X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FVamsasAppDatastore.java;h=fb6465cb93baacac99bd34d2306381e82d7049d4;hb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;hp=e21a9edbc1878f6b0e0c86dbd5c840dcb22c2a0b;hpb=9084f3744122d4c4d6ee488f9f3e428f57e800d5;p=jalview.git diff --git a/src/jalview/io/VamsasAppDatastore.java b/src/jalview/io/VamsasAppDatastore.java index e21a9ed..fb6465c 100644 --- a/src/jalview/io/VamsasAppDatastore.java +++ b/src/jalview/io/VamsasAppDatastore.java @@ -1,20 +1,19 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) - * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7) + * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation; either version 2 - * of the License, or (at your option) any later version. + * This file is part of Jalview. * - * 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 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. * - * You should have received a copy of the GNU General Public License - * along with this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + * Jalview is distributed in the hope that it will be useful, but + * WITHOUT ANY WARRANTY; without even the implied warranty + * of MERCHANTABILITY or FITNESS FOR A PARTICULAR + * PURPOSE. See the GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License along with Jalview. If not, see . */ package jalview.io; @@ -58,7 +57,9 @@ import uk.ac.vamsas.objects.utils.Properties; * "org.exolab.castor.serializer", "org.apache.xml.serialize.XMLSerilazizer"); } * */ - +/* + * TODO: check/verify consistency for vamsas sync with group associated alignment annotation + */ public class VamsasAppDatastore { /** @@ -142,11 +143,11 @@ public class VamsasAppDatastore { return cdoc.getObject((VorbaId) jv2vobj.get(jvobj)); } - // check if we're working with a string - then workaround + // 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) @@ -156,18 +157,19 @@ public class VamsasAppDatastore // 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)) + if (obj != null && !(obj instanceof Alignment)) { - Cache.log.warn("IMPLEMENTATION ERROR?: Unexpected mapping for unmapped jalview string object content:" - + seqsetidobj + " to object " + obj); + 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); + + seqsetidobj + " to another jalview dataset object " + + seqsetidobj); } } } @@ -250,10 +252,11 @@ 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 - * @return true if alignment associated with viewport was stored/synchronized to document + * title for alignment + * @return true if alignment associated with viewport was stored/synchronized + * to document */ public boolean storeVAMSAS(AlignViewport av, String aFtitle) { @@ -272,22 +275,25 @@ public class VamsasAppDatastore 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) + if (alignment != null) { dataset = (DataSet) alignment.getV_parent(); - } else { - // is the dataset already registered - dataset = (DataSet) getjv2vObj(jds); } - + else + { + // is the dataset already registered + dataset = (DataSet) getjv2vObj(jds); + } + if (dataset == null) { // it might be that one of the dataset sequences does actually have a - // binding, so search for it indirectly. If it does, then the local jalview dataset + // 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++) @@ -303,7 +309,8 @@ public class VamsasAppDatastore } else { - if (vbound.getV_parent()!=null && 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 different datasets into a single alignment in the vamsas document."); @@ -348,11 +355,14 @@ public class VamsasAppDatastore // referenced // sequences // to dataset. - Datasetsequence dssync = new jalview.io.vamsas.Datasetsequence(this, sq, dict, dataset); + Datasetsequence dssync = new jalview.io.vamsas.Datasetsequence( + this, sq, dict, dataset); sequence = (Sequence) dssync.getVobj(); - if (dssync.getModified()) { - dssmods.addElement(sequence); - }; + if (dssync.getModified()) + { + dssmods.addElement(sequence); + } + ; } if (dssmods.size() > 0) { @@ -414,8 +424,8 @@ 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), @@ -486,16 +496,17 @@ 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); } } } */ } @@ -516,6 +527,13 @@ public class VamsasAppDatastore { continue; } + if (aa[i].groupRef != null) + { + // TODO: store any group associated annotation references + Cache.log + .warn("Group associated sequence annotation is not stored in VAMSAS document."); + continue; + } if (aa[i].sequenceRef != null) { // Deal with sequence associated annotation @@ -615,11 +633,9 @@ public class VamsasAppDatastore 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); @@ -639,12 +655,13 @@ public class VamsasAppDatastore an.setGroup(Integer.toString(aa[i].graphGroup)); if (aa[i].threshold != null && aa[i].threshold.displayed) { - an.addProperty(Properties.newProperty(THRESHOLD, Properties.FLOATTYPE, "" - + aa[i].threshold.value)); + 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)); + an.addProperty(Properties.newProperty(THRESHOLD + + "Name", Properties.STRINGTYPE, "" + + aa[i].threshold.label)); } } } @@ -687,7 +704,8 @@ public class VamsasAppDatastore { TreePanel tp = (TreePanel) frames[t]; - if (tp.getViewPort().getSequenceSetId().equals(av.getSequenceSetId())) + if (tp.getViewPort().getSequenceSetId() + .equals(av.getSequenceSetId())) { DatastoreItem vtree = new jalview.io.vamsas.Tree(this, tp, jal, alignment); @@ -708,10 +726,13 @@ public class VamsasAppDatastore } /** - * 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. + * 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. + * @return true if alignment associated with this view will be stored in + * document. */ public boolean alignmentWillBeSkipped(AlignViewport av) { @@ -895,8 +916,9 @@ 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; @@ -910,21 +932,24 @@ 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) + if (valseq.getDescription() != null) { alseq.setDescription(valseq.getDescription()); - } else { + } + else + { // inherit description line from dataset. - if (alseq.getDatasetSequence().getDescription()!=null) + if (alseq.getDatasetSequence().getDescription() != null) { - alseq.setDescription(alseq.getDatasetSequence().getDescription()); + alseq.setDescription(alseq.getDatasetSequence() + .getDescription()); } } // if @@ -1008,8 +1033,7 @@ public class VamsasAppDatastore { // we only write an annotation where it really exists. Glyph ss = new Glyph(); - ss - .setDict(uk.ac.vamsas.objects.utils.GlyphDictionary.PROTEIN_SS_3STATE); + ss.setDict(uk.ac.vamsas.objects.utils.GlyphDictionary.PROTEIN_SS_3STATE); ss.setContent(String .valueOf(alan.annotations[a].secondaryStructure)); ae.addGlyph(ss); @@ -1047,12 +1071,11 @@ public class VamsasAppDatastore // bits. if (alan.getThreshold() != null && alan.getThreshold().displayed) { - an.addProperty(Properties.newProperty(THRESHOLD, Properties.FLOATTYPE, - "" - + alan.getThreshold().value)); + 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)); + an.addProperty(Properties.newProperty(THRESHOLD + "Name", + Properties.STRINGTYPE, "" + alan.getThreshold().label)); } ((DataSet) sref.getV_parent()).addDataSetAnnotations(an); bindjvvobj(alan, an); @@ -1178,24 +1201,25 @@ public class VamsasAppDatastore switch (alan.graph) { case AlignmentAnnotation.BAR_GRAPH: - an.addProperty(Properties.newProperty(DISCRETE_ANNOTATION, Properties.BOOLEANTYPE, "true")); + an.addProperty(Properties.newProperty(DISCRETE_ANNOTATION, + Properties.BOOLEANTYPE, "true")); break; case AlignmentAnnotation.LINE_GRAPH: - an.addProperty(Properties.newProperty(CONTINUOUS_ANNOTATION, Properties.BOOLEANTYPE, "true")); + an.addProperty(Properties.newProperty(CONTINUOUS_ANNOTATION, + Properties.BOOLEANTYPE, "true")); break; default: // don't add any kind of discrete or continous property info. } } - /** * get start 0) { jalview.structure.StructureSelectionManager - .getStructureSelectionManager().addMappings(mappings); + .getStructureSelectionManager(Desktop.instance).addMappings(mappings); } } } // ensure vamsas object binds to the stored views retrieved from // Jalview appdata - //jalview.structure.StructureSelectionManager - // .getStructureSelectionManager() - // .addStructureViewerListener(viewframe.alignPanel); + // jalview.structure.StructureSelectionManager + // .getStructureSelectionManager() + // .addStructureViewerListener(viewframe.alignPanel); } @@ -1440,7 +1464,8 @@ public class VamsasAppDatastore * binding tables * * @param oldjvobject - * @param newjvobject (may be null) + * @param newjvobject + * (may be null) */ private void replaceJvObjMapping(Object oldjvobject, Object newjvobject) { @@ -1451,7 +1476,7 @@ public class VamsasAppDatastore "IMPLEMENTATION ERROR: old jalview object is not bound ! (" + oldjvobject + ")"); } - if (newjvobject!=null) + if (newjvobject != null) { jv2vobj.put(newjvobject, vobject); vobj2jv.put(vobject, newjvobject); @@ -1482,8 +1507,7 @@ public class VamsasAppDatastore { // 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.", + .error("Couldn't update jalview client application data. Giving up - local settings probably lost.", e); } } @@ -1529,8 +1553,10 @@ public class VamsasAppDatastore } return mapped; } + /** * synchronize Jalview from the vamsas document + * * @return number of new views from document */ public int updateToJalview() @@ -1566,12 +1592,12 @@ public class VamsasAppDatastore // TODO: test sequence merging - we preserve existing non vamsas // sequences but add in any new vamsas ones, and don't yet update any // sequence attributes - for (i = 0; i < iSize - ; i++) + for (i = 0; i < iSize; i++) { Sequence vdseq = dataset.getSequence(i); - jalview.io.vamsas.Datasetsequence dssync = new Datasetsequence(this, vdseq); - + jalview.io.vamsas.Datasetsequence dssync = new Datasetsequence( + this, vdseq); + jalview.datamodel.SequenceI dsseq = (SequenceI) dssync.getJvobj(); if (dssync.isAddfromdoc()) { @@ -1627,7 +1653,7 @@ public class VamsasAppDatastore if (dseta.getAnnotationElementCount() == 0) { new jalview.io.vamsas.Sequencefeature(this, dseta, dsSeq); - + } else { @@ -1640,8 +1666,11 @@ public class VamsasAppDatastore .warn("Ignoring dataset annotation with annotationElements. Not yet supported in jalview."); } } - } else { - Cache.log.warn("Ignoring multiply referenced dataset sequence annotation for binding to datsaet sequence features."); + } + else + { + Cache.log + .warn("Ignoring multiply referenced dataset sequence annotation for binding to datsaet sequence features."); } } } @@ -1664,7 +1693,7 @@ public class VamsasAppDatastore jal = (av.hasHiddenRows()) ? av.getAlignment() .getHiddenSequences().getFullAlignment() : av .getAlignment(); - } + } iSize = alignment.getAlignmentSequenceCount(); boolean refreshal = false; Vector newasAnnots = new Vector(); @@ -1685,8 +1714,7 @@ 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 @@ -1723,6 +1751,7 @@ public class VamsasAppDatastore // positions. alseq.addAlignmentAnnotation(asa); bindjvvobj(asa, vasannot[a]); + refreshal = true; newasAnnots.add(asa); } else @@ -1811,8 +1840,11 @@ public class VamsasAppDatastore else { jan = getjAlignmentAnnotation(jal, an[j]); + // TODO: ensure we add the alignment annotation before the + // automatic annotation rows jal.addAnnotation(jan); bindjvvobj(jan, an[j]); + refreshal = true; } } } @@ -1828,8 +1860,10 @@ public class VamsasAppDatastore .toString()); av = alignFrame.getViewport(); newAlignmentViews.addElement(av); - String title = alignment.getProvenance().getEntry( - alignment.getProvenance().getEntryCount() - 1) + String title = alignment + .getProvenance() + .getEntry( + alignment.getProvenance().getEntryCount() - 1) .getAction(); if (alignment.getPropertyCount() > 0) { @@ -1862,6 +1896,7 @@ public class VamsasAppDatastore if (refreshal) { av.alignmentChanged(alignFrame.alignPanel); + alignFrame.alignPanel.adjustAnnotationHeight(); } } // LOAD TREES @@ -2019,16 +2054,14 @@ public class VamsasAppDatastore { if (glyphs[g] .getDict() - .equals( - uk.ac.vamsas.objects.utils.GlyphDictionary.PROTEIN_SS_3STATE)) + .equals(uk.ac.vamsas.objects.utils.GlyphDictionary.PROTEIN_SS_3STATE)) { ss = glyphs[g].getContent(); AeContent[HASSECSTR] = true; } else if (glyphs[g] .getDict() - .equals( - uk.ac.vamsas.objects.utils.GlyphDictionary.PROTEIN_HD_HYDRO)) + .equals(uk.ac.vamsas.objects.utils.GlyphDictionary.PROTEIN_HD_HYDRO)) { Cache.log.debug("ignoring hydrophobicity glyph marker."); AeContent[HASHPHOB] = true; @@ -2067,14 +2100,14 @@ public class VamsasAppDatastore 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 @@ -2121,9 +2154,8 @@ public class VamsasAppDatastore /** * @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. */ @@ -2224,11 +2256,12 @@ 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]) { @@ -2368,7 +2401,6 @@ public class VamsasAppDatastore return null; } - /** * get real bounds of a RangeType's specification. start and end are an * inclusive range within which all segments and positions lie. TODO: refactor @@ -2485,12 +2517,10 @@ 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, @@ -2555,8 +2585,8 @@ public class VamsasAppDatastore * * if (jprov != null) { entries = jprov.getEntries(); for (int i = 0; i < * entries.length; i++) { provEntry = new Entry(); try { date = new - * org.exolab.castor.types.Date(entries[i].getDate()); } catch (Exception ex) { - * ex.printStackTrace(); + * org.exolab.castor.types.Date(entries[i].getDate()); } catch (Exception ex) + * { ex.printStackTrace(); * * date = new org.exolab.castor.types.Date(entries[i].getDate()); } * provEntry.setDate(date); provEntry.setUser(entries[i].getUser()); @@ -2658,11 +2688,13 @@ public class VamsasAppDatastore Cache.log.warn("Creating new dataset for an alignment."); jal.setDataset(null); } - dataset = (DataSet) ((Alignment) getjv2vObj(viewport.getSequenceSetId())).getV_parent(); // jal.getDataset()); - if (dataset==null) + dataset = (DataSet) ((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."); + Cache.log + .error("Can't find the correct dataset for the alignment in this view. Creating new one."); } // Store any sequence mappings. @@ -2673,7 +2705,8 @@ public class VamsasAppDatastore .getCodonFrames(); for (int cf = 0; cf < cframes.length; cf++) { - if (cframes[cf].getdnaSeqs()!=null && cframes[cf].getdnaSeqs().length > 0) + if (cframes[cf].getdnaSeqs() != null + && cframes[cf].getdnaSeqs().length > 0) { jalview.datamodel.SequenceI[] dmps = cframes[cf].getdnaSeqs(); jalview.datamodel.Mapping[] mps = cframes[cf].getProtMappings(); @@ -2721,19 +2754,22 @@ public class VamsasAppDatastore } /** - * @param skipList the skipList to set + * @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) + if (dsReg == null) { dsReg = new DatastoreRegistry(); }