X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FVamsasAppDatastore.java;h=15c481df1931ba758441c1e8879dd772d4360871;hb=d3bf4ae12b72df02dee34c95da750ab38a3816b9;hp=ac00b33f60929ab0f3a2551e6f78723b961e60f3;hpb=2ac096ecd8ee1a5c11480e864fce7cf78d661c66;p=jalview.git diff --git a/src/jalview/io/VamsasAppDatastore.java b/src/jalview/io/VamsasAppDatastore.java index ac00b33..15c481d 100644 --- a/src/jalview/io/VamsasAppDatastore.java +++ b/src/jalview/io/VamsasAppDatastore.java @@ -1,31 +1,29 @@ /* - * 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 ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * - * 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. + * + * 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; @@ -35,31 +33,58 @@ 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 jalview.project.Jalview2XML; +import jalview.util.MessageManager; +import jalview.util.jarInputStreamProvider; +import jalview.viewmodel.AlignmentViewport; +import java.io.File; 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; -import uk.ac.vamsas.client.*; -import uk.ac.vamsas.objects.core.*; +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 + * TODO: check/verify consistency for vamsas sync with group associated alignment annotation */ public class VamsasAppDatastore { @@ -128,7 +153,7 @@ public class VamsasAppDatastore private void buildSkipList() { skipList = new Hashtable(); - AlignFrame[] al = Desktop.getAlignframes(); + AlignFrame[] al = Desktop.getAlignFrames(); for (int f = 0; al != null && f < al.length; f++) { skipList.put(al[f].getViewport().getSequenceSetId(), al[f]); @@ -144,11 +169,11 @@ 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) @@ -158,26 +183,27 @@ 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); } } } if (Cache.log.isDebugEnabled()) { - Cache.log.debug("Returning null VorbaID binding for jalview object " - + jvobj); + Cache.log.debug( + "Returning null VorbaID binding for jalview object " + jvobj); } return null; } @@ -193,8 +219,8 @@ public class VamsasAppDatastore if (id == null) { id = cdoc.registerObject(vobj); - Cache.log - .debug("Registering new object and returning null for getvObj2jv"); + Cache.log.debug( + "Registering new object and returning null for getvObj2jv"); return null; } if (vobj2jv.containsKey(vobj.getVorbaId())) @@ -215,7 +241,8 @@ public class VamsasAppDatastore { Cache.log.error("Failed to get id for " + (vobj.isRegisterable() ? "registerable" - : "unregisterable") + " object " + vobj); + : "unregisterable") + + " object " + vobj); } } @@ -224,16 +251,17 @@ public class VamsasAppDatastore { Cache.log.debug( "Warning? Overwriting existing vamsas id binding for " - + vobj.getVorbaId(), new Exception( - "Overwriting vamsas id binding.")); + + vobj.getVorbaId(), + new Exception(MessageManager.getString( + "exception.overwriting_vamsas_id_binding"))); } else if (jv2vobj.containsKey(jvobj) && !((VorbaId) jv2vobj.get(jvobj)).equals(vobj.getVorbaId())) { Cache.log.debug( "Warning? Overwriting existing jalview object binding for " - + jvobj, new Exception( - "Overwriting jalview object binding.")); + + jvobj, + new Exception("Overwriting jalview object binding.")); } /* * Cache.log.error("Attempt to make conflicting object binding! "+vobj+" id " @@ -252,10 +280,11 @@ 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) { @@ -274,22 +303,25 @@ 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++) @@ -305,10 +337,11 @@ 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."); + throw new Error(MessageManager.getString( + "error.implementation_error_cannot_map_alignment_sequences")); // This occurs because the dataset for the alignment we are // trying to } @@ -341,7 +374,8 @@ public class VamsasAppDatastore // flag. // this *will* break when alignment contains both nucleotide and amino // acid sequences. - String dict = jal.isNucleotide() ? uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_NA + String dict = jal.isNucleotide() + ? uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_NA : uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_AA; Vector dssmods = new Vector(); for (int i = 0; i < jal.getHeight(); i++) @@ -350,11 +384,14 @@ 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) { @@ -406,8 +443,8 @@ public class VamsasAppDatastore else { // always prepare to clone the alignment - boolean alismod = av.isUndoRedoHashModified((long[]) alignRDHash - .get(av.getSequenceSetId())); + boolean alismod = av.isUndoRedoHashModified( + (long[]) alignRDHash.get(av.getSequenceSetId())); // todo: verify and update mutable alignment props. // TODO: Use isLocked methods if (alignment.getModifiable() == null @@ -416,8 +453,8 @@ 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), @@ -427,8 +464,8 @@ public class VamsasAppDatastore { // removeValignmentSequences(alignment, docseqs); docseqs.removeAllElements(); - System.out - .println("Sequence deletion from alignment is not implemented."); + System.out.println( + "Sequence deletion from alignment is not implemented."); } if (modified) @@ -467,17 +504,18 @@ public class VamsasAppDatastore // unbind alignment from view. // create new binding and new alignment. // mark trail on new alignment as being derived from old ? - System.out - .println("update edited alignment to new alignment in document."); + System.out.println( + "update edited alignment to new alignment in document."); } } // //////////////////////////////////////////// // SAVE Alignment Sequence Features - for (int i = 0, iSize = alignment.getAlignmentSequenceCount(); i < iSize; i++) + for (int i = 0, iSize = alignment + .getAlignmentSequenceCount(); i < iSize; i++) { AlignmentSequence valseq; - SequenceI alseq = (SequenceI) getvObj2jv(valseq = alignment - .getAlignmentSequence(i)); + SequenceI alseq = (SequenceI) getvObj2jv( + valseq = alignment.getAlignmentSequence(i)); if (alseq != null && alseq.getSequenceFeatures() != null) { /* @@ -488,16 +526,17 @@ 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); } } } */ } @@ -518,10 +557,11 @@ public class VamsasAppDatastore { continue; } - if (aa[i].groupRef!=null) + 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."); + Cache.log.warn( + "Group associated sequence annotation is not stored in VAMSAS document."); continue; } if (aa[i].sequenceRef != null) @@ -536,12 +576,8 @@ 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) @@ -558,7 +594,8 @@ public class VamsasAppDatastore else { // add Alignment Annotation - uk.ac.vamsas.objects.core.AlignmentAnnotation an = (uk.ac.vamsas.objects.core.AlignmentAnnotation) getjv2vObj(aa[i]); + uk.ac.vamsas.objects.core.AlignmentAnnotation an = (uk.ac.vamsas.objects.core.AlignmentAnnotation) getjv2vObj( + aa[i]); if (an == null) { an = new uk.ac.vamsas.objects.core.AlignmentAnnotation(); @@ -607,8 +644,8 @@ public class VamsasAppDatastore ae = new AnnotationElement(); ae.setDescription(aa[i].annotations[a].description); ae.addGlyph(new Glyph()); - ae.getGlyph(0).setContent( - aa[i].annotations[a].displayCharacter); // assume + ae.getGlyph(0) + .setContent(aa[i].annotations[a].displayCharacter); // assume // jax-b // takes // care @@ -623,11 +660,10 @@ 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); @@ -647,12 +683,14 @@ 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)); } } } @@ -665,14 +703,14 @@ public class VamsasAppDatastore // LOCK METHODS) { // verify annotation - update (perhaps) - Cache.log - .info("update alignment sequence annotation. not yet implemented."); + Cache.log.info( + "update alignment sequence annotation. not yet implemented."); } else { // verify annotation - update (perhaps) - Cache.log - .info("updated alignment sequence annotation added."); + Cache.log.info( + "updated alignment sequence annotation added."); } } } @@ -684,9 +722,9 @@ public class VamsasAppDatastore // /SAVE THE TREES // ///////////////////////////////// // FIND ANY ASSOCIATED TREES - if (Desktop.desktop != null) + if (Desktop.getDesktopPane() != null) { - javax.swing.JInternalFrame[] frames = Desktop.instance + javax.swing.JInternalFrame[] frames = Desktop.getInstance() .getAllFrames(); for (int t = 0; t < frames.length; t++) @@ -695,7 +733,8 @@ 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); @@ -716,17 +755,20 @@ 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 (for all sequences, including the hidden ones!) + * 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) + public boolean alignmentWillBeSkipped(AlignmentViewport av) { return (!av.getAlignment().isAligned()); } - private void addToSkipList(AlignViewport av) + private void addToSkipList(AlignmentViewport av) { if (skipList == null) { @@ -742,18 +784,19 @@ public class VamsasAppDatastore * @param alignment * @param docseqs */ - private void removeValignmentSequences(Alignment alignment, Vector docseqs) + private void removeValignmentSequences(Alignment alignment, + Vector docseqs) { // delete these from document. This really needs to be a generic document // API function derived by CASTOR. Enumeration en = docseqs.elements(); while (en.hasMoreElements()) { - alignment.removeAlignmentSequence((AlignmentSequence) en - .nextElement()); + alignment.removeAlignmentSequence( + (AlignmentSequence) en.nextElement()); } - Entry pe = addProvenance(alignment.getProvenance(), "Removed " - + docseqs.size() + " sequences"); + Entry pe = addProvenance(alignment.getProvenance(), + "Removed " + docseqs.size() + " sequences"); en = alignment.enumerateAlignmentAnnotation(); Vector toremove = new Vector(); while (en.hasMoreElements()) @@ -792,8 +835,8 @@ public class VamsasAppDatastore en = toremove.elements(); while (en.hasMoreElements()) { - alignment - .removeAlignmentAnnotation((uk.ac.vamsas.objects.core.AlignmentAnnotation) en + alignment.removeAlignmentAnnotation( + (uk.ac.vamsas.objects.core.AlignmentAnnotation) en .nextElement()); } // TODO: search through alignment annotations to remove any references to @@ -842,17 +885,16 @@ public class VamsasAppDatastore modal = true; alseq.setName(jvalsq.getName()); } - if (jvalsq.getDescription() != null - && (alseq.getDescription() == null || !jvalsq.getDescription() - .equals(alseq.getDescription()))) + if (jvalsq.getDescription() != null && (alseq.getDescription() == null + || !jvalsq.getDescription().equals(alseq.getDescription()))) { modal = true; alseq.setDescription(jvalsq.getDescription()); } if (getjv2vObj(jvalsq.getDatasetSequence()) == null) { - Cache.log - .warn("Serious Implementation error - Unbound dataset sequence in alignment: " + Cache.log.warn( + "Serious Implementation error - Unbound dataset sequence in alignment: " + jvalsq.getDatasetSequence()); } alseq.setRefid(getjv2vObj(jvalsq.getDatasetSequence())); @@ -871,7 +913,7 @@ 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; @@ -892,8 +934,8 @@ public class VamsasAppDatastore || !valseq.getSequence().equals(alseq.getSequenceAsString())) { // this might go *horribly* wrong - alseq.setSequence(new String(valseq.getSequence()).replace( - valGapchar, gapChar)); + alseq.setSequence(new String(valseq.getSequence()) + .replace(valGapchar, gapChar)); alseq.setStart((int) valseq.getStart()); alseq.setEnd((int) valseq.getEnd()); modal = true; @@ -903,36 +945,39 @@ public class VamsasAppDatastore modal = true; alseq.setName(valseq.getName()); } - if (alseq.getDescription()==null || (valseq.getDescription() != null && !alseq.getDescription() - .equals(valseq.getDescription()))) + if (alseq.getDescription() == null || (valseq.getDescription() != null + && !alseq.getDescription().equals(valseq.getDescription()))) { alseq.setDescription(valseq.getDescription()); modal = true; } if (modal && Cache.log.isDebugEnabled()) { - Cache.log.debug("Updating apparently edited sequence " - + alseq.getName()); + Cache.log.debug( + "Updating apparently edited sequence " + alseq.getName()); } } else { - alseq = new jalview.datamodel.Sequence(valseq.getName(), valseq - .getSequence().replace(valGapchar, gapChar), (int) valseq - .getStart(), (int) valseq.getEnd()); - + alseq = new jalview.datamodel.Sequence(valseq.getName(), + valseq.getSequence().replace(valGapchar, gapChar), + (int) valseq.getStart(), (int) valseq.getEnd()); + Vobject datsetseq = (Vobject) valseq.getRefid(); if (datsetseq != null) { alseq.setDatasetSequence((SequenceI) getvObj2jv(datsetseq)); // exceptions - if (valseq.getDescription()!=null) + 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 @@ -945,8 +990,8 @@ public class VamsasAppDatastore } else { - Cache.log - .error("Invalid dataset sequence id (null) for alignment sequence " + Cache.log.error( + "Invalid dataset sequence id (null) for alignment sequence " + valseq.getVorbaId()); } bindjvvobj(alseq, valseq); @@ -1016,10 +1061,10 @@ public class VamsasAppDatastore { // we only write an annotation where it really exists. Glyph ss = new Glyph(); - ss - .setDict(uk.ac.vamsas.objects.utils.GlyphDictionary.PROTEIN_SS_3STATE); - ss.setContent(String - .valueOf(alan.annotations[a].secondaryStructure)); + ss.setDict( + uk.ac.vamsas.objects.utils.GlyphDictionary.PROTEIN_SS_3STATE); + ss.setContent( + String.valueOf(alan.annotations[a].secondaryStructure)); ae.addGlyph(ss); } an.addAnnotationElement(ae); @@ -1034,7 +1079,8 @@ public class VamsasAppDatastore // uk.ac.vamsas. // objects.core.AlignmentSequence alsref = (uk.ac.vamsas. // objects.core.AlignmentSequence) sref; - uk.ac.vamsas.objects.core.DataSetAnnotations an = (uk.ac.vamsas.objects.core.DataSetAnnotations) getjv2vObj(alan); + uk.ac.vamsas.objects.core.DataSetAnnotations an = (uk.ac.vamsas.objects.core.DataSetAnnotations) getjv2vObj( + alan); int[] gapMap = getGapMap(AlSeqMaps, alan); if (an == null) { @@ -1055,12 +1101,13 @@ 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); @@ -1077,8 +1124,8 @@ public class VamsasAppDatastore else { // verify existing alignment sequence annotation is up to date - System.out - .println("make new alignment dataset sequence annotation if modification has happened."); + System.out.println( + "make new alignment dataset sequence annotation if modification has happened."); } } @@ -1111,7 +1158,8 @@ public class VamsasAppDatastore // uk.ac.vamsas. // objects.core.AlignmentSequence alsref = (uk.ac.vamsas. // objects.core.AlignmentSequence) sref; - uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation an = (uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation) getjv2vObj(alan); + uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation an = (uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation) getjv2vObj( + alan); int[] gapMap = getGapMap(AlSeqMaps, alan); if (an == null) { @@ -1145,8 +1193,8 @@ public class VamsasAppDatastore else { // verify existing alignment sequence annotation is up to date - System.out - .println("make new alignment sequence annotation if modification has happened."); + System.out.println( + "make new alignment sequence annotation if modification has happened."); } } } @@ -1186,24 +1234,25 @@ 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 1) { // we need to close the original document view. @@ -1389,7 +1454,8 @@ public class VamsasAppDatastore // to the align frames. boolean gathered = false; String newviewid = null; - AlignedCodonFrame[] mappings = av.getAlignment().getCodonFrames(); + List mappings = av.getAlignment() + .getCodonFrames(); for (int i = 0; i < views.length; i++) { if (views[i] != av) @@ -1424,18 +1490,19 @@ public class VamsasAppDatastore { // ensure sequence mappings from vamsas document view still // active - if (mappings != null && mappings.length > 0) + if (mappings != null) { jalview.structure.StructureSelectionManager - .getStructureSelectionManager().addMappings(mappings); + .getStructureSelectionManager(Desktop.getInstance()) + .registerMappings(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); } @@ -1448,18 +1515,22 @@ public class VamsasAppDatastore * 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) { - throw new Error( - "IMPLEMENTATION ERROR: old jalview object is not bound ! (" - + oldjvobject + ")"); + // 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) + if (newjvobject != null) { jv2vobj.put(newjvobject, vobject); vobj2jv.put(vobject, newjvobject); @@ -1476,29 +1547,28 @@ public class VamsasAppDatastore { try { - jalview.gui.Jalview2XML jxml = new jalview.gui.Jalview2XML(); + Jalview2XML jxml = new Jalview2XML(); jxml.setObjectMappingTables(mapKeysToString(vobj2jv), mapValuesToString(jv2vobj)); jxml.setSkipList(skipList); if (dojvsync) { - jxml.SaveState(new JarOutputStream(cappdata - .getClientOutputStream())); + 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); + 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."); + jalview.bin.Cache.log.error( + "Couldn't access client application data for vamsas session. This is probably a vamsas client bug."); } } @@ -1537,8 +1607,10 @@ public class VamsasAppDatastore } return mapped; } + /** * synchronize Jalview from the vamsas document + * * @return number of new views from document */ public int updateToJalview() @@ -1555,8 +1627,9 @@ public class VamsasAppDatastore // ///LOAD DATASET DataSet dataset = root.getDataSet(_ds); int i, iSize = dataset.getSequenceCount(); - Vector dsseqs; - jalview.datamodel.Alignment jdataset = (jalview.datamodel.Alignment) getvObj2jv(dataset); + List dsseqs; + jalview.datamodel.Alignment jdataset = (jalview.datamodel.Alignment) getvObj2jv( + dataset); int jremain = 0; if (jdataset == null) { @@ -1574,12 +1647,12 @@ 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()) { @@ -1602,8 +1675,8 @@ 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."); @@ -1613,29 +1686,32 @@ public class VamsasAppDatastore // add any new dataset sequence feature annotations if (dataset.getDataSetAnnotations() != null) { - for (int dsa = 0; dsa < dataset.getDataSetAnnotationsCount(); dsa++) + for (int dsa = 0; dsa < dataset + .getDataSetAnnotationsCount(); dsa++) { DataSetAnnotations dseta = dataset.getDataSetAnnotations(dsa); // TODO: deal with group annotation on datset sequences. if (dseta.getSeqRefCount() == 1) { - SequenceI dsSeq = (SequenceI) getvObj2jv((Vobject) dseta - .getSeqRef(0)); // TODO: deal with group dataset + SequenceI dsSeq = (SequenceI) getvObj2jv( + (Vobject) dseta.getSeqRef(0)); // TODO: deal with group + // dataset // annotations if (dsSeq == null) { - jalview.bin.Cache.log - .warn("Couldn't resolve jalview sequenceI for dataset object reference " - + ((Vobject) dataset.getDataSetAnnotations( - dsa).getSeqRef(0)).getVorbaId() - .getId()); + jalview.bin.Cache.log.warn( + "Couldn't resolve jalview sequenceI for dataset object reference " + + ((Vobject) dataset + .getDataSetAnnotations(dsa) + .getSeqRef(0)).getVorbaId() + .getId()); } else { if (dseta.getAnnotationElementCount() == 0) { new jalview.io.vamsas.Sequencefeature(this, dseta, dsSeq); - + } else { @@ -1644,12 +1720,15 @@ public class VamsasAppDatastore // JBPNote: we could just add them to all alignments but // that may complicate cross references in the jalview // datamodel - Cache.log - .warn("Ignoring dataset annotation with annotationElements. Not yet supported in jalview."); + Cache.log.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."); } } } @@ -1657,12 +1736,13 @@ public class VamsasAppDatastore { // LOAD ALIGNMENTS from DATASET - for (int al = 0, nal = dataset.getAlignmentCount(); al < nal; al++) + for (int al = 0, nal = dataset + .getAlignmentCount(); al < nal; al++) { uk.ac.vamsas.objects.core.Alignment alignment = dataset .getAlignment(al); // TODO check this handles multiple views properly - AlignViewport av = findViewport(alignment); + AlignmentViewport av = findViewport(alignment); jalview.datamodel.AlignmentI jal = null; if (av != null) @@ -1670,9 +1750,9 @@ public class VamsasAppDatastore // TODO check that correct alignment object is retrieved when // hidden seqs exist. jal = (av.hasHiddenRows()) ? av.getAlignment() - .getHiddenSequences().getFullAlignment() : av - .getAlignment(); - } + .getHiddenSequences().getFullAlignment() + : av.getAlignment(); + } iSize = alignment.getAlignmentSequenceCount(); boolean refreshal = false; Vector newasAnnots = new Vector(); @@ -1691,10 +1771,10 @@ public class VamsasAppDatastore for (i = 0; i < iSize; i++) { AlignmentSequence valseq = alignment.getAlignmentSequence(i); - jalview.datamodel.Sequence alseq = (jalview.datamodel.Sequence) getvObj2jv(valseq); + 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 @@ -1707,7 +1787,8 @@ public class VamsasAppDatastore .getAlignmentSequenceAnnotation(); for (int a = 0; a < vasannot.length; a++) { - jalview.datamodel.AlignmentAnnotation asa = (jalview.datamodel.AlignmentAnnotation) getvObj2jv(vasannot[a]); // TODO: + jalview.datamodel.AlignmentAnnotation asa = (jalview.datamodel.AlignmentAnnotation) getvObj2jv( + vasannot[a]); // TODO: // 1:many // jalview // alignment @@ -1742,8 +1823,8 @@ public class VamsasAppDatastore // OBJECT LOCK // METHODS) { - Cache.log - .info("UNIMPLEMENTED: not recovering user modifiable sequence alignment annotation"); + Cache.log.info( + "UNIMPLEMENTED: not recovering user modifiable sequence alignment annotation"); // TODO: should at least replace with new one - otherwise // things will break // basically do this: @@ -1762,8 +1843,8 @@ 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 " @@ -1773,10 +1854,11 @@ public class VamsasAppDatastore if (newasAnnots != null && newasAnnots.size() > 0) { // Add the new sequence annotations in to the alignment. - for (int an = 0, anSize = newasAnnots.size(); an < anSize; an++) + for (int an = 0, anSize = newasAnnots + .size(); an < anSize; an++) { - jal.addAnnotation((AlignmentAnnotation) newasAnnots - .elementAt(an)); + jal.addAnnotation( + (AlignmentAnnotation) newasAnnots.elementAt(an)); // TODO: check if anything has to be done - like calling // adjustForAlignment or something. newasAnnots.setElementAt(null, an); @@ -1793,7 +1875,8 @@ public class VamsasAppDatastore for (int j = 0; j < an.length; j++) { - jalview.datamodel.AlignmentAnnotation jan = (jalview.datamodel.AlignmentAnnotation) getvObj2jv(an[j]); + jalview.datamodel.AlignmentAnnotation jan = (jalview.datamodel.AlignmentAnnotation) getvObj2jv( + an[j]); if (jan != null) { // update or stay the same. @@ -1803,16 +1886,16 @@ public class VamsasAppDatastore // jan.update(getjAlignmentAnnotation(jal, an[a])); // update // from another annotation object in place. - Cache.log - .debug("update from vamsas alignment annotation to existing jalview alignment annotation."); + Cache.log.debug( + "update from vamsas alignment annotation to existing jalview alignment annotation."); if (an[j].getModifiable() == null) // TODO: USE VAMSAS // LIBRARY OBJECT LOCK // METHODS) { // TODO: user defined annotation is totally mutable... - so // load it up or throw away if locally edited. - Cache.log - .info("NOT IMPLEMENTED - Recovering user-modifiable annotation - yet..."); + Cache.log.info( + "NOT IMPLEMENTED - Recovering user-modifiable annotation - yet..."); } // TODO: compare annotation element rows // TODO: compare props. @@ -1820,7 +1903,8 @@ 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; @@ -1835,16 +1919,18 @@ public class VamsasAppDatastore // /////////////////////////////// // construct alignment view alignFrame = new AlignFrame(jal, AlignFrame.DEFAULT_WIDTH, - AlignFrame.DEFAULT_HEIGHT, alignment.getVorbaId() - .toString()); + AlignFrame.DEFAULT_HEIGHT, + alignment.getVorbaId().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) { - for (int p = 0, pe = alignment.getPropertyCount(); p < pe; p++) + for (int p = 0, pe = alignment + .getPropertyCount(); p < pe; p++) { if (alignment.getProperty(p).getName().equals("title")) { @@ -1888,7 +1974,7 @@ public class VamsasAppDatastore TreePanel tp = null; if (vstree.isValidTree()) { - tp = alignFrame.ShowNewickTree(vstree.getNewickTree(), + tp = alignFrame.showNewickTree(vstree.getNewickTree(), vstree.getTitle(), vstree.getInputData(), 600, 500, t * 20 + 50, t * 20 + 50); @@ -1923,7 +2009,8 @@ public class VamsasAppDatastore DataSet dataset = root.getDataSet(_ds); if (dataset.getSequenceMappingCount() > 0) { - for (int sm = 0, smCount = dataset.getSequenceMappingCount(); sm < smCount; sm++) + for (int sm = 0, smCount = dataset + .getSequenceMappingCount(); sm < smCount; sm++) { Rangetype seqmap = new jalview.io.vamsas.Sequencemapping(this, dataset.getSequenceMapping(sm)); @@ -1934,10 +2021,10 @@ public class VamsasAppDatastore return newAlignmentViews.size(); } - public AlignViewport findViewport(Alignment alignment) + public AlignmentViewport findViewport(Alignment alignment) { - AlignViewport av = null; - AlignViewport[] avs = Desktop + AlignmentViewport av = null; + AlignmentViewport[] avs = Desktop .getViewports((String) getvObj2jv(alignment)); if (avs != null) { @@ -1980,11 +2067,11 @@ public class VamsasAppDatastore // may not quite cope with this (without binding an array of annotations to // a vamsas alignment annotation) // summary flags saying what we found over the set of annotation rows. - boolean[] AeContent = new boolean[] - { false, false, false, false, false }; + boolean[] AeContent = new boolean[] { false, false, false, false, + false }; int[] rangeMap = getMapping(annotation); - jalview.datamodel.Annotation[][] anot = new jalview.datamodel.Annotation[][] - { new jalview.datamodel.Annotation[rangeMap.length], + jalview.datamodel.Annotation[][] anot = new jalview.datamodel.Annotation[][] { + new jalview.datamodel.Annotation[rangeMap.length], new jalview.datamodel.Annotation[rangeMap.length] }; boolean mergeable = true; // false if 'after positions cant be placed on // same annotation row as positions. @@ -2029,18 +2116,14 @@ public class VamsasAppDatastore Glyph[] glyphs = ae[aa].getGlyph(); for (int g = 0; g < glyphs.length; g++) { - if (glyphs[g] - .getDict() - .equals( - uk.ac.vamsas.objects.utils.GlyphDictionary.PROTEIN_SS_3STATE)) + if (glyphs[g].getDict().equals( + uk.ac.vamsas.objects.utils.GlyphDictionary.PROTEIN_SS_3STATE)) { ss = glyphs[g].getContent(); AeContent[HASSECSTR] = true; } - else if (glyphs[g] - .getDict() - .equals( - uk.ac.vamsas.objects.utils.GlyphDictionary.PROTEIN_HD_HYDRO)) + else if (glyphs[g].getDict().equals( + uk.ac.vamsas.objects.utils.GlyphDictionary.PROTEIN_HD_HYDRO)) { Cache.log.debug("ignoring hydrophobicity glyph marker."); AeContent[HASHPHOB] = true; @@ -2058,8 +2141,8 @@ public class VamsasAppDatastore } else { - Cache.log - .debug("IMPLEMENTATION TODO: Ignoring unknown glyph type " + Cache.log.debug( + "IMPLEMENTATION TODO: Ignoring unknown glyph type " + glyphs[g].getDict()); } } @@ -2070,23 +2153,23 @@ public class VamsasAppDatastore AeContent[HASVALS] = true; if (ae[aa].getValueCount() > 1) { - Cache.log.warn("ignoring additional " - + (ae[aa].getValueCount() - 1) - + " values in annotation element."); + Cache.log.warn( + "ignoring additional " + (ae[aa].getValueCount() - 1) + + " values in annotation element."); } val = ae[aa].getValue(0); } if (colour == null) { anot[row][pos] = new jalview.datamodel.Annotation( - (dc != null) ? dc : "", desc, (ss != null) ? ss - .charAt(0) : ' ', val); + (dc != null) ? dc : "", desc, + (ss != null) ? ss.charAt(0) : ' ', val); } else { anot[row][pos] = new jalview.datamodel.Annotation( - (dc != null) ? dc : "", desc, (ss != null) ? ss - .charAt(0) : ' ', val, colour); + (dc != null) ? dc : "", desc, + (ss != null) ? ss.charAt(0) : ' ', val, colour); } } else @@ -2118,24 +2201,21 @@ 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. */ @@ -2182,25 +2262,30 @@ public class VamsasAppDatastore Float val = null; try { - val = new Float(props[p].getContent()); + val = Float.valueOf(props[p].getContent()); } catch (Exception e) { Cache.log.warn("Failed to parse threshold property"); } if (val != null) + { if (gl == null) { - gl = new GraphLine(val.floatValue(), "", java.awt.Color.black); + gl = new GraphLine(val.floatValue(), "", + java.awt.Color.black); } else { 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(); } } @@ -2220,8 +2305,8 @@ public class VamsasAppDatastore } if (parsedRangeAnnotation == null) { - Cache.log - .debug("Inserting empty annotation row elements for a whole-alignment annotation."); + Cache.log.debug( + "Inserting empty annotation row elements for a whole-alignment annotation."); } else { @@ -2236,11 +2321,12 @@ 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]) { @@ -2314,7 +2400,8 @@ public class VamsasAppDatastore && arow[i].description.length() < 3) { // copy over the description as the display char. - arow[i].displayCharacter = new String(arow[i].description); + arow[i].displayCharacter = new String( + arow[i].description); } } else @@ -2370,8 +2457,8 @@ public class VamsasAppDatastore } } catch (Exception e) { - Cache.log - .info("UNIMPLEMENTED : Couldn't parse non-integer group value for setting graphGroup correctly."); + Cache.log.info( + "UNIMPLEMENTED : Couldn't parse non-integer group value for setting graphGroup correctly."); } return jan; @@ -2380,7 +2467,6 @@ 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 @@ -2396,8 +2482,8 @@ public class VamsasAppDatastore int[] se = null; if (dseta.getSegCount() > 0 && dseta.getPosCount() > 0) { - throw new Error( - "Invalid vamsas RangeType - cannot resolve both lists of Pos and Seg from choice!"); + throw new Error(MessageManager.getString( + "error.invalid_vamsas_rangetype_cannot_resolve_lists")); } if (dseta.getSegCount() > 0) { @@ -2420,8 +2506,7 @@ 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(); @@ -2455,8 +2540,8 @@ public class VamsasAppDatastore int[] se = null; if (dseta.getSegCount() > 0 && dseta.getPosCount() > 0) { - throw new Error( - "Invalid vamsas RangeType - cannot resolve both lists of Pos and Seg from choice!"); + throw new Error(MessageManager.getString( + "error.invalid_vamsas_rangetype_cannot_resolve_lists")); } if (dseta.getSegCount() > 0) { @@ -2466,7 +2551,7 @@ public class VamsasAppDatastore int se_end = se[1 - se[2]] + (se[2] == 0 ? 1 : -1); for (int p = se[se[2]]; p != se_end; p += se[2] == 0 ? 1 : -1) { - posList.add(new Integer(p)); + posList.add(Integer.valueOf(p)); } } } @@ -2477,7 +2562,7 @@ public class VamsasAppDatastore for (int p = 0, pSize = dseta.getPosCount(); p < pSize; p++) { pos = dseta.getPos(p).getI(); - posList.add(new Integer(pos)); + posList.add(Integer.valueOf(pos)); } } } @@ -2497,12 +2582,12 @@ 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 + * 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 + * unit for local * @param default - * unit for mapped + * unit for mapped * @return MapList */ private jalview.util.MapList parsemapType(MapType maprange, int localu, @@ -2513,8 +2598,9 @@ public class VamsasAppDatastore int[] mappedRange = getMapping(maprange.getMapped()); long lu = maprange.getLocal().hasUnit() ? maprange.getLocal().getUnit() : localu; - long mu = maprange.getMapped().hasUnit() ? maprange.getMapped() - .getUnit() : mappedu; + long mu = maprange.getMapped().hasUnit() + ? maprange.getMapped().getUnit() + : mappedu; ml = new jalview.util.MapList(localRange, mappedRange, (int) lu, (int) mu); return ml; @@ -2524,15 +2610,15 @@ 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); } } @@ -2567,8 +2653,8 @@ 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()); @@ -2586,9 +2672,9 @@ public class VamsasAppDatastore jalview.datamodel.Provenance jprov = new jalview.datamodel.Provenance(); for (int i = 0; i < prov.getEntryCount(); i++) { - jprov.addEntry(prov.getEntry(i).getUser(), prov.getEntry(i) - .getAction(), prov.getEntry(i).getDate(), prov.getEntry(i) - .getId()); + jprov.addEntry(prov.getEntry(i).getUser(), + prov.getEntry(i).getAction(), prov.getEntry(i).getDate(), + prov.getEntry(i).getId()); } return jprov; @@ -2655,10 +2741,10 @@ public class VamsasAppDatastore return vobj2jv; } - public void storeSequenceMappings(AlignViewport viewport, String title) - throws Exception + public void storeSequenceMappings(AlignmentViewport viewport, + String title) throws Exception { - AlignViewport av = viewport; + AlignmentViewport av = viewport; try { jalview.datamodel.AlignmentI jal = av.getAlignment(); @@ -2670,39 +2756,39 @@ 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. - if (av.getAlignment().getCodonFrames() != null - && av.getAlignment().getCodonFrames().length > 0) + List cframes = av.getAlignment().getCodonFrames(); + if (cframes != null) { - jalview.datamodel.AlignedCodonFrame[] cframes = av.getAlignment() - .getCodonFrames(); - for (int cf = 0; cf < cframes.length; cf++) + for (AlignedCodonFrame acf : cframes) { - if (cframes[cf].getdnaSeqs()!=null && cframes[cf].getdnaSeqs().length > 0) + if (acf.getdnaSeqs() != null && acf.getdnaSeqs().length > 0) { - jalview.datamodel.SequenceI[] dmps = cframes[cf].getdnaSeqs(); - jalview.datamodel.Mapping[] mps = cframes[cf].getProtMappings(); + jalview.datamodel.SequenceI[] dmps = acf.getdnaSeqs(); + jalview.datamodel.Mapping[] mps = acf.getProtMappings(); for (int smp = 0; smp < mps.length; smp++) { - uk.ac.vamsas.objects.core.SequenceType mfrom = (SequenceType) getjv2vObj(dmps[smp]); + uk.ac.vamsas.objects.core.SequenceType mfrom = (SequenceType) getjv2vObj( + dmps[smp]); if (mfrom != null) { - new jalview.io.vamsas.Sequencemapping(this, mps[smp], - mfrom, dataset); + new jalview.io.vamsas.Sequencemapping(this, mps[smp], mfrom, + dataset); } else { - Cache.log - .warn("NO Vamsas Binding for local sequence! NOT CREATING MAPPING FOR " - + dmps[smp].getDisplayId(true) - + " to " + Cache.log.warn( + "NO Vamsas Binding for local sequence! NOT CREATING MAPPING FOR " + + dmps[smp].getDisplayId(true) + " to " + mps[smp].getTo().getName()); } } @@ -2711,8 +2797,9 @@ 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); } } @@ -2733,19 +2820,22 @@ 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(); }