X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FVamsasAppDatastore.java;h=d5801296ed3a0df7b410c2dfda1cf89297bcd22b;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=82e9fbabad07e34b57dc342c0a3d5e67cf1245be;hpb=8edb7ea4228bb1c112dbaa4743af9f55755557a4;p=jalview.git diff --git a/src/jalview/io/VamsasAppDatastore.java b/src/jalview/io/VamsasAppDatastore.java index 82e9fba..d580129 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 2.9) + * Copyright (C) 2015 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.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.Set; 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 { /** @@ -72,14 +105,30 @@ public class VamsasAppDatastore 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, @@ -90,6 +139,23 @@ public class VamsasAppDatastore 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]); + } } /** @@ -101,6 +167,37 @@ 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 " @@ -149,10 +246,12 @@ public class VamsasAppDatastore if (vobj2jv.containsKey(vobj.getVorbaId()) && !((VorbaId) vobj2jv.get(vobj.getVorbaId())).equals(jvobj)) { - Cache.log.debug( - "Warning? Overwriting existing vamsas id binding for " - + vobj.getVorbaId(), new Exception( - "Overwriting vamsas id binding.")); + Cache.log + .debug("Warning? Overwriting existing vamsas id binding for " + + vobj.getVorbaId(), + new Exception( + MessageManager + .getString("exception.overwriting_vamsas_id_binding"))); } else if (jv2vobj.containsKey(jvobj) && !((VorbaId) jv2vobj.get(jvobj)).equals(vobj.getVorbaId())) @@ -179,32 +278,50 @@ public class VamsasAppDatastore * put the alignment viewed by AlignViewport into cdoc. * * @param av - * alignViewport to be stored + * alignViewport to be stored * @param aFtitle - * title for alignment + * 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]); @@ -218,10 +335,12 @@ 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."); + MessageManager + .getString("error.implementation_error_cannot_map_alignment_sequences")); // This occurs because the dataset for the alignment we are // trying to } @@ -233,11 +352,13 @@ 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); nw = true; @@ -248,7 +369,6 @@ 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 @@ -262,107 +382,14 @@ public class VamsasAppDatastore // 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(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) + Datasetsequence dssync = new jalview.io.vamsas.Datasetsequence( + this, sq, dict, dataset); + sequence = (Sequence) dssync.getVobj(); + if (dssync.getModified()) { - 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) { @@ -377,24 +404,13 @@ public class VamsasAppDatastore } // 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 - - Alignment alignment = (Alignment) getjv2vObj(av.getSequenceSetId()); // bind - // to - // the - // value - // used - // to - // associate - // different - // views - // to - // same - // alignment + if (alignmentWillBeSkipped(av)) + { + // TODO: trees could be written - but for the moment we just + addToSkipList(av); + // add to the JalviewXML skipList and .. + return false; + } if (alignment == null) { @@ -435,8 +451,8 @@ public class VamsasAppDatastore { boolean modified = false; // check existing sequences in local and in document. - Vector docseqs = new Vector(alignment - .getAlignmentSequenceAsReference()); + Vector docseqs = new Vector( + alignment.getAlignmentSequenceAsReference()); for (int i = 0; i < jal.getHeight(); i++) { modified |= syncToAlignmentSequence(jal.getSequenceAt(i), @@ -456,20 +472,20 @@ public class VamsasAppDatastore { // info in the undo addProvenance(alignment.getProvenance(), "Edited"); // TODO: - // insert - // something - // sensible - // here again + // insert + // something + // sensible + // here again } else { // info in the undo addProvenance(alignment.getProvenance(), "Attributes Edited"); // TODO: - // insert - // something - // sensible - // here - // again + // insert + // something + // sensible + // here + // again } } if (alismod) @@ -507,16 +523,17 @@ 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); + * 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); } } } */ } @@ -537,6 +554,13 @@ 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 @@ -549,12 +573,8 @@ 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) @@ -628,16 +648,17 @@ 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); @@ -657,12 +678,13 @@ public class VamsasAppDatastore 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)); + an.addProperty(Properties.newProperty(THRESHOLD, + Properties.FLOATTYPE, "" + aa[i].threshold.value)); if (aa[i].threshold.label != null) { - an.addProperty(newProperty(THRESHOLD + "Name", - "string", "" + aa[i].threshold.label)); + an.addProperty(Properties.newProperty(THRESHOLD + + "Name", Properties.STRINGTYPE, "" + + aa[i].threshold.label)); } } } @@ -705,7 +727,8 @@ 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); @@ -720,8 +743,32 @@ 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); } /** @@ -860,7 +907,7 @@ public class VamsasAppDatastore * creates/syncs the jvalsq from the alignment sequence */ private boolean syncFromAlignmentSequence(AlignmentSequence valseq, - char valGapchar, char gapChar, Vector dsseqs) + char valGapchar, char gapChar, List dsseqs) { boolean modal = false; @@ -893,8 +940,8 @@ public class VamsasAppDatastore alseq.setName(valseq.getName()); } if (alseq.getDescription() == null - || (valseq.getDescription() == null || alseq.getDescription() - .equals(valseq.getDescription()))) + || (valseq.getDescription() != null && !alseq + .getDescription().equals(valseq.getDescription()))) { alseq.setDescription(valseq.getDescription()); modal = true; @@ -908,13 +955,26 @@ public class VamsasAppDatastore else { alseq = new jalview.datamodel.Sequence(valseq.getName(), valseq - .getSequence().replace(valGapchar, gapChar), (int) valseq - .getStart(), (int) valseq.getEnd()); + .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 @@ -996,8 +1056,7 @@ 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); @@ -1035,11 +1094,13 @@ public class VamsasAppDatastore // bits. if (alan.getThreshold() != null && alan.getThreshold().displayed) { - an.addProperty(newProperty(THRESHOLD, "float", "" - + alan.getThreshold().value)); + an.addProperty(Properties.newProperty(THRESHOLD, + Properties.FLOATTYPE, "" + alan.getThreshold().value)); if (alan.getThreshold().label != null) - an.addProperty(newProperty(THRESHOLD + "Name", "string", "" - + alan.getThreshold().label)); + { + an.addProperty(Properties.newProperty(THRESHOLD + "Name", + Properties.STRINGTYPE, "" + alan.getThreshold().label)); + } } ((DataSet) sref.getV_parent()).addDataSetAnnotations(an); bindjvvobj(alan, an); @@ -1165,86 +1226,25 @@ public class VamsasAppDatastore switch (alan.graph) { case AlignmentAnnotation.BAR_GRAPH: - an.addProperty(newProperty(DISCRETE_ANNOTATION, "boolean", "true")); + an.addProperty(Properties.newProperty(DISCRETE_ANNOTATION, + Properties.BOOLEANTYPE, "true")); break; case AlignmentAnnotation.LINE_GRAPH: - an.addProperty(newProperty(CONTINUOUS_ANNOTATION, "boolean", "true")); + 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; + Set mappings = av.getAlignment() + .getCodonFrames(); + for (int i = 0; i < views.length; i++) + { + if (views[i] != av) + { + AlignFrame viewframe = Desktop.getAlignFrameFor(views[i]); + if (viewframe == af) + { + gathered = true; + } + newviewid = views[i].getSequenceSetId(); + } + else + { + // lose the reference to the vamsas document created view + views[i] = null; + } + } + // close the view generated by the vamsas document synchronization + if (gathered) + { + af.closeView(av); + } + else + { + af.closeMenuItem_actionPerformed(false); + } + replaceJvObjMapping(seqsetidobj, newviewid); + seqsetidobj = newviewid; + // not sure if we need to do this: + + if (false) // mappings != null) + { + // ensure sequence mappings from vamsas document view still + // active + if (mappings != null) + { + jalview.structure.StructureSelectionManager + .getStructureSelectionManager(Desktop.instance) + .registerMappings(mappings); + } + } + } + // ensure vamsas object binds to the stored views retrieved from + // Jalview appdata + // jalview.structure.StructureSelectionManager + // .getStructureSelectionManager() + // .addStructureViewerListener(viewframe.alignPanel); + + } + + newviews = null; + newAlignmentViews.clear(); + } + + /** + * replaces oldjvobject with newjvobject in the Jalview Object <> VorbaID + * binding tables + * + * @param oldjvobject + * @param newjvobject + * (may be null) + */ + private void replaceJvObjMapping(Object oldjvobject, Object newjvobject) + { + Object vobject = jv2vobj.remove(oldjvobject); + if (vobject == null) + { + // NOTE: this happens if user deletes object in one session then updates + // from another client + throw new Error(MessageManager.formatMessage( + "error.implementation_error_old_jalview_object_not_bound", + new String[] { oldjvobject.toString() })); + } + if (newjvobject != null) + { + jv2vobj.put(newjvobject, vobject); + vobj2jv.put(vobject, newjvobject); + } + } + + /** + * Update the jalview client and user appdata from the local jalview settings + */ + public void updateJalviewClientAppdata() + { + final IClientAppdata cappdata = cdoc.getClientAppdata(); + if (cappdata != null) + { + try + { + jalview.gui.Jalview2XML jxml = new jalview.gui.Jalview2XML(); + jxml.setObjectMappingTables(mapKeysToString(vobj2jv), + mapValuesToString(jv2vobj)); + jxml.setSkipList(skipList); + if (dojvsync) + { + jxml.saveState(new JarOutputStream(cappdata + .getClientOutputStream())); + } + + } catch (Exception e) + { + // TODO raise GUI warning if user requests it. + jalview.bin.Cache.log + .error("Couldn't update jalview client application data. Giving up - local settings probably lost.", + e); + } + } + else + { + jalview.bin.Cache.log + .error("Couldn't access client application data for vamsas session. This is probably a vamsas client bug."); + } + } + + /** + * translate the Vobject keys to strings for use in Jalview2XML + * + * @param jv2vobj2 + * @return + */ + private IdentityHashMap mapValuesToString(IdentityHashMap jv2vobj2) + { + IdentityHashMap mapped = new IdentityHashMap(); + Iterator keys = jv2vobj2.keySet().iterator(); + while (keys.hasNext()) + { + Object key = keys.next(); + mapped.put(key, jv2vobj2.get(key).toString()); + } + return mapped; + } + + /** + * translate the Vobject values to strings for use in Jalview2XML + * + * @param vobj2jv2 + * @return hashtable with string values + */ + private Hashtable mapKeysToString(Hashtable vobj2jv2) + { + Hashtable mapped = new Hashtable(); + Iterator keys = vobj2jv2.keySet().iterator(); + while (keys.hasNext()) + { + Object key = keys.next(); + mapped.put(key.toString(), vobj2jv2.get(key)); + } + return mapped; + } + + /** + * synchronize Jalview from the vamsas document + * + * @return number of new views from document + */ + public int updateToJalview() { VAMSAS _roots[] = cdoc.getVamsasRoots(); @@ -1321,7 +1605,7 @@ public class VamsasAppDatastore // ///LOAD DATASET DataSet dataset = root.getDataSet(_ds); int i, iSize = dataset.getSequenceCount(); - Vector dsseqs; + List dsseqs; jalview.datamodel.Alignment jdataset = (jalview.datamodel.Alignment) getvObj2jv(dataset); int jremain = 0; if (jdataset == null) @@ -1343,25 +1627,12 @@ 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) @@ -1381,8 +1652,8 @@ 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."); @@ -1413,13 +1684,8 @@ 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 { @@ -1433,6 +1699,11 @@ public class VamsasAppDatastore } } } + else + { + Cache.log + .warn("Ignoring multiply referenced dataset sequence annotation for binding to datsaet sequence features."); + } } } if (dataset.getAlignmentCount() > 0) @@ -1443,15 +1714,19 @@ public class VamsasAppDatastore { 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 @@ -1471,8 +1746,7 @@ public class VamsasAppDatastore AlignmentSequence valseq = alignment.getAlignmentSequence(i); jalview.datamodel.Sequence alseq = (jalview.datamodel.Sequence) getvObj2jv(valseq); if (syncFromAlignmentSequence(valseq, valGapchar, gapChar, - dsseqs) - && alseq != null) + dsseqs) && alseq != null) { // updated to sequence from the document @@ -1509,6 +1783,7 @@ public class VamsasAppDatastore // positions. alseq.addAlignmentAnnotation(asa); bindjvvobj(asa, vasannot[a]); + refreshal = true; newasAnnots.add(asa); } else @@ -1539,8 +1814,8 @@ 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 " @@ -1597,8 +1872,11 @@ 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; } } } @@ -1610,10 +1888,14 @@ 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) { @@ -1640,11 +1922,13 @@ 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 @@ -1702,12 +1986,14 @@ 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)); + AlignmentViewport av = null; + AlignmentViewport[] avs = Desktop + .getViewports((String) getvObj2jv(alignment)); if (avs != null) { av = avs[0]; @@ -1715,34 +2001,6 @@ public class VamsasAppDatastore 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; @@ -1777,8 +2035,7 @@ 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], @@ -1828,16 +2085,14 @@ 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; @@ -1869,21 +2124,21 @@ 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 @@ -1915,24 +2170,21 @@ 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; } /** * @param jal - * the jalview alignment to which the annotation will be - * attached (ideally - freshly updated from corresponding - * vamsas alignment) + * the jalview alignment to which the annotation will be attached + * (ideally - freshly updated from corresponding vamsas alignment) * @param annotation * @return unbound jalview alignment annotation object. */ @@ -1985,6 +2237,7 @@ public class VamsasAppDatastore Cache.log.warn("Failed to parse threshold property"); } if (val != null) + { if (gl == null) { gl = new GraphLine(val.floatValue(), "", java.awt.Color.black); @@ -1993,11 +2246,14 @@ public class VamsasAppDatastore { gl.value = val.floatValue(); } + } } else if (props[p].getName().equalsIgnoreCase(THRESHOLD + "Name")) { if (gl == null) + { gl = new GraphLine(0, "", java.awt.Color.black); + } gl.label = props[p].getContent(); } } @@ -2033,20 +2289,21 @@ 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) { type = jalview.datamodel.AlignmentAnnotation.BAR_GRAPH; // default - // type of - // value - // annotation + // type of + // value + // annotation if (has[HASHPHOB]) { // no hints - so we ensure HPHOB display is like this. @@ -2137,6 +2394,8 @@ public class VamsasAppDatastore 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) { @@ -2145,7 +2404,7 @@ public class VamsasAppDatastore } if (annotation.getModifiable() == null || annotation.getModifiable().length() == 0) // TODO: USE VAMSAS - // LIBRARY OBJECT + // LIBRARY OBJECT // LOCK METHODS) { jan.editable = true; @@ -2156,12 +2415,12 @@ public class VamsasAppDatastore && annotation.getGroup().length() > 0) { jan.graphGroup = Integer.parseInt(annotation.getGroup()); // TODO: - // group - // similarly - // named - // annotation - // together - // ? + // group + // similarly + // named + // annotation + // together + // ? } } catch (Exception e) { @@ -2175,23 +2434,6 @@ 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 @@ -2208,7 +2450,8 @@ public class VamsasAppDatastore if (dseta.getSegCount() > 0 && dseta.getPosCount() > 0) { throw new Error( - "Invalid vamsas RangeType - cannot resolve both lists of Pos and Seg from choice!"); + MessageManager + .getString("error.invalid_vamsas_rangetype_cannot_resolve_lists")); } if (dseta.getSegCount() > 0) { @@ -2231,8 +2474,7 @@ 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(); @@ -2267,7 +2509,8 @@ public class VamsasAppDatastore if (dseta.getSegCount() > 0 && dseta.getPosCount() > 0) { throw new Error( - "Invalid vamsas RangeType - cannot resolve both lists of Pos and Seg from choice!"); + MessageManager + .getString("error.invalid_vamsas_rangetype_cannot_resolve_lists")); } if (dseta.getSegCount() > 0) { @@ -2308,12 +2551,10 @@ 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 + * where the from range is the local mapped range, and the to range + * is the 'mapped' range in the MapRangeType + * @param default unit for local + * @param default unit for mapped * @return MapList */ private jalview.util.MapList parsemapType(MapType maprange, int localu, @@ -2335,15 +2576,15 @@ 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); } } @@ -2378,8 +2619,8 @@ 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()); @@ -2466,10 +2707,10 @@ public class VamsasAppDatastore return vobj2jv; } - public void storeSequenceMappings(AlignViewport viewport, String title) + public void storeSequenceMappings(AlignmentViewport viewport, String title) throws Exception { - AlignViewport av = viewport; + AlignmentViewport av = viewport; try { jalview.datamodel.AlignmentI jal = av.getAlignment(); @@ -2481,19 +2722,25 @@ 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) + Set 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]); @@ -2516,8 +2763,48 @@ 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; } }