X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FVamsasAppDatastore.java;h=735f415206a55d692ab1c67532b4a21172b850c7;hb=9c00e25bfdf274009a471eba895f39e2fac4c0ac;hp=a9219a645786fd769d464e0dd8778c7add44ac0e;hpb=2564b4cd5f71405b3fa9155f15dedfc666448348;p=jalview.git diff --git a/src/jalview/io/VamsasAppDatastore.java b/src/jalview/io/VamsasAppDatastore.java index a9219a6..735f415 100644 --- a/src/jalview/io/VamsasAppDatastore.java +++ b/src/jalview/io/VamsasAppDatastore.java @@ -1,31 +1,26 @@ /* - * 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 - * - * This program is free software; you can redistribute it and/or + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7) + * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle + * + * This file is part of Jalview. + * + * Jalview is free software: you can redistribute it and/or * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation; either version 2 - * of the License, or (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License - * along with this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. + * + * Jalview is distributed in the hope that it will be useful, but + * WITHOUT ANY WARRANTY; without even the implied warranty + * of MERCHANTABILITY or FITNESS FOR A PARTICULAR + * PURPOSE. See the GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License along with Jalview. If not, see . */ package jalview.io; import jalview.bin.Cache; import jalview.datamodel.AlignedCodonFrame; import jalview.datamodel.AlignmentAnnotation; -import jalview.datamodel.AlignmentI; -import jalview.datamodel.AlignmentView; -import jalview.datamodel.DBRefEntry; import jalview.datamodel.GraphLine; -import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceI; import jalview.gui.AlignFrame; import jalview.gui.AlignViewport; @@ -35,14 +30,13 @@ import jalview.io.vamsas.Datasetsequence; import jalview.io.vamsas.DatastoreItem; import jalview.io.vamsas.DatastoreRegistry; import jalview.io.vamsas.Rangetype; -import jalview.util.UrlLink; - import java.io.IOException; import java.util.Enumeration; import java.util.HashMap; import java.util.Hashtable; import java.util.IdentityHashMap; import java.util.Iterator; +import java.util.List; import java.util.Vector; import java.util.jar.JarInputStream; import java.util.jar.JarOutputStream; @@ -52,13 +46,15 @@ import uk.ac.vamsas.objects.core.*; 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 { /** @@ -142,11 +138,11 @@ 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 +152,19 @@ 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); } } } @@ -181,7 +178,7 @@ public class VamsasAppDatastore } /** - * + * * @param vobj * @return Jalview datamodel object bound to the vamsas document object */ @@ -248,12 +245,13 @@ 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 +270,25 @@ 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 +304,8 @@ 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 +350,14 @@ 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 +419,8 @@ 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), @@ -481,21 +486,22 @@ public class VamsasAppDatastore /* * We do not put local Alignment Sequence Features into the vamsas * document yet. - * - * + * + * * jalview.datamodel.SequenceFeature[] features = alseq * .getSequenceFeatures(); for (int f = 0; f < features.length; f++) { * if (features[f] != null) { AlignmentSequenceAnnotation valseqf = ( - * AlignmentSequenceAnnotation) getjv2vObj(features[i]); if (valseqf == - * null) { - * + * 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 +522,13 @@ 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 @@ -528,12 +541,7 @@ 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()) - { - jvalsq = (SequenceI) jval.nextElement(); + for (SequenceI jvalsq:av.getAlignment().getSequences()) { // saveDatasetSequenceAnnotation(AlSeqMaps,(uk.ac.vamsas.objects.core.Sequence) // sref, aa[i]); if (jvalsq.getDatasetSequence() == aa[i].sequenceRef) @@ -615,11 +623,9 @@ 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 +645,13 @@ 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 +694,8 @@ 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 +716,13 @@ 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) { @@ -730,7 +741,7 @@ public class VamsasAppDatastore /** * remove docseqs from the given alignment marking provenance appropriately * and removing any references to the sequences. - * + * * @param alignment * @param docseqs */ @@ -798,7 +809,7 @@ public class VamsasAppDatastore * vamsas alignment sequence for jvalsq and adds it to the alignment if * necessary. unbounddocseq is a duplicate of the vamsas alignment sequences * and these are removed after being processed w.r.t a bound jvalsq - * + * */ private boolean syncToAlignmentSequence(SequenceI jvalsq, Alignment alignment, Vector unbounddocseq) @@ -863,7 +874,7 @@ 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; @@ -895,8 +906,9 @@ 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 +922,24 @@ 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 +1023,7 @@ 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 +1061,11 @@ 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); @@ -1145,7 +1158,7 @@ public class VamsasAppDatastore /** * set vamsas annotation object type from jalview annotation - * + * * @param an * @param alan */ @@ -1178,24 +1191,25 @@ 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); } @@ -1438,20 +1456,22 @@ public class VamsasAppDatastore /** * replaces oldjvobject with newjvobject in the Jalview Object <> VorbaID * binding tables - * + * * @param oldjvobject - * @param newjvobject (may be null) + * @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( "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 +1502,7 @@ 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); } } @@ -1496,7 +1515,7 @@ public class VamsasAppDatastore /** * translate the Vobject keys to strings for use in Jalview2XML - * + * * @param jv2vobj2 * @return */ @@ -1514,7 +1533,7 @@ public class VamsasAppDatastore /** * translate the Vobject values to strings for use in Jalview2XML - * + * * @param vobj2jv2 * @return hashtable with string values */ @@ -1529,8 +1548,10 @@ public class VamsasAppDatastore } return mapped; } + /** * synchronize Jalview from the vamsas document + * * @return number of new views from document */ public int updateToJalview() @@ -1547,7 +1568,7 @@ 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) @@ -1566,12 +1587,12 @@ 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()) { @@ -1594,8 +1615,8 @@ 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."); @@ -1627,7 +1648,7 @@ public class VamsasAppDatastore if (dseta.getAnnotationElementCount() == 0) { new jalview.io.vamsas.Sequencefeature(this, dseta, dsSeq); - + } else { @@ -1640,8 +1661,11 @@ 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 +1688,7 @@ public class VamsasAppDatastore jal = (av.hasHiddenRows()) ? av.getAlignment() .getHiddenSequences().getFullAlignment() : av .getAlignment(); - } + } iSize = alignment.getAlignmentSequenceCount(); boolean refreshal = false; Vector newasAnnots = new Vector(); @@ -1685,8 +1709,7 @@ 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 @@ -1754,8 +1777,8 @@ 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 " @@ -1812,7 +1835,8 @@ public class VamsasAppDatastore else { jan = getjAlignmentAnnotation(jal, an[j]); - // TODO: ensure we add the alignment annotation before the automatic annotation rows + // TODO: ensure we add the alignment annotation before the + // automatic annotation rows jal.addAnnotation(jan); bindjvvobj(jan, an[j]); refreshal = true; @@ -1831,8 +1855,10 @@ 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) { @@ -1956,7 +1982,7 @@ public class VamsasAppDatastore * jalview.datamodel.Annotation[] rows Two annotation rows are made if there * are distinct annotation for both at 'pos' and 'after pos' at any particular * site. - * + * * @param annotation * @return { boolean[static int constants ], int[ae.length] - map to annotated * object frame, jalview.datamodel.Annotation[], @@ -2023,16 +2049,14 @@ 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; @@ -2071,14 +2095,14 @@ 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 @@ -2125,9 +2149,8 @@ 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. */ @@ -2228,11 +2251,12 @@ 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]) { @@ -2372,12 +2396,11 @@ 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 * to vamsas utils - * + * * @param dseta * @return int[] { start, end} */ @@ -2435,7 +2458,7 @@ public class VamsasAppDatastore /** * map from a rangeType's internal frame to the referenced object's coordinate * frame. - * + * * @param dseta * @return int [] { ref(pos)...} for all pos in rangeType's frame. */ @@ -2487,14 +2510,12 @@ 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, @@ -2514,7 +2535,7 @@ public class VamsasAppDatastore /** * initialise a range type object from a set of start/end inclusive intervals - * + * * @param mrt * @param range */ @@ -2531,7 +2552,7 @@ public class VamsasAppDatastore /** * initialise a MapType object from a MapList object. - * + * * @param maprange * @param ml * @param setUnits @@ -2556,12 +2577,12 @@ public class VamsasAppDatastore * App and Action here. Provenance prov = new Provenance(); * org.exolab.castor.types.Date date = new org.exolab.castor.types.Date( new * java.util.Date()); Entry provEntry; - * + * * if (jprov != null) { entries = jprov.getEntries(); for (int i = 0; i < * entries.length; i++) { provEntry = new Entry(); try { date = new - * org.exolab.castor.types.Date(entries[i].getDate()); } catch (Exception ex) { - * ex.printStackTrace(); - * + * org.exolab.castor.types.Date(entries[i].getDate()); } catch (Exception ex) + * { ex.printStackTrace(); + * * date = new org.exolab.castor.types.Date(entries[i].getDate()); } * provEntry.setDate(date); provEntry.setUser(entries[i].getUser()); * provEntry.setAction(entries[i].getAction()); prov.addEntry(provEntry); } } @@ -2569,7 +2590,7 @@ public class VamsasAppDatastore * provEntry.setUser(System.getProperty("user.name")); // TODO: ext string * provEntry.setApp("JVAPP"); // TODO: ext string provEntry.setAction(action); * prov.addEntry(provEntry); } - * + * * return prov; } */ jalview.datamodel.Provenance getJalviewProvenance(Provenance prov) @@ -2587,7 +2608,7 @@ public class VamsasAppDatastore } /** - * + * * @return default initial provenance list for a Jalview created vamsas * object. */ @@ -2662,11 +2683,13 @@ 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. @@ -2677,7 +2700,8 @@ 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(); @@ -2725,19 +2749,22 @@ 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(); }