Update jalview dataset from vamsas."); jremain = jdataset.getHeight(); dsseqs = jdataset.getSequences(); } @@ -1195,25 +1633,12 @@ 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) @@ -1233,45 +1658,43 @@ public class VamsasAppDatastore SequenceI[] seqs = new SequenceI[dsseqs.size()]; for (i = 0, iSize = dsseqs.size(); i < iSize; i++) { - seqs[i] = (SequenceI) dsseqs.elementAt(i); - dsseqs.setElementAt(null, i); + seqs[i] = dsseqs.get(i); + dsseqs.set(i, null); } jdataset = new jalview.datamodel.Alignment(seqs); - Cache.log.debug("New vamsas dataset imported into jalview."); + Cache.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++) + 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 + 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()); + Cache.warn( + "Couldn't resolve jalview sequenceI for dataset object reference " + + ((Vobject) dataset + .getDataSetAnnotations(dsa) + .getSeqRef(0)).getVorbaId() + .getId()); } else { if (dseta.getAnnotationElementCount() == 0) { - jalview.datamodel.SequenceFeature sf = (jalview.datamodel.SequenceFeature) getvObj2jv(dseta); - if (sf == null) - { - dsSeq - .addSequenceFeature(sf = getJalviewSeqFeature(dseta)); - bindjvvobj(sf, dseta); - } + new jalview.io.vamsas.Sequencefeature(this, dseta, dsSeq); + } else { @@ -1280,34 +1703,44 @@ public class VamsasAppDatastore // 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."); + Cache.warn( + "Ignoring dataset annotation with annotationElements. Not yet supported in jalview."); } } } + else + { + Cache.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++) + for (int al = 0, nal = dataset + .getAlignmentCount(); al < nal; al++) { uk.ac.vamsas.objects.core.Alignment alignment = dataset .getAlignment(al); - AlignViewport av=findViewport(alignment); - + // TODO check this handles multiple views properly + AlignmentViewport 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 @@ -1321,10 +1754,12 @@ public class VamsasAppDatastore 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) + 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; @@ -1335,42 +1770,44 @@ public class VamsasAppDatastore .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 + 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. + // 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"); + Cache.info( + "UNIMPLEMENTED: not recovering user modifiable sequence alignment annotation"); // TODO: should at least replace with new one - otherwise // things will break // basically do this: @@ -1389,21 +1826,22 @@ public class VamsasAppDatastore SequenceI[] seqs = new SequenceI[dsseqs.size()]; for (i = 0, iSize = dsseqs.size(); i < iSize; i++) { - seqs[i] = (SequenceI) dsseqs.elementAt(i); - dsseqs.setElementAt(null, i); + seqs[i] = dsseqs.get(i); + dsseqs.set(i, null); } jal = new jalview.datamodel.Alignment(seqs); - Cache.log.debug("New vamsas alignment imported into jalview " + Cache.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++) + for (int an = 0, anSize = newasAnnots + .size(); an < anSize; an++) { - jal.addAnnotation((AlignmentAnnotation) newasAnnots - .elementAt(an)); + jal.addAnnotation( + (AlignmentAnnotation) newasAnnots.elementAt(an)); // TODO: check if anything has to be done - like calling // adjustForAlignment or something. newasAnnots.setElementAt(null, an); @@ -1420,7 +1858,8 @@ public class VamsasAppDatastore for (int j = 0; j < an.length; j++) { - jalview.datamodel.AlignmentAnnotation jan = (jalview.datamodel.AlignmentAnnotation) getvObj2jv(an[j]); + jalview.datamodel.AlignmentAnnotation jan = (jalview.datamodel.AlignmentAnnotation) getvObj2jv( + an[j]); if (jan != null) { // update or stay the same. @@ -1430,16 +1869,16 @@ public class VamsasAppDatastore // 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."); + Cache.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. - Cache.log - .info("NOT IMPLEMENTED - Recovering user-modifiable annotation - yet..."); + Cache.info( + "NOT IMPLEMENTED - Recovering user-modifiable annotation - yet..."); } // TODO: compare annotation element rows // TODO: compare props. @@ -1447,30 +1886,36 @@ 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; } } } AlignFrame alignFrame; if (av == null) { - Cache.log.debug("New alignframe for alignment " + Cache.debug("New alignframe for alignment " + alignment.getVorbaId()); // /////////////////////////////// // 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++) + 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(); } @@ -1478,14 +1923,12 @@ public class VamsasAppDatastore } // TODO: automatically create meaningful title for a vamsas // alignment using its provenance. - if (Cache.log.isDebugEnabled()) + if (Cache.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.getSequenceSetId(), alignment); } @@ -1493,11 +1936,13 @@ public class VamsasAppDatastore { // 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 @@ -1511,27 +1956,28 @@ 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); + Cache.warn("update of labels failed.", e); } } else { - Cache.log.warn("Cannot create tree for tree "+t+" in document ("+alignment.getTree(t).getVorbaId()); + Cache.warn("Cannot create tree for tree " + t + + " in document (" + + alignment.getTree(t).getVorbaId()); } } @@ -1546,7 +1992,8 @@ public class VamsasAppDatastore DataSet dataset = root.getDataSet(_ds); if (dataset.getSequenceMappingCount() > 0) { - for (int sm = 0, smCount = dataset.getSequenceMappingCount(); sm < smCount; sm++) + for (int sm = 0, smCount = dataset + .getSequenceMappingCount(); sm < smCount; sm++) { Rangetype seqmap = new jalview.io.vamsas.Sequencemapping(this, dataset.getSequenceMapping(sm)); @@ -1554,46 +2001,21 @@ public class VamsasAppDatastore } } } + return newAlignmentViews.size(); } - public AlignViewport findViewport(Alignment alignment) + public AlignmentViewport findViewport(Alignment alignment) { - AlignViewport av=null; - AlignViewport[] avs = findViewportForSequenceSetId((String)getvObj2jv(alignment)); - if (avs!=null) + AlignmentViewport av = null; + AlignmentViewport[] avs = Desktop + .getViewports((String) getvObj2jv(alignment)); + if (avs != null) { av = avs[0]; } return av; } - private AlignViewport[] findViewportForSequenceSetId(String sequenceSetId) - { - Vector viewp = new Vector(); - if (Desktop.desktop != null) - { - javax.swing.JInternalFrame[] frames = Desktop.instance.getAllFrames(); - - for (int t = 0; t < frames.length; t++) - { - if (frames[t] instanceof AlignFrame) - { - if (((AlignFrame) frames[t]).getViewport().getSequenceSetId().equals(sequenceSetId)) - { - viewp.addElement(((AlignFrame) frames[t]).getViewport()); - } - } - } - if (viewp.size()>0) - { - AlignViewport[] vp = new AlignViewport[viewp.size()]; - viewp.copyInto(vp); - return vp; - } - } - return null; - } - // bitfields - should be a template in j1.5 private static int HASSECSTR = 0; @@ -1628,14 +2050,14 @@ public class VamsasAppDatastore // 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 }; + 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], + 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. + // same annotation row as positions. if (annotation.getAnnotationElementCount() > 0) { @@ -1643,14 +2065,14 @@ 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; 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); + Cache.debug("Ignoring duplicate annotation site at " + pos); continue; } if (anot[1 - row][pos] != null) @@ -1668,29 +2090,25 @@ 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) { 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)) + 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)) + else if (glyphs[g].getDict().equals( + uk.ac.vamsas.objects.utils.GlyphDictionary.PROTEIN_HD_HYDRO)) { - Cache.log.debug("ignoring hydrophobicity glyph marker."); + Cache.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. @@ -1706,8 +2124,9 @@ public class VamsasAppDatastore } else { - Cache.log.debug("IMPLEMENTATION TODO: Ignoring unknown glyph type " - + glyphs[g].getDict()); + Cache.debug( + "IMPLEMENTATION TODO: Ignoring unknown glyph type " + + glyphs[g].getDict()); } } } @@ -1717,28 +2136,28 @@ public class VamsasAppDatastore AeContent[HASVALS] = true; if (ae[aa].getValueCount() > 1) { - Cache.log.warn("ignoring additional " - + (ae[aa].getValueCount() - 1) - + "values in annotation element."); + Cache.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); + (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 { - Cache.log.warn("Ignoring out of bound annotation element " + aa + Cache.warn("Ignoring out of bound annotation element " + aa + " in " + annotation.getVorbaId().getId()); } } @@ -1752,7 +2171,7 @@ 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; } } @@ -1765,15 +2184,13 @@ public class VamsasAppDatastore anot[1][i].description = anot[1][i].description + " (after)"; } } - return new Object[] - { AeContent, rangeMap, anot[0], anot[1] }; + 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 new Object[] { AeContent, rangeMap, anot[0], anot[1] }; } // return null; } @@ -1804,47 +2221,54 @@ 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 { - val = new Float(props[p].getContent()); - }catch (Exception e) + Float val = null; + try { - Cache.log.warn("Failed to parse threshold property"); - } - if (val!=null) - if (gl==null) + val = Float.valueOf(props[p].getContent()); + } catch (Exception e) { - gl = new GraphLine(val.floatValue(), "", java.awt.Color.black); - } else + Cache.warn("Failed to parse threshold property"); + } + if (val != null) { - gl.value = val.floatValue(); + 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(); } } @@ -1864,14 +2288,14 @@ public class VamsasAppDatastore } if (parsedRangeAnnotation == null) { - Cache.log - .debug("Inserting empty annotation row elements for a whole-alignment annotation."); + Cache.debug( + "Inserting empty annotation row elements for a whole-alignment annotation."); } else { if (parsedRangeAnnotation[3] != null) { - Cache.log.warn("Ignoring 'After' annotation row in " + Cache.warn("Ignoring 'After' annotation row in " + annotation.getVorbaId()); } jalview.datamodel.Annotation[] arow = (jalview.datamodel.Annotation[]) parsedRangeAnnotation[2]; @@ -1880,17 +2304,21 @@ 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. @@ -1950,17 +2378,20 @@ 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); + 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 + ""; - } + } } } } @@ -1969,22 +2400,28 @@ 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() + Cache.warn("Ignoring " + annotation.getLinkCount() + "links added to AlignmentAnnotation."); } - if (annotation.getModifiable() == null || annotation.getModifiable().length()==0) // 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; } @@ -1993,12 +2430,18 @@ public class VamsasAppDatastore if (annotation.getGroup() != null && annotation.getGroup().length() > 0) { - jan.graphGroup = Integer.parseInt(annotation.getGroup()); // TODO: group similarly named annotation together ? + 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."); + Cache.info( + "UNIMPLEMENTED : Couldn't parse non-integer group value for setting graphGroup correctly."); } return jan; @@ -2007,23 +2450,6 @@ 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 @@ -2039,8 +2465,8 @@ public class VamsasAppDatastore int[] se = null; if (dseta.getSegCount() > 0 && dseta.getPosCount() > 0) { - throw new Error( - "Invalid vamsas RangeType - cannot resolve both lists of Pos and Seg from choice!"); + throw new Error(MessageManager.getString( + "error.invalid_vamsas_rangetype_cannot_resolve_lists")); } if (dseta.getSegCount() > 0) { @@ -2063,8 +2489,7 @@ public class VamsasAppDatastore // 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 }; + se = new int[] { pos, pos }; for (int p = 0, pSize = dseta.getPosCount(); p < pSize; p++) { pos = dseta.getPos(p).getI(); @@ -2098,8 +2523,8 @@ public class VamsasAppDatastore int[] se = null; if (dseta.getSegCount() > 0 && dseta.getPosCount() > 0) { - throw new Error( - "Invalid vamsas RangeType - cannot resolve both lists of Pos and Seg from choice!"); + throw new Error(MessageManager.getString( + "error.invalid_vamsas_rangetype_cannot_resolve_lists")); } if (dseta.getSegCount() > 0) { @@ -2109,7 +2534,7 @@ public class VamsasAppDatastore 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)); + posList.add(Integer.valueOf(p)); } } } @@ -2120,7 +2545,7 @@ public class VamsasAppDatastore for (int p = 0, pSize = dseta.getPosCount(); p < pSize; p++) { pos = dseta.getPos(p).getI(); - posList.add(new Integer(pos)); + posList.add(Integer.valueOf(pos)); } } } @@ -2156,8 +2581,9 @@ public class VamsasAppDatastore int[] mappedRange = getMapping(maprange.getMapped()); long lu = maprange.getLocal().hasUnit() ? maprange.getLocal().getUnit() : localu; - long mu = maprange.getMapped().hasUnit() ? maprange.getMapped() - .getUnit() : mappedu; + long mu = maprange.getMapped().hasUnit() + ? maprange.getMapped().getUnit() + : mappedu; ml = new jalview.util.MapList(localRange, mappedRange, (int) lu, (int) mu); return ml; @@ -2167,15 +2593,15 @@ public class VamsasAppDatastore * initialise a range type object from a set of start/end inclusive intervals * * @param mrt - * @param range + * @param ranges */ - private void initRangeType(RangeType mrt, int[] range) + private void initRangeType(RangeType mrt, List ranges) { - for (int i = 0; i < range.length; i += 2) + for (int[] range : ranges) { Seg vSeg = new Seg(); - vSeg.setStart(range[i]); - vSeg.setEnd(range[i + 1]); + vSeg.setStart(range[0]); + vSeg.setEnd(range[1]); mrt.addSeg(vSeg); } } @@ -2210,8 +2636,8 @@ 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()); @@ -2229,9 +2655,9 @@ public class VamsasAppDatastore 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()); + jprov.addEntry(prov.getEntry(i).getUser(), + prov.getEntry(i).getAction(), prov.getEntry(i).getDate(), + prov.getEntry(i).getId()); } return jprov; @@ -2298,10 +2724,10 @@ public class VamsasAppDatastore return vobj2jv; } - public void storeSequenceMappings(AlignViewport viewport, String title) - throws Exception + public void storeSequenceMappings(AlignmentViewport viewport, + String title) throws Exception { - AlignViewport av = viewport; + AlignmentViewport av = viewport; try { jalview.datamodel.AlignmentI jal = av.getAlignment(); @@ -2310,36 +2736,42 @@ public class VamsasAppDatastore DataSet dataset = null; if (jal.getDataset() == null) { - Cache.log.warn("Creating new dataset for an alignment."); + Cache.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.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) + List cframes = av.getAlignment().getCodonFrames(); + if (cframes != null) { - jalview.datamodel.AlignedCodonFrame[] cframes = av.getAlignment() - .getCodonFrames(); - for (int cf = 0; cf < cframes.length; cf++) + for (AlignedCodonFrame acf : cframes) { - if (cframes[cf].getdnaSeqs().length > 0) + if (acf.getdnaSeqs() != null && acf.getdnaSeqs().length > 0) { - jalview.datamodel.SequenceI[] dmps = cframes[cf].getdnaSeqs(); - jalview.datamodel.Mapping[] mps = cframes[cf].getProtMappings(); + 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]); + uk.ac.vamsas.objects.core.SequenceType mfrom = (SequenceType) getjv2vObj( + dmps[smp]); if (mfrom != null) { - new jalview.io.vamsas.Sequencemapping(this, mps[smp], - mfrom, dataset); + 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 " + Cache.warn( + "NO Vamsas Binding for local sequence! NOT CREATING MAPPING FOR " + + dmps[smp].getDisplayId(true) + " to " + mps[smp].getTo().getName()); } } @@ -2348,8 +2780,48 @@ public class VamsasAppDatastore } } catch (Exception e) { - throw new Exception("Couldn't store sequence mappings for " + title, - 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; } }